scholarly journals Combined quantum mechanics/molecular mechanics (QM/MM) methods to understand the charge density distribution of estrogens in the active site of estrogen receptors

RSC Advances ◽  
2019 ◽  
Vol 9 (69) ◽  
pp. 40758-40771 ◽  
Author(s):  
C. Kalaiarasi ◽  
S. Manjula ◽  
P. Kumaradhas
Keyword(s):  
Quantum Mechanics ◽  
Molecular Recognition ◽  
Ligand Binding ◽  
Density Distribution ◽  
Charge Density ◽  
Estrogen Receptors ◽  
Molecular Mechanics ◽  
Active Site ◽  
Charge Density Distribution

The ligand binding to protein and host–guest interactions are ubiquitous for molecular recognition.

scholarly journals Conformational Flexibility and the Interaction of Huperzine A in the Active Site of Acetylcholinesterase: A Quantum Chemical and Charge Density Study

2016 ◽  
Author(s):  
Renuga Parameswari Azhagesan ◽  
Saravanan Kandasamy ◽  
Kumaradhas Poomani
Keyword(s):  
Molecular Docking ◽  
Density Distribution ◽  
Charge Density ◽  
Gas Phase ◽  
Active Site ◽  
Quantum Chemical ◽  
Conformational Flexibility ◽  
Huperzine A ◽  
Charge Density Distribution ◽  
Density Analysis

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.

Characterization of the B⋯π-system interaction via topology of the experimental charge density distribution in the crystal of 3-chloro-7α-phenyl-3-borabicyclo[3.3.1]nonane

2004 ◽  
Vol 384 (1-3) ◽  
pp. 40-44 ◽  
Author(s):  
Konstatin A Lyssenko ◽  
Mikhail Yu Antipin ◽  
Mikhail E Gurskii ◽  
Yurii N Bubnov ◽  
Anna L Karionova ◽  
...  
Keyword(s):  
Density Distribution ◽  
Charge Density ◽  
Charge Density Distribution ◽  
Experimental Charge Density

Experimental charge density distribution and its correlation to structural and optical properties of Sm 3+ doped Nd 2 O 3 nanophosphors

2017 ◽  
Vol 35 (11) ◽  
pp. 1102-1114 ◽  
Author(s):  
Morris Marieli Antoinette ◽  
S. Israel ◽  
G. Sathya ◽  
Arlin Jose Amali ◽  
John L. Berchmans ◽  
...  
Keyword(s):  
Optical Properties ◽  
Density Distribution ◽  
Charge Density ◽  
Structural And Optical Properties ◽  
Charge Density Distribution ◽  
Experimental Charge Density

scholarly journals High-throughput quantum-mechanics/molecular-mechanics (ONIOM) macromolecular crystallographic refinement withPHENIX/DivCon: the impact of mixed Hamiltonian methods on ligand and protein structure

2018 ◽  
Vol 74 (11) ◽  
pp. 1063-1077 ◽  
Author(s):  
Oleg Borbulevych ◽  
Roger I. Martin ◽  
Lance M. Westerhoff
Keyword(s):  
Quantum Mechanics ◽  
Molecular Mechanics ◽  
High Throughput ◽  
Active Site ◽  
Binding Modes ◽  
Acta Cryst ◽  
Structure Based Drug Design ◽  
Energy Functionals ◽  
Conventional Methods ◽  
The Impact

Conventional macromolecular crystallographic refinement relies on often dubious stereochemical restraints, the preparation of which often requires human validation for unusual species, and on rudimentary energy functionals that are devoid of nonbonding effects owing to electrostatics, polarization, charge transfer or even hydrogen bonding. While this approach has served the crystallographic community for decades, as structure-based drug design/discovery (SBDD) has grown in prominence it has become clear that these conventional methods are less rigorous than they need to be in order to produce properly predictive protein–ligand models, and that the human intervention that is required to successfully treat ligands and other unusual chemistries found in SBDD often precludes high-throughput, automated refinement. Recently, plugins to thePython-based Hierarchical ENvironment for Integrated Xtallography(PHENIX) crystallographic platform have been developed to augment conventional methods with thein situuse of quantum mechanics (QM) applied to ligand(s) along with the surrounding active site(s) at each step of refinement [Borbulevychet al.(2014),Acta CrystD70, 1233–1247]. This method (Region-QM) significantly increases the accuracy of the X-ray refinement process, and this approach is now used, coupled with experimental density, to accurately determine protonation states, binding modes, ring-flip states, water positions and so on. In the present work, this approach is expanded to include a more rigorous treatment of the entire structure, including the ligand(s), the associated active site(s) and the entire protein, using a fully automated, mixed quantum-mechanics/molecular-mechanics (QM/MM) Hamiltonian recently implemented in theDivConpackage. This approach was validated through the automatic treatment of a population of 80 protein–ligand structures chosen from the Astex Diverse Set. Across the entire population, this method results in an average 3.5-fold reduction in ligand strain and a 4.5-fold improvement inMolProbityclashscore, as well as improvements in Ramachandran and rotamer outlier analyses. Overall, these results demonstrate that the use of a structure-wide QM/MM Hamiltonian exhibits improvements in the local structural chemistry of the ligand similar to Region-QM refinement but with significant improvements in the overall structure beyond the active site.

Correction: Experimental and theoretical charge density distribution in Pigment Yellow 101

2015 ◽  
Vol 17 (9) ◽  
pp. 6667-6667
Author(s):  
Jonathan J. Du ◽  
Linda Váradi ◽  
Jinlong Tan ◽  
Yiliang Zhao ◽  
Paul W. Groundwater ◽  
...  
Keyword(s):  
Density Distribution ◽  
Charge Density ◽  
Chem Phys ◽  
Charge Density Distribution ◽  
Phys Chem Chem Phys

Correction for ‘Experimental and theoretical charge density distribution in Pigment Yellow 101’ by Jonathan J. Du et al., Phys. Chem. Chem. Phys., 2015, DOI: 10.1039/c4cp04302b.

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