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.     

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.     

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.     

Modeling electrochemical interfaces from ab initio molecular dynamics: water adsorption on metal surfaces at potential of zero charge

The origin of the potential difference between the potential of zero charge of a metal/water interface and the work function of the metal is a recurring issue because it is related to how water interacts with metal surface in the absence of surface charge. Recently ab initio molecular dynamics method has been used to model electrochemical interfaces to study interfacial potential and the structure of interface water. Here, we will first introduce the computational standard hydrogen electrode method, which allows for ab initio determination of electrode potentials that can be directly compared with experiment. Then, we will review the recent progress from ab initio molecular dynamics simulation in understanding the interaction between water and metal and its impact on interfacial potential. Finally, we will give our perspective for future development of ab initio computational electrochemistry.     

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.     

Ab initio dynamics with wave-packets and density matrices

Efficient methodologies to conduct simultaneous dynamics of electrons and nuclei are discussed. Particularly, attention is directed to a recent development that combines quantum dynamics with ab initio molecular dynamics. The two components of the methodology, namely, quantum dynamics and ab initio molecular dynamics, are harnessed together using a time-dependent self-consistent field-like coupling procedure. An approach to conduct quantum dynamics using an accurate banded, sparse and Toeplitz representation for the discrete free propagator is highlighted with suitable review of other related approaches. One notable feature of the method is that all important quantum dynamical effects including zero-point effects, tunneling as well as over-barrier reflections are accurately treated. Computational methodologies for improved efficiency of the quantum dynamics are also discussed. There exists a number of ways to carry out simultaneous ab initio molecular dynamics (such as Born–Oppenheimer dynamics and extended Lagrangian dynamics, Car–Parrinello dynamics being a prime example of the latter); our prime focus remains on atom-centered density-matrix propagation and Born–Oppenheimer dynamics. The electronic degrees of freedom are handled at accurate levels of density functional theory, using hybrid or gradient corrected approximations. Benchmark calculations are provided for a prototypical proton transfer system. Future generalizations and goals are discussed.     

Modeling the sorption dynamics of NaH using a reactive force field

We have parametrized a reactive force field for NaH, ReaxFF(NaH), against a training set of ab initio derived data. To ascertain that ReaxFF(NaH) is properly parametrized, a comparison between ab initio heats of formation of small representative NaH clusters with ReaxFF(NaH) was done. The results and trend of ReaxFF(NaH) are found to be consistent with ab initio values. Further validation includes comparing the equations of state of condensed phases of Na and NaH as calculated from ab initio and ReaxFF(NaH). There is a good match between the two results, showing that ReaxFF(NaH) is correctly parametrized by the ab initio training set. ReaxFF(NaH) has been used to study the dynamics of hydrogen desorption in NaH particles. We find that ReaxFF(NaH) properly describes the surface molecular hydrogen charge transfer during the abstraction process. Results on heat of desorption versus cluster size shows that there is a strong dependence on the heat of desorption on the particle size, which implies that nanostructuring enhances desorption process. To gain more insight into the structural transformations of NaH during thermal decomposition, we performed a heating run in a molecular dynamics simulation. These runs exhibit a series of drops in potential energy, associated with cluster fragmentation and desorption of molecular hydrogen. This is consistent with experimental evidence that NaH dissociates at its melting point into smaller fragments.     

"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.     

Li ion diffusion mechanisms in LiFePO4: an ab initio molecular dynamics study

The mechanisms for thermal (self) diffusion of Li ions in fully lithiated LiFePO(4) have been investigated with spin polarized ab initio molecular dynamics calculations. The effect of electron correlation is taken into account with the GGA+U formalism. It was found that Li ion diffusion is not a continuous process but through a series of jumps from one site to another. A dominant process is the hopping between neighboring Li sites around the PO(4) groups, which results in a zigzag pathway along the crystallographic b-axis. This observation is in agreement with a recent neutron diffraction experiment. A second process involves the collaborative movements of the Fe ions leading to the formation of antisite defects and promotes Li diffusion across the Li ion channels. The finding of the second mechanism demonstrates the benefit of ab initio molecular dynamics simulation in sampling diffusion pathways that may not be anticipated.     

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.     

