The interaction of proteins with silica surfaces. Part I: Ab initio modeling
Result description
Recently synthesized 2D zeolites with well-defined external surfaces have been used as model systems for the adsorption of proteins on silica materials. In this work the interaction of 19 proteinogenic amino-acid side chains in the C-beta representation and the Ace-NMe backbone model with the 2D-UTL and 2D-MWW zeolites has been investigated. The performance of different DC-DFT methods has been compared against the MP2/CBS and CCSD(T)/CBS levels of theory for cluster models of alpha-quartz and 2D-UTL. The obtained statistics clearly indicate that none of the common DC-DFT methods is capable of describing the side-chain interaction with silica surfaces within chemical accuracy (similar to 1 kcal/mol). Two different approaches have been employed to improve the accuracy: (i) the re-parameterization of the pair-wise dispersion term as proposed by Grimme 2006 and (ii) the correction scheme based on an error analysis of the vdW-DF2 functional. Both methods provide consistent and highly accurate results for external silica surfaces with and without silanol groups.
Keywords
The result's identifiers
Result code in IS VaVaI
Result on the web
DOI - Digital Object Identifier
Alternative languages
Result language
angličtina
Original language name
The interaction of proteins with silica surfaces. Part I: Ab initio modeling
Original language description
Recently synthesized 2D zeolites with well-defined external surfaces have been used as model systems for the adsorption of proteins on silica materials. In this work the interaction of 19 proteinogenic amino-acid side chains in the C-beta representation and the Ace-NMe backbone model with the 2D-UTL and 2D-MWW zeolites has been investigated. The performance of different DC-DFT methods has been compared against the MP2/CBS and CCSD(T)/CBS levels of theory for cluster models of alpha-quartz and 2D-UTL. The obtained statistics clearly indicate that none of the common DC-DFT methods is capable of describing the side-chain interaction with silica surfaces within chemical accuracy (similar to 1 kcal/mol). Two different approaches have been employed to improve the accuracy: (i) the re-parameterization of the pair-wise dispersion term as proposed by Grimme 2006 and (ii) the correction scheme based on an error analysis of the vdW-DF2 functional. Both methods provide consistent and highly accurate results for external silica surfaces with and without silanol groups.
Czech name
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Czech description
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Classification
Type
Jimp - Article in a specialist periodical, which is included in the Web of Science database
CEP classification
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OECD FORD branch
10403 - Physical chemistry
Result continuities
Project
Result was created during the realization of more than one project. More information in the Projects tab.
Continuities
P - Projekt vyzkumu a vyvoje financovany z verejnych zdroju (s odkazem do CEP)
Others
Publication year
2017
Confidentiality
S - Úplné a pravdivé údaje o projektu nepodléhají ochraně podle zvláštních právních předpisů
Data specific for result type
Name of the periodical
Computational and Theoretical Chemistry
ISSN
2210-271X
e-ISSN
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Volume of the periodical
1117
Issue of the periodical within the volume
Oct 1
Country of publishing house
NL - THE KINGDOM OF THE NETHERLANDS
Number of pages
8
Pages from-to
100-107
UT code for WoS article
000412250300012
EID of the result in the Scopus database
2-s2.0-85027218956
Basic information
Result type
Jimp - Article in a specialist periodical, which is included in the Web of Science database
OECD FORD
Physical chemistry
Year of implementation
2017