Bulletin of the Korean Chemical Society

Korean Chemical Society (대한화학회)
권호 표지
DOI QR코드

DOI QR Code

An Efficient Method to Compute Partial Atomic Charges of Large Molecules Using Reassociation of Fragments

  • Lee, Jung-Goo (Department of Physics, North Carolina State University) ;
  • Jeong, Ho-Young (Gatsby Computational Neuroscience Unit, University College London) ;
  • Lee, Ho-Sull (Kumho Chemical Laboratories)
  • Published : 2003.03.20
Download PDF
⟨ Previous Next ⟩

Abstract

Coulson (ZINDO), Mulliken $(MP2/6-31G^*)$ and Natural $(MP2/6-31G^*)$ population analyses of several large molecules were performed by the Fragment Reassociation (FR) method. The agreement between the conventional ZINDO (or conventional MP2) and FR-ZINDO (or FR-MP2) charges of these molecules was excellent. The standard deviations of the FR-ZINDO net atomic charges from the conventional ZINDO net atomic charges were 0.0008 for $C_{10}H_{22}$ (32 atoms), 0.0012 for $NH_2-C_{16}O_2H_{28}-COOH$ (53 atoms), 0.0014 for $NH_3^+-C_{16}O_2H_{28}-COOH$ (54 atoms), 0.0017 for $NH_2-C_{16}O_2H_{28}-COO^-$ (52 atoms), 0.0019 for $NH_3^+-C_{16}O_2H_{28}-COO^-$ (53 atoms), 0.0024 for a conjugated model $(O=CH-(CH=CH)_{15}-C=O-(CH=CH)_{12}-CH=CH_2)$, 118 atoms), 0.0038 for aglycoristocetin $(C_{60}N_7O_{19}H_{52}^+$, 138 atoms), 0.0023 for a polypropylene model complexed with a zirconocene catalyst $(C_{68}H-{121}Zr^+$, 190 atoms) and 0.0013 for magainin $(C_{112}N_{29}O_{28}SH_{177}$, 347 atoms), respectively. The standard deviations of the FR-MP2 Mulliken (or Natural) partial atomic charges from the conventional ones were 0.0016 (or 0.0016) for $C_{10}H_{22}$, 0.0019 (or 0.0018) for $NH_2-C_{16}O_2H_{28}-COOH$ and 0.0033 (or 0.0023) for $NH_3^+-C_{16}O_2H_{28}-COO^-$, respectively. These errors were attributed to the shape of molecules, the choice of fragments and the degree of ionic characters of molecules as well as the choice of methods. The CPU time of aglycoristocetin, conjugated model, polypropylene model complexed with zirconocene and magainin computed by the FR-ZINDO method was respectively 2, 4, 6 and 21 times faster than that by the normal ZINDO method. The CPU time of $NH_2-C_{16}O_2H_{28}-COOH\;and\;NH_3^+-C_{16}O_2H_{28}-COO^-$ computed by the FR-MP2 method was, respectively, 6 and 20 times faster than that by the normal MP2 method. The largest molecule calculated by the FR-ZINDO method was B-DNA (766 atoms). These results will enable us to compute atomic charges of huge molecules near future.

