1.3 Modelling Radicals and Their Reactivities

Abstract

In this chapter, the application of computational quantum mechanical methods to the understanding of radical reactions is introduced. For radical reactions, access to electronic configurations through quantum chemical calculations allows rationalization of unusual reactivities. Using the valence bond approach, the nature of bonding in three-electron bonds can be characterized by large resonance interactions. Similarly, some simple reactions that are commonly believed to be radical-free, such as [3 + 2] cycloadditions, are in fact governed by a high-lying biradical intermediate that helps to stabilize the transition state. More complex radical and enzymatic reactions can also be modelled, as illustrated by the example of horseradish peroxidase. These case studies show that computational analysis can complement experimental investigations and fill in the blanks to enable a more complete understanding of radical reactions.

Key words

radicals - modelling - computational chemistry - quantum mechanics - density functional theory (DFT) - radical stability - valence bond methods - two-center, three-electron bonds - enzyme catalysis - cycloaddition - electron transfer - iron catalysts - radical ions

• 1 Frisch MJ, Trucks GW, Schlegel HB, Gill PMW, Johnson BG, Robb MA, Cheeseman JR, Keith T, Petersson GA, Montgomery JA, Raghavachari K, Al-Laham MA, Zakrzewski VG, Ortiz JV, Foresman JB, Cioslowski J, Stefanov BB, Nanayakkara A, Challacombe M, Peng CY, Ayala PY, Chen W, Wong MW, Andres JL, Replogle ES, Gomperts R, Martin RL, Fox DJ, Binkley JS, Defrees DJ, Baker J, Stewart JP, Head-Gordon M, Gonzalez C, Pople JA GAUSSIAN 94, Revision B.2; Gaussian: Pittsburgh, PA 1995

• 2 Basch H, Hoz S. J. Phys. Chem. A 1997; 101: 4416

• 3 Hydrogen-Transfer Reactions. Hynes JT, Klinman JP, Limbach H.-H, Schowen RL. Wiley-VCH; Weinheim, Germany 2007

• 4 CRC Handbook of Bimolecular and Termolecular Gas Reactions. Kerr JA, Moss SJ. CRC; Boca Raton, FL 1981. 1.

• 5 Hobza P, Šponer J, Reschel T. J. Comput. Chem. 1995; 16: 1315

• 6 Bally T, Truttmann L, Dai S, Williams F. J. Am. Chem. Soc. 1995; 117: 7916

• 7 Bally T, Sastry GN. J. Phys. Chem. A 1997; 101: 7923

• 8 Zhang Y, Yang W. J. Chem. Phys. 1998; 109: 2604

• 9 Sun J, Ruzsinszky A, Perdew JP. Phys. Rev. Lett. 2015; 115: 036402

• 10 Zhao Y, Truhlar DG. Acc. Chem. Res. 2008; 41: 157

• 11 Kaduk B, Kowalczyk T, Van Voorhis T. Chem. Rev. 2012; 112: 321

• 12 Kirby JP, Roberts JA, Nocera DG. J. Am. Chem. Soc. 1997; 119: 9230

• 13 Wu Q, Van Voorhis T. J. Chem. Theory Comput. 2006; 2: 765

• 14 Hioe J, Zipse H. Org. Biomol. Chem. 2010; 8: 3609

• 15 Hioe J, Šakić D, Vrček V, Zipse H. Org. Biomol. Chem. 2015; 13: 157

• 16 Šakić D, Zipse H. Adv. Synth. Catal. 2016; 358: 3983

• 17 Meyer D, Jangra H, Walther F, Zipse H, Renaud P. Nat. Commun. 2018; 9: 4888

• 18 Baldwin JE. J. Chem. Soc., Chem. Commun. 1976; 734

• 19 Johnson CD. Acc. Chem. Res. 1993; 26: 476

• 20 Alabugin IV, Gilmore K, Manoharan M. J. Am. Chem. Soc. 2011; 133: 12608

• 21 Gilmore K, Alabugin IV. Chem. Rev. 2011; 111: 6513

• 22 Alabugin IV, Gilmore K. Chem. Commun. (Cambridge) 2013; 49: 11246

• 23 Shaik SS, Hiberty PC. A Chemistʼs Guide to Valence Bond Theory. Wiley; Hoboken, NJ 2007

• 24 Heitler W, London F. Z. Phys. 1927; 44: 455

• 25 Pauling L. J. Am. Chem. Soc. 1931; 53: 1367

• 26 Shaik S, Danovich D, Wu W, Hiberty PC. Nat. Chem. 2009; 1: 443

• 27 Shurki A, Braïda B, Wu W, In: Complementary Bonding Analysis Grabowsky S. De Gruyter STEM Berlin 2021; 157-197

