University of Southern California Dissertations and Theses

Potential-induced formation and dissociation of adducts at interfaces and adsorption of phenols onto metal electrodes

(USC Thesis Other)

Potential-induced formation and dissociation of adducts at interfaces and adsorption of phenols onto metal electrodes

PDF

Download a page range

Download transcript

Copy asset link

Request this asset

Transcript (if available)

Content Potential-Induced Formation and Dissociation of Adducts at Interfaces and Adsorption of Phenols onto Metal Electrodes by Sevan Menachekanian A Dissertation Presented to the FACULTY OF THE GRADUATE SCHOOL UNIVERSITY OF SOUTHERN CALIFORNIA In Partial Fulfillment of the Requirements for the Degree DOCTOR OF PHILOSOPHY (CHEMISTRY) August 2023 Copyright 2023 Sevan Menachekanian Acknowledgements I would like to express my deepest gratitude to my advisor, Prof. Jahan Dawlaty, for his invaluable guidance, mentorship, and support throughout my Ph.D. program. I am also grateful to Prof. Vitaly Kresin and Prof. Oleg Prezhdo for serving in my defense committee. I would like to extend my appreciation to all of my friends for their encouragement, understanding, and unwavering support during this challenging journey. Their presence and encouragement have been invaluable. I want to express my gratitude to my family for continuous support, constant encouragement, and belief in my abilities. I would like to thank all those who have played a role, whether big or small, in making this thesis possible. ii Table of Contents Acknowledgements ii List of Tables v List of Figures vi Chapter 1: Introduction 1 1.0.1 Vibrational Stark Shift Spectroscopy . . . . . . . . . . . . . . . . . . . . 1 1.0.2 Surface Enhanced Raman Spectroscopy . . . . . . . . . . . . . . . . . . . 2 1.0.3 Electro-Inductive Effect, and Ionic Structure at Electrode Interfaces . . . . 3 Chapter 2: Inductive Effect Alone Cannot Explain Lewis Adduct Formation and Disso- ciation at Electrode Interfaces 5 2.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5 2.2 Materials and Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8 2.2.1 Experimental Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . 8 2.2.2 Computational Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . 9 2.3 Results and Discussions . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 11 Chapter 3: Phenol as a Tethering Group to Metal Surfaces: Stark Response and Com- parison to Benzenethiol 26 3.1 Introduction . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26 3.2 Materials and Method . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28 3.2.1 Experimental Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . . 28 3.2.2 Computational Methods . . . . . . . . . . . . . . . . . . . . . . . . . . . 29 3.3 Results and Discussion . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30 Chapter 4: Conclusions and Future Directions 39 References 42 Appendices 56 A Supporting Information for: Inductive Effect Alone Cannot Explain Lewis Adduct Formation and Dissociation at Electrode Interfaces . . . . . . . . . . . . . . . . . 57 A.1 Cylcic V oltammetry . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 57 iii A.2 Spectroelectrochemical Cell Design . . . . . . . . . . . . . . . . . . . . . 58 A.3 Calculated Average C=C Frequency of the Marker Bands . . . . . . . . . . 64 A.4 Calculated Vibrational Frequencies . . . . . . . . . . . . . . . . . . . . . 66 A.5 Grand Potential Calculations from Periodic DFT . . . . . . . . . . . . . . 66 A.6 Sample Quantum Espresso Input Files and Optimized Geometries . . . . . 73 A.7 Sample Quantum ESPRESSO pw.x Input File . . . . . . . . . . . . . . . . 73 A.8 Sample Envrion Input File . . . . . . . . . . . . . . . . . . . . . . . . . . 75 A.9 Coordinates of Converged Structures at PZFC . . . . . . . . . . . . . . . . 76 A.10 Potential-Dependent SERS Spectra of MPy in PC at Various Electrolytes . 92 A.11 Electrochemical Impedance and Capacitance Measurements . . . . . . . . 95 B Supporting Information for: Phenol as a Tethering Group to Metal Surfaces:Stark Response and Comparison to Benzenethiol . . . . . . . . . . . . . . . . . . . . . 98 B.1 Input files . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 102 B.2 Geometry Optimization Neutral for MBN . . . . . . . . . . . . . . . . . . 107 B.3 Geometry Optimization Neutral for CP . . . . . . . . . . . . . . . . . . . 113 C Design and Optimization of a Home-Made Triple Laser Raman System . . . . . . 124 C.1 An Image of the Home-Made Raman . . . . . . . . . . . . . . . . . . . . 124 C.2 Schematic Illustration of the Home-Made Raman System. . . . . . . . . . 125 C.3 Raman Instrument Performance . . . . . . . . . . . . . . . . . . . . . . . 125 D TEMPO Project . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 126 D.1 Synthesis of Amide Diradical TEMPO . . . . . . . . . . . . . . . . . . . . 126 D.2 An Image of Diradical TEMPO Crystal . . . . . . . . . . . . . . . . . . . 126 D.3 FT-IR Spectrum of Amide Diradical TEMPO . . . . . . . . . . . . . . . . 127 D.4 Cyclic V oltammograms of Amide Diradical TEMPO . . . . . . . . . . . . 128 D.5 HNMR Data of Amide Diradical TEMPO . . . . . . . . . . . . . . . . . . 129 iv List of Tables 4.1 Effects of Li + and BF − 4 ionic strength on the formation, dissociation, and reformation. 1 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 94 4.2 Binding energy (eV) of CP (red) and MBN (blue) on an Au (111) surface at various charges (0, ±0.25, ±0.5, ±1 electron add/subtracted to the system). . . . . . . . . . 100 4.3 Nitrile bond length at various charges. . . . . . . . . . . . . . . . . . . . . . . . . 101 4.4 Nitrile frequency values at various charges from -1 to +1. . . . . . . . . . . . . . . 101 v List of Figures 2.1 (a) Lewis adducts between adsorbed MPy and BF 3 on a gold surface. (b) Re- versible electrochemical formation/dissociation of surface adduct at positive and negative potentials. The adduct formation/dissociation is reversible upon varying the electrode potential when BF 3 is supplied from Li + BF 4 − equilibrium. . . . . . . 8 2.2 (a) Raman spectra of liquid pyridine and pyridine-BF 3 adduct. (b) SERS spectra of MPy and MPy-BF 3 in acetonitrile on a gold electrode. The ring stretching (C=C) bands around 1600 cm − 1 blue shift upon adduct formation both in the bulk and on the surface. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13 2.3 SERS spectra of adduct in DCM (blue) and TEA (red). The adduct is stable in DCM but chemically dissociates upon addition of the strong Lewis base TEA. The C=C stretching marker bands red shift after adduct dissociation. . . . . . . . . . . 14 2.4 Potential-dependent SERS spectra of the MPy-BF 3 adduct on the surface. The left panel depicts the potential for each spectrum and defines the y-axis for the other two panels. The potential starts from OCP, is swept to positive potential, followed by a negative and a positive sweep to bring it back to 0 V . The right panel depicts the average frequency of the marker bands in the 1600 cm − 1 range vs applied potential. The adduct (blue spectra) is stable in a wide range of potentials between +0.5 V and -0.2 V but dissociates to MPy (red spectra) at potentials more negative than -0.5 V . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 16 2.5 SERS spectra of MPy- BF 3 (blue spectra) and MPy (red spectra) in the presence of 0.1 M LiBF 4 in propylene carbonate (middle panel). The left panel depicts the y-axis for the other two panels, corresponding to the applied potential starting from OCP and moving positive, then negative, and then positive again. The adduct breaks at negative potentials, but is regenerated upon reversal of the potential, as evidenced by the changes in the marker bands. The right panel depicts the average C=C frequency of the marker bands in the 1600 cm − 1 range vs applied potential. . 18 vi 2.6 (a) Polarizing effect of electrode potential on the strength of the Lewis bond. At positive potentials electron density is moved away from the Lewis bond and the bond weakens. The opposite is expected at negative potentials. (b) Effect of elec- trode potential on ionic structures and equilibria near the interface. We postulate a possible scenario in which at negative potentials, lithium ions aggregate near MPy and via a weak interaction with the nitrogen facilitate the formation of halogen- bridged [B 2 F 7 ] − 1 complex. At positive potentials, the lithium ions are pushed away from the interface and hence stabilize the MPy-BF 3 adduct. . . . . . . . . . 19 2.7 Analysis of the electroinductive effect from periodic DFT calculations. (a) DFT- optimized structure and (b) charge density difference plot for MPy-BF 3 * in propy- lene carbonate continuum solvent. Au, S, C, N, B, F, and H atoms are shown in gold, yellow, brown, blue, green, silver, and white, respectively. The charge density difference isosurface in (b) shows the localization of excess charge upon polarization of -0.58 V vs. PZFC. Yellow represents an increase in electron den- sity, whereas cyan represents a depletion of electron density. The isosurface level is set to 0.00025 e − /Bohr 3 . The increased charge density over the N–B bond is indicative of the electroinductive effect. (c) The N–B bond length as a function of the applied potential E, where the bond shortens (strengthens) at more negative potentials and elongates (weakens) at more positive potentials. . . . . . . . . . . . 21 2.8 Thermodynamic analysis of adduct formation. (a) DFT optimized MPy* and MPy- BF 3 * at PZFC, outlined in red and blue, respectively. (b) Corresponding grand potentialsΩ as a function of applied potential. (c) The reaction free energy∆Ω as a function of E, where∆Ω is the free energy of adduct formation, corresponding to the difference between the blue and red curves in (b) at a given value of E. . . . 22 3.1 (a) Raman spectra of 0.1 M CP and 0.1 M MBN in ethanol obtained under similar experimental conditions, revealing that their Raman cross sections are comparable. (b) SERS spectra of CP and MBN on gold, indicating successful adsorption of CP albeit with lower coverage. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 32 3.2 Frequency shift of MBN (red) and CP(blue) as a function of applied electrochem- ical potential relative to 0 V vs. Ag/AgCl. The electrode potential begins at 0 V and is swept forward to positive potentials, followed by a reverse scan to negative values, and then back to 0 V . Each frequency value represents the average of three independent measurements. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 33 3.3 Calculated nitrile stretching frequencies for MBN (red) and CP(blue) adsorbed on a slab of gold at different total net charges for the system. Consistent with experimental results, the nitrile frequency for both molecules shows a blue shift by the addition of charge to the system. . . . . . . . . . . . . . . . . . . . . . . . . . 35 3.4 Time-dependent peak Raman intensity for 1mM MBN (red), and 1mM CP in ethanol (blue). . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 36 vii 3.5 Binding energy (eV) of CP (blue) and MBN (red) on an Au (111) surface at various charges (0, ±0.25, ±0.5, ±1 electron add/subtracted to the system). Both molecules show a linear dependence by adding charge to the Au (111). MBN has a stronger binding to the gold surface with a slope of -0.33 eV/charge, while CP has a slope of -0.062 eV/charge . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 37 3.6 Charge density difference plots of MBN (a) and CP (b) calculated according to equation 2. The negative and positive charge build up are shown by red and blue colors respectively with an isovaule of 0.0025 e/Bohr 3 . The two molecules show qualitatively similar charge build up upon adsorption. However, the charge build up for MBN in the gold thiol bond region is slightly more pronounced. . . . . . . 38 4.1 Cyclic V oltametry of MPy in PC and 0.1 M LiBF 4 with a 100mV/sec scan rate. No distinct peaks associated with any Faradaic process are observed. . . . . . . . 57 4.2 An image of a home-built spectroelectrochemical cell for SERS measurements. A gold wire (1 mm thickness) is used as both the working and counter electrodes. The reference electrode is Ag/AgCl. . . . . . . . . . . . . . . . . . . . . . . . . . 58 4.3 Schematic illustration of the electrochemical cell for SERS measurements. WE: working electrode; RE: Reference electrode; CE: counter electrode. The quartz window is 3/4 inch in diameter. The reference electrode is Ag/AgCl (3 M KCl) and the counter electrode is gold. A 785 nm laser is used for all SERS measurments. . 58 4.4 An image of a gold wire (1 mm thickness with 99.99% purity) used as both work- ing and counter electrodes. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 59 4.5 An image of the gold electrodepositon solution used to make the SERS substrate. Photo courtesy of: https://goldtouchinc.com. . . . . . . . . . . . . . . . . . . . . 59 4.6 An image of the spectroelectrochemical cell under the Raman microscope. . . . . 60 4.7 SERS spectra of MPy and MPy-BF 3 in acetonitrile. The C=C marker bands of MPy in 1600 cm − 1 blue shift upon adduct formation with BF 3 . Changes in other regions are also observed . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 61 4.8 Raman spectrum of solid MPy . . . . . . . . . . . . . . . . . . . . . . . . . . . . 61 4.9 Raman spectra of bulk pyridine and bulk pyiridine-BF 3 . The marker bands in the 1600 cm − 1 undergo blue shift upon adduct formation with BF 3 . . . . . . . . . . . 62 4.10 Potential dependent SERS spectra of MPy in PC in the presence of 0.1 M NaBF 4 as electrolyte. No Raman signatures indicative of adduct formation are observed. The Raman intensity of C=C marker bands change upon application of potential, but no blue shift is observed. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 62 viii 4.11 Potential dependent spectra of MPy in PC in the presence of 0.1 M (TBA)BF 4 as electrolyte (middle panel). The left panel depicts the potential for each spectrum and defines the y-axis for the other two panels. The potential starts from OCP, is swept to positive potentials, followed by a negative and a positive sweep to bring it back to 0. No Raman blue shift above 1610 cm − 1 indicative of adduct formation is observed. The Raman intensities of marker bands change upon application of potential. The right panel depicts the average frequency of the marker bands in the 1600 cm − 1 range vs applied potential. . . . . . . . . . . . . . . . . . . . . . . . . 63 4.12 The average frequency of the marker bands vs electrode potential for MPy (red), and adduct (brown: irreversible; black: reversible). Adduct dissociates at negative potentials and the C=C marker bands undergo a red shift. The response of the adduct is distinctly different from the response of MPy. . . . . . . . . . . . . . . . 64 4.13 Potential dependent SERS specctra of adduct in PC and 0.1 M LiBF 4 (middle panel). The left panel depicts the potential for each spectrum and defines the y- axis for the other two panels. The potential starts from OCP, is swept to positive potentials, followed by a negative and a positive sweep to bring it back to 0. The right panel depicts the full width half maximum (FWHM) of the ring breathing mode as a function of applied potential. A distinct change in the spectral FWHM (from 14 to 25 cm − 1 ) is observed upon dissociation of the adduct. The potential range for this change correlates with the change in the marker bands in the 1600 cm − 1 region used in this work. . . . . . . . . . . . . . . . . . . . . . . . . . . . . 65 4.14 Schematic of the computational unit cell used for charged slab calculations in di- electric continuum propylene carbonate. . . . . . . . . . . . . . . . . . . . . . . . 67 4.15 Thermodynamic analysis of adduct formation in the presence of explicit Li + BF − 4 or Li + B 2 F − 7 ion pairs. (a) DFT-optimized geometries for MPy* + Li + B 2 F − 7 in configurations with Li + far from (light red) and close to (dark red) the Au sur- face, MPy* + Li + BF − 4 with Li + close to the Au surface (red), and MPy− BF 3 * + Li + BF − 4 with Li + close to the Au surface (blue). (b) Grand potentialsΩ as a func- tion of applied potential E. (c) Reaction free energies∆Ω as a function of E, where ∆Ω is the free energy difference between the blue curve and the lower energy red curve in (b) at a given E. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 70 4.16 Thermodynamic analysis of adduct formation in the presence of explicit Li + PC. (a) DFT-optimized geometries for MPy* with Li + PC (red) and MPy− BF 3 * with Li + PC (blue). (b) Grand potentialsΩ as a function of applied potential E. (c) Re- action free energies∆Ω as a function of E, where∆Ω is the free energy difference between the blue curve and the red curve in (b) at a given E. . . . . . . . . . . . . 71 4.17 The N–B bond length of MPy− BF 3 * as a function of the applied potential E for the different models studied: no ions, with Li + BF − 4 , and with Li + PC. In all three cases, the bond shortens (strengthens) with more negative potential and elongates (weakens) with more positive potential. . . . . . . . . . . . . . . . . . . . . . . . 72 ix 4.18 Potential dependent SERS spectra of MPy in PC in the presence of (a) 70 mM LiBF 4 and 30 mM LiTFSI, (b) 70 mM LiBF 4 and 30 mM TBABF 4 . The left panel for each spectrum depicts the potential and defines the y-axis for the right panel. The potential starts from OCP and is swept to positive potentials, followed by a negative and a positive sweep to bring it back to zero. . . . . . . . . . . . . . . . 92 4.19 Potential dependent SERS spectra of MPy in PC in the presence of (c) 50 mM LiBF 4 and 50 mM LiTFSI, (d) 50 mM LiBF 4 and 50 mM TBABF 4 . The left panel for each spectrum depicts the potential and defines the y-axis for the right panel. The potential starts from OCP and is swept to positive potentials, followed by a negative and a positive sweep to bring it back to zero. . . . . . . . . . . . . . . . 92 4.20 Potential dependent SERS spectra of MPy in PC in the presence of (e) 30 mM LiBF 4 and 70 mM LiTFSI, (f) 30 mM LiBF 4 and 70 mM TBABF 4 . The potential starts from OCP and is swept to positive potentials, followed by a negative and a positive sweep to bring it back to zero. . . . . . . . . . . . . . . . . . . . . . . . 93 4.21 Potential dependent SERS spectra of MPy in PC in the presence of (g) 10 mM LiBF 4 and 90 mM LiTFSI, (h) 10 mM LiBF 4 and 90 mM TBABF 4 . The left panel for each spectrum depicts the potential and defines the y-axis for the right panel. The potential starts from OCP and is swept to positive potentials, followed by a negative and a positive sweep to bring it back to zero. . . . . . . . . . . . . . . . 93 4.22 Potential dependent SERS spectra of MPy in the presence of 0.1 LiBF 4 /PC. The peak at 648 cm − 1 (blue spectra, left panel) may be tentatively assigned to the B-N stretching mode. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 94 4.23 Bode modulus plots of MPy SAM in 0.1 M LiBF 4 /PC at various potentials. Bode phase plots of MPy SAM in 0.1 M LiBF 4 /PC at various potentials (right panel). . . 95 4.24 Equivalent circuit model for SAM monolayer on gold in the presence of 0.1 M LiBF 4 /PC. Phase constant element (CPE) represents the EDL capacitance. R SAM is the SAM monolayer resistance, and R S is the solution resistance. . . . . . . . . 96 4.25 The plot of differential capacitance vs applied potential for the MPy SAM on Au in 0.1 M LiBF 4 /PC. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 96 4.26 Potential dependent SERS data for the nitrile stretching mode for adsorbed CP on gold (left), and for adsorbed MBN (right) . . . . . . . . . . . . . . . . . . . . . . 98 4.27 Potential dependent SERS spectra for MBN in 0.1M NaClO 4 /water. . . . . . . . . 99 4.28 Nitrile frequency shift as a function of applied electrode potential for MBN and 4-(mercaptomethyl)benzonitrile. Introducing a methylene (CH2) group disrupts the conjugation and significantly changes the Stark shift response of adsorbed molecules . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 99 x 4.29 Calculated angle of the adsorbed molecule with respect to the surface normal for CP and MBN. The data suggest that MBN exhibits a slight tilt of a few degrees compared to CP. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 100 4.30 DFT-optimized structures of neutral a) 4-mercaptobenzonitirle (MBN) and b) 4- cyanophenols (CP). Optimized coordinates in V ASP-POSCAR format are given below in the V ASP input files section of the supporting information. . . . . . . . . 100 4.31 Geometry of adsorption for CP with respect to gold surface at various charges. . . 101 4.32 Geometry of adsorption for MBN with respect to gold surface at various charges. . 101 4.33 An image of the home-made triple laser Raman system. . . . . . . . . . . . . . . 124 4.34 Schematic illustration of the home-made triple laser Raman system. . . . . . . . . 125 4.35 Raman spectra of benzonitrile taken with a Horiba XploRA Raman Microscope (blue) and the home-made Raman system (red) using a similar experimental con- ditions/settings: objective lens: 4x Olympus; Laser power: 27 mW; Laser wave- length: 785 nm; exposure time: 1 second; grating: 600 lines/mm; slit size: 50 microns. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 125 4.36 Synthesis of an amide diradical TEMPO via the reaction of disulfide dicarboxylic acid and amino TEMPO. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 126 4.37 An image of the diradical TEMPO crystal after synthesis and purification. . . . . . 126 4.38 FT-IR spectrum of the amide diradical TEMPO. . . . . . . . . . . . . . . . . . . 127 4.39 Self assembele monolayer of amide TEMPO on a gold surface. This radical can undergo one electron transfer process. . . . . . . . . . . . . . . . . . . . . . . . . 127 4.40 The cyclic voltammograms of amide SAM in 0.1 M NaClO4 in water as the sol- vent. The measurements were performed over 20 cycles, indicating the excellent stability of SAMs. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 128 4.41 Surface-tethered TEMPO-TEMPO + electrochemistry in non-aqueous electrolyte CVs obtained in 100 mM TBA + PF 6 – in DCM at various scan rates. . . . . . . . . 128 4.42 HNMR data of diradical TEMPO in the presence of Phenylhydarzine. Prior to acquiring NMR data, phenylhydrazine is utilized to reduce the TEMPO diradical. . 129 xi Chapter 1 Introduction Interfacial processes play a pivotal role in various fields of sciences, including chemistry, biol- ogy and physics. Several processes take place at metal interfaces. For example, chemical bonds can form and break, and molecules can adsorb onto the surface. The applied potential on an electrode can profoundly influence these interfacial processes as it can alter the dynamics and re- activity of molecules in close proximity to the surfaces. This interplay between applied potential and interfacial processes is particularly relevant in electrochemistry, where precise control over interfacial phenomena is crucial for optimizing electrocatalytic reactions and designing efficient energy storage and conversion devices. In this work, we investigate the reversible formation and dissociation of Lewis bonds near an electrified surface, as well as the adsorption of phenols onto metal electrodes. 1.0.1 Vibrational Stark Shift Spectroscopy Measuring the electric field near the electrode surface is challenging. One promising approach for estimating the electric field profile at the interface is Stark shift spectroscopy. 1 This method involves decorating metal surfaces with self-assembled monolayers (SAMs) and measuring the change in the frequency of a particular vibration in response to the applied potential. SAMs have been extensively used to acquire important interfacial information. 2;3;4;5 In our group, we have 1 commonly used 4-mercaptobenonitrile (MBN) SAM as a probe to investigate the interfacial elec- tric field and processes. 6;7;8;5 The nitrile frequency of MBN is sensitive to its electrostatic envi- ronment. The extent to which the vibrational frequency of a probe molecule (e.g nitrile in MBN) changes with respect to applied potential is proportional to the magnitude of the electric field, and the constant of the proportionality is called the Stark tuning rate (∆µ). One can show the relationship between the strength of the field and the corresponding frequency change as follows: ∆ν =− ∆µ· F (1.1) where∆µ is the difference between the dipole moments in the ground and the excited states, F is the strength of the field, and ∆ν is the change in vibrational frequency. Sometimes, it is conve- nient to report the Stark tuning rate using the applied electrode potential. In this work, I primarily focus on reporting the changes in frequency of nitrite with respect to the applied potential, rather than the electric field. For further insights into Stark shift spectroscopy, I refer the reader to relevant articles in the field. 9;1 Several surface spectroscopic techniques, including sum frequency gener- ation (SGF), 4 attenuated total reflection infrared spectroscopy (ATR-IR), 10;11 surface-enhanced Raman scattering (SERS), 12 Fourier-transform infrared reflection absorption spectroscopy (FT- IRRAS), 13 and surface-enhanced infrared absorption spectroscopy(SEIRAS) 14;15 are used to char- acterize the formation of SAMs and to measure the vibrational Stark shifts. Here, I will be using surface-enhanced Raman spectroscopy to confirm the formation of SAMs and report their vibra- tional Stark shifts. 1.0.2 Surface Enhanced Raman Spectroscopy Surface-enhanced Raman spectroscopy (SERS) is a powerful scattering technique for studying molecular vibrations at the interface. This method enhances Raman scattering signals from molecules adsorbed on or in close proximity to roughened metallic surfaces, including gold, silver, and cop- per. 16;17 When a laser source impinges upon a metal surface, the free electrons of metals oscillate 2 at the same frequency as the incoming light. This collective oscillation of electrons is referred to as plasmon oscillation. Plasmon oscillations enhance the electric field at the interface, resulting in an enhanced Raman scattering process. The sensitivity of Raman scattering is significantly increased when molecules are in close proximity to these metal surfaces. 18;19 The enhancement factor in SERS can be several orders of magnitude higher than in conven- tional Raman spectroscopy, enabling the detection and characterization of molecules at extremely low concentrations down to a single molecule. 20;21 SERS offers several advantages over traditional Raman spectroscopy. The enhanced signal strength allows for the detection of trace amounts of analytes, making it suitable for applications in forensic analysis 22 , biosensors 23 , pharmaceuti- cals 24 , food industry, 25 medical diagnosis, 26 photocatalysis. 27 However, it is important to note that SERS is a complex technique that requires careful experimental design and substrate prepa- ration. Factors such as the choice of the metal substrate, size and shape, and the molecular ori- entation on the surface can significantly influence the observed SERS signal. 28 Our group mem- bers have used surface Enhanced Raman spectroscopy to investigate the interfacial processes near the metal electrodes. 29;8;12;6;30 In the second half of my work, I report on the SERS spectra of adsorbed 4-mercaptobenzonitrile, and 4-cyanophenol on the gold surface. I will also report the Stark tuning rate of adsorbed 4-cyanophenol and compare the results with those obtained for 4- mercaptobenzonitrile. 1.0.3 Electro-Inductive Effect, and Ionic Structure at Electrode Interfaces A biased electrochemical interface can polarize molecules through an electro-inductive effect. 6 In the case of 4-mercaptobenzonitrile tethered to a gold electrode, the applied potential can either push the charge density from the ring toward the nitrile group or pull away from it. This can significantly impact the electronic properties of the molecules. For instance, the acidic and basic properties of the 4-mercaptobenzoic acid SAMs can be modulated by applying potential. 31;15 3 The effect of the electrode potential on the molecule can be similar to that of electro-donating or electro-withdrawing groups. For instance, the OH, NH 2 , andO – CH 3 groups are known as electro- donating groups and can push the electron density toward the benzene ring. Similarly, applying a negative potential to the electrode will have the same electro-donating effect by pushing the excess negative charge toward the benzene ring. In contrast, groups such as F, Cl, NO 2 , and COOH are electro-withdrawing groups that pull the electron density away from the benzene ring. This effect is similar to applying a positive potential to the electrode and pulling the electron density from the molecule toward the electrode. Sohini Sarkar et al. have reported this effect in great details. 