Hierarchical description of protein structure fragments obtained from analyses of promolecular electron density distributions

Leherte, Laurence

doi:10.1107/s0108767304097715

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S2 Molecular Dynamics Simulations1

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Cited by 2 publications

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“…ED parameters w' a,i (no unit) and z' a,i (bohr -2 ) coefficients as obtained to fit the Cromer-Mann parameters. The mathematical relationships and the parameter values for the atom types C, N, O, and S are given in (Leherte, 2004).…”

Section: S2 Molecular Dynamics Simulationsmentioning

confidence: 99%

Investigation of bound and unbound phosphoserine phosphatase conformations through elastic network models and molecular dynamics simulations

Leherte

Haufroid

Mirgaux

2020

Journal of Biomolecular Structure and Dynamics

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Section: S2 Molecular Dynamics Simulationsmentioning

confidence: 99%

Investigation of bound and unbound phosphoserine phosphatase conformations through elastic network models and molecular dynamics simulations

Leherte

Haufroid

Mirgaux

2020

Journal of Biomolecular Structure and Dynamics

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To What Extent are “Atoms in Molecules” Structures of Hydrocarbons Reproducible from the Promolecule Electron Densities?

Keyvani

Shahbazian

Zahedi

2016

Chemistry A European J

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The "atoms in molecules" structures of 225 unsubstituted hydrocarbons are derived from both the optimized and the promolecule electron densities. A comparative analysis demonstrates that the molecular graphs derived from these two types of electron densities at the same geometry are equivalent for almost 90 % of the hydrocarbons containing the same number and types of critical points. For the remaining 10 % of molecules, it is demonstrated that by inducing small perturbations, through the variation of the used basis set or slight changes in the used geometry, the emerging molecular graphs from both densities are also equivalent. Interestingly, the (3, -1) critical point between two "non-bonded" hydrogen atoms, which triggered "H-H bonding" controversy is also observed in the promolecule densities of certain hydrocarbons. Evidently, the topology of the electron density is not dictated by chemical bonds or strong interactions and deformations induced by the interactions of atoms in molecules have a quite marginal role, virtually null, in shaping the general traits of the topology of molecular electron densities of the studied hydrocarbons, whereas the key factor is the underlying atomic densities.

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Hierarchical description of protein structure fragments obtained from analyses of promolecular electron density distributions

Cited by 2 publications

References 3 publications

Investigation of bound and unbound phosphoserine phosphatase conformations through elastic network models and molecular dynamics simulations

Investigation of bound and unbound phosphoserine phosphatase conformations through elastic network models and molecular dynamics simulations

To What Extent are “Atoms in Molecules” Structures of Hydrocarbons Reproducible from the Promolecule Electron Densities?

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