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.

scholarly journals Molecular Dynamics Calculations of CH3Sticking Coefficient onto Diamond Surfaces

2015 ◽  
Vol 12 (8) ◽  
pp. 764-770 ◽  
Author(s):  
Laurent Schwaederlé ◽  
Pascal Brault ◽  
Cathy Rond ◽  
Alix Gicquel
Keyword(s):  
Molecular Dynamics ◽  
Diamond Surfaces ◽  
Molecular Dynamics Calculations

Molecular dynamics study of solid argon with N2, O2, and CO impurities

1982 ◽  
Vol 60 (9) ◽  
pp. 1365-1370 ◽  
Author(s):  
Shūichi Nosé ◽  
Michael L. Klein
Keyword(s):  
Experimental Data ◽  
Molecular Dynamics ◽  
Melting Point ◽  
Diatomic Molecules ◽  
Power Spectra ◽  
Preferred Orientation ◽  
Molecular Dynamics Calculations ◽  
Solid Argon

Molecular dynamics calculations employing atom–atom (exp-6) potentials are reported for solid argon in which 5% of the lattice sites are occupied by diatomic molecules. At temperatures close to the melting point (T ~ 80 K) the molecules are reorienting rapidly with no preferred orientation. Upon cooling, however, a distinct preference is observed for the crystallographic [Formula: see text] direction. Power spectra that characterize the translational and reorientational motions in the system have been evaluated. The results are discussed in light of available experimental data.

Specific osteogenesis imperfecta-related Gly substitutions in type I collagen induce distinct structural, mechanical, and dynamic characteristics

2021 ◽  
Author(s):  
Haoyuan Shi ◽  
Liming Zhao ◽  
Chenxi Zhai ◽  
Jingjie Yeo
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Bonds ◽  
Osteogenesis Imperfecta ◽  
Dynamic Characteristics ◽  
Type I Collagen ◽  
Type I ◽  
Vibrational Modes ◽  
Wild Type ◽  
Triple Helices ◽  
Dynamics Simulations

The stiffnesses, β-structures, hydrogen bonds, and vibrational modes of wild-type collagen triple helices are compared with osteogenesis imperfecta-related mutants using integrative structural and dynamic analysis via molecular dynamics simulations and...

A molecular dynamics study of ices III and V using TIP4P and TIP5P water models

2003 ◽  
Vol 81 (1-2) ◽  
pp. 11-16 ◽  
Author(s):  
R B Ayala ◽  
V Tchijov
Keyword(s):  
Experimental Data ◽  
Molecular Dynamics ◽  
Molecular Interactions ◽  
Specific Volume ◽  
Molecular Dynamics Calculations ◽  
Water Models ◽  
Good Agreement

Simulations of ices III and V are performed using molecular dynamics calculations in the NPT ensemble. To represent molecular interactions in both ices, two potentials, TIP4P and TIP5P, are used. The specific volume of ice III is calculated as a function of temperature at pressure P = 250 MPa, as well as a function of pressure at temperature T = 246 K. For ice V, the specific volume is calculated as a function of temperature at P = 500 MPa and as a function of pressure at T = 238 K. In both cases, both TIP4P and TIP5P models are used. The results of the calculations are in good agreement with the experimental data of other researchers. PACS No.: 31.15Qg

Molecular Dynamics Calculations of InSb Thermal Conductivity

2010 ◽  
Vol 297-301 ◽  
pp. 1400-1407
Author(s):  
Giovano de Oliveira Cardozo ◽  
José Pedro Rino
Keyword(s):  
Experimental Data ◽  
Thermal Conductivity ◽  
Molecular Dynamics ◽  
Infinite System ◽  
Thermal Conductivity Coefficient ◽  
Direct Method ◽  
Molecular Dynamics Calculations ◽  
Non Equilibrium Molecular Dynamics ◽  
Three Body ◽  
Non Equilibrium

Equilibrium and non-equilibrium molecular dynamics calculations of thermal conductivity coefficient are presented for bulk systems of InSb, using an effective two- and three-body inter atomic potential which demonstrated to be very transferable. In the calculations, the obtained coefficients were comparable to the experimental data. In the case of equilibrium simulations a Green-Kubo approach was used and the thermal conductivity was calculated for five temperatures between 300 K and 900 K. For the non equilibrium, or direct method, which is based on the Fourier’s law, the thermal conductivity coefficient was determined at a mean temperature of 300K. In this case it was used a pair of reservoirs, placed at a distance L from each other, and with internal temperatures fixed in 250 K, for the cold reservoir, and 350 K for the hot one. In order to obtain an approach to an infinite system coefficient, four different values of L were used, and the data was extrapolated to L→∞.