6 The applied potential can also influence the interfacial ionic structures and chemical equilib- ria at the interface. This effect arises from the electrostatic attraction or repulsion between the electrode and the ions at the interface. At positive potentials, negatively charged ions aggregate near the surface, while the positively charged ions are pushed away from the surface. On the other hand, at negative potentials, positively charged ions are more likely to populate near the electrode, and negatively charged ions are pushed away toward the bulk. This movement of ions may change the interfacial ionic structures and chemical equilibria. Despite its significance, surface scientists sometimes overlook or disregard this effect. In our work, we will discuss both the electroindic- tive effect and the field’s effect on the ionic structure and chemical equilibrium at the interface and compare which of these effects is dominant in the formation/dissociation of an interfacial pyridine – BF 3 adduct. Previously, in our group, Joel Patrow studied the formation of interfacial adduct on a gold surface. 32 Joel used sum frequency generation to observe the formation of adducts on the surface. Building upon his work, my present research aims to demonstrate the reversible formation and dissociation of pyridine – BF 3 adduct at electrified gold surfaces. The first part of this work (Chapter 2) is organized as follows. First, we introduce the concept of Lewis acid/base pairs. Second, we will cover the experimental and theoretical methods. Third, we present the experimental results supported by computations. 4 Chapter 2 Inductive Effect Alone Cannot Explain Lewis Adduct Formation and Dissociation at Electrode Interfaces 2.1 Introduction Lewis bonding is a chemical bond that involves the interaction between a Lewis base (:B) and a Lewis acid (A), resulting in the formation of an adduct (A-B): A+ :B⇌ A− B (2.1) Lewis bases have one or more unshared electrons. Lewis acids, on the other hand, are species that accept an electron pair from the Lewis bases to complete their octet or stabilize their electronic configuration. 33 Lewis acids can be neutral molecules like boron trifluoride (BF 3 ) and aluminum chloride (AlCl 3 ), or positively charged species such as metal cations. A classic example of Lewis acid-base reaction is between NH 3 and BF 3 : BF 3 + :NH 3 ⇌ F 3 B− NH 3 (2.2) The formation of Lewis bonds is important in surface chemistry. Understanding the breaking and formation of Lewis bonds at an electrified interface is relevant to a large range of phenomena, including electrocatalysis and electroadsorption. The complexities of interfacial environments and 5 associated reactions often impede a systematic understanding of this type of bond at interfaces. To address this challenge, we report the creation of a main group classic Lewis acid-base adduct on an electrode surface and its behavior under varying electrode potentials. The Lewis base is a self-assembled monolayer of mercaptopyridine and the Lewis acid is BF 3 , forming a Lewis bond between nitrogen and boron. The bond is stable at positive potentials but cleaves at potentials more negative of∼− 0.3 V vs. Ag/AgCl without an associated current. We also show that if the Lewis acid BF 3 is supplied from a reservoir of Li + BF 4 − electrolyte, the cleavage is completely re- versible. We propose that the N-B Lewis bond is affected both by the field-induced intramolecular polarization (electroinduction) and by the ionic structures and ionic equilibria near the electrode. Our results indicate that the second effect is responsible for the Lewis bond cleavage at negative potentials. This work is relevant to understanding the fundamentals of electrocatalytic and elec- troadsorption processes. In surface chemistry, such bonds describe a large range of chemical in- teractions, including a number of adsorption and electroadsorption phenomena at interfaces. Such interactions include but are not limited to adsorption of CO, CO 2 , H 2 O, and halides on metals and metal oxides. 34;35;36;37;38 Frustrated Lewis pairs (FLPs) are special cases where overlap of orbitals is sterically hindered. FLPs were first discovered several decades ago, but their applications in the field of electrocatalysis have recently received significant attention. 39;40;41 Gianetti and cowork- ers have lately introduced the carbocation-based Lewis ligands for catalysis. 42 Moreover, Lewis interactions have been shown to shift the redox potentials of electroactive species. For example, Carino et al 43 have demonstrated formation of BF 3 -quinoxiline adducts from a LiBF 4 electrolyte and subsequent modification of redox properties of the Lewis adduct. Recent work has shown that the strength of classic Lewis pairs is modified upon light excitation 44 Studying the interfacial Lewis interactions is important in electrochemistry. However, Lewis bonding is often convoluted with a range of complex phenomena at the surface, including poor characterization of surface sites and geometries, involvement of the band structure of the solids, difficulty in measurement of partial electrosorption valency of the adsorbates, and finally compet- ing reactions. 45;46;47;48 Therefore, gaining fundamental understanding requires the investigation 6 of model interfacial Lewis acid-base pairs to avoid some of these complexities. Previously, we have reported the formation of adducts between surface-bound benzonitrile and a common Lewis acid. 32 However, little is known regarding the formation and dissociation of classic Lewis bonds under applied potentials on electrode surfaces. The strength of a Lewis adduct at an interface is likely affected by many factors. The interfacial electric fields can polarize the adduct and modulate the strength of the Lewis bond. Furthermore, the electrochemical potential can affect the ionic structure and concentrations near the electrode. Therefore, in cases where ions are involved either directly or indirectly in the Lewis interactions, adduct stability can be affected by the potential. To understand how Lewis bonds break under electrochemical polarization, we have designed a classic Lewis adduct tethered to an electrode. The Lewis base is an adsorbed monolayer of 4-mercaptopyridine (MPy), and the Lewis acid is boron trifluoride BF 3 (Figure 2.1). We show spectroscopic evidence that the resulting Lewis bond can be reversibly broken and formed with relatively mild negative potentials in a net non-Faradaic process. Our technical approach is distinct from previous literature in three ways 43 . First, we have confined the adduct by tethering one of the bonding partners on the surface. This removes several ambiguities from studying these inter- actions, most importantly in resolving whether the influence of the electrode is direct or through a redox mediator. Second, we use operando vibrational spectroscopic signatures of the Lewis adduct for identifying its behavior as a function of potential. Third, we demonstrate that we can control reversibility of the adduct formation by the choice of the Lewis acid donor. These advantages give us insight into the stability of the interfacial Lewis bonds without the complications arising from the bulk reactions at an unknown distance from the electrode. Importantly, this approach allows us to more uniquely identify the influence of the interfacial electric field on the Lewis bond. We demonstrate that the Lewis adduct dissociates at a moderately negative potential and can be re- versibly formed when a reservoir of the Lewis acid is present in the electrolyte. Finally, we will present a proposed mechanism explaining the interfacial adduct’s breakdown and formation. 7 Figure 2.1: (a) Lewis adducts between adsorbed MPy and BF 3 on a gold surface. (b) Reversible electrochemical formation/dissociation of surface adduct at positive and negative potentials. The adduct formation/dissociation is reversible upon varying the electrode potential when BF 3 is sup- plied from Li + BF 4 − equilibrium. 2.2 Materials and Methods 2.2.1 Experimental Methods Solid pyridine-BF 3 was synthesized and purified according to the procedure reported in the liter- ature 49 . High purity gold (% 99.99 from Surepure Chemetals Inc.) wire of 1 mm thickness was heated and flattened to be used as the surface enhanced Raman spectroscopy (SERS) substrate. We developed a surface preparation method to make the substrate SERS-active. The gold substrate (1 cm 2 surface area) was sanded with sandpapers of increasing mesh grits (400, 1200, and 3000). After sonicating the gold wire in ethanol for approximately 10 minutes a thin layer of gold from a gold electrodeposition solution (Gold Touch Inc. Figure 4.5) was electrodeposited on the gold wire by holding the potential at -1.0 V (vs Ag/Agcl) for 300 seconds. Sanding combined with the gold electrodeposition procedure created a roughened gold surface suitable for SERS measurements. The SERS active gold wire was sonicated for 10 minutes and then soaked in a closed container filled with a 0.01 M solution of MPy for approximately 1 hour. After MPy adsorption, the gold surface was sonicated in ethanol for 5 minutes to remove any physiosorbed species. Solvents were 8 purged with N 2 gas prior to each experiment. A home-built electrochemical cell made of Teflon was designed to carry out the specrtoelectrochemical measurements. A quartz glass window with 3/4 inch diameter was incorporated into the design, permitting the laser beam into the cell (Fig- ure 4.3). SERS spectra were collected using a HORIBA XploRA microRaman Microscope (10x objective lens) with a 785 nm excitation source to reduce the likelihood of fluorescence from the samples investigated. The laser was operated at a relatively low power (< 5 mW ). SERS mea- surements for each sample were conducted without changing the laser irradiation position on the gold surface. Typical accumulation time was 30 s. A Ag/AgCl (3 M KCl) reference electrode, a gold counter electrode, and a 1010 B Gamry potentiostat were used for all electrochemical mea- surements. Impedance measurements were obtained using a Gamry Reference 3000 potentiostat. A sinusoidal potential with an amplitude of 10 mV was superimposed on various dc potentials ranging from +0.5 to -0.7 V . All impedance measurements were collected at a frequency range from 100 kHz to 1 Hz. An equivalent circuit model (Figure 4.25) adopted from the literature was used to describe the system and to measure the electrical double layer (EDL) capacitance. Echem Analyst T M software (from Gamry Inc.) was used for data fitting. All chemicals were purchased from Sigma Aldrich and used without further purification. 2.2.2 Computational Methods Spin-polarized periodic density functional theory (DFT) calculations were performed using the Quantum ESPRESSO code. 50;51 The dispersion corrected PBE-D3 functional was employed as the exchange–correlation functional. 52;53 The core electrons were treated using the optimized norm- conserving Vanderbilt pseudopotentials, and the valence states were treated using a plane-wave basis set with a wavefunction kinetic energy cutoff of 80 Ry. 54;55 Total energies were converged to a tolerance of 10 − 6 Ry, and geometry optimizations were converged to a force criterion of 10 − 3 Ry/Bohr for all unconstrained atoms. The electronic states were smeared using the first-order Methfessel–Paxton method with a smearing width of 0.01 Ry (0.136 eV). 56 DFT calculations were performed using a 3-layer 4× 4 Au(111) slab with the bottom layer constrained to its bulk 9 positions and a total cell length of 50 ˚ A along the axis normal to the surface. Adsorbed mercap- topyridine (MPy*) was optimized at three-fold hollow sites, as previous computational studies of the adsorption of similar molecules have shown that adsorption is more favorable to hollow sites than to top sites on Au(111). 57;58;59;60;61 A 2× 2× 1 k-point grid was used to sample the Brillouin zone in the slab calculations. Solvent effects were treated using the self-consistent continuum solvation model within the Environ patch to Quantum ESPRESSO, 62 in conjunction with the propylene carbonate dielectric constant of 64.0 63 and a solvent radius of 3.36 ˚ A for the solvent-aware interface correction. 64 The electrode potential was modified by changing the number of electrons in the unit cell, and the ex- cess charge was compensated by a strip of countercharge embedded in the dielectric continuum solvent as in previous studies. 65;66;67;68 The computational electrode potential E was determined from the system Fermi level and the electrostatic potential in the bulk implicit solvent. The value of E relative to the Ag/AgCl electrode was determined from previously derived empirical cor- rections, 69 as also described in recent work from our group. 70 To ensure that excess charge was localized only on one surface of the Au(111) slab, a vacuum region with a dielectric constant of 1 was added to the back side of the slab. A schematic of the dielectric regions and countercharge embedding is shown in Figure 4.14 of the Appendix. Additionally, the parabolic periodic boundary condition correction to the total energy was applied for calculations with a net charge. Coordinates of optimized geometries and sample Quantum ESPRESSO and Environ input files are provided in the Appendix. The grand potentialsΩ were calculated as a function of the applied potential E using the ex- pressions provided in the Appendix. The grand potentials were computed relative to MPy* at PZFC, and the chemical potential reference for each excess species was estimated as the DFT free energy of the species in dielectric continuum propylene carbonate. The translational and rotational entropies of the solution-phase BF 3 were estimated using the translational and rigid rotor partition functions, and these entropic contributions were assumed to be negligible for surface-adsorbed 10 species. Zero-point energy contributions of BF 3 and the adsorbed MPy and MPy-BF 3 were in- cluded using the DFT-calculated vibrational frequencies, corresponding to a∆(ZPE) of +0.16 eV upon formation of the adduct. We assumed that the change in vibrational entropies upon adduct formation would be small and therefore did not include these contributions to the calculated Ω values. We note that because of the approximations involved in the calculation of the zero-point energy and entropic contributions, they do not change as a function of applied potential and corre- spond to constant shifts of the free energy curves. Zero-point and entropy terms were not included in the free energy for other spectator species (Li + BF 4 − and Li + PC) because they are not involved in the making or breaking of chemical bonds. It is therefore assumed that differences in these terms would be negligible between the interfacial system and their corresponding chemical potential ref- erences. Further details are provided in the Appendix. 2.3 Results and Discussions We begin by presenting the vibrational spectral markers for adduct formation of pyridine-BF 3 in the bulk and on the surface. Then we will use these markers to identify formation and breakdown of the adducts under the influence of potential. Figure 2.2a shows the bulk Raman spectra of pyridine and pyridine-BF 3 adduct in the signature region. The full Raman spectrum can found in Figure 4.9. Pyridine exhibits several well-known ring stretching modes in the 1600 cm − 1 region. 71;72 Upon formation of the pyridine-BF 3 adduct, two blue shifted peaks are observed. Such an upward frequency shift for pyridine upon complex- ation with boron halides has been reported in the literature. 73;74 Our computational results also show that the ring stretching mode for MPy blue shifts by around 17 cm − 1 upon formation of the MPy-BF 3 adduct, which is in good agreement with the experimental results (Appendix). In our work, the spectral changes in the 1570-1650 cm − 1 region are most distinct. Therefore, we will use them in the electrochemical experiments as the main marker bands for identifying adduct formation/dissociation. 11 Figure 2.2 a depicts the SERS spectra of surface-adsorbed MPy and the MPy-BF 3 adduct on gold surface immersed in acetonitrile. The adduct here was prepared by treating the MPy mono- layer with BF 3 -ether. The SERS spectrum of MPy shows two distinct features corresponding to the ring stretching modes. These MPy bands have also been extensively reported in the lit- erature. 75;76;77;78;79 The surface-adsorbed MPy spectra deviate slightly from the bulk spectra of pyridine and the bulk spectra of MPy, as is common for surface-tethered species. 80 81 79 After sur- face adduct formation, similar to the bulk case, the ring stretching modes are shifted to higher frequencies. These modes have been previously used as a probe to monitor the protonation and metal complexation of MPy at the interface. 76;77;78;75 12 Figure 2.2: (a) Raman spectra of liquid pyridine and pyridine-BF 3 adduct. (b) SERS spectra of MPy and MPy-BF 3 in acetonitrile on a gold electrode. The ring stretching (C=C) bands around 1600 cm − 1 blue shift upon adduct formation both in the bulk and on the surface. To confirm the assignment, we studied the stability of the surface adduct in the presence of strong and weak Lewis bases. Figure 2.3 depicts the SERS spectra of MPy-BF 3 in a strong Lewis base (triethylamine, TEA) and a weak Lewis base (dichloromethane, DCM). The structure of the surface MPy-BF 3 adduct is preserved in DCM solution, as evidenced by its SERS spectrum. How- ever, TEA is a strong base compared to MPy and therefore dissociates the Lewis acid BF 3 from the surface, as evidenced by the spectral changes in the adduct marker bands. This further confirms 13 the identity of the adduct and shows that it can be subjected to chemical dissociation by a Lewis base stronger than MPy. Figure 2.3: SERS spectra of adduct in DCM (blue) and TEA (red). The adduct is stable in DCM but chemically dissociates upon addition of the strong Lewis base TEA. The C=C stretching marker bands red shift after adduct dissociation. Next, we evaluate whether adduct dissociation and formation can be achieved by application of an electrochemical potential. Towards this goal, we have followed two approaches. In the first approach, we treated the MPy monolayer on a gold electrode with BF 3 -ether to generate the MPy-BF 3 adduct. The electrochemical measurements were performed in tetrabutylammonium hexafluorophosphate (TBA + PF − 6 ) electrolyte in acetonitrile. In this case, when the adduct breaks down under the influence of potential, the dissociated BF 3 is dissolved in the solution and is not fully retrieved upon reversal of the potential. Therefore, we refer to this case as irreversible adduct dissociation. The experiment was repeated in other organic solvent (dichloromethane) and yielded similar results. In the second approach, we took advantage of the known equilibrium betweeen BF − 4 and BF 3 in a LiBF 4 electrolyte to generate the adduct. In this case, Li + BF 4 − is used as the 14 electrolyte in propylene carbonate solvent, and due to the LiBF 4 ⇌ BF 3 + LiF equilibrium a con- stant supply of BF 3 exists in the solution. 82;83;84;85 Therefore, when the adduct is broken, it can be regenerated upon reversal of potential. We refer to this case as the reversible adduct formation- dissociation. The solvent in the second case was chosen for consistency with previous literature supporting the liberation of BF 3 from LiBF 4 in propylene carbonate. 43 The basicity of the solvent is important for solvation of BF 3 and consequently the stability of the pyridine- BF3 adduct at the surface. Figure 2.3 shows that the adduct is stable in DCM, which is a weak Lewis base, but dissociates in TEA, which is a strong Lewis base relative to MPy. For the electrochemical experi- ments, we decided to use solvents of intermediate basicity, ACN and PC, to allow for dissociation under application of potential, while keeping the adduct intact under open circuit conditions. The enthalpies of complex formation between solvent and BF 3 , which is a proxy for basicity, for these solvents have been reported to be -10.0 kJ/mol, -60.39 kJ/mol, -64.19 kJ/mol, and -135.87 kJ/mol for DCM, ACN, PC, and TEA, respectively. 86 Figure 2.4 shows the SERS spectra for the irreversible adduct dissociation as a function of applied potential. The spectrum associated with the open circuit potential (OCP) is very similar to that at 0 V , showing the distinct signature of the adduct on the surface, namely ring stretching modes that are blue-shifted to slightly higher frequency than 1600 cm − 1 , as discussed earlier. Then the potential was swept from 0.0 V to 0.5 V and back towards negative potentials. The signature of the adduct remains intact in this range all the way up to -0.1 V . At potentials between -0.2 V and -0.4 V the peak associated with MPy (slightly lower frequency than 1600 cm − 1 ) gradually gains intensity. At potentials more negative of -0.4 V , the signature of the adduct completely disappears and the spectra indicate unadducted MPy. As explained above, because the reaction is irreversible, upon returning back to 0 V , the SERS signature of the adduct does not completely re-emerge. This is because the dissociated BF 3 , which is dissolved in the bulk solvent, is present in extremely small concentrations such that reformation of the adduct becomes difficult. To assess the evolution of the adducted and unadducted MPy at various potentials, we calcu- lated an average frequency for each spectrum in the 1600 cm − 1 range as explained in the SI and 15 shown in Figure 2.4 (right panel). This is a more suitable approach compared to following a single peak because the spectrum is structured. Figure 2.4 (right panel) shows that the average frequency in this range undergoes a red shift indicative of adduct breakdown at negative potentials. This signature is not fully recovered upon returning to 0 V . Figure 2.4: Potential-dependent SERS spectra of the MPy-BF 3 adduct on the surface. The left panel depicts the potential for each spectrum and defines the y-axis for the other two panels. The potential starts from OCP, is swept to positive potential, followed by a negative and a positive sweep to bring it back to 0 V . The right panel depicts the average frequency of the marker bands in the 1600 cm − 1 range vs applied potential. The adduct (blue spectra) is stable in a wide range of potentials between +0.5 V and -0.2 V but dissociates to MPy (red spectra) at potentials more negative than -0.5 V . The spectra for the second case, which is reversible formation/dissociation of the adduct, are shown in Figure 2.5. Prior to discussing this data, we comment on the known equilibrium between BF 4 − , BF 3 , and F − . As mentioned earlier, several authors have shown that BF 3 can be liberated from LiBF 4 based on the equilibrium BF 4 − ⇌ BF 3 + F − . 82;83;84;85 A closely related example is the work by Carino et al. where they report formation of quinoxaline-BF 3 adducts in the presence 16 of LiBF 4 . 43 Interestingly, they report that the adduct formation was only possible from a lithium salt of BF 4 − , and that tertbutyl ammonium (TBA) + and sodium Na + cations did not lead to adduct formation. We will discuss a similar observation below. In our case, upon addition of LiBF 4 to the MPy monolayer in propylene carbonate (PC) sol- vent, the adduct is formed spontaneously at OCP as evidenced by the Raman marker bands for the adduct (Figure 2.4, middle panel). Then the adduct is subjected to potential in the LiBF 4 elec- trolyte. Similar to the irreversible case described above, the adduct remains intact as the potential is swept from 0 V to 0.5 V and then back to near -0.3 V . As the potential is swept to more neg- ative values the signature of the adduct gradually disappears. At -0.5 V the adduct is completely dissociated, and the Raman spectra indicate free MPy on the surface. After adduct dissociation, the potential is swept back to positive values all the way to 0 V . In contrast to the irreversible case, the adduct begins to regenerate at -0.2 V . Similar to the irreversible case, we calculated the average frequency in the 1600 cm − 1 spectral range (Figure 2.4, right panel). These results distinctly show the frequency shift characteristic of adduct breakdown at negative potentials and its recovery with potential reversal. 17 Figure 2.5: SERS spectra of MPy- BF 3 (blue spectra) and MPy (red spectra) in the presence of 0.1 M LiBF 4 in propylene carbonate (middle panel). The left panel depicts the y-axis for the other two panels, corresponding to the applied potential starting from OCP and moving positive, then negative, and then positive again. The adduct breaks at negative potentials, but is regenerated upon reversal of the potential, as evidenced by the changes in the marker bands. The right panel depicts the average C=C frequency of the marker bands in the 1600 cm − 1 range vs applied potential. Note that several reversible features appear in the spectra at lower wavenumbers relative to the ring stretching modes. Some of them may arise from the interaction of MPy with the solvent, and therefore may contain rich information about the interface. Their exact assignment is complicated and outside the scope of this work. It is worth mentioning that all shifts in the frequency of marker bands around 1600 cm − 1 in Fig- ure 2.4 and Figure 2.5 indeed due to adduct formation and dissociation rather than the inherent re- sponse of MPy to potential due to vibrational Stark shift or peak intensity changes. To confirm this, we kept the solvent the same (propylene carbonate) but used tertbutyl ammonium (TBA) + BF 4 − as the electrolyte. As discussed earlier, Carino and co-workers reported that (TBA) + BF 4 − does not result in formation of quinoxiline-BF 3 adducts. 43 Consistent with their report, we also did not observe the signature of adduct formation in our SERS spectra (Figure 4.10 and Figure 4.11 The 18 spectra show some change in the relative intensity of the two MPy peaks, but no peaks higher in frequency than 1610 cm − 1 indicative of adduct formation were observed. The data was subjected to the same average frequency analysis to show the spectral evolution of the average frequency as a function of potential (Figure 4.11). It is very clear that the adduct formation and breakdown exhibit distinctly different behavior compared to the inherent response of MPy to potential. To investigate the underlying mechanism of the adduct dissociation at negative potentials, we consider the energetics of the adduct at the interface under the influence of electrochemical po- tential. Two main contributions influence the adduct energetics near an electrode - intramolecular inductive effect and ionic structure. Figure 2.6 illustrates these effects schematically. Figure 2.6: (a) Polarizing effect of electrode potential on the strength of the Lewis bond. At positive potentials electron density is moved away from the Lewis bond and the bond weakens. The opposite is expected at negative potentials. (b) Effect of electrode potential on ionic structures and equilibria near the interface. We postulate a possible scenario in which at negative potentials, lithium ions aggregate near MPy and via a weak interaction with the nitrogen facilitate the for- mation of halogen-bridged [B 2 F 7 ] − 1 complex. At positive potentials, the lithium ions are pushed away from the interface and hence stabilize the MPy-BF 3 adduct. 19 Below we describe the details of each one of these effects. The first arises from the molecu- lar polarization of MPy under the influence of the electric field near the electrode, also known as the electroinductive effect. 6;31 In the presence of a negative potential, the electric field points into the electrode, which is expected to polarize MPy by pushing electron density toward the nitrogen. In previous work, our groups have studied such polarizing influence of an electrode on adsorbed benzonitrile molecules using the signature Stark shift of the nitrile mode 60 . We have shown that such polarization is analogous to the effects of adding electron-donating substituents on the para terminal of the ring. 6 It is also known that when electron-donating groups are added to the para ter- minal of pyridine, its Lewis basicity increases, as evidenced by thermochemical studies. 