Abstract
Hybrid methods, combining the accuracy of Quantum Mechanics and the potency of Molecular Mechanics, the so-called QM/MM methods, arise from the desire of theoretician chemists to study electronic phenomena in large molecular systems. In this contribution, a focus, on the Physics and Chemistry on which theses methods are based on, is given. The advantages, flaws, and limitations of each type of methods are exposed. A special emphasis is put on the Local Self-Consistent Field method, developed in our group. The latest developments are detailed and illustrated by chosen examples.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Koerner T, Brown RS, Gainsforth JL, Klobulowski M (1998) Electrophilic bromination of ethylene and ethylene-d4: a combined experimental and theoretical study. J Am Chem Soc 120:5628–5636
Benkovic SJ, Hammes-Schiffer S (2003) A perspective on enzyme catalysis. Nature 5637:1196–1202
Polli D, Altoé P, Weingart O, Spillane KM, Manzoni C, Brida D, Tomasello G, Orlandi G, Kukura P, Mathies RA, Garavelli M, Cerullo G (2010) Rhodopsin isomerization probed in the visible spectral range. Nature 467:440–443
Gozem S, Schapiro I, Ferré N, Olivucci M (2012) The molecular mechanism of thermal noise in rod photoreceptors. Science 337:1225–1228
Dolmans DE, Fukumura D, Jain RK (2003) Photodynamic therapy for cancer Nature Rev. Cancer 3:380–387
Metcalfe C, Thomas JA (2003) Kinetically inert transition metal complexes that reversibly bind to DNA. Chem. Soc Rev 32(2):15–224
Zeglis BM, Pierre VC, Barton JK (2007) Metallointercalators and metalloinsertors. Chem Commun 44:4565–4579
Ortmans I, Elias B, Kelly JM, Moucheron C, Kirsch-De Mesmaeker A (2004) [RU(TAP)2(dppz)]2+: a DNA intercalating complex, which luminesces strongly in water and under goes photo-induced proton-coupled electron transfer with guanosine-5¢-monophosphate. Dalton Trans 668–676
Monari A, Rivail J-L, Assfeld X (2013) Theoretical modelling of large molecular systems. Advances in the local self consistent field method for mixed quantum mechanics/molecular mechanics calculations. Acc Chem Res 46:596–603
Monard G, Merz KM Jr (1999) Combined quantum mechanical/molecular mechanical methodologies applied to biomolecular systems. Acc Chem Rev 32:904–911
Lin H, Truhlar DG (2007) QM/MM: what we have learned, where are we, and where do we go from here? Theor Chem Acc 117:185–199
Senn HM, Thiel W (2009) QM/MM methods for biomolecular systems. Ang Chem Int 48:1198–1229
Gordon MS, Fedorov DG, Pruitt SR, Slipchenko IV (2012) Fragmentation methods: a route to accurate calculations on large molecules Chem Rev 112:632–613
Dixon SL, Merz KM Jr (1996) Semiempirical molecular-orbital calculations with linear system size scaling. J Chem Phys 104:6643–6649
Daniels AD, Millam JM, Scuseria GE (1997) Semiempirical methods with conjugate gradient density matrix search to replace diagonalization for molecular systems contianing thousands of atoms. J Chem Phys 107:425–431
Yang W, Lee TS (1995) A density matrix divide-and-conquer approach for electronic structure calculations of large molecules. J Chem Phys 103:5674–5678
Monard G, Bernal-Uruchurtu MI, van der Vaart A, Merz KM Jr, Ruiz-Lopèz MF (2005) Simulation of liquid water using semiempirical hamiltonina and the divide and conquer approach. J Phys Chem A 109:3425–3432
Tarek M, Delemotte L (2013) Omega currents in voltage-gated ion channels: what can we learn from uncovering the voltage-sensing mechanism using MD simulations? Acc Chem Res. doi:10.1021/ar300290u
Warshel A, Levitt M (1976) Theoretical studies of enzymatic reactions: dielectric, electrostatic and steric stabilization of the carbonium ion in the reaction of lysozime. J Mol Biol 103:227–249
Assfeld X, Rivail J-L (1996) Quantum chemical computations on parts of large molecules: the ab initio local self consistent field method. Chem Phys Lett 263:100–106
Jensen, F (2007) Introduction to quantum chemistry, 2nd edn. Wiley, New York
Piela L (2007) Ideas of quantum chemistry. Elsevier, Amsterdam
