Combining Self-Consistent-Charge Density-Functional Tight-Binding (SCC-DFTB) with Molecular Mechanics by the Generalized Hybrid Orbital (GHO) Method

2004 ◽  
Vol 108 (25) ◽  
pp. 5454-5463 ◽  
Author(s):  
Jingzhi Pu ◽  
Jiali Gao ◽  
Donald G. Truhlar
Keyword(s):  
Charge Density ◽  
Molecular Mechanics ◽  
Density Functional ◽  
Tight Binding ◽  
Self Consistent ◽  
Hybrid Orbital

MODELING VIBRATIONAL SPECTRA USING THE SELF-CONSISTENT CHARGE DENSITY-FUNCTIONAL TIGHT-BINDING METHOD II: INFRARED SPECTRA

2005 ◽  
Vol 04 (spec01) ◽  
pp. 639-655 ◽  
Author(s):  
HENRYK A. WITEK ◽  
KEIJI MOROKUMA ◽  
ANNA STRADOMSKA
Keyword(s):  
Charge Density ◽  
Infrared Spectra ◽  
Density Functional ◽  
Organic Molecules ◽  
Tight Binding ◽  
Additional Term ◽  
Functional Theory ◽  
Molecular Electron ◽  
Self Consistent ◽  
Energy Formula

We present an extended self-consistent charge density-functional tight-binding (SCC-DFTB) method that allows for computing vibrational infrared spectra. The extension is based on introducing an additional term in the SCC-DFTB energy formula that describes effectively the interaction of external electric field with molecular electron density distribution. The extended SCC-DFTB method is employed to model vibrational infrared spectra of 16 organic molecules. The calculated spectra are compared to experiment and to spectra obtained with density functional theory. For most of the molecules, the SCC-DFTB method reproduces the experimental spectra in a very satisfactory manner. We discuss the drawbacks and possible applications of this new scheme.

A Self-Consistent Charge Density-Functional Based Tight-Binding Scheme for Large Biomolecules

2000 ◽  
Vol 217 (1) ◽  
pp. 357-376 ◽  
Author(s):  
M. Elstner ◽  
Th. Frauenheim ◽  
E. Kaxiras ◽  
G. Seifert ◽  
S. Suhai
Keyword(s):  
Charge Density ◽  
Density Functional ◽  
Tight Binding ◽  
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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