87;86 The reverse argument holds for positive potentials behaving similar to electron-withdrawing groups. Therefore, it is expected that at negative potentials the Lewis basicity and hence the Lewis bond strength of MPy-BF3 will increase. Based on similar arguments, positive potentials are expected to weaken the Lewis bond. To elucidate the role of the electroinductive effect, we performed periodic DFT calculations of the adsorbed adduct (MPy-BF 3 *) on Au(111) shown in Figure 2.7a and Figure 2.7b shows the electron density difference at -0.58 V relative to the potential of zero free charge (PZFC). These calculations show that as the applied potential becomes more negative, the electron density at the N-B bond increases, consistent with the expectation from the electroinductive effect. To further illustrate the presence of the electroinductive effect for the adduct, the N-B bond length was calculated from DFT geometry optimizations performed at different applied potentials. These data show that the adduct bond length shortens with a more negative applied potential and elongates with a more positive applied potential (Figure 2.7c). Overall, these results suggest that the Lewis bond becomes stronger with a more negative applied potential, consistent with the presence of an electroinductive effect upon electrochemical bias. 20 Figure 2.7: Analysis of the electroinductive effect from periodic DFT calculations. (a) DFT- optimized structure and (b) charge density difference plot for MPy-BF 3 * in propylene carbonate continuum solvent. Au, S, C, N, B, F, and H atoms are shown in gold, yellow, brown, blue, green, silver, and white, respectively. The charge density difference isosurface in (b) shows the localization of excess charge upon polarization of -0.58 V vs. PZFC. Yellow represents an increase in electron density, whereas cyan represents a depletion of electron density. The isosurface level is set to 0.00025 e − /Bohr 3 . The increased charge density over the N–B bond is indicative of the electroinductive effect. (c) The N–B bond length as a function of the applied potential E, where the bond shortens (strengthens) at more negative potentials and elongates (weakens) at more positive potentials. Periodic DFT was also used to calculate potential-dependent reaction free energies for adduct formation in implicit propylene carbonate solvent. By varying the charge in the unit cell, the grand potentialsΩ of the adsorbed mercaptopyridine (MPy*) and the adsorbed adduct MPy-BF 3 * were calculated as a function of the applied potential E. Optimized structures of MPy* and MPy- BF 3 * with no added charge (i.e., at PZFC) are shown in Figure 2.8. The grand potentials were calculated relative to MPy* at PZFC, and the chemical potential reference for the excess BF 3 in the MPy-BF 3 * phase was estimated as the DFT free energy of BF 3 in dielectric continuum propylene carbonate. Figure 2.8 shows the DFT-calculatedΩ values for MPy* and MPy-BF 3 * as a function of E. The results obtained directly from DFT are shown by the markers on the plot, and a continuous function is interpolated from a cubic spline fit to the DFT data. These curves clearly show that, over a wide range of applied potentials, the free energy of the adduct MPy-BF 3 * is significantly lower than the dissociated MPy* and BF 3 . Moreover, the reaction free energy for 21 adduct formation at a given E,∆Ω(E)=Ω MPy− BF 3 ∗ (E)− Ω MPy∗ (E), becomes more negative with more negative applied potential. These results cannot account for the experimental observation that the adduct dissociates at lower potentials. Figure 2.8: Thermodynamic analysis of adduct formation. (a) DFT optimized MPy* and MPy- BF 3 * at PZFC, outlined in red and blue, respectively. (b) Corresponding grand potentialsΩ as a function of applied potential. (c) The reaction free energy∆Ω as a function of E, where∆Ω is the free energy of adduct formation, corresponding to the difference between the blue and red curves in (b) at a given value of E. The second contribution to the energetics of the adduct arises from the ionic structure and ionic equilibria in the electric double layer (EDL). It is expected that at positive (negative) potentials the EDL will be enriched in negative (positive) ions. In electrochemistry, often the interfacial ions are 22 also part of a chemical equilibrium, for example the proton-dissociation reaction. The electrode potential perturbs such equilibria, and consequently any interfacial reaction that depends on them is affected. As a case in point, the potential dependence of proton concentration at the interface is heavily studied and reported in the literature. 15;88 A similar analysis can be applied to the BF 4 − ⇌ F − + BF 3 equilibrium. The surface adduct formation is inherently tied to this equilibrium because it consumes the Lewis acid BF 3 . At positive potentials more BF 4 − is expected to be present in the double layer, while at negative potentials it is expected to be pushed away. Therefore, any surface reaction that depends on BF − 4 would become more favorable at positive potentials and less favorable at negative potentials. This scenario is depicted in Figure 2.6b. Additionally, as is reported in the literature, Li + has some affinity with Lewis bases similar to pyridine. 89 Therefore, it is plausible that at negative potentials, Li + may be drawn to the surface and interact with the nitrogen of pyridine, providing a possible explanation for the dependence of our experimental results on the presence of Li + . At the same time, the BF 4 − ion could form a fluorine-bridged [B 2 F 7 ] − 1 complex anion with BF 3 and be pushed away from the surface at negative potentials. The existence of the [B 2 F 7 ] − 1 complex has been extensively reported in the literature. 90;91;92;93;94;95 The mechanism by which the adduct dissociates for the irreversible case is likely very similar to that for the reversible case. In particular, at negative potentials, positively charged (TBA) + ions aggregate near the surface. At the same time the PF − 6 1 ions could form fluorine-bridged complex anions with BF 3 and eventually dissociate the surface adduct. To understand the influence of BF 4 − and Li + on the adduct breaking and formation, we per- formed a set of eight experiments, in which we systematically varied the concentrations of BF 4 − and Li + , while keeping the ionic strength constant. For maintaining constant ionic strength, we used tetrabutylammonium tetrafluoroborate (TBA + BF 4 − ) and lithium bis(trifluoromethanesulfonic)imide (Li + TFSI − ). The spectra from these experiments, along with a Table summarizing the results, are shown in the SI. When either the BF 4 − or the Li + concentration is below 50 mM, the adduct signature is not observed, and no signature of adduct dissociation or reformation appears as the potential is scanned. Our observations indicate that adduct formation requires at least 50 mM of 23 Li + and 50 mM of BF 4 − in the solution. In these scenarios, the dissociation potential of the adduct did not change significantly. However, the reformation potential shows more sensitivity to BF 4 − and Li + concentrations, varying between -0.2 V and +0.5 V . These results further confirm that the formation and dissociation signatures at the interface depend on both Li + and BF 4 − . To gain in- sight about any ionic structure change as a function of potential, it is reasonable to investigate the change in capacitance of the interface as a function of potential. We have performed impedance spectroscopy of the system and have observed a discontinuous change of capacitance at -0.1 V vs Ag/AgCl, which may indicate a discontinuous change in the ionic arrangement (Figure 4.25). Understanding the details of the ionic arrangement and its influence on capacitance is the subject of future experimental and computational work. In our computational work, we also considered whether the presence of explicit Li + /BF 4 − or Li + /B 2 F − 7 ion pairs near the surface would impact these thermodynamic predictions. For the MPy* state, we considered various orientations of the ion pair (Figure 4.15) The constant potential results reproduce an anticipated phenomenon, where at more negative potentials the Li + cation prefers to be close to the surface because of its favorable interaction with the more negatively charged Au surface. However, at more negative potentials, where the electroinductive effect is expected to be overcome by some other competing interaction to dissociate the adduct, MPy-BF 3 * remains lower in free energy than MPy* and the dissociated BF 3 (Figure 4.16). We observed similar trends with the inclusion of a positively charged Li + /PC near the surface (Figure 4.16). In all three scenarios (no ions, cation/anion pair, Li + /PC), the electroinductive effect persists. Notably, the potential- dependent bond lengths are nearly identical in the absence and presence of ions, suggesting that the presence of these species near the surface does not weaken the Lewis bond at more negative potentials. The use of continuum solvation, inclusion of only a single ion pair, and the lack of conformational sampling of the ion positions most likely prevents an accurate description of the ionic structure at this interface. A more elaborate molecular dynamics study with explicit solvent and all different types of ions at a charged electrode surface might provide additional insights but is beyond the scope of this work. 24 The above two mechanisms are not exclusive to each other, and they independently contribute to the energetics of interfacial reactions. However, in some cases, one or the other dominates. Note that for the case of adduct formation, these effects lead to opposite dependence of adduct stabil- ity on potential, as described above. This situation is unlike the protonation of surface-adsorbed molecules, where both the inductive effect and the ionic effect have similar consequences. In that case, a negative potential would both increase the basicity of the surface-adsorbed molecule via the inductive effect, and also increase the interfacial concentration of the protons via the double layer electrostatics. Our study is a case demonstrating the competition between these two phenomena. Our data show that the adduct is destabilized at negative potentials, whereas it remains stable at OCP and positive potentials. Therefore, we conclude that the ionic structure and equilibrium hy- pothesis (Figure 2.6) is the dominant factor in explaining the potential dependence of the Lewis bond. 25 Chapter 3 Phenol as a Tethering Group to Metal Surfaces: Stark Response and Comparison to Benzenethiol 3.1 Introduction Understanding the adsorption of organic molecules on metals is important in numerous areas of surface science, including electrocatalysis, electrosynthesis, and biosensing. While thiols are com- monly used to tether organic molecules on metals, it is desirable to broaden the range of anchoring groups. In this study, we use a combined spectroelectrochemical and computational approach to demonstrate adsorption of 4-cyanophenols (CP) on polycrystalline gold. Using the nitrile stretch- ing vibration as a marker, we confirm the adsorption of CP on the gold electrode and compare our results with those obtained for the thiol counterpart, 4-mercaptobenzonitirle (MBN). Our results reveal that CP adsorbs on the gold electrode via the OH linker as evidenced by the similarity in the direction and magnitude of the nitrite Stark shifts for CP and MBN. This finding paves the way for exploring new approaches to modify electrode surfaces for controlled reactivity. Furthermore, it highlights adsorption on metals as an important step in the electro-reactivity of phenols. Self-assembled monolayers (SAMs) are molecular assemblies with functional groups that bind to solid surfaces such as gold, silver, and copper 96 . Monolayers with thiol functional groups are 26 among the most studied SAMs. 97;98;99 Thiol SAMs have a wide range of applications in indus- try, including in electronic devices 100 , biosensors 101;102;103;104;105 , microfabrication 100;106 , batter- ies 107 , anti-corrosion coatings for metals 108;109;110 , drug delivery 111 , and catalysis 112 . Addition- ally, thiol SAMs can be used on electrode surfaces to study interfacial processes and reactions. Hildebrandt and co-workers have used thiol monolayers to study protein structure and dynam- ics 113;114;115 . Mayer and coworkers have employed aromatic SAMs 4-mercaptobenzoic acid and 4-mercaptobenzonitrile (MBN) to study acid-base interfacial equilibria 15 . Some of us have em- ployed thiol-based SAMs to study the interfacial electric field, ionic structures near the electrodes, and the formation of interfacial adducts. 4;5;7;8;30;32 . The natural analog of aromatic thiol is phenol, a very common functional group in a wide range of organic and biological molecules. Hence, it is desirable to explore the surface adsorp- tion of phenols on metal surfaces and compare the results with those of their thiol counterparts. While the interaction of aromatic thiols with metal surfaces has been widely studied, the adsorp- tion of phenols on these surfaces has received little attention. Moreover, the orientation of phenols upon adsorption on metal surfaces remains a topic of debate. One study showed that phenols and 4-cyanophenols in a basic medium adsorb onto the gold surface in a perpendicular orientation via the oxygen atom 116;117 . Reflectance and capacitance measurements have shown that phenols adsorb to the gold surface at negative potentials viaπ− interaction. However, they adopt a perpen- dicular configuration at positive potentials by forming a strong covalent bond between the oxygen atom and gold. 118 . Another research investigated the adsorption of phenols on gold in an aqueous medium. However, the study did not provide information on the phenols’ adsorption geometry 119 . A separate study demonstrated that phenols can adopt different adsorption geometries on metal surfaces depending on their concentration. Specifically, the study found that at low concentrations, phenols adsorb onto gold in a flat orientation, while at higher concentrations, they exhibit a more upright configuration 120 . The adsorption of phenols and their geometry with respect to gold sur- faces remain a topic of ongoing debate, with inconclusive reports. Hence, further investigation in 27 this area is necessary. Specifically, it is crucial to compare phenols’ adsorption behavior with thiols to understand whether phenols adsorb and behave similarly. In this work, we use vibrational spectroscopy to show the adsorption of CP on gold. Our technical and experimental approaches differ from previous work in tow key aspects. First, we use surface-enhanced Raman spectroscopy (SERS) by measuring the nitrile vibration as a marker to confirm the adsorption of CP on the gold electrode. Second, we measure the vibrational frequency of nitrile as a function of potential over a relatively wide range (+0.6 to -0.8 V vs Ag/AgCl). The observed frequency shifts due to potential are similar to that of MBN, suggesting that the adsorbed CP and MBN molecules have similar bonding structures to the substrate. The frequency change of adsorbed molecules in response to potential, known as the vibrational Stark shift, is a powerful tool for understanding the electrostatics and solvation environment of the interface. A molecule may respond to the potential if it is adsorbed to the surface or is within the electric double layer and can feel the polarization from the electrode. Our observation of the CP molecule’s Stark response and its similarity to MBN confirms that CP is adsorbed to the surface with the oxygen atom. We also used computational approaches to estimate the adsorption energies of Au-O and Au-S bonds and show the adsorption geometries for both surface-bound species. 3.2 Materials and Method 3.2.1 Experimental Methods We employed a procedure for electrode preparation and spectroelectrochemical measurements that was previously described by us 30 . In brief, A SERS substrate was prepared by heating and flatten- ing a 1 mm thick gold wire from Surepure Chemetals Inc. The gold substrate was then sanded with sandpaper until the surface became shiny, followed by sonication in ethanol for 10 minutes. Subse- quently, a thin layer of gold was deposited on the substrate using a gold electrodeposition solution (Gold Touch Inc.). The gold wire was further sonicated in ethanol for 10 minutes. Afterward, 28 it was immersed in a sealed container filled with a 10 mM solution of each chemical in ethanol for 48 hours to allow for monolayer adsorption. The gold surface was then rinsed and sonicated for 2 minutes in ethanol. A home-built cell made of Teflon was used for spechtroelectrochemi- cal measurements. SERS data were obtained using a HORIBA XploRA microRaman Microscope with a 785 nm excitation source. The typical accumulation time for data collection was around 20 seconds. Electrochemical measurements were performed using an Ag/AgCl (3 M KCl) reference electrode, a gold counter electrode, and a Gamry potentiostat (model 1010 B). All chemicals were purchased from Sigma-Aldrich without further purification. 3.2.2 Computational Methods Density functional theory (DFT) 121;122;123 ab-initio molecular dynamics (AIMD) with the projector- augmented-wave (PAW) potentials 124;125 and the Perdew-Burke-Ernzehof (PBE) functional under the generalized gradient approximation 126;127 was employed for all systems. The electronic struc- ture calculations were performed within the Vienna Ab-initio Simulation Package (V ASP) 128;129;130;131 . The PAW PBE versions included in the POTCAR files for each species were PAW-PBE Au 04Oct2007, PAW-PBE H 15Jun2001, PAW-PBE C 08Apr2002, PAW-PBE O 08Apr2002, PAW-PBE N 08Apr2002, PAW-PBE S 06Sep2000. The Au slab was built with a 111 exposed surface with a 5-layer thick- ness and 5× 5 in the x− y plane. During the V ASP calculations, we utilized a sizeable plane-wave basis energy cutoff (ENCUT) of 520 eV , a 1× 1× 1Γ centered k-point mesh to sample the Bril- louin zone. Studies of molecules adsorption on Au(111) show the need for van der Waals (vdW) dispersion interactions 132 . Thus, we implemented the Tkatchenko-Scheffler (TS) method with it- erative Hirshfeld partitioning for all the simulations. 133;134;135;136 Spin-polarized calculations were omitted since previous studies have demonstrated their negligible impact on the reported results regarding adsorption on Au(111) surfaces 137 . Given the large size of the unit cell, only the gamma point was used. This slab was constructed based on the bulk lattice constant of 4.17 ˚ A, as de- termined from previous calculations on cubic Au bulk crystal, data retrieved from the Materials Project for Au (mp-81) from database version v2022.10.28 138;139 . The bottom two layers of the 29 Au slab were frozen to the bulk geometry in all calculations. The unit cell height was also set to 39.63 ˚ A, to provide a 30 ˚ A vacuum between Au slab layers in the z-direction. The molecules were placed above the top Au layer in an fcc chemisorption site shown to be a favorable position in previous studies for thiols and oxygen on Au(111) 140;141;142;137;143 . For consistency, the oxygen molecule was also placed in the same position before optimization. Additionally, CP and MBN were spaced such that O-O and S-S have a bond distance of 14.7 ˚ A, sufficient to avoid molecule- molecule self-interactions caused by the boundary conditions of the simulations. The harmonic nitrile frequencies are computed by taking the second-order derivatives of the total energy with respect to the ions’ positions using a finite differences approach 144;145 . In order to reduce compu- tational cost, all-atom positions were fixed, except for the C and N atoms in the nitrile probe which were allowed to be displaced. The absorption energy was calculated as the difference in energy between the molecule on the Au surface E (n) Molecule on Au , and the sum of the individual components (charged Au slab E Charged Au , and the gas phase molecule E Neutral Molecule ): ∆E absorption (eV)= E Charged Molecule on Au − (E Charged Au + E Neutral Molecule ) (3.1) While the charge density shown is calculated as the difference between the density of the molecule on the Au surface ρ (charged) Molecule on Au , and the sum of the individual components (charged Au slab ρ Charged Au , and the gas phase moleculeρ Neutral Molecule ): ∆ρ =ρ Charged Molecule on Au − ρ Charged Au − ρ Neutral Molecule (3.2) 3.3 Results and Discussion First, we compare the Raman spectra of CP and MBN in bulk and adsorbed on the electrode. Figure Figure 3.1a displays the Raman spectra of bulk CP and MBN in ethanol obtained under similar experimental conditions. The Raman signal for both molecules are comparable, indicating that the nitrile stretching mode has a similar Raman cross-section for both molecules. The small 30 difference in frequency between the two is ascribable to the differences in the electron-withdrawing strengths (Hammett parameter σ p ) between SH and OH 6;146 , as well as their relative response to the hydrogen-bonding solvent. Note that this difference is not the central point of this work and will not be discussed further. Figure Figure 3.1b shows the SERS spectra of CP and MBN, prepared from a solution of similar concentration and equal soaking time (48 hours). The spectra are obtained in a 0.1 M NaClO 4 solution. The SERS signal of MBN exhibits a significant six-fold increase compared to CP. Given that the nitrile Raman cross section for CP and MBN is nearly the same in the bulk solution, it is reasonable to attribute the difference to surface coverage. This disparity in surface coverage can be attributed to the lower adsorption energy and slower adsorption kinetics of CP relative to MBN, as discussed later. 31 Figure 3.1: (a) Raman spectra of 0.1 M CP and 0.1 M MBN in ethanol obtained under similar experimental conditions, revealing that their Raman cross sections are comparable. (b) SERS spectra of CP and MBN on gold, indicating successful adsorption of CP albeit with lower coverage. Figure Figure 3.2 depicts the change in the nitrile stretching frequency of CP and MBN as a function of electrode potential in 0.1 M NaClO 4 . Each frequency value represents the average of three independent measurements on different samples recorded after applying potentials with a 0.1 V increment. All frequency values are referenced with respect to the frequency at 0 V vs. Ag/AgCl. 32 Figure 3.2: Frequency shift of MBN (red) and CP(blue) as a function of applied electrochemical potential relative to 0 V vs. Ag/AgCl. The electrode potential begins at 0 V and is swept forward to positive potentials, followed by a reverse scan to negative values, and then back to 0 V . Each frequency value represents the average of three independent measurements. The behavior of CP is qualitatively very similar to that of MBN. The potential response of CP seems to deviate slightly in the forward scan and lag behind that of MBN by about 2 cm − 1 . However, in the range of 0.4 V to -0.6 V , the behavior is very similar. Note that each trace is the average of three independent measurements on three samples. The potential-induced Stark shifts of the nitrile stretching mode for MBN have been reported in the literature 6;147;102;5;148 in the range of 5 to 8 cm − 1 /V . In this work a Stark tuning rate of 5.35 cm − 1 /V was observed in the potential range of -0.4 V to 0.6 V , which is consistent with previous reports. Note that the Stark tuning rate is influenced by several factors, including ionic strength and 5 electrolyte identity 6 . Interestingly, the Stark tuning rate for CP is 5.34 cm − 1 /V in this range, which is very similar to that of MBN. This similarity indicates that both MBN and CP have the nitrile group located 33 approximately at the same distance from the electrode and are both covalently bound to the gold electrode via the sulfur and oxygen atoms respectively. It is very unlikely that CP molecules attach to gold via the nitrogen of the nitrile group. Re- cently, it has been demonstrated that bond formation between a nitrile group and metal ions results in a significant blue shift in the nitrile frequency 149 . If CP were adsorbed onto the gold surface via the nitrile nitrogen, this would cause a significant blue shift in the nitrite frequency and likely an inverse Stark shift. We have calculated the vibrational frequency of the nitrile group for both molecules as a func- tion of potential. This was achieved by varying the charge of the metal slab from -1 to +1, as outlined in the computational methods later. It is worth noting using the PBE functional the ab- solute frequency values tend to be overestimated. Consequently, the relative trends are of primary significance and carry the relevant information. [FIGURE ] As shown in figure xxx, the nitrile frequencies of MBN consistently exhibit higher values than those of CP, irrespective of the charge levels. Translating charge into an equivalent electrochemical potential for a better comparison with experimental values presents a significant challenge. This process often necessitates the im- plementation of sophisticated methodologies, higher computational costs, and, in certain instances, an explicit account of the electrolyte 60 . Given that the exact comparison between calculated and experimental values is not the central focus of our current investigation, we have chosen to confine our discussion to a comparative analysis of the trends of CP and MBN. In agreement with experimental findings, introducing a positive charge to the system (similar to applying a positive potential to the electrode) results in an increased nitrile frequency for both MBN and CP, as illustrated in FigureFigure 3.3. Both molecules demonstrate the expected nonlinear response to changes in charge, consistent with previous theoretical and computational studies 1;6 . Detailed information on the calculated nitrile vibrational frequency across the charge range of -1 to +1 can be found in the Supporting Information. 34 Figure 3.3: Calculated nitrile stretching frequencies for MBN (red) and CP(blue) adsorbed on a slab of gold at different total net charges for the system. Consistent with experimental results, the nitrile frequency for both molecules shows a blue shift by the addition of charge to the system. Next, we investigate the kinetics of CP adsorption and compare the results to MBN. The adsorp- tion kinetics of Au-S bond have been thoroughly investigated in the literature. The typical adsorp- tion saturation (maximum coverage) for thiol derivatives on gold can range from seconds 150;151 to minutes, 152;153;154 and in some cases, it may even take several hours 155 to the monolayers to fully rearrange. Figure Figure 3.4 illustrates the peak Raman intensity as a function of time. Our experiments suggested that MBN is most ideally adsorbed from a 1 mM solution in ethanol. To the best of our knowledge, no existing literature has reported the adsorption kinetics of phenol on gold. The figure shows that the adsorption kinetics for MBN is significantly faster than CP’s. After approximately 20 min, the Raman intensity for MBN reaches a plateau, indicating adsorption saturation consistent 35 with the reported literature 152;153 . The signal for CP is, in general, about 10 times smaller in the beginning and rising much slower. Even after 40 min, it did not show a plateau. Figure 3.4: Time-dependent peak Raman intensity for 1mM MBN (red), and 1mM CP in ethanol (blue). Figure Figure 3.5 shows the binding energies for MBN and CP at various charges. At zero charge, the Au-S binding energy is -2.23 eV (-53.7 kcal/mol), which is in good agreement with the reported value in the literature 156;157 . The calculated binding energy for CP is -0.33 eV (-7.6 kcal/mol). Both molecules demonstrate a linear relationship between binding energy and adding charge to the gold slab. However, MBN displays a more negative slope (-0.33 eV/charge) than CP (-0.062 eV/charge). Noticeably, at +1 charge, the difference in binding energy is the highest. These disparities may arise from the larger polarizability of the gold-sulfur bond compared to the gold-oxygen bond. The more covalent nature of the gold-sulfur bond makes it more susceptible to electrode polarization. Additionally, previous studies have shown that 4-cyanophenols form an ordered structure on the Au (111) surface, as expected for similar phenol structures on an Au(111) surface. 158 The structural order is consistent with calculated optimized geometries utilized in this 36 study, as shown by calculated Au-O bond lengths and CP-Au angle shown in the supporting infor- mation. CP has a more perpendicular angle with respect to the surface at 89 ◦ , whereas MBN has a smaller angle to the surface 85 ◦ regardless of the charge in the system, consistent with structural ordering previously observed. Figure 3.5: Binding energy (eV) of CP (blue) and MBN (red) on an Au (111) surface at various charges (0, ±0.25, ±0.5, ±1 electron add/subtracted to the system). Both molecules show a linear dependence by adding charge to the Au (111). MBN has a stronger binding to the gold surface with a slope of -0.33 eV/charge, while CP has a slope of -0.062 eV/charge 37 Figure 3.6: Charge density difference plots of MBN (a) and CP (b) calculated according to equa- tion 2. The negative and positive charge build up are shown by red and blue colors respectively with an isovaule of 0.0025 e/Bohr 3 . The two molecules show qualitatively similar charge build up upon adsorption. However, the charge build up for MBN in the gold thiol bond region is slightly more pronounced. Next, we compare the electron densities at interfacial regions and across the molecule. Figure Figure 3.6 shows the charge density differences between free and adsorbed molecules for MBN and CP for a neutral gold slab calculated based on equation 2. The colors red and blue correspond to volumes that gain and lose electron density, respectively. The two molecules exhibit qualitatively similar behavior. A slightly higher density of electrons is observed near the Au-S bond compared to the Au-O system, indicating a stronger affinity of sulfur to to gold. Here, we investigated the adsorption of CP onto a gold surface and compared it to MBN. Our experimental and computational results suggest that CP can adsorb to the gold surface through the oxygen linker but with a lower surface coverage and slower kinetics compared to MBN. These find- ings are relevant to electrocatalysis and electroadsorption studies of molecules containing phenol derivatives. 