• 28 Hiberty PC, Humbel S, Archirel P. J. Phys. Chem. 1994; 98: 11697

• 29 Hadzic M, Braïda B, Volatron F. Org. Lett. 2011; 13: 1960

• 30 Chen Z, Chen X, Wu W. J. Chem. Phys. 2013; 138: 164120

• 31 Chen Z, Ying F, Chen X, Song J, Su P, Song L, Mo Y, Zhang Q, Wu W. Int. J. Quantum Chem. 2015; 115: 731

• 32 Braïda B, Derat E, Humbel S, Hiberty PC, Shaik S. ChemPhysChem 2012; 13: 4029

• 33 Shaik S, Shurki A. Angew. Chem. Int. Ed. 1999; 38: 586

• 34 Lai W, Li C, Chen H, Shaik S. Angew. Chem. Int. Ed. 2012; 51: 5556

• 35 Usharani D, Lai W, Li C, Chen H, Danovich D, Shaik S. Chem. Soc. Rev. 2014; 43: 4968

• 36 Shaik SS. J. Am. Chem. Soc. 1981; 103: 3692

• 37 Danovich D, Foroutan-Nejad C, Hiberty PC, Shaik S. J. Phys. Chem. A 2018; 122: 1873

• 38 Shaik S, Danovich D, Galbraith JM, Braïda B, Wu W, Hiberty PC. Angew. Chem. Int. Ed. 2020; 59: 984

• 39 Braïda B, Hazebroucq S, Hiberty PC. J. Am. Chem. Soc. 2002; 124: 2371

• 40 Fourré I, Silvi B. Heteroat. Chem. 2007; 18: 135

• 41 Borden WT, Hoffmann R, Stuyver T, Chen B. J. Am. Chem. Soc. 2017; 139: 9010

• 42 Braïda B, Hiberty PC, Savin A. J. Phys. Chem. A 1998; 102: 7872

• 43 Braïda B, Thogersen L, Wu W, Hiberty PC. J. Am. Chem. Soc. 2002; 124: 11781

• 44 Domin D, Braïda B, Bergès J. J. Phys. Chem. B 2017; 121: 9321

• 45 Anderson ME, Braïda B, Hiberty PC, Cundari TR. J. Am. Chem. Soc. 2020; 142: 3125

• 46 Wu W, Gu J, Song J, Shaik S, Hiberty PC. Angew. Chem. Int. Ed. 2009; 48: 1407

• 47 Stuyver T, Chen B, Zeng T, Geerlings P, De Proft F, Hoffmann R. Chem. Rev. 2019; 119: 11291

• 48 Braïda B, Galembeck SE, Hiberty PC. J. Chem. Theory Comput. 2017; 13: 3228

• 49 Braïda B, Lo A, Hiberty PC. ChemPhysChem 2012; 13: 811

• 50 Ess DH, Houk KN. J. Am. Chem. Soc. 2008; 130: 10187

• 51 Braïda B, Walter C, Engels B, Hiberty PC. J. Am. Chem. Soc. 2010; 132: 7631

• 52 Fruton JS. Molecules and Life: Historical Essays on the Interplay of Chemistry and Biology. Wiley-Interscience; New York 1972: 288

• 53 Dorfner R, Ferge T, Kettrup A, Zimmermann R, Yeretzian C. J. Agric. Food Chem. 2003; 51: 5768

• 54 Handbook of Metalloproteins. Messerschmidt A, Huber R, Poulos TL, Wieghardt K. Wiley; New York 2001. 1. 193-328

• 55 Poulos TL, In: The Porphyrin Handbook Kadish KM, Smith KM, Guilard R. Academic Press New York 2000; 4. 189-218

• 56 Dawson JH. Science (Washington, D. C.) 1988; 240: 433

• 57 Dawson JH, Sono M. Chem. Rev. 1987; 87: 1255

• 58 Marnett LJ, Kennedy TA, In: Cytochrome P450: Structure, Mechanisms and Biochemistry Ortiz de Montellano PR. Plenum Press New York 1995; 49-80

• 59 Poulos TL, Cupp-Vickery J, Li H, In: Cytochrome P450: Structure, Mechanisms and Biochemistry Ortiz de Montellano PR. Plenum Press New York 1995; 125-150

• 60 Meunier B, In: Biomimetic Oxidations Catalyzed by Transition Metal Complexes Meunier B. Imperial College Press UK 2000; 171-214

• 61 Meunier B. Chem. Rev. 1992; 92: 1411

• 62 Watanabe Y, In: The Porphyrin Handbook Kadish KM, Smith KM, Guilard R. Academic Press New York 2000; 4. 97-118

• 63 Poulos TL. JBIC, J. Biol. Inorg. Chem. 1996; 1: 356

• 64 Berglund GI, Carlsson GH, Smith AT, Szöke H, Henriksen A, Hajdu J. Nature (London) 2002; 417: 463

