Solvent effects on peroxynitrite structure and properties from QM/MM simulations

We have investigated the structure and the vibrational spectrum of peroxynitrite anion in aqueous solution by means of combined quantum-classical (QM/MM) molecular dynamics simulations. In our QM/MM scheme, the reactant was modeled using density functional theory with a Gaussian basis set and the solvent was described using the mean-field TIP4P and the polarizable TIP4P-FQ force fields. The choice of basis sets, functionals and force field parameters has been validated by performing calculations on isolated peroxynitrite and on small peroxynitrite-water complexes. Poor values for isolated peroxynitrite structural properties and vibrational frequencies are found for most ab initio methods, particularly regarding the ON-OO(-) bond distance and the harmonic stretching frequency, probably due to the singlet-triplet instability found in the HF wave function. On the other hand, DFT methods yield results in better agreement with high level CCSD(T) ab initio calculations. We have computed the vibrational spectrum for aqueous peroxynitrite by calculating the Fourier transform of the velocity autocorrelation function extracted from the QM-MM molecular dynamics simulations. Our computational scheme, which allows for the inclusion of both anharmonicity and solvent effects, is able to clarify previous discrepancies regarding the experimental spectra assignments and to shed light on the subtle interplay between solvation and peroxynitrite structure and properties.     

Ab initio calculations of the melting temperatures of refractory bcc metals

We present ab initio calculations of the melting temperatures for bcc metals Nb, Ta and W. The calculations combine phase coexistence molecular dynamics (MD) simulations using classical embedded-atom method potentials and ab initio density functional theory free energy corrections. The calculated melting temperatures for Nb, Ta and W are, respectively, within 3%, 4%, and 7% of the experimental values. We compare the melting temperatures to those obtained from direct ab initio molecular dynamics simulations and see if they are in excellent agreement with each other. The small remaining discrepancies with experiment are thus likely due to inherent limitations associated with exchange-correlation energy approximations within density-functional theory.     

Constrained dynamics and extraction of normal modes from ab initio molecular dynamics: application to ammonia

We present a methodology for extracting phonon data from ab initio Born-Oppenheimer molecular dynamics calculations of molecular crystals. Conventional ab initio phonon methods based on perturbations are difficult to apply to lattice modes because the perturbation energy is dominated by intramolecular modes. We use constrained molecular dynamics to eliminate the effect of bond bends and stretches and then show how trajectories can be used to isolate and define in particular, the eigenvalues and eigenvectors of modes irrespective of their symmetry or wave vector. This is done by k-point and frequency filtering and projection onto plane wave states. The method is applied to crystalline ammonia: the constrained molecular dynamics allows a significant speed-up without affecting structural or vibrational modes. All Gamma point lattice modes are isolated: the frequencies are in agreement with previous studies; however, the mode assignments are different.     

The Jahn-Teller effect of the TiIII ion in aqueous solution: extended ab initio QM/MM molecular dynamics simulations.

Combined ab initio quantum mechanical/molecular mechanical (QM/MM) molecular dynamics simulations, including only the first and the first and second hydration shells in the QM region, were performed for TiIII in aqueous solution. The hydration structure of TiIII is discussed in terms of radial distribution functions, coordination-number distributions and several angle distributions. Dynamical properties, such as librational and vibrational motions and TiIII-O vibrations, were evaluated. A fast dynamical Jahn-Teller effect of TiIII(aq) was observed in the QM/MM simulations, in particular when the second hydration shell was included into the QM region. The results justify the computational effort required for the inclusion of the second hydration shell into the QM region and show the importance of this effort for obtaining accurate hydration-shell geometries, dynamical properties, and details of the Jahn-Teller effect.     