38 Chapter 4 Conclusions and Future Directions For the first part of my thesis, I studied the behavior of classic Lewis adducts under electrochemical conditions on a surface. We have reported the formation/dissociation of a surface MPy-BF 3 adduct under applied potential. We found that the adduct breaks under negative potentials, contradicting the inductive effect’s expectations. Therefore, we conclude that the inductive effect alone is not the main driver for the stability of the adduct on the surface. Our experimental results suggest that the likely contributors to the adduct formation/dissociation are the ionic structure and concentration changes due to applying potential near the surface. Given the general importance of Lewis bond formation/dissociation at interfaces, our findings are applicable to a wide range of electrochemical processes involving Lewis pairs. Specifically, our work highlights that one cannot rely on the inductive effect alone to describe surface reactivity without considering interfacial ionic structure and chemical equilibria. In the second part of my thesis, I focused on studying the adsorption behavior of phenols on gold surfaces and compared it with that of thiols. Anuj Pennathur and I worked collaboratively on the experimental part of this project. We conclude that similar to thiols, phenols also exhibit an affinity for binding to gold surfaces through the oxygen linker. The DFT calculations for this study, performed by Carlos Mora Perez from Prof. Oleg Prezhdo’s group, indicate that phenol can adsorb to the gold surface via the oxygen linker with a nearly perpendicular geometry. However, the adsorption energy for Au-O is lower compared to the Au-S bond. In the future, I am partic- ularly interested in exploring the adsorption properties of adjacent dithiols on gold surfaces and 39 comparing the results with those of catechol. Specifically, we aim to investigate how the Stark response of a nitrile molecule changes when it is adsorbed via two oxygen or two sulfur linkers. During my Ph.D. program, I had the wonderful opportunity to engage in research across di- verse areas, including spectroscopy, optics, electrochemistry, and organic synthesis. My main area of focus was spectroelectrochemistry using SERS. I was passionate about building optical instru- ments for the lab. That is why I approached my advisor, Prof. Jahan Dawlaty, and requested laser sources and optical components to build a Raman microscope. After investing around two months, I designed and built a triple laser Raman setup shown in Figure 4.33. This Raman system oper- ates with three excitation sources (532, 633, and 785 nm). We used a range of objective lenses, including 4x, 10x, and 40x, to illuminate the sample and collect the Raman scattered light. Three longpass filters were incorporated into the design to suppress the Rayleigh line. The light was directed into the spectrometer using a combination of flat mirrors and a focusing mirror (parabolic mirror). To evaluate the performance of our homemade Raman system, we conducted a comparison with a commercially available Horiba Raman microscope, as depicted in Figure 4.35. Remarkably, the Raman spectrum of benzonitrile acquired with our homemade system exhibited a comparable quality to that obtained using the Horiba Raman microscope, indicating its high performance. Another project that Matthew V oegtle and I collaborated on involved investigating alcohol oxi- dation using TEMPO (2,2,6,6-tetramethylpiperidin-1-oxyl) and its derivatives. TEMPO is a radical with an unpaired electron that undergos electron transfer process. 159 Several research groups have previously reported on alcohol oxidation reactions involving TEMPO. 159;160;159;161;162 Matthew and I were interested in extending the catalytic ability of TEMPO to the surface by tethering it to the gold electrodes. For that purpose, we successfully synthesized (Figure 4.36) and character- ized (Figure 4.42) a diradical amide TEMPO with thiol moiety to tether it to a gold surface. The CV plots of amide TEMPO in 0.1 M NaClO 4 in water confirmed the formation of self-assembled monolayers (SAMs) on a gold surface shown in Figure 4.40. We also took the HNMR data of the diradical amide TEMPO shown in Figure 4.42. 40 Despite our successful synthesis of the TEMPO diradical, our attempts to spectroscopically observe its SAM using SERS were unsuccessful. The underlying fluorescence background from the monolayer completely overwhelmed the SERS spectrum. Even at a 785 nm laser, the fluores- cent background still existed and saturated the CCD detector. In the future, I would like to use surface-enhanced infrared absorption spectroscopy (SEIRAS) to detect the amide TEMPO SAMs. I believe SEIRAS, at least in this case, can offer two main advantages compared to SERS. Firstly, SEIRAS operates in the infrared region and produces no fluorescence background. Secondly, the C=O stretching vibration has a great absorption band in IR; therefore, the formation of aldehydes upon oxidation of alcohols can be easily detected. Alcohol oxidation is an important process in chemistry with an application in direct alcohol fuel cells. 163 The sluggish process of alcohol oxi- dation is still a big challenge. 164 I would really want to study various catalytic approaches (using TEMPO) to address its slow kinetics. I believe that new students in our lab can continue conduct- ing research in this field and develop a suitable method to spectroscopically observe the tethered TEMPO on the surface. 41 Bibliography [1] Sohini Sarkar, Cindy Tseng, Anwesha Maitra, Matthew J V oegtle, and Jahan M Dawlaty. Advances in vibrational stark shift spectroscopy for measuring interfacial electric fields. In Emerging Trends in Chemical Applications of Lasers, pages 199–224. ACS Publications, 2021. [2] Hennie Valkenier, Everardus H Huisman, Paul A van Hal, Dago M de Leeuw, Ryan C Chiechi, and Jan C Hummelen. Formation of high-quality self-assembled monolayers of conjugated dithiols on gold: base matters. Journal of the American Chemical Society, 133 (13):4930–4939, 2011. [3] Layal L Rouhana, Maroun D Moussallem, and Joseph B Schlenoff. Adsorption of short- chain thiols and disulfides onto gold under defined mass transport conditions: coverage, ki- netics, and mechanism. Journal of the American Chemical Society, 133(40):16080–16091, 2011. [4] Shayne A Sorenson, Joel G Patrow, and Jahan M Dawlaty. Solvation reaction field at the interface measured by vibrational sum frequency generation spectroscopy. Journal of the American Chemical Society, 139(6):2369–2378, 2017. [5] Joel G Patrow, Shayne A Sorenson, and Jahan M Dawlaty. Direct spectroscopic measure- ment of interfacial electric fields near an electrode under polarizing or current-carrying con- ditions. The Journal of Physical Chemistry C, 121(21):11585–11592, 2017. [6] Sohini Sarkar, Joel G Patrow, Matthew J V oegtle, Anuj K Pennathur, and Jahan M Dawlaty. Electrodes as polarizing functional groups: Correlation between hammett parameters and electrochemical polarization. The Journal of Physical Chemistry C, 123(8):4926–4937, 2019. [7] Matthew J V oegtle, Tanmoy Pal, Anuj K Pennathur, Sevan Menachekanian, Joel G Patrow, Sohini Sarkar, Qiang Cui, and Jahan M Dawlaty. Interfacial polarization and ionic struc- ture at the ionic liquid–metal interface studied by vibrational spectroscopy and molecular dynamics simulations. The Journal of Physical Chemistry B, 125(10):2741–2753, 2021. [8] Anuj K Pennathur, Matthew J V oegtle, Sevan Menachekanian, and Jahan M Dawlaty. Strong propensity of ionic liquids in their aqueous solutions for an organic-modified metal surface. The Journal of Physical Chemistry B, 124(34):7500–7507, 2020. [9] Stephen D Fried and Steven G Boxer. Measuring electric fields and noncovalent interactions using the vibrational stark effect. Accounts of chemical research, 48(4):998–1006, 2015. 42 [10] Han Wang, Ya-Wei Zhou, and Wen-Bin Cai. Recent applications of in situ atr-ir spec- troscopy in interfacial electrochemistry. Current Opinion in Electrochemistry, 1(1):73–79, 2017. [11] Davide Lotti, Peter Hamm, and Jan Philip Kraack. Surface-sensitive spectro- electrochemistry using ultrafast 2d atr ir spectroscopy. The Journal of Physical Chemistry C, 120(5):2883–2892, 2016. [12] Sohini Sarkar, Anwesha Maitra, Soumyodip Banerjee, V Sara Thoi, and Jahan M Dawlaty. Electric fields at metal–surfactant interfaces: a combined vibrational spectroscopy and ca- pacitance study. The Journal of Physical Chemistry B, 124(7):1311–1321, 2020. [13] C Quijada, A Rodes, F Huerta, and JL Vazquez. In situ ft–irras study of so2 adlayers formed on pt (111) electrodes from open-circuit adsorption in acidic media. Electrochimica acta, 44(6-7):1091–1096, 1998. [14] Akira Yamakata, Eiji Soeta, Tatsuya Ishiyama, Masatoshi Osawa, and Akihiro Morita. Real- time observation of the destruction of hydration shells under electrochemical force. Journal of the American Chemical Society, 135(40):15033–15039, 2013. [15] Murielle F Delley, Eva M Nichols, and James M Mayer. Interfacial acid–base equilibria and electric fields concurrently probed by in situ surface-enhanced infrared spectroscopy. Journal of the American Chemical Society, 143(28):10778–10792, 2021. [16] Edyta Podstawka-Proniewicz, Ilja Ignatjev, Gediminas Niaura, and Leonard M Proniewicz. Phe-metnh2 terminal bombesin subfamily peptides: potential induced changes in adsorption on ag, au, and cu electrodes monitored by sers. The Journal of Physical Chemistry C, 116 (6):4189–4200, 2012. [17] Marcela Dendisov´ a-Vyˇ skovsk´ a, Vadym Prokopec, Martin ˇ Clupek, and Pavel Matˇ ejka. Com- parison of sers effectiveness of copper substrates prepared by different methods: what are the values of enhancement factors? Journal of Raman Spectroscopy, 43(2):181–186, 2012. [18] Xiao Xia Han, Rebeca S Rodriguez, Christy L Haynes, Yukihiro Ozaki, and Bing Zhao. Surface-enhanced raman spectroscopy. Nature Reviews Methods Primers, 1(1):87, 2021. [19] Xiang Wang, Guokun Liu, Ren Hu, Maofeng Cao, Sen Yan, Yifan Bao, and Bin Ren. Prin- ciples of surface-enhanced raman spectroscopy. In Principles and Clinical Diagnostic Ap- plications of Surface-Enhanced Raman Spectroscopy, pages 1–32. Elsevier, 2022. [20] EC Le Ru, M Meyer, E Blackie, and PG Etchegoin. Advanced aspects of electromagnetic sers enhancement factors at a hot spot. Journal of Raman Spectroscopy: An International Journal for Original Work in all Aspects of Raman Spectroscopy, Including Higher Order Processes, and also Brillouin and Rayleigh Scattering, 39(9):1127–1134, 2008. [21] Katrin Kneipp, Yang Wang, Harald Kneipp, Lev T Perelman, Irving Itzkan, Ramachan- dra R Dasari, and Michael S Feld. Single molecule detection using surface-enhanced raman scattering (sers). Physical review letters, 78(9):1667, 1997. 43 [22] Marisia A Fikiet, Shelby R Khandasammy, Ewelina Mistek, Yasmine Ahmed, Lenka Hal´ amkov´ a, Justin Bueno, and Igor K Lednev. Surface enhanced raman spectroscopy: A review of recent applications in forensic science. Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, 197:255–260, 2018. [23] Penghui Li, Feng Long, Wanling Chen, Jing Chen, Paul K Chu, and Huaiyu Wang. Funda- mentals and applications of surface-enhanced raman spectroscopy–based biosensors. Cur- rent Opinion in Biomedical Engineering, 13:51–59, 2020. [24] Hulya Yilmaz, Deniz Yilmaz, Irem Culha Taskin, and Mustafa Culha. Pharmaceutical appli- cations of a nanospectroscopic technique: Surface-enhanced raman spectroscopy. Advanced Drug Delivery Reviews, 184:114184, 2022. [25] Jing Neng, Qi Zhang, and Peilong Sun. Application of surface-enhanced raman spec- troscopy in fast detection of toxic and harmful substances in food. Biosensors and Bio- electronics, 167:112480, 2020. [26] Malama Chisanga, Howbeer Muhamadali, David I Ellis, and Royston Goodacre. Enhancing disease diagnosis: biomedical applications of surface-enhanced raman scattering. Applied Sciences, 9(6):1163, 2019. [27] Quoc Khoa Doan, Manh Hong Nguyen, Cong Doanh Sai, Hong Hanh Mai, Nguyen Hai Pham, Thanh Cong Bach, Viet Tuyen Nguyen, Trong Tam Nguyen, Khac Hieu Ho, Thi Ha Tran, et al. Enhanced optical properties of zno nanorods decorated with gold nanoparti- cles for self cleaning surface enhanced raman applications. Applied Surface Science, 505: 144593, 2020. [28] Judith Langer, Dorleta Jimenez de Aberasturi, Javier Aizpurua, Ramon A Alvarez-Puebla, Baptiste Augui´ e, Jeremy J Baumberg, Guillermo C Bazan, Steven EJ Bell, Anja Boisen, Alexandre G Brolo, et al. Present and future of surface-enhanced raman scattering. ACS nano, 14(1):28–117, 2019. [29] Sohini Sarkar, Anwesha Maitra, William R Lake, Robert E Warburton, Sharon Hammes- Schiffer, and Jahan M Dawlaty. Mechanistic insights about electrochemical proton-coupled electron transfer derived from a vibrational probe. Journal of the American Chemical Soci- ety, 143(22):8381–8390, 2021. [30] Sevan Menachekanian, Matthew J V oegtle, Robert E Warburton, Sharon Hammes-Schiffer, and Jahan M Dawlaty. Inductive effect alone cannot explain lewis adduct formation and dissociation at electrode interfaces. Journal of the American Chemical Society, 145(10): 5759–5768, 2023. [31] Joon Heo, Hojin Ahn, Joonghee Won, Jin Gyeong Son, Hyun Kyong Shon, Tae Geol Lee, Sang Woo Han, and Mu-Hyun Baik. Electro-inductive effect: Electrodes as functional groups with tunable electronic properties. Science, 370(6513):214–219, 2020. [32] Joel G Patrow, Yi Wang, and Jahan M Dawlaty. Interfacial lewis acid–base adduct formation probed by vibrational spectroscopy. The journal of physical chemistry letters, 9(13):3631– 3638, 2018. 44 [33] Gilbert Newton Lewis. Valence and the Structure of Atoms and Molecules. Number 14. Chemical Catalog Company: New York, 1923. [34] Paramita Saha, Sk Amanullah, and Abhishek Dey. Selectivity in electrochemical co2 reduc- tion. Accounts of Chemical Research, 55(2):134–144, 2022. [35] Lingling Peng, Mingzhen Shi, Yi Pan, Zhuoheng Tu, Xingbang Hu, Xiaomin Zhang, and Youting Wu. Ultrahigh carbon monoxide capture by novel protic cuprous-functionalized dicationic ionic liquids through complexation interactions. Chemical Engineering Journal, 451:138519, 2023. [36] Oluwaseun Romiluyi, Yannick Eatmon, Ruihao Ni, Barry P Rand, and Paulette Clancy. The efficacy of lewis affinity scale metrics to represent solvent interactions with reagent salts in all-inorganic metal halide perovskite solutions. Journal of Materials Chemistry A, 9(22): 13087–13099, 2021. [37] Jinsun Lee, Ashwani Kumar, Min Gyu Kim, Taehun Yang, Xiaodong Shao, Xinghui Liu, Yang Liu, Yeseul Hong, Amol R Jadhav, Mengfang Liang, et al. Single-metal-atom dopants increase the lewis acidity of metal oxides and promote nitrogen fixation. ACS Energy Let- ters, 6(12):4299–4308, 2021. [38] Vera Bolis, Claudia Busco, and Piero Ugliengo. Thermodynamic study of water adsorption in high-silica zeolites. The Journal of Physical Chemistry B, 110(30):14849–14859, 2006. [39] Wenwen Lin, Hao Chen, Gaobo Lin, Siyu Yao, Zihao Zhang, Jizhen Qi, Meizan Jing, Weiyu Song, Jing Li, Xi Liu, et al. Creating frustrated lewis pairs in defective boron carbon ni- tride for electrocatalytic nitrogen reduction to ammonia. Angewandte Chemie International Edition, 61(36):e202207807, 2022. [40] Menglei Yuan, Honghua Zhang, Yong Xu, Rongji Liu, Rui Wang, Tongkun Zhao, Jingxian Zhang, Zhanjun Liu, Hongyan He, Chao Yang, et al. Artificial frustrated lewis pairs facil- itating the electrochemical n2 and co2 conversion to urea. Chem Catalysis, 2(2):309–320, 2022. [41] Douglas W Stephan. Diverse uses of the reaction of frustrated lewis pair (flp) with hydrogen. Journal of the American Chemical Society, 143(48):20002–20014, 2021. [42] Liangyong Mei, Jos´ e M Veleta, Jan Bloch, Hannah J Goodman, Dominic Pierce-Navarro, Alejandro Villalobos, and Thomas L Gianetti. Tunable carbocation-based redox active am- biphilic ligands: synthesis, coordination and characterization. Dalton Transactions, 49(45): 16095–16105, 2020. [43] Emily V Carino, Charles E Diesendruck, Jeffrey S Moore, Larry A Curtiss, Rajeev S As- sary, and Fikile R Brushett. Bf 3-promoted electrochemical properties of quinoxaline in propylene carbonate. RSC Advances, 5(24):18822–18831, 2015. [44] Matthew J V oegtle and Jahan M Dawlaty. Can brønsted photobases act as lewis photobases? Journal of the American Chemical Society, 144(18):8178–8184, 2022. 45 [45] Andrew R Akbashev. Electrocatalysis on oxide surfaces: Fundamental challenges and op- portunities. Current Opinion in Electrochemistry, 35:101095, 2022. [46] Zhenyu Sun, Tao Ma, Hengcong Tao, Qun Fan, and Buxing Han. Fundamentals and chal- lenges of electrochemical co2 reduction using two-dimensional materials. Chem, 3(4):560– 587, 2017. [47] Fayez Nasir Al-Rowaili, Aqil Jamal, Mohammad S Ba Shammakh, and Azeem Rana. A review on recent advances for electrochemical reduction of carbon dioxide to methanol us- ing metal–organic framework (mof) and non-mof catalysts: challenges and future prospects. ACS Sustainable Chemistry & Engineering, 6(12):15895–15914, 2018. [48] Song Jin, Zhimeng Hao, Kai Zhang, Zhenhua Yan, and Jun Chen. Advances and challenges for the electrochemical reduction of co2 to co: from fundamentals to industrialization. Ange- wandte Chemie, 133(38):20795–20816, 2021. [49] Etienne Ch´ enard, Andre Sutrisno, Lingyang Zhu, Rajeev S Assary, Jeffrey A Kowalski, John L Barton, Jeffery A Bertke, Danielle L Gray, Fikile R Brushett, Larry A Curtiss, et al. Synthesis of pyridine–and pyrazine–bf3 complexes and their characterization in solution and solid state. The Journal of Physical Chemistry C, 120(16):8461–8471, 2016. [50] Paolo Giannozzi, Stefano Baroni, Nicola Bonini, Matteo Calandra, Roberto Car, Carlo Cavazzoni, Davide Ceresoli, Guido L Chiarotti, Matteo Cococcioni, Ismaila Dabo, et al. Quantum espresso: a modular and open-source software project for quantum simulations of materials. Journal of physics: Condensed matter, 21(39):395502, 2009. [51] Paolo Giannozzi, Oliviero Andreussi, Thomas Brumme, Oana Bunau, M Buongiorno Nardelli, Matteo Calandra, Roberto Car, Carlo Cavazzoni, Davide Ceresoli, Matteo Cococ- cioni, et al. Advanced capabilities for materials modelling with quantum espresso. Journal of physics: Condensed matter, 29(46):465901, 2017. [52] John P Perdew, Kieron Burke, and Matthias Ernzerhof. Generalized gradient approximation made simple. Physical review letters, 77(18):3865–3868, 1996. [53] Stefan Grimme, Jens Antony, Stephan Ehrlich, and Helge Krieg. A consistent and accu- rate ab initio parametrization of density functional dispersion correction (dft-d) for the 94 elements h-pu. The Journal of chemical physics, 132(15):154104, 2010. [54] DR Hamann. Optimized norm-conserving vanderbilt pseudopotentials. Physical Review B, 88(8):085117, 2013. [55] Martin Schlipf and Franc ¸ois Gygi. Optimization algorithm for the generation of oncv pseu- dopotentials. Computer Physics Communications, 196:36–44, 2015. [56] MPAT Methfessel and AT Paxton. High-precision sampling for brillouin-zone integration in metals. Physical Review B, 40:3616–3621, Aug 1989. 46 [57] Xia Stammer, Katrin Tonigold, Asif Bashir, Daniel K¨ afer, Osama Shekhah, Christian H¨ uls- busch, Martin Kind, Axel Groß, and Christof W¨ oll. A highly ordered, aromatic biden- tate self-assembled monolayer on au (111): a combined experimental and theoretical study. Physical Chemistry Chemical Physics, 12(24):6445–6454, 2010. [58] Jan Kucera and Axel Gross. Adsorption of 4-mercaptopyridine on au (111): a periodic dft study. Langmuir, 24(24):13985–13992, 2008. [59] Eduardo Alejandro Ramirez, Emiliano Cort´ es, Aldo Alberto Rubert, P Carro, G Ben´ ıtez, Maria Elena Vela, and Roberto Carlos Salvarezza. Complex surface chemistry of 4- mercaptopyridine self-assembled monolayers on au (111). Langmuir, 28(17):6839–6847, 2012. [60] Zachary K Goldsmith, Maxim Secor, and Sharon Hammes-Schiffer. Inhomogeneity of in- terfacial electric fields at vibrational probes on electrode surfaces. ACS central science, 6 (2):304–311, 2020. [61] Aimin Ge, Georg Kastlunger, Jinhui Meng, Per Lindgren, Jia Song, Qiliang Liu, Alexander Zaslavsky, Tianquan Lian, and Andrew A Peterson. On the coupling of electron transfer to proton transfer at electrified interfaces. Journal of the American Chemical Society, 142(27): 11829–11834, 2020. [62] Oliviero Andreussi, Ismaila Dabo, and Nicola Marzari. Revised self-consistent contin- uum solvation in electronic-structure calculations. The Journal of chemical physics, 136 (6):064102, 2012. [63] Larry Simeral and Ralph L Amey. Dielectric properties of liquid propylene carbonate. The Journal of Physical Chemistry, 74(7):1443–1446, 1970. [64] Oliviero Andreussi, Nicolas Georg Hormann, Francesco Nattino, Giuseppe Fisicaro, Stefan Goedecker, and Nicola Marzari. Solvent-aware interfaces in continuum solvation. Journal of chemical theory and computation, 15(3):1996–2009, 2019. [65] Georg Kastlunger, Per Lindgren, and Andrew A Peterson. Controlled-potential simulation of elementary electrochemical reactions: proton discharge on metal surfaces. The Journal of Physical Chemistry C, 122(24):12771–12781, 2018. [66] Nicolas G Hormann, Oliviero Andreussi, and Nicola Marzari. Grand canonical simulations of electrochemical interfaces in implicit solvation models. The Journal of chemical physics, 150(4):041730, 2019. [67] Phillips Hutchison, Robert E Warburton, Alexander V Soudackov, and Sharon Hammes- Schiffer. Multicapacitor approach to interfacial proton-coupled electron transfer thermody- namics at constant potential. The Journal of Physical Chemistry C, 125(40):21891–21901, 2021. [68] Phillips Hutchison, Peter S Rice, Robert E Warburton, Simone Raugei, and Sharon Hammes-Schiffer. Multilevel computational studies reveal the importance of axial ligand for 47 oxygen reduction reaction on fe–n–c materials. Journal of the American Chemical Society, 144(36):16524–16534, 2022. [69] Nicolas G Hormann, Zhendong Guo, Francesco Ambrosio, Oliviero Andreussi, Alfredo Pasquarello, and Nicola Marzari. Absolute band alignment at semiconductor-water inter- faces using explicit and implicit descriptions for liquid water. npj Computational Materials, 5(1):1–6, 2019. [70] Pallavi Sarkar, Shubhajit Das, and Swapan K Pati. Investigating tetrel-based neutral frus- trated lewis pairs for hydrogen activation. Inorganic Chemistry, 60(20):15180–15189, 2021. [71] F Partal Urena, M Fernandez Gomez, JJ L´ opez Gonz´ alez, and E Martınez Torres. A new insight into the vibrational analysis of pyridine. Spectrochimica Acta Part A: Molecular and Biomolecular Spectroscopy, 59(12):2815–2839, 2003. [72] Marco Pagliai, Luca Bellucci, Maurizio Muniz-Miranda, Gianni Cardini, and Vincenzo Schettino. A combined raman, dft and md study of the solvation dynamics and the ad- sorption process of pyridine in silver hydrosols. Physical Chemistry Chemical Physics, 8 (1):171–178, 2006. [73] No N Greenwood and K Wade. 232. complexes of boron trichloride with pyridine and piperidine. Journal of the Chemical Society (Resumed), pages 1130–1141, 1960. [74] M Taillandier and E Taillandier. Complexes par transfert de charge en spectroscopie in- frarouge pyridine-bf3. Spectrochimica Acta Part A: Molecular Spectroscopy, 25(11):1807– 1814, 1969. [75] Xingjuan Zhao, Shirley Campbell, Patrick Z El-Khoury, Yuechen Jia, Gregory Q Wallace, Audrey Claing, C Geraldine Bazuin, and Jean-Francois Masson. Surface-enhanced raman scattering optophysiology nanofibers for the detection of heavy metals in single breast can- cer cells. ACS sensors, 6(4):1649–1662, 2021. [76] Hee Sook Jung, Kwan Kim, and Myung Soo Kim. Raman spectroscopic investigation of the adsorption of 4-mercaptopyridine on a silver-sol surface. Journal of molecular structure, 407(2-3):139–147, 1997. [77] Jiawen Hu, Bing Zhao, Weiqing Xu, Bofu Li, and Yuguo Fan. Surface-enhanced raman spectroscopy study on the structure changes of 4-mercaptopyridine adsorbed on silver sub- strates and silver colloids. Spectrochimica Acta Part A: Molecular and Biomolecular Spec- troscopy, 58(13):2827–2834, 2002. [78] Nungnit Wattanavichean, Matthew Gilby, Richard J Nichols, and Heike Arnolds. Detec- tion of metal–molecule–metal junction formation by surface enhanced raman spectroscopy. Analytical chemistry, 91(4):2644–2651, 2019. [79] Ling Zhang, Ying Bai, Zhiguo Shang, Yanke Zhang, and Yujun Mo. Experimental and theoretical studies of raman spectroscopy on 4-mercaptopyridine aqueous solution and 4- mercaptopyridine/ag complex system. Journal of Raman Spectroscopy: An International 48 Journal for Original Work in all Aspects of Raman Spectroscopy, Including Higher Order Processes, and also Brillouin and Rayleigh Scattering, 38(9):1106–1111, 2007. [80] Hao Guo, Li Ding, and Yujun Mo. Adsorption of 4-mercaptopyridine onto laser-ablated gold, silver and copper oxide films: A comparative surface-enhanced raman scattering in- vestigation. Journal of Molecular Structure, 991(1-3):103–107, 2011. [81] Yanwen Chao, Qun Zhou, Yan Li, Yuerong Yan, Ying Wu, and Junwei Zheng. Potential dependent surface-enhanced raman scattering of 4-mercaptopyridine on electrochemically roughened silver electrodes. The Journal of Physical Chemistry C, 111(45):16990–16995, 2007. [82] Bruce H Lipshutz, Joseph J Pegram, and Matthew C Morey. Chemistry of β- trimethylsilylethanol. ii. a new method for protection of an anomeric center in pyranosides. Tetrahedron Letters, 22(46):4603–4606, 1981. [83] RJ Gillespie, JS Hartman, and M Parekh. Solvent effects on the boron–fluorine coupling constant and on fluorine exchange in the tetrafluoroborate anion. Canadian Journal of Chemistry, 46(10):1601–1610, 1968. [84] Douglas A Smith and KN Houk. Libf4: A mild lewis acid for intramolecular diels-alder reactions. Tetrahedron letters, 32(12):1549–1552, 1991. [85] Martin Kilpatrick and Fred E Luborsky. The dissociation of fluoborate ion in anhydrous hydrofluoric acid1, 2. Journal of the American Chemical Society, 76(22):5863–5865, 1954. [86] Pierre Charles Maria and Jean Francois Gal. A lewis basicity scale for nonprotogenic sol- vents: enthalpies of complex formation with boron trifluoride in dichloromethane. The Journal of Physical Chemistry, 89(7):1296–1304, 1985. [87] Christian Laurence and Jean-Franc ¸ois Gal. Lewis basicity and affinity scales: data and measurement. John Wiley & Sons, 2009. [88] Paul B Dorain, K Ulrich V on Raben, and Richard K Chang. V oltage dependence of the ph at the interface of a ag electrode: A sers measurement of a phosphate-phosphoric acid system. Surface science, 148(2-3):439–452, 1984. [89] Hajime Tsunekawa, Akiko Narumi, Mitsuru Sano, Akio Hiwara, Miho Fujita, and Haruhiko Yokoyama. Solvation and ion association studies of libf4- propylenecarbonate and libf4- propylenecarbonate- trimethyl phosphate solutions. The Journal of Physical Chemistry B, 107(39):10962–10966, 2003. [90] Philipp Bertocco, Christoph Bolli, Bruno A Correia Bicho, Carsten Jenne, Berrin Erken, Risto S Laitinen, Helene A Seeger, and Teemu T Takaluoma. Theoretical and synthetic study on the existence, structures, and bonding of the halide-bridged [b2x7]-(x= f, cl, br, i) anions. Inorganic Chemistry, 55(7):3599–3604, 2016. 49 [91] M Watanabe, M Sato, A Nagasawa, M Kai, I Motoyama, and T Takayama. Analytical and inorganic-a better synthesis of biruthenocene and molecular structures of (ruiicp (c5h4c5h4) cpru1vncc 2) h5)-(bf4)(b2f7) ch3no2,(ru (sup ii) cp (2, 2’-bipyridine)-(p-benzoquinone)) bf4. Bulletin of the Chemical Society of Japan, 72(4):715–724, 1999. [92] S Brownstein and J Paasivirta. Complexes of boron trifluoride with fluoborates. Canadian journal of Chemistry, 43(6):1645–1649, 1965. [93] P Braunstein, L Douce, J Fischer, Norman C Craig, G Goetz-Grandmont, and D Matt. Synthesis and crystal structure of cis-[pd{Ph2PCH2C (O) Ph} 2]-[bf4][b2f7]. unexpected formation and first structural characterisation of the heptafluorodiborate anion b2f7-. Inor- ganica chimica acta, 194(2):151–156, 1992. [94] Keith E Johnson, W David Chandler, and Brad D Fahlman. Molten salt and related acids. ECS Proceedings Volumes, 1996(1):92, 1996. [95] Stephen D Williams, Warren Harper, Gleb Mamantov, Louis J Tortorelli, and George Shankle. Ab initio mo study of selected aluminum and boron chlorides and fluorides: Comparison with 11b nmr spectra of a tetrachloroborate melt. Journal of computational chemistry, 17(15):1696–1711, 1996. [96] Abraham Ulman. Ultrathin organic films: From langmuir-blodgett to self assembly. 1991. [97] GE Poirier and ED Pylant. The self-assembly mechanism of alkanethiols on au (111). Science, 272(5265):1145–1148, 1996. [98] Paul E Laibinis, Marye Anne Fox, John P Folkers, and George M Whitesides. Comparisons of self-assembled monolayers on silver and gold: mixed monolayers derived from hs (ch2) 21x and hs (ch2) 10y (x, y= ch3, ch2oh) have similar properties. Langmuir, 7(12):3167– 3173, 1991. [99] Ralph G Nuzzo and David L Allara. Adsorption of bifunctional organic disulfides on gold surfaces. Journal of the American Chemical Society, 105(13):4481–4483, 1983. [100] Mandeep Singh, Navpreet Kaur, and Elisabetta Comini. The role of self-assembled mono- layers in electronic devices. Journal of Materials Chemistry C, 8(12):3938–3955, 2020. [101] Jung Wook Lee, Sang Jun Sim, Sung Min Cho, and Jeewon Lee. Characterization of a self-assembled monolayer of thiol on a gold surface and the fabrication of a biosensor chip based on surface plasmon resonance for detecting anti-gad antibody. Biosensors and Bio- electronics, 20(7):1422–1427, 2005. [102] M S´ anchez-Paniagua, S Palenzuela-Batista, CL Manzanares-Palenzuela, and B L´ opez-Ruiz. Electrochemical genosensor for klotho detection based on aliphatic and aromatic thiols self- assembled monolayers. Talanta, 212:120735, 2020. [103] Ratna Nurmalasari, Shabarni Gaffar, Yeni W Hartati, et al. Label-free electrochemical dna biosensor for the detection of mycobacterium tuberculosis using gold electrode modified by self-assembled monolayer of thiol. Procedia Chemistry, 17:111–117, 2015. 