Cramer CJ (2004) Essentials of computational chemistry, 2nd edn. Wiley, New York
van Gunsteren WF, Berendsen HJC (1987) Groningen Molecular Simulation (GROMOS) library manual. Biomos, Groningen
Allinger NL, Yuh YH, Lii JH (1989) Molecular mechanics. The MM3 force field for hydrocarbons. J Am Chem Soc 111:8551–8566
Pearlman DA, Case DA, Caldwell JW, Ross WS, Cheatham TE. III, DeBolt S, Ferguson D, Seibel G, Kollman P (1995) AMBER, a package of computer programs for applying molecular mechanics, normal mode analysis, molecular dynamics and free energy calculations to simulate structural and energetic properties of molecules. Comput Phys Commun 91:1–41
MacKerell AD Jr, Bashford D, Bellott M, Dunbrack RL Jr, Evanseck JD, Field MJ, Fischer S, Gao J, Guo H, Ha S, Joseph-McCarthy D, Kuchnir L, Kuczera K, Lau F. TK, Mattos C, Michnick S, Ngo T, Nguyen DT, Prodhom B, Reiher WE III, Roux B, Schlenkrich M, Smith JC, Stote R, Straub J, Watanabe W, Wiórkiewicz-Kuczera J, Yin D, Karplus M (1998) All-atom empirical potential for molecular modeling and dynamics studies of proteins. J Phys Chem B 102:3586–3616
Dang LX, Chang T-M (1997) Molecular dynamics study of water clusters, liquid and liquid–vapor interface of water with many-body potentials. J Chem Phys 106:8149–8159
Dupuis M, Aida M, Kawashima Y, Hirao K (2002) A polarizable mixed hamiltonian model of electronic structure for micro-solvated excited states. I energy and gradients formulation and application to formaldehyde (1A2) J Chem Phys 117:1242–1255
Gresh N, Andrés Cisneros G, Darden TA, Piquemal J-P (2007) Anisotropic, polarizable molecular mechanics studies of inter- and intramolecular interactions and ligand–macromolecule-complexes. A bottom-up strategy. J Chem Theory Comput 3:1960–1986
Field MJ, Bash PA, Kearplus M (1990) A combined quantum mechanical and molecular mechanical potential for molecular dynamic simulations J Comput Chem 11:700–733
Kaminski GA, Jorgensen WL (1998) A quantum mechanical and molecular mechanical method based on cm1a charges: applications to solvent effects on organic equilibria and reactions. J Phys Chem B 102:1787–1796
Ferré N, Olivucci M (2003) The amide bond: pitfalls and drawback of the link atom scheme. J Mol Struct (Theochem) 632:71–84
Antes I, Thiel W (1999) Adjusted connection atoms for combined quantum mechanical and molecular mechanical methods. J Phys Chem A 103:9290–9295
Ranganathan S, Gready JE (1997) Hybrid quantum and molecular mechanical (QM/MM) studies on the pyruvate to l-lactate interconversion in l-lactate dehydrogenase. J Phys Chem B 101:5614–5618
Swart M (2003) AddRemove: a new link model for use in QM/MM studies. Int J Quantum Chem 91:177–183
Das D, Eurenius KP, Billings EM, Sherwood P, Chatfield DC, Hodoscek M, Brook BR (2002) Optimization of quantum mechanical molecular mechanical partitioning schemes: Gaussian delocalization of molecular mechanical charges and the double link atom method. J Chem Phys 117:10534–10547
Di Labio 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
Zhang Y, Lee T-S, Yang W (1999) A pseudobond approach to combining quantum mechanical and molecular mechanical methods. J Chem Phys 110:46–54
Xiao C, Zhang Y (2007) Design-atom approach for quantum mechanical/molecular mechanical covalent boundary: a design-carbon atom with five valence electrons. J Chem Phys 127:124102
Ferenczy GG, Rivail J-L, Surjan PR, Naray-Szabo G (1992) NDDO fragment self-consistent-field approximation for large electronic systems. J Comput Chem 13:830–837
Théry V, Rinaldi D, Rivail J-L, Maigret B, Ferenczy GG (1994) Quantum mechanical computations on very large molecular systems: the local self-consistent field method. J Comput Chem 15:269–282
Stewart JJP (1989) Optimization of parameters for semiempirical methods I. Method J Comput Chem 10:209–220
Gao G, Amara P, Alhambra C, Field MJ (1998) A generalized hybrid orbital (GHO) method for the treatment of boundary atoms in combined QM/MM calculations. J Phys Chem A 102:4714–4721
Pu J, Gao J, 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
