Abstract
Some recent applications of density functional theory (DFT) are described and specifically the review addresses the activation of small molecules such as water, molecular oxygen and its reduced congeners, nitrogen oxides and oxyanions, sulfide, sulfur oxides and oxyanions, carbon dioxide, organic compounds, halogens, molecular hydrogen, and protons. A range of predictions on geometry, electronic structure, and spectroscopic properties are made and binding energies and activation energies are critically reviewed.
Graphical Abstract
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
Abbreviations
- CANH:
-
Carbonic anhydrase
- CPOI:
-
Chloroperoxidase
- DFT:
-
Density functional theory
- Fe-SOD:
-
Iron-containing SOD
- MM:
-
Molecular mechanics
- MPO:
-
Myeloperoxidase
- Ni-SOD:
-
Nickel-containing SOD
- NOR:
-
Nitric oxide reductase
- P450NOR:
-
P450-like nitric oxide reductase
- P450:
-
Cytochrome P450
- QM:
-
Quantum mechanics
- SOD:
-
Superoxide dismutase
- SOR:
-
Superoxide reductase
- TD-DFT:
-
Time-dependent DFT
- TSR:
-
Two-state reactivity
- VPO:
-
Vanadium-containing peroxidase
References
Tolman WB (2006) Activation of small molecules: organometallic and bioinorganic perspectives. Wiley, New York, 382 pp
Kraatz HB, Metzler-Nolte N (2006) Concepts and models in bioinorganic chemistry. Wiley-VCH, Weinheim
Zhao Y, Truhlar DG (2006) Acc Chem Res 41:157
Hersleth HP, Ryde U, Rydberg P, Gorbitz CH, Andersson KK (2006) J Inorg Biochem 100:460
Groves JT (2006) J Inorg Biochem 100:434
Decker A, Clay MD, Solomon EI (2006) J Inorg Biochem 100:697
Green MT, Dawson JH, Gray HB (2004) Science 304:1653
Silaghi-Dumitrescu R, Silaghi-Dumitrescu I (2004) Rev Roum Chim 3–4:257
Silaghi-Dumitrescu R (2006) Studia Univ Babes-Bolyai Chemia 51:167
Rydberg P, Sigfridsson E, Ryde U (2004) J Biol Inorg Chem 9:203
Jensen KP, Roos BO, Ryde U (2005) J Inorg Biochem 99:45–54
Silaghi-Dumitrescu R (2003) Eur J Inorg Chem 1048
Silaghi-Dumitrescu R (2008) Revue Roumaine de Chimie 53:1149
Silaghi-Dumitrescu R (2004) J Biol Inorg Chem 9:471
Stone KL, Behan RK, Green MT (2006) Proc Natl Acad Sci USA 103:12307
Stone KL, Hoffart LM, Behan RK, Krebs C, Green MT (2006) J Am Chem Soc 128:6147
Green MT (2006) J Am Chem Soc 128:1902
Behan RK, Hoffart LM, Stone KL, Krebs C, Green MT (2006) J Am Chem Soc 128:11471
Behan RK, Green MT (2006) J Inorg Biochem 100:448
Stone KL, Behan RK, Green MT (2005) Proc Natl Acad Sci USA 102:16563
Silaghi-Dumitrescu R, Reeder BJ, Nicholls P, Cooper CE, Wilson MT (2007) Biochem J 403:391
Silaghi-Dumitrescu R (2005) Studia Univ Babes-Bolyai Chemia 50:17
Shaik S, de Visser SP, Kumar D (2004) J Biol Inorg Chem 9:661
Silaghi-Dumitrescu R (2007) Rev Chim 58:461
Silaghi-Dumitrescu R, Makarov SV, Uta M-M, Dereven’kov IA, Stuzhin PA (2011) New J Chem 35:1140
Lassalle-Kaiser B, Hureau C, Pantazis DA, Pushkar Y, Guillot R, Yachandra VK, Yano J, Neese F, Anxolabéhère-Mallart E (2010) Energy Environ Sci 3:924
Silaghi-Dumitrescu R (2010) New J Chem 34:1830
Bassan A, Blomberg MR, Siegbahn PE (2004) J Biol Inorg Chem 9:439