50 [104] Yu-Sin Wang, Shuehlin Yau, Lai-Kwan Chau, Ameen Mohamed, and Chun-Jen Huang. Functional biointerfaces based on mixed zwitterionic self-assembled monolayers for biosensing applications. Langmuir, 35(5):1652–1661, 2018. [105] AKM Kafi, M Naqshabandi, Mashitah M Yusoff, and Maxwell J Crossley. Improved per- oxide biosensor based on horseradish peroxidase/carbon nanotube on a thiol-modified gold electrode. Enzyme and microbial technology, 113:67–74, 2018. [106] K Kołczyk-Siedlecka, R Bernasconi, A Lucotti, P Zabinski, and L Magagnin. Self- assembled monolayers assisted all wet metallization of su-8 negative tone photoresist. Jour- nal of The Electrochemical Society, 167(14):142506, 2020. [107] Ruowei Yi, Yayun Mao, Yanbin Shen, and Liwei Chen. Self-assembled monolayers for batteries. Journal of the American Chemical Society, 143(33):12897–12912, 2021. [108] Judit Telegdi. Formation of self-assembled anticorrosion films on different metals. Materi- als, 13(22):5089, 2020. [109] Vinodh K Korrapati, Nico Scharnagl, Dietmar Letzig, and Mikhail L Zheludkevich. Self- assembled layers for the temporary corrosion protection of magnesium-az31 alloy. Corro- sion Science, 169:108619, 2020. [110] Chandrabhan Verma, Salhah Hamed Alrefaee, Kyong Yop Rhee, MA Quraishi, and Eno E Ebenso. Thiol (-sh) substituent as functional motif for effective corrosion protection: A review on current advancements and future directions. Journal of Molecular Liquids, 324: 115111, 2021. [111] Angela Bui, Steven G Guillen, Andy Sua, Travis C Nguyen, Angel Ruiz, Lester Carachure, Mark DR Weber, Araseli Cortez, and Fangyuan Tian. Iron-containing metal-organic frame- work thin film as a drug delivery system. Colloids and Surfaces A: Physicochemical and Engineering Aspects, 650:129611, 2022. [112] Faysal M Al Khulaifi, Yousef A Alsunni, Charles B Musgrave, Adam Holewinski, and J Will Medlin. Impact of pretreatment and thiol modifiers on the partial oxidation of glutaralde- hyde using pd/al2o3. Applied Catalysis A: General, page 119229, 2023. [113] Damian Alvarez-Paggi, Wiebke Meister, Uwe Kuhlmann, Inez Weidinger, Katalin Tenger, Laszlo Zimanyi, Gabor Rakhely, Peter Hildebrandt, and Daniel H Murgida. Disentangling electron tunneling and protein dynamics of cytochrome c through a rationally designed sur- face mutation. The Journal of Physical Chemistry B, 117(20):6061–6068, 2013. [114] Anja Kranich, Hoang Khoa Ly, Peter Hildebrandt, and Daniel H Murgida. Direct observa- tion of the gating step in protein electron transfer: Electric-field-controlled protein dynam- ics. Journal of the American Chemical Society, 130(30):9844–9848, 2008. [115] Nattawadee Wisitruangsakul, Ingo Zebger, Khoa H Ly, Daniel H Murgida, Sanong Ekgasit, and Peter Hildebrandt. Redox-linked protein dynamics of cytochrome c probed by time- resolved surface enhanced infrared absorption spectroscopy. Physical chemistry chemical physics, 10(34):5276–5286, 2008. 51 [116] Katherine M Richard and Andrew A Gewirth. In situ stm and ir studies of phenoxide elec- trooxidation on au (111) electrode surfaces. The Journal of Physical Chemistry, 99(32): 12288–12293, 1995. [117] Katherine M Richard and Andrew A Gewirth. Effects of ring substitution on the binding and oxidation of cyanophenols on au (111) electrodes. The Journal of Physical Chemistry, 100(17):7204–7211, 1996. [118] Reynaldo Oscar Lezna, NR De Tacconi, Silvia Adriana Centeno, and Alejandro Jorge Arvia. Adsorption of phenol on gold as studied by capacitance and reflectance measurements. Langmuir, 7(6):1241–1246, 1991. [119] Dragica Chamovska and Aleksandra Porjazoska Kujundziski. Adsorption of phenol on poly- crystalline gold from aqueous solutions. Journal of Engineering & Processing Management, 11(1):51–54, 2019. [120] Silke Schomaker and Rudolf Holze. An in situ vibrational spectroscopic investigation of the adsorption of phenol on a gold electrode. Zeitschrift f¨ ur Physikalische Chemie, 185(1): 17–32, 1994. [121] P. Hohenberg and W. Kohn. Inhomogeneous electron gas. Phys. Rev., 136:B864–B871, Nov 1964. doi: 10.1103/PhysRev.136.B864. [122] W. Kohn and L. J. Sham. Self-consistent equations including exchange and correlation effects. Phys. Rev., 140:A1133–A1138, Nov 1965. [123] W. Kohn. Nobel lecture: Electronic structure of matter—wave functions and density func- tionals. Rev. Mod. Phys., 71:1253–1266, Oct 1999. [124] G. Kresse and D. Joubert. From ultrasoft pseudopotentials to the projector augmented-wave method. Phys. Rev. B, 59:1758–1775, Jan 1999. [125] P. E. Bl¨ ochl. Projector augmented-wave method. Phys. Rev. B, 50:17953–17979, Dec 1994. [126] John P. Perdew, Kieron Burke, and Matthias Ernzerhof. Generalized gradient approximation made simple. Phys. Rev. Lett., 77:3865–3868, Oct 1996. [127] John P. Perdew, Kieron Burke, and Yue Wang. Generalized gradient approximation for the exchange-correlation hole of a many-electron system. Phys. Rev. B, 54:16533–16539, Dec 1996. [128] G. Kresse and J. Hafner. Ab initio molecular dynamics for liquid metals. Phys. Rev. B, 47: 558–561, Jan 1993. [129] G. Kresse and J. Hafner. Ab initio molecular-dynamics simulation of the liquid-metal– amorphous-semiconductor transition in germanium. Phys. Rev. B, 49:14251–14269, May 1994. [130] Efficiency of ab-initio total energy calculations for metals and semiconductors using a plane- wave basis set. Computational Materials Science, 6(1):15–50, 1996. ISSN 0927-0256. 52 [131] G. Kresse and J. Furthm¨ uller. Efficient iterative schemes for ab initio total-energy calcula- tions using a plane-wave basis set. Phys. Rev. B, 54:11169–11186, Oct 1996. [132] E. Pensa, A. A. Rubert, G. Benitez, P. Carro, A. Gonz´ alez Orive, A. Hern´ andez Creus, R. C. Salvarezza, and C. Vericat. Are 4-mercaptobenzoic acid self assembled monolayers on au(111) a suitable system to test adatom models? The Journal of Physical Chemistry C, 116(49):25765–25771, 2012. doi: 10.1021/jp306545v. [133] Tomas Bucko, Sebastien Lebegue, Jurgen Hafner, and Janos G Angyan. Improved density dependent correction for the description of london dispersion forces. Journal of chemical theory and computation, 9(10):4293–4299, 2013. [134] Tom´ aˇ s Buˇ cko, S´ ebastien Leb` egue, J´ anos G ´ Angy´ an, and J¨ urgen Hafner. Extending the appli- cability of the tkatchenko-scheffler dispersion correction via iterative hirshfeld partitioning. The Journal of chemical physics, 141(3):034114, 2014. [135] Patrick Bultinck, Christian Van Alsenoy, Paul W Ayers, and Ramon Carb´ o-Dorca. Critical analysis and extension of the hirshfeld atoms in molecules. The Journal of chemical physics, 126(14):144111, 2007. [136] Torsten Kerber, Marek Sierka, and Joachim Sauer. Application of semiempirical long-range dispersion corrections to periodic systems in density functional theory. Journal of compu- tational chemistry, 29(13):2088–2097, 2008. [137] Thomas A. Baker, Cynthia M. Friend, and Efthimios Kaxiras. Atomic oxygen adsorption on au(111) surfaces with defects. The Journal of Physical Chemistry C, 113(8):3232–3238, 2009. [138] The Materials Project. Materials data on au by materials project. [139] Anubhav Jain, Shyue Ping Ong, Geoffroy Hautier, Wei Chen, William Davidson Richards, Stephen Dacek, Shreyas Cholia, Dan Gunter, David Skinner, Gerbrand Ceder, and Kristin A. Persson. Commentary: The Materials Project: A materials genome approach to accelerating materials innovation. APL Materials, 1(1):011002, 07 2013. ISSN 2166-532X. [140] Zachary K. Goldsmith, Maxim Secor, and Sharon Hammes-Schiffer. Inhomogeneity of interfacial electric fields at vibrational probes on electrode surfaces. ACS Central Science, 6(2):304–311, 2020. doi: 10.1021/acscentsci.9b01297. PMID: 32123749. [141] Henrik Gr¨ onbeck, Alessandro Curioni, and Wanda Andreoni. Thiols and disulfides on the au(111) surface: the headgroupgold interaction. Journal of the American Chemical Society, 122(16):3839–3842, 2000. [142] Yohaselly Santiago-Rodriguez, Jeffrey A. Herron, Maria C. Curet-Arana, and Manos Mavrikakis. Atomic and molecular adsorption on au(111). Surface Science, 627, 5 2014. ISSN 0039-6028. [143] Cao Jianming, Wu Naijuan, Qi Shangxue, Feng Kean, and M S Zei. Chemisorption of oxygen on au(111) surface. Chinese Physics Letters, 6(2):92, feb 1989. 53 [144] Yvon Le Page and Paul Saxe. Symmetry-general least-squares extraction of elastic data for strained materials from ab initio calculations of stress. Phys. Rev. B, 65:104104, Feb 2002. [145] Xifan Wu, David Vanderbilt, and D. R. Hamann. Systematic treatment of displacements, strains, and electric fields in density-functional perturbation theory. Phys. Rev. B, 72:035105, Jul 2005. [146] Corwin Hansch, A Leo, and RW Taft. A survey of hammett substituent constants and resonance and field parameters. Chemical reviews, 91(2):165–195, 1991. [147] Haotian Shi, Zhi Cai, Joel Patrow, Bofan Zhao, Yi Wang, Yu Wang, Alexander Benderskii, Jahan Dawlaty, and Stephen B Cronin. Monitoring local electric fields at electrode surfaces using surface enhanced raman scattering-based stark-shift spectroscopy during hydrogen evolution reactions. ACS applied materials & interfaces, 10(39):33678–33683, 2018. [148] Demelza Wright, Sara Sangtarash, Niclas S Mueller, Qianqi Lin, Hatef Sadeghi, and Jeremy J Baumberg. Vibrational stark effects: Ionic influence on local fields. The jour- nal of physical chemistry letters, 13(22):4905–4911, 2022. [149] Anwesha Maitra, Pratyusha Das, Barry C Thompson, and Jahan M Dawlaty. Distinguishing between the electrostatic effects and explicit ion interactions in a stark probe. The Journal of Physical Chemistry B, 2023. [150] Farid Bensebaa, Raluca V oicu, Laurent Huron, Thomas H Ellis, and Erik Kruus. Kinetics of formation of long-chain n-alkanethiolate monolayers on polycrystalline gold. Langmuir, 13(20):5335–5340, 1997. [151] HM Schessler, DS Karpovich, and GJ Blanchard. Quantitating the balance between en- thalpic and entropic forces in alkanethiol/gold monolayer self assembly. Journal of the American Chemical Society, 118(40):9645–9651, 1996. [152] Marco Bieri and Thomas B¨ urgi. Adsorption kinetics of l-glutathione on gold and structural changes during self-assembly: an in situ atr-ir and qcm study. Physical Chemistry Chemical Physics, 8(4):513–520, 2006. [153] Laura G Carrascosa, Lidia Mart´ ınez, Yves Huttel, Elisa Rom´ an, and Laura M Lechuga. Understanding the role of thiol and disulfide self-assembled dna receptor monolayers for biosensing applications. European Biophysics Journal, 39:1433–1444, 2010. [154] Sheng Liao, Yitzhak Shnidman, and Abraham Ulman. Adsorption kinetics of rigid 4- mercaptobiphenyls on gold. Journal of the American Chemical Society, 122(15):3688– 3694, 2000. [155] Nupur Garg, Jonathan M Friedman, and T Randall Lee. Adsorption profiles of chelating aromatic dithiols and disulfides: comparison to those of normal alkanethiols and disulfides. Langmuir, 16(9):4266–4271, 2000. 54 [156] Ralph G Nuzzo, Bernard R Zegarski, and Lawrence H Dubois. Fundamental studies of the chemisorption of organosulfur compounds on gold (111). implications for molecular self- assembly on gold surfaces. Journal of the American Chemical Society, 109(3):733–740, 1987. [157] C Vericat, ME Vela, G Benitez, P Carro, and RC Salvarezza. Self-assembled monolayers of thiols and dithiols on gold: new challenges for a well-known system. Chemical Society Reviews, 39(5):1805–1834, 2010. [158] Katherine M. Richard and Andrew A. Gewirth. Effects of ring substitution on the binding and oxidation of cyanophenols on au(111) electrodes. The Journal of Physical Chemistry, 100(17):7204–7211, 1996. doi: 10.1021/jp953709e. [159] Jordan E Nutting, Mohammad Rafiee, and Shannon S Stahl. Tetramethylpiperidine n-oxyl (tempo), phthalimide n-oxyl (pino), and related n-oxyl species: electrochemical properties and their use in electrocatalytic reactions. Chemical reviews, 118(9):4834–4885, 2018. [160] Mohammad Rafiee, Zachary M Konz, Matthew D Graaf, Hannes F Koolman, and Shannon S Stahl. Electrochemical oxidation of alcohols and aldehydes to carboxylic acids catalyzed by 4-acetamido-tempo: An alternative to “anelli” and “pinnick” oxidations. ACS Catalysis, 8(7):6738–6744, 2018. [161] Astrid E Delorme, Victor Sans, Peter Licence, and Darren A Walsh. Tuning the reactivity of tempo during electrocatalytic alcohol oxidations in room-temperature ionic liquids. ACS Sustainable Chemistry & Engineering, 7(13):11691–11699, 2019. [162] Joseph T Hill-Cousins, Jekaterina Kuleshova, Robert A Green, Peter R Birkin, Derek Pletcher, Toby J Underwood, Stuart G Leach, and Richard CD Brown. Tempo-mediated electrooxidation of primary and secondary alcohols in a microfluidic electrolytic cell. Chem- SusChem, 5(2):326–331, 2012. [163] Horacio R Corti and Ernesto R Gonzalez. Direct alcohol fuel cells. Materials, Performance, Durability and Applications, Springer, Amsterdam, 2014. [164] Mohammad Bagher Askari, Parisa Salarizadeh, Amirkhosro Beheshti-Marnani, and Anto- nio Di Bartolomeo. Nio-co3o4-rgo as an efficient electrode material for supercapacitors and direct alcoholic fuel cells. Advanced Materials Interfaces, 8(15):2100149, 2021. [165] Allen J. Bard and Larry R. Faulkner. Electrochemical Methods: Fundamentals and Appli- cations. Wiley, 2nd edition, 2001. [166] William M Haynes, David R Lide, and Thomas J Bruno. CRC handbook of chemistry and physics. CRC press, 2016. [167] Ethan C Lambert, Benjamin W Stratton, and Nathan I Hammer. Raman spectroscopic and quantum chemical investigation of the pyridine-borane complex and the effects of dative bonding on the normal modes of pyridine. ACS omega, 7(15):13189–13195, 2022. 55 [168] JD Odom, JA Barnes, BA Hudgens, and JR Durig. Spectra and structure of boron-nitrogen compounds. ii. infrared and raman spectra of trimethylamine-borane. The Journal of Phys- ical Chemistry, 78(15):1503–1509, 1974. [169] Dana N Reinemann, Ashley M Wright, Jonathan D Wolfe, Gregory S Tschumper, and Nathan I Hammer. Vibrational spectroscopy of n-methyliminodiacetic acid (mida)-protected boronate ester: Examination of the b–n dative bond. The Journal of Physical Chemistry A, 115(24):6426–6431, 2011. [170] Eric R Dionne, Fadwa Ben Amara, and Antonella Badia. An electrochemical immittance analysis of the dielectric properties of self-assembled monolayers. Canadian Journal of Chemistry, 98(9):471–479, 2020. [171] Lesia V Protsailo and W Ronald Fawcett. Electrochemical impedance spectroscopy at alkanethiol-coated gold in propylene carbonate. Langmuir, 18(23):8933–8941, 2002. 56 Appendices A Supporting Information for: Inductive Effect Alone Cannot Explain Lewis Adduct Formation and Dissociation at Electrode Interfaces A.1 Cylcic Voltammetry Figure 4.1: Cyclic V oltametry of MPy in PC and 0.1 M LiBF 4 with a 100mV/sec scan rate. No distinct peaks associated with any Faradaic process are observed. 57 A.2 Spectroelectrochemical Cell Design Figure 4.2: An image of a home-built spectroelectrochemical cell for SERS measurements. A gold wire (1 mm thickness) is used as both the working and counter electrodes. The reference electrode is Ag/AgCl. Figure 4.3: Schematic illustration of the electrochemical cell for SERS measurements. WE: working electrode; RE: Reference electrode; CE: counter electrode. The quartz window is 3/4 inch in diameter. The reference electrode is Ag/AgCl (3 M KCl) and the counter electrode is gold. A 785 nm laser is used for all SERS measurments. 58 Figure 4.4: An image of a gold wire (1 mm thickness with 99.99% purity) used as both working and counter electrodes. Figure 4.5: An image of the gold electrodepositon solution used to make the SERS substrate. Photo courtesy of: https://goldtouchinc.com. 59 Figure 4.6: An image of the spectroelectrochemical cell under the Raman microscope. 60 . Figure 4.7: SERS spectra of MPy and MPy-BF 3 in acetonitrile. The C=C marker bands of MPy in 1600 cm − 1 blue shift upon adduct formation with BF 3 . Changes in other regions are also observed . Figure 4.8: Raman spectrum of solid MPy 61 Figure 4.9: Raman spectra of bulk pyridine and bulk pyiridine-BF 3 . The marker bands in the 1600 cm − 1 undergo blue shift upon adduct formation with BF 3 . Figure 4.10: Potential dependent SERS spectra of MPy in PC in the presence of 0.1 M NaBF 4 as electrolyte. No Raman signatures indicative of adduct formation are observed. The Raman intensity of C=C marker bands change upon application of potential, but no blue shift is observed. 62 Figure 4.11: Potential dependent spectra of MPy in PC in the presence of 0.1 M (TBA)BF 4 as electrolyte (middle panel). The left panel depicts the potential for each spectrum and defines the y-axis for the other two panels. The potential starts from OCP, is swept to positive potentials, followed by a negative and a positive sweep to bring it back to 0. No Raman blue shift above 1610 cm − 1 indicative of adduct formation is observed. The Raman intensities of marker bands change upon application of potential. The right panel depicts the average frequency of the marker bands in the 1600 cm − 1 range vs applied potential. 63 Figure 4.12: The average frequency of the marker bands vs electrode potential for MPy (red), and adduct (brown: irreversible; black: reversible). Adduct dissociates at negative potentials and the C=C marker bands undergo a red shift. The response of the adduct is distinctly different from the response of MPy. A.3 Calculated Average C=C Frequency of the Marker Bands We have calculated the average C=C Raman shift of marker bands in the range of 1560 - 1660 cm − 1 for each potential increment using the following formula: <ν >= ∑ I(ν)ν ∑ I(ν) (A.1) whereν is the frequency and I(ν) is the Raman intensity. 64 Figure 4.13: Potential dependent SERS specctra of adduct in PC and 0.1 M LiBF 4 (middle panel). The left panel depicts the potential for each spectrum and defines the y-axis for the other two panels. The potential starts from OCP, is swept to positive potentials, followed by a negative and a positive sweep to bring it back to 0. The right panel depicts the full width half maximum (FWHM) of the ring breathing mode as a function of applied potential. A distinct change in the spectral FWHM (from 14 to 25 cm − 1 ) is observed upon dissociation of the adduct. The potential range for this change correlates with the change in the marker bands in the 1600 cm − 1 region used in this work. 65 A.4 Calculated Vibrational Frequencies Vibrational frequencies were calculated within the harmonic approximation using the PHonon code (ph.x) in the Quantum ESPRESSO package. 51;51 The phonon calculations were performed at zero charge in vacuum without the dielectric continuum solvent, as the PHonon.x code is not currently compatible with the Environ module for solvation. To simplify the vibrational analysis and to reduce computational expense, we assumed that the vibrations of surface Au atoms would not significantly impact the predicted C=C ring breathing modes. As such, the Au atoms were frozen (i.e., mass of Au atoms→∞) in the phonon calculations and the adsorbed MPy and MPy- BF 3 species were allowed to vibrate. The C=C ring breathing modes were identified for the MPy* and MPy− BF 3 * from the eigenvectors of the mass-weighted Hessian matrix. The calculated fre- quencies were 1785.0 cm − 1 and 1801.9 cm − 1 for MPy* and MPy− BF 3 *, respectively. Although DFT significantly overestimates the absolute values of the frequencies, the trends in the computed frequencies can still provide useful comparison to experiment, and we compute a blueshift of 17 cm − 1 upon formation of the Lewis adduct. The absolute frequency estimates could be improved with the inclusion of implicit or explicit solvent and by including anharmonic effects. We do not anticipate that these effects would impact the qualitative trends. The calculated frequencies of MPy*, MPy− BF 3 *, and BF 3 were also used to compute zero-point energies for the grand potential calculations. A.5 Grand Potential Calculations from Periodic DFT A representative depiction of the computational unit cell used in the periodic DFT studies is shown in Figure 4.14 The dielectric continuum propylene carbonate (ε =ε PC = 64.0) is included on one side of the Au slab, and vacuum (ε = ε vac = 1.0) is included on the other side. This setup is intended to localize excess charge on only one side of the surface and to allow the electrostatic potential in the bulk continuum solvent to converge to a constant value. Excess charge added to the system is compensated by an equivalent countercharge embedded in the continuum solvent. The countercharge region is denoted by the orange strip in Figure 4.14. 66 Figure 4.14: Schematic of the computational unit cell used for charged slab calculations in dielec- tric continuum propylene carbonate. The relative free energies of MPy* and MPy− BF 3 * were analyzed within the grand canonical ensemble. The free energy is computed as the grand potentialΩ, which is the Legendre transform of the Hemholtz free energy (equivalent to the Gibbs free energy in this analysis): Ω= G− ∑ i N i µ i (A.2) where G is the Gibbs free energy, µ i is the (electro)chemical potential of component i, and N i is the number of particles of type i. Because the electrochemical potential of the electrons is related to the electrode potential E, the potential-dependent grand potentialΩ(E) can be expressed as follows: Ω(E)= U DFT [q(E)]+ ZPE− T S− G ref − qE− ∑ i N i µ i (A.3) In eq A.3, U DFT is the DFT electronic energy, ZPE is the zero-point energy, T S is the entropic contribution to the free energy, and q is the net charge added to the system. In the above expression, only the N i µ i terms associated with excess components are included explicitly, and the remaining terms are combined into G ref , a consistent reference state chosen for this thermodynamic analysis. Here, the reference state is chosen to be the MPy* system with no net charge, i.e., at PZFC, where q = 0. The value of E in eq A.3 is determined from the DFT-calculated Fermi energy ε F and the bulk implicit solvent electrostatic potential φ S by the expression E = φ S − ε F /e. For comparison to experiment, the values of E are subsequently converted to the Ag/AgCl reference 67 electrode based on previously determined electrostatic potential offsets between implicit water and vacuum of 0.33 V 69 . The E o of the Ag/AgCl electrode is 0.197 V vs. the standard hydrogen electrode (SHE). Because SHE is≈ 4.11 V vs. implicit water 69 , Ag/AgCl is≈ 4.31 V vs. implicit water. 165 Thus 4.31 V is subtracted from the values of E in eq A.3 to convert between an implicit water and Ag/AgCl reference. Although these calculations were performed in implicit propylene carbonate, we applied this offset previously determined for implicit water due to the absence of similar correction schemes for propylene carbonate in the literature. This approximation introduces a constant shift in the magnitude of E vs the Ag/AgCl reference and does not impact trends in the reaction free energies∆Ω or bond lengths as a function of applied potential. Here, we assume that G ref ≈ U DFT MPy∗ (q= 0)+ ZPE(MPy)*. The entropy of surface-adsorbed MPy* and MPy− BF 3 * is not included in these calculations because T∆S changes for surface species (associated with formation of an N− B bond) are assumed to be small. The value of µ BF 3 includes the ZPE of gas-phase BF 3 (calculated to be 0.41 eV), as well as the TS contributions for rotational entropy (0.29 eV from a rigid rotor approximation) and translational entropy (calculated to be 0.40 eV using the Sackur− Tetrode equation). We note that the translational entropy is an overestimate because of the high vapor pressure of BF 3 relative to ideal gas conditions. The other µ i in eq A.3 are approximated by the DFT energies of relevant reference compounds, e.g., isolated solution-phase propylene carbonate. We assume that the zero-point energy and entropic contribu- tions to the free energy mostly cancel for these other species because they are not directly involved in bond forming and breaking. For the example presented in the main text of MPy* and MPy− BF 3 * in the absence of ions, the only excess component is the BF 3 Lewis acid, and thusµ BF 3 ≈ U DFT BF 3 +ZPE BF 3 − T S BF 3 , where U DFT BF 3 is the DFT energy of a BF 3 molecule in dielectric continuum propylene carbonate. With the approximations above, the grand potential is computed as Ω(E)= U DFT [q(E)]+ ZPE− G ref − N BF 3 µ BF 3 − qE (A.4) 68 We also performed calculations that included an extra Li + BF − 4 ion pair. In its dissociated state, this case corresponds to MPy* and a solvated Li + B 2 F − 7 near the Au surface. For the intact Lewis adduct, MPy− BF 3 *, a solvated Li + BF − 4 ion pair is included near the Au surface. Although these calculations include Li + BF − 4 or Li + B 2 F − 7 ion pairs, each of them is charge neutral, so the electrostatic contributions to the electrochemical potentials cancel. Because this excess Li + BF − 4 ion pair is not involved in forming or breaking new bonds, the zero-point energy and entropic contributions to the free energy are assumed to cancel relative to the reference chemical potential of this specie, µ Li + BF − 4 . Thus, we do not include these contributions in U DFT and assume that µ Li + BF − 4 ≈ U DFT Li + BF − 4 . Furthermore, the DFT energy of a solvated Li + BF − 4 ion pair is used in the grand potential calculations because its DFT energy is lower than the solvated Li + B 2 F − 7 compound. This implies that Li + B 2 F − 7 is likely to dissociate into Li + BF − 4 and BF 3 in the bulk solution, making the dissociated state the appropriate chemical potential reference in the grand canonical ensemble. The resulting grand potential is Ω(E)= U DFT [q(E)]+ ZPE− G ref − N BF 3 µ BF 3 − N Li + BF − 4 µ Li + BF − 4 − qE (A.5) The DFT-optimized structures and thermodynamic analysis with the inclusion of these ions are shown in Figure 4.15. Notably, the constant potential analysis of the grand potentials suggests that for the dissociated MPy* + Li + B 2 F − 7 state, the Li + cation prefers to be close to the Au electrode surface at lower potentials and then prefers to be further away from the Au electrode at higher potentials. This phenomenon is indicated by the intersecting light and dark red curves around 0.6 V vs. Ag/AgCl in Figure 4.15b. However, the associated MPy− BF 3 * adduct remains lower in free energy at all potentials studied. 69 Figure 4.15: Thermodynamic analysis of adduct formation in the presence of explicit Li + BF − 4 or Li + B 2 F − 7 ion pairs. (a) DFT-optimized geometries for MPy* + Li + B 2 F − 7 in configurations with Li + far from (light red) and close to (dark red) the Au surface, MPy* + Li + BF − 4 with Li + close to the Au surface (red), and MPy− BF 3 * + Li + BF − 4 with Li + close to the Au surface (blue). (b) Grand potentialsΩ as a function of applied potential E. (c) Reaction free energies∆Ω as a function of E, where∆Ω is the free energy difference between the blue curve and the lower energy red curve in (b) at a given E. We performed a similar analysis including a Li + ion near the surface, this time coordinated to a propylene carbonate (PC) molecule, such that it is not charge compensated (Figure 4.16). In this case, the (electro)chemical potentials of the Li + cation and the neutral propylene carbonate molecule are treated separately because the electrochemical potential of Li + is dependent upon the applied potential. Ω(E)= U DFT [q(E)]+ ZPE− G ref − N BF 3 µ BF 3 − N PC µ PC − N Li +[µ ◦ Li − e(E− E Li/Li +)] − qE (A.6) As above, we assume that µ PC ≈ U DFT PC because propylene carbonate is not directly involved in the association or dissociation of the adduct. The electrochemical potential of the Li + ion, ˜ µ Li + =µ ◦ Li − e(E− E Li/Li +), is calculated using the chemical potential of bulk BCC lithium metal (µ ◦ Li ≈ U DFT Li ) and the potential relative to the Li/Li + reference electrode, E− E Li/Li +. The value of 70 E− E Li/Li + is determined using the potential offsets discussed above, along with the known value of E Li/Li + =− 3.04 V vs. SHE. 166 This is analogous to the electrochemical potential treatment of protons relative to the standard hydrogen electrode in grand canoncial treatments of proton-coupled electron transfer reactions. 66;67;68 . Again, we find similar trends in the reaction free energies as in the cases without ions and with the Li + BF − 4 /Li + B 2 F − 7 ion pairs. In addition to the reaction free energies∆Ω becoming more neg- ative with more reducing potentials in all cases, the inductive effect is consistent for MPy− BF 3 * across all three models based on the trends in N− B bond lengths (Figure 4.16). Figure 4.16: Thermodynamic analysis of adduct formation in the presence of explicit Li + PC. (a) DFT-optimized geometries for MPy* with Li + PC (red) and MPy− BF 3 * with Li + PC (blue). (b) Grand potentialsΩ as a function of applied potential E. (c) Reaction free energies∆Ω as a function of E, where∆Ω is the free energy difference between the blue curve and the red curve in (b) at a given E. 71 Figure 4.17: The N–B bond length of MPy− BF 3 * as a function of the applied potential E for the different models studied: no ions, with Li + BF − 4 , and with Li + PC. In all three cases, the bond shortens (strengthens) with more negative potential and elongates (weakens) with more positive potential. 