Theoretical Study of Na Clusters by First Principle Molecular Dynamics Calculations

1999 ◽  
Vol 16 (4) ◽  
pp. 262-263 ◽  
Author(s):  
Chang-rong Su ◽  
Jie Zhu ◽  
Jia-ming Li ◽  
Jin-long Yang
Keyword(s):  
Molecular Dynamics ◽  
Theoretical Study ◽  
First Principle ◽  
Molecular Dynamics Calculations

Effects of Chlorine on Aluminum Refining: A Review and an Ab Initio Molecular Dynamics Study

2011 ◽  
Vol 467-469 ◽  
pp. 1404-1409 ◽  
Author(s):  
Yan Liu ◽  
Bao De Sun ◽  
Jun Wang ◽  
Yong Bing Dai
Keyword(s):  
Experimental Data ◽  
Molecular Dynamics ◽  
Ab Initio ◽  
Hydrogen Diffusion ◽  
Liquid Aluminum ◽  
Refining Process ◽  
Ab Initio Molecular Dynamics ◽  
Molecular Dynamics Calculations ◽  
Comprehensive Introduction ◽  
Diffusion Of Hydrogen

A comprehensive introduction of current aluminum refining technology is reviewed in this work especially the effects of chlorine on refining process is discussed. The mechanism of chlorine on improving hydrogen diffusion has been studied by ab initio molecular dynamics calculations and we obtain the diffusivity of hydrogen in liquid aluminum which is in agreement with the experimental data. It can be concluded that the diffusion of hydrogen in aluminum melts can be enhanced on the presence of chlorine.

Sub-THz specific relaxation times of hydrogen bond oscillations in E.coli thioredoxin. Molecular dynamics and statistical analysis

2014 ◽  
Vol 171 ◽  
pp. 179-193 ◽  
Author(s):  
Tatiana Globus ◽  
Igor Sizov ◽  
Boris Gelmont
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Bond ◽  
Relaxation Time ◽  
Hydrogen Bonds ◽  
Spectral Resolution ◽  
Relaxation Times ◽  
Low Frequency ◽  
Thz Spectroscopy ◽  
Vibrational Modes ◽  
Covalent Bonds

Hydrogen bonds (H-bonds) in biological macromolecules are important for the molecular structure and functions. Since interactions via hydrogen bonds are weaker than covalent bonds, it can be expected that atomic movements involving H-bonds have low frequency vibrational modes. Sub-Terahertz (sub-THz) vibrational spectroscopy that combines measurements with molecular dynamics (MD) computational prediction has been demonstrated as a promising approach for biological molecule characterization. Multiple resonance absorption lines have been reported. The knowledge of relaxation times of atomic oscillations is critical for the successful application of THz spectroscopy for hydrogen bond characterization. The purpose of this work is to use atomic oscillations in the 0.35–0.7 THz range, found from molecular dynamic (MD) simulations of E.coli thioredoxin (2TRX), to study relaxation dynamics of two intra-molecular H-bonds, O⋯H–N and O⋯H–C. Two different complimentary techniques are used in this study, one is the analysis of the statistical distribution of relaxation time and dissipation factor values relevant to low frequency oscillations, and the second is the analysis of the autocorrelation function of low frequency quasi-periodic movements. By studying hydrogen bond atomic displacements, it was found that the atoms are involved in a number of collective oscillations, which are characterized by different relaxation time scales ranging from 2–3 ps to more than 150 ps. The existence of long lasting relaxation processes opens the possibility to directly observe and study H-bond vibrational modes in sub-THz absorption spectra of bio-molecules if measured with an appropriate spectral resolution. The results of measurements using a recently developed frequency domain spectroscopic sensor with a spectral resolution of 1 GHz confirm the MD analysis.

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