Quantum wavepacket ab initio molecular dynamics: an approach for computing dynamically averaged vibrational spectra including critical nuclear quantum effects

We have introduced a computational methodology to study vibrational spectroscopy in clusters inclusive of critical nuclear quantum effects. This approach is based on the recently developed quantum wavepacket ab initio molecular dynamics method that combines quantum wavepacket dynamics with ab initio molecular dynamics. The computational efficiency of the dynamical procedure is drastically improved (by several orders of magnitude) through the utilization of wavelet-based techniques combined with the previously introduced time-dependent deterministic sampling procedure measure to achieve stable, picosecond length, quantum-classical dynamics of electrons and nuclei in clusters. The dynamical information is employed to construct a novel cumulative flux/velocity correlation function, where the wavepacket flux from the quantized particle is combined with classical nuclear velocities to obtain the vibrational density of states. The approach is demonstrated by computing the vibrational density of states of [Cl-H-Cl]-, inclusive of critical quantum nuclear effects, and our results are in good agreement with experiment. A general hierarchical procedure is also provided, based on electronic structure harmonic frequencies, classical ab initio molecular dynamics, computation of nuclear quantum-mechanical eigenstates, and employing quantum wavepacket ab initio dynamics to understand vibrational spectroscopy in hydrogen-bonded clusters that display large degrees of anharmonicities.     

An ab initio force field for the cofactors of bacterial photosynthesis

This article presents a new ab initio force field for the cofactors of bacterial photosynthesis, namely quinones and bacteriochlorophylls. The parameters has been designed to be suitable for molecular dynamics simulations of photosynthetic proteins by being compatible with the AMBER force field. To our knowledge, this is the first force field for photosynthetic cofactors based on a reliable set of ab initio density functional reference data for methyl bacteriochlorophyll a, methyl bacteriopheophytin a, and of a derivative of ubiquinone. Indeed, the new molecular mechanics force field is able to reproduce very well not only the experimental and ab initio structural properties and the vibrational spectra of the molecules, but also the eigenvectors of the molecular normal modes. For this reason it might also be helpful to understand vibrational spectroscopy results obtained on reaction center proteins.     

Structure and dynamics of homoleptic beryllocenes: a solid-state 9Be and 13C NMR study

The correlation between anisotropic 9Be NMR (quadrupolar and chemical shielding) interactions and the structure and dynamics in [Cp2Be], [Cp2*Be], and [(C5Me4H)2Be] is examined by solid-state 9Be NMR spectroscopy, as well as by ab initio and hybrid density functional theory calculations. The 9Be quadrupole coupling constants in the three compounds correspond well to the relative degrees of spherical ground-state electronic symmetry of the environment about beryllium. Theoretical computations of NMR interaction tensors are in excellent agreement with experimental values and aid in understanding the origins of NMR interaction tensors and their correlation to molecular symmetry. Variable-temperature (VT) 9Be and 13C NMR experiments reveal a highly fluxional structure in the condensed phase of [Cp2Be]. In particular, the pathway by which the Cp rings of [Cp2Be] 'invert' coordination modes is examined in detail using hybrid density functional theory in order to inspect variations of the 9Be NMR interaction tensors. The activation energy for the 'inversion' process is found to be 36.9 kJ mol(-1) from chemical exchange analysis of 13C VT CP/MAS NMR spectra. The low-temperature (ca. -100 degrees C) X-ray crystal structures of all three compounds have been collected and refined, and are in agreement with previously reported structures. In addition, the structure of the same Cp2Be crystal was determined at 20 degrees C and displays features consistent with increased intramolecular motion, supporting observations by 9Be VT NMR spectroscopy.     

"Pump-probe" atom-centered density matrix propagation studies to gauge anharmonicity and energy repartitioning in atmospheric reactive adducts: case study of the OH + isoprene and OH + butadiene reaction intermediates

Time-resolved "pump-probe" ab initio molecular dynamics studies are constructed to probe the stability of reaction intermediates, the mechanism of energy transfer, and energy repartitioning, for moieties involved during the interaction of volatile organic compunds with hydroxyl radical. These systems are of prime importance in the atmosphere. Specifically, the stability of reaction intermediates of hydroxyl radical adducts to isoprene and butadiene molecules is used as a case study to develop novel computational techniques involving "pump-probe" ab initio molecular dynamics. Starting with the various possible hydroxyl radical adducts to isoprene and butadiene, select vibrational modes of each of the adducts are populated with excess energy to mimic the initial conditions of an experiment. The flow of energy into the remaining modes is then probed by subjecting the excited adducts to ab initio molecular dynamics simulations. It is found that the stability of the adducts arises directly due to the anhormonically driven coupling of the modes to facilitate repartitioning of the excess vibrational energy. This kind of vibrational repartitioning has a critical influence on the energy density.     

