Crystal structure, quantum chemical and theoretical charge density analysis of 5‑bromo-2-(4-methylbenzyl)-6-(4-nitrophenyl)imidazo[2,1-b][1,3,4] thiadiazole

2020 ◽  
Vol 25 ◽  
pp. 100326
Author(s):  
A. Sowmya ◽  
G.N. Anil Kumar ◽  
Sujeet Kumar ◽  
Subhas S. Karki
ChemInform ◽  
2010 ◽  
Vol 41 (13) ◽  
Author(s):  
T. Noritake ◽  
M. Aoki ◽  
M. Matsumoto ◽  
K. Miwa ◽  
S. Towata ◽  
...  

Author(s):  
Gautam R. Desiraju

Three approaches to the exploration of the crystal structure landscape are outlined. These are crystal structure prediction, non-ambient crystallography and charge density analysis.


Author(s):  
Renuga Parameswari Azhagesan ◽  
Saravanan Kandasamy ◽  
Kumaradhas Poomani

Huperzine A is an herbal reversible inhibitor of Acetylcholinesterase (AChE). A molecular docking analysis on Huperzine A molecule has been carried out to understand its structure, conformational flexibility, intermolecular interaction and the binding affinity in the active site of AChE enzyme. Further, the charge density distribution of huperzine A molecule (lifted from the active site of AChE) was determined from the high level quantum chemical calculations coupled with charge density analysis. The binding affinity of Huperzine A towards AChE was calculated from the molecular docking; the lowest docked energy is -8.46 kcal/mol. In the active site, huperzine A molecule interacts with acyl binding pocket-Phe330 of AChE, that is, the bicyclo ring group of huperzine A forms an intermolecular interaction with the oxygen atom of main chain of the amino acid residue Phe330 at the distances 3.02 and 3.25 Å respectively. On the other hand, a gas phase study on huperzine A molecule also performed using HF and DFT (B3LYP) methods with the basis set 6-311G**. The molecular structure, conformation, and the charge density distribution of huperzine A molecule in the gas phase have determined using quantum chemical calculations and the charge density analysis. The comparative studies between the gas phase and the active site forms of huperzine A molecule, explicitly reveals the degree of conformational modification and the charge density redistribution of huperzine A when present in the active site. The dipole moment of the molecule in the active site is 6.85 D, which is slightly higher than its gas phase value (5.91 D). The electrostatic potential (ESP) surface of active site molecule clearly shows the strong electronegative and positive ESP regions of the molecule, which are the expected strong reactive locations of the molecule.


Author(s):  
Philip Coppens

The number of reflection intensities measured in a crystallographic experiment is large, and commonly exceeds the number of parameters to be determined. It was first realized by Hughes (1941) that such an overdetermination is ideally suited for the application of the least-squares methods of Gauss (see, e.g., Whittaker and Robinson 1967), in which an error function S, defined as the sum of the squares of discrepancies between observation and calculation, is minimized by adjustment of the parameters of the observational equations. As least-squares methods are computationally convenient, they have largely replaced Fourier techniques in crystal structure refinement. In addition to the positional and thermal parameters of the atoms, least-squares procedures are used to determine the scale of the data, and parameters such as mosaic spread or particle size, which influence the intensities through multiple-beam effects (Becker and Coppens 1974a, b, 1975). It is not an exaggeration to say that modern crystallography is, to a large extent, made possible by the use of least-squares methods. Similarly, least-squares techniques play a central role in the charge density analysis with the scattering formalisms described in the previous chapter. The following description follows closely the treatment given by Hamilton (1964).


2005 ◽  
Vol 393 (1-2) ◽  
pp. 264-268 ◽  
Author(s):  
T. Noritake ◽  
H. Nozaki ◽  
M. Aoki ◽  
S. Towata ◽  
G. Kitahara ◽  
...  

ChemInform ◽  
2005 ◽  
Vol 36 (29) ◽  
Author(s):  
T. Noritake ◽  
H. Nozaki ◽  
M. Aoki ◽  
S. Towata ◽  
G. Kitahara ◽  
...  

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