Abstract
▪ Abstract Recent applications of density functional theory to biologically relevant metal centers are reviewed. The emphasis is on reaction mechanisms, structures, and modeling. The accuracy of different functionals is discussed for standard benchmark tests of first- and second-row molecules and for transition metal systems. Modeling aspects of the protein metal complexes are discussed regarding both the size of the model being treated quantum mechanically and the treatment of the protein surrounding it. To illustrate the effects, structures computed without the effects of the protein are compared with experimental structures from enzymes, and results from simple dielectric models of the protein for electron transfer processes are described. The choice of spin state is discussed for multimetal complexes. Examples of mechanisms studied recently by density functional theory are described, such as O2and methane activation in methane monooxygenase and O2formation in photosystem II.
References
116
Referenced
211
10.1016/S0959-440X(98)80048-1
- Noodleman L, Li J, Zhaox G, Richardson WH. 1997. InMethods in Chemistry and Materials Science, ed. M Springborg, pp. 149–88. New York: Wiley
10.1006/jmbi.1996.0484
{'key': 'b4', 'first-page': '2255', 'volume': '3', 'author': 'Ryde U', 'year': '1998', 'journal-title': 'Encycl. Comput. Chem.'}
/ Encycl. Comput. Chem. by Ryde U (1998)10.1021/ja9805268
10.1021/cr00023a010
10.1021/ja963939m
10.1246/cl.1997.1213
10.1007/s007750050239
10.1007/s007750050238
10.1021/ja00041a032
10.1021/ja9642323
10.1021/ic9514307
10.1021/ja982290d
10.1021/jp972207t
{'key': 'b16', 'author': 'Rod TH', 'journal-title': 'Phys. Rev. Lett.'}
/ Phys. Rev. Lett. by Rod TH10.1039/a607136h
10.1002/(SICI)1097-461X(1996)58:1<109::AID-QUA10>3.0.CO;2-2
10.1021/ic960102j
10.1021/ja962305c
10.1021/ja962455n
10.1021/jp9813241
10.1021/jp982321r
10.1021/ic970396o
10.1021/ja971681+
{'key': 'b26', 'author': 'Pavlov M', 'year': '1999', 'journal-title': 'Int. J. Quantum Chem.-Biophys. Quarterly'}
/ Int. J. Quantum Chem.-Biophys. Quarterly by Pavlov M (1999)- Stein M, Lubitz W. 1998. InMagnetic Resonance and Related Phenonmena, ed. D Zussow, F Lendzian, W Lubitz, pp. 820–21. Berlin: Tech. Univ. Berlin
- Deleted in proof
{'key': 'b29', 'volume-title': 'Density-Functional Theory of Atoms and Molecules.', 'author': 'Parr RG', 'year': '1989'}
/ Density-Functional Theory of Atoms and Molecules. by Parr RG (1989)10.1021/cr00005a001
-
Salahub DR. 1987. InAb initio Methods in Quantum Chemistry: Part II Advances in Chemical Physics 68, ed. KP Lawley, pp. 447–520. Chichester, UK: Wiley-Intersci.
(
10.1002/9780470142943.ch8
) - Deleted in proof
10.1103/PhysRevA.38.3098
10.1063/1.462066
10.1063/1.463343
10.1063/1.464913
10.1021/j100096a001
10.1103/PhysRevB.37.785
10.1139/p80-159
10.1103/PhysRevB.45.13244
- Perdew JP. 1991. InElectronic Structure of Solids, ed, P Ziesche, H Eischrig. Berlin: Akademie
10.1103/PhysRevB.46.6671
10.1007/BF01028401
-
Bauschlicher CWJr , Ricca A, Partridge H, Langhoff SR. 1997. InRecent Advances in Density Functional Methods, Part 2, ed. DP Chong, p. 165. Singapore: World Sci.
