Comparison of the Hydrogen Bond Interaction Dynamics in the Guanine and Cytosine Crystals: Ab Initio Molecular Dynamics and Spectroscopic Study

2019 ◽  
Vol 123 (50) ◽  
pp. 10757-10763 ◽  
Author(s):  
Mateusz Z. Brela ◽  
Oskar Klimas ◽  
Ewa Surmiak ◽  
Marek Boczar ◽  
Takahito Nakajima ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Bond ◽  
Spectroscopic Study ◽  
Ab Initio ◽  
Ab Initio Molecular Dynamics ◽  
Hydrogen Bond Interaction ◽  
Interaction Dynamics ◽  
Bond Interaction

AN AB INITIO MOLECULAR DYNAMICS STUDY ON THE SOLVATION OF FORMATE ION AND FORMIC ACID IN WATER

2012 ◽  
Vol 11 (05) ◽  
pp. 1019-1032 ◽  
Author(s):  
QIUBO CHEN ◽  
ZHIFENG LIU ◽  
CHEE HOW WONG
Keyword(s):  
Molecular Dynamics ◽  
Formic Acid ◽  
Ab Initio ◽  
Thermal Dissociation ◽  
Ab Initio Molecular Dynamics ◽  
Water Molecules ◽  
Hydrogen Bond Interaction ◽  
Acidic Dissociation ◽  
Partial Dissociation ◽  
Dynamics Simulations

Formate ion and formic acid are linked in water by the equilibrium for the acidic dissociation of formic acid, which as the simplest carboxylic acid is an important model system. In this study, the microscopic details of the solvation around a formate ion and around a formic acid molecule in aqueous solution are explored by ab initio molecular dynamics simulations, at 300, 500, 700, and 900 K. The formate ion exerts a strong influence on the surrounding solvent molecules by hydrogen bonding, which restricts the access of other water molecules. With rising temperature, the hydrogen bonds are disrupted, and the space around formic acid becomes more accessible. Solvation of the formic acid is marked by its partial dissociation to produce a proton, and the hydrogen bond interaction around a formic acid is not as strong as that around a formate ion. The acidic dissociation becomes less favorable as temperature rises, which indicates a lesser catalytic role for the water molecules in the thermal dissociation of formic acid.

Bifurcated Hydrogen Bond in Lithium Nitrate Trihydrate Probed by ab Initio Molecular Dynamics

2012 ◽  
Vol 116 (9) ◽  
pp. 2147-2153 ◽  
Author(s):  
Francesco Muniz-Miranda ◽  
Marco Pagliai ◽  
Gianni Cardini ◽  
Roberto Righini
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Bond ◽  
Ab Initio ◽  
Ab Initio Molecular Dynamics ◽  
Lithium Nitrate ◽  
Nitrate Trihydrate ◽  
Bifurcated Hydrogen Bond

Zero-point fluctuation of hydrogen bond in water dimer from ab initio molecular dynamics

2020 ◽  
Vol 29 (10) ◽  
pp. 103101
Author(s):  
Wan-Run Jiang ◽  
Rui Wang ◽  
Xue-Guang Ren ◽  
Zhi-Yuan Zhang ◽  
Dan-Hui Li ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Bond ◽  
Ab Initio ◽  
Zero Point ◽  
Water Dimer ◽  
Ab Initio Molecular Dynamics

scholarly journals Probing the Molecular Mechanism of Rifampin Resistance Caused by the Point Mutations S456L and D441V on Mycobacterium tuberculosis RNA Polymerase through Gaussian Accelerated Molecular Dynamics Simulation

2020 ◽  
Vol 64 (7) ◽  
Author(s):  
Qianqian Zhang ◽  
Shuoyan Tan ◽  
Tong Xiao ◽  
Hongli Liu ◽  
Syed Jawad Ali Shah ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Bond ◽  
Drug Resistance ◽  
Mycobacterium Tuberculosis ◽  
Rna Polymerase ◽  
Resistance Mechanism ◽  
Hydrogen Bond Interaction ◽  
Content Type ◽  
Accelerated Molecular Dynamics ◽  
Bond Interaction

ABSTRACT Rifampin is the first-line antituberculosis drug, with Mycobacterium tuberculosis RNA polymerase as the molecular target. Unfortunately, M. tuberculosis strains that are resistant to rifampin have been identified in clinical settings, which limits its therapeutic effects. In clinical isolates, S531L and D516V (in Escherichia coli) are two common mutated codons in the gene rpoB, corresponding to S456L and D441V in M. tuberculosis. However, the resistance mechanism at the molecular level is still elusive. In this work, Gaussian accelerated molecular dynamics simulations were performed to uncover the resistance mechanism of rifampin due to S456L and D441V mutations at the atomic level. The binding free energy analysis revealed that the reduction in the ability of two mutants to bind rifampin is mainly due to a decrease in electrostatic interaction, specifically, a decrease in the energy contribution of the R454 residue. R454 acts as an anchor and forms stable hydrogen bond interaction with rifampin, allowing rifampin to be stably incorporated in the center of the binding pocket. However, the disappearance of the hydrogen bond between R454 and the mutated residues increases the flexibility of the side chain of R454. The conformation of R454 changes, and the hydrogen bond interaction between it and rifampin is disrupted. As result, the rifampin molecule moves to the outside of the pocket, and the binding affinity decreases. Overall, these findings can provide useful information for understanding the drug resistance mechanism of rifampin and also can give theoretical guidance for further design of novel inhibitors to overcome the drug resistance.

Ab initio calculations on the hydrogen bond interaction between diacetamide and ammonia

1997 ◽  
Vol 404 (1-2) ◽  
pp. 75-82 ◽  
Author(s):  
Minh Tho Nguyen ◽  
Natalie Leroux ◽  
Thérèse Zeegers-Huyskens
Keyword(s):  
Hydrogen Bond ◽  
Ab Initio Calculations ◽  
Ab Initio ◽  
Hydrogen Bond Interaction ◽  
Bond Interaction
Sign in / Sign up

Export Citation Format

Share Document