Interpretation of the electronic spectra of Fe and Co porphyrins based on quantum-chemical calculations by the density functional method

Deamidation of asparagine (Asn) residues is a nonenzymatic post-translational modification of proteins. Asn deamidation is associated with pathogenesis of age-related diseases and hypofunction of monoclonal antibodies. Deamidation rate is known to be affected by the residue following Asn on the carboxyl side and by secondary structure. Information about main-chain conformation of Asn residues is necessary to accurately predict deamidation rate. In this study, the effect of main-chain conformation of Asn residues on deamidation rate was computationally investigated using molecular dynamics (MD) simulations and quantum chemical calculations. The results of MD simulations for γS-crystallin suggested that frequently deamidated Asn residues have common main-chain conformations on the N-terminal side. Based on the simulated structure, initial structures for the quantum chemical calculations were constructed and optimized geometries were obtained using the B3LYP density functional method. Structures that were frequently deamidated had a lower activation energy barrier than that of the little deamidated structure. We also showed that dihydrogen phosphate and bicarbonate ions are important catalysts for deamidation of Asn residues.

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Vibrational Study and Electronic Parameters of "2-Diphenylphosphanyl- 6-fluoro-pyridine"using First Principle

SAMRIDDHI A Journal of Physical Sciences Engineering and Technology ◽

10.18090/samriddhi.v9i02.10873 ◽

2017 ◽

Vol 9 (02) ◽

pp. 125-130

Author(s):

Tanveer Hasan ◽

P. K. Singh ◽

S. H. Mehdi

Keyword(s):

Title Compound ◽

Quantum Chemical ◽

Density Functional ◽

Density Functional Method ◽

Vibrational Analysis ◽

Functional Method ◽

Orbital Energy ◽

Electronic Parameters ◽

Chemical Studies ◽

Equilibrium Geometries

Vibrational investigations along with theoretical quantum chemical studies on “2-Diphenylphosphanyl-6-fluoro-pyridine (C17H14NFP)” have been carried out. The quantum chemical density functional method at B3LYP/3-21Glevel is used to obtain the equilibrium geometries of the title compound. We have also performed vibrational analysis of the title compound at their equilibrium geometries and established the complete assignments of the significant vibrational modes. Electronic parameters such as HOMO, LUMO and frontier orbital energy band gap, has been calculated. Besides it the thermodynamical parameters like internal thermal energy, entropy and constant volume specific heat capacity have been calculated.

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Comprehensive conformational analysis of 2'-deoxyuridine by quantum-chemical density functional method

Biopolymers and Cell ◽

10.7124/bc.000746 ◽

2006 ◽

Vol 22 (5) ◽

pp. 384-389 ◽

Cited By ~ 3

Author(s):

R. O. Zhurakivsky ◽

D. M. Hovorun

Keyword(s):

Conformational Analysis ◽

Quantum Chemical ◽

Density Functional ◽

Density Functional Method ◽

Functional Method

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Vibrational Investigation of "2-Arsanyl-Pyridine" Using First Principle

SAMRIDDHI A Journal of Physical Sciences Engineering and Technology ◽

10.18090/samriddhi.v9i01.8330 ◽

2017 ◽

Vol 9 (01) ◽

pp. 01-04

Author(s):

Tanveer Hasan ◽

P. K. Singh

Keyword(s):

Title Compound ◽

Quantum Chemical ◽

Density Functional ◽

Density Functional Method ◽

Vibrational Analysis ◽

Functional Method ◽

Perfect Agreement ◽

Chemical Studies ◽

Quantum Chemical Studies ◽

Equilibrium Geometries

Spectroscopic investigations along with theoretical quantum chemical studies on “2-Arsanyl-Pyridine (C5H7AsN)” have been carried out. The quantum chemical density functional method at B3LYP/6-31+g(d,p) level, is used to obtain the equilibrium geometries of the title compound. We have also performed vibrational analysis of the title compound at their equilibrium geometries and established the complete assignments of the significant vibrational modes. The calculated vibrational frequencies are shown to be in perfect agreement with the theoretically observed FTIR spectra of the molecule under study.

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