Abstract
To obtain stable states (SS) and transition states (TS) in chemical reactions in condensed phase, the free energy gradient (FEG) method was proposed in 1998 as an optimization method on a multidimensional free energy surface (FES). Analogous to the method for the Born Oppenheimer potential energy surface (PES) using ab initio molecular orbital calculation, the FEG method utilizes the force and Hessian on the FES, which can be adiabatically calculated by molecular dynamics (MD) or Monte Carlo (MC) methods, and, originally, the free energy (FE) perturbation theory. In fact, since then, a number of excellent approximate methods have been developed, e.g., the averaged solvent electrostatic potential (ASEP)/MD method and the average solvent electrostatic configuration (ASEC) method. In this chapter, the FEG methodology is reviewed in general and a future perspective to explore the FE landscape is introduced together with several applications of these methods. Based on computational demands and on the numerical accuracy, we believe that a family of the FEG methodologies should become more efficient as one strategic setting and will play promising and important roles to survey condensed state chemistry on the basis of recent supercomputing technology.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
(a) Okuyama-Yoshida N, Nagaoka M, Yamabe T (1998) Int J Quantum Chem 70:95 (b) Nagaoka M, Okuyama-Yoshida N, Yamabe T (1998) J Phys Chem A 102:8202 (c) Okuyama-Yoshida N, Nagaoka M, Yamabe T (1998) J Phys Chem A 102: 282
(a) Okuyama-Yoshida N, Kataoka K, Nagaoka M, Yamabe T (2000) J Chem Phys 113:3519 (b) Hirao H, Nagae Y, Nagaoka M (2001) Chem Phys Lett 348:350
(a) Nagae Y, Oishi Y, Naruse N, Nagaoka M (2003) J Chem Phys 110:4555 (b) Nagaoka M, Nagae Y, Koyano Y, Oishi Y (2006) J Phys Chem A 110:4555
(a) Koyano Y, Takenaka N, Nakagawa Y, Nagaoka M (2010) Bull Chem Soc Jpn 83:486 (b) Takenaka N, Kitamura Y, Koyano Y, Asada T, Nagaoka M (2011) Theor Chem Acc 130:215
Malaspina T, Coutinho K, Canuto S (2002) J Chem Phys 117:1692
Coutinho K, Rivelino R, Georg HC, Canuto S (2008) In: Canuto S (ed) Solvation effects in molecules and biomolecules. Challenges and advances in computational chemistry and physics, vol 6. Springer, London, pp 159–189
Georg HC, Coutinho K, Canuto S (2006) Chem Phys Lett 429:119
Georg HC, Coutinho K, Canuto S (2007) J Chem Phys 126:034507
(a) Fukui K (1981) Acc Chem Res 14:363 (b) Fukui K (1982) Angew Chem Int Ed 21:801
(a) Warshel A, Levitt M (1976) J Mol Biol 103:227 (b) Singh UC, Kollman PA (1986) J Comput Chem 7:718 (c) Field MJ, Bash PA, Karplus MA (1990) J Comput Chem 11:700
Luque FJ, Reuter N, Cartier A, Ruiz-López MF (2000) J Phys Chem A 104:10923
(a) Okamoto T, Yamada K, Koyano Y, Asada T, Koga N, Nagaoka M (2011) J Comput Chem 32:932 (b) Okamoto T, Ishikawa T, Koyano Y, Yamamoto N, Kuwata K, Nagaoka M (2013) Bull Chem Soc Jpn 86:210
Yamada K, Koyano Y, Okamoto T, Asada T, Koga N, Nagaoka M (2011) J Comput Chem 32:3092
Sanchez ML, Aguilar MA, Olivares del Valle FJ (1997) J Comput Chem 18:313
