Modeling a liquid crystal dynamics by atomistic simulation with an ab initio derived force field

Atomistic molecular dynamics (MD) simulations of 4-n-pentyl 4'-cyano-biphenyl (5CB) have been performed, adopting a specific ab initio derived force field. Two state points in the nematic phase and three in the isotropic phase, as determined in a previous work, have been considered. At each state point, at least 10 ns have been produced, allowing us to accurately calculate single-molecule properties. In the isotropic phase, the values of the translational diffusion coefficient, and even more so the activation energy for the process, agree well with experimental data. Qualitatively, also the dynamic anisotropy of the nematic phase is correctly accounted for. Rotational diffusion coefficients, which describe spinning and tumbling motions, fall well within the range of experimental values. The reorientational dynamics of our model 5CB covers diverse time regimes. The longest one is strongly temperature dependent and characterized by a relaxation time in accord with experimental dielectric relaxation data. Shear viscosity and Landau-de Gennes relaxation times, typically collective variables, reproduce the experimental results very well in the isotropic phase. In the nematic phase, despite a large statistical uncertainty due to the extremely slow relaxation of the correlation functions involved, our simulation yields the correct relative order of the three experimental Miesowicz viscosities.     

Adsorption isotherm and other properties of methane in zeolite A from an intermolecular potential derived from ab initio calculations

A classical Lennard-Jones potential is derived from a fit to the ab initio energies obtained from an all-electron mixed-basis calculation for methane in zeolite LTA. The potential predicts the heat of adsorption, adsorption isotherm, and self-diffusivity of methane in excellent agreement with experiment. This study suggests, for the first time, that ab initio energies-in addition to experimental data-can form a good basis for derivation of accurate classical potentials between organic and inorganic elements.     

An interaction potential between an alanine zwitterion and a water molecule based on ab initio calculations

Interaction energies between an alanine zwitterion and a water molecule at 150 different positions and orientations have been calculated using the ab initio method with the minimal basis set and employing the counterpoise method to eliminate the basis set superposition error. Dispersion energies are estimated using the Slater–Kirkwood formula. Out of a total of 150 computed interaction energies, 140 whose SCF interaction energies are below 5 kcal/mol have been fitted with a summation of atom-atom pair potentials in the form of the Lennard–Jones potential plus an electrostatic term. The standard deviation for this fitting is 0.49 kcal/mol. A sampling scheme regarding geometrical configurations is presented. Twenty rays are uniformly drawn from the origin of coordinates, a floatable division with equal ratios is made along each ray, and one of 60 orientations is randomly taken as the orientation of a water molecule. A nonlinear fitting method is used with a restriction on the sign change of fitting coefficients.     

Liquid crystal properties of the n-alkyl-cyanobiphenyl series from atomistic simulations with ab initio derived force fields

Lengthy molecular dynamics (MD) simulations were performed at constant atmospheric pressure and different temperatures for the series of the 4-n-alkyl-4'-cyanobiphenyls (nCB) with n = 6, 7, and 8. The accurate atomistic force field (Bizzarri, M.; Cacelli, I.; Prampolini, G; Tani, A. J. Phys. Chem. A 2004, 108, 10336), successfully employed to reproduce thermodynamic and transport properties of the 5CB molecule, has here been extended to higher homologues. Nematic and isotropic phases were found for all members of the series, and also, a smectic phase was (tentatively) identified for 8CB at 1 atm and 300 K. Transition temperatures reproduce the experimental values within +/-10 K. Also, structural properties as second and fourth rank orientational order parameters are in good agreement with the corresponding experimental quantities. This means that the well-known odd-even effect, observed for many properties along the nCB series, is well reproduced, despite the narrow range of oscillations, e.g., in clearing temperatures. A detailed analysis of the correlation between molecular properties and odd-even effects is presented.     

