Abstract
About 35 years after its first suggestion, QM/MM became the standard theoretical approach to investigate enzymatic structures and processes. The success is due to the ability of QM/MM to provide an accurate atomistic picture of enzymes and related processes. This picture can even be turned into a movie if nuclei-dynamics is taken into account to describe enzymatic processes. In the field of organic chemistry, QM/MM methods are used to a much lesser extent although almost all relevant processes happen in condensed matter or are influenced by complicated interactions between substrate and catalyst. There is less importance for theoretical organic chemistry since the influence of nonpolar solvents is rather weak and the effect of polar solvents can often be accurately described by continuum approaches. Catalytic processes (homogeneous and heterogeneous) can often be reduced to truncated model systems, which are so small that pure quantum-mechanical approaches can be employed. However, since QM/MM becomes more and more efficient due to the success in software and hardware developments, it is more and more used in theoretical organic chemistry to study effects which result from the molecular nature of the environment. It is shown by many examples discussed in this review that the influence can be tremendous, even for nonpolar reactions. The importance of environmental effects in theoretical spectroscopy was already known. Due to its benefits, QM/MM can be expected to experience ongoing growth for the next decade.
In the present chapter we give an overview of QM/MM developments and their importance in theoretical organic chemistry, and review applications which give impressions of the possibilities and the importance of the relevant effects. Since there is already a bunch of excellent reviews dealing with QM/MM, we will discuss fundamental ingredients and developments of QM/MM very briefly with a focus on very recent progress. For the applications we follow a similar strategy.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Himo F (2006) Quantum chemical modeling of enzyme active sites and reaction mechanisms. Theor Chem Acc 116:232–240
Siegbahn PEM, Blomberg MRA (2000) Transition-metal systems in biochemistry studied by high-accuracy quantum chemical methods. Chem Rev 100:421–437
Siegbahn PEM, Borowski T (2006) Modeling enzymatic reactions involving transition metals. Acc Chem Res 39:729–738
Hu LH et al (2009) Do quantum mechanical energies calculated for small models of protein-active sites converge? J Phys Chem A 113:11793–11800
Warshel A, Levitt M (1976) Theoretical studies of enzymic reactions - dielectric, electrostatic and steric stabilization of carbonium-ion in reaction of lysozyme. J Mol Biol 103:227–249
Field MJ, Bash PA, Karplus M (1990) A combined quantum-mechanical and molecular mechanical potential for molecular-dynamics simulations. J Comput Chem 11:700–733
Brooks BR et al (2009) CHARMM – Chemistry at HARvard Macromolecular Mechanics (22 and higher) available at: http://www.charmm.org
ISI Web of Knowledge at http://www.isiknowledge.com. Accessed 2011
Gao J (1996) Hybrid quantum and molecular mechanical simulations: an alternative avenue to solvent effects in organic chemistry. Acc Chem Res 29:298–305
Gao J (2007) Methods and applications of combined quantum mechanical and molecular mechanical potentials. In: Lipkowitz KB, Boyd DB (eds) Reviews in computational chemistry. Wiley, New York
Cunningham MA, Bash PA (1997) Computational enzymology. Biochimie 79:687–689
Gao J (1998) Hybrid quantum mechanical/molecular mechanical (QM/MM) methods. In: Schleyer PV et al (eds) Encyclopedia of computational chemistry. Wiley, Chichester
Amara P, Field MJ (1998) Combined Q/M. In: Schleyer PV et al (eds) Encyclopedia of computational chemistry. Wiley, Chichester
Ruiz-López MF, Rivail J-L (1998) Combined quantum mechanics and molecular mechanics approaches to chemical and biochemical reactivity. In: Schleyer PV et al (eds) Encyclopedia of computational chemistry. Wiley, Chichester
Merz KMJ, Stanton RV (1998) Divide and conquer for semiempirical MO methods. In: Schleyer PV (ed) Encyclopedia of computational chemistry. Wiley, Chichester
Friesner RA, Beachy MD (1998) Quantum mechanical calculations on biological systems. Curr Opin Struct Biol 8:257–262
Beck B, Clark T (1998) Some biological applications of semiempirical MO theory. Perspect Drug Discov 9–11:131–159
Mordasini TZ, Thiel W (1998) Combined quantum mechanical and molecular mechanical approaches. Chimia 52:288–291
Monard G, Merz KM (1999) Combined quantum mechanical/molecular mechanical methodologies applied to biomolecular systems. Acc Chem Res 32:904–911
Hillier IH (1999) ChemInform abstract: chemical reactivity studied by hybrid QM/MM methods. ChemInform 30:45–52
Amara P, Field MJ (1999) Hybrid potentials for large molecular systems. In: Leszczynski J (ed) Computational molecular biology. Elsevier, Amsterdam
Bruice TC, Kahn K (2000) Computational enzymology. Curr Opin Chem Biol 4:540–544
Sherwood P (2000) Hybrid quantum mechanics/molecular mechanics approaches. In: Grotendorst J (ed) Modern methods and algorithms of quantum chemistry 2. John von Neumann Institute of Computing, Jülich
Lyne PD, Walsh OA (2001) Computer simulation of biochemical reactions with QM-MM methods. In: Becker OM et al (eds) Computational biochemistry and biophysics. Decker, New York
Mulholland AJ (2001) The QM/MM approach to enzymatic reactions. In: Eriksson LA (ed) Theoretical biochemistry: processes and properties of biological systems. Elsevier, Amsterdam
Field MJ (2002) Simulating enzyme reactions: challenges and perspectives. J Comput Chem 23:48–58
Gogonea V (2002) The QM/MM method. An overview. Internet Electron J Mol Des 1:173–184
Gao JL, Truhlar DG (2002) Quantum mechanical methods for enzyme kinetics. Annu Rev Phys Chem 53:467–505
Monard G et al (2003) Determination of enzymatic reaction pathways using QM/MM methods. Int J Quantum Chem 93:229–244
Ridder L, Mulholland AJ (2003) Modeling biotransformation reactions by combined quantum mechanical/molecular mechanical approaches: from structure to activity. Curr Top Med Chem 3:1241–1256
Náray-Szabó G, Berente I (2003) Computer modelling of enzyme reactions. J Mol Struct THEOCHEM 666–667:637–644
Ryde U (2003) Combined quantum and molecular mechanics calculations on metalloproteins. Curr Opin Chem Biol 7:136–142
Kästner J (2011) QM/MM: Quantenmechanik und empirische Kraftfelder. Nachr Chem 59:286–288
Zhang R et al (2010) A guide to QM/MM methodology and applications. In: Sabin JR, Brandas E (eds) Advances in quantum chemistry. Elsevier Academic, San Diego
Chen X et al (2011) Reaction pathway and free energy profile for butyrylcholinesterase-catalyzed hydrolysis of acetylcholine. J Phys Chem B 115:1315–1322
van der Kamp MW et al (2008) Biomolecular simulation and modelling: status, progress and prospects. J R Soc Interface 5:S173–S190
Sierka M, Sauer J (2005) Hybrid quantum mechanics/molecular mechanics methods and their application. In: Yip S (ed) Handbook of materials modeling. Springer, Dordrecht
Eichler U, Kolmel CM, Sauer J (1997) Combining ab initio techniques with analytical potential functions for structure predictions of large systems: method and application to crystalline silica polymorphs. J Comput Chem 18:463–477
Sauer J, Sierka M (2000) Combining quantum mechanics and interatomic potential functions in ab initio studies of extended systems. J Comput Chem 21:1470–1493
Sherwood P et al (1997) Computer simulation of zeolite structure and reactivity using embedded cluster methods. Faraday Discuss 106:79–92
French SA et al (2003) Identification and characterization of active sites and their catalytic processes - the Cu/ZnO methanol catalyst. Top Catal 24:161–172
Catlow CRA et al (2005) Computational approaches to the determination of active site structures and reaction mechanisms in heterogeneous catalysts. Philos T R Soc A 363:913–936
Sokol AA et al (2004) Hybrid QM/MM embedding approach for the treatment of localized surface states in ionic materials. Int J Quantum Chem 99:695–712
Sherwood P et al (2003) QUASI: a general purpose implementation of the QM/MM approach and its application to problems in catalysis. J Mol Struct-Theochem 632:1–28
Bernstein N, Kermode JR, Csanyi G (2009) Hybrid atomistic simulation methods for materials systems. Rep Prog Phys 72:1–25
Acevedo O, Jorgensen WL (2010) Advances in quantum and molecular mechanical (QM/MM) simulations for organic and enzymatic reactions. Acc Chem Res 43:142–151
Hu H, Yang WT (2009) Development and application of ab initio QM/MM methods for mechanistic simulation of reactions in solution and in enzymes. J Mol Struct-Theochem 898:17–30
Rode BM et al (2005) Coordination and ligand exchange dynamics of solvated metal ions. Coord Chem Rev 249:2993–3006
Hu H, Yang WT (2008) Free energies of chemical reactions in solution and in enzymes with ab initio quantum mechanics/molecular mechanics methods. Annu Rev Phys Chem 59:573–601
Bearpark MJ et al (2007) CASSCF calculations for photoinduced processes in large molecules: choosing when to use the RASSCF, ONIOM and MMVB approximations. J Photochem Photobiol A 190:207–227
Bearpark MJ et al (2006) Excited states of conjugated hydrocarbons using the molecular mechanics-valence bond (MMVB) method: Conical intersections and dynamics. Theor Chem Acc 116:670–682
Garavelli M (2006) Computational organic photochemistry: strategy, achievements and perspectives. Theor Chem Acc 116:87–105
Blancafort L et al (2005) Computational investigations of photochemical reaction mechanisms. In: Kutateladze AG (ed) Computational methods in photochemistry. Taylor & Francis, Boca Raton
Corbeil CR, Moitessier N (2010) Theory and application of medium to high throughput prediction method techniques for asymmetric catalyst design. J Mol Catal A-Chem 324:146–155
Balcells D, Maseras F (2007) Computational approaches to asymmetric synthesis. New J Chem 31:333–343
Maldonado AG, Rothenberg G (2010) Predictive modeling in homogeneous catalysis: a tutorial. Chem Soc Rev 39:1891–1902
Menikarachchi LC, Gascon JA (2010) QM/MM approaches in medicinal chemistry research. Curr Top Med Chem 10:46–54
Gao JL, Thompson MA (1998) Combined quantum mechanical and molecular mechanical methods. American Chemical Society, Washington
Senn HM, Thiel W (2007) QM/MM studies of enzymes. Curr Opin Chem Biol 11:182–187
Senn HM, Thiel W (2009) QM/MM methods for biomolecular systems. Angew Chem Int Ed 48:1198–1229
Lin H, Truhlar DG (2007) QM/MM: what have we learned, where are we, and where do we go from here? Theor Chem Acc 117:185–199
Senn HM, Thiel W (2007) QM/MM methods for biological systems. In: Reiher M (ed) Atomistic approaches in modern biology: from quantum chemistry to molecular simulations. Springer, Berlin
Hsiao YW, Drakenberg T, Ryde U (2005) NMR structure determination of proteins supplemented by quantum chemical calculations: detailed structure of the Ca2+ sites in the EGF34 fragment of protein S. J Biomol NMR 31:97–114
Lennartz C et al (2002) Enzymatic reactions of triosephosphate isomerase: a theoretical calibration study. J Phys Chem B 106:1758–1767
Jensen F (2007) Introduction to computational chemistry. Wiley, Chichester
Cramer CJ (2003) Essentials of computational chemistry. Wiley, Chichester
Koch W, Holthausen MC (2001) A chemist's guide to density functional theory. Wiley-VCH, Weinheim
Sousa SF, Fernandes PA, Ramos MJ (2007) General performance of density functionals. J Phys Chem A 111:10439–10452
Szabo A, Ostlund NS (1996) Modern quantum chemistry. Dover Publications, Inc, New York
Helgaker T, Jorgensen P, Olsen J (2000) Molecular electronic-structure theory. Wiley, Chichester
Schutz M, Manby FR (2003) Linear scaling local coupled cluster theory with density fitting. Part I: 4-external integrals. Phys Chem Chem Phys 5:3349–3358
Werner HJ, Manby FR, Knowles PJ (2003) Fast linear scaling second-order Moller-Plesset perturbation theory (MP2) using local and density fitting approximations. J Chem Phys 118:8149–8160
Schutz M (2002) A new, fast, semi-direct implementation of linear scaling local coupled cluster theory. Phys Chem Chem Phys 4:3941–3947
Werner HJ, Manby FR (2006) Explicitly correlated second-order perturbation theory using density fitting and local approximations. J Chem Phys 124:12
Claeyssens F et al (2006) High-accuracy computation of reaction barriers in enzymes. Angew Chem Int Ed 45:6856–6859
Mata RA et al (2008) Toward accurate barriers for enzymatic reactions: QM/MM case study on p-hydroxybenzoate hydroxylase. J Chem Phys 128:8
Mulholland AJ (2007) Chemical accuracy in QM/MM calculations on enzyme-catalysed reactions. Chem Cent J 1:5
Torrie GM, Valleau JP (1974) Monte-Carlo free-energy estimates using non-Boltzmann sampling - Application to subcritical Lennard-Jones fluid. Chem Phys Lett 28:578–581
Valleau JP, Torrie GMA (1977) A guide for Monte Carlo for statistical mechanics. In: Berne BJ (ed) Statistical mechanics. Plenum, New York
Ridder L et al (2002) Quantum mechanical/molecular mechanical free energy simulations of the glutathione S-transferase (M1-1) reaction with phenanthrene 9,10-oxide. J Am Chem Soc 124:9926–9936
Senn HM, Thiel S, Thiel W (2005) Enzymatic hydroxylation in p-hydroxybenzoate hydroxylase: a case study for QM/MM molecular dynamics. J Chem Theory Comput 1:494–505
Engels B, Peyerimhoff SD (1989) Theoretical-study of FC2H4. J Phys Chem-Us 93:4462–4470
Peric M, Engels B, Peyerimhoff SD (1995) Ab initio study of the Renner-Teller effect in the X2Πu electronic-state of B2H +2 . J Mol Spectrosc 171:494–503
Engels B (1994) A detailed study of the configuration selected multireference configuration-interaction method combined with perturbation-theory to correct the wave-function. J Chem Phys 100:1380–1386
Muhlhauser M et al (1994) Ab-initio investigation of the stability of Si3C3 clusters and their structural and bonding features. Z Phys D Atom Mol Cl 32:113–123
Musch PW et al (2002) On the regioselectivity of the cyclization of enyne-ketenes: a computational investigation and comparison with the Myers-Saito and Schmittel reaction. J Am Chem Soc 124:1823–1828
Schmittel M et al (1998) Two novel thermal biradical cyclizations in theory and experiment: new synthetic routes to 6H-indolo 2,3-b quinolines and 2-amino-quinolines from enyne-carbodiimides. Angew Chem Int Ed 37:2371–2373
Schmittel M et al (2001) Ring size effects in the C2-C6 biradical cyclisation of enyne-allenes and the relevance for neocarzinostatin. J Chem Soc Perkin Trans 2 1331–1339
Engels B et al (1998) Regioselectivity of biradical cyclizations of enyne-allenes: influence of substituents on the switch from the Myers-Saito to the novel C2-C6 cyclization. Angew Chem Int Ed 37:1960–1963
Christl M, Engels B (2009) Stable five-membered-ring allenes with second-row elements only: not allenes, but zwitterions. Angew Chem Int Ed 48:1538–1539
Schoneboom JC et al (2003) Computational assessment of the electronic structure of 1-azacyclohexa-2,3,5-triene (3 delta(2)-1H-pyridine) and its benzo derivative (3 delta(2)-1H-quinoline) as well as generation and interception of 1-methyl-3 delta(2)-1H-quinoline. Chem-Eur J 9:4641–4649
Engels B et al (2002) Cycloallenes. Part 17. Computational assessment of the electronic structures of cyclohexa-1,2,4-triene, 1-oxacyclohexa-2,3,5-triene (3 delta(2)-pyran), their benzo derivatives, and cyclohexa-1,2-diene. An experimental approach to 3 delta(2)-pyran. J Am Chem Soc 124:287–297
Musch PW, Engels B (2001) The importance of the ene reaction for the C2-C6 cyclization of enyne-allenes. J Am Chem Soc 123:5557–5562
Shaik S et al (2010) P450 enzymes: their structure, reactivity, and selectivity-modeled by QM/MM calculations. Chem Rev 110:949–1017
Sit PHL et al (2010) Quantum mechanical and quantum mechanical/molecular mechanical studies of the iron-dioxygen intermediates and proton transfer in superoxide reductase. J Chem Theory Comput 6:2896–2909
Scherlis DA et al (2007) Simulation of heme using DFT+U: a step toward accurate spin-state energetics. J Phys Chem B 111:7384–7391
Cococcioni M, de Gironcoli S (2005) Linear response approach to the calculation of the effective interaction parameters in the LDA+U method. Phys Rev B 71:16
Kulik HJ et al (2006) Density functional theory in transition-metal chemistry: a self-consistent Hubbard U approach. Phys Rev Lett 97:4
Bikiel DE et al (2006) Modeling heme proteins using atomistic simulations. Phys Chem Chem Phys 8:5611–5628
Sit PHL, Cococcioni M, Marzari N (2007) Car-Parrinello molecular dynamics in the DFT+U formalism: structure and energetics of solvated ferrous and ferric ions. J Electroanal Chem 607:107–112
Toniolo A et al (2004) QM/MM connection atoms for the multistate treatment of organic and biological molecules. Theor Chem Acc 111:270–279
Toniolo A, Granucci G, Martinez TJ (2003) Conical intersections in solution: a QM/MM study using floating occupation semiempirical configuration interaction wave functions. J Phys Chem A 107:3822–3830
Martinez TJ (2006) Insights for light-driven molecular devices from ab initio multiple spawning excited-state dynamics of organic and biological chromophores. Acc Chem Res 39:119–126
Marques MAL, Rubio A (2009) Time-dependent density-functional theory. Phys Chem Chem Phys 11:4436
