NDLI: Theoretical study of anticancer drug trans-[Pd(dmnp)$_{2}$Cl$_{2}$] binding to DNA purine bases, phosphate group and amino acid residues

Content Provider	Springer Nature Link
Author	Jiang, Bo Zhou, Lixin
Copyright Year	2011
Abstract	The reaction mechanism of the binding of the completely hydrolyzed trans-[Pd(dmnp)$_{2}$Cl$_{2}$] (dmnp = 2,6-dimethyl-4-nitropyridine) complexes to DNA and peptides was investigated computationally using model molecules and density functional theory calculations at the B3LYP level. To test the solvent effect, single-point energy calculations for the structures optimized in all reactions were conducted by employing the polarizable continuum model (IEF-PCM). The pentammineruthenium fragment had been intensively studied and also constituted a good model for antitumor trans-[Pd(dmnp)$_{2}$Cl$_{2}$], while the considered bases/ligands had been chosen as models for the main binding sites of DNA, nucleobases, and phosphate backbone and proteins, nitrogen-containing histidyl, and sulfur-containing residue such as methionine or cysteine. The activation free energies had been calculated for all the considered metal binding sites both in the gas phase and in solution and allowed building a binding affinity order for the considered nucleic acid or protein binding sites. Additionally, to better understand the interactions between the compounds and binding sites, the natural orbital population analysis (NPA) was adopted for every stationary point to employ the mutative trend of the net charge on the three important atoms which directly related to the reactions.
Starting Page	1353
Ending Page	1364
Page Count	12
File Format	PDF
ISSN	10400400
Journal	Structural Chemistry
Volume Number	22
Issue Number	6
e-ISSN	15729001
Language	English
Publisher	Springer US
Publisher Date	2011-07-12
Publisher Place	Boston
Access Restriction	One Nation One Subscription (ONOS)
Subject Keyword	DFT Trans-[Pd(dmnp)$_{2}$Cl$_{2}$] DNA purine bases Phosphate group Amino acid residues Hydrogen bond Theoretical and Computational Chemistry Physical Chemistry Computer Applications in Chemistry
Content Type	Text
Resource Type	Article
Subject	Physical and Theoretical Chemistry Condensed Matter Physics

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