Ab initio molecular dynamics study of liquid methanol

We present a density-functional theory based molecular-dynamics study of the structural, dynamical, and electronic properties of liquid methanol under ambient conditions. The calculated radial distribution functions involving the oxygen and hydroxyl hydrogen show a pronounced hydrogen bonding and compare well with recent neutron diffraction data, except for an underestimate of the oxygen–oxygen correlation. We observe that, in line with infrared spectroscopic data, the hydroxyl stretching mode is significantly red-shifted in the liquid. A substantial enhancement of the dipole moment is accompanied by significant fluctuations due to thermal motion. Our results provide valuable data for improvement of empirical potentials.     

Ab initio molecular dynamics calculations to study catalysis

The modern versions of the density functional theory (DFT), especially those using the generalized gradient approximation (GGA), have reached (almost) chemical accuracy and thus can be applied to study problems of real chemical interest such as catalysis. The important equations for the DFT, the local density approximation (LDA), and GGA are given. The full-potential linearized augmented plane wave method (LAPW) is used to check the accuracy of GGA in solids. The basic concepts of the ab initio molecular dynamics (MD) method by Car and Parrinello and its recent implementation using the projector augmented Wave (PAW) method which use a similar augmentation as LAPW are described. PAW applications to ferrocene and beryllocene are summarized, which illustrate that vibrational or fluxional behavior are well described. Sodalite, an aluminosilicate, is discussed as a generic zeolite in comparison with gmelinite. A study of the dynamics of such a system allows the determination of, e.g., the proton stretch vibrations which can be related to infrared spectra. This is illustrated for the OH stretch vibration of the acid site in silicon-rich sodalite. With this methodology, we are able to study the interaction of methanol trapped inside the cage structure of silicon-rich sodalite and to gain new insight into crucial steps of catalytic reactions, namely, the hydrogen-bonding and the possible protonation in this system, or a proton-exchange reaction. The strategies for parallelizing the PAW code are outlined. © 1997 John Wiley & Sons, Inc.     

Ab initio model potential and molecular dynamics simulation of Ag6 clusters

We present an approach to generate a model potential with parameters fitted to ab initio energetic surfaces. The potential includes two-, three- and four-body terms. Each of them consists of an exponential exchange and dispersion terms. The analytical form of the latter was taken from perturbation theory up to fourth order. We illustrate the present approach by constructing an ab initio model potential for the Ag₆ cluster. A molecular dynamics simulation using this potential reveals interesting features in the isomerization of the C _2v structure. A two step isomerization transition is observed: First, at temperatures around 350 K, the cluster structures fluctuate between two-dimensional isomers. At higher temperatures (450 K), fast transitions occur between two- and three-dimensional cluster configurations.     

Ab initio molecular dynamics study of formate ion hydration

We perform ab initio molecular dynamics simulations of the aqueous formate ion. The mean number of water molecules in the first solvation shell, or the hydration number, of each formate oxygen is found to be consistent with recent experiments. Our ab initio pair correlation functions, however, differ significantly from many classical force field results and hybrid quantum mechanics/molecular mechanics predictions. They yield roughly one less hydrogen bond between each formate oxygen and water than force field or hybrid methods predict. Both the BLYP and PW91 exchange correlation functionals give qualitatively similar results. The time dependence of the hydration numbers are examined, and Wannier function techniques are used to analyze electronic configurations along the molecular dynamics trajectory.     

Ab initio mass tensor molecular dynamics

Mass tensor molecular dynamics method was first introduced by Bennett [J. Comput. Phys. 19, 267 (1975)] for efficient sampling of phase space through the use of generalized atomic masses. Here, we show how to apply this method to ab initio molecular dynamics simulations with minimal computational overhead. Test calculations on liquid water show a threefold reduction in computational effort without making the fixed geometry approximation. We also present a simple recipe for estimating the optimal atomic masses using only the first derivatives of the potential energy.     

