A method to incorporate the radial distribution function of bulk fluid into the density functional approximation

2001 ◽  
Vol 115 (5) ◽  
pp. 2212-2218 ◽  
Author(s):  
Shiqi Zhou
Keyword(s):  
Distribution Function ◽  
Radial Distribution Function ◽  
Radial Distribution ◽  
Density Functional ◽  
Bulk Fluid ◽  
Functional Approximation

The Influence of Hydrogen atoms on the Performance of Radial Distribution Function Based Descriptors in the Chemoinformatic Studies of HIV-1 Prote-ase Complexes with Inhibitors.

2020 ◽  
Vol 17 ◽  
Author(s):  
Jurica Novak ◽  
Maria A. Grishina ◽  
Vladimir A. Potemkin
Keyword(s):  
Distribution Function ◽  
Radial Distribution Function ◽  
Radial Distribution ◽  
Current Model ◽  
Direct Interaction ◽  
Hydroxyl Group ◽  
Linear Regression Method ◽  
Hydrogen Atoms ◽  
Protease Enzyme ◽  
Hiv 1

: In this letter the newly introduced approach based on the radial distribution function (RDF) weighted by the number of va-lence shell electrons is applied for a series of HIV-1 protease enzyme and its complexes with inhibitors to evaluate the influ-ence of hydrogen atoms on the performance of the model. The multiple linear regression method was used for the selection of the relevant descriptors. Two groups of residues having dominant contribution to the RDF descriptor are identified as relevant for the inhibition. In the first group are residues like Arg8, Asp25, Thr26, Gly27 and Asp29, which establish direct interaction with the inhibitor, while the second group consists of the amino acids at the interface of the two homodimer sub-units or with the solvent. The crucial motif pointed out by our approach as the most important for inhibition of the enzyme’s activity and present in all inhibitors is hydroxyl group that establish hydrogen bond with Asp25 side chain. Additionally, the comparison to the model without hydrogen showed that both models are of similar quality, but the downside of the current model is the need for the determination of residues’ protonation states.

Effect of Substrate Temperature and Incident Energy for Alloyzation of Co onto Cu(001) Substrate

2008 ◽  
Vol 47-50 ◽  
pp. 375-378 ◽  
Author(s):  
Zheng Han Hong ◽  
Shun Fa Hwang ◽  
Te Hua Fang
Keyword(s):  
Molecular Dynamics ◽  
Distribution Function ◽  
Substrate Temperature ◽  
Radial Distribution Function ◽  
Radial Distribution ◽  
Incident Energy

The mixing situation of Co atoms implanting onto Cu(001) substrate is investigated with regard to incident energy and substrate temperature by molecular dynamics. The results indicate that higher substrate temperature and/or incident energy will result in higher intermixing between the incident atoms and the substrate atoms. Furthermore, the value of the first peak of the radial distribution function (RDF) becomes lower and wider for the Co-Cu system as the substrate temperature and/or incident energy are increased.

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