(
10.1142/9789812819468_0006
) - Deleted in proof
- Deleted in proof
10.1063/1.460205
-
Armentrout PB, Kickel BL. 1995. InOrganometallic Ion Chemistry, ed. BS Freiser, pp. 1–45. Dordrecht, Germany: Kluwer
(
10.1007/978-94-009-0111-7_1
) 10.1063/1.471673
10.1021/jp972531o
- Blomberg MRA, Siegbahn PEM. Unpublished data
10.1021/j100100a015
10.6028/jres.074A.019
10.1021/om00067a012
10.1021/ja00034a004
{'key': 'b56', 'author': 'Koch W', 'year': '1999', 'journal-title': 'Encycl. Comput. Chem.'}
/ Encycl. Comput. Chem. by Koch W (1999)10.1021/j100069a011
10.1021/ja00326a004
10.1007/BF00020428
- Babcock GT. 1995. InPhotosynthesis from Light to Biosphere, ed. P Mathis, 2:209. Dordrecht, Germany: Kluwer
10.1021/ja00146a017
10.1126/science.7569922
- Mayer JM. Personal communication
10.1063/1.477267
10.1063/1.475007
10.1063/1.476577
- Handy NC. Personal communication
- Becke AD. Personal communication
- Scuseria GE. Personal communication
10.1007/s007750050169
10.1002/prot.340190405
10.1126/science.271.5254.1397
10.1021/jp972072r
- Roos BO, Andersson K, Fülscher MP, Malmqvist P-Å, Serrano-Andrés L, et al. 1996. InAdvances in Chemical Physics: New Methods in Computational Quantum Mechanics, ed. I Prigogine, SA Rice, 93:219–331. New York: Wiley
10.1073/pnas.59.2.498
- Fraústo da Silvia JJR, Williams RJP. 1991. InBiological Chemistry of the Elements, pp. 182–84. Oxford: Clarendon
10.1111/j.1432-1033.1995.363_b.x
10.1080/02603598308078118
10.1111/j.1432-1033.1994.tb19044.x
- Levitt M. 1974. InPeptides, Polypeptides and Proteins, ed. ER Blout, FA Bovey, M Goodman, J Lotan, pp. 207–16. New York: Wiley
- Fersht A. 1985. InEnzyme Structure and Mechanims, pp. 341–42. New York: Frieman
- Warshel A. 1991.Computer Modelling of Chemical Reactions in Enzymes and Solutions, pp. 209–11. New York: Wiley
10.1016/S0969-2126(94)00094-8
{'key': 'b84', 'volume-title': 'Gaussian 94 Revision B.2.', 'author': 'Frisch MJ', 'year': '1995'}
/ Gaussian 94 Revision B.2. by Frisch MJ (1995)10.1126/science.2675313
10.1016/0005-2728(84)90205-6
10.1016/0005-2728(86)90243-4
10.1021/bi00192a014
10.1021/jp980753w
{'key': 'b90', 'author': 'Siegbahn PEM', 'year': '1999', 'journal-title': 'Inorg. Chem.'}
/ Inorg. Chem. by Siegbahn PEM (1999)10.1021/ja9805270
10.1016/0009-2614(88)80378-6
10.1016/0009-2614(94)01221-0
- Noodleman L, Case DA, Baerends EJ. 1991. InDensity Functional Methods in Chemistry, ed. JK Labanowski, JW Andzelm, Ch. 8. New York: Springer
10.1021/jp960713x
10.1021/ja00105a033
10.1021/cr00027a011
10.1021/cr9500489
10.1126/science.275.5299.515
10.1021/cr950052k
- Siegbahn PEM. 1997. InMolecular Modeling and Dynamics of Bioinorganic Systems, ed. P Comba, L Banci, pp. 233–53. Dordrecht, Germany: Kluwer Academic
10.1073/pnas.92.8.3209
10.1038/373580a0
10.1021/ja962270g
10.1038/385126a0
{'key': 'b106', 'author': 'Sigfridsson E', 'year': '1999', 'journal-title': 'J. Biol. Inorg. Chem.'}
/ J. Biol. Inorg. Chem. by Sigfridsson E (1999)10.1021/ja974110q
10.1021/ja981059x
10.1021/jp9632955
10.1021/j100072a027
10.1021/jp953543h
10.1007/s007750050166
10.1021/ja970574c
10.1016/S0009-2614(97)00492-2
10.1021/jp9722115
10.1002/chem.19970030523
Dates
Type | When |
---|---|
Created | 23 years ago (July 27, 2002, 7:46 a.m.) |
Deposited | 1 year, 7 months ago (Jan. 6, 2024, 12:10 a.m.) |
Indexed | 1 month, 3 weeks ago (July 2, 2025, 12:17 p.m.) |
Issued | 25 years, 10 months ago (Oct. 1, 1999) |
Published | 25 years, 10 months ago (Oct. 1, 1999) |
Published Print | 25 years, 10 months ago (Oct. 1, 1999) |
@article{Siegbahn_1999, title={D<scp>ENSITY</scp>F<scp>UNCTIONAL</scp>T<scp>HEORY OF</scp>B<scp>IOLOGICALLY</scp>R<scp>ELEVANT</scp>M<scp>ETAL</scp>C<scp>ENTERS</scp>}, volume={50}, ISSN={1545-1593}, url={http://dx.doi.org/10.1146/annurev.physchem.50.1.221}, DOI={10.1146/annurev.physchem.50.1.221}, number={1}, journal={Annual Review of Physical Chemistry}, publisher={Annual Reviews}, author={Siegbahn, Per E. M. and Blomberg, Margareta R. A.}, year={1999}, month=oct, pages={221–249} }