Dreuw A, Head-Gordon M (2005) Single-reference ab initio methods for the calculation of excited states of large molecules. Chem Rev 105:4009–4037
Caricato M et al (2009) Using the ONIOM hybrid method to apply equation of motion CCSD to larger systems: benchmarking and comparison with time-dependent density functional theory, configuration interaction singles, and time-dependent Hartree-Fock. J Chem Phys 131:12
Dinh PM, Reinhard PG, Suraud E (2010) Dynamics of clusters and molecules in contact with an environment. Phys Rep 485:43–107
Parac M et al (2010) QM/MM calculation of solvent effects on absorption spectra of guanine. J Comput Chem 31:90–106
Sanchez-Garcia E, Doerr M, Thiel W (2010) QM/MM Study of the absorption spectra of DsRed.M1 chromophores. J Comput Chem 31:1603–1612
Yanai T, Tew DP, Handy NC (2004) A new hybrid exchange-correlation functional using the Coulomb-attenuating method (CAM-B3LYP). Chem Phys Lett 393:51–57
Peach MJG et al (2006) Assessment of a Coulomb-attenuated exchange-correlation energy functional. Phys Chem Chem Phys 8:558–562
Rohrdanz MA, Herbert JM (2008) Simultaneous benchmarking of ground- and excited-state properties with long-range-corrected density functional theory. J Chem Phys 129:034107
Fan P-D, Valiev M, Kowalski K (2008) Large-scale parallel calculations with combined coupled cluster and molecular mechanics formalism: excitation energies of zinc-porphyrin in aqueous solution. Chem Phys Lett 458:205–209
Dreuw A, Head-Gordon M (2004) Failure of time-dependent density functional theory for long-range charge-transfer excited states: the zincbacteriochlorin-bacterlochlorin and bacteriochlorophyll-spheroidene complexes. J Am Chem Soc 126:4007–4016
Tozer DJ et al (1999) Does density functional theory contribute to the understanding of excited states of unsaturated organic compounds? Mol Phys 97:859–868
Moret ME et al (2005) Quantum mechanical/molecular mechanical (OM/MM) car-parrinello simulations in excited states. Chimia 59:493–498
Grimm S, Nonnenberg C, Frank I (2003) Restricted open-shell Kohn-Sham theory for pi-pi(*) transitions. I. Polyenes, cyanines, and protonated imines. J Chem Phys 119:11574–11584
Nonnenberg C, Grimm S, Frank I (2003) Restricted open-shell Kohn-Sham theory for pi-pi(*) transitions. II. Simulation of photochemical reactions. J Chem Phys 119:11585–11590
Rohrig UF et al (2003) QM/MM Car-Parrinello molecular dynamics study of the solvent effects on the ground state and on the first excited singlet state of acetone in water. Chemphyschem 4:1177–1182
Masson F et al (2009) A QM/MM investigation of thymine dimer radical anion splitting catalyzed by DNA photolyase. Chemphyschem 10:400–410
Langer H, Doltsinis NL (2003) Excited state tautomerism of the DNA base guanine: a restricted open-shell Kohn-Sham study. J Chem Phys 118:5400–5407
Ben-Nun M, Quenneville J, Martinez TJ (2000) Ab initio multiple spawning: photochemistry from first principles quantum molecular dynamics. J Phys Chem A 104:5161–5175
Ben-Nun M, Martinez TJ (2002) Ab initio quantum molecular dynamics. In: Prigogine I, Rice SA (eds) Advances in chemical physics. Wiley, New York
Manthe U, Koppel H (1990) Dynamics on potential-energy surfaces with a conical intersection - adiabatic, intermediate, and diabatic behavior. J Chem Phys 93:1658–1669
Manthe U, Koppel H, Cederbaum LS (1991) Dissociation and predissociation on coupled electronic potential-energy surfaces - a 3-dimensional wave packet dynamic study. J Chem Phys 95:1708–1720
Klessinger M, Michl J (1995) Excited states and photochemistry of organic molecules. VCH, New York
Robb MA, Bernardi F, Olivucci M (1995) Conical intersections as a mechanistic feature of organic-photochemistry. Pure Appl Chem 67:783–789
Yarkony DR (1996) Diabolical conical intersections. Rev Mod Phys 68:985–1013
Turro NJ (1991) Modern molecular photochemistry. University Science Books, Sausalito
Heller EJ (1981) Frozen Gaussians - a very simple semi-classical approximation. J Chem Phys 75:2923–2931
Virshup AM et al (2009) Photodynamics in complex environments: ab initio multiple spawning quantum mechanical/molecular mechanical dynamics. J Phys Chem B 113:3280–3291
Garcia JI et al (2007) QM/MM modeling of enantioselective pybox-ruthenium- and box-copper-catalyzed cyclopropanation reactions: scope, performance, and applications to ligand design. Chem-Eur J 13:4064–4073
Levine BG, Martinez TJ (2007) Isomerization through conical intersections. Annu Rev Phys Chem 58:613–634
Bearpark MJ, Larkin SM, Vreven T (2008) Searching for conical intersections of potential energy surfaces with the ONIOM method: application to previtamin D. J Phys Chem A 112:7286–7295
Sicilia F et al (2008) New algorithms for optimizing and linking conical intersection points. J Chem Theory Comput 4:257–266
Tokmachev AM et al (2010) Fluorescence of the perylene radical cation and an inaccessible D-0/D-1 conical intersection: an MMVB, RASSCF, and TD-DFT computational study. J Chem Phys 132:9
Dewar MJS, Thiel W (1977) Ground-states of molecules.38. MNDO method - approximations and parameters. J Am Chem Soc 99:4899–4907
Dewar MJS, Thiel W (1977) Ground-states of molecules. 39. MNDO results for molecules containing hydrogen, carbon, nitrogen, and oxygen. J Am Chem Soc 99:4907–4917
Dewar MJS et al (1985) The development and use of quantum-mechanical molecular-models. 76. AM1 - a new general-purpose quantum-mechanical molecular-model. J Am Chem Soc 107:3902–3909
Stewart JJP (1989) Optimization of parameters for semiempirical methods. 1. Method. J Comput Chem 10:209–220
Stewart JJP (1989) Optimization of parameters for semiempirical methods. 2. Applications. J Comput Chem 10:221–264
Stewart JJP (1991) Optimization of parameters for semiempirical methods. 3. Extension of Pm3 to Be, Mg, Zn, Ga, Ge, As, Se, Cd, In, Sn, Sb, Te, Hg, Tl, Pb, and Bi. J Comput Chem 12:320–341
Elstner M (2006) The SCC-DFTB method and its application to biological systems. Theor Chem Acc 116:316–325
Elstner M et al (1998) Self-consistent-charge density-functional tight-binding method for simulations of complex materials properties. Phys Rev B 58:7260–7268
Repasky MP, Chandrasekhar J, Jorgensen WL (2002) PDDG/PM3 and PDDG/MNDO: improved semiempirical methods. J Comput Chem 23:1601–1622
Weber W, Thiel W (2000) Orthogonalization corrections for semiempirical methods. Theor Chem Acc 103:495–506
Tuttle T, Thiel W (2008) OMx-D: semiempirical methods with orthogonalization and dispersion corrections. Implementation and biochemical application. Phys Chem Chem Phys 10:2159–2166
Silva-Junior MR, Thiel W (2010) Benchmark of electronically excited states for semiempirical methods: MNDO, AM1, PM3, OM1, OM2, OM3, INDO/S, and INDO/S2. J Chem Theory Comput 6:1546–1564
Sattelmeyer KW, Tubert-Brohman I, Jorgensen WL (2006) NO-MNDO: reintroduction of the overlap matrix into MNDO. J Chem Theory Comput 2:413–419
Rocha GB et al (2006) RM1: a reparameterization of AM1 for H, C, N, O, P, S, F, Cl, Br, and I. J Comput Chem 27:1101–1111
Feng F et al (2009) Can semiempirical quantum models calculate the binding energy of hydrogen bonding for biological systems? J Theor Comput Chem 8:691–711
Stewart JJP (2007) Optimization of parameters for semiempirical methods V: modification of NDDO approximations and application to 70 elements. J Mol Model 13:1173–1213
Danilov VI, Stewart JJP, van Mourik T (2007) A PM6 study of the “hydration shell” of nucleic acid 64 bases in small water clusters. J Biomol Struct Dyn 24:64
Kruger T et al (2005) Validation of the density-functional based tight-binding approximation method for the calculation of reaction energies and other data. J Chem Phys 122:5
Yang Y et al (2007) Extension of the self-consistent-charge density-functional tight-binding method: third-order expansion of the density functional theory total energy and introduction of a modified effective coulomb interaction. J Phys Chem A 111:10861–10873
Schaefer P, Riccardi D, Cui Q (2005) Reliable treatment of electrostatics in combined QM/MM simulation of macromolecules. J Chem Phys 123:014905
Riccardi D, Schaefer P, Cui Q (2005) pKa calculations in solution and proteins with QM/MM free energy perturbation simulations: a quantitative test of QM/MM protocols. J Phys Chem B 109:17715–17733
Riccardi D et al (2006) Development of effective quantum mechanical/molecular mechanical (QM/MM) methods for complex biological processes. J Phys Chem B 110:6458–6469
Sattelmeyer KW, Tirado-Rives J, Jorgensen WL (2006) Comparison of SCC-DFTB and NDDO-based semiempirical molecular orbital methods for organic molecules. J Phys Chem A 110:13551–13559
Otte N, Scholten M, Thiel W (2007) Looking at self-consistent-charge density functional tight binding from a semiempirical perspective. J Phys Chem A 111:5751–5755
Seabra GD, Walker RC, Roitberg AE (2009) Are current semiempirical methods better than force fields? A study from the thermodynamics perspective. J Phys Chem A 113:11938–11948
McNamara JP et al (2004) Towards a quantum mechanical force field for carbohydrates: a reparametrized semi-empirical MO approach. Chem Phys Lett 394:429–436
Sattelle BM, Almond A (2010) Less is more when simulating unsulfated glycosaminoglycan 3D-structure: comparison of GLYCAM06/TIP3P, PM3-CARB1/TIP3P, and SCC-DFTB-D/TIP3P predictions with experiment. J Comput Chem 31:2932–2947
Shaik S, Hiberty PC (2008) A chemist's guide to valence bond theory. Wiley, Hoboken
Shaik S, Shurki A (1999) Valence bond diagrams and chemical reactivity. Angew Chem Int Ed 38:586–625
Shaik SS (1989) A Qualitative Valence Bond Approach to Organic Reactions. In: Bertrán J, Csizmadia GI (eds) New theoretical concepts for understanding organic reactions. Kluwer Academic Publishers, Dordrecht
Shaik SS, Hilberty PC (1991) Theoretical concepts for chemical bonding. Springer, Berlin
Hilberty PC, Shaik S (2002) BOVB - a valence bond method incorporating static and dynamic electron correlation effects. In: Cooper DL (ed) Valence bond theory. Elsevier, Amsterdam
Aqvist J, Warshel A (1993) Simulation of enzyme-reactions using valence-bond force-fields and other hybrid quantum-classical approaches. Chem Rev 93:2523–2544
Warshel A, Weiss RM (1980) An empirical valence bond approach for comparing reactions in solutions and in enzymes. J Am Chem Soc 102:6218–6226
Warshel A (1991) Modeling of chemical reactions in enzymes and solutions. Wiley, New York
Shurki A, Warshel A (2003) Protein simulations. Academic, San Diego
Warshel A (2003) Computer simulations of enzyme catalysis: methods, progress, and insights. Annu Rev Biophys Biomol Struct 32:425–443
Leach AR (2001) Molecular modelling. Pearson Education Limited, Harlow
Shurki A, Crown HA (2005) Hybrid ab initio VB/MM method - a valence bond ride through classical landscapes. J Phys Chem B 109:23638–23644
Bearpark MJ et al (1997) Benchmarking the molecular mechanics valence bond method: photophysics of styrene and indene. J Phys Chem A 101:8395–8401
Bearpark MJ, Boggio-Pasqua M (2003) Excited states of conjugated hydrocarbon radicals using the molecular mechanics - valence bond (MMVB) method. Theor Chem Acc 110:105–114
Bearpark MJ et al (1994) Molecular mechanics valence-bond methods for large active spaces - application to conjugated polycyclic-hydrocarbons. Chem Phys Lett 217:513–519
Blancafort L et al (2003) A valence-bond-based complete-active-space self-consistent-field method for the evaluation of bonding in organic molecules. Theor Chem Acc 110:92–99
Garavelli M et al (2003) A simple approach for improving the hybrid MMVB force field: application to the photoisomerization of s-cis butadiene. J Comput Chem 24:1357–1363
Durand P, Malrieu JP (2007) Effective Hamiltonians and pseudo-operators as tools for rigorous modelling. Adv Chem Phys 67:321–412
Bernardi F et al (1988) Parametrization of a Heitler-London valence bond Hamiltonian from complete-active-space self-consistent-field computations - an application to chemical-reactivity. J Chem Phys 89:6365–6375
Said M, Maynau D, Malrieu JP (1984) Excited-state properties of linear polyenes studied through a nonempirical Heisenberg Hamiltonian. J Am Chem Soc 106:580–587
Said M et al (1984) A nonempirical Heisenberg Hamiltonian for the study of conjugated hydrocarbons - ground-state conformational studies. J Am Chem Soc 106:571–579
Allinger NL (1976) Calculation of molecular structure and energy by force-field methods. Adv Phys Org Chem 13:1–82
Allinger NL (1977) Conformational-analysis.130. MM2 - hydrocarbon force-field utilizing V1 and V2 torsional terms. J Am Chem Soc 99:8127–8134
Bernardi F, Olivucci M, Robb MA (1992) Simulation of MC-SCF results on covalent organic multibond reactions - molecular mechanics with valence bond (MM-VB). J Am Chem Soc 114:1606–1616
Warshel A (1991) Computer modelling of chemical reactions in enzymes and solutions. Wiley, New York
Chang YT, Minichino C, Miller WH (1992) Classical trajectory studies of the molecular dissociation dynamics of formaldehyde: H2CO → H2 + CO. J Chem Phys 96:4341–4355
Grochowski P et al (1996) Density functional based parametrization of a valence bond method and its applications in quantum classical molecular dynamics simulations of enzymatic reactions. Int J Quantum Chem 60:1143–1164
Albu TV, Corchado JC, Truhlar DG (2001) Molecular mechanics for chemical reactions: a standard strategy for using multiconfiguration molecular mechanics for variational transition state theory with optimized multidimensional tunneling. J Phys Chem A 105:8465–8487
Wei W, Zhong SJ, Shaik S (1998) VBDFT(s): a Huckel-type semi-empirical valence bond method scaled to density functional energies. Application to linear polyenes. Chem Phys Lett 292:7–14
Wu W, Shaik S (1999) VB-DFT: a nonempirical hybrid method combining valence bond theory and density functional energies. Chem Phys Lett 301:37–42
Wu W et al (2000) Using valence bond theory to understand electronic excited states: application to the hidden excited state (21Ag) of C2nH2n+2 (n = 2-14) polyenes. J Phys Chem A 104:8744–8758
Wu W et al (2001) VBDFT(s) - a semi-empirical valence bond method: application to linear polyenes containing oxygen and nitrogen heteroatoms. Phys Chem Chem Phys 3:5459–5465
Sharir-Ivry A et al (2010) VB/MM protein landscapes: a study of the SN2 reaction in haloalkane dehalogenase. J Phys Chem B 114:2212–2218
Cornell WD et al (1995) A 2nd generation force-field for the simulation of proteins, nucleic-acids, and organic-molecules. J Am Chem Soc 117:5179–5197
Kollman P et al (1998) AMBER: a program for simulation of biological and organic molecules. In: Schleyer PV et al (eds) Encyclopedia of computational chemistry. Wiley, Chichester
Wang J, Cieplak P, Kollman PA (2000) How well does a restrained electrostatic potential (RESP) model perform in calculating conformational energies of organic and biological molecules? J Comput Chem 21:1049–1074
Duan Y et al (2003) A point-charge force field for molecular mechanics simulations of proteins based on condensed-phase quantum mechanical calculations. J Comput Chem 24:1999–2012
MacKerell AD et al (1998) All-atom empirical potential for molecular modeling and dynamics studies of proteins. J Phys Chem B 102:3586–3616
MacKerell ADJ et al (1998) Protein force fields. Wiley, Chichester
Foloppe N, MacKerell JAD (2000) All-atom empirical force field for nucleic acids: I. Parameter optimization based on small molecule and condensed phase macromolecular target data. J Comput Chem 21:86–104
MacKerell AD, Banavali NK (2000) All-atom empirical force field for nucleic acids: II. Application to molecular dynamics simulations of DNA and RNA in solution. J Comput Chem 21:105–120
MacKerell JAD (2001) Atomistic models and force fields. In: Becker OM et al (eds) Computational biochemistry and biophysics. Dekker, New York
van Gunsteren WF, Daura X, Mark AE (1998) GROMOS force field. In: Schleyer Pv et al (eds) Encyclopedia of computational chemistry. Wiley, Chichester
Scott WRP et al (1999) The GROMOS biomolecular simulation program package. J Phys Chem A 103:3596–3607
van Gunsteren WF et al (1996) Gromos – GROningen MOlecular Simulation computer program package (GROMOS96) available at: http://www.gromos.net/
Jorgensen WL, Maxwell DS, Tirado-Rives J (1996) Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids. J Am Chem Soc 118:11225–11236
Jorgensen WL (1998) OPLS force fields. In: Schleyer Pv et al (eds) Encyclopedia of computational chemistry. Wiley, Chichester
Kaminski GA et al (2001) Evaluation and reparametrization of the OPLS-AA force field for proteins via comparison with accurate quantum chemical calculations on peptides. J Phys Chem B 105:6474–6487
Allinger NL, Kok RA, Imam MR (1988) Hydrogen-bonding in MM2. J Comput Chem 9:591–595
Allinger NL, Yuh YH, Lii JH (1989) Molecular mechanics - the MM3 force-field for hydrocarbons. 1. J Am Chem Soc 111:8551–8566
Lii JH, Allinger NL (1989) Molecular mechanics - The MM3 force-field for hydrocarbons. 3. The vanderwaals potentials and crystal data for aliphatic and aromatic-hydrocarbons. J Am Chem Soc 111:8576–8582
Lii JH, Allinger NL (1989) Molecular mechanics - the MM3 force-field for hydrocarbons. 2. Vibrational frequencies and thermodynamics. J Am Chem Soc 111:8566–8575