Reaction path potential for complex systems derived from combined ab initio quantum mechanical and molecular mechanical calculations

Combined ab initio quantum mechanical and molecular mechanical calculations have been widely used for modeling chemical reactions in complex systems such as enzymes, with most applications being based on the determination of a minimum energy path connecting the reactant through the transition state to the product in the enzyme environment. However, statistical mechanics sampling and reaction dynamics calculations with a combined ab initio quantum mechanical (QM) and molecular mechanical (MM) potential are still not feasible because of the computational costs associated mainly with the ab initio quantum mechanical calculations for the QM subsystem. To address this issue, a reaction path potential energy surface is developed here for statistical mechanics and dynamics simulation of chemical reactions in enzymes and other complex systems. The reaction path potential follows the ideas from the reaction path Hamiltonian of Miller, Handy and Adams for gas phase chemical reactions but is designed specifically for large systems that are described with combined ab initio quantum mechanical and molecular mechanical methods. The reaction path potential is an analytical energy expression of the combined quantum mechanical and molecular mechanical potential energy along the minimum energy path. An expansion around the minimum energy path is made in both the nuclear and the electronic degrees of freedom for the QM subsystem internal energy, while the energy of the subsystem described with MM remains unchanged from that in the combined quantum mechanical and molecular mechanical expression and the electrostatic interaction between the QM and MM subsystems is described as the interaction of the MM charges with the QM charges. The QM charges are polarizable in response to the changes in both the MM and the QM degrees of freedom through a new response kernel developed in the present work. The input data for constructing the reaction path potential are energies, vibrational frequencies, and electron density response properties of the QM subsystem along the minimum energy path, all of which can be obtained from the combined quantum mechanical and molecular mechanical calculations. Once constructed, it costs much less for its evaluation. Thus, the reaction path potential provides a potential energy surface for rigorous statistical mechanics and reaction dynamics calculations of complex systems. As an example, the method is applied to the statistical mechanical calculations for the potential of mean force of the chemical reaction in triosephosphate isomerase.     

Structure and dynamics of mesogens using intermolecular potentials derived from ab initio calculations

A method for the calculation of the two-body intermolecular potential which can be applied to large molecules is presented. Each monomer is fragmented in a number of moieties whose interaction energies are used to recover the interaction energy of the whole dimer. For these reasons this strategy has been called fragmentation reconstruction method (FRM). By a judicious choice of the fragmentation scheme it is shown that very accurate interaction energies can be obtained. The sampling of the potential energy surface of a dimer is then used to obtain intermolecular force fields at several levels of complexity, suitable to be employed in bulk phase computer simulations. Applications are presented for benzene and for some mesogenic molecules which constitute the principal interest of the authors. A number of properties ranging from phase stability, thermodynamic quantities, orientational order parameter and collective dynamics properties are computed and discussed.     

Monte Carlo simulation of liquid hydroxylamine using ab initio intermolecular potential functions

A potential model for intermolecular interactions between hydroxylamine (NH₂OH) molecules based on ab initio quantum mechanical calculations is reviewed and critically assessed by analyzing results from a Monte Carlo simulation of liquid hydroxylamine. The liquid structure is studied in detail using radial, energy, and angular distribution functions, coordination numbers, and their distribution. Results indicate a large first solvation shell (5.3 Å), which contains 13 molecules, out of which only 4 are truly bonded by nonlinear, low-energy hydrogen bonds. These are of either the OH…O or the OH…N type, as NH…O and NH…N linear bonds are considerably suppressed, and no cyclic dimers are found. The dependence of the structural and physical properties on the simulation characteristics has also been investigated.     

Viscosities of liquid CdTe near melting point from ab initio molecular-dynamics calculations

Recent experimental results for the viscosity of liquid CdTe exhibit disparate behavior as a function of temperature. While some measurements show the expected Arrhenius-type behavior, other measurements show an anomalous temperature dependence indicating an increase in viscosity with increasing temperature. We present ab initio molecular-dynamics simulations of liquid cadmium telluride near its melting point and use the Stokes-Einstein relation to extract values of the viscosity constant. We find no anomalous behavior; the viscosity decreases monotonically with temperature and is consistent with an Arrhenius like behavior. Although calculated values are slightly smaller than those measured, the predicted activation energy agrees well with experiment.     