Pu J, Gao J, Truhlar DG (2004) Combining self-consistent-charge density-functional tight-binding (SCC-DFTB) with molecular mechanics by the generalized hybrid orbital (GHO) method. J Phys Chem A 108:5454–5463
Pu J, Truhlar DG (2005) Redristributed charge and dipole schemes for combined quantum mechanical and molecular mechanical calculations J Phys Chem A 109:3991–4004
Maseras F, Morokuma K (1995) IMOMM, a new integrated ab initio + molecular mechanics geometry optimization scheme of equilibrium structure and transition states. J Comput Chem 16:1170–1179
Celebi N, Ángyán JG, Dehez F, Millot C, Chipot C (2000) Distributed polarizabilities derived from induction energies: a finite perturbation approach. J Chem Phys 112:2709–2717
Dehez F, Soetens JC, Chipot C, Ángyán JG, Millot C (2000) Determination of distributed polarizabilities from a statistical analysis of induction energies. J Phys Chem A 104:1293–1303
Martin M, Aguilar M, Chalmet S, Ruiz-Lopez MF (2001) An iterative procedure to determinate Lennard–Jone parameters for their use in quantum mechanics/molecular mechanics liquid state simulations. 284:607–614
Dehez F, Chipot C, Millot C, Ángyán JG (2001) Fast and accurate determination of induction energies: reduction of topologically distributed polarizability models. Chem Phys Lett 338:180–188
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 100:14492–14507
Jacquemin D, Perpète EA, Laurent AD, Assfeld X, Adamo C (2009) Spectral properties of self-assembled squaraine–tetralactam: a theoretical assessment. Phys Chem Chem Phys 11:1258–1262
Laurent AD, Assfeld X (2010) Effect of the enhanced cyan fluorescent proteinic framework on the UV/visible absorption spectra of some chromophores. Interdisc Sci Comput Life Sci 2:38–47
Monari A, Very T, Rivail J-L, Assfeld X (2012) A QM/MM study on the spinach plastocyanin: redox properties and absorption spectra. Comp Theoret Chem 990:119–125
Monari A, Very T, Rivail J-L, Assfeld X (2012) Effects of mutations on the absorption spectrum of copper proteins: a QM/MM study Theor Chem Acc 131:1221
Very T, Despax S, Hébraud P, Monari A, Assfeld X (2012) Spectral properties of polypyridyl ruthenium complex intercalated in DNA: theoretical insights on the surrounding effects for [Ru(dppz)(bpy)2]2+.Phys Chem Chem Phys 14:12496–12504
Chantzis A, Very T, Monari A, Assfeld X (2012) Improved treatment of surrounding effects: UV/vis absorption properties of a solvated Ru(II) complex. J Chem Theory Comp 8:1536
Etienne T, Very T, Perpète EA, Monari A, Assfeld X (2013) A QM/MM study of the absorption spectrum of harmane in water solution and interacting with DNA: the crucial role of dynamic effects J Phys Chem B 117:4973–4980
Moreau Y, Loss P-F, Assfeld X (2004) Solvent effects on the asymmetric Diels–Alder reaction between cyclopentadiene and (–)-menthyl acrylate revisited with the three-layer hybrid local self-consistent field/molecular mechanics/self-consistent reaction field method. Theor Chem Acc 112: 228–239
Ferré N, Assfeld X (2002) Application of the local self-consistent-field method to core-ionized and core-excited molecules, polymers, and proteins: true orthogonality between ground and excited states. J Chem Phys 117:4119–4125
Loos PF, Assfeld X (2007) Core-ionized and core-excited states of macromolecules. Int J Quantum Chem 107:2243–2252
Ferré N, Assfeld X, Rivail J-L (2002) Specific force field determination for the hybrid ab initio QM/MM LSCF method. J Comput Chem 23:610–624
Fornili A, Loos P-F, Sironi M, Assfeld X (2006) Frozen core orbitals as an alternative to specific frontier bond potential in hybrid quantum mechanics/molecular mechanics methods. Chem Phys Lett 427:236–240
Loos P-F, Fornili A, Sironi M, Assfeld X (2007) Removing extra frontier parameters in QM/MM methods: a tentative with the local self-consistent field approach. Comput Lett 4:473–486
Loos P-F, Assfeld X (2007) On the frontier bond location in the QM/MM description of peptides and proteins. AIP Conf Proc 963:308–315