Silaghi-Dumitrescu R, Cooper CE (2005) Dalton Trans 3477
Silaghi-Dumitrescu R (2004) Inorg Chem 43:3715
Silaghi-Dumitrescu R, Makarov SV (2012) Int J Quant Chem 112:900
Silaghi-Dumitrescu R, Mich M, Matyas C, Cooper CE (2012) Nitric Oxide 26:27
Balcells D, Moles P, Blakemore JD, Raynaud C, Brudvig GW, Crabtree RH, Eisenstein O (2009) Dalton Trans 5989
Balcells D, Raynaud C, Crabtree RH, Eisenstein O (2009) Chem Commun (Camb) 1772
Silaghi-Dumitrescu R (2007) Studia Universitatis Babes-Bolyai Chemia 103
Silaghi-Dumitrescu R (2007) Studia Universitatis Babes-Bolyai Chemia 2:127
Silaghi-Dumitrescu R, Silaghi-Dumitrescu I, Coulter ED, Kurtz DM Jr (2003) Inorg Chem 42:446
Silaghi-Dumitrescu R (2009) J Mol Graph Model 28:156
Katona G, Carpentier P, Niviere V, Amara P, Adam V, Ohana J, Tsanov N, Bourgeois D (2007) Science 316:449
Pelmenschikov V, Siegbahn PE (2005) Inorg Chem 44:3311
Bonnot F, Molle T, Menage S, Moreau Y, Duval S, Favaudon V, Houee-Levin C, Niviere V (2012) J Am Chem Soc 134:5120–5130
Kurtz DM Jr (2004) Acc Chem Res 37:902
Ames W, Pantazis DA, Krewald V, Cox N, Messinger J, Lubitz W, Neese F (2011) J Am Chem Soc 133:19743
Cox N, Rapatskiy L, Su JH, Pantazis DA, Sugiura M, Kulik L, Dorlet P, Rutherford AW, Neese F, Boussac A, Lubitz W, Messinger J (2011) J Am Chem Soc 133:3635
Duboc C, Collomb MN, Pecaut J, Deronzier A, Neese F (2008) Chemistry 14:6498
Zein S, Kulik LV, Yano J, Kern J, Pushkar Y, Zouni A, Yachandra VK, Lubitz W, Neese F, Messinger J (2008) Philos Trans R Soc Lond B Biol Sci 363:1167
Silaghi-Dumitrescu R (2009) Revue Roumaine de Chimie 54:513
Silaghi-Dumitrescu R, Silaghi-Dumitrescu I (2005) Chemtracts Inorg Chem 18:595
Lancaster KM, Roemelt M, Ettenhuber P, Hu Y, Ribbe MW, Neese F, Bergmann U, DeBeer S (2011) Science 334:974
Silaghi-Dumitrescu R (2005) J Mol Struct Theochem 722:233
Blomberg LM, Blomberg MRA, Siegbahn PEM (2004) J Biol Inorg Chem 9:923–935
Yi J, Orville AM, Skinner JM, Skinner MJ, Richter-Addo GB (2010) Biochemistry 49:5969–5971
Yi J, Heinecke J, Tan H, Ford PC, Richter-Addo GB (2009) J Am Chem Soc 131:18119
Zahran ZN, Chooback L, Copeland DM, West AH, Richter-Addo GB (2008) J Inorg Biochem 102:216
Yi J, Safo MK, Richter-Addo GB (2008) Biochemistry 47:8247
Copeland DM, Soares AS, West AH, Richter-Addo GB (2006) J Inorg Biochem 100:1413
Perissinotti LL, Marti MA, Doctorovich F, Luque FJ, Estrin DA (2008) Biochemistry 47:9793
Silaghi-Dumitrescu R (2006) J Inorg Biochem 100:396
Simon J, Kern M, Hermann B, Einsle O, Butt JN (2011) Biochem Soc Trans 39:1864
Zhou J, He Q, Hemme CL, Mukhopadhyay A, Hillesland K, Zhou A, He Z, Van Nostrand JD, Hazen TC, Stahl DA, Wall JD, Arkin AP (2011) Nat Rev Microbiol 9:452
Crane BR, Siegel LM, Getzoff ED (1995) Science 270:59
Pietri R, Roman-Morales E, Lopez-Garriga J (2011) Antioxid Redox Signal 15:393
Salnikov DS, Silaghi-Dumitrescu R, Makarov SV, van Eldik R, Boss GR (2012) Dalton Trans 40:9831
Silaghi-Dumitrescu R (2010) J Mol Struct Theochem 942:15
Putz MV, Russo N, Sicilia E (2004) J Comput Chem 25:994–1003
Putz MV (2008) MATCH Commun Math Comput Chem 60:845