Interpolating moving least-squares methods for fitting potential energy surfaces: an application to the H2CN unimolecular reaction

Classical trajectories have been used to compute rates for the unimolecular reaction H2CN-->H+HCN on a fitted ab initio potential energy surface (PES). The ab initio energies were obtained from CCSD(T)/aug-cc-pvtz electronic structure calculations. The ab initio energies were fitted by the interpolating moving least-squares (IMLS) method. This work continues the development of the IMLS method for producing ab initio PESs for use in molecular dynamics simulations of many-atom systems. A dual-level scheme was used in which the preliminary selection of data points was done using a low-level theory and the points used for fitting the final PES were obtained at the desired higher level of theory. Classical trajectories were used on various low-level IMLS fits to tune the fit to the unimolecular reaction under study. Procedures for efficiently picking data points, selecting basis functions, and defining cutoff limits to exclude distant points were investigated. The accuracy of the fitted PES was assessed by comparing interpolated values of quantities to the corresponding ab initio values. With as little as 330 ab initio points classical trajectory rate constants were converged to 5%-10% and the rms error over the six-dimensional region sampled by the trajectories was a few tenths of a kcal/mol.     

Molecular dynamics and metadynamics simulations of [2 + 2] photocycloaddition

Triplet state mechanism of [2 + 2] photocycloaddition forming a cyclobutane ring from two ethylenes is investigated in the context of photocatalysis. High‐level ab initio calculations are combined with ab initio adiabatic molecular dynamics and ab initio metadynamics for rare events modeling. In a photocatalytic scheme, a reactant reaches the triplet state either via intersystem crossing (ISC) or triplet sensitization. The model system adopts a biradical structure, which represents energy intersection with the ground state. The system either completes cyclization or undergoes fragmentation into two olefinic units. The potential and free energy surfaces of the cyclobutane/ethylenes system are mapped with multireference approaches describing possible reaction pathways. To obtain a full picture of a double bond photoreactivity, ab initio adiabatic dynamical calculations were used to estimate reaction yields and to model the effects of excess energy. The potential use of density functional theory based approaches for [2 + 2] photocycloaddition was investigated for future simulations and design of realistic photocatalytic systems. Dynamical aspects of [2 + 2] photocycloaddition via a triplet state manifold are investigated by combining ab initio multireference methods and ab initio molecular dynamics and metadynamics. The reaction pathways are studied for a model system of two ethylenes forming a cyclobutane ring to provide a basis for further studies on design of photocatalytic systems.     

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.     

Approaches to the solvation of the molecular probe N-methyl-6-quinolone in its excited state

The molecular probe N-methyl-6-quinolone (MQ) gives experimental access to its local chemical environment, e.g. inside a biomolecule. Using ab initio molecular dynamics (MD), it is possible to simulate the time evolution of the Stokes shift as a function of the actual atomistic coupling to the surrounding hydrogen bond network and thus obtain a comprehensive view of the local environment. In contrast to ground state ab initio MD simulations, the choice of a method for excited state MD is nontrivial. Here, we develop a simple and accurate model for the solvation dynamics of MQ in its first excited state.     

Accelerating chemical reactions: exploring reactive free-energy surfaces using accelerated ab initio molecular dynamics

A biased potential molecular dynamics simulation approach, accelerated molecular dynamics (AMD), has been implemented in the framework of ab initio molecular dynamics for the study of chemical reactions. Using two examples, the double proton transfer reaction in formic acid dimer and the hypothetical adiabatic ring opening and subsequent rearrangement reactions in methylenecyclopropane, it is demonstrated that ab initio AMD can be readily employed to efficiently explore the reactive potential energy surface, allowing the prediction of chemical reactions and the identification of metastable states. An adaptive variant of the AMD method is developed, which additionally affords an accurate representation of both the free-energy surface and the mechanism associated with the chemical reaction of interest and can also provide an estimate of the reaction rate.     