Allinger NL, Chen KS, Lii JH (1996) An improved force field (MM4) for saturated hydrocarbons. J Comput Chem 17:642–668
Ma BY et al (1996) Systematic comparison of experimental, quantum mechanical, and molecular mechanical bond lengths for organic molecules. J Phys Chem-Us 100:8763–8769
Nevins N, Chen KS, Allinger NL (1996) Molecular mechanics (MM4) calculations on alkenes. J Comput Chem 17:669–694
Nevins N, Lii JH, Allinger NL (1996) Molecular mechanics (MM4) calculations on conjugated hydrocarbons. J Comput Chem 17:695–729
Lifson S, Warshel A (1968) Consistent force field for calculations of conformations vibrational spectra and enthalpies of cycloalkane and n-alkane molecules. J Chem Phys 49:5116
Warshel A, Levitt M, Lifson S (1970) Consistent force field for calculation of vibrational spectra and conformations of some amides and lactam rings. J Mol Spectrosc 33:84
Warshel A, Lifson S (1970) Consistent force field calculations. 2. Crystal structures, sublimation energies, molecular and lattice vibrations, molecular conformations, and enthalpies of alkanes. J Chem Phys 53:582
Liang CX et al (1994) Ab-initio studies of lipid model species. 2. Conformational-analysis of inositols. J Am Chem Soc 116:3904–3911
Maple JR et al (1994) Derivation of class-II force-fields. 1. Methodology and quantum force-field for the alkyl functional-group and alkane molecules. J Comput Chem 15:162–182
Halgren TA (1996) Merck molecular force field. 1. Basis, form, scope, parameterization, and performance of MMFF94. J Comput Chem 17:490–519
Halgren TA (1996) Merck molecular force field. 2. MMFF94 van der Waals and electrostatic parameters for intermolecular interactions. J Comput Chem 17:520–552
Halgren TA (1996) Merck molecular force field. 3. Molecular geometries and vibrational frequencies for MMFF94. J Comput Chem 17:553–586
Halgren TA (1996) Merck molecular force field. 5. Extension of MMFF94 using experimental data, additional computational data, and empirical rules. J Comput Chem 17:616–641
Halgren TA (1999) MMFF VII. Characterization of MMFF94, MMFF94s, and other widely available force fields for conformational energies and for intermolecular-interaction energies and geometries. J Comput Chem 20:730–748
Halgren TA (1999) MMFF VI. MMFF94s option for energy minimization studies. J Comput Chem 20:720–729
Halgren TA, Nachbar RB (1996) Merck molecular force field. 4. Conformational energies and geometries for MMFF94. J Comput Chem 17:587–615
Rappe AK et al (1992) UFF, a full periodic-table force-field for molecular mechanics and molecular-dynamics simulations. J Am Chem Soc 114:10024–10035
Casewit CJ, Colwell KS, Rappe AK (1992) Application of a universal force-field to organic-molecules. J Am Chem Soc 114:10035–10046
Mayo SL, Olafson BD, Goddard WA (1990) Dreiding - a generic force-field for molecular simulations. J Phys Chem-Us 94:8897–8909
Lindahl E, Hess B, van der Spoel D (2001) GROMACS 3.0: a package for molecular simulation and trajectory analysis. J Mol Model 7:306–317
van der Spoel D et al (2005) GROMACS: fast, flexible, and free. J Comput Chem 26:1701–1718
Clark M, Cramer RD, Vanopdenbosch N (1989) Validation of the general-purpose tripos 5.2 force-field. J Comput Chem 10:982–1012
Hagler AT, Dauber P, Lifson S (1979) Consistent force-field studies of inter-molecular forces in hydrogen-bonded crystals. 3. C=O…H-O hydrogen-bond and the analysis of the energetics and packing of carboxylic-acids. J Am Chem Soc 101:5131–5141
Hobza P et al (1997) Performance of empirical potentials (AMBER, CFF95, CVFF, CHARMM, OPLS, POLTEV), semiempirical quantum chemical methods (AM1, MNDO/M, PM3), and ab initio Hartree-Fock method for interaction of DNA bases: comparison with nonempirical beyond Hartree-Fock results. J Comput Chem 18:1136–1150
Hornak V et al (2006) Comparison of multiple amber force fields and development of improved protein backbone parameters. Proteins 65:712–725
Hu H, Elstner M, Hermans J (2003) Comparison of a QM/MM force field and molecular mechanics force fields in simulations of alanine and glycine "dipeptides" (Ace-Ala-Nme and Ace-Gly-Nme) in water in relation to the problem of modeling the unfolded peptide backbone in solution. Proteins 50:451–463
Gundertofte K, Liljefors T, Norrby PO (1996) A comparison of conformational energies calculated by several molecular mechanics methods. J Comput Chem 17:429–449
Ponder JW, Case DA (2003) Force fields for protein simulations. In: Richards FM, Eisendberg DS, Kuriyan J (eds) Protein simulations. Elsevier Academic, Amsterdam
MacKerell AD (2004) Empirical force fields for biological macromolecules: overview and issues. J Comput Chem 25:1584–1604
Okur A et al (2003) Using PC clusters to evaluate the transferability of molecular mechanics force fields for proteins. J Comput Chem 24:21–31
Wikipedia, the free encyclopedia: force field (chemistry) at http://en.wikipedia.org/wiki/Force_field_%28chemistry%29. Accessed: March 2011
Imberty A, Perez S (2000) Structure, conformation, and dynamics of bioactive oligosaccharides: theoretical approaches and experimental validations. Chem Rev 100:4567–4588
Kirschner KN et al (2008) GLYCAM06: a generalizable biomolecular force field. Carbohydrates. J Comput Chem 29:622–655
Tessier MB et al (2008) Extension of the GLYCAM06 biomolecular force field to lipids, lipid bilayers and glycolipids. Mol Simul 34:349–363
Hemmingsen L et al (2004) Evaluation of carbohydrate molecular mechanical force fields by quantum mechanical calculations. Carbohydr Res 339:937–948
Swope WC et al (2008) COMP 327-Comprehensive comparison and assessment of force fields for pharmaceutical applications by computation of hydration free energy. Abstr Pap Am Chem S 236
Vanommeslaeghe K, Acharya C, MacKerell AD (2008) COMP 6-development of parameters for the CHARMM general force field. Abstr Pap Am Chem S 236
Vanommeslaeghe K et al (2010) CHARMM general force field: a force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields. J Comput Chem 31:671–690
Sherrill CD et al (2009) Assessment of standard force field models against high-quality ab initio potential curves for prototypes of pi-pi, CH/pi, and SH/pi interactions. J Comput Chem 30:2187–2193
Jeziorski B, Moszynski R, Szalewicz K (1994) Perturbation-theory approach to intermolecular potential-energy surfaces of van-der-Waals complexes. Chem Rev 94:1887–1930
van der Avoird A et al (1980) Ab initio studies of the interactions in vanderwaals molecules. Top Curr Chem 93:1–51
Hesselmann A, Korona T (2011) On the accuracy of DFT-SAPT, MP2, SCS-MP2, MP2C, and DFT plus Disp methods for the interaction energies of endohedral complexes of the C60 fullerene with a rare gas atom. Phys Chem Chem Phys 13:732–743
Hobza P et al (2010) Stabilization and structure calculations for noncovalent interactions in extended molecular systems based on wave function and density functional theories. Chem Rev 110:5023–5063
Hohenstein EG, Sherrill CD (2010) Density fitting of intramonomer correlation effects in symmetry-adapted perturbation theory. J Chem Phys 133:014101
Jansen G et al (2008) Stacking energies for average B-DNA structures from the combined density functional theory and symmetry-adapted perturbation theory approach. J Am Chem Soc 130:1802
Jansen G, Tekin A (2007) How accurate is the density functional theory combined with symmetry-adapted perturbation theory approach for CH-pi and pi-pi interactions? A comparison to supermolecular calculations for the acetylene-benzene dimer. Phys Chem Chem Phys 9:1680–1687
Mooij WTM et al (1999) Transferable ab initio intermolecular potentials. 1. Derivation from methanol dimer and trimer calculations. J Phys Chem A 103:9872–9882
Chipot C et al (2009) Polarizable intermolecular potentials for water and benzene interacting with halide and metal ions. J Chem Theory Comput 5:3022–3031
Hloucha M, Sum AK, Sandler SI (2000) Computer simulation of acetonitrile and methanol with ab initio-based pair potentials. J Chem Phys 113:5401–5406
Jansen G, Torheyden M (2006) A new potential energy surface for the water dimer obtained from separate fits of ab initio electrostatic, induction, dispersion and exchange energy contributions. Mol Phys 104:2101–2138
Li X et al (2006) Interaction energies between glycopeptide antibiotics and substrates in complexes determined by X-ray crystallography: application of a theoretical databank of aspherical atoms and a symmetry-adapted perturbation theory-based set of interatomic potentials. Acta Crystallogr D 62:639–647
Misquitta AJ, Totton TS, Kraft M (2010) A first principles development of a general anisotropic potential for polycyclic aromatic hydrocarbons. J Chem Theory Comput 6:683–695
Mitchell JBO, Price SL (2000) A systematic nonempirical method of deriving model intermolecular potentials for organic molecules: application to amides. J Phys Chem A 104:10958–10971
van der Avoird A, Szalewicz K, Leforestier C (2009) Towards the complete understanding of water by a first-principles computational approach. Chem Phys Lett 482:1–14
Goodman JM, Paton RS (2009) Hydrogen bonding and pi-stacking: how reliable are force fields? A critical evaluation of force field descriptions of nonbonded interactions. J Chem Inf Model 49:944–955
Sponer J et al (2009) Balance of attraction and repulsion in nucleic-acid base stacking: CCSD(T)/complete-basis-set-limit calculations on uracil dimer and a comparison with the force-field description. J Chem Theory Comput 5:1524–1544
Sponer J et al (2010) Reference MP2/CBS and CCSD(T) quantum-chemical calculations on stacked adenine dimers. Comparison with DFT-D, MP2.5, SCS(MI)-MP2, M06-2X, CBS(SCS-D) and force field descriptions. Phys Chem Chem Phys 12:3522–3534
Zgarbova M et al (2010) Large-scale compensation of errors in pairwise-additive empirical force fields: comparison of AMBER intermolecular terms with rigorous DFT-SAPT calculations. Phys Chem Chem Phys 12:10476–10493
Corry B et al (2010) Molecular dynamics simulations of structure and dynamics of organic molecular crystals. Phys Chem Chem Phys 12:14916–14929
Hobza P et al (2010) On the reliability of the AMBER force field and its empirical dispersion contribution for the description of noncovalent complexes. Chemphyschem 11:2399–2408
Tateno M, Hagiwara Y (2009) Evaluation of stabilization energies in π–π and cation–π interactions involved in biological macromolecules by ab initio calculations. J Phys Condens Matter 21:064243
Wetmore SD, Rutledge LR (2010) The assessment of density functionals for DNA-protein stacked and T-shaped complexes. Can J Chem 88:815–830
Tafipolsky M, Engels B (2011) Accurate intermolecular potentials with physically grounded electrostatics. J Chem Theory Comput 7:1791–1803
Head-Gordon T et al (2010) Current status of the AMOEBA polarizable force field. J Phys Chem B 114:2549–2564
Ponder JW et al (2010) Tinker – software tools for molecular modelling (5.1) available at: http://dasher.wustl.edu/tinker
van der Avoird A et al (2010) Vibration-rotation-tunneling states of the benzene dimer: an ab initio study. Phys Chem Chem Phys 12:8219–8240
Spackman MA (2006) The use of the promolecular charge density to approximate the penetration contribution to intermolecular electrostatic energies. Chem Phys Lett 418:158–162
Spackman MA (1986) A simple quantitative model of hydrogen-bonding. J Chem Phys 85:6587–6601
Gordon MS, Slipchenko LV (2009) Damping functions in the effective fragment potential method. Mol Phys 107:999–1016
Piquemal JP et al (2008) Simple formulas for improved point-charge electrostatics in classical force fields and hybrid quantum mechanical/molecular mechanical embedding. Int J Quantum Chem 108:1905–1912
Pedersen LG et al (2010) Gaussian multipole model (GMM). J Chem Theory Comput 6:190–202
Wang B, Truhlar DG (2010) Including charge penetration effects in molecular modeling. J Chem Theory Comput 6:3330–3342
Singh UC, Kollman PA (1986) A combined ab initio quantum-mechanical and molecular mechanical method for carrying out simulations on complex molecular-systems - applications to the CH3Cl+Cl− exchange-reaction and gas-phase protonation of polyethers. J Comput Chem 7:718–730
Bakowies D, Thiel W (1996) Hybrid models for combined quantum mechanical and molecular mechanical approaches. J Phys Chem-Us 100:10580–10594
Gao J (1997) Energy components of aqueous solution: insight from hybrid QM/MM simulations using a polarizable solvent model. J Comput Chem 18:1061–1071
Gao JL, Byun K (1997) Solvent effects on the n->pi transition of pyrimidine in aqueous solution. Theor Chem Acc 96:151–156
Thompson MA (1996) QM/MMpol: a consistent model for solute/solvent polarization. Application to the aqueous solvation and spectroscopy of formaldehyde, acetaldehyde, and acetone. J Phys Chem-Us 100:14492–14507
Thompson MA, Schenter GK (1995) Excited-states of the bacteriochlorophyll-B dimer of Rhodopseudomonas-viridis - a QM/MM study of the photosynthetic reaction-center that includes MM polarization. J Phys Chem-Us 99:6374–6386
Cornell WD et al (1996) A second generation force field for the simulation of proteins, nucleic acids, and organic molecules (vol 117, pg 5179, 1995). J Am Chem Soc 118:2309
Kunz APE, Eichenberger AP, van Gunsteren WF (2011) A simple, efficient polarizable molecular model for liquid carbon tetrachloride. Mol Phys 109:365–372
Kunz APE, van Gunsteren WF (2009) Development of a nonlinear classical polarization model for liquid water and aqueous solutions: COS/D. J Phys Chem A 113:11570–11579
Geerke DP, Van Gunsteren WF (2007) The performance of non-polarizable and polarizable force-field parameter sets for ethylene glycol in molecular dynamics simulations of the pure liquid and its aqueous mixtures. Mol Phys 105:1861–1881
Grossfield A, Ren PY, Ponder JW (2003) Ion solvation thermodynamics from simulation with a polarizable force field. J Am Chem Soc 125:15671–15682
Maple JR et al (2005) A polarizable force field and continuum solvation methodology for modeling of protein-ligand interactions. J Chem Theory Comput 1:694–715
Oostenbrink C et al (2004) A biomolecular force field based on the free enthalpy of hydration and solvation: the GROMOS force-field parameter sets 53A5 and 53A6. J Comput Chem 25:1656–1676
Chang TM, Dang LX (2005) Liquid-vapor interface of methanol-water mixtures: a molecular dynamics study. J Phys Chem B 109:5759–5765
Patel SA, Brooks CL (2006) Revisiting the hexane-water interface via molecular dynamics simulations using nonadditive alkane-water potentials. J Chem Phys 124:204706
Warshel A, Kato M, Pisliakov AV (2007) Polarizable force fields: history, test cases, and prospects. J Chem Theory Comput 3:2034–2045
Harder E et al (2008) Understanding the dielectric properties of liquid amides from a polarizable force field. J Phys Chem B 112:3509–3521
Xie WS et al (2007) Development of a polarizable intermolecular potential function (PIPF) for liquid amides and alkanes. J Chem Theory Comput 3:1878–1889
Rick SW, Stuart SJ (2003) Potentials and algorithms for incorporating polarizability in computer simulations. In: Lipkowitz KB, Boyd DB (eds) Reviews in computational chemistry. Wiley, New York
Yu HB, van Gunsteren WF (2005) Accounting for polarization in molecular simulation. Comput Phys Commun 172:69–85
van Belle D et al (1987) Calculations of electrostatic properties in proteins - analysis of contributions from induced protein dipoles. J Mol Biol 198:721–735
Vesely FJ (1977) N-Particle dynamics of polarizable Stockmayer-type molecules. J Comput Phys 24:361–371
Straatsma TP, McCammon JA (1990) Molecular dynamics simulations with interaction potentials including polarization development of a noniterative method and application to water. Mol Simul 5:181–192
Drude P (1902) The theory of optics. Longmans, Green and Co, New York
Rick SW, Stuart SJ, Berne BJ (1994) Dynamical fluctuating charge force-fields - application to liquid water. J Chem Phys 101:6141–6156
Anisimov VM et al (2005) Determination of electrostatic parameters for a polarizable force field based on the classical Drude oscillator. J Chem Theory Comput 1:153–168
Cieplak P, Caldwell J, Kollman P (2001) Molecular mechanical models for organic and biological systems going beyond the atom centered two body additive approximation: aqueous solution free energies of methanol and N-methyl acetamide, nucleic acid base, and amide hydrogen bonding and chloroform/water partition coefficients of the nucleic acid bases. J Comput Chem 22:1048–1057
Cieplak P et al (2009) Polarization effects in molecular mechanical force fields. J Phys Condens Matter 21:21
Patel S, Brooks CL (2004) CHARMM fluctuating charge force field for proteins: I parameterization and application to bulk organic liquid simulations. J Comput Chem 25:1–15
Patel S, Mackerell AD, Brooks CL (2004) CHARMM fluctuating charge force field for proteins: II Protein/solvent properties from molecular dynamics simulations using a nonadditive electrostatic model. J Comput Chem 25:1504–1514
Vorobyov IV, Anisimov VM, MacKerell AD (2005) Polarizable empirical force field for alkanes based on the classical drude oscillator model. J Phys Chem B 109:18988–18999
Wang ZX et al (2006) Strike a balance: optimization of backbone torsion parameters of AMBER polarizable force field for simulations of proteins and peptides. J Comput Chem 27:781–790
