Molecular dynamics simulation study of water structure and dynamics on the gold electrode surface with adsorbed 4-mercaptobenzonitrile.

Understanding water dynamics at charged interfaces is of great importance in various fields, such as catalysis, biomedical processes, and solar cell materials. In this study, we implemented molecular dynamics simulations of a system of pure water interfaced with Au electrodes, on one side of which 4-mercaptobenzonitrile (4-MBN) molecules are adsorbed. We calculated time correlation functions of various dynamic quantities, such as the hydrogen bond status of the N atom of the adsorbed 4-MBN molecules, the rotational motion of the water OH bond, hydrogen bonds between 4-MBN and water, and hydrogen bonds between water molecules in the interface region. Using the Luzar-Chandler model, we analyzed the hydrogen bond dynamics between a 4-MBN and a water molecule. The dynamic quantities we calculated can be divided into two categories: those related to the collective behavior of interfacial water molecules and the H-bond interaction between a water molecule and the CN group of 4-MBN. We found that these two categories of dynamic quantities exhibit opposite trends in response to applied potentials on the Au electrode. We anticipate that the present work will help improve our understanding of the interfacial dynamics of water in various electrolyte systems.

The hydrogen-bonding dynamics of water to a nitrile-functionalized electrode is modulated by voltage according to ultrafast 2D IR spectroscopy.

We report the hydrogen-bonding dynamics of water to a nitrile-functionalized and plasmonic electrode surface as a function of applied voltage. The surface-enhanced two-dimensional infrared spectra exhibit hydrogen-bonded and non-hydrogen-bonded nitrile features in similar proportions, plus cross peaks between the two. Isotopic dilution experiments show that the cross peaks arise predominantly from chemical exchange between hydrogen-bonded and non-hydrogen-bonded nitriles. The chemical exchange rate depends upon voltage, with the hydrogen bond of the water to the nitriles breaking 2 to 3 times slower (>63 vs. 25 ps) under a positive as compared to a negative potential. Spectral diffusion created by hydrogen-bond fluctuations occurs on a ~1 ps timescale and is moderately potential-dependent. Timescales from molecular dynamics simulations agree qualitatively with the experiment and show that a negative voltage causes a small net displacement of water away from the surface. These results show that the voltage applied to an electrode can alter the timescales of solvent motion at its interface, which has implications for electrochemically driven reactions.

Machine Learning Approach for Describing Water OH Stretch Vibrations.

A machine learning approach employing neural networks is developed to calculate the vibrational frequency shifts and transition dipole moments of the symmetric and antisymmetric OH stretch vibrations of a water molecule surrounded by water molecules. We employed the atom-centered symmetry functions (ACSFs), polynomial functions, and Gaussian-type orbital-based density vectors as descriptor functions and compared their performances in predicting vibrational frequency shifts using the trained neural networks. The ACSFs perform best in modeling the frequency shifts of the OH stretch vibration of water among the types of descriptor functions considered in this paper. However, the differences in performance among these three descriptors are not significant. We also tried a feature selection method called CUR matrix decomposition to assess the importance and leverage of the individual functions in the set of selected descriptor functions. We found that a significant number of those functions included in the set of descriptor functions give redundant information in describing the configuration of the water system. We here show that the predicted vibrational frequency shifts by trained neural networks successfully describe the solvent-solute interaction-induced fluctuations of OH stretch frequencies.

Vibrational Spectroscopic Map, Vibrational Spectroscopy, and Intermolecular Interaction.