• 65 Harris DL. Curr. Opin. Chem. Biol. 2001; 5: 724

• 66 Harris DL, Loew GH. J. Porphyrins Phthalocyanines 2001; 5: 334

• 67 Loew GH, Kert CJ, Hjelmeland LM, Kirchner RF. J. Am. Chem. Soc. 1977; 99: 3534

• 68 Du P, Loew GH. Biophys. J. 1995; 68: 69

• 69 Loew GH, Axe FU, Collins JR, Du P. Inorg. Chem. 1991; 30: 2291

• 70 Deeth RJ. J. Am. Chem. Soc. 1999; 121: 6074

• 71 Green MT. J. Am. Chem. Soc. 2000; 122: 9495

• 72 de Visser SP, Shaik S, Sharma PK, Kumar D, Thiel W. J. Am. Chem. Soc. 2003; 125: 15779

• 73 Kuramochi H, Noodleman L, Case DA. J. Am. Chem. Soc. 1997; 119: 11442

• 74 Rydberg P, Sigfridsson E, Ryde U. JBIC, J. Biol. Inorg. Chem. 2004; 9: 203

• 75 Antony J, Grodzicki M, Trautwein AX. J. Phys. Chem. A 1997; 101: 2692

• 76 La Mar GN, de Ropp JS, Smith KM, Langry KC. J. Biol. Chem. 1981; 256: 237

• 77 Thanabal V, La Mar GN, de Ropp JS. Biochemistry 1988; 27: 5400

• 78 de Ropp JS, Sham S, Asokan A, Newmyer S, Ortiz de Montellano PR, La Mar GN. J. Am. Chem. Soc. 2002; 124: 11029

• 79 Wirstam M, Blomberg MRA, Siegbahn PEM. J. Am. Chem. Soc. 1999; 121: 10178

• 80 Menyhárd DK, Náray-Szabó G. J. Phys. Chem. B 1999; 103: 227

• 81 Zazza C, Sanna N, Tatoli S, Aschi M, Palma A. Int. J. Quantum Chem. 2010; 110: 352

• 82 Vidossich P, Alfonso-Prieto M, Rovira C. J. Inorg. Biochem. 2012; 117: 292

• 83 Hersleth H.-P, Ryde U, Rydberg P, Görbitz CH, Andersson KK. J. Inorg. Biochem. 2006; 100: 460

• 84 Warshel A, Levitt M. J. Mol. Biol. 1976; 103: 227

• 85 Dapprich S, Komáromi I, Byun KS, Morokuma K, Frisch MJ. J. Mol. Struct.: THEOCHEM 1999; 461–462: 1

• 86 Sherwood P, de Vries AH, Guest MF, Schreckenbach G, Catlow CRA, French SA, Sokol AA, Bromley ST, Thiel W, Turner AJ, Billeter S, Terstegen F, Thiel S, Kendrick J, Rogers SC, Casci J, Watson M, King F, Karlsen E, Sjøvoll M, Fahmi A, Schafer A, Lennartz C. J. Mol. Struct.: THEOCHEM 2003; 632: 1

• 87 Derat E, Cohen S, Shaik S, Altun A, Thiel W. J. Am. Chem. Soc. 2005; 127: 13611

• 88 Heimdal J, Rydberg P, Ryde U. J. Phys. Chem. B 2008; 112: 2501

• 89 Poulos TL, Kraut J. J. Biol. Chem. 1980; 255: 8199

• 90 Derat E, Shaik S. J. Phys. Chem. B 2006; 110: 10526

• 91 Rodríguez-López JN, Gilabert MA, Tudela J, Thorneley RNF, García-Cánovas F. Biochemistry 2000; 39: 13201

• 92 Derat E, Shaik S, Rovira C, Vidossich P, Alfonso-Prieto M. J. Am. Chem. Soc. 2007; 129: 6346

• 93 Vidossich P, Fiorin G, Alfonso-Prieto M, Derat E, Shaik S, Rovira C. J. Phys. Chem. B 2010; 114: 5161

• 94 Zazza C, Aschi M, Palma A. Chem. Phys. Lett. 2006; 428: 152

• 95 Tatoli S, Zazza C, Sanna N, Palma A, Aschi M. Biophys. Chem. 2009; 141: 87

• 96 Zazza C, Palma A, Sanna N, Tatoli S, Aschi M. J. Phys. Chem. B 2010; 114: 6817

• 97 Roth JP, Cramer CJ. J. Am. Chem. Soc. 2008; 130: 7802

• 98 Derat E, Shaik S. J. Am. Chem. Soc. 2006; 128: 13940

• 99 Rovira C, Fita I. J. Phys. Chem. B 2003; 107: 5300

• 100 Derat E, Shaik S. J. Am. Chem. Soc. 2006; 128: 8185

• 101 Meunier B, de Visser SP, Shaik S. Chem. Rev. 2004; 104: 3947

• 102 Li P, Soudackov AV, Hammes-Schiffer S. J. Am. Chem. Soc. 2018; 140: 3068