Decomposing total IR spectra of aqueous systems into solute and solvent contributions: a computational approach using maximally localized Wannier orbitals

The theoretical principles underpinning the calculation of infrared spectra for condensed-phase systems in the context of ab initio molecular dynamics have been recently developed in literature. At present, most ab initio molecular dynamics calculations are restricted to relatively small systems and short simulation times. In this paper we devise a method that allows well-converged results for infrared spectra from ab initio molecular dynamics simulations using small systems and short trajectories characteristic of simulations typically performed in practice. We demonstrate the utility of our approach by computing the imaginary part of the dielectric constant epsilon"(omega) for H2O and D2O in solid and liquid phases and show that it compares well with experimental data. We further demonstrate that maximally localized Wannier orbitals can be used to separate the individual contributions of different molecular species to the linear spectrum of complex systems. The new spectral decomposition method is shown to be useful in present-day ab initio molecular dynamics calculations to compute the magnitude of the "continuous absorption" generated by excess protons in aqueous solutions with good accuracy even when other species present in the solutions absorb strongly in the same frequency window.     

Glycosidic linkage conformation of methyl-alpha-mannopyranoside

We study the preferred conformation of the glycosidic linkage of methyl-alpha-mannopyranoside in the gas phase and in aqueous solution. Results obtained utilizing Car-Parrinello molecular dynamics (CPMD) simulations are compared to those obtained from classical molecular dynamics (MD) simulations. We describe classical simulations performed with various water potential functions to study the impact of the chosen water potential on the predicted conformational preference of the glycosidic linkage of the carbohydrate in aqueous solution. In agreement with our recent studies, we find that results obtained with CPMD simulations differ from those obtained from classical simulations. In particular, this study shows that the trans (t) orientation of the glycosidic linkage of methyl-alpha-mannopyranoside is preferred over its gauche anticlockwise (g-) orientation in aqueous solution. CPMD simulations indicate that this preference is due to intermolecular hydrogen bonding with surrounding water molecules, whereas no such information could be demonstrated by classical MD simulations. This study emphasizes the importance of ab initio MD simulations for studying the structural properties of carbohydrates in aqueous solution.     

Calculation of Raman optical activity spectra of methyl-β-D-glucose incorporating a full molecular dynamics simulation of hydration effects

We report calculations of the Raman and Raman optical activity (ROA) spectra of methyl-β-D-glucose utilizing density functional theory combined with molecular dynamics (MD) simulations to provide an explicit hydration environment. This is the first report of such combination of MD simulations with ROA ab initio calculations. We achieve a significant improvement in accuracy over the more commonly used gas phase and polarizable continuum model (PCM) approaches, resulting in an excellent level of agreement with the experimental spectrum. Modeling the ROA spectra of carbohydrates has until now proven a notoriously difficult challenge due to their sensitivity to the effects of hydration on the molecular vibrations involving each of the chiral centers. The details of the ROA spectrum of methyl-β-D-glucose are found to be highly sensitive to solvation effects, and these are correctly predicted for the first time including those originating from the highly sensitive low frequency vibrational modes. This work shows that a thorough consideration of the role of water is pivotal for understanding the vibrational structure of carbohydrates and presents a new and powerful tool for characterizing carbohydrate structure and conformational dynamics in solution.     

An extended ab initio QM/MM MD approach to structure and dynamics of Zn(II) in aqueous solution

Structural and dynamical properties of Zn(II) in aqueous solution were investigated, based on an ab initio quantum mechanical/molecular mechanical (QM/MM) molecular dynamics simulation at double-zeta Hartree-Fock quantum mechanical level including the first and second hydration shells into the QM region. The inclusion of the second shell in the QM region resulted in significant changes in the properties of the hydrate. The first shell coordination number was found to be 6, the second shell consists of approximately 14 water molecules. The structural properties were determined in terms of RDF, ADF, tilt and theta angle distributions, while dynamics were characterized by mean ligand residence times, ion-ligand stretching frequencies and the vibrational and librational motions of water ligands.     

