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Experimental and theoretical studies have highlighted protonated water clusters (PWCs) as important models of the excess proton in aqueous systems. A significant focus has been characterizing the spectral signatures associated with different excess proton solvation motifs. Accurate vibrational frequency calculations are crucial for connecting the measured spectra to the structure of PWCs. In this paper, we extend and characterize a coupled local mode (CLM) approach for calculating the infrared spectra of PWCs using the H + ( H 2 O) 4 cluster as a benchmark system. The CLM method is relatively low cost and incorporates the anharmonicity and coupling of OH vibrations. Here, we demonstrate the accuracy of the technique compared to experiments. We also illustrate the dependence of calculated spectral features on the underlying electronic structure theory and basis sets used in the local mode frequency and coupling calculations. [ABSTRACT FROM AUTHOR]

Solvation dynamics in ionic liquids show features that are often associated with supercooled liquids, including "stretched" nonexponential relaxation. To better understand the mechanism behind the stretching, the nonlinear mode-correlation methods proposed in Paper I [S. R. Hodge and M. A. Berg, J. Chem. Phys. 155, 024122 (2021)] are applied to a simulation of a prototypical ionic liquid. A full Green's function is recovered. In addition, specific tests for non-Gaussian dynamics are made. No deviations from Gaussian dynamics are found. This finding is incompatible with rate heterogeneity as a cause of the nonexponential relaxation and appears to be in conflict with an earlier multidimensional analysis of the same data. Although this conflict is not resolved here, this work does demonstrate the practicality of mode-correlation analysis in the face of finite datasets and calculations. [ABSTRACT FROM AUTHOR]

Fewest-switches surface hopping (FSSH) is combined with transition path sampling (TPS) to produce a new method called nonadiabatic path sampling (NAPS). The NAPS method is validated on a model electron transfer system coupled to a Langevin bath. Numerically exact rate constants are computed using the reactive flux (RF) method over a broad range of solvent frictions that span from the energy diffusion (low friction) regime to the spatial diffusion (high friction) regime. The NAPS method is shown to quantitatively reproduce the RF benchmark rate constants over the full range of solvent friction. Integrating FSSH within the TPS framework expands the applicability of both approaches and creates a new method that will be helpful in determining detailed mechanisms for nonadiabatic reactions in the condensed-phase. [ABSTRACT FROM AUTHOR]

Molecular quantum-dot cellular automata is a computing paradigm in which digital information is encoded by the charge configuration of a mixed-valence molecule. General-purpose computing can be achieved by arranging these compounds on a substrate and exploiting intermolecular Coulombic coupling. The operation of such a device relies on nonequilibrium electron transfer (ET), whereby the time-varying electric field of one molecule induces an ET event in a neighboring molecule. The magnitude of the electric fields can be quite large because of close spatial proximity, and the induced ET rate is a measure of the nonequilibrium response of the molecule. We calculate the electric-field-driven ET rate for a model mixed-valence compound. The mixed-valence molecule is regarded as a two-state electronic system coupled to a molecular vibrational mode, which is, in turn, coupled to a thermal environment. Both the electronic and vibrational degrees-of-freedom are treated quantum mechanically, and the dissipative vibrational-bath interaction is modeled with the Lindblad equation. This approach captures both tunneling and nonadiabatic dynamics. Relationships between microscopic molecular properties and the driven ET rate are explored for two time-dependent applied fields: an abruptly switched field and a linearly ramped field. In both cases, the driven ET rate is only weakly temperature dependent. When the model is applied using parameters appropriate to a specific mixed-valence molecule, diferrocenylacetylene, terahertz-range ET transfer rates are predicted. [ABSTRACT FROM AUTHOR]

Low-temperature scanning tunneling microscopy is used to observe self-assembled structures of ferrocenedicarboxylic acid (Fc(COOH)2) on the Au(111) surface. The surface is prepared by pulse-deposition of Fc(COOH)2 dissolved in methanol, and the solvent is evaporated before imaging. While the rows of hydrogen-bonded dimers that are common for carboxylic acid species are observed, the majority of adsorbed Fc(COOH)2 is instead found in six-molecule clusters with a well-defined and chiral geometry. The coverage and distribution of these clusters are consistent with a random sequential adsorption model, showing that solution-phase species are determinative of adsorbate distribution for this system under these reaction conditions. [ABSTRACT FROM AUTHOR]