Computer simulation of trifluoromethane properties with ab initio force field

Intermolecular interaction potentials of the trifluoromethane dimer in 15 orientations have been calculated using the Hartree‐Fock (HF) self‐consistent theory and the second‐order Møller‐Plesset (MP2) perturbation theory. Single point energies at important geometries were also calibrated by the coupled cluster with single and double and perturbative triple excitation [CCSD(T)] calculations. We have employed Pople's medium size basis sets [up to 6‐311++G(3df,3pd)] and Dunning's correlation consistent basis sets (up to aug‐cc‐pVQZ). Basis set limit potential values were obtained through well‐studied extrapolation methods. The calculated MP2 potential data were employed to parameterize a 5‐site force field for molecular simulations. We performed molecular dynamics simulations using the constructed ab initio force field and compared the simulation results with experiments. Quantitative agreements for the atom‐wise radial distribution functions and the self‐diffusion coefficients over a wide range of experimental conditions can be obtained, thus validating the ab initio force field without using experimental data a priori. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011     

Nuclear momentum distribution in solid and liquid HF from ab initio calculation

A calculation of nuclear momentum distribution of liquid and solid hydrogen fluoride was performed. In both systems, density functional theory generalized gradient approximation functional of Perdew, Burke, and Ernzerhof was used for the calculation: for liquid hydrogen fluoride, using an atom centered basis set for an isolated molecule with optimized geometry, and for solid hydrogen fluoride using plane-wave basis sets on optimized orthorhombic crystal cell. For liquid hydrogen fluoride, a semiclassical approach was adopted with the vibrational contribution to momentum distribution obtained from the density functional theory calculation and translational and rotational contributions calculated classically. Nuclear momentum distribution in the solid hydrogen fluoride was calculated entirely quantum mechanically using phonon dispersion and vibrational density of states calculated in the framework of plane-wave density functional theory. Theoretical results were contrasted with recently obtained results of Compton (deep inelastic) neutron scattering on liquid and solid hydrogen fluoride. In case of liquid hydrogen fluoride, almost a perfect agreement between theory and experiment was achieved within the harmonic Born-Oppenheimer approximation. For the solid system under investigation, the harmonic approximation leads to small (4%) overestimation of the square root of the second moment indicating that neutron Compton scattering technique is sensitive to proton delocalization due to hydrogen bonding in solid hydrogen fluoride.     

A re-interpretation of the UV-photoelectron spectra of dewar benzene,norbornadiene and barrelene by ab initio configuration interaction calculations

Ab initio configuration interaction calculations of the ground and cationic states of Dewar benzene, norbornadiene and barrelene have enabled a firm assignment of the uv-photoelectron spectra in the range 8–16 eV to be made. Many of the states are of Koopman's one-electron process type, and the order of states is close to that of the SCF double zeta ground state calculations. A number of shake-up doublet states were computed, and for barrelene at least, these appear from about 12 eV onwards; the lowest lying triplet and singlet states for barrelene were computed at 3.82 and 6.04 eV, respectively, and most of the low-lying shake-up states are related to this HOMO—LUMO pair of transitions.     

Structure change of liquid GaSb under pressure: an ab initio molecular-dynamics simulation

We have performed ab initio molecular-dynamics simulation of liquid GaSb (l-GaSb) up to 20.0 GPa. The calculated structure factors are consistent with the recent experimental results, and the partial structure parameters show that the structure of l-GaSb under pressure contracts nonuniformly. In the whole calculated pressure region, the contraction of l-GaSb can be divided into three substages: 1.8-5.4, 5.4-10.0, and 10.0-20.0 GPa. It is further confirmed by analyzing the bond-angle distributions of Ga-Ga-Ga and Sb-Sb-Sb that the rearrangement of Sb atoms under pressure plays a crucial role in the structure change of l-GaSb.     

