Car-Parrinello Molecular Dynamics Calculations Research Articles

Circumambulatory Rearrangement with Characteristics of a 2:1 Covalent Molecular Bevel Gear

anti-W(CO)(5)-complexed 9-methyl-9-phosphabicyclo[6.1.0]nonatriene represents a covalently interlocked molecular bevel gear. Correlated movement of the phosphorus atom and the eight-membered ring by way of a "walk" rearrangement makes gear slippage impossible. The gearing motion is transferred to the four-toothed W(CO)(5) propeller connected to the rotating phosphorus atom, enabling a gearing ratio of 2:1 according to B3LYP and Car-Parrinello Molecular Dynamics calculations. Methyl substitution of the eight-membered ring tempers the gearing process, with the PMeW(CO)(5) entity passing the substituted carbon atom only at temperatures above 50 degrees C.

The Isobutylene−Isobutane Alkylation Process in Liquid HF Revisited

Details on the mechanism of HF catalyzed isobutylene-isobutane alkylation were investigated. On the basis of available experimental data and high-level quantum chemical calculations, a detailed reaction mechanism is proposed taking into account solvation effects of the medium. On the basis of our computational results, we explain why the density of the liquid media and stirring rates are the most important parameters to achieve maximum yield of alkylate, in agreement with experimental findings. The ab initio Car-Parrinello molecular dynamics calculations show that isobutylene is irreversibly protonated in the liquid HF medium at higher densities, leading to the ion pair formation, which is shown to be a minimum on the potential energy surface after optimization using periodic boundary conditions. The HF medium solvates preferentially the fluoride anion, which is found as solvated [FHF](-) or solvated F(-.)(HF)(3). On the other hand, the tert-butyl cation is weakly solvated, where the closest HF molecules appear at a distance of about 2.9 Angstrom with the fluorine termination of an HF chain.

Dual-resolution coarse-grained simulation of the bisphenol-A-polycarbonate/nickel interface.

We present a dual-resolution coarse-graining scheme for efficient molecular dynamics simulations of bisphenol-A-polycarbonate (BP-A-PC) liquids in contact with a (111) nickel surface. The essential feature of this model is the strong adsorption of phenoxy chain ends, and the absence of adsorption by other parts of the chains. Details of how phenoxy chain ends interact with the nickel surface were extracted from Car-Parrinello molecular dynamics calculations of adsorption of phenol on nickel. These calculations show that phenol adsorption on nickel is short ranged (<3 A) and strongly dependent on the C1-C4 orientation of the ring. The structure of BP-A-PC prevents internal phenylene groups from interacting with the surface, due to steric hindrances from the noninteracting isopropylidenes. These dependencies are incorporated in the coarse-grained model of the BP-A-PC chain by resolving chain-terminating carbonate groups with atomistic detail, while the rest of the chain is represented by coarsened "beads." This allows specification of the C1-C4 orientation of the terminal phenoxy groups, while overall allowing for system equilibration with reasonable computer time. We simulate liquids of up to 240 chains of ten chemical repeat units, confined in a slit pore formed by two frozen (111) planes of atoms with the lattice spacing of nickel. We find that the strong adsorption of chain ends has a large effect on the liquid structure through a distance of more than two bulk radii of gyration from the surface. These effects are explained by a competition among single- and double-end adsorption, and dense packing. The structure of the interface less than 10 A from the wall is greatly sensitive to the orientational dependence of the phenoxy adsorption.

Proton tunneling in fatty acid/soap crystals?

Fatty acids and acid/soap crystals have a bilayer structure, which is held together by hydrogen bonding between head groups. The present ab initio Car–Parrinello molecular dynamics calculations suggest that proton tunneling or sharing along such hydrogen bonds could be the key structural features in the acid/soap crystal but not in the pure acid. This effect seems to be due to sodium cations, which induce a dramatic shortening of the hydrogen bond and its signature should be visible in the experimental vibrational spectra.

The inelastic incoherent neutron spectrum of crystalline oxamide: experiment and simulation of a solid

The inelastic neutron scattering spectrum of crystalline oxamide, CO(NH 2)–CO(NH 2), is reported and compared with the results of Hartree–Fock and density functional theory calculations on a pentamer cluster model and the results of Car–Parrinello molecular dynamics calculations for the periodic crystal. All four hydrogen atoms of this centrosymmetric, planar sheet molecular crystal are involved in CO–H–N hydrogen bonds. It is shown that all three of these simulations provide reasonable descriptions of the inelastic neutron scattering spectra and thus of the hydrogen bond dynamics. There is no evidence for unusual structural or dynamic effects beyond those typically associated with H-bond formation. It is argued that a polymolecular approach is needed in order to provide an adequate treatment of such strongly hydrogen bonded systems.

Structural and dynamical behavior of an azide anion in water from ab initio molecular dynamics calculations

The solvation of an azide anion in deuterated water has been investigated using density functional theory based Car–Parrinello molecular dynamics calculations. The first solvation shell of the anion was found to contain between five and six hydrogen bonded water molecules, compared to the six to seven waters found in analogous classical studies based on empirical potentials. The stretching modes of the azide ion in solution and in the gas phase are both red shifted by more than 10% compared to experiment. In agreement with inferences from experiment, the asymmetric ν 3 mode of azide in solution relaxes on a picosecond time scale. The calculated solvent shift of this mode is about +80 cm −1 , which is somewhat greater than the measured value of +57 cm −1 .