Keywords

References

  1. Jensen, F. Introduction to Computational Chemistry; Wiley &Sons: Chichester, 1999; Chapter 9.
  2. Rappe, A. K.; Goddard III, W. A. J. Phys. Chem. 1991, 95, 3358. https://doi.org/10.1021/j100161a070
  3. Mulliken, R. S. J. Chem. Phys. 1955, 23, 1833. https://doi.org/10.1063/1.1740588
  4. Singh, U. C.; Kollman, P. A. J. Comput. Chem. 1984, 5, 129. https://doi.org/10.1002/jcc.540050204
  5. Stone, A. J.; Alderton, M. Mol. Phys. 1985, 56, 1047. https://doi.org/10.1080/00268978500102891
  6. Chirlian, L. E.; Francl, M. M. J. Comput. Chem. 1987, 8, 894. https://doi.org/10.1002/jcc.540080616
  7. Breneman, C. M.; Wiberg, K. B. J. Comput. Chem. 1990, 11, 361. https://doi.org/10.1002/jcc.540110311
  8. Williams, D. E. Rev. Comput. Chem. 1991, 2, 219. https://doi.org/10.1002/9780470125793.ch6
  9. Reynolds, C. A.; Essex, J. W.; Richards, W. G. J. Am. Chem. Soc.1992, 114, 9075. https://doi.org/10.1021/ja00049a045
  10. Aleman, C.; Orozro, M.; Luque, F. J. Chem. Phys. 1994, 189, 573. https://doi.org/10.1016/0301-0104(94)00310-6
  11. Koch, U.; Egert, E. J. Comput. Chem. 1995, 16, 937. https://doi.org/10.1002/jcc.540160803
  12. Marynick, D. S. J. Comput. Chem. 1997, 18, 955. https://doi.org/10.1002/(SICI)1096-987X(199705)18:7<955::AID-JCC7>3.0.CO;2-Q
  13. Swart, M.; Duijnen, P. T. v.; Snijders, J. G. J. Comput. Chem.2001, 22, 79. https://doi.org/10.1002/1096-987X(20010115)22:1<79::AID-JCC8>3.0.CO;2-B
  14. Bader, R. F. W. Atoms in Molecules - A Quantum Theory; Oxford:London, 1990.
  15. Cioslowski, J. J. Am. Chem. Soc. 1989, 111, 8333. https://doi.org/10.1021/ja00204a001
  16. Cioslowski, J. J. Chem. Phys. Lett. 1992, 189, 524. https://doi.org/10.1016/0009-2614(92)85244-5
  17. Foster, J. P.; Weinhold, F. J. Am. Chem. Soc. 1980, 102, 7211. https://doi.org/10.1021/ja00544a007
  18. Reed, A. E.; Weinhold, F. J. Chem. Phys. 1983, 78, 4066. https://doi.org/10.1063/1.445134
  19. Reed, A. E.; Weinstock, R. B.; Weinhold, F. J. Chem. Phys. 1985,83, 735. https://doi.org/10.1063/1.449486
  20. Reed, A. E.; Curtiss, L. A.; Weinhold, F. Chem. Rev. 1988, 88,899. https://doi.org/10.1021/cr00088a005
  21. Weinhold, F.; Carpenter, J. E. The Structure of Small Molecules and Ions; Plenum: 1988; p 227.
  22. Lee, J.-G.; Friesner, R. A. J. Phys. Chem. 1993, 97, 3515. https://doi.org/10.1021/j100116a013
  23. Van der Vaart, A.; Gogonea, V.; Dixon, S. L.; Merz, K. M., Jr. J.Comput. Chem. 2000, 21, 1494. https://doi.org/10.1002/1096-987X(200012)21:16<1494::AID-JCC6>3.0.CO;2-4
  24. Bellido, M. N.; Rullmann, J. A. C. J. Comput. Chem. 1989, 10, 479. https://doi.org/10.1002/jcc.540100405
  25. Young, L.; Topol, I. A.; Rashin, A. A.; Burt, S. K. J. Comput. Chem. 1997, 18, 522. https://doi.org/10.1002/(SICI)1096-987X(199703)18:4<522::AID-JCC6>3.0.CO;2-V
  26. Dardenne, L. E.; Werneck, A. S.; Oliveira Neto, M.; Bisch, P. M.J. Comput. Chem. 2000, 22, 689. https://doi.org/10.1002/jcc.1037
  27. ZINDO, User Guide, version 95.0/3.0.0, BIOSYM/MolecularSimulations: 1995.
  28. Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.;Robb, M. A.; Cheeseman, J. R.; Zakrzewski, V. G.; Montgomery,J. A.; Stratmann, Jr., R. E.; Burant, J. C.; Dapprich, S.; Millam, J.M.; Daniels, A. D.; Kudin, K. N.; Strain, M. C.; Farkas, O.;Tomasi, J.; Barone, V.; Cossi, M.; Cammi, R.; Mennucci, B.;Pomelli, C.; Adamo, C.; Clifford, S.; Ochterski, J.; Petersson, G.A.; Ayala, P. Y.; Cui, Q.; Morokuma, K.; Malick, D. K.; Rabuck,A. D.; Raghavachari, K.; Foresman, J. B.; Cioslowski, J.; Ortiz, J.V.; Baboul, A. G.; Stefanov, B. B.; Liu, G.; Liashenko, A.;Piskorz, P.; Komaromi, I.; Gomperts, R.; Martin, R. L.; Fox, D. J.;Keith, T.; Al-Laham, M. A.; Peng, C. Y.; Nanayakkara, A.;Gonzalez, C.; Challacombe, M.; Gill, P. M. W.; Johnson, B. G.;Chen, W.; Wong, M. W.; Andres, J. L.; Head-Gordon, M.;Replogle, E. S.; Pople, J. A. Gaussian 98 (Revision A.7),Gaussian, Inc.: Pittsburgh, PA, 1998.

Cited by

  1. Fragment-based prediction of skin sensitization using recursive partitioning vol.25, pp.9, 2011, https://doi.org/10.1007/s10822-011-9472-7
  2. BN-Substituted fullerenes C60−2x (BN) x : a computational 11B and 15N NMR study vol.23, pp.6, 2012, https://doi.org/10.1007/s11224-012-0002-6
  3. Exploring 11B and 15N NMR parameters of C70−2x (BN) x fullerenes (x = 3–25) in connection with local structures and curvature effects: a DFT study vol.145, pp.3, 2014, https://doi.org/10.1007/s00706-013-1103-7
  4. Evaluation of on-cage phosphorus doping of hydrogenated silicon fullerenes: a computational study vol.25, pp.1, 2014, https://doi.org/10.1007/s11224-013-0243-z
  5. (SiH)48X12 Heterofullerenes with the Group III and V Dopants: A DFT Prediction of Geometry, Stability, and Electronic Structure vol.25, pp.2, 2014, https://doi.org/10.1007/s10876-013-0630-z
  6. Physical Chemistry Research Articles Published in the Bulletin of the Korean Chemical Society: 2003-2007 vol.29, pp.2, 2008, https://doi.org/10.5012/bkcs.2008.29.2.450
  7. Structural determination of large molecules through the reassembly of optimized fragments vol.27, pp.3, 2003, https://doi.org/10.1016/j.jmgm.2008.06.004
  8. Ionization of biological molecules by multicharged ions using the stoichiometric model vol.53, pp.5, 2020, https://doi.org/10.1088/1361-6455/ab6052