Vibrational spectroscopy is an essential tool in chemical analyses, biological assays, and studies of functional materials. Over the past decade, various coherent nonlinear vibrational spectroscopic techniques have been developed and enabled researchers to study time-correlations of the fluctuating frequencies that are directly related to solute-solvent dynamics, dynamical changes in molecular conformations and local electrostatic environments, chemical and biochemical reactions, protein structural dynamics and functions, characteristic processes of functional materials, and so on. In order to gain incisive and quantitative information on the local electrostatic environment, molecular conformation, protein structure and interprotein contacts, ligand binding kinetics, and electric and optical properties of functional materials, a variety of vibrational probes have been developed and site-specifically incorporated into molecular, biological, and material systems for time-resolved vibrational spectroscopic investigation. However, still, an all-encompassing theory that describes the vibrational solvatochromism, electrochromism, and dynamic fluctuation of vibrational frequencies has not been completely established mainly due to the intrinsic complexity of intermolecular interactions in condensed phases. In particular, the amount of data obtained from the linear and nonlinear vibrational spectroscopic experiments has been rapidly increasing, but the lack of a quantitative method to interpret these measurements has been one major obstacle in broadening the applications of these methods. Among various theoretical models, one of the most successful approaches is a semiempirical model generally referred to as the vibrational spectroscopic map that is based on a rigorous theory of intermolecular interactions. Recently, genetic algorithm, neural network, and machine learning approaches have been applied to the development of vibrational solvatochromism theory. In this review, we provide comprehensive descriptions of the theoretical foundation and various examples showing its extraordinary successes in the interpretations of experimental observations. In addition, a brief introduction to a newly created repository Web site (http://frequencymap.org) for vibrational spectroscopic maps is presented. We anticipate that a combination of the vibrational frequency map approach and state-of-the-art multidimensional vibrational spectroscopy will be one of the most fruitful ways to study the structure and dynamics of chemical, biological, and functional molecular systems in the future.

Machine learning approach for describing vibrational solvatochromism.

Machine learning is becoming a more and more versatile tool describing condensed matter systems. Here, we employ the feed-forward and the convolutional neural networks to describe the frequency shifts of the amide I mode vibration of N-methylacetamide (NMA) in water. For a given dataset of configurations of an NMA molecule solvated by water, we obtained comparable or improved results for describing vibrational solvatochromic frequency shift with the neural network approach, compared to the previously developed differential evolution algorithm approach. We compared the performance of the atom centered symmetry functions (ACSFs) and simple polynomial functions as descriptors for the solvated system and found that the polynomial function performs better than the ACSFs employed in the description of the amide I vibrational solvatochromism.

Differential evolution algorithm approach for describing vibrational solvatochromism.

We model the solvation-induced vibrational frequency shifts of the amide I and amide II modes of N-methylacetamide in water and the nitrile stretch mode of acetonitrile in water by expressing the frequency shift as a polynomial function expanded by the inverse power of interatomic distances. The coefficients of the polynomial are optimized to minimize the deviation between the predicted frequency shifts and those calculated with quantum chemistry methods. Here, we show that a differential evolution algorithm combined with singular value decomposition is useful to find the optimum set of coefficients of polynomial terms. The differential evolution optimization shows that only a few terms in the polynomial are dominant in the contribution to the vibrational frequency shifts. We anticipate that the present work paves the way for further developing different genetic algorithms and machine learning schemes for their applications to vibrational spectroscopic studies.

Stability, Molecular Sieving, and Ion Diffusion Selectivity of a Lamellar Membrane from Two-Dimensional Molybdenum Disulfide.

Two-dimensional (2D) subnanometer channels allow unique mass transport promising for molecular sieving. New 2D channels of MoS2 nanosheets allow one to understand molecular transmission and separation, unlike the graphene oxide counterpart containing various defects and cationic metal contaminants. Membranes from layered MoS2 platelets show extraordinary stability in an aqueous environment and compatibility with polymer filters, both beneficial to efficient manufacturing. Sharing gas-tightness and unimpeded water vapor permeation with a graphene oxide membrane, our lamellar MoS2 membrane demonstrates a molecular sieving property for organic vapor for the first time. The MoS2 membrane also reveals diffusion selectivity of aqueous ions, attributable to the energy penalty in bulk-to-2D dimensional transition. These newly revealed properties of the lamellar membrane full of angstrom-sized 2D channels point to membrane technology applications for energy and environment.

Selective nitrogen capture by porous hybrid materials containing accessible transition metal ion sites.