72 A.6 Sample Quantum Espresso Input Files and Optimized Geometries A.7 Sample Quantum ESPRESSO pw.x Input File &c o n t r o l c a l c u l a t i o n = ’ r e l a x ’ p s e u d o d i r = ’ . / ’ o u t d i r = ’ . / ’ t i t l e = ’ au111 . t h i o p y r a d i n e . fcc ’ p r e f i x = ’ au111 . t h i o p y r a d i n e . fcc ’ n s t e p = 499 / & SYSTEM ntyp = 5 , n a t = 59 , i b r a v = 0 e c u t w f c = 80 , t o t c h a r g e = 0 n s p i n = 2 s t a r t i n g m a g n e t i z a t i o n ( 1 ) = 0 . 0 s m e a r i n g = ’mp’ d e g a u s s = 0 . 0 1 o c c u p a t i o n s = ’ smearing ’ i n p u t d f t = ’ pbe ’ vdw corr = ’ d f t −d3 ’ / &e l e c t r o n s s t a r t i n g p o t = ’ f i l e ’ 73 ! s t a r t i n g w f c = ’ f i l e ’ mixing mode = ’ l o c a l −TF ’ m i x i n g b e t a = 0 . 5 , mixing ndim = 12 , m i x i n g f i x e d n s = 12 , e l e c t r o n m a x s t e p =50000 , c o n v t h r = 1 . 0 d−6 d i a g o f u l l a c c = . t r u e . / &i o n s / K POINTS { a u t o m a t i c } 2 2 1 0 0 0 ATOMIC SPECIES Au 196.97 Au ONCV PBE − 1 . 0 . upf C 12.011 C ONCV PBE − 1 . 0 . upf H 1 . 0 0 H ONCV PBE − 1 . 0 . upf S 32.06 S ONCV PBE − 1 . 1 . upf N 14.007 N ONCV PBE − 1 . 0 . upf CELL PARAMETERS ( angstrom ) 11.7634284118194046 0.0000000000000000 0.0000000000000000 5.8817142059097023 10.1874278402352356 0.0000000000000000 0.0000000000000000 0.0000000000000000 50.0000000000000000 ATOMIC POSITIONS ( angstrom ) { i n s e r t ato mi c c o o r d i n a t e s} 74 A.8 Sample Envrion Input File & ENVIRON v e r b o s e = 2 e n v i r o n t h r = 1 . d−1 e n v i r o n t y p e = ’ i n p u t ’ e n v e l e c t r o s t a t i c = . t r u e . e n v s t a t i c p e r m i t t i v i t y = 6 4 . 0D0 ! e n v e x t e r n a l c h a r g e s = 1 e n v d i e l e c t r i c r e g i o n s = 1 / & BOUNDARY s o l v e n t m o d e = ’ e l e c t r o n i c ’ s o l v e n t r a d i u s = 6.348672397 ! r p c = 6.348672397 Bohr / &ELECTROSTATIC p b c c o r r e c t i o n = ’ p a r a b o l i c ’ pbc dim = 2 p b c a x i s = 3 t o l = 1 . d −11 mix = 0 . 6 s o l v e r = ’ i t e r a t i v e ’ a u x i l i a r y = ’ f u l l ’ / ! EXTERNAL CHARGES { angstrom} ! CHARGE 3 . 5 3 . 5 29. 30 0 . 5 2 3 DIELECTRIC REGIONS { angstrom} 1 . 0 1 . 0 5 . 5 5 . 5 5 . 0 0 5 . 0 0 0 . 5 2 3 75 A.9 Coordinates of Converged Structures at PZFC MPy*: Au 1.470428550 0.848952320 10.000000000 0 0 0 Au 4.411285650 0.848952320 10.000000000 0 0 0 Au 2.940857100 3.395809280 10.000000000 0 0 0 Au 5.881714210 3.395809280 10.000000000 0 0 0 Au 4.411285650 5.942666240 10.000000000 0 0 0 Au 7.352142750 5.942666240 10.000000000 0 0 0 Au 5.881714200 8.489523200 10.000000000 0 0 0 Au 8.822571310 8.489523200 10.000000000 0 0 0 Au 7.352142760 0.848952320 10.000000000 0 0 0 Au 10.292999860 0.848952320 10.000000000 0 0 0 Au 8.822571310 3.395809280 10.000000000 0 0 0 Au 11.763428420 3.395809280 10.000000000 0 0 0 Au 10.292999860 5.942666240 10.000000000 0 0 0 Au 13.233856960 5.942666240 10.000000000 0 0 0 Au 11.763428410 8.489523200 10.000000000 0 0 0 Au 14.704285520 8.489523200 10.000000000 0 0 0 Au −0.000000007 1.687463516 12.357996303 Au 2.993257263 1.728757756 12.400800268 Au 1.475139991 4.230718864 12.381186845 Au 4.442550448 4.220705329 12.512884090 Au 0.000000000 0.013969380 14.771705923 Au 2.905838047 −0.091679515 14.756242392 Au 1.373044303 2.557039056 14.765172903 Au 4.105844642 2.367259556 14.895112940 Au 2.960390354 6.791125753 12.381543512 76 Au 5.881714200 6.696824181 12.436575494 Au 4.421198202 9.337350351 12.355176871 Au 7.342230214 9.337350333 12.355176876 Au 2.876416602 5.131728102 14.725877754 Au 5.881714196 5.484335663 15.014793229 Au 4.363121507 7.734406104 14.762458838 Au 7.400306917 7.734406080 14.762458833 Au 5.881714189 1.710972219 12.504134379 Au 8.770171151 1.728757762 12.400800263 Au 7.320877965 4.220705341 12.512884105 Au 10.288288415 4.230718856 12.381186845 Au 5.881714217 −0.095394659 14.726256764 Au 8.857590352 −0.091679511 14.756242387 Au 7.657583763 2.367259562 14.895112951 Au 10.390384099 2.557039053 14.765172879 Au 8.803038054 6.791125766 12.381543516 Au 11.763428412 6.783458785 12.399462667 Au 10.282079692 9.338633437 12.377753323 Au 13.244777135 9.338633423 12.377753298 Au 8.887011813 5.131728103 14.725877770 Au 11.763428397 5.122207689 14.813146861 Au 10.312793130 7.618273190 14.815518727 Au 13.214063696 7.618273196 14.815518718 N 5.881714183 3.296242318 20.721062041 C 5.881714215 4.457830702 20.049496087 C 5.881714201 4.546926778 18.657693064 C 5.881714190 3.354547968 17.935000421 77 C 5.881714198 2.131351879 18.606917807 C 5.881714214 2.162971891 19.999894039 H 5.881714216 5.370271180 20.648432212 H 5.881714216 5.515431468 18.161639344 S 5.881714203 3.392183563 16.153673602 H 5.881714178 1.182599128 18.074315040 H 5.881714190 1.227236752 20.561497132 MPy− BF 3 *: Au 1.470428550 0.848952320 10.000000000 0 0 0 Au 4.411285650 0.848952320 10.000000000 0 0 0 Au 2.940857100 3.395809280 10.000000000 0 0 0 Au 5.881714210 3.395809280 10.000000000 0 0 0 Au 4.411285650 5.942666240 10.000000000 0 0 0 Au 7.352142750 5.942666240 10.000000000 0 0 0 Au 5.881714200 8.489523200 10.000000000 0 0 0 Au 8.822571310 8.489523200 10.000000000 0 0 0 Au 7.352142760 0.848952320 10.000000000 0 0 0 Au 10.292999860 0.848952320 10.000000000 0 0 0 Au 8.822571310 3.395809280 10.000000000 0 0 0 Au 11.763428420 3.395809280 10.000000000 0 0 0 Au 10.292999860 5.942666240 10.000000000 0 0 0 Au 13.233856960 5.942666240 10.000000000 0 0 0 Au 11.763428410 8.489523200 10.000000000 0 0 0 Au 14.704285520 8.489523200 10.000000000 0 0 0 Au 0.000086561 1.689443557 12.362520080 Au 2.989485087 1.727905680 12.401253385 Au 1.473297544 4.232731665 12.383061407 78 Au 4.439499253 4.221034758 12.510910747 Au 0.000088843 0.012286348 14.778617610 Au 2.898422133 −0.096155073 14.766034454 Au 1.373222488 2.559968201 14.771692862 Au 4.108232858 2.357387551 14.889722028 Au 2.959647952 6.793825401 12.383491972 Au 5.881727287 6.703160908 12.429610687 Au 4.422584535 9.339585197 12.358916574 Au 7.340979132 9.339601195 12.358959645 Au 2.875301492 5.131209670 14.726208023 Au 5.881770025 5.467118240 14.981045914 Au 4.363504569 7.728182346 14.766821679 Au 7.400112940 7.728284516 14.766827990 Au 5.881698175 1.716751641 12.495959289 Au 8.774045541 1.727868966 12.401043510 Au 7.324161826 4.221184167 12.510730722 Au 10.290267233 4.232718281 12.383045951 Au 5.881734536 −0.090987529 14.718131622 Au 8.865245496 −0.096280078 14.765997346 Au 7.655529320 2.357190644 14.889051975 Au 10.390560515 2.559937653 14.771647556 Au 8.803925080 6.793841575 12.383450804 Au 11.763529591 6.788014765 12.401823593 Au 10.278974075 9.341225863 12.379904330 Au 13.248026081 9.341249737 12.379924833 Au 8.888376492 5.131325811 14.726152359 Au 11.763518498 5.124555195 14.818514344 79 Au 10.314240557 7.620768376 14.818364030 Au 13.212803514 7.620763934 14.818329637 N 5.875624667 3.331955318 20.694385119 C 5.879570994 4.508852780 20.035955577 C 5.883265496 4.564559445 18.652916122 C 5.883577158 3.365253474 17.938175696 C 5.883239244 2.145137181 18.622651784 C 5.879329920 2.169334294 20.003008389 H 5.877157989 5.406354296 20.646066671 H 5.885225067 5.527559214 18.149939032 S 5.882897091 3.391408107 16.165031249 H 5.885248362 1.192145080 18.101525662 H 5.876140328 1.254427173 20.588262964 F 7.103341192 2.688039932 22.693024436 B 5.883075808 3.260129821 22.310534108 F 4.809503923 2.446356037 22.692274775 F 5.746938969 4.556464958 22.806998081 MPy* + Li + B 2 F − 7 (Li near surface): Au 1.470428550 0.848952320 10.000000000 0 0 0 Au 4.411285650 0.848952320 10.000000000 0 0 0 Au 2.940857100 3.395809280 10.000000000 0 0 0 Au 5.881714210 3.395809280 10.000000000 0 0 0 Au 4.411285650 5.942666240 10.000000000 0 0 0 Au 7.352142750 5.942666240 10.000000000 0 0 0 Au 5.881714200 8.489523200 10.000000000 0 0 0 Au 8.822571310 8.489523200 10.000000000 0 0 0 Au 7.352142760 0.848952320 10.000000000 0 0 0 80 Au 10.292999860 0.848952320 10.000000000 0 0 0 Au 8.822571310 3.395809280 10.000000000 0 0 0 Au 11.763428420 3.395809280 10.000000000 0 0 0 Au 10.292999860 5.942666240 10.000000000 0 0 0 Au 13.233856960 5.942666240 10.000000000 0 0 0 Au 11.763428410 8.489523200 10.000000000 0 0 0 Au 14.704285520 8.489523200 10.000000000 0 0 0 Au −0.000480403 1.687612660 12.363403242 Au 2.981727262 1.723869463 12.397969947 Au 1.473836049 4.234267810 12.385083982 Au 4.427674539 4.229410487 12.510629823 Au 0.007114766 0.017040160 14.783326190 Au 2.906836039 −0.092131796 14.776900789 Au 1.372101238 2.566238782 14.777549317 Au 4.110916213 2.372630565 14.866355920 Au 2.953642971 6.797872730 12.386668080 Au 5.882333051 6.704264528 12.437489129 Au 4.418917191 9.343234594 12.360626187 Au 7.337178902 9.341437669 12.365127477 Au 2.866565800 5.139993049 14.735234671 Au 5.872832029 5.482356170 15.003446065 Au 4.360258110 7.738418212 14.766312157 Au 7.405053319 7.730786540 14.776136007 Au 5.877720285 1.708770706 12.507474721 Au 8.765388981 1.733055924 12.411317743 Au 7.305136746 4.214881731 12.488897454 Au 10.294245321 4.232046049 12.373644538 81 Au 5.881186373 −0.096130799 14.735744673 Au 8.863719015 −0.085404108 14.766972625 Au 7.665180071 2.370438697 14.921691974 Au 10.391329108 2.564083657 14.767407390 Au 8.804961965 6.809518694 12.373734956 Au 11.761050740 6.794531504 12.405186471 Au 10.280027106 9.346461938 12.386962955 Au 13.244579059 9.341925096 12.385459941 Au 8.864005046 5.132639582 14.676192603 Au 11.754066774 5.127541688 14.811128571 Au 10.310136075 7.614064184 14.832436217 Au 13.208836275 7.623630657 14.838612966 N 5.751627712 3.227710047 20.715486184 C 5.698345654 4.397476690 20.061529885 C 5.729682532 4.509525308 18.670881732 C 5.827132627 3.331643128 17.931584104 C 5.885071433 2.100254782 18.585333910 C 5.841146537 2.108800660 19.978147352 H 5.629429106 5.297134612 20.674668242 H 5.679347615 5.483492701 18.188355444 S 5.873600601 3.393097976 16.150882753 H 5.961554376 1.162747105 18.038361508 H 5.880418465 1.165529608 20.525016019 Li 9.791708706 4.987207887 18.386637036 F 9.839993139 8.170737344 21.173741117 B 9.268061645 7.158337050 21.909525838 F 10.488858606 6.382280846 22.589841565 82 F 8.617488764 6.215775407 21.146725624 F 8.550502168 7.596492898 22.997335697 F 11.931356319 6.053404182 20.732422459 B 11.603976033 5.452220283 21.926874930 F 12.612448575 5.475814953 22.861111913 F 11.003916390 4.222130938 21.781866470 MPy− BF 3 * + Li + BF − 4 : Au 1.470428550 0.848952320 10.000000000 0 0 0 Au 4.411285650 0.848952320 10.000000000 0 0 0 Au 2.940857100 3.395809280 10.000000000 0 0 0 Au 5.881714210 3.395809280 10.000000000 0 0 0 Au 4.411285650 5.942666240 10.000000000 0 0 0 Au 7.352142750 5.942666240 10.000000000 0 0 0 Au 5.881714200 8.489523200 10.000000000 0 0 0 Au 8.822571310 8.489523200 10.000000000 0 0 0 Au 7.352142760 0.848952320 10.000000000 0 0 0 Au 10.292999860 0.848952320 10.000000000 0 0 0 Au 8.822571310 3.395809280 10.000000000 0 0 0 Au 11.763428420 3.395809280 10.000000000 0 0 0 Au 10.292999860 5.942666240 10.000000000 0 0 0 Au 13.233856960 5.942666240 10.000000000 0 0 0 Au 11.763428410 8.489523200 10.000000000 0 0 0 Au 14.704285520 8.489523200 10.000000000 0 0 0 Au 0.001908214 1.680585810 12.371666466 Au 2.981576925 1.719729576 12.404633684 Au 1.474025421 4.225642988 12.385339367 Au 4.430131853 4.221217738 12.513050679 83 Au −0.000861355 0.006204085 14.804329834 Au 2.899420688 −0.098053150 14.792542419 Au 1.373106127 2.555691300 14.790120615 Au 4.106981300 2.356696917 14.883929647 Au 2.956502007 6.792880752 12.390187621 Au 5.876849824 6.717820641 12.427386305 Au 4.419052150 9.342765691 12.369815699 Au 7.335367846 9.343640803 12.370937787 Au 2.868046322 5.131453496 14.732749067 Au 5.880490865 5.468595428 14.944926911 Au 4.354646462 7.729416206 14.784277924 Au 7.400801732 7.729406663 14.778262409 Au 5.876261805 1.709605370 12.506055379 Au 8.774647723 1.722039853 12.407569452 Au 7.309239428 4.215009928 12.479264062 Au 10.296737543 4.224697930 12.371482117 Au 5.879463099 −0.096316292 14.733784781 Au 8.859575151 −0.093802219 14.788393540 Au 7.664766465 2.369011949 14.888971185 Au 10.394036841 2.551871653 14.776333315 Au 8.802558293 6.808099600 12.373406816 Au 11.765737390 6.796342311 12.405005356 Au 10.275318449 9.345941712 12.389868249 Au 13.245401724 9.344984046 12.388592378 Au 8.877025916 5.129000293 14.667496314 Au 11.761654581 5.120240407 14.805073977 Au 10.313123387 7.613815746 14.827171100 84 Au 13.211132206 7.621299168 14.838771444 N 5.866047451 3.330975989 20.672614949 C 5.858243591 4.509927535 20.020185265 C 5.863681721 4.574016020 18.637497246 C 5.881176351 3.378443743 17.917240955 C 5.892629522 2.155032509 18.595696151 C 5.883621385 2.171990074 19.976107844 H 5.847366423 5.403887929 20.634632129 H 5.851065949 5.541772673 18.143505224 S 5.884209396 3.402356496 16.144635624 H 5.906093680 1.203901117 18.071367866 H 5.888042729 1.255961983 20.558904976 F 7.087689930 2.675619030 22.670593794 B 5.871270845 3.254331688 22.291186912 F 4.794065941 2.440783121 22.663983652 F 5.736384399 4.548881162 22.788652224 Li 9.860050610 5.314841726 18.337715183 B 10.300565961 6.060743974 21.810292524 F 11.214456706 5.060898392 21.389612261 F 10.437952563 6.275927664 23.201660049 F 8.979927251 5.642031446 21.518137178 F 10.575006744 7.263810580 21.108793838 MPy* + Li + PC : Au 1.470428550 0.848952320 10.000000000 0 0 0 Au 4.411285650 0.848952320 10.000000000 0 0 0 Au 2.940857100 3.395809280 10.000000000 0 0 0 Au 5.881714210 3.395809280 10.000000000 0 0 0 85 Au 4.411285650 5.942666240 10.000000000 0 0 0 Au 7.352142750 5.942666240 10.000000000 0 0 0 Au 5.881714200 8.489523200 10.000000000 0 0 0 Au 8.822571310 8.489523200 10.000000000 0 0 0 Au 7.352142760 0.848952320 10.000000000 0 0 0 Au 10.292999860 0.848952320 10.000000000 0 0 0 Au 8.822571310 3.395809280 10.000000000 0 0 0 Au 11.763428420 3.395809280 10.000000000 0 0 0 Au 10.292999860 5.942666240 10.000000000 0 0 0 Au 13.233856960 5.942666240 10.000000000 0 0 0 Au 11.763428410 8.489523200 10.000000000 0 0 0 Au 14.704285520 8.489523200 10.000000000 0 0 0 Au 0.007772418 1.688484732 12.429802945 Au 2.957563956 1.729029928 12.426790136 Au 1.468816208 4.246138984 12.436709753 Au 4.425269544 4.248848581 12.549342027 Au −0.006259949 0.058348837 14.924027228 Au 2.913955042 −0.077613522 14.887121211 Au 1.362412851 2.600774332 14.918023379 Au 4.094485316 2.390193889 14.880419796 Au 2.952005856 6.818269963 12.434605836 Au 5.878517113 6.729148746 12.504866502 Au 4.426315874 9.345875695 12.420635319 Au 7.332808205 9.356829500 12.419710852 Au 2.857710276 5.171245921 14.796612126 Au 5.879225545 5.547243972 15.126113803 Au 4.354406618 7.777603303 14.892404667 86 Au 7.399197419 7.777742383 14.882658902 Au 5.877395968 1.709783474 12.529016598 Au 8.807961725 1.721811447 12.418994859 Au 7.310955303 4.234445304 12.505991008 Au 10.322395304 4.235362160 12.412587852 Au 5.876986983 −0.098618052 14.789223726 Au 8.840250040 −0.075292747 14.890476901 Au 7.666802558 2.398331069 14.860535197 Au 10.395552212 2.601305971 14.897268051 Au 8.808273492 6.841696790 12.403031241 Au 11.767290605 6.803359632 12.484666823 Au 10.276139065 9.347361824 12.429087559 Au 13.255945307 9.338658826 12.432169529 Au 8.878825372 5.168671093 14.688718998 Au 11.754118102 5.158115985 14.970085215 Au 10.305280051 7.630185521 14.991086874 Au 13.207036195 7.638655608 15.013135908 N 5.965996260 3.209393591 20.730265242 C 5.959745469 4.384194887 20.077196684 C 5.925146693 4.500690585 18.690159231 C 5.904673799 3.329504229 17.926861130 C 5.903809184 2.095439743 18.586467963 C 5.932753116 2.094332764 19.977513849 H 5.983610893 5.283948401 20.694335106 H 5.919212372 5.478367336 18.211051294 S 5.886360780 3.406736208 16.156482759 H 5.880556385 1.161045942 18.028229009 87 H 5.929755410 1.145494711 20.516887040 O 10.282813586 6.036353890 23.290986087 O 9.856116421 6.736045442 21.212491460 O 10.774810747 4.694698491 21.536233842 C 9.556268801 7.303427147 23.470215687 C 9.584997082 7.889683432 22.056335305 C 10.229993666 8.137172752 24.529681142 C 10.342055868 5.734159469 21.980207943 H 8.536979886 7.026028623 23.765887359 H 8.632103729 8.325928472 21.748389052 H 10.401195398 8.610017783 21.918744577 H 10.211920160 7.626152615 25.498156937 H 9.693386344 9.087607436 24.635006244 H 11.268611296 8.351576787 24.251776408 Li 9.518209981 5.003341195 18.411641430 MPy− BF 3 * + Li + PC: Au 1.470428550 0.848952320 10.000000000 0 0 0 Au 4.411285650 0.848952320 10.000000000 0 0 0 Au 2.940857100 3.395809280 10.000000000 0 0 0 Au 5.881714210 3.395809280 10.000000000 0 0 0 Au 4.411285650 5.942666240 10.000000000 0 0 0 Au 7.352142750 5.942666240 10.000000000 0 0 0 Au 5.881714200 8.489523200 10.000000000 0 0 0 Au 8.822571310 8.489523200 10.000000000 0 0 0 Au 7.352142760 0.848952320 10.000000000 0 0 0 Au 10.292999860 0.848952320 10.000000000 0 0 0 Au 8.822571310 3.395809280 10.000000000 0 0 0 88 Au 11.763428420 3.395809280 10.000000000 0 0 0 Au 10.292999860 5.942666240 10.000000000 0 0 0 Au 13.233856960 5.942666240 10.000000000 0 0 0 Au 11.763428410 8.489523200 10.000000000 0 0 0 Au 14.704285520 8.489523200 10.000000000 0 0 0 Au 0.009115346 1.685216200 12.427189038 Au 2.958705494 1.719488156 12.414611162 Au 1.474527189 4.238503571 12.430795645 Au 4.431717114 4.234279493 12.547512991 Au −0.001314672 0.038915951 14.922454675 Au 2.912288788 −0.090978112 14.900078160 Au 1.370797920 2.584620018 14.910084564 Au 4.102822878 2.369399579 14.869155707 Au 2.956865530 6.811482438 12.432732225 Au 5.879905180 6.732117660 12.472306557 Au 4.431472755 9.343166455 12.426026707 Au 7.338349544 9.353141396 12.417706045 Au 2.866995259 5.155568560 14.788627918 Au 5.894426877 5.513719950 15.043430470 Au 4.354826295 7.752061789 14.895358431 Au 7.402259895 7.762751462 14.869348812 Au 5.882788939 1.700252595 12.527042118 Au 8.820061103 1.707015839 12.404833759 Au 7.311264379 4.216017054 12.496035593 Au 10.324736941 4.231478626 12.402816639 Au 5.883527058 −0.106661768 14.787473961 Au 8.849360500 −0.098287423 14.909670664 89 Au 7.672989055 2.371058732 14.839768380 Au 10.402197411 2.583603144 14.889058438 Au 8.811187349 6.833484118 12.400066500 Au 11.773682718 6.801963520 12.466494861 Au 10.277999852 9.344710931 12.429899012 Au 13.262634404 9.334245928 12.433920423 Au 8.881235042 5.144556618 14.673143646 Au 11.761652823 5.142491470 14.933151969 Au 10.310187110 7.618895904 14.952396838 Au 13.208602134 7.624249095 15.002119920 N 5.908696025 3.325645962 20.686555408 C 5.922868219 4.506497554 20.027184827 C 5.919463599 4.566568592 18.647873616 C 5.905368931 3.372237604 17.911864415 C 5.894499454 2.150034841 18.605786272 C 5.895259706 2.165763595 19.983227008 H 5.934652212 5.401368841 20.641119244 H 5.926815069 5.531169785 18.147059544 S 5.898853748 3.404056764 16.155982946 H 5.883656012 1.201335552 18.075322030 H 5.883044545 1.248590099 20.566256542 F 7.126948198 2.650876577 22.680878018 B 5.919291673 3.251491883 22.289898459 F 4.828211862 2.461985661 22.685700616 F 5.816235533 4.550885148 22.795208488 O 10.266228112 6.028797457 23.205732989 O 9.796952005 6.815124810 21.167304561 90 O 10.715548028 4.759896143 21.388278067 C 9.553746973 7.291353069 23.454783276 C 9.539879502 7.931265100 22.063437133 C 10.266070061 8.083840109 24.520505856 C 10.296041128 5.781515926 21.883588746 H 8.542455317 7.008991268 23.772304414 H 8.575241748 8.369815488 21.800151691 H 10.343234264 8.665790370 21.928923587 H 10.292223866 7.530161552 25.465058676 H 9.727045299 9.024011971 24.689088768 H 11.290501088 8.318466652 24.207994809 Li 9.582453896 5.283294372 18.361371506 91 A.10 Potential-Dependent SERS Spectra of MPy in PC at Various Electrolytes Figure 4.18: Potential dependent SERS spectra of MPy in PC in the presence of (a) 70 mM LiBF 4 and 30 mM LiTFSI, (b) 70 mM LiBF 4 and 30 mM TBABF 4 . The left panel for each spectrum depicts the potential and defines the y-axis for the right panel. The potential starts from OCP and is swept to positive potentials, followed by a negative and a positive sweep to bring it back to zero. Figure 4.19: Potential dependent SERS spectra of MPy in PC in the presence of (c) 50 mM LiBF 4 and 50 mM LiTFSI, (d) 50 mM LiBF 4 and 50 mM TBABF 4 . The left panel for each spectrum depicts the potential and defines the y-axis for the right panel. The potential starts from OCP and is swept to positive potentials, followed by a negative and a positive sweep to bring it back to zero. 92 Figure 4.20: Potential dependent SERS spectra of MPy in PC in the presence of (e) 30 mM LiBF 4 and 70 mM LiTFSI, (f) 30 mM LiBF 4 and 70 mM TBABF 4 . The potential starts from OCP and is swept to positive potentials, followed by a negative and a positive sweep to bring it back to zero. Figure 4.21: Potential dependent SERS spectra of MPy in PC in the presence of (g) 10 mM LiBF 4 and 90 mM LiTFSI, (h) 10 mM LiBF 4 and 90 mM TBABF 4 . The left panel for each spectrum depicts the potential and defines the y-axis for the right panel. The potential starts from OCP and is swept to positive potentials, followed by a negative and a positive sweep to bring it back to zero. 93 Table 4.1: Effects of Li + and BF − 4 ionic strength on the formation, dissociation, and reformation. 1 1 Experiment 1 refers to Figure 5 in the manuscript, and experiments 2-9 refer to Figures above. Figure 4.22: Potential dependent SERS spectra of MPy in the presence of 0.1 LiBF 4 /PC. The peak at 648 cm − 1 (blue spectra, left panel) may be tentatively assigned to the B-N stretching mode. 94 It seems reasonable to look for the Raman signature of the B-N bond vibration as a signature of the adduct formation/dissociation. However, the assignment of the vibrational frequencies of that bond has been debated in the literature. The vibrational frequency of B-N bond can be mixed with pyridine’s other vibrational modes. According to a recent study by Ethan C. Lambert et al, the B-N modes for the pyridine-BH 3 adduct are strongly coupled to the pyridine’s vibration and appear at around 695 and 1085 cm − 1 167 . J.D. Odom et al suggest that the B-N stretching mode is around 610-680 cm − 1 and is strongly mixed with the N-C vibration. 168 Dana N. Reinemann et al show that the B-N stretching mode lies in the range of 560-650 cm − 1 . 169 Our potential dependent spectra show the disappearance of a peak at 648 cm − 1 (Figure 4.22), which is consistent with bond break- ing based on the ring modes. However, we exercise caution in making a firm assignment of this feature, especially given that a new blue-shifted peak appears concurrent with its disappearance. A.11 Electrochemical Impedance and Capacitance Measurements Figure 4.23: Bode modulus plots of MPy SAM in 0.1 M LiBF 4 /PC at various potentials. Bode phase plots of MPy SAM in 0.1 M LiBF 4 /PC at various potentials (right panel). 95 Figure 4.24: Equivalent circuit model for SAM monolayer on gold in the presence of 0.1 M LiBF 4 /PC. Phase constant element (CPE) represents the EDL capacitance. R SAM is the SAM monolayer resistance, and R S is the solution resistance. Figure 4.25: The plot of differential capacitance vs applied potential for the MPy SAM on Au in 0.1 M LiBF 4 /PC. From the impedance spectra, we have inferred the capacitance as a function of potential after fitting the impedance data to the equivalent circuit model. 170;171 . The capacitance shows a non-monotonic behavior as a function of potential. Especially, prior to the potential for adduct dissociation (0.1 V vs Ag/AgCl), an abrupt change in capacitance, followed by continuing decline of capacitance with 96 more negative potential is observed. We hypothesize that these observations may correlate with our proposed ionic structure change discussed in the paper. 97 B Supporting Information for: Phenol as a Tethering Group to Metal Surfaces:Stark Response and Comparison to Benzenethiol Figure 4.26: Potential dependent SERS data for the nitrile stretching mode for adsorbed CP on gold (left), and for adsorbed MBN (right) . 98 Figure 4.27: Potential dependent SERS spectra for MBN in 0.1M NaClO 4 /water. Figure 4.28: Nitrile frequency shift as a function of applied electrode potential for MBN and 4- (mercaptomethyl)benzonitrile. Introducing a methylene (CH2) group disrupts the conjugation and significantly changes the Stark shift response of adsorbed molecules 99 Figure 4.29: Calculated angle of the adsorbed molecule with respect to the surface normal for CP and MBN. The data suggest that MBN exhibits a slight tilt of a few degrees compared to CP. Figure 4.30: DFT-optimized structures of neutral a) 4-mercaptobenzonitirle (MBN) and b) 4- cyanophenols (CP). Optimized coordinates in V ASP-POSCAR format are given below in the V ASP input files section of the supporting information. Table 4.2: Binding energy (eV) of CP (red) and MBN (blue) on an Au (111) surface at various charges (0, ±0.25, ±0.5, ±1 electron add/subtracted to the system). Binding energy (eV) -1 -0.75 -0.5 -0.25 0 0.25 0.5 0.75 1 S -1.99 -2.03 -2.09 -2.16 -2.23 -2.32 -2.42 -2.52 -2.64 O -0.34 -0.33 -0.32 -0.32 -0.33 -0.35 -0.38 -0.42 -0.47 100 Table 4.3: Nitrile bond length at various charges. C-N Bond -1 -0.75 -0.5 -0.25 0 0.25 0.5 0.75 1 S 1.16999 1.16896 1.16924 1.1691 1.16896 1.16859 1.16858 1.16855 1.16842 O 1.17097 1.17045 1.17026 1.16994 1.16968 1.16947 1.16953 1.16929 1.16937 Table 4.4: Nitrile frequency values at various charges from -1 to +1. Freq -1 -0.75 -0.5 -0.25 0 0.25 0.5 0.75 1 S 2239.035 2241.456 2246.398 2248.109 2250.268 2252.912 2253.608 2254.022 2255.072 O 2232.21 2236.169 2238.221 2241.151 2242.86 2244.022 2242.72 2243.501 2241.407 Figure 4.31: Geometry of adsorption for CP with respect to gold surface at various charges. Figure 4.32: Geometry of adsorption for MBN with respect to gold surface at various charges. 101 B.1 Input files V ASP input files: INCAR (Geometry Optimization) General characteristics • System = Mol A u CalculationTitlePREC= Accurate Options : Normal—Single—Accurate • • ENCUT = 520 Kinetic Energy(eV) Converge • ISTART = 0 Job: 0-new 1-cont 2-samecut • ICHARG = 2 Charge density: 1-file 2-atom 10-cons 11-DOS/BANDS • ISPIN = 1 Spin Polarize: 1-No 2-Yes • LWA VE = False Write the WA VECAR • LCHARG = False Write the CHGCAR Electronic Relaxation (SCF) • NELM = 200 Max Number of Elec Self Cons Steps • NELMIN = 4 Min Number of ESC steps • NELMDL = 6 Number of non-SC at the beginning • EDIFF = 1.0E-08 Stopping criteria for ESC • LREAL = Auto Real space projection • ALGO = Normal Electronic algorithm minimization: Normal| VeryFast| Fast| Conjugate VDW Corrections • IVDW = 21 11-D3, 12-D3 B J,20− T S,21− T S/H Ionic Relaxation • EDIFFG = -0.01 Stopping criteria for ionic self-cons steps 102 • NSW = 200 Max Number of ISC steps: 0-Single Point • IBRION = 2 Ionic Relaxation Method: 0-MD 1-qNewton-RaphsonElectronic 2-CG • ISIF = 2 Stress and Relaxation: 1-Single Point 2-Ion 3-Full • SIGMA = 0.05 Insulators/semiconductors=0.1 metals=0.05 • ISMEAR = 0 Partial Occupancies for each Orbital: 0-Gaussian -1-Fermi -4 tetrahe- dron -5 tetrahedron/Bl¨ ochl -5 DOS, -2 from file, -1 Fermi Smear, 0 Gaussian Smear • ISYM = 0 Parallelization • NPAR = 8 cores per band sqrt num of cores: set to 8 if using 4 nodes with 16 cores each Here is the LaTeX-compatible representation of the second V ASP input file: INCAR (Static Energy/Charge) General characteristics • System = Mol Au Calculation Title • PREC = Accurate Options: Normal| Single| Accurate • ENCUT = 520 Kinetic Energy(eV) Converge • ISTART = 0 Job: 0-new 1-cont 2-samecut • ICHARG = 2 Charge density: 1-file 2-atom 10-cons 11-DOS/BANDS • ISPIN = 1 Spin Polarize: 1-No 2-Yes • LWA VE = True Write the WA VECAR • LCHARG = True Write the CHGCAR Electronic Relaxation (SCF) • NELM = 200 Max Number of Elec Self Cons Steps 103 • NELMIN = 4 Min Number of ESC steps • NELMDL = 6 Number of non-SC at the beginning • EDIFF = 1.0E-08 Stopping criteria for ESC • LREAL = Auto Real space projection • ALGO = Normal Electronic algorithm minimization: Normal| VeryFast| Fast| Conjugate VDW Corrections • IVDW = 21 11-D3, 12-D3 BJ, 20-TS, 21-TS/H Ionic Relaxation • EDIFFG = -0.01 Stopping criteria for ionic self-cons steps • NSW = 0 Max Number of ISC steps: 0-Single Point • IBRION = 2 Ionic Relaxation Method: 0-MD 1-qNewton-RaphsonElectronic 2-CG • ISIF = 1 Stress and Relaxation: 1-Single Point 2-Ion 3-Full • SIGMA = 0.05 Insulators/semiconductors=0.1 metals=0.05 • ISMEAR = 0 Partial Occupancies for each Orbital: 0-Gaussian -1-Fermi -4 tetrahe- dron -5 tetrahedron/Bl¨ ochl -5 DOS, -2 from file, -1 Fermi Smear, 0 Gaussian Smear • ISYM = 0 Parallelization • NPAR = 8 cores per band sqrt num of cores: set to 8 if using 4 nodes with 16 cores each Here is the LaTeX-compatible representation of the third V ASP input file: INCAR (Frequency) General characteristics • System = Mol Au Calculation Title 104 • PREC = Accurate Options: Normal| Single| Accurate • ENCUT = 520 Kinetic Energy(eV) Converge • ISTART = 0 Job: 0-new 1-cont 2-samecut • ICHARG = 2 Charge density: 1-file 2-atom 10-cons 11-DOS/BANDS • ISPIN = 1 Spin Polarize: 1-No 2-Yes • LWA VE = False Write the WA VECAR • LCHARG = False Write the CHGCAR Electronic Relaxation (SCF) • NELM = 200 Max Number of Elec Self Cons Steps • NELMIN = 4 Min Number of ESC steps • NELMDL = 6 Number of non-SC at the beginning • EDIFF = 1.0E-08 Stopping criteria for ESC • LREAL = Auto Real space projection • ALGO = Normal Electronic algorithm minimization: Normal| VeryFast| Fast| Conjugate VDW Corrections • IVDW = 21 11-D3, 12-D3 BJ, 20-TS, 21-TS/H Ionic Relaxation • EDIFFG = -0.01 Stopping criteria for ionic self-cons steps • NSW = 200 Max Number of ISC steps: 0-Single Point • IBRION = 5 Ionic Relaxation Method: 0-MD 1-qNewton-RaphsonElectronic 2-CG 105 • ISIF = 2 Stress and Relaxation: 1-Single Point 2-Ion 3-Full • SIGMA = 0.05 Insulators/semiconductors=0.1 metals=0.05 • ISMEAR = 0 Partial Occupancies for each Orbital: 0-Gaussian -1-Fermi -4 tetrahe- dron -5 tetrahedron/Bl¨ ochl -5 DOS, -2 from file, -1 Fermi Smear, 0 Gaussian Smear • ISYM = 0 Parallelization • NPAR = 8 cores per band sqrt num of cores: set to 8 if using 4 nodes with 16 cores each Here is the LaTeX-compatible representation of the KPOINTS section followed by the POTCAR- list: KPOINTS • Regular k-point mesh • 0 ! 