Insights into intermolecular interactions, electrostatic properties and the stability of C646 in the binding pocket of p300 histone acetyltransferase enzyme: a combined molecular dynamics and charge density study

2017 ◽  
Vol 36 (12) ◽  
pp. 3246-3264 ◽  
Author(s):  
Magudeeswaran Sivanandam ◽  
Kandasamy Saravanan ◽  
Poomani Kumaradhas
Author(s):  
Chinnasamy Kalaiarasi ◽  
Christy George ◽  
Rajesh G. Gonnade ◽  
Venkatesha R. Hathwar ◽  
Kumaradhas Poomani

Metronidazole is a radiosensitizer; it crystallizes in the monoclinic system with space group P21/c. The crystal structure of metronidazole has been determined from high-resolution X-ray diffraction measurements at 90 K with a resolution of (sin θ/λ)max = 1.12 Å−1. To understand the charge-density distribution and the electrostatic properties of metronidazole, a multipole model refinement was carried out using the Hansen–Coppens multipole formalism. The topological analysis of the electron density of metronidazole was performed using Bader's quantum theory of atoms in molecules to determine the electron density and the Laplacian of the electron density at the bond critical point of the molecule. The experimental results have been compared with the corresponding periodic theoretical calculation performed at the B3LYP/6-31G** level using CRYSTAL09. The topological analysis reveals that the N—O and C—NO2 exhibit less electron density as well as negative Laplacian of electron density. The molecular packing of crystal is stabilized by weak and strong inter- and intramolecular hydrogen bonding and H...H interactions. The topological analysis of O—H...N, C—H...O and H...H intra- and intermolecular interactions was also carried out. The electrostatic potential of metronidazole, calculated from the experiment, predicts the possible electrophilic and nucleophilic sites of the molecule; notably, the hydroxyl and the nitro groups exhibit large electronegative regions. The results have been compared with the corresponding theoretical results.


RSC Advances ◽  
2014 ◽  
Vol 4 (101) ◽  
pp. 57823-57833 ◽  
Author(s):  
G. Rajalakshmi ◽  
Mysore S. Pavan ◽  
P. Kumaradhas

The experimental and theoretical charge density analysis of ethionamide molecule provides the topological and the electrostatic properties, which allows the understanding of the nature of intra- and intermolecular interactions.


2015 ◽  
Vol 17 (21) ◽  
pp. 14177-14184 ◽  
Author(s):  
L.-C. Wu ◽  
W.-C. Chung ◽  
C.-C. Wang ◽  
G.-H. Lee ◽  
S.-I. Lu ◽  
...  

The location of bond critical points (red dots) and its associated bond path (black line) provide the evidence on the existence of the weak intermolecular interactions of the π–π interactions between triazole rings of atrz molecules in crystal with the close ring distance of 3.17 Å.


2011 ◽  
Vol 989 (1-3) ◽  
pp. 122-130 ◽  
Author(s):  
Arputharaj David Stephen ◽  
Reji Thomas ◽  
Ponnusamy Srinivasan ◽  
Vijayan Narayayanasamy ◽  
Poomani Kumaradhas

2011 ◽  
Vol 295-297 ◽  
pp. 1505-1509 ◽  
Author(s):  
Ying Xia Qi ◽  
Hua Zhang ◽  
Sheng Xi Zhao

Molecular dynamics simulations are carried out to investigate the effect of the occupation of the cages on the stability of sI CO2 hydrates. Three types of cage occupations are concerned. The TIP4P/EPM2/DUAN potential models are used for the water-water, CO2-CO2, water-CO2 intermolecular interactions. The simulation results show that the occupation of the large cage is preferable compared to the occupation of the small cage. It may be induced that the hydration number of sI CO2 hydrates is mostly to be 9.


2011 ◽  
Vol 966 (1-3) ◽  
pp. 259-264 ◽  
Author(s):  
Gnanasekaran Rajalakshmi ◽  
Balu Devipriya ◽  
Azhagesan Renuga Parameswari ◽  
Arputharaj David Stephen ◽  
Poomani Kumaradhas

2020 ◽  
Vol 1220 ◽  
pp. 128714
Author(s):  
Chinnasamy Kalaiarasi ◽  
Magudeeswaran Sivanandam ◽  
Suresh Suganya ◽  
George Christy ◽  
Rajesh G. Gonnade ◽  
...  

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