Banks JL et al (1999) Parametrizing a polarizable force field from ab initio data. I. The fluctuating point charge model. J Chem Phys 110:741–754
Kaminski GA et al (2004) Development of an accurate and robust polarizable molecular mechanics force field from ab initio quantum chemistry. J Phys Chem A 108:621–627
Kaminski GA et al (2002) Development of a polarizable force field for proteins via ab initio quantum chemistry: first generation model and gas phase tests. J Comput Chem 23:1515–1531
Xie WS, Gao JL (2007) Design of a next generation force field: the X-POL potential. J Chem Theory Comput 3:1890–1900
Cho AE et al (2005) Importance of accurate charges in molecular docking: quantum mechanical/molecular mechanical (QM/MM) approach. J Comput Chem 26:915–931
Friesner RA (2006) Modeling polarization in proteins and protein-ligand complexes: methods and preliminary results. Adv Protein Chem 72:79
Illingworth CJR et al (2006) Classical polarization in hybrid QM/MM methods. J Phys Chem A 110:6487–6497
Kaminski S et al (2010) Vibrational Raman spectra from the self-consistent charge density functional tight binding method via classical time-correlation functions. J Chem Theory Comput 6:1240–1255
Lopes PEM, Roux B, MacKerell AD (2009) Molecular modeling and dynamics studies with explicit inclusion of electronic polarizability: theory and applications. Theor Chem Acc 124:11–28
Geerke DP, van Gunsteren WF (2007) Calculation of the free energy of polarization: quantifying the effect of explicitly treating electronic polarization on the transferability of force-field parameters. J Phys Chem B 111:6425–6436
Lin ZX, Schmid N, van Gunsteren WF (2011) The effect of using a polarizable solvent model upon the folding equilibrium of different -peptides. Mol Phys 109:493–506
Illingworth CJR et al (2008) Toward a consistent treatment of polarization in model QM/MM calculations. J Phys Chem A 112:12151–12156
Swope WC, Horn HW, Rice JE (2010) Accounting for polarization cost when using fixed charge force fields. II. Method and application for computing effect of polarization cost on free energy of hydration. J Phys Chem B 114:8631–8645
Biswas PK, Gogonea V (2008) A polarizable force-field model for quantum-mechanical-molecular-mechanical Hamiltonian using expansion of point charges into orbitals. J Chem Phys 129:154108
Pliego JR (2011) Shells theory of solvation and the long-range born correction. Theor Chem Acc 128:275–283
Jiang W et al (2011) High-performance scalable molecular dynamics simulations of a polarizable force field based on classical drude oscillators in NAMD. J Phys Chem Lett 2:87–92
Stillinger FH, Rahman A (1974) Improved simulation of liquid water by molecular-dynamics. J Chem Phys 60:1545–1557
Phillips JC et al (2005) Scalable molecular dynamics with NAMD. J Comput Chem 26:1781–1802
Zhang Y, Lin H (2008) Flexible-boundary quantum-mechanical/molecular-mechanical calculations: partial charge transfer between the quantum-mechanical and molecular-mechanical subsystems. J Chem Theory Comput 4:414–425
Zhang Y, Lin H, Truhlar DG (2007) Self-consistent polarization of the boundary in the redistributed charge and dipole scheme for combined quantum-mechanical and molecular-mechanical calculations. J Chem Theory Comput 3:1378–1398
Hamad S, Woodley SM, Catlow CRA (2009) Experimental and computational studies of ZnS nanostructures. Mol Simul 35:1015–1032
Catlow CRA et al (2008) Zinc oxide: a case study in contemporary computational solid state chemistry. J Comput Chem 29:2234–2249
To J et al (2008) Hybrid QM/MM investigations into the structure and properties of oxygen-donating species in TS-1. J Phys Chem C 112:7173–7185
Goumans TPM et al (2008) Hydrogenation of CO on a silica surface: an embedded cluster approach. J Chem Phys 128:6
Goumans TPM, Catlow CRA, Brown WA (2008) Catalysis of addition reactions by a negatively charged silica surface site on a dust grain. J Phys Chem C 112:15419–15422
Adriaens DA et al (2010) Computational study of carbonyl sulphide formation on model interstellar dust grains. J Phys Chem C 114:1892–1900
Goumans TPM et al (2009) An embedded cluster study of the formation of water on interstellar dust grains. Phys Chem Chem Phys 11:5431–5436
Goumans TPM et al (2009) Formation of H2 on an olivine surface: a computational study. Mon Not R Astron Soc 393:1403–1407
Olsen JM, Aidas K, Kongsted J (2010) Excited states in solution through polarizable embedding. J Chem Theory Comput 6:3721–3734
Slipchenko LV (2010) Solvation of the excited states of chromophores in polarizable environment: orbital relaxation versus polarization. J Phys Chem A 114:8824–8830
Mata RA, Cabral BJC (2010) QM/MM approaches to the electronic spectra of hydrogen-bonding systems with connection to many-body decomposition schemes. In: Sabin JR, Brandas, E, Canuto S (eds) Advances in quantum chemistry. Elsevier Academic, San Diego
Yoo S et al (2008) Solvent effects on optical properties of molecules: a combined time-dependent density functional theory/effective fragment potential approach. J Chem Phys 129:144112
Fujimoto K, Yang WT (2008) Density-fragment interaction approach for quantum-mechanical/molecular-mechanical calculations with application to the excited states of a Mg(2+)-sensitive dye. J Chem Phys 129:054102
Fux S et al (2010) Accurate frozen-density embedding potentials as a first step towards a subsystem description of covalent bonds. J Chem Phys 132:164101
Neugebauer J et al (2010) A subsystem TDDFT approach for solvent screening effects on excitation energy transfer couplings. J Chem Theory Comput 6:1843–1851
Neugebauer J et al (2005) An explicit quantum chemical method for modeling large solvation shells applied to aminocoumarin C151. J Phys Chem A 109:7805–7814
Neugebauer J et al (2005) The merits of the frozen-density embedding scheme to model solvatochromic shifts. J Chem Phys 122:094115
Neugebauer J et al (2005) Modeling solvent effects on electron-spin-resonance hyperfine couplings by frozen-density embedding. J Chem Phys 123:114101
Ranaghan KE, Mulholland AJ (2010) Investigations of enzyme-catalysed reactions with combined quantum mechanics/molecular mechanics (QM/MM) methods. Int Rev Phys Chem 29:65–133
Maseras F, Morokuma K (1995) IMOMM - a new integrated ab-initio plus molecular mechanics geometry optimization scheme of equilibrium structures and transition-states. J Comput Chem 16:1170–1179
Matsubara T, Sieber S, Morokuma K (1996) A test of the new “integrated MO + MM” (IMOMM) method for the conformational energy of ethane and n-butane. Int J Quantum Chem 60:1101–1109
Froese RDJ, Morokuma K (1999) IMOMO-G2MS approaches to accurate calculations of bond dissociation energies of large molecules. J Phys Chem A 103:4580–4586
Humbel S, Sieber S, Morokuma K (1996) The IMOMO method: integration of different levels of molecular orbital approximations for geometry optimization of large systems: test for n-butane conformation and SN2 reaction: RCl + Cl. J Chem Phys 105:1959–1967
Froese RDJ, Morokuma K (1996) The IMOMO and IMOMM methods for excited states. A study of the adiabatic S0->T1, T2 excitation energies of cyclic alkenes and enones. Chem Phys Lett 263:393–400
Svensson M et al (1996) ONIOM: a multilayered integrated MO+MM method for geometry optimizations and single point energy predictions. A test for Diels-Alder reactions and Pt(P(t-Bu)3)2 + H2 oxidative addition. J Phys Chem-Us 100:19357–19363
Dapprich S et al (1999) A new ONIOM implementation in Gaussian98. Part I. The calculation of energies, gradients, vibrational frequencies and electric field derivatives. J Mol Struct-Theochem 461:1–21
Vreven T et al (2006) Combining quantum mechanics methods with molecular mechanics methods in ONIOM. J Chem Theory Comput 2:815–826
Vreven T et al (2003) Geometry optimization with QM/MM, ONIOM, and other combined methods. I. Microiterations and constraints. J Comput Chem 24:760–769
Ryde U (1996) The coordination of the catalytic zinc ion in alcohol dehydrogenase studied by combined quantum-chemical and molecular mechanics calculations. J Comput Aided Mol Des 10:153–164
Ryde U, Olsson MHM (2001) Structure, strain, and reorganization energy of blue copper models in the protein. Int J Quantum Chem 81:335–347
Zhang YK, Lee TS, Yang WT (1999) A pseudobond approach to combining quantum mechanical and molecular mechanical methods. J Chem Phys 110:46–54
Nicoll RM et al (2001) Quantum mechanical/molecular mechanical methods and the study of kinetic isotope effects: modelling the covalent junction region and application to the enzyme xylose isomerase. Theor Chem Acc 106:105–112
Reuter N et al (2000) Frontier bonds in QM/MM methods: a comparison of different approaches. J Phys Chem A 104:1720–1735
Hall RJ et al (2000) Aspects of hybrid QM/MM calculations: the treatment of the QM/MM interface region and geometry optimization with an application to chorismate mutase. J Comput Chem 21:1433–1441
Amara P, Field MJ (2003) Evaluation of an ab initio quantum mechanical/molecular mechanical hybrid-potential link-atom method. Theor Chem Acc 109:43–52
Lin H, Truhlar DG (2005) Redistributed charge and dipole schemes for combined quantum mechanical and molecular mechanical calculations. J Phys Chem A 109:3991–4004
Konig PH et al (2005) A critical evaluation of different QM/MM frontier treatments with SCC-DFTB as the QM method. J Phys Chem B 109:9082–9095
Assfeld X, Rivail JL (1996) Quantum chemical computations on parts of large molecules: the ab initio local self consistent field method. Chem Phys Lett 263:100–106
Pu JZ, Gao JL, Truhlar DG (2004) Generalized hybrid orbital (GHO) method for combining ab initio Hartree-Fock wave functions with molecular mechanics. J Phys Chem A 108:632–650
Jung J et al (2007) New implementation of a combined quantum mechanical and molecular mechanical method using modified generalized hybrid orbitals. J Chem Phys 127:204102
Bessac F et al (2003) Effective group potentials: a powerful tool for hybrid QM/MM methods? J Mol Struct-Theochem 632:43–59
Day PN et al (1996) An effective fragment method for modeling solvent effects in quantum mechanical calculations. J Chem Phys 105:1968–1986
Adamovic I, Freitag MA, Gordon MS (2003) Density functional theory based effective fragment potential method. J Chem Phys 118:6725–6732
Adamovic I, Gordon MS (2006) Methanol-water mixtures: a microsolvation study using the effective fragment potential method. J Phys Chem A 110:10267–10273
Netzloff HM, Gordon MS (2004) The effective fragment potential: small clusters and radial distribution functions. J Chem Phys 121:2711–2714
Poteau R et al (2001) Effective group potentials. 1. Method. J Phys Chem A 105:198–205
Poteau R et al (2001) Effective group potentials. 2. Extraction and transferability for chemical groups involved in covalent or donor-acceptor bonds. J Phys Chem A 105:206–214
Exner TE, Mezey PG (2003) Ab initio quality properties for macromolecules using the ADMA approach. J Comput Chem 24:1980–1986
Exner TE, Mezey PG (2005) Evaluation of the field-adapted ADMA approach: absolute and relative energies of crambin and derivatives. Phys Chem Chem Phys 7:4061–4069
Eckard S, Exner TE (2006) Generalized hybrid orbitals in the FA-ADMA method. Z Phys Chem 220:927–944
DiLabio GA, Hurley MM, Christiansen PA (2002) Simple one-electron quantum capping potentials for use in hybrid QM/MM studies of biological molecules. J Chem Phys 116:9578–9584
Moon S, Christiansen PA, DiLabio GA (2004) Quantum capping potentials with point charges: a simple QM/MM approach for the calculation of large-molecule NMR shielding tensors. J Chem Phys 120:9080–9086
Jardillier N, Goursot A (2008) One-electron quantum capping potential for hybrid QM/MM studies of silicate molecules and solids. Chem Phys Lett 454:65–69
Ohnishi YY et al (2008) Frontier orbital consistent quantum capping potential (FOC-QCP) for bulky ligand of transition metal complexes. J Phys Chem A 112:1946–1955
Komin S, Sebastiani D (2009) Optimization of capping potentials for spectroscopic parameters in hybrid quantum mechanical/mechanical modeling calculations. J Chem Theory Comput 5:1490–1498
Wang B, Truhlar DG (2010) Combined quantum mechanical and molecular mechanical methods for calculating potential energy surfaces: tuned and balanced redistributed-charge algorithm. J Chem Theory Comput 6:359–369
DiLabio GA, Wolkow RA, Johnson ER (2005) Efficient silicon surface and cluster modeling using quantum capping potentials. J Chem Phys 122:5
Goedecker S, Teter M, Hutter J (1996) Separable dual-space Gaussian pseudopotentials. Phys Rev B 54:1703–1710
Hartwigsen C, Goedecker S, Hutter J (1998) Relativistic separable dual-space Gaussian pseudopotentials from H to Rn. Phys Rev B 58:3641–3662
Schiffmann C, Sebastiani D (2011) Artificial bee colony optimization of capping potentials for hybrid QM/MM calculations. J Chem Theory Comput 7:1307–1315
Brown SP, Spiess HW (2001) Advanced solid-state NMR methods for the elucidation of structure and dynamics of molecular, macromolecular, and supramolecular systems. Chem Rev 101:4125–4155
Schulz-Dobrick M et al (2005) Determining the geometry of hydrogen bonds in solids with picometer accuracy by quantum chemical calculations and NMR spectroscopy. Chemphyschem 6:315–327
Spiess HW (2003) Nuclear magnetic resonance spectroscopy in macromolecular science. Macromol Chem Phys 204:340–346
Press WH et al (1992) Numerical recipes. Cambridge University Press, Cambridge, UK
Karaboga D, Akay B (2009) A survey: algorithms simulating bee swarm intelligence. Artif Intell Rev 31:61–85
Karaboga D, Basturk B (2007) A powerful and efficient algorithm for numerical function optimization: artificial bee colony (ABC) algorithm. J Global Optim 39:459–471
Karaboga D, Basturk B (2008) On the performance of artificial bee colony (ABC) algorithm. Appl Soft Comput 8:687–697
Moon S, Patchkovskii S, Salahub DR (2003) QM/MM calculations of EPR hyperfine coupling constants in blue copper proteins. J Mol Struct-Theochem 632:287–295
Kerdcharoen T, Liedl KR, Rode BM (1996) A QM/MM simulation method applied to the solution of Li+ in liquid ammonia. Chem Phys 211:313–323
Hofer TS et al (2005) Structure and dynamics of solvated Sn(II) in aqueous solution: an ab initio QM/MM MD approach. J Am Chem Soc 127:14231–14238
Schwenk CF, Loeffler HH, Rode BM (2003) Structure and dynamics of metal ions in solution: QM/MM molecular dynamics simulations of Mn2+ and V2+. J Am Chem Soc 125:1618–1624
Rode BM, Schwenk CF, Tongraar A (2004) Structure and dynamics of hydrated ions-new insights through quantum mechanical simulations. J Mol Liq 110:105–122
Kerdcharoen T, Morokuma K (2002) ONIOM-XS: an extension of the ONIOM method for molecular simulation in condensed phase. Chem Phys Lett 355:257–262
Kerdcharoen T, Morokuma K (2003) Combined quantum mechanics and molecular mechanics simulation of Ca2+/ammonia solution based on the ONIOM-XS method: octahedral coordination and implication to biology. J Chem Phys 118:8856–8862
Morokuma K (2003) ONIOM and its applications to material chemistry and catalyses. Bull Korean Chem Soc 24:797–801
Heyden A, Lin H, Truhlar DG (2007) Adaptive partitioning in combined quantum mechanical and molecular mechanical calculations of potential energy functions for multiscale simulations. J Phys Chem B 111:2231–2241
Zhang Y, Lin H (2010) Flexible-boundary QM/MM calculations: II. Partial charge transfer across the QM/MM boundary that passes through a covalent bond. Theor Chem Acc 126:315–322
Nielsen SO et al (2010) Recent progress in adaptive multiscale molecular dynamics simulations of soft matter. Phys Chem Chem Phys 12:12401–12414
Hofer TS et al (2010) Simulations of liquids and solutions based on quantum mechanical forces. In: vanEldik R, Harvey J (eds) Advances in inorganic chemistry: theoretical and computational inorganic chemistry, Vol 62. Elsevier Academic, San Diego
Darden T, York D, Pedersen L (1993) Particle mesh Ewald - an N.log(N) method for Ewald sums in large systems. J Chem Phys 98:10089–10092
York DM, Darden TA, Pedersen LG (1993) The effect of long-range electrostatic interactions in simulations of macromolecular crystals - a comparison of the Ewald and truncated list methods. J Chem Phys 99:8345–8348
Essmann U et al (1995) A smooth particle mesh Ewald method. J Chem Phys 103:8577–8593
Nam K, Gao JL, York DM (2005) An efficient linear-scaling Ewald method for long-range electrostatic interactions in combined QM/MM calculations. J Chem Theory Comput 1:2–13
Walker RC, Crowley MF, Case DA (2008) The implementation of a fast and accurate QM/MM potential method in Amber. J Comput Chem 29:1019–1031
Laino T et al (2005) An efficient real space multigrid OM/MM electrostatic coupling. J Chem Theory Comput 1:1176–1184
Laino T et al (2006) An efficient linear-scaling electrostatic coupling for treating periodic boundary conditions in QM/MM simulations. J Chem Theory Comput 2:1370–1378
Berkowitz M, McCammon JA (1982) Molecular-dynamics with stochastic boundary-conditions. Chem Phys Lett 90:215–217
Brunger A, Brooks CL, Karplus M (1984) Stochastic boundary-conditions for molecular-dynamics simulations of St2 water. Chem Phys Lett 105:495–500
Brooks CL, Karplus M (1983) Deformable stochastic boundaries in molecular-dynamics. J Chem Phys 79:6312–6325
