Advertisement

Molecular Tailoring: An Art of the Possible for Ab Initio Treatment of Large Molecules and Molecular Clusters

  • Anuja P. Rahalkar
  • Sachin D. Yeole
  • V. Ganesh
  • Shridhar R. GadreEmail author
Chapter
Part of the Challenges and Advances in Computational Chemistry and Physics book series (COCH, volume 13)

Abstract

Divide-and-conquer (DC) type methods are being actively developed in order to break the bottleneck of high scaling order of ab initio calculations of large molecules. Molecular Tailoring Approach (MTA) is one of such early attempts, which scissors the parent molecular system into subsystems (fragments). The properties of these subsystems are stitched back in order to estimate those for the parent system. Inclusion-exclusion principle from set theory is incorporated into MTA, which allows accurate estimation of electronic energy, energy-gradients and Hessian. This Chapter summarizes the algorithm, equations as well as basic parameters for obtaining an optimal fragmentation for a given molecule. The fragmentation in MTA is exclusively based on distance-criterion allowing its application to a general class of molecules. Further, the versatility of this method with respect to the level of theory [Hartree-Fock (HF) method, Møller-Plesset second order perturbation theory (MP2) and Density Functional Theory (DFT)] as well as the basis set is illustrated. Apart from earlier benchmarks, a few new test cases including geometry optimization of variety of molecules, benzene clusters, polyaromatic hydrocarbons, metal cluster and a protein with charged centers are presented in this Chapter.

Keywords

Molecular tailoring approach (MTA) Linear scaling methods Hartree-Fock (HF) Theory Density functional theory (DFT) Møller-Plesset second order perturbation (MP2) theory π-conjugation Large molecules 

Notes

Acknowledgments

Authors thank the Center for Development of Advanced Computing (C-DAC), Pune; Naval Research Board (NRB), New Delhi and Center for Advanced Studies (CAS) program in Chemistry supported by the University Grants Commission (UGC), New Delhi for financial assistance and computational resource availability. APR is grateful to the Council of Scientific and Industrial Research (CSIR), New Delhi for funding. SRG is thankful to Department of Science and Technology (DST), New Delhi for the award of a J. C. Bose Fellowship to him.

