scholarly journals Anharmonic calculations of vibrational spectra for molecular adsorbates: A divide-and-conquer semiclassical molecular dynamics approach

2020 ◽  
Vol 152 (10) ◽  
pp. 104104 ◽  
Author(s):  
Marco Cazzaniga ◽  
Marco Micciarelli ◽  
Francesco Moriggi ◽  
Agnes Mahmoud ◽  
Fabio Gabas ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Vibrational Spectra ◽  
Divide And Conquer ◽  
Molecular Adsorbates

Structural stabilities and transformations in cationized asparagine at finite temperatures: An ab initio molecular dynamics study

2014 ◽  
Vol 13 (04) ◽  
pp. 1450024
Author(s):  
Shoutian Sun ◽  
Jianwen Liu ◽  
Zhi-Feng Liu
Keyword(s):  
Molecular Dynamics ◽  
Ab Initio ◽  
Structural Transformation ◽  
Vibrational Spectra ◽  
Room Temperature ◽  
Ab Initio Molecular Dynamics ◽  
And Shifts ◽  
Torsional Angles

The cationic complexes of Asparagine (Asn), M +( Asn ), with M + = Li +, Na +, K +, Cs +, and H +, are models for studying the interaction between cations and Asn. Ab initio molecular dynamics (AIMD) method is employed to simulate their behavior at finite temperatures. Structural transformation between conformers is observed, which becomes progressively easier as the cation varies from Li +, to Na +, K +, Cs +, and H +. The fluctuation of the M +– N and M +– O distances and rotation of torsional angles are significant even at room temperature for K +, Cs + and H +. Vibrational profiles based on AIMD trajectories provide insights into the broadening and shifts in relative intensities observed in the vibrational spectra measured by infrared multi-photon dissociation (IRMPD) experiments.

Vibrational spectra and molecular dynamics of 1,2-di-(p-XC6H4)ethanes (X=Br,NO2)

2001 ◽  
Author(s):  
D. I. Kamalova ◽  
S. A. Petrova ◽  
A. B. Remizov ◽  
R. A. Skochilov
Keyword(s):  
Molecular Dynamics ◽  
Vibrational Spectra

Reactive Molecular Dynamics Simulations, Data Analytics and Visualization

2015 ◽  
Vol 1756 ◽  
Author(s):  
Priya Vashishta ◽  
Rajiv K. Kalia ◽  
Aiichiro Nakano ◽  
Ying Li ◽  
Ken-ichi Nomura ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Production ◽  
Density Functional ◽  
Silica Surface ◽  
Hydrogen Gas ◽  
Divide And Conquer ◽  
List Type ◽  
Reactive Molecular Dynamics ◽  
Production Of Hydrogen ◽  
Blue Gene

ABSTRACTMultimillion-atom reactive molecular dynamics (RMD) and large quantum molecular dynamics (QMD) simulations are used to investigate structural and dynamical correlations under highly nonequilibrium conditions and reactive processes in nanostructured materials under extreme conditions. This paper discusses four simulations:1.RMD simulations of heated aluminum nanoparticles have been performed to study the fast oxidation reaction processes of the core (aluminum)-shell (alumina) nanoparticles and small complexes.2.Cavitation bubbles readily occur in fluids subjected to rapid changes in pressure. We have used billion-atom RMD simulations on a 163,840-processor Blue Gene/P supercomputer to investigate chemical and mechanical damages caused by shock-induced collapse of nanobubbles in water near silica surface. Collapse of an empty nanobubble generates high-speed nanojet, resulting in the formation of a pit on the surface. The gas-filled bubbles undergo partial collapse and consequently the damage on the silica surface is mitigated.3.Our QMD simulation reveals rapid hydrogen production from water by an Al superatom. We have found a low activation-barrier mechanism, in which a pair of Lewis acid and base sites on the Aln surface preferentially catalyzes hydrogen production.4.We have introduced an extension of the divide-and-conquer (DC) algorithmic paradigm called divide-conquer-recombine (DCR) to perform large QMD simulations on massively parallel supercomputers, in which interatomic forces are computed quantum mechanically in the framework of density functional theory (DFT). A benchmark test on an IBM Blue Gene/Q computer exhibits an isogranular parallel efficiency of 0.984 on 786,432 cores for a 50.3 million-atom SiC system. As a test of production runs, LDC-DFT-based QMD simulation involving 16,661 atoms was performed on the Blue Gene/Q to study on-demand production of hydrogen gas from water using LiAl alloy particles.

A Theoretical Study Of The Energetics And Vibrational Spectra Of Oxygenated (100) Diamond Surfaces

1995 ◽  
Vol 416 ◽  
Author(s):  
S. Skokov ◽  
B. Weiner ◽  
M. Frenklach
Keyword(s):  
Experimental Data ◽  
Molecular Dynamics ◽  
Hydrogen Bonds ◽  
Vibrational Spectra ◽  
Theoretical Study ◽  
Local Environment ◽  
Hydroxyl Groups ◽  
Vibrational Modes ◽  
Diamond Surfaces ◽  
Molecular Dynamics Calculations

ABSTRACTStatic quantum ab initio and quantum semiempirical molecular dynamics calculations were employed to study reconstructions of (100) diamond surfaces in presence of hydrogen and oxygen. The results indicate that the energetically most favorable structures of oxygenated surfaces are those with chemisorbed hydroxyl groups. It was found that hydrogen bonds are formed among chemisorbed oxygenated species. The formation of these hydrogen bonds is shown to be an important factor in stabilization of adlayers. A number of important vibrational modes characteristic of oxygenated diamond surfaces were identified. The analysis of surface vibrational spectra demonstrates the influence of the local environment on the position of vibrational modes and can be useful for interpretation of experimental data.

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