Role of the exchange-correlation potential in ab initio electron transport calculations

The effect of the exchange-correlation potential in ab initio electron transport calculations is investigated by constructing optimized effective potentials using different energy functionals or the electron density from second-order perturbation theory. The authors calculate electron transmission through two atomic chain systems, one with charge transfer and one without. Dramatic effects are caused by two factors: changes in the energy gap and the self-interaction error. The error in conductance caused by the former is about one order of magnitude while that caused by the latter ranges from several times to two orders of magnitude, depending on the coupling strength and charge transfer. The implications for accurate quantum transport calculations are discussed.     

Q-branch linewidths of N2 perturbed by H2: experiments and quantum calculations from an ab initio potential

In this work the authors present an experimental and theoretical study about the Q-branch lines' broadening coefficients of N2 perturbed by H2. Experimental values for these parameters have been obtained at 440 and 580 K, and quantum calculations have been performed using a new ab initio potential energy surface, obtained by quantum chemistry methods. The results of these calculations are compared to experimental data obtained previously at 77 and 298 K [L. Gomez et al., Mol. Phys. 104, 1869 (2006)] and to the present measurements. A satisfactory agreement is obtained for the whole range of temperatures used in the experiments.     

Linewidths of C2H2 perturbed by H2: experiments and calculations from an ab initio potential

In this work we present a theoretical and experimental study of the acetylene-hydrogen system. A potential surface considering rigid monomers has been obtained by ab initio quantum chemistry methods. This 4-dimensional potential is further employed to compute, using the close-coupling approach and the coupled-states approximation, pressure broadening coefficients of C(2)H(2) isotropic Raman Q lines over a temperature range of 77 to 2000 K. Experimental data for the acetylene nu(2) Raman lines broadened by molecular hydrogen are obtained using stimulated Raman spectroscopy. The comparison of theoretical values with experimental data at 143 K is promising. Approximations to increase the computational efficiency are proposed.     

Heuristic intermolecular potential function for the methane–water interaction based on ab initio quantum-mechanical calculations

An analytical potential function for the pairwise interaction of methane and water is reported. The function is representative of 225 ab initio quantum-mechanical calculations of the intermolecular interaction using 6–31G self-consistent-field molecular-orbital theory. The statistical parameters of the curve fitting are given and isoenergy contour maps of the interaction energy are presented and discussed.     

The Rydberg states of trans-1,3-5-hexatriene from ab initio and configuration interaction calculations

Self-consistent ab initio and configuration interaction (CI) calculations are presented for the Rydberg states of the trans-1,3,5-hexatriene molecule. Seven Rydberg series were identified, four optically allowed (ns, nd _{s ²}, nd ₂₉) and three optically forbidden (np _z, np _y, np _z). These present results plus previous calculations on the valence states are used to assign the transitions observed in the ultraviolet (UV), electron-impact (EI) and two-photon spectra of this molecule.     

Ab initio CI calculations on benzene with an extended basis set

An extended basis set of triple zeta plus polarization quality is employed to carry out configuration interaction (CI ) calculations of the three lowest singlet and triplet excited states of benzene. The CI calculation is carried out by taking into account single and double excitations of π and σ electrons. In the CI , composite natural orbitals (CNO s), which are constructed from the natural orbitals of the ground state of ethylene, are used as virtual orbitals. The aim of using CNOs is to reduce the number of virtual orbitals to be used in constructing configuration-state functions, thus cutting down CI dimensions without losing reasonable accuracy. The excitation energies resulting from the CI are in fairly good agreement with experiment. The root mean square of the deviation is 0.22 eV for the six calculated energies and the largest disagreement is 0.37 eV for the third singlet excited state. To obtain better excitation energies by an ab initio calculation, it seems likely that we need to take into account more electron correlation than in the present calculation. © 1994 John Wiley & Sons, Inc.