Direct ab initio MD study on the interaction of hydroperoxy radical (HOO) with water molecules

2010 ◽  
Vol 12 (15) ◽  
pp. 3904 ◽  
Author(s):  
Hiroto Tachikawa ◽  
Shigeaki Abe
Keyword(s):  
Ab Initio ◽  
Water Molecules ◽  
Hydroperoxy Radical ◽  
Ab Initio Md

scholarly journals QM AND AB INITIO INVESTIGATION ON THE HYDROGEN BONDING, NMR CHEMICAL SHIFTS AND SOLVENT EFFECTS ON THE DPPE

2010 ◽  
Vol 7 (3) ◽  
pp. 260-272
Author(s):  
M. Monajjemi ◽  
A. Nouri ◽  
H. Monajemi
Keyword(s):  
Hydrogen Bonding ◽  
Ab Initio ◽  
Atomic Orbital ◽  
Theoretical Data ◽  
Basis Sets ◽  
Stable Complex ◽  
Head Group ◽  
Water Molecules ◽  
Hartree Fock ◽  
Zwitterionic Form

The hydrogen bonding effects that were produced from interaction of membrane lipid dipalmitoylphosphatidyl-ethanolamine (DPPE) with 1-5 water molecules, has been theoretically  investigated through the quantum mechanical calculations at the Hartree-Fock level of theory and the 3-21G, 6-31G and 6-31G* basis sets with the computational package of Gaussian 98. According to the obtained results of the structural optimization of the isolated DPPE in the gas phase, we can see the evidences of interactions in the head group of this macromolecule (from the molecular point of view we have a proton transfer from the ammonium group to the phosphate oxygen of zwitterionic form. As we know that the hydrogen bonding of DPPE with water molecules which have surrounded its head group plays an important role in the permeability of DPPE. So, in order to understand the microscopic physico-chemical nature of this subject we have analyzed bond and torsion angles of DPPE before and after added water molecules.  In this paper we have theoretically studied the complexes DPPE with water molecules which have surrounded its head group. As mentioned before, this theoretically study has been done through Hartree-Fock level of theory by using simple basis sets. Theoretical data shows that the interaction of head group of DPPE with water molecules causes some changes in the geometry of DPPE which were explained by the contribution of zwitterionic form of DPPE macromolecule, and finally hydrated DPPE becomes stable complex. Comparison between theoretical and experimental geometry data of DPPE macromolecule shows that the calculation at the HF/3-21 level of theory produces results which they are in better agreement with the experimental data. Moreover the hydrogen bonding effects on the NMR shielding tensor of selected atoms in the hydrated complexes of DPPE were reported. The ";Gauge Including Atomic Orbitals"; (GIAO) approaches within the SCF-Hartree-Fock approximation have been used in order to investigate the influence of hydrogen bonding of DPPE-water complex on the shielding tensors. Finally, the solvent affects on the stability of DPPE macromolecule, dipole moment and atomic charge of some selected atoms of DPPE molecule was discussed using Onsager model and Merz-Singh-Kolman schema.   Keywords  : Gauge Including Atomic Orbital, DPPE, hydrogen bonding, solvation, quantum mechanics, ab initio

scholarly journals Automated generation of radical species in crystalline carbohydrate using ab initio MD simulations

2014 ◽  
Vol 16 (32) ◽  
pp. 17196-17205 ◽  
Author(s):  
Siv G. Aalbergsjø ◽  
Ewald Pauwels ◽  
Andy Van Yperen-De Deyne ◽  
Veronique Van Speybroeck ◽  
Einar Sagstuen
Keyword(s):  
Charge Transfer ◽  
Hydrogen Bonds ◽  
Ab Initio ◽  
Md Simulations ◽  
Radical Species ◽  
Automated Generation ◽  
Ab Initio Md

Stabilization of radical products is connected to charge transfer along hydrogen bonds.

Ab Initio and DFT Study on Cyclophosphamide: Anticancer and Immunomodulating Agents

2018 ◽  
Vol 71 (7) ◽  
pp. 511 ◽  
Author(s):  
Giuseppe Bruno
Keyword(s):  
Ab Initio ◽  
Electronic Properties ◽  
Quantum Chemical ◽  
Immunosuppressive Agents ◽  
Water Molecules ◽  
Frontier Molecular Orbitals ◽  
Germ Cell Tumours ◽  
Antineoplastic Chemotherapy ◽  
Over Time ◽  
Ab Initio And Dft

Cyclophosphamide is presently the most frequently used drug for antineoplastic chemotherapy. It has shown a great response in the treatment of human malignancies including leukemia, lymphoma, germ cell tumours, medulloblastomas, and carcinomas of the breast, lung, and cervix. Cyclophosphamide is also one of the most important immunosuppressive agents. This study investigates the quantum-chemical electronic properties of cyclophosphamide, as well as some of its metabolites, which are computed using ab-initio and DFT calculations. The interaction energy calculations between water molecules and the cyclophosphamide show how, in the solid state, the presence of water of crystallisation will make cyclophosphamide more stable over time. Atomic charges, dipole moment, frontier molecular orbitals, electrostatic potential isosurface, geometric parameters, and proton affinity on every nitrogen site enable the characterisation of the electronic properties and clearly illustrate the reactive sites that could be associated with this biologically important class of molecules.

The multiple dissociation constants of glutathione disulfide: interpreting experimental pH-titration curves with ab initio MD simulations

2019 ◽  
Vol 21 (18) ◽  
pp. 9212-9217 ◽  
Author(s):  
Vaishali Arunachalam ◽  
Anil Kumar Tummanapelli ◽  
Sukumaran Vasudevan
Keyword(s):  
Complex Systems ◽  
Ab Initio ◽  
Dissociation Constants ◽  
Md Simulations ◽  
Glutathione Disulfide ◽  
Ph Titration ◽  
Titration Curves ◽  
Ab Initio Md

Dissociation constants calculated from ab initio MD simulations can aid the interpretation of the pH-titration curves of complex systems.

Effect of water on gas explosions: combined ReaxFF and ab initio MD calculations

RSC Advances ◽  
2014 ◽  
Vol 4 (66) ◽  
pp. 35048 ◽  
Author(s):  
Zheng-Hua He ◽  
Xi-Bo Li ◽  
Wen-Jun Zhu ◽  
Li-Min Liu ◽  
Guang-Fu Ji
Keyword(s):  
Ab Initio ◽  
Effect Of Water ◽  
Gas Explosions ◽  
Ab Initio Md
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