Selective dinitrogen binding to transition metal ions mainly covers two strategic domains: biological nitrogen fixation catalysed by metalloenzyme nitrogenases, and adsorptive purification of natural gas and air. Many transition metal-dinitrogen complexes have been envisaged for biomimetic nitrogen fixation to produce ammonia. Inspired by this concept, here we report mesoporous metal-organic framework materials containing accessible Cr(III) sites, able to thermodynamically capture N2 over CH4 and O2. This fundamental study integrating advanced experimental and computational tools confirmed that the separation mechanism for both N2/CH4 and N2/O2 gas mixtures is driven by the presence of these unsaturated Cr(III) sites that allows a much stronger binding of N2 over the two other gases. Besides the potential breakthrough in adsorption-based technologies, this proof of concept could open new horizons to address several challenges in chemistry, including the design of heterogeneous biomimetic catalysts through nitrogen fixation.

The critical size of hydrogen-bonded alcohol clusters as effective Brønsted bases in solutions.

The alkyl oxonium ion, which is a protonated alcohol, has long been proposed as a key reaction intermediate in alcohol dehydration. Nonetheless, the dynamics and structure of this simple but important intermediate species have not been adequately examined due to the transient nature of the oxonium ion. Here, we devised a model system for the key step in the alcohol dehydration reaction, in which a photoacid transfers a proton to alcohols of different basicity in the acetonitrile solvent. Using time-resolved spectroscopy and computation, we have found that the linkage of at least two alcohol molecules via hydrogen bonding is critical for their enhanced reactivity and extraction of the proton from the acid. This finding addresses the cooperative role of the simplest organic protic compounds, namely alcohols, in nonaqueous acid-base reactions.

Alcohol Dimer is Requisite to Form an Alkyl Oxonium Ion in the Proton Transfer of a Strong (Photo)Acid to Alcohol.

Alcohols, the simplest amphiprotic organic compounds, can exhibit either acidic or basic behavior by donating or accepting a proton. In this study, proton dissociation of a model photoacid in solution is explored by using time-resolved spectroscopy, revealing quantitatively for the first time that alcohol acts as a Brønsted base because of H-bonded cluster formation to enhance the reactivity. The protonated alcohol cluster, the alkyl oxonium ion, can be regarded as a key reaction intermediate in the well-established alcohol dehydration reaction. This finding signifies, as in water, the cooperativity of protic solvent molecules to facilitate nonaqueous acid-base reactions.

A mixed quantum-classical molecular dynamics study of anti-tetrol and syn-tetrol dissolved in liquid chloroform: hydrogen-bond structure and its signature on the infrared absorption spectrum.

The intramolecular hydrogen-bond structure of stereoselectively synthesized syn-tetrol and anti-tetrol dissolved in deuterated chloroform is investigated via a mixed quantum-classical molecular dynamics simulation. An extensive conformational analysis is performed in order to determine the dominant conformations, the distributions among them, and their sensitivity to the method for assigning partial charges (RESP vs AM1-BCC). The signature of the conformational distribution and method of assigning partial charges on the infrared absorption spectra is analyzed in detail. The relationship between the spectra and the underlying hydrogen-bond structure is elucidated.

A mixed quantum-classical molecular dynamics study of anti-tetrol and syn-tetrol dissolved in liquid chloroform II: infrared emission spectra, vibrational excited-state lifetimes, and nonequilibrium hydrogen-bond dynamics.

The effect of vibrational excitation and relaxation of the hydroxyl stretch on the hydrogen-bond structure and dynamics of stereoselectively synthesized syn-tetrol and anti-tetrol dissolved in deuterated chloroform are investigated via a mixed quantum-classical molecular dynamics simulation. Emphasis is placed on the changes in hydrogen-bond structure upon photoexcitation and the nonequilibrium hydrogen-bond dynamics that follows the subsequent relaxation from the excited to the ground vibrational state. The propensity to form hydrogen bonds is shown to increase upon photoexcitation of the hydroxyl stretch, thereby leading to a sizable red-shift of the infrared emission spectra relative to the corresponding absorption spectra. The vibrational excited state lifetimes are calculated within the framework of Fermi's golden rule and the harmonic-Schofield quantum correction factor, and found to be sensitive reporters of the underlying hydrogen-bond structure. The energy released during the relaxation from the excited to the ground state is shown to break hydrogen bonds involving the relaxing hydroxyl. The spectral signature of this nonequilibrium relaxation process is analyzed in detail.

