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At least 1,243 records · Page 69
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DOE OSTI2015

A hybrid framework of first principles molecular orbital calculations and a three-dimensional integral equation theory for molecular liquids: Multi-center molecular Ornstein–Zernike self-consistent field approach

In this study, we reported the development of a new quantum mechanics/molecular mechanics (QM/MM)-type framework to describe chemical processes in solution by combining standard molecular-orbital calculations with a three-dimensional formalism of integral equation theory for molecular liquids (multi-center molecular Ornstein–Zernike (MC-MOZ) method). The theoretical procedure is very similar to the 3D-reference interaction site model self-consistent field (RISM-SCF) approach. Since the MC-MOZ method is highly parallelized for computation, the present approach has the potential to be one of the most efficient procedures to treat chemical processes in solution. Benchmark tests to check the validity of this approach were performed for two solute (solute water and formaldehyde) systems and a simple S{sub N}2 reaction (Cl{sup −} + CH{sub 3}Cl → ClCH{sub 3} + Cl{sup −}) in aqueous solution. The results for solute molecular properties and solvation structures obtained by the present approach were in reasonable agreement with those obtained by other hybrid frameworks and experiments. In particular, the results of the proposed approach are in excellent agreements with those of 3D-RISM-SCF.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2015

A modified two-state empirical valence bond model for proton transport in aqueous solutions

A detailed analysis of the proton solvation structure and transport properties in aqueous solutions is performed using classical molecular dynamics simulations. A refined two-state empirical valence bond (aTS-EVB) method, which is based on the EVB model of Walbran and Kornyshev and the anharmonic water force field, is developed in order to describe efficiently excess proton transport via the Grotthuss mechanism. The new aTS-EVB model clearly satisfies the requirement for simpler and faster calculation, because of the simplicity of the two-state EVB algorithm, while providing a better description of diffusive dynamics of the excess proton and water in comparison with the previous two-state EVB models, which significantly improves agreement with the available experimental data. The results of activation energies for the excess proton and water calculated between 300 and 340 K (the temperature range used in this study) are also found to be in good agreement with the corresponding experimental data.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2015

Solute location in a nanoconfined liquid depends on charge distribution

Nanostructured materials that can confine liquids have attracted increasing attention for their diverse properties and potential applications. Yet, significant gaps remain in our fundamental understanding of such nanoconfined liquids. Using replica exchange molecular dynamics simulations of a nanoscale, hydroxyl-terminated silica pore system, we determine how the locations explored by a coumarin 153 (C153) solute in ethanol depend on its charge distribution, which can be changed through a charge transfer electronic excitation. The solute position change is driven by the internal energy, which favors C153 at the pore surface compared to the pore interior, but less so for the more polar, excited-state molecule. This is attributed to more favorable non-specific solvation of the large dipole moment excited-state C153 by ethanol at the expense of hydrogen-bonding with the pore. It is shown that a change in molecule location resulting from shifts in the charge distribution is a general result, though how the solute position changes will depend upon the specific system. This has important implications for interpreting measurements and designing applications of mesoporous materials.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2015

Absolute shielding scales for Al, Ga, and In and revised nuclear magnetic dipole moments of {sup 27}Al, {sup 69}Ga, {sup 71}Ga, {sup 113}In, and {sup 115}In nuclei

We present coupled cluster calculations of NMR shielding constants of aluminum, gallium, and indium in water-ion clusters. In addition, relativistic and dynamical corrections and the influence of the second solvation shell are evaluated. The final NMR shielding constants define new absolute shielding scales, 600.0 ± 4.1 ppm, 2044.4 ± 31.4 ppm, and 4507.7 ± 63.7 ppm for aluminum, gallium, and indium, respectively. The nuclear magnetic dipole moments for {sup 27}Al, {sup 69}Ga, {sup 71}Ga, {sup 113}In, and {sup 115}In isotopes are corrected by combining the computed shielding constants with experimental NMR frequencies. The absolute magnitude of the correction increases along the series and for indium isotopes it reaches approximately −8.0 × 10{sup −3} of the nuclear magneton.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2015

Elucidation of reactive wavepackets by two-dimensional resonance Raman spectroscopy