Ab initio ground and excited state potential energy surfaces for NO-Kr complex and dynamics of Kr solids with NO impurity

The intermolecular potentials for the NO(X 2Pi)-Kr and NO(A 2Sigma+)-Kr systems have been calculated using highly accurate ab initio calculations. The spin-restricted coupled cluster method for the ground 1 2A' state [NO(X 2Pi)-Kr] and the multireference singles and doubles configuration interaction method for the excited 2 2A' state [NO(A 2Sigma+)-Kr], respectively, were used. The potential energy surfaces (PESs) show two linear wells and one that is almost in the perpendicular position. An analytical representation of the PESs has been constructed for the triatomic systems and used to carry out molecular dynamics (MD) simulations of the NO-doped krypton matrix response after excitation of NO. MD results are shown comparatively for three sets of potentials: (1) anisotropic ab initio potentials [NO molecule direction fixed during the dynamics and considered as a point (its center of mass)], (2) isotropic ab initio potentials (isotropic part in a Legendre polynomial expansion of the PESs), and (3) fitted Kr-NO potentials to the spectroscopic data. An important finding of this work is that the anisotropic and isotropic ab initio potentials calculated for the Kr-NO triatomic system are not suitable for describing the dynamics of structural relaxation upon Rydberg excitation of a NO impurity in the crystal. However, the isotropic ab initio potential in the ground state almost overlaps the published experimental potential, being almost independent of the angle asymmetry. This fact is also manifested in the radial distribution function around NO. However, in the case of the excited state the isotropic ab initio potential differs from the fitted potentials, which indicates that the Kr-NO interaction in the matrix is quite different because of the presence of the surrounding Kr atoms acting on the NO molecule. MD simulations for isotropic potentials reasonably reproduce the experimental observables for the femtosecond response and the bubble size but do not match spectroscopic results. A general overall view of the results suggests that, when the Kr-NO interaction takes place inside the matrix, potentials are rather symmetric and less repulsive than those for the triatomic system.     

Ab initio potential-energy surfaces for complex, multichannel systems using modified novelty sampling and feedforward neural networks

A neural network/trajectory approach is presented for the development of accurate potential-energy hypersurfaces that can be utilized to conduct ab initio molecular dynamics (AIMD) and Monte Carlo studies of gas-phase chemical reactions, nanometric cutting, and nanotribology, and of a variety of mechanical properties of importance in potential microelectromechanical systems applications. The method is sufficiently robust that it can be applied to a wide range of polyatomic systems. The overall method integrates ab initio electronic structure calculations with importance sampling techniques that permit the critical regions of configuration space to be determined. The computed ab initio energies and gradients are then accurately interpolated using neural networks (NN) rather than arbitrary parametrized analytical functional forms, moving interpolation or least-squares methods. The sampling method involves a tight integration of molecular dynamics calculations with neural networks that employ early stopping and regularization procedures to improve network performance and test for convergence. The procedure can be initiated using an empirical potential surface or direct dynamics. The accuracy and interpolation power of the method has been tested for two cases, the global potential surface for vinyl bromide undergoing unimolecular decomposition via four different reaction channels and nanometric cutting of silicon. The results show that the sampling methods permit the important regions of configuration space to be easily and rapidly identified, that convergence of the NN fit to the ab initio electronic structure database can be easily monitored, and that the interpolation accuracy of the NN fits is excellent, even for systems involving five atoms or more. The method permits a substantial computational speed and accuracy advantage over existing methods, is robust, and relatively easy to implement.     

Intramolecular SN2 reaction caused by photoionization of benzene chloride-NH3 complex: direct ab initio molecular dynamics study

Ionization processes of chlorobenzene-ammonia 1:1 complex (PhCl-NH3) have been investigated by means of full dimensional direct ab initio molecular dynamics (MD) method, static ab initio calculations, and density functional theory (DFT) calculations. The static ab initio and DFT calculations of neutral PhCl-NH3 complex showed that one of the hydrogen atoms of NH3 orients toward a carbon atom in the para-position of PhCl. The dynamics calculation for ionization of PhCl-NH3 indicated that two reaction channels are competitive with each other as product channels: one is an intramolecular SN2 reaction expressed by a reaction scheme [PhCl-NH3]+-->SN2 intermediate complex-->PhNH3++Cl, and the other is ortho-NH3 addition complex (ortho complex) in which NH3 attacks the ortho-carbon of PhCl+ and the trajectory leads to a bound complex expressed by (PhCl-NH3)+. The mechanism of the ionization of PhCl-NH3 is discussed on the basis of the theoretical results.