scholarly journals Mechanisms of Deamidation of Asparagine Residues and Effects of Main-Chain Conformation on Activation Energy

2020 ◽  
Vol 21 (19) ◽  
pp. 7035
Author(s):  
Koichi Kato ◽  
Tomoki Nakayoshi ◽  
Eiji Kurimoto ◽  
Akifumi Oda
Keyword(s):  
Activation Energy ◽  
Quantum Chemical Calculations ◽  
Quantum Chemical ◽  
Density Functional ◽  
Main Chain ◽  
Density Functional Method ◽  
Md Simulations ◽  
Chain Conformation ◽  
Dihydrogen Phosphate ◽  
Chain Conformations

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.

THE ROLE OF SUBSTRATE IN PACKING STRUCTURES OF SEXITHIOPHENES ON AG (111) SURFACE: MOLECULAR DYNAMICS SIMULATIONS AND QUANTUM CHEMICAL CALCULATIONS

2009 ◽  
Vol 08 (04) ◽  
pp. 677-690 ◽  
Author(s):  
JIN WEN ◽  
JING MA
Keyword(s):  
Molecular Dynamics ◽  
Quantum Chemical Calculations ◽  
Quantum Chemical ◽  
Density Functional ◽  
Md Simulations ◽  
Site Preference ◽  
Functional Theory ◽  
The Density Functional Theory ◽  
Dynamics Simulations

Packing structures and orientation of sexithiophene (6T) molecules on Ag (111) surface are investigated by molecular dynamics (MD) simulations and quantum chemical calculations. Both the cluster and the slab models are employed. The density functional theory and molecular mechanism calculations demonstrate a weak physisorption and little site-preference in thiophene/ Ag (111) system. The MD simulations show that in the first layer close to the surface, the nearly coplanar 6T strips lie parallel with long axes deviating from [Formula: see text] direction about 20° – 30° and 75° – 90°. The average adsorption height of the monolayer is about 3.2 Å with most of the sulfur atoms in thienyl rings sitting on the bridge site of Ag (111) surface. The 6T molecules tend to take tilted orientations when they are far away from the surface. The packing structures of 6T layers deposited on the surface resulted from the competition between the molecule–substrate and intermolecular interactions.

A density functional theory insight into the structure and reactivity of diphenyltin(IV) derivative of glycylphenylalanine

2016 ◽  
Vol 39 (3-4) ◽  
Author(s):  
Sandeep Pokharia ◽  
Rachana Joshi ◽  
Mamta Pokharia ◽  
Swatantra Kumar Yadav ◽  
Hirdyesh Mishra
Keyword(s):  
Density Functional Theory ◽  
Quantum Chemical Calculations ◽  
Quantum Chemical ◽  
Density Functional ◽  
Functional Theory ◽  
Insight Into

AbstractThe quantum-chemical calculations based on density functional theory (DFT) have been performed on the diphenyltin(IV) derivative of glycyl-phenylalanine (H

scholarly journals Quantum Chemical Calculations on Locked Nucleic Acid based Modifications: A Density Functional Theory (DFT) Study

2020 ◽  
Author(s):  
Mallikarjunachari Uppuladinne ◽  
Dikshita Dowerah ◽  
Uddhavesh Sonavane ◽  
Suvendra Kumar Ray ◽  
Ramesh Deka ◽  
...  
Keyword(s):  
Density Functional Theory ◽  
Nucleic Acid ◽  
Quantum Chemical Calculations ◽  
Quantum Chemical ◽  
Density Functional ◽  
Locked Nucleic Acid ◽  
Dft Study ◽  
Functional Theory

Can silylenes rival transition metal systems in bond-strengthening π-back donation? A computational investigation

2014 ◽  
Vol 50 (62) ◽  
pp. 8522-8525 ◽  
Author(s):  
Amrita Pal ◽  
Kumar Vanka
Keyword(s):  
Density Functional Theory ◽  
Transition Metal ◽  
Quantum Chemical Calculations ◽  
Quantum Chemical ◽  
Density Functional ◽  
Computational Investigation ◽  
Functional Theory ◽  
Silylene Complexes ◽  
Back Donation ◽  
Full Quantum

Full quantum chemical calculations with density functional theory (DFT) show that bond-strengthening back-donation to a π-diborene, recently discovered for transition metal systems (Braunschweig and co-workers, Nat. Chem., 2013, 5, 115–121), would be just as favored for Main Group silylene complexes.

DFT Studies and Quantum Chemical Calculations of Benzoyl Thiourea Derivatives Linked with Morpholine and Piperidine for the Evaluation of Antifungal Activity

2022 ◽  
Vol 12 ◽  
Author(s):  
Rameshwar K. Dongare ◽  
Shaukatali N. Inamdar ◽  
Radhakrishnan M. Tigote
Keyword(s):  
Antifungal Activity ◽  
Quantum Chemical Calculations ◽  
Quantum Chemical ◽  
Density Functional ◽  
Basis Set ◽  
Functional Study ◽  
Chemical Parameters ◽  
Thiourea Derivatives ◽  
Quantum Chemical Parameters ◽  
B3lyp Method

Herein, we report the density functional study of benzoyl thiourea derivatives linked to morpholine and piperidine to evaluate their antifungal activity. Overall six compounds BTP 1-3 and BTM 4-6 were optimized with DFT using the B3LYP method with 6-31G(d,p) basis set. The molecular geometry, bond lengths, bond angles, atomic charges and HOMO-LUMO energy gap have been investigated. The structural parameters have been compared with the reported experimental results and structure- antifungal activity relationship is explored in details. The calculated results from DFT were discussed using all Quantum chemical parameters of the compounds. Introduction: Benzoyl thiourea derivatives linked with morpholine and piperidine were reported to have good antifungal activity. Objective: To find the correlations between the quantum chemical calculations and the antifungal activity for the benzoyl thiourea derivatives linked with morpholine and piperidine. Method: Optimization was carried out with DFT using B3LYP method utilizing 6-31G(d,p) basis set. Results: A good correlation between the quantum chemical calculations and the antifungal activity for the benzoyl thiourea derivatives linked with morpholine and piperidine was found. Conclusion: The DFT study of benzoyl thiourea derivatives linked to morpholine and piperidine was evaluated for their antifungal activity and it showed good correlations of activity with the quantum chemical parameters.

Sign in / Sign up

Export Citation Format

Share Document