Solvation dynamics of formylperylene dissolved in methanol-acetonitrile liquid mixtures: a molecular dynamics study.

The solvation dynamics of formylperylene in methanol/acetonitrile liquid mixtures have been experimentally observed to slow down with increasing concentration of methanol. We present results from equilibrium and nonequilibrium molecular dynamics simulations that relate the slowdown to the formation of a hydrogen-bonded methanol oligomer, which is hydrogen-bonded to the carbonyl group of formylperylene.

A mixed quantum-classical molecular dynamics study of the hydroxyl stretch in methanol/carbon tetrachloride mixtures III: nonequilibrium hydrogen-bond dynamics and infrared pump-probe spectra.

We present a mixed quantum-classical molecular dynamics study of the nonequilibrium hydrogen-bond dynamics following vibrational energy relaxation of the hydroxyl stretch in a 10 mol % methanol/carbon tetrachloride mixture and pure methanol. The ground and first-excited energy levels and wave functions are identified with the eigenvalues and eigenfunctions of the hydroxyl's adiabatic Hamiltonian and as such depend parametrically on the configuration of the remaining, classically treated, degrees of freedom. The dynamics of the classical degrees of freedom are in turn governed by forces obtained by taking the expectation value of the force with respect to the ground or excited vibrational wave functions. Polarizable force fields and nonlinear mapping relations between the hydroxyl transition frequencies and dipole moments and the electric field along the hydroxyl bond are used, which were previously shown to quantitatively reproduce the experimental infrared steady-state absorption spectra and excited state lifetime [Kwac, K.; Geva, E. J. Phys. Chem. B 2011, 115, 9184; 2012, 116, 2856]. The relaxation from the first-excited state to the ground state is treated as a nonadiabatic transition. Within the mixed quantum-classical treatment, relaxation from the excited state to the ground state is accompanied by a momentum-jump in the classical degrees of freedom, which is in turn dictated by the nonadiabatic coupling vector. We find that the momentum jump leads to breaking of hydrogen bonds involving the relaxing hydroxyl, thereby blue-shifting the transition frequency by more than the Stokes shift between the steady-state emission and absorption spectra. The subsequent nonequilibrium relaxation toward equilibrium on the ground state potential energy surface is thereby accompanied by red shifting of the transition frequency. The signature of this nonequilibrium relaxation process on the pump-probe spectrum is analyzed in detail. The calculated pump-probe spectrum is found to be in reasonable agreement with experiment, thereby providing further credibility to the underlying force fields and mixed quantum-classical methodology.

Mixed quantum-classical molecular dynamics study of the hydroxyl stretch in methanol/carbon-tetrachloride mixtures II: excited state hydrogen bonding structure and dynamics, infrared emission spectrum, and excited state lifetime.