Kis Z, Silaghi-Dumitrescu R (2010) Int J Quant Chem 110:1848
Silaghi-Dumitrescu R, Makarov SV (2010) J Biol Inorg Chem 15:977
Grodkowski J, Dhanasekaran T, Neta P, Hambright P, Brunschwig BS, Shinozaki K, Fujita E (2000) J Phys Chem A 104:11332
Makarov SV, Salnikov DS, Pogorelova AS, Kis Z, Silaghi-Dumitrescu R (2008) J Porph Phthalocyan 12:1096
Silaghi-Dumitrescu R, Makarov SV (2010) Eur J Inorg Chem 34:1830
Silaghi-Dumitrescu R (2008) Eur J Inorg Chem 5404
Geethalakshmi KR, Waller MP, Thiel W, Buhl M (2009) J Phys Chem B 113:4456
Zhang Y, Gascon JA (2008) J Inorg Biochem 102:1684
Schweitzer A, Gutmann T, Wachtler M, Breitzke H, Buchholz A, Plass W, Buntkowsky G (2008) Solid State Nucl Magn Reson 34:52
Wikete C, Wu P, Zampella G, De Gioia L, Licini G, Rehder D (2007) Inorg Chem 46:196
Zampella G, Fantucci P, Pecoraro VL, De Gioia L (2006) Inorg Chem 45:7133
Dey A (2011) J Am Chem Soc 132:13892
Leidel N, Chernev P, Havelius KG, Ezzaher S, Ott S, Haumann M (2012) Inorg Chem 51:4546
Baffert C, Bertini L, Lautier T, Greco C, Sybirna K, Ezanno P, Etienne E, Soucaille P, Bertrand P, Bottin H, Meynial-Salles I, De Gioia L, Leger C (2011) J Am Chem Soc 133:2096
Kachmar A, Vetere V, Maldivi P, Franco AA (2010) J Phys Chem A 114:11861
Greco C, Fantucci P, De Gioia L, Suarez-Bertoa R, Bruschi M, Talarmin J, Schollhammer P (2010) Dalton Trans 39:7320
Ryde U, Greco C, De Gioia L (2010) J Am Chem Soc 132:4512
Surawatanawong P, Tye JW, Darensbourg MY, Hall MB (2010) Dalton Trans 39:3093
Yang X, Hall MB (2009) J Am Chem Soc 131:10901
Bertini L, Greco C, De Gioia L, Fantucci P (2009) J Phys Chem A 113:5657
Jayapal P, Sundararajan M, Hillier IH, Burton NA (2008) Phys Chem Chem Phys 10:4249
Jayapal P, Robinson D, Sundararajan M, Hillier IH, McDouall JJ (2008) Phys Chem Chem Phys 10:1734
Fiedler AT, Brunold TC (2005) Inorg Chem 44:9322
Justice AK, De Gioia L, Nilges MJ, Rauchfuss TB, Wilson SR, Zampella G (2008) Inorg Chem 47:7405
Zhou T, Mo Y, Zhou Z, Tsai K (2005) Inorg Chem 44:4941
Petrenko T, Neese F (2007) J Chem Phys 127:164319
Ganyushin D, Neese F (2008) J Chem Phys 128:114117
Pantazis DA, Orio M, Petrenko T, Zein S, Bill E, Lubitz W, Messinger J, Neese F (2009) Chemistry 15:5108
Ganyushin D, Neese F (2006) J Chem Phys 125:24103
Acknowledgment
Funding from the Romanian Ministry for Education and Research project PCCE 140/2008 is gratefully acknowledged.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2013 Springer-Verlag Berlin Heidelberg
About this chapter
Cite this chapter
Silaghi-Dumitrescu, R. (2013). Redox Activation of Small Molecules at Biological Metal Centers. In: Putz, M., Mingos, D. (eds) Applications of Density Functional Theory to Biological and Bioinorganic Chemistry. Structure and Bonding, vol 150. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-32750-6_3
Download citation
DOI: https://doi.org/10.1007/978-3-642-32750-6_3
Published:
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-642-32749-0
Online ISBN: 978-3-642-32750-6
eBook Packages: Chemistry and Materials ScienceChemistry and Material Science (R0)