0 -¿ determine number of k points automatically • Gamma ! generate a Gamma centered mesh • 1 1 1 ! subdivisions N 1, N 2 and N 3 along the reciprocal lattice vectors • 0 0 0 ! optional shift of the mesh (s 1, s 2, s 3) POTCAR-list • Au: PAW PBE Au 04Oct2007 • N: PAW PBE N 08Apr2002 • C: PAW PBE C 08Apr2002 • H: PAW PBE H 15Jun2001 • O: PAW PBE O 08Apr2002 • S: PAW PBE S 06Sep2000 106 B.2 Geometry Optimization Neutral for MBN POSCAR (Optimized Geometry Neutral: MBZ) Sulfur 1.00000000000000 14.7477998734000000 0.0000000000000000 0.0000000000000000 -7.3738999367000000 12.7719693403000001 0.0000000000000000 0.0000000000000000 0.0000000000000000 39.6332015990999977 Au S N C H 125 1 1 7 5 Selective dynamics Direct 0.1333300020000010 0.0666700009999985 0.0000000000000000 F F F 0.3333300050000005 0.0666700009999985 0.0000000000000000 F F F 0.5333300229999978 0.0666700009999985 0.0000000000000000 F F F 0.7333300109999996 0.0666700009999985 0.0000000000000000 F F F 0.9333299990000015 0.0666700009999985 0.0000000000000000 F F F 0.1333300020000010 0.2666699890000004 0.0000000000000000 F F F 0.3333300050000005 0.2666699890000004 0.0000000000000000 F F F 0.5333300229999978 0.2666699890000004 0.0000000000000000 F F F 0.7333300109999996 0.2666699890000004 0.0000000000000000 F F F 0.9333299990000015 0.2666699890000004 0.0000000000000000 F F F 0.1333300020000010 0.4666700069999976 0.0000000000000000 F F F 0.3333300050000005 0.4666700069999976 0.0000000000000000 F F F 0.5333300229999978 0.4666700069999976 0.0000000000000000 F F F 0.7333300109999996 0.4666700069999976 0.0000000000000000 F F F 0.9333299990000015 0.4666700069999976 0.0000000000000000 F F F 107 0.1333300020000010 0.6666700239999983 0.0000000000000000 F F F 0.3333300050000005 0.6666700239999983 0.0000000000000000 F F F 0.5333300229999978 0.6666700239999983 0.0000000000000000 F F F 0.7333300109999996 0.6666700239999983 0.0000000000000000 F F F 0.9333299990000015 0.6666700239999983 0.0000000000000000 F F F 0.1333300020000010 0.8666700120000002 0.0000000000000000 F F F 0.3333300050000005 0.8666700120000002 0.0000000000000000 F F F 0.5333300229999978 0.8666700120000002 0.0000000000000000 F F F 0.7333300109999996 0.8666700120000002 0.0000000000000000 F F F 0.9333299990000015 0.8666700120000002 0.0000000000000000 F F F 0.0000000000000000 0.0000000000000000 0.0607599989999983 F F F 0.2000000029999995 0.0000000000000000 0.0607599989999983 F F F 0.4000000059999991 0.0000000000000000 0.0607599989999983 F F F 0.6000000240000034 0.0000000000000000 0.0607599989999983 F F F 0.8000000119999982 0.0000000000000000 0.0607599989999983 F F F 0.0000000000000000 0.2000000029999995 0.0607599989999983 F F F 0.2000000029999995 0.2000000029999995 0.0607599989999983 F F F 0.4000000059999991 0.2000000029999995 0.0607599989999983 F F F 0.6000000240000034 0.2000000029999995 0.0607599989999983 F F F 0.8000000119999982 0.2000000029999995 0.0607599989999983 F F F 0.0000000000000000 0.4000000059999991 0.0607599989999983 F F F 0.2000000029999995 0.4000000059999991 0.0607599989999983 F F F 0.4000000059999991 0.4000000059999991 0.0607599989999983 F F F 0.6000000240000034 0.4000000059999991 0.0607599989999983 F F F 0.8000000119999982 0.4000000059999991 0.0607599989999983 F F F 0.0000000000000000 0.6000000240000034 0.0607599989999983 F F F 0.2000000029999995 0.6000000240000034 0.0607599989999983 F F F 108 0.4000000059999991 0.6000000240000034 0.0607599989999983 F F F 0.6000000240000034 0.6000000240000034 0.0607599989999983 F F F 0.8000000119999982 0.6000000240000034 0.0607599989999983 F F F 0.0000000000000000 0.8000000119999982 0.0607599989999983 F F F 0.2000000029999995 0.8000000119999982 0.0607599989999983 F F F 0.4000000059999991 0.8000000119999982 0.0607599989999983 F F F 0.6000000240000034 0.8000000119999982 0.0607599989999983 F F F 0.8000000119999982 0.8000000119999982 0.0607599989999983 F F F 0.0669353353772593 0.1336458211244600 0.1191733915068130 T T T 0.2678214884495306 0.1356163187020301 0.1193292499754469 T T T 0.4667297147376390 0.1333388749501563 0.1192967534601989 T T T 0.6667737581269840 0.1331084514613844 0.1193228030047090 T T T 0.8669882059954841 0.1330115413533221 0.1192186799407149 T T T 0.0678119453239899 0.3344390998359034 0.1196008025531616 T T T 0.2681977761278779 0.3354263639851447 0.1198640935297388 T T T 0.4671682093761588 0.3354024412620332 0.1197822975209635 T T T 0.6664733739233059 0.3334661550030890 0.1193384347261924 T T T 0.8668940952801780 0.3332195507180009 0.1193186835996515 T T T 0.0670958500247900 0.5330542318480859 0.1192448980290330 T T T 0.2678400177512925 0.5325853741029851 0.1196710808925665 T T T 0.4664562110339032 0.5335753782646734 0.1204044756697260 T T T 0.6645387444647968 0.5327422428793611 0.1198166373653168 T T T 0.8666302294797664 0.5332033561299162 0.1192903607328607 T T T 0.0671456149860482 0.7336916108888766 0.1188580385835852 T T T 0.2678398979925591 0.7323154796129344 0.1192196018002585 T T T 0.4677458022093937 0.7322896633758519 0.1196934892445522 T T T 0.6647279193363447 0.7317030661607371 0.1198877599175233 T T T 109 0.8642405490292308 0.7319502089267049 0.1193759827274116 T T T 0.0673584070835845 0.9324774879847836 0.1190132244695909 T T T 0.2663152296097704 0.9328668452881160 0.1188624272514968 T T T 0.4670659611002558 0.9329191408324913 0.1192424328027806 T T T 0.6657284009423062 0.9321835854099648 0.1196102241733965 T T T 0.8664004338335735 0.9330051248607345 0.1191798112667330 T T T 0.1321739735898414 0.0641159932181198 0.1773093298818423 T T T 0.3318564565788901 0.0638598519829916 0.1773040611985132 T T T 0.5340051388670385 0.0664006885095486 0.1779000355119799 T T T 0.7341447398771231 0.0665308149996433 0.1778647776675685 T T T 0.9335031079515980 0.0663929434224365 0.1780213561247072 T T T 0.1331257901500348 0.2650539221090906 0.1775793129916735 T T T 0.3318481874270311 0.2643412371144639 0.1783151082580958 T T T 0.5319119145860363 0.2653140164489816 0.1774668576126510 T T T 0.7336457855343049 0.2663524120746357 0.1778448760623599 T T T 0.9334716342190099 0.2658815929037179 0.1778617641019536 T T T 0.1343088969838253 0.4693235715341788 0.1782128017572182 T T T 0.3348041156633814 0.4682719152028633 0.1808304005420674 T T T 0.5315943089014938 0.4680188393079062 0.1807302578818792 T T T 0.7347747177378720 0.4679888653232291 0.1774748876645999 T T T 0.9337206149859799 0.4660312543575458 0.1778898153278690 T T T 0.1334778314910220 0.6675619036185376 0.1776366500736313 T T T 0.3323253297993890 0.6682294094928488 0.1781100791207115 T T T 0.5324498321207324 0.6651191795606604 0.1808864780376911 T T T 0.7354871669546725 0.6676185275285634 0.1784673662266082 T T T 0.9364146012574773 0.6680995622017477 0.1773064872983210 T T T 0.1346314875876400 0.8654319530513149 0.1784127195229744 T T T 110 0.3326607709599075 0.8669443066858729 0.1776305550431033 T T T 0.5309540494581709 0.8658665235532536 0.1782305600638395 T T T 0.7349973238409128 0.8666953231923348 0.1776155669496055 T T T 0.9356592795084273 0.8674990283369564 0.1773326149751214 T T T 0.9993699104105402 0.0001711256323784 0.2390857064489470 T T T 0.1985257454688386 0.9984902322326717 0.2386207715106717 T T T 0.6045432002275863 0.0053345835519449 0.2388817969610063 T T T 0.4022727268429631 0.0027176791355175 0.2383171234216017 T T T 0.1887658344848526 0.1892585744189454 0.2383008513485959 T T T 0.9960647541126328 0.1975007608895728 0.2392151096284724 T T T 0.8022055144835746 0.0035828091915124 0.2392055252006854 T T T 0.1890626281680770 0.3933317117581067 0.2367120697802921 T T T 0.3837379474505210 0.3702121861727246 0.2391391914753458 T T T 0.6049384783779932 0.3952121581107075 0.2360646869980823 T T T 0.8002011684721329 0.1997679649389697 0.2388683566552892 T T T 0.9948320737140663 0.3954547659265130 0.2388743436109167 T T T 0.6024651648120073 0.1991868963486247 0.2385812171609392 T T T 0.3997765013767615 0.1903203866619961 0.2379417342053956 T T T 0.8010769726380936 0.3975473582343981 0.2385614013242178 T T T 0.9981340854721862 0.5978163117487971 0.2382849945859356 T T T 0.3860431967194342 0.6158216375673438 0.2386749631641688 T T T 0.1855106757724194 0.5924704168964174 0.2403215299394603 T T T 0.0017571286020636 0.8016592670224764 0.2386273734726210 T T T 0.8106353509532740 0.6003208453606176 0.2379775511048860 T T T 0.6301895202420029 0.6149052964776651 0.2395343204750301 T T T 0.1970844218386532 0.8031121768811136 0.2405688358611665 T T T 0.4073663893874037 0.8153397402947123 0.2403114628011592 T T T 111 0.8103061670235209 0.8106192125371238 0.2383369630144409 T T T 0.6065350261872920 0.8107399015237395 0.2367434460809688 T T T 0.4674050297468147 0.5321774987060086 0.2707456855126424 T T T 0.4892574605134009 0.4947710758333475 0.4501823008560624 T T T 0.4718056509902190 0.5243790419843228 0.3152103222379374 T T T 0.3899499195657559 0.4392791892344678 0.3321533018597861 T T T 0.5576249919067974 0.6024361466896196 0.3329880996827564 T T T 0.3942142962198384 0.4320522131549643 0.3670256261121457 T T T 0.5618153750289239 0.5951193216435525 0.3678716880306210 T T T 0.4802922568829550 0.5097542666329562 0.3851362447791363 T T T 0.4851814471156546 0.5016203035909210 0.4209053103127460 T T T 0.2657733470992736 0.7339336845235152 0.2563485047475945 T T T 0.3241256849993786 0.3788955284653956 0.3178788139447954 T T T 0.6209360109009079 0.6676325158823393 0.3193531666958053 T T T 0.3314512428238639 0.3660637585952100 0.3804845405544966 T T T 0.6284168136516245 0.6548610209458000 0.3819621244584321 T T T 112 B.3 Geometry Optimization Neutral for CP POSCAR (Optimized Geometry Neutral: CP) Oxygen 1.00000000000000 14.7477998734000000 0.0000000000000000 0.0000000000000000 -7.3738999367000000 12.7719693403000001 0.0000000000000000 0.0000000000000000 0.0000000000000000 39.6332015990999977 Au O N C H 125 1 1 7 5 Selective dynamics Direct 0.1333300020000010 0.0666700009999985 0.0000000000000000 F F F 0.3333300050000005 0.0666700009999985 0.0000000000000000 F F F 0.5333300229999978 0.0666700009999985 0.0000000000000000 F F F 0.7333300109999996 0.0666700009999985 0.0000000000000000 F F F 0.9333299990000015 0.0666700009999985 0.0000000000000000 F F F 0.1333300020000010 0.2666699890000004 0.0000000000000000 F F F 0.3333300050000005 0.2666699890000004 0.0000000000000000 F F F 0.5333300229999978 0.2666699890000004 0.0000000000000000 F F F 0.7333300109999996 0.2666699890000004 0.0000000000000000 F F F 0.9333299990000015 0.2666699890000004 0.0000000000000000 F F F 0.1333300020000010 0.4666700069999976 0.0000000000000000 F F F 0.3333300050000005 0.4666700069999976 0.0000000000000000 F F F 0.5333300229999978 0.4666700069999976 0.0000000000000000 F F F 0.7333300109999996 0.4666700069999976 0.0000000000000000 F F F 0.9333299990000015 0.4666700069999976 0.0000000000000000 F F F 113 0.1333300020000010 0.6666700239999983 0.0000000000000000 F F F 0.3333300050000005 0.6666700239999983 0.0000000000000000 F F F 0.5333300229999978 0.6666700239999983 0.0000000000000000 F F F 0.7333300109999996 0.6666700239999983 0.0000000000000000 F F F 0.9333299990000015 0.6666700239999983 0.0000000000000000 F F F 0.1333300020000010 0.8666700120000002 0.0000000000000000 F F F 0.3333300050000005 0.8666700120000002 0.0000000000000000 F F F 0.5333300229999978 0.8666700120000002 0.0000000000000000 F F F 0.7333300109999996 0.8666700120000002 0.0000000000000000 F F F 0.9333299990000015 0.8666700120000002 0.0000000000000000 F F F 0.0000000000000000 0.0000000000000000 0.0607599989999983 F F F 0.2000000029999995 0.0000000000000000 0.0607599989999983 F F F 0.4000000059999991 0.0000000000000000 0.0607599989999983 F F F 0.6000000240000034 0.0000000000000000 0.0607599989999983 F F F 0.8000000119999982 0.0000000000000000 0.0607599989999983 F F F 0.0000000000000000 0.2000000029999995 0.0607599989999983 F F F 0.2000000029999995 0.2000000029999995 0.0607599989999983 F F F 0.4000000059999991 0.2000000029999995 0.0607599989999983 F F F 0.6000000240000034 0.2000000029999995 0.0607599989999983 F F F 0.8000000119999982 0.2000000029999995 0.0607599989999983 F F F 0.0000000000000000 0.4000000059999991 0.0607599989999983 F F F 0.2000000029999995 0.4000000059999991 0.0607599989999983 F F F 0.4000000059999991 0.4000000059999991 0.0607599989999983 F F F 0.6000000240000034 0.4000000059999991 0.0607599989999983 F F F 0.8000000119999982 0.4000000059999991 0.0607599989999983 F F F 0.0000000000000000 0.6000000240000034 0.0607599989999983 F F F 0.2000000029999995 0.6000000240000034 0.0607599989999983 F F F 114 0.4000000059999991 0.6000000240000034 0.0607599989999983 F F F 0.6000000240000034 0.6000000240000034 0.0607599989999983 F F F 0.8000000119999982 0.6000000240000034 0.0607599989999983 F F F 0.0000000000000000 0.8000000119999982 0.0607599989999983 F F F 0.2000000029999995 0.8000000119999982 0.0607599989999983 F F F 0.4000000059999991 0.8000000119999982 0.0607599989999983 F F F 0.6000000240000034 0.8000000119999982 0.0607599989999983 F F F 0.8000000119999982 0.8000000119999982 0.0607599989999983 F F F 0.0668419722876899 0.1333519375879540 0.1192430153116466 T T T 0.2674986667624878 0.1345637933690094 0.1193067131782227 T T T 0.4667925278251343 0.1330556318266397 0.1193672197351545 T T T 0.6669200689538085 0.1331223770228195 0.1193899581554902 T T T 0.8669837764042310 0.1329980769929051 0.1192715446805889 T T T 0.0675335991067439 0.3341307122769073 0.1196369962584811 T T T 0.2677216782423930 0.3346935625933163 0.1197788090643982 T T T 0.4673652553088601 0.3348539955530865 0.1197434770834948 T T T 0.6667395746636879 0.3333007560992612 0.1193930524548890 T T T 0.8668846675500650 0.3330882174136878 0.1193891006084128 T T T 0.0669595823168315 0.5330003813274703 0.1193010808670184 T T T 0.2672319017377334 0.5322304579087528 0.1195632136287742 T T T 0.4666044420409141 0.5334109429158428 0.1201436891037809 T T T 0.6651667922376788 0.5326669761142268 0.1197451358228363 T T T 0.8669789489533517 0.5332310090739248 0.1193663620233502 T T T 0.0670362552837932 0.7335948034618452 0.1190516431648709 T T T 0.2670916497225458 0.7329173600909398 0.1190689531001839 T T T 0.4677640463144510 0.7327483423131557 0.1195700997257981 T T T 0.6652768479172247 0.7322540062606679 0.1197891152353857 T T T 115 0.8653881440230996 0.7324847074333962 0.1193162867759815 T T T 0.0673968891218248 0.9325877648586574 0.1192214250547884 T T T 0.2664302808630410 0.9329741503137463 0.1190548965329388 T T T 0.4670101570479469 0.9330503728315047 0.1193005784428507 T T T 0.6658500490328239 0.9324426019253446 0.1196355811865105 T T T 0.8666297810811555 0.9331432810081880 0.1192422899369091 T T T 0.1322420606689438 0.0644316180712475 0.1776061396291171 T T T 0.3323843847325296 0.0640356498021562 0.1776211676406885 T T T 0.5341501949404072 0.0662768143368201 0.1780282084069133 T T T 0.7343194151065637 0.0665105114616721 0.1779839720393613 T T T 0.9336426925072725 0.0663709205596037 0.1781640794631055 T T T 0.1329228545746830 0.2651339146027638 0.1777573567644033 T T T 0.3314398981720555 0.2626183272239438 0.1778306129514799 T T T 0.5326400396330602 0.2651775658839238 0.1776433914909578 T T T 0.7338766590741838 0.2661375818928889 0.1780063461232167 T T T 0.9334796378160822 0.2656593162320042 0.1779841003589943 T T T 0.1339800876313002 0.4686276253172661 0.1783802081323531 T T T 0.3344636766365572 0.4675702107530204 0.1798853006528664 T T T 0.5324117802389401 0.4677341172404394 0.1799990627063817 T T T 0.7348864826398076 0.4674214095234068 0.1776445039630168 T T T 0.9337359957182556 0.4658539608449587 0.1780277611050924 T T T 0.1330062131057347 0.6669562953926284 0.1778840401131123 T T T 0.3311892866822903 0.6687834933996111 0.1773240585790783 T T T 0.5324301630746673 0.6655373324962661 0.1799179789966009 T T T 0.7373571085127993 0.6685848453564243 0.1778740819033674 T T T 0.9359945958339788 0.6676778869052316 0.1776192627996717 T T T 0.1346873222666589 0.8653668045981588 0.1785712498941527 T T T 116 0.3330605131014151 0.8669951599284240 0.1778854859733479 T T T 0.5313480778899830 0.8660004566373561 0.1783825736255601 T T T 0.7348559205770420 0.8670668508055537 0.1777585448662104 T T T 0.9356054726227963 0.8677932471726969 0.1776064835629910 T T T 0.9999821941283772 0.0001969767598283 0.2391920286687918 T T T 0.1991154060742036 0.9989617531926015 0.2385902784535267 T T T 0.6042287278851283 0.0037706340449630 0.2387435392869113 T T T 0.4022743915010868 0.0020283572820636 0.2383300423955782 T T T 0.1913906970232577 0.1916352334376257 0.2385340760175489 T T T 0.9975080947326447 0.1981615889534070 0.2391459226211610 T T T 0.8018977880923139 0.0025866370786401 0.2391320380131507 T T T 0.1933533320818877 0.3951859334578200 0.2371086544095017 T T T 0.3872912434640545 0.3760255577977731 0.2369268800289292 T T T 0.6035350183178908 0.3965705895745860 0.2364412714172444 T T T 0.8004801962318773 0.1995390163558421 0.2389728761856164 T T T 0.9962433858288995 0.3957536575097572 0.2387494230264397 T T T 0.6024072438757899 0.1993161885680031 0.2385854136119616 T T T 0.4005332409075817 0.1923734682121555 0.2382592276370034 T T T 0.8007257149766984 0.3976192758803189 0.2385886100721764 T T T 0.9980247330445184 0.5977536712531227 0.2383297093062172 T T T 0.3885703183767685 0.6113259670247191 0.2364020322760943 T T T 0.1881061112224378 0.5923105779777933 0.2405198942773482 T T T 0.0011182852755258 0.8009622037889623 0.2385894533164796 T T T 0.8077285107020685 0.5995336007542822 0.2382605589374500 T T T 0.6242106190856462 0.6129849485084148 0.2370279069865333 T T T 0.1975626335152011 0.8024722662760131 0.2402994990129836 T T T 0.4076638259511939 0.8118575427192846 0.2405115217263928 T T T 117 0.8085553791422918 0.8088216032256096 0.2385342167887806 T T T 0.6048389896539236 0.8067241944156246 0.2371165938957071 T T T 0.4711741691691134 0.5293104958651131 0.2700386923140111 T T T 0.4756371642897003 0.5168395804299210 0.4405963345174230 T T T 0.4715731475187446 0.5277037431657124 0.3043011161417351 T T T 0.3875252832517814 0.4462913177037426 0.3219896158162970 T T T 0.5559173476755517 0.6072464120147499 0.3224202109853910 T T T 0.3882923036426023 0.4438165944718118 0.3569934777464760 T T T 0.5568047373054421 0.6049073642371250 0.3574349227671350 T T T 0.4731241131909423 0.5229699297824547 0.3751731361936348 T T T 0.4744630975107086 0.5197087869679374 0.4111131514956117 T T T 0.2665945246755480 0.7333847931390541 0.2565898474903253 T T T 0.3223053968995510 0.3850284629597612 0.3076848448490287 T T T 0.6206210600723956 0.6702296790092115 0.3084593585480721 T T T 0.3234553193601448 0.3802920467042860 0.3706220118224955 T T T 0.6225668691219184 0.6662399661308390 0.3714061160443090 T T T POSCAR (Optimized Geometry Neutral: CP) Oxygen 1.00000000000000 14.7477998734000000 0.0000000000000000 0.0000000000000000 -7.3738999367000000 12.7719693403000001 0.0000000000000000 0.0000000000000000 0.0000000000000000 39.6332015990999977 Au O N C H 125 1 1 7 5 Selective dynamics 118 Direct 0.1333300020000010 0.0666700009999985 0.0000000000000000 F F F 0.3333300050000005 0.0666700009999985 0.0000000000000000 F F F 0.5333300229999978 0.0666700009999985 0.0000000000000000 F F F 0.7333300109999996 0.0666700009999985 0.0000000000000000 F F F 0.9333299990000015 0.0666700009999985 0.0000000000000000 F F F 0.1333300020000010 0.2666699890000004 0.0000000000000000 F F F 0.3333300050000005 0.2666699890000004 0.0000000000000000 F F F 0.5333300229999978 0.2666699890000004 0.0000000000000000 F F F 0.7333300109999996 0.2666699890000004 0.0000000000000000 F F F 0.9333299990000015 0.2666699890000004 0.0000000000000000 F F F 0.1333300020000010 0.4666700069999976 0.0000000000000000 F F F 0.3333300050000005 0.4666700069999976 0.0000000000000000 F F F 0.5333300229999978 0.4666700069999976 0.0000000000000000 F F F 0.7333300109999996 0.4666700069999976 0.0000000000000000 F F F 0.9333299990000015 0.4666700069999976 0.0000000000000000 F F F 0.1333300020000010 0.6666700239999983 0.0000000000000000 F F F 0.3333300050000005 0.6666700239999983 0.0000000000000000 F F F 0.5333300229999978 0.6666700239999983 0.0000000000000000 F F F 0.7333300109999996 0.6666700239999983 0.0000000000000000 F F F 0.9333299990000015 0.6666700239999983 0.0000000000000000 F F F 0.1333300020000010 0.8666700120000002 0.0000000000000000 F F F 0.3333300050000005 0.8666700120000002 0.0000000000000000 F F F 0.5333300229999978 0.8666700120000002 0.0000000000000000 F F F 0.7333300109999996 0.8666700120000002 0.0000000000000000 F F F 0.9333299990000015 0.8666700120000002 0.0000000000000000 F F F 0.0000000000000000 0.0000000000000000 0.0607599989999983 F F F 119 0.2000000029999995 0.0000000000000000 0.0607599989999983 F F F 0.4000000059999991 0.0000000000000000 0.0607599989999983 F F F 0.6000000240000034 0.0000000000000000 0.0607599989999983 F F F 0.8000000119999982 0.0000000000000000 0.0607599989999983 F F F 0.0000000000000000 0.2000000029999995 0.0607599989999983 F F F 0.2000000029999995 0.2000000029999995 0.0607599989999983 F F F 0.4000000059999991 0.2000000029999995 0.0607599989999983 F F F 0.6000000240000034 0.2000000029999995 0.0607599989999983 F F F 0.8000000119999982 0.2000000029999995 0.0607599989999983 F F F 0.0000000000000000 0.4000000059999991 0.0607599989999983 F F F 0.2000000029999995 0.4000000059999991 0.0607599989999983 F F F 0.4000000059999991 0.4000000059999991 0.0607599989999983 F F F 0.6000000240000034 0.4000000059999991 0.0607599989999983 F F F 0.8000000119999982 0.4000000059999991 0.0607599989999983 F F F 0.0000000000000000 0.6000000240000034 0.0607599989999983 F F F 0.2000000029999995 0.6000000240000034 0.0607599989999983 F F F 0.4000000059999991 0.6000000240000034 0.0607599989999983 F F F 0.6000000240000034 0.6000000240000034 0.0607599989999983 F F F 0.8000000119999982 0.6000000240000034 0.0607599989999983 F F F 0.0000000000000000 0.8000000119999982 0.0607599989999983 F F F 0.2000000029999995 0.8000000119999982 0.0607599989999983 F F F 0.4000000059999991 0.8000000119999982 0.0607599989999983 F F F 0.6000000240000034 0.8000000119999982 0.0607599989999983 F F F 0.8000000119999982 0.8000000119999982 0.0607599989999983 F F F 0.0668419722876899 0.1333519375879540 0.1192430153116466 T T T 0.2674986667624878 0.1345637933690094 0.1193067131782227 T T T 0.4667925278251343 0.1330556318266397 0.1193672197351545 T T T 120 0.6669200689538085 0.1331223770228195 0.1193899581554902 T T T 0.8669837764042310 0.1329980769929051 0.1192715446805889 T T T 0.0675335991067439 0.3341307122769073 0.1196369962584811 T T T 0.2677216782423930 0.3346935625933163 0.1197788090643982 T T T 0.4673652553088601 0.3348539955530865 0.1197434770834948 T T T 0.6667395746636879 0.3333007560992612 0.1193930524548890 T T T 0.8668846675500650 0.3330882174136878 0.1193891006084128 T T T 0.0669595823168315 0.5330003813274703 0.1193010808670184 T T T 0.2672319017377334 0.5322304579087528 0.1195632136287742 T T T 0.4666044420409141 0.5334109429158428 0.1201436891037809 T T T 0.6651667922376788 0.5326669761142268 0.1197451358228363 T T T 0.8669789489533517 0.5332310090739248 0.1193663620233502 T T T 0.0670362552837932 0.7335948034618452 0.1190516431648709 T T T 0.2670916497225458 0.7329173600909398 0.1190689531001839 T T T 0.4677640463144510 0.7327483423131557 0.1195700997257981 T T T 0.6652768479172247 0.7322540062606679 0.1197891152353857 T T T 0.8653881440230996 0.7324847074333962 0.1193162867759815 T T T 0.0673968891218248 0.9325877648586574 0.1192214250547884 T T T 0.2664302808630410 0.9329741503137463 0.1190548965329388 T T T 0.4670101570479469 0.9330503728315047 0.1193005784428507 T T T 0.6658500490328239 0.9324426019253446 0.1196355811865105 T T T 0.8666297810811555 0.9331432810081880 0.1192422899369091 T T T 0.1322420606689438 0.0644316180712475 0.1776061396291171 T T T 0.3323843847325296 0.0640356498021562 0.1776211676406885 T T T 0.5341501949404072 0.0662768143368201 0.1780282084069133 T T T 0.7343194151065637 0.0665105114616721 0.1779839720393613 T T T 0.9336426925072725 0.0663709205596037 0.1781640794631055 T T T 121 0.1329228545746830 0.2651339146027638 0.1777573567644033 T T T 0.3314398981720555 0.2626183272239438 0.1778306129514799 T T T 0.5326400396330602 0.2651775658839238 0.1776433914909578 T T T 0.7338766590741838 0.2661375818928889 0.1780063461232167 T T T 0.9334796378160822 0.2656593162320042 0.1779841003589943 T T T 0.1339800876313002 0.4686276253172661 0.1783802081323531 T T T 0.3344636766365572 0.4675702107530204 0.1798853006528664 T T T 0.5324117802389401 0.4677341172404394 0.1799990627063817 T T T 0.7348864826398076 0.4674214095234068 0.1776445039630168 T T T 0.9337359957182556 0.4658539608449587 0.1780277611050924 T T T 0.1330062131057347 0.6669562953926284 0.1778840401131123 T T T 0.3311892866822903 0.6687834933996111 0.1773240585790783 T T T 0.5324301630746673 0.6655373324962661 0.1799179789966009 T T T 0.7373571085127993 0.6685848453564243 0.1778740819033674 T T T 0.9359945958339788 0.6676778869052316 0.1776192627996717 T T T 0.1346873222666589 0.8653668045981588 0.1785712498941527 T T T 0.3330605131014151 0.8669951599284240 0.1778854859733479 T T T 0.5313480778899830 0.8660004566373561 0.1783825736255601 T T T 0.7348559205770420 0.8670668508055537 0.1777585448662104 T T T 0.9356054726227963 0.8677932471726969 0.1776064835629910 T T T 0.9999821941283772 0.0001969767598283 0.2391920286687918 T T T 0.1991154060742036 0.9989617531926015 0.2385902784535267 T T T 0.6042287278851283 0.0037706340449630 0.2387435392869113 T T T 0.4022743915010868 0.0020283572820636 0.2383300423955782 T T T 0.1913906970232577 0.1916352334376257 0.2385340760175489 T T T 0.9975080947326447 0.1981615889534070 0.2391459226211610 T T T 0.8018977880923139 0.0025866370786401 0.2391320380131507 T T T 122 0.1933533320818877 0.3951859334578200 0.2371086544095017 T T T 0.3872912434640545 0.3760255577977731 0.2369268800289292 T T T 0.6035350183178908 0.3965705895745860 0.2364412714172444 T T T 0.8004801962318773 0.1995390163558421 0.2389728761856164 T T T 0.9962433858288995 0.3957536575097572 0.2387494230264397 T T T 0.6024072438757899 0.1993161885680031 0.2385854136119616 T T T 0.4005332409075817 0.1923734682121555 0.2382592276370034 T T T 0.8007257149766984 0.3976192758803189 0.2385886100721764 T T T 0.9980247330445184 0.5977536712531227 0.2383297093062172 T T T 0.3885703183767685 0.6113259670247191 0.2364020322760943 T T T 0.1881061112224378 0.5923105779777933 0.2405198942773482 T T T 0.0011182852755258 0.8009622037889623 0.2385894533164796 T T T 0.8077285107020685 0.5995336007542822 0.2382605589374500 T T T 0.6242106190856462 0.6129849485084148 0.2370279069865333 T T T 0.1975626335152011 0.8024722662760131 0.2402994990129836 T T T 0.4076638259511939 0.8118575427192846 0.2405115217263928 T T T 0.8085553791422918 0.8088216032256096 0.2385342167887806 T T T 0.6048389896539236 0.8067241944156246 0.2371165938957071 T T T 0.4711741691691134 0.5293104958651131 0.2700386923140111 T T T 0.4756371642897003 0.5168395804299210 0.4405963345174230 T T T 0.4715731475187446 0.5277037431657124 0.3043011161417351 T T T 0.3875252832517814 0.4462913177037426 0.3219896158162970 T T T 0.5559173476755517 0.6072464120147499 0.3224202109853910 T T T 0.3882923036426023 0.4438165944718118 0.3569934777464760 T T T 0.5568047373054421 0.6049073642371250 0.3574349227671350 T T T 0.4731241131909423 0.5229699297824547 0.3751731361936348 T T T 0.4744630975107086 0.5197087869679374 0.4111131514956117 T T T 123 0.2665945246755480 0.7333847931390541 0.2565898474903253 T T T 0.3223053968995510 0.3850284629597612 0.3076848448490287 T T T 0.6206210600723956 0.6702296790092115 0.3084593585480721 T T T 0.3234553193601448 0.3802920467042860 0.3706220118224955 T T T 0.6225668691219184 0.6662399661308390 0.3714061160443090 T T T C Design and Optimization of a Home-Made Triple Laser Raman System C.1 An Image of the Home-Made Raman Figure 4.33: An image of the home-made triple laser Raman system. 124 C.2 Schematic Illustration of the Home-Made Raman System. Figure 4.34: Schematic illustration of the home-made triple laser Raman system. C.3 Raman Instrument Performance Figure 4.35: Raman spectra of benzonitrile taken with a Horiba XploRA Raman Microscope (blue) and the home-made Raman system (red) using a similar experimental conditions/settings: objective lens: 4x Olympus; Laser power: 27 mW; Laser wavelength: 785 nm; exposure time: 1 second; grating: 600 lines/mm; slit size: 50 microns. 125 D TEMPO Project D.1 Synthesis of Amide Diradical TEMPO Figure 4.36: Synthesis of an amide diradical TEMPO via the reaction of disulfide dicarboxylic acid and amino TEMPO. D.2 An Image of Diradical TEMPO Crystal Figure 4.37: An image of the diradical TEMPO crystal after synthesis and purification. 126 D.3 FT-IR Spectrum of Amide Diradical TEMPO Figure 4.38: FT-IR spectrum of the amide diradical TEMPO. Figure 4.39: Self assembele monolayer of amide TEMPO on a gold surface. This radical can undergo one electron transfer process. 127 D.4 Cyclic Voltammograms of Amide Diradical TEMPO Figure 4.40: The cyclic voltammograms of amide SAM in 0.1 M NaClO4 in water as the solvent. The measurements were performed over 20 cycles, indicating the excellent stability of SAMs. Figure 4.41: Surface-tethered TEMPO-TEMPO + electrochemistry in non-aqueous electrolyte CVs obtained in 100 mM TBA + PF 6 – in DCM at various scan rates. 128 D.5 HNMR Data of Amide Diradical TEMPO Figure 4.42: HNMR data of diradical TEMPO in the presence of Phenylhydarzine. Prior to acquir- ing NMR data, phenylhydrazine is utilized to reduce the TEMPO diradical. 129