Lee FS, Warshel A (1992) A local reaction field method for fast evaluation of long-range electrostatic interactions in molecular simulations. J Chem Phys 97:3100–3107
Tironi IG et al (1995) A generalized reaction field method for molecular-dynamics simulations. J Chem Phys 102:5451–5459
Beglov D, Roux B (1994) Finite representation of an infinite bulk system - solvent boundary potential for computer-simulations. J Chem Phys 100:9050–9063
Benighaus T, Thiel W (2011) Long-range electrostatic effects in QM/MM studies of enzymatic reactions: application of the solvated macromolecule boundary potential. J Chem Theory Comput 7:238–249
Im W, Berneche S, Roux B (2001) Generalized solvent boundary potential for computer simulations. J Chem Phys 114:2924–2937
Thiel W, Benighaus T (2008) Efficiency and accuracy of the generalized solvent boundary potential for hybrid QM/MM simulations: implementation for semiempirical Hamiltonians. J Chem Theory Comput 4:1600–1609
Thiel W, Benighaus T (2009) A general boundary potential for hybrid QM/MM simulations of solvated biomolecular systems. J Chem Theory Comput 5:3114–3128
Wales DJ (2003) Energy landscapes. Cambridge University Press, Cambridge
Moult J et al (2009) Critical assessment of methods of protein structure prediction—round VIII. Proteins Struct Funct Bioinf 77:1–4
Klahn M et al (2005) On possible pitfalls in ab initio quantum mechanics/molecular mechanics minimization approaches for studies of enzymatic reactions. J Phys Chem B 109:15645–15650
Christen M, van Gunsteren WF (2008) On searching in, sampling of, and dynamically moving through conformational space of biomolecular systems: a review. J Comput Chem 29:157–166
Oakley MT et al (2008) Search strategies in structural bioinformatics. Curr Protein Pept Sci 9:260–274
van Gunsteren WF et al (2006) Biomolecular modeling: goals, problems, perspectives. Angew Chem Int Ed 45:4064–4092
Chen IJ, Foloppe N (2011) Is conformational sampling of drug-like molecules a solved problem? Drug Dev Res 72:85–94
Chen IJ, Foloppe N (2010) Drug-like bioactive structures and conformational coverage with the ligprep/confgen suite: comparison to programs MOE and catalyst. J Chem Inf Model 50:822–839
Chen IJ, Foloppe N (2008) Conformational sampling of druglike molecules with MOE and catalyst: implications for pharmacophore modeling and virtual screening. J Chem Inf Model 48:1773–1791
Bruccoleri RE, Karplus M (1987) Prediction of the folding of short polypeptide segments by uniform conformational sampling. Biopolymers 26:137–168
Gippert GP, Wright PE, Case DA (1998) Distributed torsion angle grid search in high dimensions: a systematic approach to NMR structure determination. J Biomol NMR 11:241–263
Sadowski J, Bostrom J (2006) MIMUMBA revisited: torsion angle rules for conformer generation derived from X-ray structures. J Chem Inf Model 46:2305–2309
Smellie A et al (2003) Conformational analysis by intersection: CONAN. J Comput Chem 24:10–20
Chandrasekhar J, Saunders M, Jorgensen WL (2001) Efficient exploration of conformational space using the stochastic search method: application to beta-peptide oligomers. J Comput Chem 22:1646–1654
Chen JH, Im W, Brooks CL (2005) Application of torsion angle molecular dynamics for efficient sampling of protein conformations. J Comput Chem 26:1565–1578
Glen RC, Payne AWR (1995) A genetic algorithm for the automated generation of molecules within constraints. J Comput Aided Mol Des 9:181–202
Scheraga HA et al (1999) Surmounting the multiple-minima problem in protein folding. J Global Optim 15:235–260
Bohm G (1996) New approaches in molecular structure prediction. Biophys Chem 59:1–32
Floudas CA, Klepeis JL, Pardalos PM (1999) Global optimization approaches in protein folding and peptide docking. American Mathematical Society, New Jersey
Leach AR (1991) A survey of methods for searching the conformational space of small and medium-sized molecules. In: Lipkowitz KB, Boyd DB (eds) Reviews in computational chemistry. VCH, New York
Neumaier A (1997) Molecular modeling of proteins and mathematical prediction of protein structure. Siam Rev 39:407–460
Li ZQ, Laidig KE, Daggett V (1998) Conformational search using a molecular dynamics-minimization procedure: applications to clusters of coulombic charges, Lennard-Jones particles, and waters. J Comput Chem 19:60–70
Vengadesan K, Gautham N (2005) A new conformational search technique and its applications. Curr Sci India 88:1759–1770
Kostrowicki J, Scheraga HA (1992) Application of the diffusion equation method for global optimization to oligopeptides. J Phys Chem-Us 96:7442–7449
Chang G, Guida WC, Still WC (1989) An internal coordinate Monte-Carlo method for searching conformational space. J Am Chem Soc 111:4379–4386
Morales LB, Gardunojuarez R, Romero D (1991) Applications of simulated annealing to the multiple-minima problem in small peptides. J Biomol Struct Dyn 8:721–735
Wilson SR et al (1991) Applications of simulated annealing to the conformational-analysis of flexible molecules. J Comput Chem 12:342–349
Grubmuller H (1995) Predicting slow structural transitions in macromolecular systems: conformational flooding. Phys Rev E Stat Phys Plasmas Fluids Relat Interdiscip Topics 52:2893–2906
Huber T, Torda AE, van Gunsteren WF (1994) Local elevation: a method for improving the searching properties of molecular dynamics simulation. J Comput Aided Mol Des 8:695–708
Iannuzzi M, Laio A, Parrinello M (2003) Efficient exploration of reactive potential energy surfaces using Car-Parrinello molecular dynamics. Phys Rev Lett 90:238302
Yang YD, Liu HY (2006) Genetic algorithms for protein conformation sampling and optimization in a discrete backbone dihedral angle space. J Comput Chem 27:1593–1602
Nanias M et al (2005) Protein structure prediction with the UNRES force-field using replica-exchange Monte Carlo-with-minimization; comparison with MCM, CSA, and CFMC. J Comput Chem 26:1472–1486
Grebner C et al (2011) Efficiency of tabu-search-based conformational search algorithms. J Comput Chem 32:2245–2253
Chu CM, Alsberg BK (2010) A knowledge-based approach for screening chemical structures within de novo molecular evolution. J Chemom 24:9
Sakae Y et al (2011) New conformational search method using genetic algorithm and knot theory for proteins. Pac Symp Biocomput 217–228
Watts KS et al (2010) ConfGen: a conformational search method for efficient generation of bioactive conformers. J Chem Inf Model 50:534–546
Ling S, Gutowski M (2011) SSC: a tool for constructing libraries for systematic screening of conformers. J Comput Chem 32:2047–2054, Published online in Wiley Online Library (wileyonlinelibrary.com; DOI 10.1002/jcc.21774)
Goldstein M, FredJ E, Gerber RB (2011) A new hybrid algorithm for finding the lowest minima of potential surfaces: approach and application to peptides. J Comput Chem 32:1785–1800, Published online in Wiley Online Library (wileyonlinelibrary.com; DOI 10.1002/jcc.21775)
Wales DJ, Doye JPK (1997) Global optimization by basin-hopping and the lowest energy structures of Lennard-Jones clusters containing up to 110 atoms. J Phys Chem A 101:5111–5116
Grebner C, Engels B (2012) A new tabu-search-based algorithm for solvation of proteins (in preparation)
Henkelman G, Jónsson H (1999) A dimer method for finding saddle points on high dimensional potential surfaces using only first derivatives. J Chem Phys 111:7010–7022
Kästner J, Sherwood P (2008) Superlinearly converging dimer method for transition state search. J Chem Phys 128:014106
Heyden A, Bell AT, Keil FJ (2005) Efficient methods for finding transition states in chemical reactions: comparison of improved dimer method and partitioned rational function optimization method. J Chem Phys 123:224101
Honda S et al (2004) 10 residue folded peptide designed by segment statistics. Structure 12:1507–1518
Satoh D et al (2006) Folding free-energy landscape of a 10-residue mini-protein, chignolin. FEBS Lett 580:3422–3426
Suenaga A et al (2007) Folding dynamics of 10-residue beta-hairpin peptide chignolin. Chem Asian J 2:591–598
Henkelman G, Jóhannesson G, Jónsson H (2000) Methods for finding saddle points and minimum energy paths. In: Schwartz SD (ed) Progress in theoretical chemistry and physics. Kluwer Academic, New York, page 269–3000
Baker J (1986) An algorithm for the location of transition-states. J Comput Chem 7:385–395
Banerjee A et al (1985) Search for stationary-points on surface. J Phys Chem-Us 89:52–57
Cerjan CJ, Miller WH (1981) On finding transition-states. J Chem Phys 75:2800–2806
Simons J et al (1983) Walking on potential-energy surfaces. J Phys Chem-Us 87:2745–2753
Henkelman G, Jónsson H (2000) Improved tangent estimate in the nudged elastic band method for finding minimum energy paths and saddle points. J Chem Phys 113:9978–9985
Quapp W, Bofill JM (2010) A comment to the nudged elastic band method. J Comput Chem 31:2526–2531
Sheppard D, Terrell R, Henkelman G (2008) Optimization methods for finding minimum energy paths. J Chem Phys 128:134106
Peters B et al (2004) A growing string method for determining transition states: comparison to the nudged elastic band and string methods. J Chem Phys 120:7877–7886
Woodcock HL et al (2003) Exploring the quantum mechanical/molecular mechanical replica path method: a pathway optimization of the chorismate to prephenate Claisen rearrangement catalyzed by chorismate mutase. Theor Chem Acc 109:140–148
Henkelman G, Uberuaga BP, Jónsson H (2000) A climbing image nudged elastic band method for finding saddle points and minimum energy paths. J Chem Phys 113:9901–9904
Goodrow A, Bell AT, Head-Gordon M (2008) Development and application of a hybrid method involving interpolation and ab initio calculations for the determination of transition states. J Chem Phys 129:174109
Goodrow A, Bell AT, Head-Gordon M (2009) Transition state-finding strategies for use with the growing string method. J Chem Phys 130:244108
Goodrow A, Bell AT, Head-Gordon M (2010) A strategy for obtaining a more accurate transition state estimate using the growing string method. Chem Phys Lett 484:392–398
Shang C, Liu ZP (2010) Constrained Broyden minimization combined with the dimer method for locating transition state of complex reactions. J Chem Theory Comput 6:1136–1144
Schwartz SD, Schramm VL (2009) Enzymatic transition states and dynamic motion in barrier crossing. Nat Chem Biol 5:552–559
Peter C et al (2004) Estimating entropies from molecular dynamics simulations. J Chem Phys 120:2652–2661
Zhang Y, Liu H, Yang W (2000) Free energy calculation on enzyme reactions with an efficient iterative procedure to determine minimum energy paths on a combined ab initio QM/MM potential energy surface. J Chem Phys 112:3483–3492
Torrie GM, Valleau JP (1977) Nonphysical sampling distributions in Monte Carlo free-energy estimation: umbrella sampling. J Comput Phys 23:187–199
Laio A, Parrinello M (2002) Escaping free-energy minima. Proc Natl Acad Sci USA 99:12562–12566
Hu H, Lu Z, Yang W (2007) QM/MM minimum free-energy path: methodology and application to triosephosphate isomerase. J Chem Theory Comput 3:390–406
Jorgensen WL (1989) Free energy calculations: a breakthrough for modeling organic chemistry in solution. Acc Chem Res 22:184–189
Rod TH, Ryde U (2005) Accurate QM/MM free energy calculations of enzyme reactions: methylation by catechol O-methyltransferase. J Chem Theory Comput 1:1240–1251
Valiev M et al (2007) Hybrid approach for free energy calculations with high-level methods: application to the SN2 reaction of CHCl3 and OH- in water. J Chem Phys 127:051102
Zwanzig RW (1954) High-temperature equation of state by a perturbation method. I. Nonpolar gases. J Chem Phys 22:1420–1426
Hori K et al (2011) A free-energy perturbation method based on Monte Carlo simulations using quantum mechanical calculations (QM/MC/FEP method): application to highly solvent-dependent reactions. J Comput Chem 32:778–786
Kästner J et al (2006) QM/MM free-energy perturbation compared to thermodynamic integration and umbrella sampling: application to an enzymatic reaction. J Chem Theory Comput 2:452–461
Senn HM et al (2009) Finite-temperature effects in enzymatic reactions - insights from QM/MM free-energy simulations. Can J Chem 87:1322–1337
Maurer P, Iftimie R (2010) Combining ab initio quantum mechanics with a dipole-field model to describe acid dissociation reactions in water: first-principles free energy and entropy calculations. J Chem Phys 132:074112
Sheppard AN, Acevedo O (2009) Multidimensional exploration of valley-ridge inflection points on potential-energy surfaces. J Am Chem Soc 131:2530–2540
Kirkwood JG (1935) Statistical mechanics of fluid mixtures. J Chem Phys 3:300
Sharma R et al (2008) A computational study of the intramolecular deprotonation of a carbon acid in aqueous solution. Phys Chem Chem Phys 10:2475–2487
Xie H-B et al (2010) Reaction mechanism of monoethanolamine with CO2 in aqueous solution from molecular modeling. J Phys Chem A 114:11844–11852
Yonezawa Y et al (2009) Intra- and intermolecular interaction inducing pyramidalization on both sides of a proline dipeptide during isomerization: an ab initio QM/MM molecular dynamics simulation study in explicit water. J Am Chem Soc 131:4535–4540
Yonezawa Y, Standley DM, Nakamura H (2011) Degree of pyramidality governs the height and peak position of the free-energy-barrier for the cis-trans isomerization of N-Methylacetamide. Chem Phys Lett 503:139–144
Alfonso-Prieto M et al (2009) The molecular mechanism of the catalase reaction. J Am Chem Soc 131:11751–11761
Petersen L et al (2009) Mechanism of cellulose hydrolysis by inverting GH8 endoglucanases: a QM/MM metadynamics study. J Phys Chem B 113:7331–7339
Stanton CL et al (2007) QM/MM metadynamics study of the direct decarboxylation mechanism for orotidine-5-monophosphate decarboxylase using two different QM regions: acceleration too small to explain rate of enzyme catalysis. J Phys Chem B 111:12573–12581
Ayala PY, Schlegel HB (1997) A combined method for determining reaction paths, minima, and transition state geometries. J Chem Phys 107:375
Zeng XC et al (2009) Calculating solution redox free energies with ab initio quantum mechanical/molecular mechanical minimum free energy path method. J Chem Phys 130:164111
Hu H, Yang W (2010) Elucidating solvent contributions to solution reactions with ab initio QM/MM methods. J Phys Chem B 114:2755–2759
Hu H, Boone A, Yang W (2008) Mechanism of OMP decarboxylation in orotidine 5'-monophosphate decarboxylase. J Am Chem Soc 130:14493–14503
Kirkilionis M (2010) Exploration of cellular reaction systems. Brief Bioinform 11:153–178
Simonson T (2008) Dielectric relaxation in proteins: the computational perspective. Photosynth Res 97:21–32
Jensen JH et al (2005) Prediction and rationalization of protein pKa values using QM and QM/MM methods. J Phys Chem A 109:6634–6643
Buback V et al (2009) Rational design of improved aziridine-based inhibitors of cysteine proteases. J Phys Chem B 113:5282–5289
Helten H, Schirmeister T, Engels B (2004) Model calculations about the influence of protic environments on the alkylation step of epoxide, aziridine, and thiirane based cysteine protease inhibitors. J Phys Chem A 108:7691–7701
Paasche A et al (2009) Origin of the reactivity differences of substituted aziridines: CN vs CC bond breakages. J Org Chem 74:5244–5249
Vicik R et al (2006) Rational design of aziridine-containing cysteine protease inhibitors with improved potency: studies on inhibition mechanism. ChemMedChem 1:1021–1028
Reuter W, Engels B, Peyerimhoff SD (1992) Reaction of singlet and triplet methylene with ethene - a multireference configuration-interaction study. J Phys Chem-Us 96:6221–6232
Barone V, Cossi M (1998) Quantum calculation of molecular energies and energy gradients in solution by a conductor solvent model. J Phys Chem A 102:1995–2001
Klamt A, Eckert F, Arlt W (2010) COSMO-RS: an alternative to simulation for calculating thermodynamic properties of liquid mixtures. In: Prausnitz JM, Doherty MF, Segalman MA (eds) Annual review of chemical and biomolecular engineering, Vol 1 Annual Reviews, Palo Alto
Klamt A et al (1998) Refinement and parametrization of COSMO-RS. J Phys Chem A 102:5074–5085
Klamt A, Schuurmann G (1993) COSMO – a new approach to dielectric screening in solvents with explicit expressions for the screening energy and its gradient. J Chem Soc Perkin Trans 2 799–805
Ruiz-Lopez MF (2008) The multipole moment expansion solvent continuum model: a brief review. In: Canuto S (ed) Solvation effects on molecules and biomolecules: computational methods and applications. Springer
Schafer A et al (2000) COSMO implementation in TURBOMOLE: extension of an efficient quantum chemical code towards liquid systems. Phys Chem Chem Phys 2:2187–2193
Tomasi J (2004) Thirty years of continuum solvation chemistry: a review, and prospects for the near future. Theor Chem Acc 112:184–203
Tomasi J, Mennucci B, Cammi R (2005) Quantum mechanical continuum solvation models. Chem Rev 105:2999–3093
Zhan CG (2011) Development and application of first-principles electronic structure approach for molecules in solution based on fully polarizable continuum model. Acta Phys Chim Sin 27:1–10
Barone V, Biczysko M, Brancato G (2010) Extending the range of computational spectroscopy by QM/MM approaches: time-dependent and time-independent routes. In: Sabin JR, Brandas E, Canuto S (eds) Advances in quantum chemistry. Elsevier Academic, San Diego