Ab initio molecular dynamics of protonated water clusters by integrated multicenter molecular-orbital method

To analyze large-scale cluster systems theoretically, we recently developed an "integrated multicenter molecular-orbital" (IMiC-MO) method. This method calculates the force of an entire system by dividing the system into small regions. We used the method to analyze the effect of cluster size and the process of hydrogen bond network (HBN) growth to form H(+)(H(2)O)(n) (n = 9, 17, and 33) clusters. Our simulations reveal that H(3)O(+) and water molecules in the first solvation shell function take an important role to grow the HBN. In addition, the number of hydrogen donors in each water molecule is strongly related to the shape of the HBN.     

Ab initio study on the adsorption and dissociation process of methanol on a silver surface

The geometries of methanol adsorbed on an oxygen-free silver surface, a promoted silver surface and an oxygen preadsorbed silver surface were optimized at the MP2 level and the energies were calculated at the MP4 level. Our calculations showed that weak physisorption of methanol occurs on the clean silver surface, but stable molecular chemisorption occurs in the other two cases. The adsorption and dissociation process of methanol was postulated to occur via two pathways, i.e. the Eley-Rideal mode and the Langmuir-Hinshelwood mode. The calculations also showed that the presence of atomic oxygen at a silver surface is essential for the cleavage of the OH bond in the methanol. The dissociation of methanol in the Langmuir-Hinshelwood mode has a small energy barrier but has no energy barrier in the Eley-Rideal mode.     

Ab initio molecular orbital theory study of GaAs clusters: The geometry

We have studied the structure and geometry of neutral and charged atomic clusters consisting of Ga and As atoms via ab initio Hartree–Fock (HF) and second‐order Møller–Plesset methods. The Ga_mAs_n cluster with m≠n composition prefers a nontetrahedral geometry in the charge neutral (q=0) state. These clusters tend to be stable in tetrahedral geometry when appropriately charged. The Ga_mAs_n cluster with m=n composition (1:1 ratio of Ga to As atoms) tends to be stable in a tetrahedral geometry in the charge neutral (q=0) state. With increasing size of the cluster, the geometry of Ga_nAs_n cluster approaches the zinc‐belende‐type crystalline structure. © 2000 John Wiley & Sons, Inc. Int J Quant Chem 77: 563–573, 2000     

Ab initio study of molecular oxygen adsorption on Pu (111) surface

Using the generalized gradient approximation to density functional theory (DFT), molecular and dissociative oxygen adsorptions on a Pu (111) surface has been studied in detail. Dissociative adsorption with a layer‐by‐layer alternate spin arrangement of the plutonium layer is found to be energetically more favorable, and adsorption of oxygen does not change this feature. Hor1 (O₂ is parallel to the surface and lattice vectors) approach on the center2 (center of the unit cell, where there is a Pu atom directly below on the third layer) site, both without and with spin polarization, was found to be the preferred chemisorbed site among all cases studied with chemisorption energies of 8.365 and 7.897 eV, respectively. The second‐highest chemisorption energy occurs at the Ver (O₂ is vertical to the surface) approach of the bridge site with chemisorption energies of 8.294 eV (non‐spin‐polarized) and 7.859 eV (spin‐polarized), respectively. We find that 5f electrons are more localized in the spin‐polarized case than the non‐spin‐polarized counterparts. Localization of the 5f electrons is higher in the oxygen‐adsorbed plutonium layers compared with the bare layers. The ionic part of O? Pu bonding plays a significant role in the chemisorption process, along with Pu 5f? O 2p hybridization. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005     

Ab initio molecular dynamics study of the hydrolysis reaction of diborane

The hydrolysis reaction of the diborane molecule in aqueous solution has been studied by a series of Car-Parrinello Molecular Dynamics simulations in the Blue Moon Ensemble. The total reaction has been divided into two parts: one dealing with the breaking of B(2)H(6) molecule and the formation of a BH(4)(-) ion, a H(2)BOH molecule and a H(+) ion; the second leads to the formation of two hydrogen molecules and another H(2)BOH molecule, starting from BH(4)(-), two water molecules and a H(+) ion. The total reaction studied in this work has been B(2)H(6) + 2H(2)O --> 2H(2)BOH + 2H(2). We have described both structurally and electronically the reagents and the products through the radial distribution functions and the Wannier Function Center positions calculations, with attention to the solvent effects on the compounds. The free energy barrier value for the first part of the reaction and a detailed mechanisms for both parts have been reported. An interesting behavior of BH(3) and H(2) molecules in solution has been observed. They form a quite stable three center bond between the electron pair of the hydrogen molecule and the empty orbital of the boron atom in BH(3), which has been described from both a structural and electronic point of view.     

