Molecular dynamics simulations of ion solvation by flexible-boundary QM/MM: On-the-fly partial charge transfer between QM and MM subsystems

2014 ◽  
Vol 35 (24) ◽  
pp. 1778-1788 ◽  
Author(s):  
Soroosh Pezeshki ◽  
Hai Lin
Keyword(s):  
Molecular Dynamics ◽  
Charge Transfer ◽  
Molecular Dynamics Simulations ◽  
Ion Solvation ◽  
Partial Charge ◽  
Partial Charge Transfer ◽  
Dynamics Simulations

scholarly journals The SAMPL4 hydration challenge: evaluation of partial charge sets with explicit-water molecular dynamics simulations

2014 ◽  
Vol 28 (3) ◽  
pp. 277-287 ◽  
Author(s):  
Hari S. Muddana ◽  
Neil V. Sapra ◽  
Andrew T. Fenley ◽  
Michael K. Gilson
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Partial Charge ◽  
Dynamics Simulations ◽  
Explicit Water

scholarly journals Atomistic mechanism of graphene growth on a SiC substrate: Large-scale molecular dynamics simulations based on a new charge-transfer bond-order type potential

2018 ◽  
Vol 97 (12) ◽  
Author(s):  
So Takamoto ◽  
Takahiro Yamasaki ◽  
Jun Nara ◽  
Takahisa Ohno ◽  
Chioko Kaneta ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Charge Transfer ◽  
Molecular Dynamics Simulations ◽  
Bond Order ◽  
Large Scale ◽  
Order Type ◽  
Graphene Growth ◽  
Dynamics Simulations ◽  
Type Potential

scholarly journals Ab initio molecular dynamics simulations of aluminum ion solvation in water clusters

2000 ◽  
Vol 322 (6) ◽  
pp. 447-453 ◽  
Author(s):  
M.I. Lubin ◽  
E.J. Bylaska ◽  
J.H. Weare
Keyword(s):  
Molecular Dynamics ◽  
Ab Initio ◽  
Molecular Dynamics Simulations ◽  
Water Clusters ◽  
Ion Solvation ◽  
Ab Initio Molecular Dynamics ◽  
Aluminum Ion ◽  
Dynamics Simulations

Molecular-dynamics simulations of solvent effects in the intramolecular charge transfer of 4-(N,N-dimethylamino)benzonitrile

2000 ◽  
Vol 2 (19) ◽  
pp. 4341-4353 ◽  
Author(s):  
Wibke Sudholt ◽  
Arnulf Staib ◽  
Andrzej L. Sobolewski ◽  
Wolfgang Domcke
Keyword(s):  
Molecular Dynamics ◽  
Charge Transfer ◽  
Molecular Dynamics Simulations ◽  
Solvent Effects ◽  
Intramolecular Charge Transfer ◽  
Dynamics Simulations

Ion solvation in polarizable water: molecular dynamics simulations

1991 ◽  
Vol 113 (7) ◽  
pp. 2481-2486 ◽  
Author(s):  
Liem X. Dang ◽  
Julia E. Rice ◽  
James Caldwell ◽  
Peter A. Kollman
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Ion Solvation ◽  
Dynamics Simulations

Multi-Million Atom Molecular-Dynamics Simulations of Stresses in Si(111)/Si3N4 Nanopixels

1999 ◽  
Vol 592 ◽  
Author(s):  
Martina E. Bachlechner ◽  
Andrey Omeltchenko ◽  
Phillip Walsh ◽  
Aiichiro Nakano ◽  
Rajiv K. Kalia ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Charge Transfer ◽  
Molecular Dynamics Simulations ◽  
Electronic Structure Calculations ◽  
Parallel Computers ◽  
Dynamics Simulations ◽  
Three Body ◽  
Stress Domains ◽  
Structure Calculations ◽  
Weber Potential

ABSTRACTThe stress distribution in Si(111)/Si3N4(0001) and Si(111)/a-Si3N4 nanopixels are studied using molecular dynamics simulations on parallel computers. Bulk Si is described by the Stillinger-Weber potential and Si3N4 is represented by a combination of two- and three-body interactions that include steric, charge transfer, polarizability and covalent forces. The charge transfer at the interface is extracted from self-consistent electronic structure calculations. The molecular dynamics simulations for Si(111)/a-Si3N4 nanopixels involve two pixel sizes: 25nm and 54 nm (the systems consist of 3.7 million and 10 million atoms, respectively). In both systems we find stress domains at the interface, which extend into the silicon substrate. The nature of the stress domains is discussed.

scholarly journals Electronic Circular Dichroism Spectra of DNA Quadruple Helices Studied by Molecular Dynamics Simulations and Excitonic Calculations Including Charge Transfer States

Molecules ◽  
2021 ◽  
Vol 26 (16) ◽  
pp. 4789
Author(s):  
Haritha Asha ◽  
James A. Green ◽  
Lara Martinez-Fernandez ◽  
Luciana Esposito ◽  
Roberto Improta
Keyword(s):  
Molecular Dynamics ◽  
Circular Dichroism ◽  
Charge Transfer ◽  
Molecular Dynamics Simulations ◽  
Thermal Fluctuations ◽  
Telomeric Sequence ◽  
Quadruple Helix ◽  
Electronic Circular Dichroism ◽  
Dynamics Simulations ◽  
Circular Dichroïsm

We here investigate the Electronic Circular Dichroism (ECD) Spectra of two representative Guanine-rich sequences folded in a Quadruple helix (GQ), by using a recently developed fragment diabatisation based excitonic model (FrDEx). FrDEx can include charge transfer (CT) excited states and consider the effect of the surrounding monomers on the local excitations (LEs). When applied to different structures generated by molecular dynamics simulations on a fragment of the human telomeric sequence (Tel21/22), FrDEx provides spectra fully consistent with the experimental one and in good agreement with that provided by quantum mechanical (QM) method used for its parametrization, i.e., TD-M05-2X. We show that the ECD spectrum is moderately sensitive to the conformation adopted by the bases of the loops and more significantly to the thermal fluctuations of the Guanine tetrads. In particular, we show how changes in the overlap of the tetrads modulate the intensity of the ECD signal. We illustrate how this correlates with changes in the character of the excitonic states at the bottom of the La and Lb bands, with larger LE and CT involvement of bases that are more closely stacked. As an additional test, we utilised FrDEx to compute the ECD spectrum of the monomeric and dimeric forms of a GQ forming sequence T30695 (5’TGGGTGGGTGGGTGGG3’), i.e., a system containing up to 24 Guanine bases, and demonstrated the satisfactory reproduction of the experimental and QM reference results. This study provides new insights on the effects modulating the ECD spectra of GQs and, more generally, further validates FrDEx as an effective tool to predict and assign the spectra of closely stacked multichromophore systems.

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