Barone V, Improta R, Rega N (2008) Quantum mechanical computations and spectroscopy: from small rigid molecules in the gas phase to large flexible molecules in solution. Acc Chem Res 41:605–616
Barone V, Polimeno A (2007) Integrated computational strategies for UV/vis spectra of large molecules in solution. Chem Soc Rev 36:1724–1731
Pedone A, Biczysko M, Barone V (2010) Environmental effects in computational spectroscopy: accuracy and interpretation. Chemphyschem 11:1812–1832
Curutchet C et al (2009) Electronic energy transfer in condensed phase studied by a polarizable QM/MM model. J Chem Theory Comput 5:1838–1848
Difley S et al (2010) Electronic properties of disordered organic semiconductors via QM/MM simulations. Acc Chem Res 43:995–1004
Endres F (2010) Physical chemistry of ionic liquids. Phys Chem Chem Phys 12:1648
Fanfrlik J et al (2008) Interpretation of protein/ligand crystal structure using QM/MM calculations: case of HIV-1 protease/metallacarborane complex. J Phys Chem B 112:15094–15102
Helten H, Schirmeister T, Engels B (2005) Theoretical studies about the influence of different ring substituents on the nucleophilic ring opening of three-membered heterocycles and possible implications for the mechanisms of cysteine protease inhibitors. J Org Chem 70:233–237
Peters MB, Raha K, Merz KM (2006) Quantum mechanics in structure-based drug design. Curr Opin Drug Discov Devel 9:370–379
Raha K et al (2007) The role of quantum mechanics in structure-based drug design. Drug Discov Today 12:725–731
LaPointe SM, Weaver DF (2007) A review of density functional theory quantum mechanics as applied to pharmaceutically relevant systems. Curr Comput Aided Drug Des 3:290–296
Cavalli A, Carloni P, Recanatini M (2006) Target-related applications of first principles quantum chemical methods in drug design. Chem Rev 106:3497–3519
Mladenovic M et al (2007) The importance of the active site histidine for the activity of epoxide- or aziridine-based inhibitors of cysteine proteases. ChemMedChem 2:120–128
Mladenovic M et al (2008) Atomistic insights into the inhibition of cysteine proteases: first QM/MM calculations clarifying the stereoselectivity of epoxide-based inhibitors. J Phys Chem B 112:11798–11808
Mladenovic M et al (2008) Atomistic insights into the inhibition of cysteine proteases: first QM/MM calculations clarifying the regiospecificity and the inhibition potency of epoxide- and aziridine-based inhibitors. J Phys Chem B 112:5458–5469
Mladenovic M et al (2009) Environmental effects on charge densities of biologically active molecules: do molecule crystal environments indeed approximate protein surroundings? J Phys Chem B 113:5072–5082
Warren JG et al (2010) Conformational preferences of pro line analogues with a fused benzene ring. J Phys Chem B 114:11761–11770
Gleeson MP, Gleeson D (2009) QM/MM calculations in drug discovery: a useful method for studying binding phenomena? J Chem Inf Model 49:670–677
Horowitz G (1998) Organic field-effect transistors. Adv Mater 10:365–377
Forrest SR (2004) The path to ubiquitous and low-cost organic electronic appliances on plastic. Nature 428:911–918
Gratzel M (2003) Dye-sensitized solar cells. J Photochem Photobiol C 4:145–153
Gregg BA, Hanna MC (2003) Comparing organic to inorganic photovoltaic cells: theory, experiment, and simulation. J Appl Phys 93:3605–3614
Bredas JL et al (2009) Molecular understanding of organic solar cells: the challenges. Acc Chem Res 42:1691–1699
May V, Kühn O (2004) Charge and energy transfer dynamics in molecular systems. Wiley-VCH, Weinheim
Forrest SR (1997) Ultrathin organic films grown by organic molecular beam deposition and related techniques. Chem Rev 97:1793–1896
Pullerits T, Sundstrom V (1996) Photosynthetic light-harvesting pigment-protein complexes: toward understanding how and why. Acc Chem Res 29:381–389
Grimsdale AC, Mullen K (2005) The chemistry of organic nanomaterials. Angew Chem Int Ed 44:5592–5629
Poulsen L et al (2007) Three-dimensional energy transport in highly luminescent host-guest crystals: a quantitative experimental and theoretical study. J Am Chem Soc 129:8585–8593
Herbst W, Hunger K (1997) Industrial organic pigments: production, properties, applications. Wiley-VCH, Weinheim
Klebe G et al (1989) Crystallochromy as a solid-state effect - correlation of molecular-conformation, crystal packing and color in perylene-3,4-9,10-bis(dicarboximide) pigments. Acta Crystallogr B 45:69–77
Graser F, Hadicke E (1984) Crystal-structure and color of perylene-3,4-9,10-bis(dicarboximide) pigments. 2. Liebigs Ann Chem 483–494
Forster T (1948) Zwischenmolekulare Energiewanderung Und Fluoreszenz. Ann Phys-Berlin 2:55–75
Forster T (1949) Experimentelle Und Theoretische Untersuchung Des Zwischenmolekularen Übergangs Von Elektronenanregungsenergie. Z Naturforsch A 4:321–327
Forster T (1969) Excimers. Angew Chem Int Ed 8:333
Eisenschlitz R, London F (1930) Über das Verhältnis der van der Waalschen Kräfte zu den Homöopolaren Bindungskräften. Zeitschr f Physik 60:491–527
Beljonne D et al (2011) Electronic processes at organic-organic interfaces: insight from modeling and implications for opto-electronic devices. Chem Mater 23:591–609
Bredas JL et al (2004) Charge-transfer and energy-transfer processes in pi-conjugated oligomers and polymers: a molecular picture. Chem Rev 104:4971–5003
Hennebicq E et al (2005) Exciton migration in rigid-rod conjugated polymers: an improved Forster model. J Am Chem Soc 127:4744–4762
Cornil J et al (2001) Interchain interactions in organic pi-conjugated materials: impact on electronic structure, optical response, and charge transport. Adv Mater 13:1053–1067
Hwang I, Scholes GD (2011) Electronic energy transfer and quantum-coherence in pi-conjugated polymers. Chem Mater 23:610–620
Olaya-Castro A, Scholes GD (2011) Energy transfer from Forster-Dexter theory to quantum coherent light-harvesting. Int Rev Phys Chem 30:49–77
Scholes GD (2003) Long-range resonance energy transfer in molecular systems. Annu Rev Phys Chem 54:57–87
Scholz R et al (2005) Investigation of molecular dimers in alpha-PTCDA by ab initio methods: binding energies, gas-to-crystal shift, and self-trapped excitons. Phys Rev B 72:18
Hoffmann M et al (2000) The lowest energy Frenkel and charge-transfer excitons in quasi-one-dimensional structures: application to MePTCDI and PTCDA crystals. Chem Phys 258:73–96
Gisslen L, Scholz R (2009) Crystallochromy of perylene pigments: interference between Frenkel excitons and charge-transfer states. Phys Rev B 80:23
Fink RF et al (2008) Ab initio configuration interaction description of excitation energy transfer between closely packed molecules. Chem Phys 343:353–361
Fink RF et al (2008) Assessment of quantum chemical methods and basis sets for excitation energy transfer. Chem Phys 346:275–285
Fink RF et al (2008) Exciton trapping in pi-conjugated materials: a quantum-chemistry-based protocol applied to perylene bisimide dye aggregates. J Am Chem Soc 130:12858
Zhao HM et al (2009) Understanding ground- and excited-state properties of perylene tetracarboxylic acid bisimide crystals by means of quantum chemical computations. J Am Chem Soc 131:15660–15668
Burquel A et al (2006) Pathways for photoinduced charge separation and recombination at donor-acceptor heterojunctions: the case of oligophenylenevinylene-perylene bisimide complexes. J Phys Chem A 110:3447–3453
Guthmuller J, Zutterman F, Champagne B (2009) Multimode simulation of dimer absorption spectra from first principles calculations: application to the 3,4,9,10-perylenetetracarboxylic diimide dimer. J Chem Phys 131:8
Beljonne D et al (2000) Interchain interactions in conjugated materials: the exciton model versus the supermolecular approach. J Chem Phys 112:4749–4758
Liu W et al (2011) Assessment of TD-DFT- and TD-HF-based approaches for the prediction of exciton coupling parameters, potential energy curves and electronic characters of electronically excited aggregates. J Comput Chem 32:1971–1981
Marcus Y (1988) Ionic-radii in aqueous-solutions. Chem Rev 88:1475–1498
Marcus Y (2009) Effect of ions on the structure of water: structure making and breaking. Chem Rev 109:1346–1370
Ohtaki H, Radnai T (1993) Structure and dynamics of hydrated ions. Chem Rev 93:1157–1204
Feig M (2010) Modelling solvent environments: applications to simulations of biomolecules. Wiley-VCH, Weinheim
Bernal JD (1937) An attempt at a molecular theory of liquid structure. Trans Faraday Soc 33:27–40
Bennetto HP, Caldin EF (1971) Solvent effects on kinetics of reactions of nickel(II) and cobalt(II) ions with 2,2′-bipyridyl and 2,2′,2′′-terpyridyl. J Chem Soc A 2191
Bennetto HP, Caldin EF (1971) Kinetics of solvent exchange and ligand substitution reactions of metal ions in relation to structural properties of solvent. J Chem Soc A 2198
Bennetto HP, Caldin EF (1971) Kinetics of reaction of nickel(II) ions with 2,2′-bipyridyl in water-methanol mixtures. J Chem Soc A 2207
Frank HS, Wen W-Y (1957) Ion-solvent interaction. Structural aspects of ion-solvent interaction in aqueous solutions: a suggested picture of water structure. Discuss Faraday Soc 24:133–140
Tongraar A, Liedl KR, Rode BM (1997) Solvation of Ca2+ in water studied by Born-Oppenheimer ab initio QM/MM dynamics. J Phys Chem A 101:6299–6309
Tongraar A, Liedl KR, Rode BM (1998) Born-Oppenheimer ab initio QM/MM dynamics simulations of Na+ and K+ in water: from structure making to structure breaking effects. J Phys Chem A 102:10340–10347
Tongraar A, Liedl KR, Rode BM (1998) The hydration shell structure of Li+ investigated by Born-Oppenheimer ab initio QM/MM dynamics. Chem Phys Lett 286:56–64
Tongraar A et al (2010) Structure of the hydrated Ca2+ and Cl−: combined X-ray absorption measurements and QM/MM MD simulations study. Phys Chem Chem Phys 12:10876–10887
Azam SS, ul Zaheer H, Fatmi MQ (2010) Classical and QM/MM MD simulations of sodium(I) and potassium(I) ions in aqueous solution. J Mol Liq 153:95–100
Bucher D et al (2010) Coordination numbers of K+ and Na+ ions inside the selectivity filter of the KcsA potassium channel: insights from first principles molecular dynamics. Biophys J 98:L47–L49
Truong TN, Stefanovich EV (1996) Development of a perturbative approach for Monte Carlo simulations using a hybrid ab initio QM/MM method. Chem Phys Lett 256:348–352
Tongraar A, Hannongbua S (2008) Solvation structure and dynamics of ammonium (NH +4 ) in liquid ammonia studied by HF/MM and B3LYP/MM molecular dynamics simulations. J Phys Chem B 112:885–891
Intharathep P, Tongraar A, Sagarik K (2005) Structure and dynamics of hydrated NH +4 : an ab initio QM/MM molecular dynamics simulation. J Comput Chem 26:1329–1338
Intharathep P, Tongraar A, Sagarik K (2006) Ab initio QM/MM dynamics of H3O+ in water. J Comput Chem 27:1723–1732
Takenaka N, Koyano Y, Nagaoka M (2010) Microscopic hydration mechanism in the ammonia dissolution process: importance of the solute QM polarization. Chem Phys Lett 485:119–123
Mohammed AM et al (2005) Quantum mechanical/molecular mechanical molecular dynamic simulation of zinc(II) ion in water. J Mol Liq 119:55–62
Vchirawongkwin V et al (2007) Ti(I) - the strongest structure-breaking metal ion in water? A quantum mechanical/molecular mechanical simulation study. J Comput Chem 28:1006–1016
Vchirawongkwin V et al (2007) Quantum mechanical/molecular mechanical simulations of the T1(III) ion in water. J Comput Chem 28:1057–1067
Fatmi MQ et al (2005) An extended ab initio QM/MM MD approach to structure and dynamics of Zn(II) in aqueous solution. J Chem Phys 123:054514
Fatmi MQ et al (2007) Stability of different zinc(II)-diamine complexes in aqueous solution with respect to structure and dynamics: a QM/MM MD study. J Phys Chem B 111:151–158
Fatmi MQ, Hofer TS, Rode BM (2010) The stability of Zn(NH3) 2+4 in water: a quantum mechanical/molecular mechanical molecular dynamics study. Phys Chem Chem Phys 12:9713–9718
Pham VT et al (2010) The solvent shell structure of aqueous iodide: X-ray absorption spectroscopy and classical, hybrid QM/MM and full quantum molecular dynamics simulations. Chem Phys 371:24–29
Tongraar A, Hannongbua S, Rode BM (2010) QM/MM MD simulations of iodide ion (I−) in aqueous solution: a delicate balance between ion-water and water-water H-bond interactions. J Phys Chem A 114:4334–4339
Yagasaki T, Saito S, Ohmine I (2010) Effects of nonadditive interactions on ion solvation at the water/vapor interface: a molecular dynamics study. J Phys Chem A 114:12573–12584
Hinteregger E et al (2010) Structure and dynamics of the chromate ion in aqueous solution. An ab initio QMCF-MD simulation. Inorg Chem 49:7964–7968
Pribil AB et al (2008) Structure and dynamics of phosphate ion in aqueous solution: an ab initio QMCF MD study. J Comput Chem 29:2330–2334
Pribil AB et al (2008) Quantum mechanical simulation studies of molecular vibrations and dynamics of oxo-anions in water. Chem Phys 346:182–185
Tongraar A, Rode BM (2003) The hydration structures of F− and Cl− investigated by ab initio QM/MM molecular dynamics simulations. Phys Chem Chem Phys 5:357–362
Tongraar A, Tangkawanwanit P, Rode BM (2006) A combined QM/MM molecular dynamics simulations study of nitrate anion (NO −3 ) in aqueous solution. J Phys Chem A 110:12918–12926
Kubozono Y et al (1994) An EXAFS investigation of local-structure around Rb+ in aqueous-solution. Z Naturforsch A 49:727–729
Munozpaez A et al (1995) EXAFS investigation of the 2nd hydration shell of metal-cations in dilute aqueous-solutions. Physica B 208:395–397
Munozpaez A, Pappalardo RR, Marcos ES (1995) Determination of the 2nd hydration shell of Cr3+ and Zn2+ in aqueous-solutions by extended X-ray-absorption fine-structure. J Am Chem Soc 117:11710–11720
Yaita T, Ito D, Tachimori S (1998) La-139 NMR relaxation and chemical shift studies in the aqueous nitrate and chloride solutions. J Phys Chem B 102:3886–3891
Chizhik VI et al (2002) Microstructure and dynamics of electrolyte solutions containing polyatomic ions by NMR relaxation and molecular dynamics simulation. J Mol Liq 98–9:173–182
Kaatze U (1983) Dielectric effects in aqueous-solutions of 1-1, 2-1, and 3-1 valent electrolytes - kinetic depolarization, saturation, and solvent relaxation. Z Phys Chem Neue Fol 135:51–75
Bopp P, Jancsó G, Heinzinger K (1983) An improved potential for non-rigid water molecules in the liquid phase. Chem Phys Lett 98:129–133
Jancso G, Bopp P, Heinzinger K (1984) Molecular dynamics study of high-density liquid water using a modified central-force potential. Chem Phys 85:377–387
Jorgensen WL et al (1983) Comparison of simple potential functions for simulating liquid water. J Chem Phys 79:926–935
Matsuoka O, Clementi E, Yoshimine M (1976) CI study of water dimer potential surface. J Chem Phys 64:1351–1361
Rowlinson JS (1951) The lattice energy of ice and the 2nd virial coefficient of water vapour. Trans Faraday Soc 47:120–129
Stillinger FH, Rahman A (1978) Revised central force potentials for water. J Chem Phys 68:666–670
Aguilar CM, De Almeida WB, Rocha WR (2008) Solvation and electronic spectrum of Ni2+ ion in aqueous and ammonia solutions: a sequential Monte Carlo/TD-DFT study. Chem Phys 353:66–72
Beret EC et al (2009) Opposite effects of successive hydration shells on the aqua ion structure of metal cations. Mol Simul 35:1007–1014
Eilmes A, Kubisiak P (2010) Relative complexation energies for Li+ ion in solution: molecular level solvation versus polarizable continuum model study. J Phys Chem A 114:973–979
Mallik BS, Semparithi A, Chandra A (2008) A first principles theoretical study of vibrational spectral diffusion and hydrogen bond dynamics in aqueous ionic solutions: D2O in hydration shells of Cl− ions. J Chem Phys 129:194512
Men CJ, Tao FM (2007) Hydration and dissociation of calcium hydroxide in water clusters: a quantum chemical study. J Theor Comput Chem 6:595–609
Xenides D, Randolf BR, Rode BM (2006) Hydrogen bonding in liquid water: an ab initio QM/MM MD simulation study. J Mol Liq 123:61–67
Armunanto R, Schwenk CF, Rode BM (2005) Ab initio QM/MM simulation of Ag+ in 18.6% aqueous ammonia solution: structure and dynamics investigations. J Phys Chem A 109:4437–4441
Santosh MS et al (2010) Molecular dynamics investigation of dipeptide - transition metal salts in aqueous solutions. J Phys Chem B 114:16632–16640
Marchi M, Sprik M, Klein ML (1990) Solvation and ionization of alkali-metals in liquid-ammonia - a path integral Monte-Carlo study. J Phys Condens Matter 2:5833–5848
Andzelm J, Kolmel C, Klamt A (1995) Incorporation of solvent effects into density-functional calculations of molecular-energies and geometries. J Chem Phys 103:9312–9320
Cossi M et al (2002) New developments in the polarizable continuum model for quantum mechanical and classical calculations on molecules in solution. J Chem Phys 117:43–54
Eckert F, Klamt A (2002) Fast solvent screening via quantum chemistry: COSMO-RS approach. AIChE J 48:369–385
Acevedo O, Jorgensen WL (2006) Solvent effects on organic reactions from QM/MM simulations. In: David CS (ed) Annual reports in computational chemistry. Elsevier, New Haven
Vayner G et al (2004) Steric retardation of SN2 reactions in the gas phase and solution. J Am Chem Soc 126:9054–9058
