Ab initio STO-nG Hartree-Fock-Roothaan calculations of the ammonia-formic acid complex as a model for hydrogen bonding in crystalline amino acids

1985 ◽  
Vol 89 (3) ◽  
pp. 524-532 ◽  
Author(s):  
Julia Parra-Mouchet ◽  
William H. Fink ◽  
Charles P. Nash
Keyword(s):  
Amino Acids ◽  
Hydrogen Bonding ◽  
Formic Acid ◽  
Ab Initio ◽  
Acid Complex ◽  
Hartree Fock ◽  
Crystalline Amino Acids

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

A spectroscopic and ab initio study of the hydrogen peroxide–formic acid complex: hindering the internal motion of H2O2

2018 ◽  
Vol 20 (33) ◽  
pp. 21345-21351 ◽  
Author(s):  
Leo Yuxiu Li ◽  
Nathan A. Seifert ◽  
Fan Xie ◽  
Matthias Heger ◽  
Yunjie Xu ◽  
...  
Keyword(s):  
Hydrogen Peroxide ◽  
Formic Acid ◽  
Ab Initio ◽  
Internal Motion ◽  
Ab Initio Study ◽  
Acid Complex

Hydrogen peroxide imprints its chirality onto the H2O2–formic acid complex, which results in an asymmetric tunnelling potential.

Ab Initio Calculations of Supramolecular Recognition Modes. Cyclic versus Noncyclic Hydrogen Bonding in the Formic Acid/Formamide System

1994 ◽  
Vol 98 (26) ◽  
pp. 6459-6467 ◽  
Author(s):  
Thomas Neuheuser ◽  
Bernd A. Hess ◽  
Christiane Reutel ◽  
Edwin Weber
Keyword(s):  
Hydrogen Bonding ◽  
Formic Acid ◽  
Ab Initio Calculations ◽  
Ab Initio

scholarly journals Theoretical Ab initio and Density Functional Study of the Hydrogen Bonding Nature Between the Pyridine-nitrogenic Base Pairs

2012 ◽  
Vol 4 (2) ◽  
pp. 419
Author(s):  
M. J. Al-anber
Keyword(s):  
Hydrogen Bonding ◽  
Ab Initio ◽  
Point Mutation ◽  
Density Functional ◽  
Bonding Energy ◽  
Functional Study ◽  
Geometrical Parameters ◽  
Base Pairs ◽  
Hartree Fock ◽  
Significant Point

The pyridine interact with two nitrogenic bases (adenine and uracil) so that they may cause a significant point mutation. The results of theoretical ab initio study on the hydrogen bonding energies of pyridine with the adenine and uracil are reported. The geometries of the local minima for all suggested cases  were optimized with Restricted Hartree-Fock RHF/cc-pVDZ and then density functional B3LYP/cc-pVDZ. The geometrical parameters, relative stability, interaction energies and nature of hydrogen bonding energy are reported. Also, focus on the range of the hydrogen bonding energy and the flexibility of the rotation angle in the P:A¹ base pair have been investigated. Additionally, the influence of the hydrogen bonding energy with the dihedral angle between the two planes of the adenine and the pyridine in the P:A¹  pair are studied. The pyridine with the adenine and uracil may be classified as multi-point mutation. In general, enzymes may have three mechanisms to recorrect the errors in the DNA and the RNA. Keywords:   Ab initio; Density funtional theory; Mutating; Pyridine ; DNA. © 2012 JSR Publications. ISSN: 2070-0237 (Print); 2070-0245 (Online). All rights reserved. doi: http://dx.doi.org/10.3329/jsr.v4i2.8721 J. Sci. Res. 4 (2), 419-425 (2012)  

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