The ability of fewest switches surface hopping (FSSH) approach, where the classical degrees of freedom are coupled to an implicit Langevin bath, to establish and maintain an appropriate thermal equilibrium was evaluated in the context of a three site model for electron transfer. The electron transfer model consisted of three coupled diabatic states that each depends harmonically on the collective bath coordinate. This results in three states with increasing energy in the adiabatic representation. The adiabatic populations and distributions of the collective solvent coordinate were monitored during the course of 250 ns FSSH-Langevin (FSSH-L) simulations performed at a broad range of temperatures and for three different nonadiabatic coupling strengths. The agreement between the FSSH-L simulations and numerically exact results for the adiabatic population ratios and solvent coordinate distributions was generally favorable. The FSSH-L method produces a correct Boltzmann distribution of the solvent coordinate on each of the adiabats, but the integrated populations are slightly incorrect because FSSH does not rigorously obey detailed balance. The overall agreement is better at high temperatures and for high nonadiabatic coupling, which agrees with a previously reported analytical and simulation analysis [J. R. Schmidt, P. V. Parandekar, and J. C. Tully, J. Chem. Phys. 129, 044104 (2008)] on a two-level system coupled to a classical bath. [ABSTRACT FROM AUTHOR]

The utility of α-carbon deuterium-labeled bonds (Cα–D) as infrared reporters of local peptide conformation was investigated for two model dipeptide compounds: Cα–D labeled alanine dipeptide (Adp-d1) and Cα–D2 labeled glycine dipeptide (Gdp-d2). These model compounds adopt structures that are analogous to the motifs found in larger peptides and proteins. For both Adp-d1 and Gdp-d2, we systematically mapped the entire conformational landscape in the gas phase by optimizing the geometry of the molecule with the values of φ and ψ, the two dihedral angles that are typically used to characterize the backbone structure of peptides and proteins, held fixed on a uniform grid with 7.5° spacing. Since the conformations were not generally stationary states in the gas phase, we then calculated anharmonic Cα–D and Cα–D2 stretch transition frequencies for each structure. For Adp-d1 the Cα–D stretch frequency exhibited a maximum variability of 39.4 cm-1 between the six stable structures identified in the gas phase. The Cα–D2 frequencies of Gdp-d2 show an even more substantial difference between its three stable conformations: there is a 40.7 cm-1 maximum difference in the symmetric Cα–D2 stretch frequencies and an 81.3 cm-1 maximum difference in the asymmetric Cα–D2 stretch frequencies. Moreover, the splitting between the symmetric and asymmetric Cα–D2 stretch frequencies of Gdp-d2 is remarkably sensitive to its conformation. [ABSTRACT FROM AUTHOR]

Infrared spectroscopy is a versatile technique for probing the structure and dynamics of condensed-phase systems. Simulating infrared absorption spectra with molecular dynamics (MD) offers a powerful means to establish a molecular-level interpretation of experimental results, as well as a basis for the parametrization of more accurate simulation force-fields. Two distinct methods for the calculation of infrared absorption line shapes of high-frequency (hω/kBT>1) vibrational probes from MD simulations are examined: The classical dipole approximation (CDA) and the fluctuating frequency approximation (FFA). Although these two formalisms result in expressions for the infrared absorption line shape that appear very different, both approximations are shown to yield identical results for the infrared line shape of a harmonic system in the condensed-phase. The equivalence of the FFA and CDA is also demonstrated in the case where the transition dipole of the oscillator fluctuates in response to the environment (i.e., where the Condon approximation has been relaxed). Finally we examine the effects of solute anharmonicity and demonstrate that the CDA and FFA are not equivalent in general, and the magnitude of the deviations increases with anharmonicity. We conclude that the calculation of infrared absorption line shapes via the CDA is a promising alternative to the FFA approach in cases where it may be difficult or undesirable to employ the latter, particularly when the effects of anharmonicity are small. [ABSTRACT FROM AUTHOR]