References

  1. 1.
    Schmidt MW, Baldridge KK, Boatz JA, Elbert ST, Gordon MS, Jensen JH, Koseki S, Matsunaga N, Nguyen KA, Su SJ, Windus TL, Dupuis, M, Montgomery JA (1993) J Comput Chem 14:1347. For further details, see: http://www.msg.ameslab.gov/GAMESS/GAMESS.html CrossRefGoogle Scholar
  2. 2.
    Gaussian 03, Revision C.02, Frisch MJ, Trucks GW, Schlegel HB, Scuseria GE, Robb MA, Cheeseman JR, Montgomery Jr JA, VrevenT, Kudin KN, Burant JC, Millam JM, Iyengar SS, Tomasi J, Barone V, Mennucci B, Cossi M, Scalmani G, Rega N, Petersson GA, Nakatsuji H, Hada M, Ehara M, Toyota K, Fukuda R, Hasegawa J, Ishida M, Nakajima T, Honda Y, Kitao O, Nakai H, Klene M. Li X, Knox JE, Hratchian HP, Cross JB, Bakken V, Adamo C, Jaramillo J, Gomperts R, Stratmann RE, Yazyev O, Austin AJ, Cammi R, Pomelli C, Ochterski JW, Ayala PY, Morokuma K, Voth GA, Salvador P, Dannenberg JJ, Zakrzewski, VG, Dapprich S, Daniels AD, Strain MC, Farkas O, Malick DK, Rabuck AD, Raghavachari K, Foresman JB, Ortiz JV, Cui Q, Baboul AG, Clifford Cioslowski J, Stefanov BB, Liu G, Liashenko A, Piskorz P. Komaromi I, Martin RL, Fox DJ, Keith T, Al-Laham MA, Peng CY, Nanayakkara A, Challacombe M, Gill PMW, Johnson B, Chen W, Wong MW, Gonzalez C, Pople JA (2004) Gaussian, Inc., Wallingford, CTGoogle Scholar
  3. 3.
    TURBOMOLE V6.0 2009, a development of University of Karlsruhe and Forschungszentrum Karlsruhe GmbH, 1989–2007, TURBOMOLE GmbH, since 2007; available from the website: http://www.turbomole.com
  4. 4.
    Barden C, Schaefer HF III, Pure J (2000) Appl Chem 72:1405CrossRefGoogle Scholar
  5. 5.
    (a) Becke AD (1993) J Chem Phys 98:5648; (b) Lee C, Yang W, Parr RG (1988) Phys Rev B 37:785CrossRefGoogle Scholar
  6. 6.
    Zhao Y, Truhlar DG (2006) J Phys Chem A (2006) 110:13126; Valero Z, Costa R, Moreitra IPR, Truhlar DG, (2008) F Illas 128:114103CrossRefGoogle Scholar
  7. 7.
    (a) Gadre SR, Kulkarni SA, Limaye AC, Shirsat RN (1991) Zeit Phys-D : Atoms, Molecules and Clusters 18:357(b) Shirsat RN, Limaye AC, Gadre SR (1993) J Comput Chem 14:445 (c) Limaye AC, Gadre SR (1994) J Chem Phys 100 1303CrossRefGoogle Scholar
  8. 8.
    Ufimtsev IS, Martinez TJ (2009) J Chem Theory Comput 5:2619CrossRefGoogle Scholar
  9. 9.
    The package PetaChem, for quantum chemical calculations on graphics processors, available at http://www.petachem.com
  10. 10.
    Saebo S, Pulay P (1988) J Chem Phys 88:1884CrossRefGoogle Scholar
  11. 11.
    Schütz M, Hetzer G, Werner H-J (1999) J Chem Phys 111:5691.CrossRefGoogle Scholar
  12. 12.
    (a) Ishimura K, Pulay P, Nagase S (2006) J Comput Chem 27:407 (b) Ishimura K, Pulay P, Nagase S (2007) J Comput Chem 28:2034(c) Katouda M, Nagase S (2009) Int J Quant Chem 109:2121Google Scholar
  13. 13.
    Feyereisen M, Fitzgerald G, Komornicki A (1993) Chem Phys Lett 208:359CrossRefGoogle Scholar
  14. 14.
    Weigend F, Häser M, Patzelt H, Ahlrichs R (1998) Chem Phys Lett 294:143CrossRefGoogle Scholar
  15. 15.
    Spangler D, Christoffersen RE (1980) Int J Quant Chem 17:1075CrossRefGoogle Scholar
  16. 16.
    Yang W (1991) Phys Rev A 44:7823CrossRefGoogle Scholar
  17. 17.
    Lee C, Yang W (1992) J Chem Phys 96:2408CrossRefGoogle Scholar
  18. 18.
    Zhao Q, Yang W (1995) J Chem Phys 102:9598CrossRefGoogle Scholar
  19. 19.
    Gadre SR, Shirsat RN, Limaye AC (1994) J Phys Chem 98:9165CrossRefGoogle Scholar
  20. 20.
    Babu K, Gadre SR (2003) J Comp Chem 24:484CrossRefGoogle Scholar
  21. 21.
    Babu K, Ganesh V, Gadre SR, Ghermani NE (2004) Theor Chem Acc 111:255CrossRefGoogle Scholar
  22. 22.
    Gadre SR, Babu K, Ganesh V (2005) In: Maheshwari SN (ed) Recent trends in practice and theory of information technology: proceedings of nrb seminar, Viva Books, New Delhi, p 86Google Scholar
  23. 23.
    Gadre SR, Ganesh V (2006) J Theory Comput Chem 5:835CrossRefGoogle Scholar
