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 molecular dynamics simulation of a room temperature ionic liquid

Ab initio molecular dynamics simulations have been performed for the first time on the room-temperature organic ionic liquid dimethyl imidazolium chloride [DMIM][Cl] using density functional theory. The aim is to compare the local liquid structure with both that obtained from two different classical force fields and from neutron scattering experiments. The local structure around the cation shows significant differences compared to both the classical calculations and the neutron results. In particular, and unlike in the gas-phase ion pair, chloride ions tend to be located near a ring C-H proton in a position suggesting hydrogen bonding. The results are used to suggest ways in which the classical potentials may be improved.     

Ab initio molecular dynamics simulations of local structure of supercooled Ni

We report results of first-principles molecular dynamics simulations for stable and undercooled nickel liquids. The calculated structure factors as a function of temperature are discussed with respect to recent experimental measurements. In addition, structural analysis using bonding orientational order and three-dimensional pair analysis techniques have been performed in detail and the effect of undercooling on the microstructure has been analyzed. More particularly, we show the importance of fivefold symmetry local structures.     

Ab initio folding of helix bundle proteins using molecular dynamics simulations

We have demonstrated that ab initio fast folding simulations at 400 K using a GB implicit solvent model with an all-atom based force field can describe the spontaneous formation of nativelike structures for the 36-residue villin headpiece and the 46-residue fragment B of Staphylococcal protein A. An implicit solvent model combined with high-temperature MD makes it possible to perform direct folding simulations of small- to medium-sized proteins by reducing the computational requirements tremendously. In the early stage of folding of the villin headpiece and protein A, initial hydrophobic collapse and rapid formation of helices were found to play important roles. For protein A, the third helix forms first in the early stage of folding and exhibits higher stability. The free energy profiles calculated from the folding simulations suggested that both of the helix-bundle proteins show a two-state thermodynamic behavior and protein A exhibits rather broad native basins.     

Ab initio based force field and molecular dynamics simulations of crystalline TATB

An all-atom force field for 1,3,5-triamino-2,4,6-trinitrobenzene (TATB) is presented. The classical intermolecular interaction potential for TATB is based on single-point energies determined from high-level ab initio calculations of TATB dimers. The newly developed potential function is used to examine bulk crystalline TATB via molecular dynamics simulations. The isobaric thermal expansion and isothermal compression under hydrostatic pressures obtained from the molecular dynamics simulations are in good agreement with experiment. The calculated volume-temperature expansion is almost one dimensional along the c crystallographic axis, whereas under compression, all three unit cell axes participate, albeit unequally.     

Ab initio molecular dynamics simulations of the Li4F4 cluster

Molecular dynamics simulations have been performed directly on the ab initio potential energy surface of Li₄F₄, which was generated within the Hartree-Fock approximation using a Gaussian basis set (split valence contraction). Trajectories at different temperatures yield the temperature dependence of the infrared spectra and the photoelectron spectra. For the infrared spectra comparison is made with MD results using a shell model ion pair potential function.     

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 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 simulations of the liquid/vapor interface of sulfuric acid solutions

Ab initio molecular dynamics simulations of the liquid-vapor interface are presented for thin slabs of 72 water molecules containing a single molecule of sulfuric acid. Trajectories in the 306-330 K range are calculated for two functionals with double- and triple-ζ quality basis sets. Comparisons are made between BLYP and HCTH/120 results for the slab simulations and for bulk simulations of one H(2)SO(4) in a periodic box with 63 waters. Good agreement is found with the available experimental data and the results of other relevant AIMD studies with respect to ionization of the acid, size of the coordination shells, partitioning of the ions with the hydronium exhibiting a surface preference and the anions in the interior, and the orientational distributions for the hydronium ions and for the surface/subsurface water molecules. The major differences in the performance of the two functionals are attributable to the greater basicity of the anion oxygen atoms with the HCTH functional and the more structured aqueous solution with BLYP. The enhanced basicity results in larger aqueous coordination shells for the anion oxygens. The structuring of the BLYP aqueous solution is observed in the corrugation of the water density profile, the higher first peak in g(OO)(r), and a smaller water self-diffusion constant. This structuring with the BLYP functional yields anion hydrogen bonds that endure longer and where the dissociated ions more rapidly and directly segregate in the slab. The simulations indicate that aqueous surfaces containing ionizable diprotic acids can be modeled with rather modest sized systems and be informative.     

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 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 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 molecular dynamics of liquid 1,3-dimethylimidazolium chloride

Density-functional-based Car-Parrinello molecular dynamics (CPMD) simulations have been performed for the ionic liquid 1,3-dimethylimidazolium chloride, [dmim]Cl, at 438 K. The local structure of the liquid is described in terms of various partial radial distribution functions and anisotropic spatial distributions, which reveal a significant extent of hydrogen bonding. The cation-anion distribution simulated with the BP86 functional is in qualitative agreement with the structural model derived from neutron diffraction data for the liquid, whereas the theoretical cation-cation distribution shows less satisfactory accord. Population analyses indicate noticeable charge transfer from anions to cations, and specific CH...Cl hydrogen bonds are characterized in terms of donor-acceptor interactions between lone pairs on Cl and antibonding sigma(CH) orbitals.     