Traditional second-order kinetic theories fail to describe sub-picosecond photochemical reactions when solvation and vibrational dephasing undermine the assumption of equilibrium initial conditions. Four-wave mixing spectroscopies may reveal insights into such non-equilibrium processes but are limited by the single “population time” available in these types of experiments. Here, we use two-dimensional resonance Raman (2DRR) spectroscopy to expose correlations between coherent nuclear motions of the reactant and product in the photodissociation reaction of triiodide. It is shown that the transition of a nuclear wavepacket from the reactant (triiodide) to product (diiodide) states gives rise to a unique pattern of 2DRR resonances. Peaks associated with this coherent reaction mechanism are readily assigned, because they are isolated in particular quadrants of the 2DRR spectrum. A theoretical model in which the chemical reaction is treated as a vibronic coherence transfer transition from triiodide to diiodide reproduces the patterns of 2DRR resonances detected in experiments. These signal components reveal correlation between the nonequilibrium geometry of triiodide and the vibrational coherence frequency of diiodide. The 2DRR signatures of coherent reaction mechanisms established in this work may generalize to studies of ultrafast energy and charge transfer processes.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2015

Role of excited state solvent fluctuations on time-dependent fluorescence Stokes shift

We explore the connection between the solvation dynamics of a chromophore upon photon excitation and equilibrium fluctuations of the solvent. Using molecular dynamics simulations, fluorescence Stokes shift for the tryptophan in Staphylococcus nuclease was examined using both nonequilibrium calculations and linear response theory. When the perturbed and unperturbed surfaces exhibit different solvent equilibrium fluctuations, the linear response approach on the former surface shows agreement with the nonequilibrium process. This agreement is excellent when the perturbed surface exhibits Gaussian statistics and qualitative in the case of an isomerization induced non-Gaussian statistics. However, the linear response theory on the unperturbed surface breaks down even in the presence of Gaussian fluctuations. Experiments also provide evidence of the connection between the excited state solvent fluctuations and the total fluorescence shift. These observations indicate that the equilibrium statistics on the excited state surface characterize the relaxation dynamics of the fluorescence Stokes shift. Our studies specifically analyze the Gaussian fluctuations of the solvent in the complex protein environment and further confirm the role of solvent fluctuations on the excited state surface. The results are consistent with previous investigations, found in the literature, of solutes dissolved in liquids.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2015

Coronene molecules in helium clusters: Quantum and classical studies of energies and configurations

Coronene-doped helium clusters have been studied by means of classical and quantum mechanical (QM) methods using a recently developed He–C{sub 24}H{sub 12} global potential based on the use of optimized atom-bond improved Lennard-Jones functions. Equilibrium energies and geometries at global and local minima for systems with up to 69 He atoms were calculated by means of an evolutive algorithm and a basin-hopping approach and compared with results from path integral Monte Carlo (PIMC) calculations at 2 K. A detailed analysis performed for the smallest sizes shows that the precise localization of the He atoms forming the first solvation layer over the molecular substrate is affected by differences between relative potential minima. The comparison of the PIMC results with the predictions from the classical approaches and with diffusion Monte Carlo results allows to examine the importance of both the QM and thermal effects.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2015

A molecularly based theory for electron transfer reorganization energy

Using field-theoretic techniques, we develop a molecularly based dipolar self-consistent-field theory (DSCFT) for charge solvation in pure solvents under equilibrium and nonequilibrium conditions and apply it to the reorganization energy of electron transfer reactions. The DSCFT uses a set of molecular parameters, such as the solvent molecule’s permanent dipole moment and polarizability, thus avoiding approximations that are inherent in treating the solvent as a linear dielectric medium. A simple, analytical expression for the free energy is obtained in terms of the equilibrium and nonequilibrium electrostatic potential profiles and electric susceptibilities, which are obtained by solving a set of self-consistent equations. With no adjustable parameters, the DSCFT predicts activation energies and reorganization energies in good agreement with previous experiments and calculations for the electron transfer between metallic ions. Because the DSCFT is able to describe the properties of the solvent in the immediate vicinity of the charges, it is unnecessary to distinguish between the inner-sphere and outer-sphere solvent molecules in the calculation of the reorganization energy as in previous work. Furthermore, examining the nonequilibrium free energy surfaces of electron transfer, we find that the nonequilibrium free energy is well approximated by a double parabola for self-exchange reactions, but the curvature of the nonequilibrium free energy surface depends on the charges of the electron-transferring species, contrary to the prediction by the linear dielectric theory.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2015