Abstract (if available)

Abstract Interfacial processes play a pivotal role in various fields of sciences, including chemistry, biology and physics. Several processes take place at metal interfaces. For example, chemical bonds can form and break, and molecules can adsorb onto the surface. The applied potential on an electrode can profoundly influence these interfacial processes as it can alter the dynamics and reactivity of molecules in close proximity to the surfaces. This interplay between applied potential and interfacial processes is particularly relevant in electrochemistry, where precise control over interfacial phenomena is crucial for optimizing electrocatalytic reactions and designing efficient energy storage and conversion devices. In this work, we investigate the reversible formation and dissociation of Lewis bonds near an electrified surface, as well as the adsorption of phenols onto metal electrodes.

Linked assets

University of Southern California Dissertations and Theses

Conceptually similar

PDF

Water partitioning between the bulk and an electrode surface

PDF

Elucidating local electric fields and ion adsorption using benzonitrile: vibrational spectroscopic studies at interfaces and in bulk

PDF

Probing charge transfer and electric fields at the bulk and interface using vibrational spectroscopy

PDF

Molecular orientation and structure of hydrogen bonds at water interfaces

PDF

Interfacial polarization and photobasicity: spectroscopic studies of the electrode environment and photochemical effects

PDF

Vibrational sum frequency generation studies of electrode interfaces

PDF

Nonlinear spectroscopy of chemical phenomena at interfaces: carrier trapping and local electric fields

PDF

Computational spectroscopy in gas and condensed phases

PDF

Asymmetric response and the reorientation of interfacial water with respect to applied electric fields

PDF

Two-coordinate coinage metal complexes for solar fuels and organic LED chemistry

PDF

Excited state proton transfer in quinoline photobases

PDF

Controlled heteroatom functionalization of carbon-carbon bonds by aerobic oxidation

PDF

Ultrafast dynamics of excited state intra- and intermolecular proton transfer in nitrogen containing photobases

PDF

Vibrational spectroscopy and molecular orientation at interfaces: correlating the structure of a material's surface to its properties

PDF

Monitoring local electric fields, charge densities at electrode surfaces using in-situ graphene/surface enhanced Raman spectroscopy (GERS/SERS) based Stark-shifts

PDF

Molecular orientation from sum frequency generation spectroscopy: case study of water and methyl vibrations

PDF

Catalysis for solar fuels production: molecular and materials approaches

PDF

Modeling x-ray spectroscopy in condensed phase

PDF

Hot electron driven photocatalysis and plasmonic sensing using metallic gratings

PDF

Dissociation energy and dynamics of HCl and aromatic-water clusters

Asset Metadata

Creator Menachekanian, Sevan (author)

Core Title Potential-induced formation and dissociation of adducts at interfaces and adsorption of phenols onto metal electrodes

School College of Letters, Arts and Sciences

Degree Doctor of Philosophy

Degree Program Chemistry

Degree Conferral Date 2023-08

Publication Date 07/18/2023

Defense Date 07/18/2023

Publisher University of Southern California (original), University of Southern California. Libraries (digital)

Tag OAI-PMH Harvest,spectroscopy

Format theses (aat)

Language English

Contributor Electronically uploaded by the author (provenance)

Advisor Dawlaty, Jahan (committee chair)

Creator Email menachek@usc.edu,sevan_777@yahoo.com

Permanent Link (DOI) https://doi.org/10.25549/usctheses-oUC113281403

Unique identifier UC113281403

Identifier etd-Menachekan-12105.pdf (filename)

Legacy Identifier etd-Menachekan-12105

Document Type Dissertation

Format theses (aat)

Rights Menachekanian, Sevan

Internet Media Type application/pdf

Type texts

Source 20230719-usctheses-batch-1070 (batch), University of Southern California (contributing entity), University of Southern California Dissertations and Theses (collection)

Access Conditions The author retains rights to his/her dissertation, thesis or other graduate work according to U.S. copyright law. Electronic access is being provided by the USC Libraries in agreement with the author, as the original true and official version of the work, but does not grant the reader permission to use the work if the desired use is covered by copyright. It is the author, as rights holder, who must provide use permission if such use is covered by copyright.

Repository Name University of Southern California Digital Library

Repository Location USC Digital Library, University of Southern California, University Park Campus MC 2810, 3434 South Grand Avenue, 2nd Floor, Los Angeles, California 90089-2810, USA

Repository Email cisadmin@lib.usc.edu