Ab initio centroid path integral molecular dynamics: application to vibrational dynamics of diatomic molecular systems

An ab initio centroid molecular dynamics (CMD) method is developed by combining the CMD method with the ab initio molecular orbital method. The ab initio CMD method is applied to vibrational dynamics of diatomic molecules, H2 and HF. For the H2 molecule, the temperature dependence of the peak frequency of the vibrational spectral density is investigated. The results are compared with those obtained by the ab initio classical molecular dynamics method and exact quantum mechanical treatment. It is shown that the vibrational frequency obtained from the ab initio CMD approaches the exact first excitation frequency as the temperature lowers. For the HF molecule, the position autocorrelation function is also analyzed in detail. The present CMD method is shown to well reproduce the exact quantum result for the information on the vibrational properties of the system.     

Towards accurate solvation dynamics of divalent cations in water using the polarizable amoeba force field: From energetics to structure

Molecular dynamics simulations were performed using a modified amoeba force field to determine hydration and dynamical properties of the divalent cations Ca2+ and Mg2+. The extension of amoeba to divalent cations required the introduction of a cation specific parametrization. To accomplish this, the Thole polarization damping model parametrization was modified based on the ab initio polarization energy computed by a constrained space orbital variation energy decomposition scheme. Excellent agreement has been found with condensed phase experimental results using parameters derived from gas phase ab initio calculations. Additionally, we have observed that the coordination of the calcium cation is influenced by the size of the periodic water box, a recurrent issue in first principles molecular dynamics studies.     

Vibrational echo spectroscopy of aqueous sodium bromide solutions from first principles simulations

A theoretical study of the time-dependent vibrational echo spectroscopy of sodium bromide solutions in deuterated water at two different concentrations of 0.5 and 5.0 M and at temperatures of 300 and 350 K is presented using the method of ab initio molecular dynamics simulations. The instantaneous fluctuations in frequencies of local OD stretch modes are calculated using time-series analysis of the simulated trajectories. The third-order polarization and intensities of three pulse photon-echo are calculated from ab initio simulations. The timescales of vibrational spectral diffusion are determined from the frequency time correlation functions (FTCF) and short-time slope of three pulse photon echo (S3PE) calculated within the second-order cumulant and Condon approximations. It is found that under ambient conditions, the rate of vibrational spectral diffusion becomes slower with increase in ionic concentration. Decay of S3PE calculated for different systems give timescales, which are in close agreement with those of FTCF and also with the results of experimental time-dependent vibrational spectroscopic experiments. © 2019 Wiley Periodicals, Inc.     

Simulations of structure and vibrational spectra of deoxyoctanucleotides

Combined molecular dynamics and ab initio computations were applied for analysis of infrared absorption and vibrational circular dichroism spectra of deoxyoctanucleotides. Unlike for previous idealized models, molecular geometries of these shorter DNA fragments in solutions were obtained as dynamic averages from simulations in a periodic water box. Vibrational spectra for the whole octamers including hydrogen-bonded solvent molecules were simulated on the basis of density-functional calculations on small fragments and subsequent transfer of molecular property tensors. Explicit and continuum solvent models were compared. Apparently, the DNA segments retain an approximate B-conformation in the aqueous solutions, but the terminal base pairs significantly deviate from the planar arrangement and the vibrational circular dichroism spectrum for (CG)(2) nucleotide indicates a larger average helical twist. Sodium counterions moved freely around the molecule during the simulation and do not influence spectral intensities. Simulated absorption spectra faithfully reproduced the experimental signal of principal functional groups, while only qualitative agreement was obtained for the dependence on the basis sequence.     

