Modeling zinc in biomolecules with the self consistent charge-density functional tight binding (SCC-DFTB) method: Applications to structural and energetic analysis
✍ Scribed by Marcus Elstner; Qiang Cui; Petra Munih; Efthimios Kaxiras; Thomas Frauenheim; Martin Karplus
- Publisher
- John Wiley and Sons
- Year
- 2003
- Tongue
- English
- Weight
- 777 KB
- Volume
- 24
- Category
- Article
- ISSN
- 0192-8651
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✦ Synopsis
Abstract
Parameters for the zinc ion have been developed in the self‐consistent charge density functional tight‐binding (SCC‐DFTB) framework. The approach was tested against B3LYP calculations for a range of systems, including small molecules that contain the typical coordination environment of zinc in biological systems (cysteine, histidine, glutamic/aspartic acids, and water) and active site models for a number of enzymes such as alcohol dehydrogenase, carbonic anhydrase, and aminopeptidase. The SCC‐DFTB approach reproduces structural and energetic properties rather reliably (e.g., total and relative ligand binding energies and deprotonation energies of ligands and barriers for zinc‐assisted proton transfers), as compared with B3LYP/6‐311+G** or MP2/6‐311+G** calculations. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 565–581, 2003