Ab initio molecular dynamics of heme in cytochrome c

Ab initio molecular dynamics (AIMD) calculations, based on the Car-Parrinello method, have been carried out for three models of heme c that is present in cytochrome c. Both the reduced (Fe(II)) and oxidized (Fe(III)) forms have been analyzed. The simplest models (1R and 1O, respectively) consist of a unsubstituted porphyrin (with no side chains) and two axially coordinated imidazole and ethylmethylthioether ligands. Density functional theory optimizations of these models confirm the basic electronic features and are the starting point for building more complex derivatives. AIMD simulations were performed after reaching the thermal stability at T = 300 K. The evolution of the Fe-L(ax) bond strengths is examined together with the relative rotations of the imidazole and methionine about the axial vector, which appear rather independent from each other. The next models (2R and 2O) contain side chains at the heme to better simulate the actual active site. It is observed that two adjacent propionate groups induce some important effects. The axial Fe-Sdelta bond is only weakened in 2R but is definitely cleaved in the oxidized species 2O. Also the mobility of the Im ligand seems to be reduced by the formation of a strong hydrogen bond that involves the Im Ndelta1-Hdelta1 bond and one carboxylate group. In 2O the interaction becomes so strong that a proton transfer occurs and the propionic acid is formed. Finally, the models 3 include a free N-methyl-acetamide molecule to mimic a portion of the protein backbone. This influences the orientation of carboxylate groups and limits the amount of their hydrogen bonding with the Im ligand. Residual electrostatic interactions are maintained, which are still able to modulate the dissociation of the methionine from the heme.     

Ab initio molecular dynamics with dual basis set methods

On-the-fly, ab initio classical molecular dynamics are demonstrated with an underlying dual basis set potential energy surface. Dual-basis self-consistent field (Hartree-Fock and density functional theory) and resolution-of-the-identity second-order M?ller-Plesset perturbation theory (RI-MP2) dynamics are tested for small systems, including the water dimer. The resulting dynamics are shown to be faithful representations of their single-basis analogues for individual trajectories, as well as vibrational spectra. Computational cost savings of 58% are demonstrated for SCF methods, even relative to Fock-extrapolated dynamics, and savings are further increased to 71% with RI-MP2. Notably, these timings outperform an idealized estimate of extended-Lagrangian molecular dynamics. The method is subsequently demonstrated on the vibrational absorption spectrum of two NO(+)(H?O)? isomers and is shown to recover the significant width of the shared-proton bands observed experimentally.     

Ab initio pair potentials for the ionic lithium-formate system

The potential energy surfaces for the interatomic interaction in the Li⁺HCOO^– system have been investigated byab initio methods within the rigid-molecule approximation. Analytical potential expressions were fitted to 133 calculated SCF energies for the Li⁺-HCOO^– interaction, 42 SCF energies for the Li⁺-Li⁺ interaction, and 332 SCF energies for the HCOO^–-HCOO^– interaction. The global minimum on the Li⁺-HCOO^– surface is –170 kcal/mol and corresponds to the lithium ion lying on the C₂ axis of the formate ion at 2.2 Å from the carbon atom on the oxygen side. The cation-cation and anion-anion interactions are repulsive everywhere, although the potential surface is markedly anisotropic for the HCOO^–-HCOO^– interaction.     

Molecular dynamics simulations of the surface tension of ionic liquids

We report molecular dynamics computer simulations of the surface tension and interfacial thickness of ionic liquid-vapor interfaces modeled with a soft core primitive model potential. We find that the surface tension shows an anomalous oscillatory behavior with interfacial area. This observation is discussed in terms of finite size effects introduced by the periodic boundary conditions employed in computer simulations. Otherwise we show that the thickness of the liquid-vapor interface increases with surface area as predicted by the capillary wave theory. Data on the surface tension of size-asymmetric ionic liquids are reported and compared with experimental data of molten salts. Our data suggest that the surface tensions of size-asymmetric ionic liquids do not follow a corresponding states law.     

Ab initio molecular dynamics simulation of a water-hydrogen fluoride equimolar mixture.

Hydrogen fluoride and water can be mixed in any proportion. The resulting solutions have unique acidic properties. In particular, hydrogen fluoride undergoes a weak-to-strong acidity transition with increasing concentration of HF To supplement the knowledge already obtained on dilute or moderately concentrated solutions and gas-phase aggregates, an equimolar mixture is studied here by Car-Parrinello molecular dynamics. The natures of the ions and of the complexes formed in the equimolar liquid were determined. Specifically, H3O+, H5O2+, FH-OH2, and HF2- were spontaneously obtained while only hydronium and fluoride ions pre-exist in the equimolar crystal. The behaviour of the proton in the equimolar liquid was compared with mixtures of other proportions simulated previously in an attempt to relate proton dynamics to acidity. In the same way, the behaviour of HF2- was also examined. In this case, proton localization and transfer appeared to be driven by the fluctuating environment of the solvated ion.     

Ab initio Ehrenfest dynamics

We present an ab initio direct Ehrenfest dynamics scheme using a three time-step integrator. The three different time steps are implemented with nuclear velocity Verlet, nuclear-position-coupled midpoint Fock integrator, and time-dependent Hartree-Fock with a modified midpoint and unitary transformation algorithm. The computational cost of the ab initio direct Ehrenfest dynamics presented here is found to be only a factor of 2-4 larger than that of Born-Oppenheimer (BO) dynamics. As an example, we compute the vibration of the NaCl molecule and the intramolecular torsional motion of H2C=NH2+ by Ehrenfest dynamics compared with BO dynamics. For the vibration of NaCl with an initial kinetic energy of 1.16 eV, Ehrenfest dynamics converges to BO dynamics with the same vibrational frequency. The intramolecular rotation of H2C=NH2+ produces significant electronic excitation in the Ehrenfest trajectory. The amount of nonadiabaticity, suggested by the amplitude of the coherent progression of the excited and ground electronic states, is observed to be directly related to the strength of the electron-nuclear coupling. Such nonadiabaticity is seen to have a significant effect on the dynamics compared with the adiabatic approximation.