Adsorption and dissociation of water molecules at the α-Al2O3(0001) surface: A 2-dimensional hybrid self-consistent charge density functional based tight-binding/molecular mechanics molecular dynamics (2D SCC-DFTB/MM MD) simulation study

2019 ◽  
Vol 164 ◽  
pp. 195-204 ◽  
Author(s):  
Niko Prasetyo ◽  
Thomas S. Hofer
Keyword(s):  
Molecular Dynamics ◽  
Charge Density ◽  
Simulation Study ◽  
Density Functional ◽  
Md Simulation ◽  
Tight Binding ◽  
Water Molecules ◽  
Self Consistent ◽  
Α Al2o3 ◽  
Adsorption And Dissociation

A SELF-CONSISTENT-CHARGE DENSITY-FUNCTIONAL TIGHT-BINDING THEORY BASED MOLECULAR DYNAMICS SIMULATION OF A ZWITTERIONIC GLYCINE IN AN EXPLICIT WATER ENVIRONMENT

2013 ◽  
Vol 12 (04) ◽  
pp. 1350019 ◽  
Author(s):  
Y. ZHAI ◽  
Y. L. ZHAO
Keyword(s):  
Molecular Dynamics ◽  
Amino Acids ◽  
Charge Density ◽  
Density Functional ◽  
Water Environment ◽  
Tight Binding ◽  
Water Molecules ◽  
Binding Theory ◽  
Self Consistent ◽  
The Impact

A zwitterionic glycine (zGLY) is adopted as an example to study the impact of water environment (310 H2O molecules) on the molecular structure and energetics using a self-consistent-charge density-functional tight-binding theory based molecular dynamics (SCC-DFTB/MD) method. It is found that maximal eight hydrogen bonds could be formed simultaneously between eight water molecules and the zGLY. The ability of the COO- terminal to adsorb water molecules is stronger than the [Formula: see text] terminal with respect to hydrogen bonding with more water molecules and exhibits lower adiabatic adsorption energies. The zGLY's intramolecular hydrogen bond appeared unpredictably, without involving any proton transfer and generally helpful for enhancing the system stability. Water molecules play an important role to stabilize the zwitterionic amino acids and restrain the proton migration from the [Formula: see text] to the COO− group. Our results show that the SCC-DFTB/MD method could successfully describe geometry dynamical evolutions and energetics of biomolecules in a nanoscale simulation with the presence of a large number of water molecules. Our study not only verified the feasibility of a QM level methodology for describing the aqueous states of biochemical molecules, but also gave a clear evidence for the impact of water environment on amino acids.

EFFECTS AND ROLE OF WATER ENVIRONMENT ON A GEMINAL HYDROXYLATED SILICA SURFACE — SELF-CONSISTENT CHARGE DENSITY FUNCTIONAL TIGHT BINDING THEORY BASED MOLECULAR DYNAMICS SIMULATION

2012 ◽  
Vol 11 (01) ◽  
pp. 155-162 ◽  
Author(s):  
Y. L. ZHAO
Keyword(s):  
Hydrogen Bonds ◽  
Charge Density ◽  
Density Functional ◽  
Silica Surface ◽  
Water Environment ◽  
Tight Binding ◽  
Dynamics Simulation ◽  
Water Molecules ◽  
Self Consistent ◽  
The Impact

The presence of aqueous solution is inevitable in complex systems involving biological and material components and could affect the interaction between them substantially. To properly simulate such an interaction system, it is necessary to quantitatively explore the effects and specific roles of the water environment on the material surface. In this work, a silica surface was adopted as an example to study the impact of water environment ( 144H2O ) on the structure and energetics using a self-consistent charge density functional tight binding/molecular dynamic method. First, we demonstrated that the silica surface in a vacuum involves a large deformation due to the formation of hydrogen bonds among the surface silanols; in contrast, the deformation is eased in water environment because water molecules could locate in between the silanols and form many hydrogen bonds with the silanols. Therefore, water molecules play an important role to maintain surface from not getting heavily deformed. Our work not only tested the feasible computational methodology of studying nanoscale large systems under water environment at a quantum-mechanical level of theory, but also provided clear evidence on the impact of water environment to the inorganic surface.

scholarly journals Ewald summation on a helix: A route to self-consistent charge density-functional based tight-binding objective molecular dynamics

2013 ◽  
Vol 139 (9) ◽  
pp. 094110 ◽  
Author(s):  
I. Nikiforov ◽  
B. Hourahine ◽  
B. Aradi ◽  
Th. Frauenheim ◽  
T. Dumitrică
Keyword(s):  
Molecular Dynamics ◽  
Charge Density ◽  
Density Functional ◽  
Tight Binding ◽  
Ewald Summation ◽  
Self Consistent
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