Abstract
The combination of molecular mechanics and quantum mechanics (QM/MM) is gaining increasing application in solvation problems. One possibility that has been explored is to use the MM and QM sequentially. This has the advantage that statistically converged results can be ensured. In addition, convergence with the size (number of explicit solvent molecules) can also be easily explored. The disadvantage is that uncoupling the QM and the MM imposes special consideration for including the solute polarization. These aspects are considered here, where a detailed analysis is made of the statistical correlation and the statistical inefficiency. An iterative procedure to include the solute polarization is discussed and examples are presented. Examples are also given to illustrate the different aspects, especially the size and statistical convergence. Finally, the possibility and implementation of using just one average configuration to obtain, from a single QM calculation, the same average of the statistically converged value is discussed
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Yabuzaki T, Kinoshita T et al (1995) Z Phys B 98:367
Tabbert B, Günther H et al (1997) J Low Temp Phys 109:653
Ludwig V, Mukherjee PK, et al (2005) Phys Rev A 72:062714–1
Reichardt C (2003) Solvents and solvent effects in organic chemistry, 3rd edn. Wiley-VCH, Weinheim
Onsager L (1936) J Am Chem Soc 58:1486
Kirkwood JG (1934) J Chem Phys 2:351
Tapia O, Goscinski O (1975) Mol Phys 29:1653
Rivail JL, Rinaldi D (1976) Chem Phys 18:233
Rinaldi D, Rivail JL (1973) Theor Chim Acta 32:57
Tomasi J (2004) Theor Chem Acc 112:184
Miertus S, Scrocco E et al (1981) Chem Phys 55:117
Tomasi J, Persico M (1994) Chem Rev 94:2027
Tomasi J, Mennucci B et al (2005) Chem Rev 105:2999
Foresman JB, Keith TA et al (1996) J Phys Chem 100:16098
Mikkelsen KV, Ågren H, et al (1988) J Chem Phys 89:3086
Kongsted J, Osted A et al (2003) J Chem Phys 119:10519
Grozema FC. van Duijnen Th P (1998) J Phys Chem A 102:7984
Jensen L, van Duijnen Th P et al (2003) J Chem Phys 118:514
Klamt A, Schüürmann G (1993) J Chem Soc Perkins T 2:799
Monte SA, Muller T et al (2004) Theor Chem Acc 111:78
Blair JT, Krogh-Jespersen K et al (1989) J Am Chem Soc 111:6948
Warshell A, Levitt M (1976) J Mol Biol 103:227
Gao JL (1996) in: Lipkowitz KB, Boyd DB (eds) Reviews of Computational Chemistry, vol 7. New York, p. 119
Ruiz-López MF (ed) (2003) J Mol Struct (Theochem) 632, special issue on Combined QM/MM calculations in chemistry and biochemistry, p 1
Orozco M, Luque FJ (2000) Chem Rev 100:4187.
Cramer CJ (2004) Essentials of computational chemistry: Theories and models, 2 nd edn. Wiley, Chichester
Lin H, Truhlar DG (2007) Theor Chem Acc 117:185
Allen MP, Tildesley DJ (1987) Computer Simulation of Liquids, Oxford, Clarendon
Zeng J, Hush NS et al (1993) J Chem Phys 99:1508
Zeng J, Craw JS et al (1994) J Phys Chem 98:11075
Canuto S, Coutinho K (1997) Adv Quantum Chem 28:89
Canuto S, Coutinho K (2000) Int J Quantum Chem 77:192
Field MJ, Bash PA et al (1990) J Comput Chem 11:700
Gao JL, Luque FJ et al (1993) J Chem Phys 98:2975
Almeida TS, Coutinho K et al (2007) J Chem Phys 128:014506
Besley NA, Oakley MT et al (2004) J Am Chem Soc 126:13502
Coutinho K, Oliveira MJ et al (1998) Int J Quantum Chem 66:249
Chatfield C (1984) The analysis of time series. An introduction, Chapman and Hall, London
