Recent density functional theory model calculations of drug metabolism by cytochrome P450

2012 ◽  
Vol 256 (11-12) ◽  
pp. 1137-1150 ◽  
Author(s):  
Dongmei Li ◽  
Yong Wang ◽  
Keli Han
Keyword(s):  
Density Functional Theory ◽  
Cytochrome P450 ◽  
Drug Metabolism ◽  
Density Functional ◽  
Theory Model ◽  
Functional Theory ◽  
Model Calculations

Reciprocal Polarizable Embedding with a Transferable H2O Potential Function II: Application to (H2O)n Clusters & Liquid Water

2019 ◽  
Author(s):  
Asmus Ougaard Dohn ◽  
Elvar Jónsson ◽  
Hannes Jonsson
Keyword(s):  
Density Functional Theory ◽  
Liquid Water ◽  
Density Functional ◽  
Water Clusters ◽  
Theory Model ◽  
Coupling Scheme ◽  
Functional Theory ◽  
Total Polarization ◽  
Electrostatic Embedding ◽  
Polarizable Embedding

The manuscript analyzes the accuracy of our recently developed reciprocal polarizable embedding scheme, where a density functional theory model of the QM region is coupled to a dipole- and quadrupole polarizable water potential of the MM region. We present calculations of water clusters and liquid water where we analyze the energy, atomic forces and total polarization to demonstrate that artifacts in energy and polarization introduced by the QM/MM coupling are small and well-behaved. Furthermore, our methodology improves the consistency of the structure of optimized water hexamer geometries when compared to results obtained with models that neglect polarization. Additionally, the manuscript provides evidence that our coupling scheme eliminates artifacts in the structure of liquid water obtained with simpler electrostatic embedding models.

scholarly journals DFT Modelling of Tripeptides (Lysine-Tryptophan-Lysine) Interacting with Single Walled Carbon Nanotubes

2010 ◽  
Vol 7 (3) ◽  
pp. 870-874 ◽  
Author(s):  
Navaratnarajah Kuganathan
Keyword(s):  
Density Functional Theory ◽  
Charge Transfer ◽  
Density Functional ◽  
Single Walled Carbon Nanotubes ◽  
Binding Energies ◽  
Functional Theory ◽  
Model Calculations ◽  
Walled Carbon Nanotubes ◽  
Dft Modelling ◽  
Covalent Nature

Model calculations are performed to predict the nature of interaction between SWNT and a tripeptide (Lys-Trp-Lys) and to calculate the binding energies and charge transfer between these two species using density functional theory. DFT calculations indicate that the interaction is of a non covalent nature. Minimal charge transfer is observed between SWNT and Lys-Trp-Lys.

Reciprocal Polarizable Embedding with a Transferable H2O Potential Function II: Application to (H2O)n Clusters & Liquid Water

2019 ◽  
Author(s):  
Asmus Ougaard Dohn ◽  
Elvar Jónsson ◽  
Hannes Jonsson
Keyword(s):  
Density Functional Theory ◽  
Liquid Water ◽  
Density Functional ◽  
Water Clusters ◽  
Theory Model ◽  
Coupling Scheme ◽  
Functional Theory ◽  
Total Polarization ◽  
Electrostatic Embedding ◽  
Polarizable Embedding

The manuscript analyzes the accuracy of our recently developed reciprocal polarizable embedding scheme, where a density functional theory model of the QM region is coupled to a dipole- and quadrupole polarizable water potential of the MM region. We present calculations of water clusters and liquid water where we analyze the energy, atomic forces and total polarization to demonstrate that artifacts in energy and polarization introduced by the QM/MM coupling are small and well-behaved. Furthermore, our methodology improves the consistency of the structure of optimized water hexamer geometries when compared to results obtained with models that neglect polarization. Additionally, the manuscript provides evidence that our coupling scheme eliminates artifacts in the structure of liquid water obtained with simpler electrostatic embedding models.

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