Structure of phosphorus-selenium glasses: results from ab initio molecular dynamics simulations

Car-Parrinello molecular dynamics calculations have been carried out for phosphorus-selenium mixtures of compositions corresponding to overall stoichiometrics PSe and P2Se. Comparison of the calculated structure factors with those obtained in neutron scattering experiements suggests that the real materials are characterized by the presence of substantial numbers of well defined molecular units.

Ab Initio Molecular Dynamics Study of Crystalline Nitric Acid Trihydrate

Ab initio based Car-Parrinello molecular dynamics calculations (CPMD) have been used to investigate the properties of crystalline nitric acid trihydrate (NAT) at 195 K. The crystal unit cell consists of four formula units of NAT and nominally contains the ions NO3- and H3O+ plus H2O molecules. Reversible proton-transfer events were observed between unique H3O+ and neighboring H2O pairs, which occur throughout the crystal. Full proton transfer to form a new neighboring H3O+ molecule was a rare event. The motion of this mobile proton was associated with hyperextension of the covalent oxygen−hydrogen of H3O+, whose stretch frequency was observed in corresponding power spectra. Calculations showed that a classical free energy of 3.3 kBT was required for the proton to reach the center of the oxygen−oxygen pair. Crystalline NAT was further characterized by calculated equilibrium averages, structural properties, and vibrational spectra.

Static and ab Initio Molecular Dynamics Study of the Titanium(IV)-Constrained Geometry Catalyst (CpSiH2NH)Ti-R+. 2. Chain Termination and Long Chain Branching

We present a comprehensive survey of chain termination and long chain branching processes for the “constrained-geometry” olefin polymerization catalyst (CpSiH2NH)Ti-R+ (R = ethyl, propyl) based on static and dynamic density functional theory. Car-Parrinello molecular dynamics calculations are used to locate reaction pathways and estimate free energies of activation, and conventional static calculations are used to ascertain stationary points and relative energies. We have examined three distinct chain termination processes: (a) β-hydrogen transfer to the monomer, (b) β-hydrogen transfer to the metal, and (c) olefin C−H σ-bond metathesis. We find alternative (a) to be the most viable one [ΔH⧧el(R = ethyl) = 32 kJ/mol; ΔF⧧(R = ethyl) = 40.1; ΔF⧧(R = propyl) = 43 ± 8 kJ/mol at 300 K], whereas pathways (b) [ΔH⧧el(R = propyl) = 67; ΔF⧧(R = propyl) = 57 ± 3 at 300 K] and (c) [ΔH⧧el(R = ethyl) = 93; ΔF⧧(R = ethyl) = 91.7 kJ/mol; ΔF⧧(R = propyl) = 87 ± 5 at 300 K] have much higher activation barriers. In addition, we investigated an unconventional long chain branching mechanism (d), where a polymer chain binds to the metal center in an η2-agostic fashion via aliphatic hydrogens, followed by activation of one aliphatic C−H bond and transfer of the hydrogen to the α-carbon (σ-bond metathesis). For this process we have found a large electronic barrier of ΔH⧧el(R = ethyl) = 77 kJ/mol and a free energy barrier of ΔF⧧(R = ethyl) = 72.3 kJ/mol; ΔF⧧(R = propyl) = 70 ± 3 kJ/mol at 300 K. On the basis of our data, we favor the conventional long chain branching mechanism consisting of chain termination via mechanism (a) to produce a vinyl-terminated chain and reincorporation of the terminated chain into the polymer. In this study we have calculated free energy barriers for each of the aforementioned processes by a conventional static calculations and by a Car-Parrinello “first principles” molecular dynamics simulations. The agreement of the two methods is exceptional, demonstrating utility of first principles molecular dynamics to determine free energy barriers.

Supercell calculation of relaxation at the vacancy in diamond

Supercells consisting of 63 and 64 atoms are used to evaluate lattice relaxation at the vacancy in diamond using plane waves with soft and hard pseudopotentials. Car-Parrinello molecular dynamics calculations are undertaken allowing both nearest neighbour and second nearest neighbour atoms to move. Results are compared with static calculations where only the nearest atoms to the vacancy move.

First-principles simulation of phosphorus-selenium systems

Car-Parrinello molecular dynamics calculations have been carried out for a single P 4Se 3 molecule and for an amorphous system of 72 atoms of overall stoichiometry P 2Se. A systematic study has been made of the effects of variation in the basis set energy cutoff on the calculated bond lengths and vibrational frequencies of the isolated molecule. We find that when a sufficiently large cutoff is used the calculated values are in good agreement with experiment. The simulation of the amorphous system was initiated from a configuration consisting of eight P 4Se 3 molecules and 16 added phosphorus atoms, prepared by a classical molecular dynamics calculation. After a total of approximately 10 ps Car-Parrinello simulation, only two molecules remained intact, but a variety of other partly ordered local structures were generated, including rings of phosphorus atoms and distorted versions of the P 4Se 3 molecule in which bonds between basal phosphorus atoms had broken.

Method of Car-Parrinello Molecular Dynamics Calculations with Conservation of Total Energy

A method is presented to carry out molecular dynamics calculations with the optimized electron configuration at each time step and with the conservation of the total energy of the system of atoms. Although an example of calculations within the tight-binding approximation is presented, the method can also be used in ab initio calculations. A method to obtain each eigenstate of the one-electron hamiltonian by the use of the steepest-descent equation of motion is also presented. Moreover, a feature of the flow of the electron configuration in the configuration space which is governed by the steepest-descent equation of motion is discussed.