Acevedo O, Jorgensen WL (2005) Influence of inter- and intramolecular hydrogen bonding on Kemp decarboxylations from QM/MM simulations. J Am Chem Soc 127:8829–8834
Acevedo O, Jorgensen WL (2006) Medium effects on the decarboxylation of a biotin model in pure and mixed solvents from QM/MM simulations. J Org Chem 71:4896–4902
Acevedo O, Jorgensen WL (2004) Solvent effects and mechanism for a nucleophilic aromatic substitution from QM/MM simulations. Org Lett 6:2881–2884
Chen X et al (2009) Steric and solvation effects in ionic SN2 reactions. J Am Chem Soc 131:16162–16170
Geerke DP et al (2007) Combined QM/MM molecular dynamics study on a condensed-phase SN2 reaction at nitrogen: the effect of explicitly including solvent polarization. J Chem Theory Comput 3:1499–1509
Singleton DA et al (2003) Mechanism of ene reactions of singlet oxygen. A two-step no-intermediate mechanism. J Am Chem Soc 125:1319–1328
Thompson JD, Cramer CJ, Truhlar DG (2003) Parameterization of charge model 3 for AM1, PM3, BLYP, and B3LYP. J Comput Chem 24:1291–1304
Acevedo O, Squillacote ME (2008) A new solvent-dependent mechanism for a triazolinedione ene reaction. J Org Chem 73:912–922
Acevedo O, Jorgensen WL (2006) Cope elimination: elucidation of solvent effects from QM/MM simulations. J Am Chem Soc 128:6141–6146
Acevedo O, Jorgensen WL (2007) Understanding rate accelerations for Diels-Alder reactions in solution using enhanced QM/MM methodology. J Chem Theory Comput 3:1412–1419
Acevedo O, Jorgensen WL, Evanseck JD (2007) Elucidation of rate variations for a Diels-Alder reaction in ionic liquids from QM/MM simulations. J Chem Theory Comput 3:132–138
Chandrasekhar J, Shariffskul S, Jorgensen WL (2002) QM/MM simulations for Diels-Alder reactions in water: contribution of enhanced hydrogen bonding at the transition state to the solvent effect. J Phys Chem B 106:8078–8085
Jorgensen WL et al (1994) Investigation of solvent effects on pericyclic-reactions by computer-simulations. J Chem Soc Faraday Trans 90:1727–1732
Thomas LL, Tirado-Rives J, Jorgensen WL (2010) Quantum mechanical/molecular mechanical modeling finds Diels-Alder reactions are accelerated less on the surface of water than in water. J Am Chem Soc 132:3097–3104
Gunaydin H et al (2007) Computation of accurate activation barriers for methyl-transfer reactions of sulfonium and ammonium salts in aqueous solution. J Chem Theory Comput 3:1028–1035
Lebrero MCG, Estrin DA (2007) QM-MM investigation of the reaction of peroxynitrite with carbon dioxide in water. J Chem Theory Comput 3:1405–1411
Alexandrova AN, Jorgensen WL (2007) Why urea eliminates ammonia rather than hydrolyzes in aqueous solution. J Phys Chem B 111:720–730
Estiu G, Merz KM (2004) Enzymatic catalysis of urea decomposition: elimination or hydrolysis? J Am Chem Soc 126:11832–11842
Jung YS, Marcus RA (2007) On the theory of organic catalysis on water. J Am Chem Soc 129:5492–5502
Jung YS, Marcus RA (2010) Protruding interfacial OH groups and 'on-water' heterogeneous catalysis. J Phys Condens Matter 22:284117
Narayan S et al (2005) "On water": unique reactivity of organic compounds in aqueous suspension. Angew Chem Int Ed 44:3275–3279
Zheng YY, Zhang JP (2010) Catalysis in the oil droplet/water interface for aromatic Claisen rearrangement. J Phys Chem A 114:4325–4333
Acevedo O, Armacost K (2010) Claisen rearrangements: insight into solvent effects and "on water" reactivity from QM/MM simulations. J Am Chem Soc 132:1966–1975
Marcus RA (2010) Spiers memorial lecture interplay of theory and computation in chemistry-examples from on-water organic catalysis, enzyme catalysis, and single-molecule fluctuations. Faraday Discuss 145:9–14
Radak BK et al (2009) Modeling reactive scattering of F(2P) at a liquid squalane interface: a hybrid QM/MM molecular dynamics study. J Phys Chem A 113:7218–7226
Sambasivarao SV, Acevedo O (2009) Development of OPLS-AA force field parameters for 68 unique ionic liquids. J Chem Theory Comput 5:1038–1050
Gao JL (1991) A priori computation of a solvent-enhanced SN2 reaction profile in water - the Menshutkin reaction. J Am Chem Soc 113:7796–7797
Arantes GM, Ribeiro MCC (2008) A microscopic view of substitution reactions solvated by ionic liquids. J Chem Phys 128:114503
Aggarwal A et al (2002) The role of hydrogen bonding in controlling the selectivity of Diels-Alder reactions in room-temperature ionic liquids. Green Chem 4:517–520
Ananikov VP, Musaev DG, Morokuma K (2010) Real size of ligands, reactants and catalysts: studies of structure, reactivity and selectivity by ONIOM and other hybrid computational approaches. J Mol Catal A-Chem 324:104–119
Qin S et al (2008) Computational investigation on stereochemistry in titanium-salicylaldehydes-catalyzed cyanation of benzaldehyde. J Org Chem 73:4840–4847
Drudis-Sole G et al (2008) DFT/MM study on copper-catalyzed cyclopropanation - enantioselectivity with no enthalpy barrier. Eur J Org Chem 5614–5621
Curet-Arana MC et al (2008) Quantum chemical determination of stable intermediates for alkene epoxidation with Mn-porphyrin catalysts. J Mol Catal A-Chem 285:120–127
Brookes NJ et al (2009) The influence of peripheral ligand bulk on nitrogen activation by three-coordinate molybdenum complexes - a theoretical study using the ONIOM method. J Comput Chem 30:2146–2156
Balcells D, Maseras F, Ujaque G (2005) Computational rationalization of the dependence of the enantioselectivity on the nature of the catalyst in the vanadium-catalyzed oxidation of sulfides by hydrogen peroxide. J Am Chem Soc 127:3624–3634
Drudis-Sole G et al (2005) A QM/MM study of the asymmetric dihydroxylation of terminal aliphatic n-alkenes with OsO4(DHQD)2PYDZ: enantioselectivity as a function of chain length. Chem-Eur J 11:1017–1029
Feldgus S, Landis CR (2000) Large-scale computational modeling of [Rh(DuPHOS)]+-catalyzed hydrogenation of prochiral enamides: reaction pathways and the origin of enantioselection. J Am Chem Soc 122:12714–12727
Feldgus S, Landis CR (2001) Origin of enantioreversal in the rhodium-catalyzed asymmetric hydrogenation of prochiral enamides and the effect of the alpha-substituent. Organometallics 20:2374–2386
French SA et al (2004) Active sites for heterogeneous catalysis by functionalisation of internal and external surfaces. Catal Today 93–95:535–540
Santra S et al (2009) Adsorption of dioxygen to copper in CuHY zeolite. Phys Chem Chem Phys 11:8855–8866
Sklenak S et al (2009) Aluminium siting in the ZSM-5 framework by combination of high resolution Al-27 NMR and DFT/MM calculations. Phys Chem Chem Phys 11:1237–1247
Zeng XC et al (2008) Ab initio quantum mechanical/molecular mechanical simulation of electron transfer process: fractional electron approach. J Chem Phys 128:124510
Shavitt I (1985) Geometry and singlet-triplet energy-gap in methylene - a critical-review of experimental and theoretical determinations. Tetrahedron 41:1531–1542
Harrison JF (1974) Structure of methylene. Acc Chem Res 7:378–384
Borden WT, Davidson ER (1979) Singlet-triplet energy separations in some hydrocarbon diradicals. Annu Rev Phys Chem 30:125–153
Leopold DG et al (1985) Methylene - a study of the x 3B1 and a 1A1 states by photoelectron-spectroscopy of CH −2 and CD2. J Chem Phys 83:4849–4865
Schaefer HF (1986) Methylene - a paradigm for computational quantum-chemistry. Science 231:1100–1107
Hayashi S, Taikhorshid E, Schulten K (2009) Photochemical reaction dynamics of the primary event of vision studied by means of a hybrid molecular simulation. Biophys J 96:403–416
Roca-Sanjuan D et al (2009) DNA nucleobase properties and photoreactivity: modeling environmental effects. Pure Appl Chem 81:743–754
Rossle SC, Frank I (2009) First-principles simulation of photoreactions in biological systems. Front Biosci 14:4862–4877
Wanko M et al (2006) Computational photochemistry of retinal proteins. J Comput Aided Mol Des 20:511–518
Ryde U (2007) Accurate metal-site structures in proteins obtained by combining experimental data and quantum chemistry. Dalton Trans 607-625
Hersleth HP et al (2006) Structures of the high-valent metal-ion haem-oxygen intermediates in peroxidases, oxygenases and catalases. J Inorg Biochem 100:460–476
Kallrot N et al (2005) Theoretical study of structure of catalytic copper site in nitrite reductase. Int J Quantum Chem 102:520–541
Nilsson K et al (2004) The protonation status of compound II in myoglobin, studied by a combination of experimental data and quantum chemical calculations: quantum refinement. Biophys J 87:3437–3447
Nilsson K, Ryde U (2004) Protonation status of metal-bound ligands can be determined by quantum refinement. J Inorg Biochem 98:1539–1546
Rulisek L, Ryde U (2006) Structure of reduced and oxidized manganese superoxide dismutase: a combined computational and experimental approach. J Phys Chem B 110:11511–11518
Ryde U, Nilsson K (2003) Quantum refinement - a combination of quantum chemistry and protein crystallography. J Mol Struct-Theochem 632:259–275
Ryde U, Nilsson K (2003) Quantum chemistry can locally improve protein crystal structures. J Am Chem Soc 125:14232–14233
Ryde U, Olsen L, Nilsson K (2002) Quantum chemical geometry optimizations in proteins using crystallographic raw data. J Comput Chem 23:1058–1070
Soderhjelm P, Ryde U (2006) Combined computational and crystallographic study of the oxidised states of NiFe hydrogenase. J Mol Struct-Theochem 770:199–219
Ryde U, Greco C, De Gioia L (2010) Quantum refinement of FeFe hydrogenase indicates a dithiomethylamine ligand. J Am Chem Soc 132:4512
Ryde U et al (2007) Identification of the peroxy adduct in multicopper oxidases by a combination of computational chemistry and extended X-ray absorption fine-structure measurements. J Am Chem Soc 129:726–727
Hsiao YW et al (2006) EXAFS structure refinement supplemented by computational chemistry. Phys Rev B 74:214101
Hsiao Y-W, Ryde U (2006) Interpretation of EXAFS spectra for sitting-atop complexes with the help of computational methods. Inorg Chim Acta 359:1081–1092
Yu N et al (2006) Assigning the protonation states of the key aspartates in beta-secretase using QM/MM X-ray structure refinement. J Chem Theory Comput 2:1057–1069
Hudecova J et al (2010) Side chain and flexibility contributions to the Raman optical activity spectra of a model cyclic hexapeptide. J Phys Chem A 114:7642–7651
Bour P et al (2008) Vibrational circular dichroism and IR spectral analysis as a test of theoretical conformational modeling for a cyclic hexapeptide. Chirality 20:1104–1119
Gauss J (1992) Calculation of NMR chemical-shifts at 2nd-order many-body perturbation-theory using gauge-including atomic orbitals. Chem Phys Lett 191:614–620
Gauss J (1993) Effects of electron correlation in the calculation of nuclear-magnetic-resonance chemical-shifts. J Chem Phys 99:3629–3643
Buehl M et al (1999) The DFT route to NMR chemical shifts. J Comput Chem 20:91–105
Malkina OL et al (1998) Spin-orbit corrections to NMR shielding constants from density functional theory. How important are the two-electron terms? Chem Phys Lett 296:93–104
Pickard CJ, Mauri F (2001) All-electron magnetic response with pseudopotentials: NMR chemical shifts. Phys Rev B 63:245101
Vaara J et al (2001) Study of relativistic effects on nuclear shieldings using density-functional theory and spin-orbit pseudopotentials. J Chem Phys 114:61–71
Arnold WD, Oldfield E (2000) The chemical nature of hydrogen bonding in proteins via NMR: J-couplings, chemical shifts, and AIM theory. J Am Chem Soc 122:12835–12841
Autschbach J, Ziegler T (2000) Nuclear spin-spin coupling constants from regular approximate relativistic density functional calculations. II. Spin-orbit coupling effects and anisotropies. J Chem Phys 113:9410–9418
Benedict H et al (2000) Nuclear scalar spin-spin couplings and geometries of hydrogen bonds. J Am Chem Soc 122:1979–1988
Helgaker T, Jaszunski M, Ruud K (1999) Ab initio methods for the calculation of NMR shielding and indirect spin-spin coupling constants. Chem Rev 99:293–352
Helgaker T, Watson M, Handy NC (2000) Analytical calculation of nuclear magnetic resonance indirect spin-spin coupling constants at the generalized gradient approximation and hybrid levels of density-functional theory. J Chem Phys 113:9402–9409
Beer M, Kussmann J, Ochsenfeld C (2011) Nuclei-selected NMR shielding calculations: a sublinear-scaling quantum-chemical method. J Chem Phys 134:15
Kussmann J, Ochsenfeld C (2007) Linear-scaling method for calculating nuclear magnetic resonance chemical shifts using gauge-including atomic orbitals within Hartree-Fock and density-functional theory. J Chem Phys 127:16
Ochsenfeld C, Kussmann J, Koziol F (2004) Ab initio NMR spectra for molecular systems with a thousand and more atoms: a linear scaling method. Angew Chem Int Ed 43:4485–4489
Ciofini I (2004) Use of continuum models in magnetic resonance parameter calculation. In: Kaupp M, Buehl M, Malkin VG (eds) Calculation of NMR and EPR parameters. Wiley VCH Verlag GmbH & Co. KGaA, Weinheim
Pickard CJ, Mauri F (2004) Calculations of magnetic resonance parameters in solids and liquids using periodic boundary conditions. In: Kaupp M, Buehl M, Malkin VG (eds) Calculation of NMR and EPR parameters. Wiley VCH Verlag GmbH & Co. KGaA, Weinheim
Johnson ER, DiLabio GA (2009) Convergence of calculated nuclear magnetic resonance chemical shifts in a protein with respect to quantum mechanical model size. J Mol Struct-Theochem 898:56–61
Pedone A et al (2008) Accurate first-principle prediction of 29Si and 17O NMR parameters in SiO2 polymorphs: the cases of zeolites sigma-2 and ferrierite. J Chem Theory Comput 4:2130–2140
Heine T et al (2001) Performance of DFT for 29Si NMR chemical shifts of silanes. J Phys Chem A 105:620–626
van Wüllen C (2004) Chemical shifts with Hartree-Fock and density functional methods. In: Kaupp M, Buehl M, Malkin VG (eds) Calculation of NMR and EPR parameters. Wiley VCH Verlag GmbH & Co. KGaA, Weinheim
Gauss J, Stanton JF (2004) Electron-correlated methods for the calculation of NMR chemical shifts. In: Kaupp M, Buehl M, Malkin VG (eds) Calculation of NMR and EPR parameters. Wiley VCH Verlag GmbH & Co. KGaA, Weinheim
Helgaker T, Pecul M (2004) Spin-spin coupling constants with HF and DFT methods. In: Kaupp M, Buehl M, Malkin VG (eds) Calculations of NMR and EPR parameters. Wiley VCH, Weinheim
Bjornsson R, Fruchtl H, Buehl M (2011) 51V NMR parameters of VOCl3: static and dynamic density functional study from the gas phase to the bulk. Phys Chem Chem Phys 13:619–627
Geethalakshmi KR et al (2009) 51V NMR chemical shifts calculated from QM/MM models of peroxo forms of vanadium haloperoxidases. J Phys Chem B 113:4456–4465
Gester RM et al (2009) NMR chemical shielding and spin-spin coupling constants of liquid NH3: a systematic investigation using the sequential QM/MM method. J Phys Chem A 113:14936–14942
Harriman JE (1978) Theoretical foundations of electronic spin resonance. Academic, New York
Kaupp M, Buehl M, Malkin VG (2004) Calculation of NMR and EPR parameters. Wiley VCH Verlag GmbH & Co. KGaA, Weinheim
Weltner W (1983) Magnetic atoms and molecules. Van Nostrand Reinhold Company Inc., New York
Goldfarb D (2009) Modern EPR spectroscopy: beyond the EPR spectrum. Phys Chem Chem Phys 11:6553–6554
McWeeny R (1970) Spins in chemistry. Academic, New York
Lushington GH (2000) Small closed-form CI expansions for electronic g-tensor calculations. J Phys Chem A 104:2969–2974
Lushington GH, Bundgen P, Grein F (1995) Ab-initio study of molecular g-tensors. Int J Quantum Chem 55:377–392
Lushington GH, Grein F (1997) Multireference configuration interaction calculations of electronic g-tensors for NO2, H2O+, and CO+. J Chem Phys 106:3292–3300
Schreckenbach G, Ziegler T (1997) Calculation of the G-tensor of electron paramagnetic resonance spectroscopy using gauge-including atomic orbitals and density functional theory. J Phys Chem A 101:3388–3399
Malkina OL et al (2000) Density functional calculations of electronic g-tensors using spin-orbit pseudopotentials and mean-field all-electron spin-orbit operators. J Am Chem Soc 122:9206–9218
Kaupp M et al (2002) Calculation of electronic g-tensors for transition metal complexes using hybrid density functionals and atomic meanfield spin-orbit operators. J Comput Chem 23:794–803
Bolvin H (2006) An alternative approach to the g-matrix: theory and applications. Chemphyschem 7:1575–1589
Brownridge S et al (2003) Efficient calculation of electron paramagnetic resonance g-tensors by multireference configuration interaction sum-over-state expansions, using the atomic mean-field spin-orbit method. J Chem Phys 118:9552–9562
Delabie A et al (2002) The siting of Cu(II) in mordenite: a theoretical spectroscopic study. Phys Chem Chem Phys 4:134–145
Gilka N, Tatchen J, Marian CM (2008) The g-tensor of AlO: principal problems and first approaches. Chem Phys 343:258–269
Neese F (2007) Analytic derivative calculation of electronic g-tensors based on multireference configuration interaction wavefunctions. Mol Phys 105:2507–2514
Neyman KM et al (2002) Calculation of electronic g-tensors using a relativistic density functional Douglas-Kroll method. J Phys Chem A 106:5022–5030
Vahtras O, Engstrom M, Schimmelpfennig B (2002) Electronic g-tensors obtained with the mean-field spin-orbit Hamiltonian. Chem Phys Lett 351:424–430