  24. 24.
    Ganesh V, Dongare RK, Balanarayan P, Gadre SR (2006) J Chem Phys 125:104109CrossRefGoogle Scholar
  25. 25.
    Gadre SR, Rahalkar AP, Ganesh V (2006) Indian Assoc Nucl Chem Allied Sci Bull 4:267Google Scholar
  26. 26.
    Elango M, Subramanian V, Rahalkar AP, Gadre SR, Sathyamurthy N (2008) J Phys Chem A 112:7699CrossRefGoogle Scholar
  27. 27.
    Rahalkar AP, Ganesh V, Gadre SR (2008) J Chem Phys 129:234101CrossRefGoogle Scholar
  28. 28.
    WebProp: Web Interface for Ab Initio Calculation of Molecular One-Electron Properties. Available for free academic use at http://chem.unipune.ernet.in/~tcg/webprop/ See: Ganesh V, Kavathekar R, Rahalkar AP, Gadre SR (2008) J Comput Chem 29:488CrossRefGoogle Scholar
  29. 29.
    WebMTA: Web interface for Ab Initio Calculations using Molecular Tailoring Approach. Available for free academic use at http://chem.unipune.ernet.in/~tcg/mtaweb See: Kavathekar R, Khire S, Ganesh V, Rahalkar AP, Gadre SR (2009) J Comp Chem 30:1167CrossRefGoogle Scholar
  30. 30.
    Kitaura K, Ikeo E, Asada T, Nakano T, Uebayasi M (1999) Chem Phys Lett 313:701CrossRefGoogle Scholar
  31. 31.
    Fedorov DG, Kitaura K (2004) J Chem Phys 120:6832CrossRefGoogle Scholar
  32. 32.
    Fedorov DG, Ishida T, Uebayasi M, Kitaura K (2007) J Phys Chem A 111:2722CrossRefGoogle Scholar
  33. 33.
    Fedorov DG, Jensen JH, Deka RC, Kitaura K (2008) J Phys Chem A 112:11808CrossRefGoogle Scholar
  34. 34.
    Sawada T, Fedorov DG, Kitaura K (2009) Int J Quant Chem 109:2033CrossRefGoogle Scholar
  35. 35.
    Fedorov DG, Ishimura K, Ishida T, Kitaura K, Pulay P, Nagase S (2007) J Comp Chem 28:1476CrossRefGoogle Scholar
  36. 36.
    Rahalkar AP, Katouda M, Gadre SR, Nagase S (2010) J Comput Chem 31:2405Google Scholar
  37. 37.
    Li S, Ma J, Jiang Y (2002) J Comp Chem 23:237CrossRefGoogle Scholar
  38. 38.
    Huo W, Fang T, Li W, Yu JG, Li S (2008) J Phys Chem A 112:10864CrossRefGoogle Scholar
  39. 39.
    Zhang DW, Zhang JZH (2003) J Chem Phys 119:3599CrossRefGoogle Scholar
  40. 40.
    Deev V, Collins MA (2005) J Chem Phys 122:154102CrossRefGoogle Scholar
  41. 41.
    Collins MA (2007) J Chem Phys 127:024104CrossRefGoogle Scholar
  42. 42.
    Bettens RPA, Lee AM (2006) J Phys Chem A 110:8777CrossRefGoogle Scholar
  43. 43.
    Akama T, Kobayashi M, Nakai H (2007) J Comp Chem 28:2003CrossRefGoogle Scholar
  44. 44.
    Kobayashi M, Nakai H (2009) Int J Quant Chem 109:2227CrossRefGoogle Scholar
  45. 45.
    Jovan JKV, Gadre SR (2008) J Chem Phys 129:164314CrossRefGoogle Scholar
  46. 46.
    Yeole SD, Gadre SR (2010) J Chem Phys 132:094102CrossRefGoogle Scholar
  47. 47.
    The package MeTA Studio available at: http://code.google.com/p/metastudio/. See Ganesh V (2009) J Comp Chem 30:661CrossRefGoogle Scholar
  48. 48.
    Qiu L, Pabit SA, Roitberg AE, Hagen SJ (2002) J Am Chem Soc 124:12952CrossRefGoogle Scholar
  49. 49.
    Mahadevi S, Rahalkar AP, Gadre SR, Sastry GN (2010) J Chem Phys 133:164308Google Scholar
  50. 50.
    Jovan JKV, Gadre SR (2009) Int J Quant Chem 109:2238CrossRefGoogle Scholar
  51. 51.
    Shirsat RN, Bapat SV, Gadre SR (1992) Chem Phys Lett 200:373CrossRefGoogle Scholar
  52. 52.
    Kulkarni AD, Ganesh V, Gadre SR (2004) J Chem Phys 121:5043CrossRefGoogle Scholar
  53. 53.
    Kohn W (1996) Phys Rev Lett 76:3168CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media B.V. 2011

Authors and Affiliations

  • Anuja P. Rahalkar
    • 1
    • 2
  • Sachin D. Yeole
    • 1
    • 2
  • V. Ganesh
    • 3
  • Shridhar R. Gadre
    • 1
    • 2
    Email author
  1. 1.Department of ChemistryUniversity of PunePuneIndia
  2. 2.Department of ChemistryIIT KanpurKanpurIndia
  3. 3.Department of Computer ScienceAustralian National UniversityCanberraAustralia

Personalised recommendations