Local structure of liquid Ti: Ab initio molecular dynamics study

Local order of liquid Ti is studied by ab initio molecular dynamics to address the unique liquid structure factor in experiments reported recently. The present study reveals that the local order of liquid Ti is in the form of fragments of the distorted icosahedral short range order, where the distortion is induced by strong bond order effects. We show that the fragments in the short-bond rich region separated from the background liquid account for the pronounced feature in structure factor of liquid Ti.     

Ab initio static and molecular dynamics study of 4-styrylpyridine.

We report an in‐depth theoretical study of 4‐styrylpyridine in its singlet S₀ ground state. The geometries and the relative stabilities of the trans and cis isomers were investigated within density functional theory (DFT) as well as within Hartree–Fock (HF), second‐order Møller–Plesset (MP2), and coupled cluster (CC) theories. The DFT calculations were performed using the B3LYP and PBE functionals, with basis sets of different qualities, and gave results that are very consistent with each other. The molecular structure is thus predicted to be planar at the energy minimum, which is associated with the trans conformation, and to become markedly twisted at the minimum of higher energy, which is associated with the cis conformation. The results of the calculations performed with the post‐HF methods approach those obtained with the DFT methods, provided that the level of treatment of the electronic correlation is high enough and that sufficiently flexible basis sets are used. Calculations carried out within DFT also allowed the determination of the geometry and the energy of the molecule at the biradicaloid transition state associated with the thermal cis?trans isomerization and at the transition states associated with the enantiomerization of the cis isomer and with the rotations of the pyridinyl and phenyl groups in the trans and cis isomers. Car–Parrinello molecular dynamics simulations were also performed at 50, 150, and 300 K using the PBE functional. The studies allowed us to evidence the highly flexible nature of the molecule in both conformations. In particular, the trans isomer was found to exist mainly in a nonplanar form at finite temperatures, while the rotation of the pyridinyl ring in the cis isomer was incidentally observed to take place within ≈1 ps during the simulation carried out at 150 K on this isomer.     

Ab initio molecular dynamics simulation of ionic liquids

Ab initio Car-Parinnello molecular dynamics is used to simulate the structure and the dynamics of 1-butyl-3-methylimidazolium iodide ([bmim]I) ionic liquid at 300 K. Site-site pair correlation functions reveal that the anion has a strong interaction with any three C-H's of the imidazolium ring. The ring bends over and wraps around the anion such that the two nitrogen atoms take a distance to the anion. Electron donating butyl group contributes the electronic polarization in addition to geometrical (out-of-plane) polarization of the ring due to the liquid environment. This facilitates bending of the ring along the axis passing through nitrogen atoms. The average bending angle depends largely on the alkyl chain length and slightly on the anion type. Redistribution of electron density over the ring caused by the electron donating alkyl group provides additional independent evidence to the instability of lattice structure, hence the low melting point of the ionic liquid. Simulated viscosity and diffusion coefficients of [bmim]I are in quite agreement with the experiments.     

Ab initio SCF molecular dynamics: Exploring the potential energy surface of small silicon clusters

A few classical nuclear trajectories at finite temperature have been calculated from ab initio SCF energy gradients. They have been used as an alternative means to search for local minimum energy structures on the Born–Oppenheimer surfaces for some elemental silicon clusters. The approach is found to be beneficial in yielding different structures of silicon clusters. In other cases, the trajectories stay trapped in only one region of the phase space.     

