Reaction Mechanism of Ru(II) Piano-Stool Complexes: Umbrella Sampling QM/MM MD Study
The result's identifiers
Result code in IS VaVaI
<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F00216208%3A11320%2F14%3A10286196" target="_blank" >RIV/00216208:11320/14:10286196 - isvavai.cz</a>
Result on the web
<a href="http://dx.doi.org/10.1002/jcc.23639" target="_blank" >http://dx.doi.org/10.1002/jcc.23639</a>
DOI - Digital Object Identifier
<a href="http://dx.doi.org/10.1002/jcc.23639" target="_blank" >10.1002/jcc.23639</a>
Alternative languages
Result language
angličtina
Original language name
Reaction Mechanism of Ru(II) Piano-Stool Complexes: Umbrella Sampling QM/MM MD Study
Original language description
Biologically relevant interactions of piano-stool ruthenium(II) complexes with ds-DNA are studied in this article by hybrid quantum mechanics-molecular mechanics (QM/MM) computational technique. The whole reaction mechanism is divided into three phases:(i) hydration of the [Ru-II(H-6 -benzene)(en) Cl](+) complex, (ii) monoadduct formation between the resulting aqua-Ru(II) complex and N7 position of one of the guanines in the ds-DNA oligomer, and (iii) formation of the intrastrand Ru(II) bridge (cross-link) between two adjacent guanines. Free energy profiles of all the reactions are explored by QM/MM MD umbrella sampling approach where the Ru(II) complex and two guanines represent a quantum core, which is described by density functional theory methods.The combined QM/MM scheme is realized by our own software, which was developed to couple several quantum chemical programs (in this study Gaussian 09) and Amber 11 package. Calculated free energy barriers of the both ruthenium hydration
Czech name
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Czech description
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Classification
Type
J<sub>x</sub> - Unclassified - Peer-reviewed scientific article (Jimp, Jsc and Jost)
CEP classification
BJ - Thermodynamics
OECD FORD branch
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Result continuities
Project
<a href="/en/project/GAP208%2F12%2F0622" target="_blank" >GAP208/12/0622: Interactions of organometallic antitumor compounds with nucleic acids and proteins: study of sequence and substrate selectivity</a><br>
Continuities
P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)
Others
Publication year
2014
Confidentiality
S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů
Data specific for result type
Name of the periodical
Journal of Computational Chemistry
ISSN
0192-8651
e-ISSN
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Volume of the periodical
35
Issue of the periodical within the volume
19
Country of publishing house
US - UNITED STATES
Number of pages
11
Pages from-to
1446-1456
UT code for WoS article
000337641400005
EID of the result in the Scopus database
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