On the reliability of the corrected semiempirical quantum chemical method (PM6-DH2) for assigning the protonation states in HIV-1 protease/inhibitor complexes

Result code in IS VaVaI
<a href="https://www.isvavai.cz/riv?ss=detail&h=RIV%2F61388963%3A_____%2F11%3A00368013" target="_blank" >RIV/61388963:_____/11:00368013 - isvavai.cz</a>
Result on the web
<a href="http://dx.doi.org/10.1135/cccc2011035" target="_blank" >http://dx.doi.org/10.1135/cccc2011035</a>
DOI - Digital Object Identifier
<a href="http://dx.doi.org/10.1135/cccc2011035" target="_blank" >10.1135/cccc2011035</a>

Result language
angličtina
Original language name
On the reliability of the corrected semiempirical quantum chemical method (PM6-DH2) for assigning the protonation states in HIV-1 protease/inhibitor complexes
Original language description
A novel computational protocol for studying protonation in protein/ligand complexes is presented. We use a QM/MM approach in which the large QM part (the ligand and the active site) are treated using the corrected semiempirical method PM6-DH2, while theMM part (the rest of the protein and the surrounding solvent) are calculated using MM/GB method. This approach is applied to two model systems, the carboxylate pairs in HIV-1 protease/inhibitor complexes. The computationally more costly DFT optimizationsare performed for a smaller QM part as a check of the correctness. Proton transfer (PT) phenomena occur at both the PM6-D2 and DFT levels, which underlines the requirement for a QM approach. The barriers of PT are checked in model carboxylic acid pairsusing the highly accurate MP2 and CCSD(T) values. An important result of this study is the fine-tuning of the protocol which can be used in further applications; its limitations are also shown, pointing to future developments.
Czech name
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Czech description
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Type
J<sub>x</sub> - Unclassified - Peer-reviewed scientific article (Jimp, Jsc and Jost)
CEP classification
CF - Physical chemistry and theoretical chemistry
OECD FORD branch
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Project
Result was created during the realization of more than one project. More information in the Projects tab.
Continuities
Z - Vyzkumny zamer (s odkazem do CEZ)

Publication year
2011
Confidentiality
S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů

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