Ab initio investigation of benzene clusters: molecular tailoring approach

An exhaustive study on the clusters of benzene (Bz)(n), n = 2-8, at MP2/6-31++G(??) level of theory is reported. The relative strengths of CH-π and π-π interactions in these aggregates are examined, which eventually govern the pattern of cluster formation. A linear scaling method, viz., molecular tailoring approach (MTA), is efficiently employed for studying the energetics and growth patterns of benzene clusters consisting up to eight benzene (Bz) units. Accuracy of MTA-based calculations is appraised by performing the corresponding standard calculations wherever possible, i.e., up to tetramers. For benzene tetramers, the error introduced in energy is of the order of 0.1 mH (～0.06 kcal/mol). Although for higher clusters the error may build up, further corrections based on many-body interaction energy analysis substantially reduce the error in the MTA-estimate. This is demonstrated for a prototypical case of benzene hexamer. A systematic way of building up a cluster of n monomers (n-mer) which employs molecular electrostatic potential of an (n-1)-mer is illustrated. The trends obtained using MTA method are essentially identical to those of the standard methods in terms of structure and energy. In summary, this study clearly brings out the possibility of effecting such large calculations, which are not possible conventionally, by the use of MTA without a significant loss of accuracy.     

Ab initio molecular dynamics using hybrid density functionals

Ab initio molecular dynamics simulations with hybrid density functionals have so far found little application due to their computational cost. In this work, an implementation of the Hartree-Fock exchange is presented that is specifically targeted at ab initio molecular dynamics simulations of medium sized systems. We demonstrate that our implementation, which is available as part of the CP2K/Quickstep program, is robust and efficient. Several prescreening techniques lead to a linear scaling cost for integral evaluation and storage. Integral compression techniques allow for in-core calculations on systems containing several thousand basis functions. The massively parallel implementation respects integral symmetry and scales up to hundreds of CPUs using a dynamic load balancing scheme. A time-reversible multiple time step scheme, exploiting the difference in computational efficiency between hybrid and local functionals, brings further time savings. With extensive simulations of liquid water, we demonstrate the ability to perform, for several tens of picoseconds, ab initio molecular dynamics based on hybrid functionals of systems in the condensed phase containing a few thousand Gaussian basis functions.     

Ab initio molecular dynamics study of H2 formation inside POSS compounds

The mechanism and dynamics of the formation of a hydrogen molecule by incorporating two hydrogen atoms in a stepwise manner into the cavity of some POSS (polyhedral oligomeric silsesquioxanes) compounds has been investigated by ab initio molecular orbital and ab initio molecular dynamics (AIMD) methods. The host molecules in the present reactions are two types of POSS, T(8) ([HSiO(1.5)](8)) and T(12)(D(2d)) ([HSiO(1.5)](12)). AIMD simulations were performed at the CASSCF level of theory, in which two electrons and two orbitals of the colliding hydrogen atoms are included in the active space. The trajectories were started by inserting the second hydrogen atom into the hydrogen atom-encapsulated-POSS (H + H@T(n) → H(2)@T(n); n = 8 and 12). In many cases, the gradual formation of a hydrogen molecule has been observed after frequent collisions of two hydrogen atoms within the cages. The effect of the introduction of an argon atom in T(12) is discussed as well.     

Ab initio molecular dynamics study of glycine intramolecular proton transfer in water

We use ab initio molecular-dynamics simulations to quantify structural and thermodynamic properties of a model proton transfer reaction that converts a neutral glycine molecule, stable in the gas phase, to the zwitterion that predominates in aqueous solution. We compute the potential of mean force associated with the direct intramolecular proton transfer event in glycine. Structural analyses show that the average hydration number (N(w)) of glycine is not constant along the reaction coordinate, but rather progresses from N(w) = 5 in the neutral molecule to N(w) = 8 for the zwitterion. We report the free-energy difference between the neutral and charged glycine molecules, and the free-energy barrier to proton transfer. Finally, we identify the approximations inherent in our method and estimate the corresponding corrections to our reported thermodynamic predictions.