We present a mixed quantum-classical molecular dynamics study of the hydrogen-bonding structure and dynamics of a vibrationally excited hydroxyl stretch in methanol/carbon-tetrachloride mixtures. The adiabatic Hamiltonian of the quantum-mechanical hydroxyl is diagonalized on-the-fly to obtain the ground and first-excited adiabatic energy levels and wave functions which depend parametrically on the instantaneous configuration of the classical degrees of freedom. The dynamics of the classical degrees of freedom are determined by Hellmann-Feynman forces obtained by taking the expectation value of the force with respect to the ground or excited vibrational wave functions. Polarizable force fields are used which were previously shown to reproduce the experimental infrared absorption spectrum rather well, for different isotopomers and over a wide composition range [Kwac, K.; Geva, E. J. Phys. Chem. B 2011, 115, 9184]. We show that the agreement of the absorption spectra with experiment can be further improved by accounting for the dependence of the dipole moment derivatives on the configuration of the classical degrees of freedom. We find that the propensity of a methanol molecule to form hydrogen bonds increases upon photoexcitation of its hydroxyl stretch, thereby leading to a sizable red-shift of the corresponding emission spectrum relative to the absorption spectrum. Treating the relaxation from the first excited to the ground state as a nonadiabatic process, and calculating its rate within the framework of Fermi's golden rule and the harmonic-Schofield quantum correction factor, we were able to predict a lifetime which is of the same order of magnitude as the experimental value. The experimental dependence of the lifetime on the transition frequency is also reproduced. Nonlinear mapping relations between the hydroxyl transition frequency and bond length in the excited state and the electric field along the hydroxyl bond axis are established. These mapping relations make it possible to reduce the computational cost of the mixed quantum-classical treatment to that of a fully classical treatment.

A mixed quantum-classical molecular dynamics study of the hydroxyl stretch in methanol/carbon tetrachloride mixtures: equilibrium hydrogen-bond structure and dynamics at the ground state and the infrared absorption spectrum.

We present a mixed quantum-classical molecular dynamics study of the structure and dynamics of the hydroxyl stretch in methanol/carbon tetrachloride mixtures. One of the methanol molecules is tagged, and its hydroxyl stretch is treated quantum-mechanically, while the remaining degrees of freedom are treated classically. The adiabatic Hamiltonian of the quantum-mechanical hydroxyl is diagonalized on-the-fly to obtain the corresponding adiabatic energy levels and wave functions which depend parametrically on the instantaneous configuration of the classical degrees of freedom. The dynamics of the classical degrees of freedom are in turn affected by the quantum-mechanical state of the tagged hydroxyl stretch via the corresponding Hellmann-Feynman forces. The ability of five different force-field combinations to reproduce the experimental absorption infrared spectrum of the hydroxyl stretch is examined for different isotopomers and on a wide range of compositions. It is found that, in addition to accounting for the anharmonic nature of the hydroxyl stretch, one also has to employ polarizable force fields and account for the damping of the polarizability at short distances. The equilibrium ground-state hydrogen-bonding structure and dynamics is analyzed, and its signature on the absorption infrared spectrum of the hydroxyl stretch is investigated in detail. Five different hydroxyl stretch subpopulations are identified and spectrally assigned: monomers (α), hydrogen-bond acceptors (ß), hydrogen-bond donors (γ), simultaneous hydrogen-bond donors and acceptors (δ), and simultaneous hydrogen-bond donors and double-acceptors (ε). The fundamental transition frequencies of the α and ß subpopulations are found to be narrowly distributed and to overlap, thereby giving rise to a single narrow band whose intensity is significantly diminished by rotational relaxation. The fundamental transition frequency distributions of the γ, δ, and ε subpopulations are found to be broader and to partially overlap, thereby giving rise to a single broad band which is red-shifted relative to the αß band. The γδε band is also found to be inhomogeneously broadened and unaffected by rotational relaxation. The exchange rates between the different subpopulations and corresponding branching ratios are reported and explained. Finally, nonlinear mapping relations between the hydroxyl transition frequency and bond length and the electric field along the hydroxyl bond axis are established, which can be used to reduce the computational cost of the mixed quantum-classical treatment to that of a purely classical molecular dynamics simulation.

Classical and quantum mechanical/molecular mechanical molecular dynamics simulations of alanine dipeptide in water: comparisons with IR and vibrational circular dichroism spectra.