Kendal MG (1973) Time Series, Griffin, London
Krätschmer R, Binder K et al (1976) J Stat Phys 15:267
Caprihan A, Seymour JD (2000) J Mag Res 144:96
Coutinho K, Canuto S et al (2000) J Chem Phys 112:9874
Müller-Krumbhaar H, Binder K (1973) J Stat Phys 8:1
Tang S, Landau DP (1987) Phys Rev B 36:567
Friedberg R, Cameron JE (1970) J Chem Phys 52:6049
Malaspina T, Coutinho K et al (2002) J Chem Phys 117:1692
Canuto S, Coutinho K et al (2002) Adv Quantum Chem 41:161
Coutinho K, Cabral BJC et al (2004) Chem Phys Lett 399:534
Coutinho K, Canuto S (1997) DICE: A Monte Carlo program for molecular liquid simulation, University of São Paulo, Brazil
Georg HC, Coutinho K et al (2007) J Chem Phys 126:034507
Almeida KJ, Coutinho K et al (2001) Phys Chem Chem Phys 3:1583
Hernandez MZ, Longo R et al (2004) Phys Chem Chem Phys 6:2088
Coutinho K, Canuto S (2000) J Chem Phys 113:9132
Coutinho K, Canuto S (2003) J Mol Struct (Theochem) 632:235
Coutinho K, Ludwig V et al (2004) Phys Rev E 69:619021–1
Guedes RC, Coutinho K et al (2003) J Phys Chem B 107:4304
Guedes RC, Coutinho K et al (2003) J Phys Chem A 107:9197
Ludwig V, Coutinho K et al (2004) Phys Rev B 70:214110–1
Canuto S, Coutinho K et al (2005) Adv Quantum Chem 48:141
Lima MCP, Coutinho K et al (2006) J Phys Chem A 110:7253
Fileti EE, Georg HC et al (2007) J Braz Chem Soc 18:74
Couto PC, Cabral BJC et al (2006) Chem Phys Lett 429:129
Coutinho K, Canuto S (2006) in: Maroulis G (ed) Atoms, Molecules and Clusters in Electric Fields. Theoretical Approaches to the Calculation of Electric Polarizability. Imperial College Press, London, p 405
Ludwig V, Coutinho K et al (2003) Int J Quantum Chem 95:572
Liptay W (1966), in: Sinanoglu O (ed) Modern quantum chemistry, Acad. Press, N.Y., Part II, p 173
Bayliss NS, Hulme L (1953) Aust J Chem 6:257
Jorgensen WL, Chandrasekhar J et al (1984) J Am Chem Soc 106:6638
McDonald IR, Bounds DG et al (1982) Mol Phys 45:521
Berendsen HJC, Postman JPM et al (1981) Interaction models for water in relation to protein hydration. In: Pullman B (ed) Intermolecular forces. Dordrecht, Reidel, p. 331
Ridley J, Zerner MC (1973) Theor Chim Acta 32:111
Zerner MC (2000) ZINDO: A semi-empirical program package, University of Florida, Gainesville, FL, USA
Rivelino R, Maniero AM et al (2006) Carbon 44:2925
Rivelino R, Mota FB (2007) Nano Lett 7:1526
Li L, Bedrov D et al (2005) Phys Rev E 71:011502
Werder T, Walther JH et al (2003) Phys Chem B 107:1345
Mahoney MW. Jorgensen WL (2000) J Chem Phys 112:8910
Zerner MC (1990) Semiempirical molecular orbital methods. In: Lipkowitz KB Boyd DB (eds) Reviews of computational chemistry, VCH, New York, vol 25, p. 313
Canuto S, Coutinho K et al (2000) J Chem Phys 112:7293
Ordejón P, Artacho E, et al (1996) Phys Rev B 53:10441
Soler JM, Artacho E et al (2002) Phys: Condens Matter 14:2745
Ceperley DM, Alder BJ (1980) Phys Rev Lett 45:566
Perdew JP, Zunger A (1981) Phys Rev B 23:5048
Becke AD (1998) Phys Rev A 38:3098
Lee C, Yang W et al (1998) Phys Rev B 37:785
Troullier N, Martins JL (1991) Phys Rev B 43:1993
Junquera J, Paz O et al (2001) Phys Rev B 64:235111
Artacho E, Sánchez-Portal D et al (1999) Phys Status Solidi B 215:809
Ordejón P (2000) Phys Status Solidi B 217:335
Choudhury NJ (2006) Chem Phys 125:034502
Steiner T (2002) Biophys Chem 95:195
Andrievsky GV, Klochkov VK et al (2002) Chem Phys Lett 364:8
