Molecular Dynamics Study and Electronic Structure Evolution of a DNA Duplex d(CCCGATCGGG)2

2011 ◽  
Vol 115 (8) ◽  
pp. 1760-1766 ◽  
Author(s):  
Basab Chattopadhyay ◽  
Monika Mukherjee
Keyword(s):  
Molecular Dynamics ◽  
Electronic Structure ◽  
Structure Evolution ◽  
Dna Duplex

scholarly journals Sensitivity of Intra- and Intermolecular Interactions of Benzo[h]quinoline from Car–Parrinello Molecular Dynamics and Electronic Structure Inspection

2021 ◽  
Vol 22 (10) ◽  
pp. 5220
Author(s):  
Jarosław J. Panek ◽  
Joanna Zasada ◽  
Bartłomiej M. Szyja ◽  
Beata Kizior ◽  
Aneta Jezierska
Keyword(s):  
Molecular Dynamics ◽  
Electronic Structure ◽  
Hydrogen Bonds ◽  
Density Functional ◽  
Quantum Effects ◽  
Potential Of Mean Force ◽  
Probability Density Distribution ◽  
Donor And Acceptor ◽  
Nuclear Quantum Effects ◽  
Vibrational Features

The O-H...N and O-H...O hydrogen bonds were investigated in 10-hydroxybenzo[h]quinoline (HBQ) and benzo[h]quinoline-2-methylresorcinol complex in vacuo, solvent and crystalline phases. The chosen systems contain analogous donor and acceptor moieties but differently coupled (intra- versus intermolecularly). Car–Parrinello molecular dynamics (CPMD) was employed to shed light onto principle components of interactions responsible for the self-assembly. It was applied to study the dynamics of the hydrogen bonds and vibrational features as well as to provide initial geometries for incorporation of quantum effects and electronic structure studies. The vibrational features were revealed using Fourier transformation of the autocorrelation function of atomic velocity and by inclusion of nuclear quantum effects on the O-H stretching solving vibrational Schrödinger equation a posteriori. The potential of mean force (Pmf) was computed for the whole trajectory to derive the probability density distribution and for the O-H stretching mode from the proton vibrational eigenfunctions and eigenvalues incorporating statistical sampling and nuclear quantum effects. The electronic structure changes of the benzo[h]quinoline-2-methylresorcinol dimer and trimers were studied based on Constrained Density Functional Theory (CDFT) whereas the Electron Localization Function (ELF) method was applied for all systems. It was found that the bridged proton is localized on the donor side in both investigated systems in vacuo. The crystalline phase simulations indicated bridged proton-sharing and transfer events in HBQ. These effects are even more pronounced when nuclear quantization is taken into account, and the quantized Pmf allows the proton to sample the acceptor area more efficiently. The CDFT indicated the charge depletion at the bridged proton for the analyzed dimer and trimers in solvent. The ELF analysis showed the presence of the isolated proton (a signature of the strongest hydrogen bonds) only in some parts of the HBQ crystal simulation. The collected data underline the importance of the intramolecular coupling between the donor and acceptor moieties.

Enhanced Fast Response to Hg0 by Adsorption-Induced Electronic Structure Evolution of Ti2C Nanosheet

2021 ◽  
pp. 148925
Author(s):  
Tao Yang ◽  
Xingang Jiang ◽  
Wencai Yi ◽  
Xiaomin Cheng ◽  
Tiexin Cheng
Keyword(s):  
Electronic Structure ◽  
Fast Response ◽  
Structure Evolution

Molecular Dynamics Study Of Si/Si3N4 Interface

1996 ◽  
Vol 446 ◽  
Author(s):  
Martina E. Bachlechner ◽  
Ingvar Ebbsjö ◽  
Rajiv K. Kalia ◽  
Priya Vashishta
Keyword(s):  
Molecular Dynamics ◽  
Electronic Structure ◽  
Charge Transfer ◽  
Md Simulations ◽  
Electronic Structure Calculations ◽  
Interface Structure ◽  
Bond Bending ◽  
Three Body ◽  
Structure Calculations ◽  
Weber Potential

AbstractStructural correlations at the Si(111)/Si3N4(0001) interface are studied using the molecular dynamics (MD) method. In the bulk, Si is described by the Stillinger-Weber potential and Si3N4 by an interaction potential which contains two-body (steric, Coulomb, electronic polarizabilities) and three-body (bond bending and stretching) terms. At the interface, the charge transfer from silicon to nitrogen is taken from LCAO electronic structure calculations. Using these Si, Si3N4 and interface interactions in MD simulations, the interface structure (atomic positions, bond lengths, and bond angles) is determined. Results for fracture in silicon are also presented.

scholarly journals Phase transition and electronic structure evolution of MoTe2 induced by W substitution

2018 ◽  
Vol 98 (14) ◽  
Author(s):  
Wencan Jin ◽  
Theanne Schiros ◽  
Yi Lin ◽  
Junzhang Ma ◽  
Rui Lou ◽  
...  
Keyword(s):  
Phase Transition ◽  
Electronic Structure ◽  
Structure Evolution

Nanosecond Molecular Dynamics of Zipper-like DNA Duplex Structures Containing Sheared G·A Mismatch Pairs

2000 ◽  
Vol 122 (31) ◽  
pp. 7564-7572 ◽  
Author(s):  
Nad'a Špačková ◽  
Imre Berger ◽  
Jiří Šponer
Keyword(s):  
Molecular Dynamics ◽  
Dna Duplex

Unconventional Electronic Structure Evolution with Hole Doping inBi2Sr2CaCu2O8+δ: Angle-Resolved Photoemission Results

1996 ◽  
Vol 76 (25) ◽  
pp. 4841-4844 ◽  
Author(s):  
D. S. Marshall ◽  
D. S. Dessau ◽  
A. G. Loeser ◽  
C-H. Park ◽  
A. Y. Matsuura ◽  
...  
Keyword(s):  
Electronic Structure ◽  
Structure Evolution ◽  
Hole Doping
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