The DOI matches its Crossref record; 15 of the 15 references it cites were found in a registry or an index.
Modeling Enzymatic Reactions Involving Transition Metals
Abstract
High-accuracy quantum chemistry has now been applied for almost 10 years to biological problems involving transition metal active sites. The leading theoretical method is hybrid density functional theory (DFT), usually with the B3LYP functional. The chemical models vary in size, commonly from 30 to 100 atoms treated fully quantum mechanically. Two schools exist, one using the smallest possible adequate models and the other using as large models as possible and sometimes including the entire enzyme by combining quantum mechanics with molecular mechanics. In our group, we have found that the latter approach, which is much more time-consuming and error prone, is seldom needed. In this Account, methods and models will be described and examples of recent applications given. The examples are chosen to illustrate trends and to show cases where theory has predicted new mechanisms not suggested previously.
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Citations
Cites
Theoretical Perspective on the Structure and Mechanism of Cytochrome P450 Enzymes
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Mechanism of Dioxygen Activation in 2‐Oxoglutarate‐Dependent Enzymes: A Hybrid DFT Study
Borowski, T., Bassan, A., & Siegbahn, P. E. M. (2004) · Chemistry – A European Journal · doi:10.1002/chem.200305306 · Cited by 175
Self-citationBassan, A., Blomberg, M. R. A., Siegbahn, P. E. M., & QUE, L. J. (2002) · Journal of the American Chemical Society · doi:10.1021/ja026488g · Cited by 156
Self-citationA Mechanism from Quantum Chemical Studies for Methane Formation in Methanogenesis
Pelmenschikov, V., Blomberg, M. R. A., Siegbahn, P. E. M., & Crabtree, R. H. (2002) · Journal of the American Chemical Society · doi:10.1021/ja011664r · Cited by 119
Self-citationA theoretical study on the binding of O2, NO and CO to heme proteins
Blomberg, L. M., Blomberg, M. R. A., & Siegbahn, P. E. M. (2005) · Journal of Inorganic Biochemistry · doi:10.1016/j.jinorgbio.2005.02.014 · Cited by 102
Self-citationTargeting of HIV- and SIV-Infected Cells by CD4-Chemokine Receptor Pseudotypes
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Self-citationJohnson-Winters, K. L., Purpero, V. M., Kavana, M., Nelson, T., & Moran, G. R. (2003) · Biochemistry · doi:10.1021/bi026499m · Cited by 83
Catalytic Reaction Mechanism of Homogentisate Dioxygenase: A Hybrid DFT Study
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Self-citationBorowski, T., Bassan, A., & Siegbahn, P. E. M. (2004) · Inorganic Chemistry · doi:10.1021/ic035395c · Cited by 45
Self-citation
Cited by
Density functional theory for transition metals and transition metal chemistry
Cramer, C. J., & Truhlar, D. G. (2009) · Physical Chemistry Chemical Physics · doi:10.1039/b907148b · Cited by 1,648
Reactivity of High-Valent Iron–Oxo Species in Enzymes and Synthetic Reagents: A Tale of Many States
Shaik, S., Hirao, H., & Kumar, D. (2007) · Accounts of Chemical Research · doi:10.1021/ar600042c · Cited by 555
Structural Survey of Zinc-Containing Proteins and Development of the Zinc AMBER Force Field (ZAFF)
Peters, M. B., Yang, Y., Wang, B., Füsti-Molnár, L., Weaver, M. N., & Merz, K. M. (2010) · Journal of Chemical Theory and Computation · doi:10.1021/ct1002626 · Cited by 501
The quantum chemical cluster approach for modeling enzyme reactions
Siegbahn, P. E. M., & Himo, F. (2011) · WIREs Computational Molecular Science · doi:10.1002/wcms.13 · Cited by 288
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Metadata
- Authors
- Siegbahn, P. E. M., & Borowski, T.
- Venue
- Accounts of Chemical Research
- Publisher
- American Chemical Society (ACS)
- Published
- 2006-07-13
- Volume
- 39
- Issue
- 10
- Pages
- 729-738
- ISSN
- 0001-4842 (ISSN-L)
- 1520-4898
- OpenAlex
- W2119292856
- Cited by
- 309
- References
- 15
- FWCI
- 12.03
- Type
- journal article
- Language
- en
- Open access
- closed
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