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Recent developments of the quantum chemical cluster approach for modeling enzyme reactions
KTH, School of Biotechnology (BIO), Theoretical Chemistry.
2009 (English)In: Journal of Biological Inorganic Chemistry, ISSN 0949-8257, E-ISSN 1432-1327, Vol. 14, no 5, 643-651 p.Article, review/survey (Refereed) Published
Abstract [en]

The quantum chemical cluster approach for modeling enzyme reactions is reviewed. Recent applications have used cluster models much larger than before which have given new modeling insights. One important and rather surprising feature is the fast convergence with cluster size of the energetics of the reactions. Even for reactions with significant charge separation it has in some cases been possible to obtain full convergence in the sense that dielectric cavity effects from outside the cluster do not contribute to any significant extent. Direct comparisons between quantum mechanics (QM)-only and QM/molecular mechanics (MM) calculations for quite large clusters in a case where the results differ significantly have shown that care has to be taken when using the QM/MM approach where there is strong charge polarization. Insights from the methods used, generally hybrid density functional methods, have also led to possibilities to give reasonable error limits for the results. Examples are finally given from the most extensive study using the cluster model, the one of oxygen formation at the oxygen-evolving complex in photosystem II.

Place, publisher, year, edition, pages
2009. Vol. 14, no 5, 643-651 p.
Keyword [en]
Computational chemistry, Density functional theory, Molecularmodeling, Photosynthesis, site arginine residues, hydrogen-halide-lyase, 4-oxalocrotonate, tautomerase, photosystem-ii, halohydrin dehalogenases, haloalcohol, dehalogenase, nife-hydrogenase, qm/mm methods, mechanism, resolution
Identifiers
URN: urn:nbn:se:kth:diva-18509DOI: 10.1007/s00775-009-0511-yISI: 000266924400001Scopus ID: 2-s2.0-67649476220OAI: oai:DiVA.org:kth-18509DiVA: diva2:336556
Note
QC 20100525Available from: 2010-08-05 Created: 2010-08-05 Last updated: 2017-12-12Bibliographically approved

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