Redox levels in aqueous solution: Effect of van der Waals interactions and hybrid functionals

We investigate redox levels in aqueous solution using a combination of ab initio molecular dynamics (MD) simulations and thermodynamic integration methods. The molecular dynamics are performed with both the semilocal Perdew-Burke-Ernzerhof functional and a nonlocal functional (rVV10) accounting for van der Waals (vdW) interactions. The band edges are determined through three different schemes, namely, from the energy of the highest occupied and of the lowest unoccupied Kohn-Sham states, from total-energy differences, and from a linear extrapolation of the density of states. It is shown that the latter does not depend on the system size while the former two are subject to significant finite-size effects. For the redox levels, we provide a formulation in analogy to the definition of charge transition levels for defects in crystalline materials. We consider the H{sup +}/H{sub 2} level defining the standard hydrogen electrode, the OH{sup −}/OH{sup ∗} level corresponding to the oxidation of the hydroxyl ion, and the H{sub 2}O/OH{sup ∗} level for the dehydrogenation of water. In spite of the large structural modifications induced in liquid water, vdW interactions do not lead to any significant structural effect on the calculated band gap and band edges. The effect on the redox levels is also small since the solvation properties of ionic species are little affected by vdW interactions. Since the electronic properties are not significantly affected by the underlying structural properties, it is justified to perform hybrid functional calculations on the configurations of our MD simulations. The redox levels calculated as a function of the fraction α of Fock exchange are found to remain constant, reproducing a general behavior previously observed for charge transition levels of defects. Comparison with experimental values shows very good agreement. At variance, the band edges and the band gap evolve linearly with α. For α ≃ 0.40, we achieve a band gap, band-edge positions, and redox levels in overall good agreement with experiment.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2015

Electronic excitation of molecules in solution calculated using the symmetry-adapted cluster–configuration interaction method in the polarizable continuum model

The effects from solvent environment are specific to the electronic states; therefore, a computational scheme for solvent effects consistent with the electronic states is necessary to discuss electronic excitation of molecules in solution. The PCM (polarizable continuum model) SAC (symmetry-adapted cluster) and SAC-CI (configuration interaction) methods are developed for such purposes. The PCM SAC-CI adopts the state-specific (SS) solvation scheme where solvent effects are self-consistently considered for every ground and excited states. For efficient computations of many excited states, we develop a perturbative approximation for the PCM SAC-CI method, which is called corrected linear response (cLR) scheme. Our test calculations show that the cLR PCM SAC-CI is a very good approximation of the SS PCM SAC-CI method for polar and nonpolar solvents.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2015

Development of a model electronic Hamiltonian for understanding electronic relaxation dynamics of [Fe(bpy){sub 3}]{sup 2+} through molecular dynamics simulations

A model electronic Hamiltonian of [Fe(bpy){sub 3}]{sup 2+}, which was recently refined for use in molecular dynamics simulations, is reviewed with some additional results. In particular, the quality of the refined model Hamiltonian is examined in terms of the vibrational frequencies and solvation structures of the lowest singlet and quintet states.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗
DOE OSTI2016

Super-Maxwellian helium evaporation from pure and salty water

Helium atoms evaporate from pure water and salty solutions in super-Maxwellian speed distributions, as observed experimentally and modeled theoretically. The experiments are performed by monitoring the velocities of dissolved He atoms that evaporate from microjets of pure water at 252 K and 4–8.5 molal LiCl and LiBr at 232–252 K. The average He atom energies exceed the flux-weighted Maxwell-Boltzmann average of 2RT by 30% for pure water and 70% for 8.5m LiBr. Classical molecular dynamics simulations closely reproduce the observed speed distributions and provide microscopic insight into the forces that eject the He atoms from solution. Comparisons of the density profile and He kinetic energies across the water-vacuum interface indicate that the He atoms are accelerated by He–water collisions within the top 1-2 layers of the liquid. We also find that the average He atom kinetic energy scales with the free energy of solvation of this sparingly soluble gas. This free-energy difference reflects the steeply decreasing potential of mean force on the He atoms in the interfacial region, whose gradient is the repulsive force that tends to expel the atoms. The accompanying sharp decrease in water density suppresses the He–water collisions that would otherwise maintain a Maxwell-Boltzmann distribution, allowing the He atom to escape at high energies. Helium is especially affected by this reduction in collisions because its weak interactions make energy transfer inefficient.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2016