Ultrafast vibrational spectroscopy experiments, together with molecular-level theoretical interpretation, can provide important information about the structure and dynamics of complex condensed phase systems, including liquids. The theoretical challenge is to calculate the instantaneous vibrational frequencies of a molecule in contact with a molecular environment, accurately and quickly, and to this end a number of different methods have been developed. In this paper we critically analyze these different methods by comparing their results to accurate benchmark calculations on azide/water clusters. We also propose an optimized quantum mechanics/molecular mechanics method, which for this problem is superior to the other methods. [ABSTRACT FROM AUTHOR]

In the context of vibrational spectroscopy in liquids, non-Condon effects refer to the dependence of the vibrational transition dipole moment of a particular molecule on the rotational and translational coordinates of all the molecules in the liquid. For strongly hydrogen-bonded systems, such as liquid water, non-Condon effects are large. That is, the bond dipole derivative of an OH stretch depends strongly on its hydrogen-bonding environment. Previous calculations of nonlinear vibrational spectroscopy in liquids have not included these non-Condon effects. We find that for water, inclusion of these effects is important for an accurate calculation of, for example, homodyned and heterodyned three-pulse echoes. Such echo experiments have been “inverted” to obtain the OH stretch frequency time-correlation function, but by necessity the Condon and other approximations are made in this inversion procedure. Our conclusion is that for water, primarily because of strong non-Condon effects, this inversion may not lead to the correct frequency time-correlation function. Nevertheless, one can still make comparison between theory and experiment by calculating the experimental echo observables themselves. [ABSTRACT FROM AUTHOR]

Vibrational echo correlation spectroscopy experiments on the OD stretch of dilute HOD in H2O are used to probe the structural dynamics of water. A method is demonstrated for combining correlation spectra taken with different infrared pulse bandwidths (pulse durations), making it possible to use data collected from many experiments in which the laser pulse properties are not identical. Accurate measurements of the OD stretch anharmonicity (162 cm-1) are presented and used in the data analysis. In addition, the recent accurate determination of the OD vibrational lifetime (1.45 ps) and the time scale for the production of vibrational relaxation induced broken hydrogen bond “photoproducts” (∼2 ps) aid in the data analysis. The data are analyzed using time dependent diagrammatic perturbation theory to obtain the frequency time correlation function (FTCF). The results are an improved FTCF compared to that obtained previously with vibrational echo correlation spectroscopy. The experimental data and the experimentally determined FTCF are compared to calculations that employ a polarizable water model (SPC-FQ) to calculate the FTCF. The SPC-FQ derived FTCF is much closer to the experimental results than previously tested nonpolarizable water models which are also presented for comparison. © 2004 American Institute of Physics. [ABSTRACT FROM AUTHOR]

Kwac and Cho [J. Chem. Phys. 119, 2247 (2003)] have recently developed a combined electronic structure/molecular dynamics approach to vibrational spectroscopy in liquids. The method involves fitting ab initio vibrational frequencies for a solute in a cluster of solvent molecules to a linear combination of the electrostatic potentials on the solute atoms due to the charges on the solvent molecules. These authors applied their method to the N-methylacetamide-D/D2O system. We (S. A. Corcelli, C. P. Lawrence, and J. L. Skinner, [J. Chem. Phys. 120, 8107 (2004)]) have recently explored a closely related method, where instead of the electrostatic potential, the solute vibrational frequencies are fit to the components of the electric fields on the solute atoms due to the solvent molecules. We applied our method to the HOD/D2O and HOD/H2O systems. In order to make a direct comparison of these two approaches, in this paper we apply their method to the water system, and our method to the N-methylacetamide system. For the water system we find that the electric field method is superior to the potential approach, as judged by comparison with experiments for the absorption line shape. For the N-methylacetamide system the two methods are comparable. © 2004 American Institute of Physics. [ABSTRACT FROM AUTHOR]