Martin ME, Sánchez ML, Olivares del Valle FJ, Aguilar MA (2002) J Chem Phys 116:1613
Galván IF, Sánchez ML, Martín ME, Olivares del Valle FJ, Aguilar MA (2003) J Chem Phys 118:255
Coutinho K, Georg HC, Fonseca TL, Ludwig V, Canuto S (2007) Chem Phys Lett 437:148
Georg HC, Canuto S (2012) J Phys Chem B 116:11247
Matubayasi N, Nakahara M (2000) J Chem Phys 113:6070
Matubayasi N, Nakahara M (2002) J Chem Phys 117:3605
Impey RW, Klein ML (1984) Chem Phys Lett 104:579
Gao J, Xia X, George TF (1993) J Phys Chem 97:9241
Keal TW, Helgaker T, Salek P, Tozer DJ (2006) Chem Phys Lett 425:163
Provasi PF, Aucar GA, Sauer SPA (2001) J Chem Phys 115:1324
Jensen F (2006) J Chem Theory Comput 2:1360
(a) Bernheim RA, Batiz-Hernandez H (1964) J Chem Phys 40:3446 (b) Alei Jr M, Florin AE, Litchman WM, O’Brien JF (1971) J Phys Chem 75:932 (c) Litchman WM, Alei Jr M, Florin AE (1969) J Chem Phys 50:1897 (d) Jameson CJ, Jameson AK, Cohen SM, Parker H, Oppusunggu D, Burrel PM, Wille S (1981) J Chem Phys 74:1608
Gester RM, Georg HC, Canuto S, Caputo MC, Provasi PF (2009) J Phys Chem A 113:14936
Moriarty NW, Karlström G (1997) J Chem Phys 106:6470
(a) Ichikawa K, Kameda Y, Yamaguchi T, Wakita H, Misawa M (1991) Mol Phys 73:79 (b) Lide DR (ed) (2007) CRC handbook of chemistry and physics, 87th edn. Taylor and Francis, Boca Raton (c) Benedict WS, Gailar N, Plyler EK (1956) J Chem Phys 24:1139
Chalmet S, Ruiz-Lopez MS (2001) J Chem Phys 115:5220
Tu Y, Laaksonen A (2000) Chem Phys Lett 329:283
Guedes RC, Coutinho K, Cabral BJC, Canuto S (2003) Chem Phys Lett 369:345
Wasylischen RE, Friedrich JO (1987) Can J Chem 65:2238
Burnett LJ, Zeltmann AH (1974) J Chem Phys 60:4636
Hermida-Ramón JM, Öhrn A, Karlström G (2007) J Phys Chem B 111:11511
Godfrey PD, Brown RD, Hunter AN (1997) J Mol Struct 413–414:405
Merrick JP (2007) J Phys Chem A 111:11683
Foresman JB, Frisch AE (1996) Exploring chemistry with electronic structure methods, 2nd edn. Gaussian Inc., Pittsburgh
Hermansson K (1993) J Chem Phys 99:861
Benedict WS, Gailar N, Plyler EK (1956) J Chem Phys 24:1139
Ford TA, Falk M (1968) Can J Chem 46:3579
Bertie JE, Lan Z (1996) Appl Spectrosc 50:1047
Nagaoka M, Yu I, Takayanagi M (2009) In: Leitner DM, Straub JE (eds) Proteins: energy, heat and signal flow, Computation in chemistry. CRC Press, Boca Raton, pp 149–196
Kitamura Y, Takenaka N, Koyano Y, Nagaoka M, J Chem Phys, submitted for publication
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2014 Springer Science+Business Media New York
About this chapter
Cite this chapter
Georg, H.C., Fernandes, T.S., Canuto, S., Takenaka, N., Kitamura, Y., Nagaoka, M. (2014). A Combination of the Sequential QM/MM and the Free Energy Gradient Methodologies with Applications. In: Leszczynski, J., Shukla, M. (eds) Practical Aspects of Computational Chemistry III. Springer, Boston, MA. https://doi.org/10.1007/978-1-4899-7445-7_8
Download citation
DOI: https://doi.org/10.1007/978-1-4899-7445-7_8
Published:
Publisher Name: Springer, Boston, MA
Print ISBN: 978-1-4899-7444-0
Online ISBN: 978-1-4899-7445-7
eBook Packages: Chemistry and Materials ScienceChemistry and Material Science (R0)