Intermolecular diatomic energies of a hydrogen dimer with non-Born–Oppenheimer nuclear and electron wave packets

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mentioning

confidence: 83%

“…12 In this Communication, we extend it to a real-time condensed-phase simulation method of nuclear and electron wave packet molecular dynamics (NEWPMD) for liquid p-H 2 .…”

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confidence: 99%

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Communication: Quantum molecular dynamics simulation of liquid para-hydrogen by nuclear and electron wave packet approach

Hyeon‐Deuk

Ando

2014

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“…The combination of EWP and PP VB has been demonstrated to yield accurate potential energy curves for H 2 , LiH, CH 2 , and H 2 O. [12][13][14] We start by considering a H 2 dimer and denote the four electrons (4e) by a, b, c, and d, and the four nuclei (4n) by A, B, C, and D. Here, the nuclei (A, B) and electrons (a, b) form one hydrogen molecule, while the remaining (C, D) and (c, d) compose another hydrogen molecule. The time-dependent total wave function ψ(t), where the EWP pairs (a, b) and (c, d) are coupled in the singlet configuration, is introduced as…”

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confidence: 99%

Investigations of α-helix↔β-sheet transition pathways in a miniprotein using the finite-temperature string method

Ovchinnikov

Karplus

2014

A parallel implementation of the finite-temperature string method is described, which takes into account the invariance of coordinates with respect to rigid-body motions. The method is applied to the complex α-helix↔β-sheet transition in a β-hairpin miniprotein in implicit solvent, which exhibits much of the complexity of conformational changes in proteins. Two transition paths are considered, one derived from a linear interpolant between the endpoint structures and the other derived from a targeted dynamics simulation. Two methods for computing the conformational free energy (FE) along the string are compared, a restrained method, and a tessellation method introduced by E. Vanden-Eijnden and M. Venturoli [J. Chem. Phys. 130, 194103 (2009)]. It is found that obtaining meaningful free energy profiles using the present atom-based coordinates requires restricting sampling to a vicinity of the converged path, where the hyperplanar approximation to the isocommittor surface is sufficiently accurate. This sampling restriction can be easily achieved using restraints or constraints. The endpoint FE differences computed from the FE profiles are validated by comparison with previous calculations using a path-independent confinement method. The FE profiles are decomposed into the enthalpic and entropic contributions, and it is shown that the entropy difference contribution can be as large as 10 kcal/mol for intermediate regions along the path, compared to 15–20 kcal/mol for the enthalpy contribution. This result demonstrates that enthalpic barriers for transitions are offset by entropic contributions arising from the existence of different paths across a barrier. The possibility of using systematically coarse-grained representations of amino acids, in the spirit of multiple interaction site residue models, is proposed as a means to avoid ad hoc sampling restrictions to narrow transition tubes.

“…11 We recently proposed a simulation method of nuclear and electron wave packet molecular dynamics (NEWPMD) based on non-empirical ab initio intra-and inter-molecular interactions of non-spherical hydrogen molecules where a) kim@kuchem.kyoto-u.ac.jp important NQEs of a hydrogen nucleus are non-perturbatively taken into account. [25][26][27] It reproduces the long-range dispersion interaction depending on an intermolecular angle and thus gives the correct structures and transport properties such as diffusion coefficients and viscosities of liquid H 2 under vapor pressure without any empirical parameters. 25,26 This paper reports the first study with the NEWPMD method on real-time dynamics of low-pressure H 2 molecular solids.…”

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confidence: 99%

Communication: Dynamical and structural analyses of solid hydrogen under vapor pressure

Hyeon‐Deuk

Ando

2015

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Nuclear quantum effects play a dominant role in determining the phase diagram of H2. With a recently developed quantum molecular dynamics simulation method, we examine dynamical and structural characters of solid H2 under vapor pressure, demonstrating the difference from liquid and high-pressure solid H2. While stable hexagonal close-packed lattice structures are reproduced with reasonable lattice phonon frequencies, the most stable adjacent configuration exhibits a zigzag structure, in contrast with the T-shape liquid configuration. The periodic angular distributions of H2 molecules indicate that molecules are not a completely free rotor in the vapor-pressure solid reflecting asymmetric potentials from surrounding molecules on adjacent lattice sites. Discrete jumps of librational and H–H vibrational frequencies as well as H–H bond length caused by structural rearrangements under vapor pressure effectively discriminate the liquid and solid phases. The obtained dynamical and structural information of the vapor-pressure H2 solid will be useful in monitoring thermodynamic states of condensed hydrogens.