Vancoillie S, Malmqvist P-Å, Pierloot K (2007) Calculation of EPR g tensors for transition-metal complexes based on multiconfigurational perturbation theory (CASPT2). Chemphyschem 8:1803–1815
van Lenthe E, Wormer PES, van der Avoird A (1997) Density functional calculations of molecular g-tensors in the zero-order regular approximation for relativistic effects. J Chem Phys 107:2488–2498
Gauss J, Kallay M, Neese F (2009) Calculation of electronic g-tensors using coupled cluster theory. J Phys Chem A 113:11541–11549
Arbuznikov AV et al (2002) Validation study of meta-GGA functionals and of a model exchange-correlation potential in density functional calculations of EPR parameters. Phys Chem Chem Phys 4:5467–5474
Arbuznikov AV, Kaupp M (2004) Unrestricted open-shell Kohn-Sham scheme with local hybrid exchange-correlation potentials: improved calculation of electronic g-tensors for transition-metal complexes. Chem Phys Lett 391:16–21
Arbuznikov AV, Kaupp M (2005) Localized hybrid exchange-correlation potentials for Kohn-Sham DFT calculations of NMR and EPR parameters. Int J Quantum Chem 104:261–271
Engels B, Peyerimhoff SD, Davidson ER (1987) Calculation of hyperfine coupling-constants - an ab initio MRD CI study for nitrogen to analyze the effects of basis-sets and CI parameters. Mol Phys 62:109–127
Knight LB et al (1987) Electron-spin-resonance and ab initio theoretical-studies of the cation radicals 14N4+ and 15N4+ - the trapping of ion neutral reaction-products in neon matrices at 4-K. J Chem Phys 87:885–897
Feller D, Davidson ER (1984) Ab initio configuration-interaction calculations of the hyperfine-structure in small radicals. J Chem Phys 80:1006–1017
Chipman DM (1983) Theoretical-study of the properties of methyl radical. J Chem Phys 78:3112–3132
Suter HU, Huang MB, Engels B (1994) A multireference configuration-interaction study of the hyperfine-structure of the molecules CCO, CNN, and NCN in their triplet ground-states. J Chem Phys 101:7686–7691
Engels B et al (1992) Study of the hyperfine coupling-constants (14N And 1H) of the NH2 molecules in the X2B1 ground-state and the A2A1 excited-state. J Chem Phys 96:4526–4535
Engels B, Peyerimhoff SD (1988) Study of the 1s and 2s shell contributions to the isotropic hyperfine coupling-constant in nitrogen. J Phys B-At Mol Opt Phys 21:3459–3471
Engels B et al (1988) The hyperfine coupling-constants of the 5 lowest states of CH - an ab initio MRDCI study. Chem Phys Lett 152:397–401
Barone V et al (2009) Magnetic interactions in phenyl-bridged nitroxide diradicals: conformational effects by multireference and broken symmetry DFT approaches. J Phys Chem A 113:15150–15155
Svistunenko DA, Jones GA (2009) Tyrosyl radicals in proteins: a comparison of empirical and density functional calculated EPR parameters. Phys Chem Chem Phys 11:6600–6613
Munzarova M, Kaupp M (1999) A critical validation of density functional and coupled-cluster approaches for the calculation of EPR hyperfine coupling constants in transition metal complexes. J Phys Chem A 103:9966–9983
Munzarova ML, Kubacek P, Kaupp M (2000) Mechanisms of EPR hyperfine coupling in transition metal complexes. J Am Chem Soc 122:11900–11913
Arbuznikov AV, Vaara J, Kaupp M (2004) Relativistic spin-orbit effects on hyperfine coupling tensors by density-functional theory. J Chem Phys 120:2127–2139
Suter HU et al (1994) Difficulties in the calculation of electron-spin-resonance parameters using density-functional methods. Chem Phys Lett 230:398–404
Fangstrom T et al (1997) Structure and dynamics of the silacyclobutane radical cation, studied by ab initio and density functional theory and electron spin resonance spectroscopy. J Chem Phys 107:297–306
Huang MB et al (1995) Multireference configuration-interaction and density-functional study of the azetidine radical-cation and the neutral azetidin-1-Yl radical. J Phys Chem-Us 99:9724–9729
Suter HU, Engels B (1996) An ab initio determination of the magnetic hyperfine structure of C2 in the four lowest triplet states. Chem Phys Lett 261:644–650
Cimino P et al (2010) Interplay of stereo-electronic, environmental, and dynamical effects in determining the EPR parameters of aromatic spin-probes: INDCO as a test case. Phys Chem Chem Phys 12:3741–3746
Engels B, Suter HU, Peric M (1996) Ab initio investigation of vibrational effects on magnetic hyperfine coupling constants in the X3Σ −g state of B2H2. J Phys Chem-Us 100:10121–10122
Peric M, Engels B (1992) Ab initio calculation of the vibronically averaged values for the hyperfine coupling-constants in NH2, NHD, and ND2. J Chem Phys 97:4996–5006
Staikova M et al (1993) Ab-initio calculations of the vibronically averaged hyperfine coupling-constants in the 12Πu (X2B1, A2A1) state of the water cation. Mol Phys 80:1485–1497
Pavone M et al (2007) Interplay of intrinsic, environmental, and dynamic effects in tuning the EPR parameters of nitroxides: further insights from an integrated computational approach. J Phys Chem B 111:8928–8939
Funken K et al (1990) Study of the hyperfine coupling-constants of the molecules NH2, NHD and ND2. Chem Phys Lett 172:180–186
Peric M, Engels B, Peyerimhoff SD (1991) Ab initio investigation of the vibronic structure of the C2H spectrum - calculation of the hyperfine coupling-constants for the 3 lowest-lying electronic states. J Mol Spectrosc 150:56–69
Peric M, Engels B, Peyerimhoff SD (1991) Ab initio investigation of the vibronic structure of the C2H SPECTRUM - computation of the vibronically averaged values for the hyperfine coupling-constants. J Mol Spectrosc 150:70–85
Brancato G et al (2005) A mean field approach for molecular simulations of fluid systems. J Chem Phys 122:154109
Brancato G, Rega N, Barone V (2006) Reliable molecular simulations of solute-solvent systems with a minimum number of solvent shells. J Chem Phys 124:214505
Brancato G, Rega N, Barone V (2007) Unraveling the role of stereo-electronic, dynamical, and environmental effects in tuning the structure and magnetic properties of glycine radical in aqueous solution at different pH values. J Am Chem Soc 129:15380–15390
Brancato G, Rega N, Barone V (2008) A hybrid explicit/implicit solvation method for first-principle molecular dynamics simulations. J Chem Phys 128:144501
Rega N, Brancato G, Barone V (2006) Non-periodic boundary conditions for ab initio molecular dynamics in condensed phase using localized basis functions. Chem Phys Lett 422:367–371
Cossi M et al (1996) Ab initio study of solvated molecules: a new implementation of the polarizable continuum model. Chem Phys Lett 255:327–335
Naumov S, Reinhold J, Beckert D (2003) Investigation of the molecular structure of the radical anions of some pyrimidine-type bases in aqueous solution by comparison of calculated hyperfine coupling constants with EPR results. Phys Chem Chem Phys 5:64–72
Cances E, Mennucci B (2001) Comment on “reaction field treatment of charge penetration”. J Chem Phys 114:4744–4745
Cossi M et al (2001) Polarizable dielectric model of solvation with inclusion of charge penetration effects. J Chem Phys 114:5691–5701
Cossi M et al (2003) Energies, structures, and electronic properties of molecules in solution with the C-PCM solvation model. J Comput Chem 24:669–681
Lu JM et al (2001) A Fourier transform EPR study of uracil and thymine radical anions in aqueous solution. Phys Chem Chem Phys 3:952–956
Houriez C et al (2009) Further insights into the environmental effects on the computed hyperfine coupling constants of nitroxides in aqueous solution. J Phys Chem B 113:15047–15056
Houriez C et al (2010) Structure and spectromagnetic properties of the superoxide radical adduct of DMPO in water: elucidation by theoretical investigations. J Phys Chem B 114:11793–11803
Adamo C et al (1999) Tuning of structural and magnetic properties of nitronyl nitroxides by the environment. A combined experimental and computational study. J Phys Chem A 103:3481–3488
Barone V et al (1998) Assessment of a combined QM/MM approach for the study of large nitroxide systems in vacuo and in condensed phases. J Am Chem Soc 120:7069–7078
Barone V, Cimino P (2009) Validation of the B3LYP/N07D and PBE0/N07D computational models for the calculation of electronic g-tensors. J Chem Theory Comput 5:192–199
Barone V et al (1993) Ab-initio configuration-interaction calculation of isotropic spin-densities in nitronyl and iminonitroxides. New J Chem 17:545–549
Beyer M et al (2003) Synthesis of novel aromatic nitroxides as potential DNA intercalators. An EPR spectroscopical and DFT computational study. J Org Chem 68:2209–2215
Cirujeda J et al (2000) Spin density distribution of a-nitronyl aminoxyl radicals from experimental and ab initio calculated ESR isotropic hyperfine coupling constants. J Am Chem Soc 122:11393–11405
di Matteo A et al (1999) Intrinsic and environmental effects in the physico-chemical properties of nitroxides. The case of 2-phenyl-4,4,5,5-tetramethyl-4,5-dihydro-1H-imidazol-1-oxyl 3-oxide. Chem Phys Lett 310:159–165
Mattar SM, Stephens AD (2000) UB1LYP hybrid density functional studies of the 2,2,6,6-tetramethyl-4-piperidone-oxyl (TEMPONE) hyperfine tensors. Chem Phys Lett 319:601–610
Stipa P (2006) A multi-step procedure for evaluating the EPR parameters of indolinonic aromatic aminoxyls: a combined DFT and spectroscopic study. Chem Phys 323:501–510
Zheludev A et al (1994) Spin-density in a nitronyl nitroxide free-radical - polarized neutron-diffraction investigation and ab-initio calculations. J Am Chem Soc 116:2019–2027
Colombo MC et al (2008) Copper binding sites in the C-terminal domain of mouse prion protein: a hybrid (QM/MM) molecular dynamics study. Proteins 70:1084–1098
Sinnecker S, Neese F (2006) QM/MM calculations with DFT for taking into account protein effects on the EPR and optical spectra of metalloproteins. Plastocyanin as a case study. J Comput Chem 27:1463–1475
Bernini C et al (2011) EPR parameters of amino acid radicals in P. eryngii versatile peroxidase and its W164Y variant computed at the QM/MM level. Phys Chem Chem Phys 13:5078–5098
Neese F (2003) A spectroscopy oriented configuration interaction procedure. J Chem Phys 119:9428–9443
Mattar SM, Durelle J (2010) Calculation of the 4,5-dihydro-1,3,2-dithiazolyl radical g-tensor components by the coupled-perturbed Kohn-Sham hybrid density functional and configuration interaction methods: a comparative study. Magn Reson Chem 48:S122–S131
Engels B (1991) Estimation of the influence of the configurations neglected within truncated multireference CI wave-functions on molecular-properties. Chem Phys Lett 179:398–404
Mattar SM (1999) Calculation of the 1H 13C, 14N and 33S hyperfine tensors of the 1,3,2-dithiazol-2-yl radical using hybrid density functionals. Chem Phys Lett 300:545–552
Arrondo JLR et al (1993) Quantitative studies of the structure of proteins in solution by Fourier-transform infrared-spectroscopy. Prog Biophys Mol Biol 59:23–56
Elliot A, Ambrose EJ (1950) Structure of synthetic polypeptides. Nature 165:921–922
Bour P, Keiderling TA (1993) Ab-initio simulations of the vibrational circular-dichroism of coupled peptides. J Am Chem Soc 115:9602–9607
Berova N, Nakanishi K, Woody RW (2000) Circular dichroism principles and applications. Wiley VCH, New York
Barron LD, Hecht L, Bell AD (1996) Vibrational Raman optical activity of biomolecules. In: Fasman GD (ed) Circular dichroism and the conformational analysis of biomolecules. Plenum, New York
Keiderling TA, Kubelka J, Hilario J (2006) Vibrational circular dichroism of biopolymers. Summary of methods and applications. In: Braiman MS, Gregoriou VG (eds) Vibrational spectroscopy of biological and polymeric materials. CRC, New York
Barron LD, Buckingham AD (1971) Rayleigh and Raman scattering from optically active molecules. Mol Phys 20:1111–1119
Barron LD, Buckingham AD (1975) Rayleigh and Raman optical-activity. Annu Rev Phys Chem 26:381–396
Barron LD, Buckingh AD (1973) Raman circular intensity differential observations on some monoterpenes. J Chem Soc Chem Commun 152–153
Nafie LA, Keiderling TA, Stephens PJ (1976) Vibrational circular-dichroism. J Am Chem Soc 98:2715–2723
Polavarapu PL (1990) Ab initio vibrational Raman and Raman optical-activity spectra. J Phys Chem-Us 94:8106–8112
Jalkanen KJ et al (2003) Vibrational analysis of various isotopomers of L-alanyl-L-alanine in aqueous solution: vibrational absorption, vibrational circular dichroism, Raman, and Raman optical activity spectra. Int J Quantum Chem 92:239–259
Stephens PJ et al (1994) Ab-initio calculation of vibrational absorption and circular-dichroism spectra using density-functional force-fields. J Phys Chem-Us 98:11623–11627
Jeon J, Cho M (2010) Direct quantum mechanical/molecular mechanical simulations of two-dimensional vibrational responses: N-methylacetamide in water. New J Phys 12:065001
Poully JC, Gregoire G, Schermann JP (2009) Evaluation of the ONIOM method for interpretation of infrared spectra of gas-phase molecules of biological interest. J Phys Chem A 113:8020–8026
Misra N et al (2010) Vibrational analysis of boldine hydrochloride using QM/MM approach. Spectrosc-Int J 24:483–499
Amadei A et al (2010) Theoretical-computational modelling of infrared spectra in peptides and proteins: a new frontier for combined theoretical-experimental investigations. Curr Opin Struct Biol 20:155–161
Daidone I et al (2010) On the origin of IR spectral changes upon protein folding. Chem Phys Lett 488:213–218
Horspool W, Armesto D (1992) Organic photochemistry: a comprehensive treatment. Ellis Horwood Limited, West Sussex
Dutoi AD et al (2010) Tracing molecular electronic excitation dynamics in real time and space. J Chem Phys 132:144302
Moret ME et al (2010) Electron localization dynamics in the triplet excited state of [Ru(bpy)3]2+ in aqueous solution. Chem-Eur J 16:5889–5894
Abel S et al (2011) Molecular simulations of dodecyl-beta-maltoside micelles in water: influence of the headgroup conformation and force field parameters. J Phys Chem B 115:487–499
Kistler KA, Matsika S (2009) Solvatochromic shifts of uracil and cytosine using a combined multireference configuration interaction/molecular dynamics approach and the fragment molecular orbital method. J Phys Chem A 113:12396–12403
Kistler KA, Matsika S (2010) Photophysical pathways of cytosine in aqueous solution. Phys Chem Chem Phys 12:5024–5031
Olsen JM et al (2010) Solvatochromic shifts in uracil: a combined MD-QM/MM study. J Chem Theory Comput 6:249–256
Oncak M, Lischka H, Slavicek P (2010) Photostability and solvation: photodynamics of microsolvated zwitterionic glycine. Phys Chem Chem Phys 12:4906–4914
Loos PF et al (2008) Theoretical investigation of the geometries and UV-vis spectra of poly(L-glutamic acid) featuring a photochromic azobenzene side chain. J Chem Theory Comput 4:637–645
Grimme S, Waletzke M (1999) A combination of Kohn-Sham density functional theory and multi-reference configuration interaction methods. J Chem Phys 111:5645–5655
Eckert-Maksic M et al (2010) Matrix-controlled photofragmentation of formamide: dynamics simulation in argon by nonadiabatic QM/MM method. Phys Chem Chem Phys 12: 12719–12726
Ruckenbauer M et al (2010) Azomethane: nonadiabatic photodynamical simulations in solution. J Phys Chem A 114:12585–12590
Koch DM et al (2006) Nonadiabatic trajectory studies of NaI(H2O)n photodissociation dynamics. J Phys Chem A 110:1438–1454
Malaspina T, Coutinho K, Canuto S (2008) Analyzing the n ->pi* electronic transition of formaldehyde in water. A sequential Monte Carlo/time-dependent density functional theory. J Braz Chem Soc 19:305–311
Nielsen CB et al (2007) Density functional self-consistent quantum mechanics/molecular mechanics theory for linear and nonlinear molecular properties: applications to solvated water and formaldehyde. J Chem Phys 126:154112
Lin YL, Gao J (2007) Solvatochromic shifts of the n → π* transition of acetone from steam vapor to ambient aqueous solution: a combined configuration interaction QM/MM simulation study incorporating solvent polarization. J Chem Theory Comput 3:1484–1493
Wallqvist A, Ahlstrom P, Karlstrom G (1990) A new intermolecular energy calculation scheme - applications to potential surface and liquid properties of water. J Phys Chem-Us 94:1649–1656
Hermida-Ramon JM, Ohrn A, Karlstrom G (2009) Aqueous solvent effects on structure and lowest electronic transition of methylene peroxide in an explicit solvent model. Chem Phys 359:118–125
Acknowledgement
Financial support by the DFG (Deutsche Forschungsgemeinschaft) in the framework of the SFB 630 and the GRK1221 and by the Volkswagen Stiftung is gratefully acknowledged.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2012 Springer-Verlag Berlin Heidelberg
About this chapter
Cite this chapter
Schmidt, T.C. et al. (2012). QM/MM Investigations Of Organic Chemistry Oriented Questions. In: Kirchner, B. (eds) Electronic Effects in Organic Chemistry. Topics in Current Chemistry, vol 351. Springer, Berlin, Heidelberg. https://doi.org/10.1007/128_2011_309
Download citation
DOI: https://doi.org/10.1007/128_2011_309
Published:
Publisher Name: Springer, Berlin, Heidelberg
Print ISBN: 978-3-662-43581-6
Online ISBN: 978-3-662-43582-3
eBook Packages: Chemistry and Materials ScienceChemistry and Material Science (R0)