Ferré N, Assfeld X (2003) A new three-layer hybrid method (LSCF/MM/Madelung) devoted to the study of chemical reactivity in zeolites. Preliminary results. J Mol Struct (Theochem) 632:83–90
Loos PF, Assfeld X (2007) Self-consistent strictly localized orbitals. J Chem Theory Comput 3:1047–1053
Boys SF (1960) Construction of some molecular orbitals to be approximately invariant for changes from one molecule to another. Rev Mod Phys 32:296–299
Monard G, Loos M, Théry V, Baka K, Rivail JL (1996) Hybrid classical quantum force field for modeling very large molecules. Int J Quantum Chem 58:153–159
Foster JM, Boys SF (1960) Canonical configurational interaction procedure. Rev Mod Phys 32:300–302
Magnasco V, Perico A (1967) Uniform localization of atomic and molecular orbitals. I. J Chem Phys 47:971–981
Weinstein H, Pauncz R (1968) Molecular orbital set determined by a localization procedure. Symp Faraday Soc 2:23–31
Pipek J, Mezey PG (1989) A fast intrinsic localization procedure applicable for ab initio and semiempirical linear combination of atomic orbital wave functions. J Chem Phys 90:4916–4926
Fornili A, Moreau Y, Sironi M, Assfeld X (2006) On the suitability of strictly localized orbitals for hybrid QM/MM calculations. J Comput Chem 27:515–523
Sironi M, Famulari A (2000) An orthogonal approach to determine extremely localised molecular orbitals. Theor Chem Acc 103:417–422
Antonczak S, Monard G, Ruiz-López MF, Rivail J-L (1998) Modeling of peptide hydrolysis by thermolysin. A semiempirical and QM/MM study. J Am Chem Soc. 120:8825–8833
Fornili A, Sironi M, Raimondi M (2003) Determination of extremely localized molecular orbitals and their application to quantum mechanics/molecular mechanics methods and to the study of intramolecular hydrogen bonding. J Mol Struct (Theochem) 632:157–172
Genoni A, Ghitti M, Pieraccini S, Sironi M (2005) A novel extremely localized molecular orbitals based technique for the one-electron density matrix computation. Chem Phys Lett 415:256–260
Ruiz-Pernia J, Luk L, Garcia-Meseguer R, Marti S, Loveridge J, Tuñón I, Moliner V, Allemann R (2013) Increased dynamic effects in a catalytically compromised variant of Escherichia coli dihydrofolate reductase. J Am Chem Soc. doi:10.1021/ja410519h
Luk L, Ruiz-Pernia J, Dawson W, Roca M, Loveridge J, Glowacki D, Harvey J, Mulholland A, Tuñón I, Moliner V, Allemann R (2013) Unravelling the role of protein dynamics in dihydrofolate reductase catalysis. Proc Nat Acad Sci U S A 110:16344–16349
Jacquemin D, Mennucci B, Adamo C (2011) Excited-state calculations with TD-DFT: from benchmarcks to simulations in complex environments. Phys Chem Chem Phys 13:16987–16998
Gonzaléz L, Escudero D, Serrano-Andrés (2012) Progress and challenges in the calculation of electronic excited states. Chem Phys Chem 13:28–51
Laurent AD, Jacquemin D (2013) TD-DFT benchmarks: a review. Int J Quant Chem. doi:10.1002/qua.24438
Clark KM, Yu Y, Marshall NM, Sieracki NA, Nilges MJ, Blackburn NJ., van de Donk WA., Lu Y (2010) Transforming a blue copper into a red copper protein: engineering cystein and homocystein into the axial position of azurin using site-directed mutagenesis and expressed protein ligation. J Am Chem Soc 132:10093–10101
Abtouche S, Very T, Monari A, Brahimi M, Assfeld X (2013) Insights on the interactions of polychlorobiphenyl with nucleic acid base. J Mol Model 19:581–588
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2014 Springer Science+Business Media Dordrecht
About this chapter
Cite this chapter
Monari, A., Assfeld, X. (2014). Hybrid QM/MM Methods: Treating Electronic Phenomena in Very Large Molecular Systems. In: Gorb, L., Kuz'min, V., Muratov, E. (eds) Application of Computational Techniques in Pharmacy and Medicine. Challenges and Advances in Computational Chemistry and Physics, vol 17. Springer, Dordrecht. https://doi.org/10.1007/978-94-017-9257-8_1
Download citation
DOI: https://doi.org/10.1007/978-94-017-9257-8_1
Published:
Publisher Name: Springer, Dordrecht
Print ISBN: 978-94-017-9256-1
Online ISBN: 978-94-017-9257-8
eBook Packages: Chemistry and Materials ScienceChemistry and Material Science (R0)