We have implemented the combined quantum mechanical (QM)/molecular mechanical (MM) molecular dynamics (MD) simulations of alanine dipeptide in water along with the polarizable and nonpolarizable classical MD simulations with different models of water. For the QM/MM MD simulation, the alanine dipeptide is treated with the AM1 or PM3 approximations and the fluctuating solute dipole moment is calculated by the Mulliken population analysis. For the classical MD simulations, the solute is treated with the polarizable or nonpolarizable AMBER and polarizable CHARMM force fields and water is treated with the TIP3P, TIP4P, or TIP5P model. It is found that the relative populations of right-handed alpha-helix and extended beta and P(II) conformations in the simulation trajectory strongly depend on the simulation method. For the QM/MM MD simulations, the PM3/MM shows that the P(II) conformation is dominant, whereas the AM1/MM predicts that the dominant conformation is alpha(R). Polarizable CHARMM force field gives almost exclusively P(II) conformation and other force fields predict that both alpha-helical and extended (beta and P(II)) conformations are populated with varying extents. Solvation environment around the dipeptide is investigated by examining the radial distribution functions and numbers and lifetimes of hydrogen bonds. Comparing the simulated IR and vibrational circular dichroism spectra with experimental results, we concluded that the dipeptide adopts the P(II) conformation and PM3/MM, AMBER03 with TIP4P water, and AMBER polarizable force fields are acceptable for structure determination of the dipeptide considered in this paper.

Phenol-benzene complexation dynamics: quantum chemistry calculation, molecular dynamics simulations, and two dimensional IR spectroscopy.

Molecular dynamics (MD) simulations and quantum mechanical electronic structure calculations are used to investigate the nature and dynamics of the phenol-benzene complex in the mixed solvent, benzene/CCl4. Under thermal equilibrium conditions, the complexes are continuously dissociating and forming. The MD simulations are used to calculate the experimental observables related to the phenol hydroxyl stretching mode, i.e., the two dimensional infrared vibrational echo spectrum as a function of time, which directly displays the formation and dissociation of the complex through the growth of off-diagonal peaks, and the linear absorption spectrum, which displays two hydroxyl stretch peaks, one for the complex and one for the free phenol. The results of the simulations are compared to previously reported experimental data and are found to be in quite reasonable agreement. The electronic structure calculations show that the complex is T shaped. The classical potential used for the phenol-benzene interaction in the MD simulations is in good accord with the highest level of the electronic structure calculations. A variety of other features is extracted from the simulations including the relationship between the structure and the projection of the electric field on the hydroxyl group. The fluctuating electric field is used to determine the hydroxyl stretch frequency-frequency correlation function (FFCF). The simulations are also used to examine the number distribution of benzene and CCl4 molecules in the first solvent shell around the phenol. It is found that the distribution is not that of the solvent mole fraction of benzene. There are substantial probabilities of finding a phenol in either a pure benzene environment or a pure CCl4 environment. A conjecture is made that relates the FFCF to the local number of benzene molecules in phenol's first solvent shell.

Non-Gaussian statistics of amide I mode frequency fluctuation of N-methylacetamide in methanol solution: linear and nonlinear vibrational spectra.

By carrying out molecular dynamics simulations of an N-methylacetamide (NMA) in methanol solution, the amide I mode frequency fluctuation and hydrogen bonding dynamics were theoretically investigated. Combining an extrapolation formula developed from systematic ab initio calculation studies of NMA-(CH3OH)n clusters with a classical molecular dynamics simulation method, we were able to quantitatively describe the solvatochromic vibrational frequency shift induced by the hydrogen-bonding interaction between NMA and solvent methanol. It was found that the fluctuating amide I mode frequency distribution is notably non-Gaussian and it can be decomposed into two Gaussian peaks that are associated with two distinctively different solvation structures. The ensemble-average-calculated linear response function associated with the IR absorption is found to be oscillating, which is in turn related to the doublet amide I band shape. Numerically calculated infrared absorption spectra are directly compared with experiment and the agreement was found to be excellent. By using the Onsager's regression hypothesis, the rate constants of the interconversion process between the two solvation structures were obtained. Then, the nonlinear response functions associated with two-dimensional infrared pump-probe spectroscopy were simulated. The physics behind the two-dimensional line shape and origin of the cross peaks in the time-resolved pump-probe spectra is explained and the result is compared with 2D spectra experimentally measured recently by Woutersen et al.