scholarly journals A Modified QM/MM Hamiltonian with the Self-Consistent-Charge Density-Functional-Tight-Binding Theory for Highly Charged QM Regions

2012 ◽  
Vol 8 (11) ◽  
pp. 4293-4304 ◽  
Author(s):  
Guanhua Hou ◽  
Xiao Zhu ◽  
Marcus Elstner ◽  
Qiang Cui
Keyword(s):  
Charge Density ◽  
Density Functional ◽  
Tight Binding ◽  
The Self ◽  
Binding Theory ◽  
Self Consistent

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.

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