We apply the combined electronic structure/molecular dynamics approach of Corcelli, Lawrence, and Skinner [J. Chem. Phys. 120, 8107 (2004)] to the fluctuating charge (SPC-FQ) model of liquid water developed by Rick, Stuart, and Berne [J. Chem. Phys. 101, 6141 (1994)]. For HOD in H2O the time scale for the long-time decay of the OD stretch frequency time-correlation function, which corresponds to the time scale for hydrogen-bond rearrangement in the liquid, is about 1.5 ps. This result is significantly longer than the 0.9 ps decay previously calculated for the nonpolarizable SPC/E water model. Our results for the SPC-FQ model are in better agreement with recent vibrational echo experiments.© 2004 American Institute of Physics. [ABSTRACT FROM AUTHOR]

We present a new approach that combines electronic structure methods and molecular dynamics simulations to investigate the infrared spectroscopy of condensed phase systems. This approach is applied to the OH stretch band of dilute HOD in liquid D2O and the OD stretch band of dilute HOD in liquid H2O for two commonly employed models of water, TIP4P and SPC/E. Ab initio OH and OD anharmonic transition frequencies are calculated for 100 HOD·(D2O)n and HOD·(H2O)n (n=4–9) clusters randomly selected from liquid water simulations. A linear empirical relationship between the ab initio frequencies and the component of the electric field from the solvent along the bond of interest is developed. This relationship is used in a molecular dynamics simulation to compute frequency fluctuation time-correlation functions and infrared absorption line shapes. The normalized frequency fluctuation time-correlation functions are in good agreement with the results of previous theoretical approaches. Their long-time decay times are 0.5 ps for the TIP4P model and 0.9 ps for the SPC/E model, both of which appear to be somewhat too fast compared to recent experiments. The calculated line shapes are in good agreement with experiment, and improve upon the results of previous theoretical approaches. The methods presented are simple, and transferable to more complicated systems. © 2004 American Institute of Physics. [ABSTRACT FROM AUTHOR]

We present an efficient method for computing thermal reaction rate constants that can be applied to systems in which transitions from reactant to product are infrequent. The method can be applied to high-dimensional, disordered systems which exhibit too many transition states to be identified, and for which useful reaction coordinates cannot be easily defined. The focus of our method is the time correlation function C(t), the normalized partition function for trajectories that begin in the reactant region and end in the product region after a time t; the time derivative of C(t) is the reaction rate constant, k(t). We use an umbrella potential to select initial positions from improbable regions of the reactant configuration space. We then compute C(t) directly by choosing random thermal momenta and asking if the resulting dynamical trajectory reaches the product region in time t. Since dynamical trajectories are run on the true potential energy surface, without the umbrella, re-crossing effects are included correctly. The initial condition bias introduced by the umbrella is removed by a weighting factor. We test the method on a simple two dimensional model potential and on a model for the isomerization of a diatomic in a Weeks-Chandler-Andersen fluid, and show that it gives accurate and precise rates with substantial reduction in computer time. [ABSTRACT FROM AUTHOR]

Vibrational states as high as n = 15 have been experimentally observed in CO molecules adsorbed in a monolayer on the NaCl(100) surface after pumping the n = 0 → 1 vibrational transition with a short (5 µs) infrared laser pulse. These high states become populated from successive single vibrational quantum exchanges between CO molecules on the surface, CO(m)+CO(n) → CO(m - 1 ) + CO(n + 1 ), mediated by dipole-dipole interactions and driven by the anharmonicity of the CO bond vibration. The rates for all of the possible channels of vibrational energy flow in the CO/NaCl(100) system, exchange, relaxation, and fluorescence, were calculated using perturbation theory for a model in which the CO bond vibration is treated as a Morse oscillator and is coupled to a bath of harmonic oscillators with a Debye density of states representing the underlying NaC1 substrate. These rates form a Master equation that governs the overall vibrational population dynamics of CO molecules in the monolayer, and was solved using kinetic Monte Carlo (KMC) techniques. Time-dependent vibrational population distributions, P[sub n] (t), representing the probability of finding a CO molecule in the monolayer in vibrational state n at time t, were obtained from the KMC simulations. The results are in good accord with experiment. The maximum achievable excitation is found to be limited by a crossover in the vibrational relaxation and excitation transfer rates with increasing quantum number. [ABSTRACT FROM AUTHOR]