DFT study on the attacking mechanisms of H and OH radicals to G-C and A-T base pairs in water

To elucidate the effect of radicals on DNA base pairs, we investigated the attacking mechanism of OH and H radicals to the G-C and A-T base pairs, using the density functional theory (DFT) calculations in water approximated by the continuum solvation model. The DFT calculations revealed that the OH radical abstracts the hydrogen atom of a NH{sub 2} group of G or A base and induces a tautomeric reaction for an A-T base pair more significantly than for a G-C base pair. On the other hand, the H radical prefers to bind to the Cytosine NH{sub 2} group of G-C base pair and induce a tautomeric reaction from G-C to G*-C*, whose activation free energy is considerably small (−0.1 kcal/mol) in comparison with that (42.9 kcal/mol) for the reaction of an A-T base pair. Accordingly, our DFT calculations elucidated that OH and H radicals have a significant effect on A-T and G-C base pairs, respectively. This finding will be useful for predicting the effect of radiation on the genetic information recorded in the base sequences of DNA duplexes.

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DOE OSTI2016

Quantum cluster equilibrium model of N-methylformamide–water binary mixtures

The established quantum cluster equilibrium (QCE) approach is refined and applied to N-methylformamide (NMF) and its aqueous solution. The QCE method is split into two iterative cycles: one which converges to the liquid phase solution of the QCE equations and another which yields the gas phase. By comparing Gibbs energies, the thermodynamically stable phase at a given temperature and pressure is then chosen. The new methodology avoids metastable solutions and allows a different treatment of the mean-field interactions within the gas and liquid phases. These changes are of crucial importance for the treatment of binary mixtures. For the first time in a QCE study, the cis-trans-isomerism of a species (NMF) is explicitly considered. Cluster geometries and frequencies are calculated using density functional theory (DFT) and complementary coupled cluster single point energies are used to benchmark the DFT results. Independent of the selected quantum-chemical method, a large set of clusters is required for an accurate thermodynamic description of the binary mixture. The liquid phase of neat NMF is found to be dominated by the cyclic trans-NMF pentamer, which can be interpreted as a linear trimer that is stabilized by explicit solvation of two further NMF molecules. This cluster reflects the known hydrogen bond network preferences of neat NMF.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2016

Triplet excited electronic state switching induced by hydrogen bonding: A transient absorption spectroscopy and time-dependent DFT study

The solvent plays a decisive role in the photochemistry and photophysics of aromatic ketones. Xanthone (XT) is one such aromatic ketone and its triplet-triplet (T-T) absorption spectra show intriguing solvatochromic behavior. Also, the reactivity of XT towards H-atom abstraction shows an unprecedented decrease in protic solvents relative to aprotic solvents. Therefore, a comprehensive solvatochromic analysis of the triplet-triplet absorption spectra of XT was carried out in conjunction with time dependent density functional theory using the ad hoc explicit solvent model approach. A detailed solvatochromic analysis of the T-T absorption bands of XT suggests that the hydrogen bonding interactions are different in the corresponding triplet excited states. Furthermore, the contributions of non-specific and hydrogen bonding interactions towards differential solvation of the triplet states in protic solvents were found to be of equal magnitude. The frontier molecular orbital and electron density difference analysis of the T{sub 1} and T{sub 2} states of XT indicates that the charge redistribution in these states leads to intermolecular hydrogen bond strengthening and weakening, respectively, relative to the S{sub 0} state. This is further supported by the vertical excitation energy calculations of the XT-methanol supra-molecular complex. The intermolecular hydrogen bonding potential energy curves obtained for this complex in the S{sub 0}, T{sub 1}, and T{sub 2} states support the model. In summary, we propose that the different hydrogen bonding mechanisms exhibited by the two lowest triplet excited states of XT result in a decreasing role of the nπ{sup ∗} triplet state, and are thus responsible for its reduced reactivity towards H-atom abstraction in protic solvents.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2016