Andrievsky GV, Klochkov VK et al (1999) Chem Phys Lett 300:392
Andrievsky GV, Klochkov VK et al (2005) Fullerenes, Nanotubes, Carbon Nanostruct 13:363
Dhawan A, Taurozzi JS et al (2006) Environ Sci Technol 40:7394
Scharff P, Risch K et al (2004) Carbon 42:1203
Prylutskyy YI, Durov SS et al (2001) Int J Thermophys 22:943
Sayes CM, Fortner JD et al (2004) Nano Lett 4:1881
Jorgensen WL (ed) special issue no. 6 (2007) J Chem Theo Comput 3:1877–2145
Ohba T, Ikawa S (1991) Mol Phys 73:985
Jensen L, Swart M et al (2005) J Chem Phys 122:034103
Cornell WD, Cieplack P et al (1995) J Am Chem Soc 117:5179
Jorgensen WL. Tirado-Rives J (1988) J Am Chem Soc 110:1657
McDonald NA, Carlson HA et al (1997) J Phys Org Chem 10:563
Rivelino R, Cabral BJC et al (2005) Chem Phys Lett 407:13
Jorgensen WL, McDonald NA et al (1995) J Am Chem Soc 117:11809
Dang LX, Rice JE et al (1991) J Am Chem Soc 113:2481
Meng EC, Cieplak V et al (1994) J Am Chem Soc 116:12061
Soto P, Mark AE (2002) J Phys Chem B 106:12830
Breneman CM, Wiberg KB (1990) J Comput Chem 11:361
Besler BH, Merz KM et al (1990) J Comput Chem 11:431
Georg HC, Coutinho K et al (2006) Chem Phys Lett 429:119
Martín ME, Sánchez ML et al (2000) J Chem Phys 113:6308
Ten-no S, Hirata F et al (1994) J Chem Phys 100:7443
Kongsted J, Osted A et al (2004) J Chem Phys 121:8435
Öhrn A, Karlström G (2006) Mol Phys 104:3087
Kawashima Y, Dupuis M et al (2002) J Chem Phys 117:248
Aidas K, Kongsted J et al (2005) J Phys Chem A 109:8001
Öhrn A, Karlström G (2007) Theor Chem Acc 117:441
Hayes WP. Timmons CJ (1965) Spectrochim Acta 21:529
Bayliss NS, McRae EG (1954) J Phys Chem 58:1006
Bayliss NS, Wills-Johnson G (1968) Spectrochim Acta, Part A 24:551
Frisch MJ et al (2004) Gaussian 03, Revision D.01; Gaussian, Inc., Wallingford CT
Peter R, Dreizler H (1965) Z Naturforsch A 20:301
Röhrig UF, Frank I, et al (2003) Chem Phys Phys Chem 4:1177
Barker JW, Noe LJ (1972) J Chem Phys 57:3035
Lide DR (1993) Handbook of Chemistry and Physics, CRC Press, Boca Raton
Dilling WL (1966) J Org Chem 31:1045
Urahata S, Canuto S (2000) Int J Quantum Chem 80:1062
Couto PC, Guedes RC et al (2003) J Chem Phys 119:7344
Sánchez ML, Aguilar MA et al (1997) J Comput Chem 18:313
Sánchez ML, Aguilar MA et al (1998)J Mol Struct (Theochem) 426:181
Sánchez ML, Martín ME et al (2002) J Phys Chem 106:4813
Coutinho K, Georg HC et al (2007) Chem Phys Lett 437:148
Pavone M, Crescenzi O et al (2006) Theor Chem Acc 116:456
Mennucci B, Martinez JM et al (2001) J Phys Chem A 105:7287
Acknowledgment
This work has been partially supported by the Brazilian agencies FAPESP, CNPq, RENAMI and CAPES.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2008 Springer Science+Business Media B.V.
About this chapter
Cite this chapter
Coutinho, K., Rivelino, R., Georg, H.C., Canuto, S. (2008). The Sequential qm/mm Method and its Applications to Solvent Effects in Electronic and Structural Properties of Solutes. In: Canuto, S. (eds) Solvation Effects on Molecules and Biomolecules. Challenges and Advances in Computational Chemistry and Physics, vol 6. Springer, Dordrecht. https://doi.org/10.1007/978-1-4020-8270-2_7
Download citation
DOI: https://doi.org/10.1007/978-1-4020-8270-2_7
Published:
Publisher Name: Springer, Dordrecht
Print ISBN: 978-1-4020-8269-6
Online ISBN: 978-1-4020-8270-2
eBook Packages: Chemistry and Materials ScienceChemistry and Material Science (R0)