Force-field parametrization and molecular dynamics simulations of p-menthan-3,9-diols: a family of amphiphilic compounds derived from terpenoids

A set of amphiphilic p-menthan-3,9-diols have been investigated by molecular dynamics simulations. These are four stereoisomers than can be specifically obtained from two terpenoids widely used in biorganic chemistry. For this purpose, the p-menthan-3,9-diols have been explicitly parametrized using both semiempirical and ab initio quantum mechanical calculations. The reliability of these parameters has been validated by predicting different molecular and thermodynamic properties. Molecular dynamics simulations in aqueous solution have been performed with the new parameters. The results provide useful insights about the conformational properties of this family of compounds and the formation of intra- and intermolecular hydrogen bonds.     

Simulations of vibrational spectra from classical trajectories: calibration with ab initio force fields

An algorithm allowing simulating vibrational spectra from classical time-dependent trajectories was applied for infrared absorption, vibrational circular dichroism, Raman, and Raman optical activity of model harmonic systems. The implementation of the theory within the TINKER molecular dynamics (MD) program package was tested with ab initio harmonic force fields in order to determine the feasibility for more extended MD simulations. The results suggest that sufficiently accurate frequencies can be simulated with integration time steps shorter than about 0.5 fs. For a given integration time step, lower vibrational frequencies ( approximately 0-2000 cm(-1)) could be reproduced with a higher accuracy than higher-frequency vibrational modes (e.g., O-H and C-H stretching). In principle, the algorithm also provides correct intensities for ideal systems. In applied simulations, however, the intensity profiles are affected by an unrealistic energy distribution between normal modes and a slow energy relaxation. Additionally, the energy fluctuations may cause weakening of the intensities on average. For ab initio force fields, these obstacles could be overcome by an arbitrary normal mode energy correction. For general MD simulations, averaging of many shorter MD trajectories started with randomly distributed atomic velocities provided the best spectral shapes. alpha-pinene, D-gluconic acid, formaldehyde dimer, and the acetylprolineamide molecule were used in the tests.     

Ab initio studies of the electronic structure and density of states of metallic beryllium

Hartree–Fock–Roothaan studies are reported for low-lying electronic states of metallic beryllium as modeled by a moiety of 135 beryllium atoms. The system corresponds to 16 coordination shells of a central Be with internuclear separations derived from the lattice constants of the bulk metal. The calculations become tractable by use of the full D_3h symmetry of the system at both the integrals and self-consistent-field stages and by employing ab initio effective potentials for the 1s electrons of each beryllium atom. Ionization potentials, binding energies, orbital energies, electric field gradients, nuclear-electrostatic potentials, diamagnetic shielding constants, second moments, and Mulliken populations are calculated for selected electronic states. The calculated ionization potential for the lowest state agrees to within 10% of the experimental bulk work function. A density-of-states analysis for that state is reported and compared with band structure calculations.     

Solvation of propylene oxide in water: vibrational circular dichroism, optical rotation, and computer simulation studies

The solvation of propylene oxide (PO) in water has been studied using vibrational circular dichroism (VCD) spectroscopy, optical rotation dispersion (ORD) spectroscopy, molecular dynamics simulations, and ab initio calculations. VCD and ORD measurements were carried out for PO as neat liquid, in CCl4, and in water solutions. The classical molecular dynamics simulations were carried out for the PO + water binary mixtures at different concentrations, and the solvation information was derived from the radial distribution functions obtained in the simulations. The total number of water molecules within the closest vicinity of PO was predicted to be about 3. The geometry optimizations, vibrational frequencies, and VCD intensities were evaluated for the PO monomer and the PO-(H2O)n clusters with n = 1-3 , using density functional theory calculations at the B3LYP/aug-cc-pVTZ level of theory. The chirality transfer VCD feature, which is a direct result of the explicit H-bonding between water and the chiral PO solute, was detected experimentally at the water bending band region. This feature exhibits high sensitivity to the solvation structure around PO. Comparison of the calculated and experimental chirality transfer features leads to the conclusion that the PO-water binary complex is the dominating species in aqueous solution at room temperature and the anti conformation, where water is on the opposite side of the oxirane ring of the PO methyl group, is preferred over the syn one. This conclusion is also supported by the complementary ORD studies. Possible contributions from the ternary and quaternary PO-water complexes are also discussed.