The nature of the CO{sub 2}{sup −} radical anion in water

The reductive conversion of CO{sub 2} into industrial products (e.g., oxalic acid, formic acid, methanol) can occur via aqueous CO{sub 2}{sup −} as a transient intermediate. While the formation, structure, and reaction pathways of this radical anion have been modelled for decades using various spectroscopic and theoretical approaches, we present here, for the first time, a vibrational spectroscopic investigation in liquid water, using pulse radiolysis time-resolved resonance Raman spectroscopy for its preparation and observation. Excitation of the radical in resonance with its 235 nm absorption displays a transient Raman band at 1298 cm{sup −1}, attributed to the symmetric CO stretch, which is at ∼45 cm{sup −1} higher frequency than in inert matrices. Isotopic substitution at C ({sup 13}CO{sub 2}{sup −}) shifts the frequency downwards by 22 cm{sup −1}, which confirms its origin and the assignment. A Raman band of moderate intensity compared to the stronger 1298 cm{sup −1} band also appears at 742 cm{sup −1} and is assignable to the OCO bending mode. A reasonable resonance enhancement of this mode is possible only in a bent CO{sub 2}{sup −}(C{sub 2v}/C{sub s}) geometry. These resonance Raman features suggest a strong solute-solvent interaction, the water molecules acting as constituents of the radical structure, rather than exerting a minor solvent perturbation. However, there is no evidence of the non-equivalence (C{sub s}) of the two CO bonds. A surprising resonance Raman feature is the lack of overtones of the symmetric CO stretch, which we interpret due to the detachment of the electron from the CO{sub 2}{sup −} moiety towards the solvation shell. Electron detachment occurs at the energies of 0.28 ± 0.03 eV or higher with respect to the zero point energy of the ground electronic state. The issue of acid-base equilibrium of the radical, which has been in contention for decades, as reflected in a wide variation in the reported pK{sub a} (−0.2 to 3.9), has been resolved. A value of 3.4 ± 0.2 measured in this work is consistent with the vibrational properties, bond structure, and charge distribution in aqueous CO{sub 2}{sup −}.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2016

Perspective: Polarizable continuum models for quantum-mechanical descriptions

Polarizable continuum solvation models are nowadays the most popular approach to describe solvent effects in the context of quantum mechanical calculations. Unexpectedly, despite their widespread use in all branches of quantum chemistry and beyond, important aspects of both their theoretical formulation and numerical implementation are still not completely understood. In particular, in this perspective we focus on the numerical issues of their implementation when applied to large systems and on the theoretical framework needed to treat time dependent problems and excited states or to deal with electronic correlation. Possible extensions beyond a purely electrostatic model and generalizations to environments beyond common solvents are also critically presented and discussed. Finally, some possible new theoretical approaches and numerical strategies are suggested to overcome the obstacles which still prevent a full exploitation of these models.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2016

Effect of ethanol concentrations on temperature driven structural changes of chymotrypsin inhibitor 2

A series of atomistic molecular dynamics (MD) simulations of a small enzymatic protein Chymotrypsin Inhibitor 2 (CI2) in water-ethanol mixed solutions were carried out to explore the underlying mechanism of ethanol driven conformational changes of the protein. Efforts have been made to probe the influence of ethanol concentrations ranging from 0% to 75% (v/v) at ambient condition (300 K (T1)) and at elevated temperatures (375 K (T2) and 450 K (T3)) to investigate the temperature induced conformational changes of the protein further. Our study showed that the effect of varying ethanol concentrations on protein’s structure is almost insignificant at T1 and T2 temperatures whereas at T3 temperature, partial unfolding of CI2 in 10% ethanol solution followed by full unfolding of the protein at ethanol concentrations above 25% occurs. However, interestingly, at T3 temperature CI2’s native structure was found to be retained in pure water (0% ethanol solution) indicating that the cosolvent ethanol do play an important role in thermal denaturation of CI2. Such observations were quantified in the light of root-mean-square deviations (RMSDs) and radius of gyration. Although higher RMSD values of β-sheet over α-helix indicate complete destruction of the β-structure of CI2 at high ethanol concentrations, the associated time scale showed that the faster melting of α-helix happens over β-sheet. Around 60%-80% of initial native contacts of the protein were found broken with the separation of hydrophobic core consisting eleven residues at ethanol concentrations greater than 25%. This leads protein to expand with the increase in solvent accessible surface area. The interactions between protein and solvent molecules showed that protein’s solvation shell preferred to accommodate ethanol molecules as compared to water thereby excluded water molecules from CI2’s surface. Further, concentration dependent differential self-aggregation behavior of ethanol is likely to regulate the replacement of relatively fast diffused water by low diffused ethanol molecules from protein’s surface during the unfolding process.

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