Force-field and quantum-mechanical binding study of selected SAMPL3 host-guest complexes

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• 作者：Nobuko Hamaguchi (1)
  Laszlo Fusti-Molnar (1)
  Stanislaw Wlodek (1) stan@eyesopen.com
• 关键词：Binding thermodynamics – Synthetic receptors – Intermolecular potential
• 刊名：Journal of Computer-Aided Molecular Design
• 出版年：2012
• 出版时间：May 2012
• 年：2012
• 卷：26
• 期：5
• 页码：577-582
• 全文大小：346.4 KB
• 参考文献：1. Wall SD, Meadows E, Barbour L, Gokel G (2000) Proc Natl Acad Sci 97:6271
  2. Pal A, Bérubé M, Hall DG (2110) Angew Chem Int Ed 49:1492
  3. Mazik M, Hartmann A (2010) Beilstein J Org Chem 6(9). doi:10.3762/bjoc.6.9
  4. Castilla A, Conn M, Ballester P (2010) Beilstein J Org Chem 6(5). doi:10.3762/bjoc.6.5
  5. Rekharsky M, Inoue Y (2007) Netsu Sokutei 34:232
  6. Ma D, Zavalij Y, Isaacs L (2010) J Org Chem 75:4786
  7. Fred2.2.5 (2010) OpenEye Scientific Software, Inc., Santa Fe
  8. Omega2.4.3 (2006) OpenEye Scientific Software, Inc., Santa Fe
  9. Szybki1.5.0 (2010) OpenEye Scientific Software, Inc., Santa Fe
  10. Wlodek S, Skillman A, Nicholls A (2010) J Chem Theory Comput 6:2140
  11. Pierotti R (1976) Chem Rev 76:717
  12. Grant J, Pickup B, Sykes M, Kitchen C, Nicholls A (2007) Chem Phys Lett 441:163
  13. Stone A (1981) Chem Phys Lett 83:233
  14. Stone A (2005) J Chem Theory Comput 1:1128
  15. Schmidt M, Baldridge K, Boatz J, Elbert S, Gordon M, Jensen J, Koseki S, Matsunaga N, Nguyen K, Su S, Windus T, Dupuis M, Montgomery J (1993) J Comput Chem 14:1347
  16. Molnar LF, He X, Wang B, Merz K (2009) J Chem Phys 131:065102
  17. Kim J, Jung I, Kim S, Lee E, Kang J, Sakamoto S, Yamaguchi K, Kim K (2000) J Am Chem Soc 122:540
  18. Knox C, Law V, Jewison T, Liu P, Ly S, Frolkis A, Pon A, Banco K, Mak C, Neveu V, Djoumbou Y, Eisner R, Guo A, Wishart D (2011) Nucleic Acids Res 39:D1035
  19. Civalleri B, Zicovich-Wilson C, Valenzano L, Ugliengo P (2008) CrystEngComm 10:405
  20. Kelly C, Cramer C, Truhlar D (2006) J Phys ChemA 110:2493
  21. Bryantsev V, Diallo M, Goddard-III W (2008) J Phys ChemB 112:9709
  22. da Silva E, Svendsena H, Merz K (2009) J Phys ChemA 113:6404
  23. Grant J, Pickup B, Nicholls A (2001) J Comput Chem 22:608
  24. Burgess J (1978) Metal ions in solution. Ellis Horwood Ltd., Chichester
  25. Szmap1.0.0 (2010) OpenEye Scientific Software, Inc., Santa Fe
• 作者单位：1. OpenEye Scientific Software, 9 Bisbee Court, Suite D, Santa Fe, NM 87508, USA
• ISSN：1573-4951

文摘

A Merck molecular force field classical potential combined with Poisson-Boltzmann electrostatics (MMFF/PB) has been used to estimate the binding free energy of seven guest molecules (six tertiary amines and one primary amine) into a synthetic receptor (acyclic cucurbit[4]uril congener) and two benzimidazoles into cyclic cucurbit[7]uril (CB[7]) and cucurbit[8]uril (CB[8]) hosts. In addition, binding enthalpies for the benzimidazoles were calculated with density functional theory (DFT) using the B3LYP functional and a polarizable continuum model (PCM). Although in most cases the MMFF/PB approach returned reasonable agreements with the experiment (±2 kcal/mol), significant, much larger deviations were reported in the case of three host-guest pairs. All four binding enthalpy predictions with the DFT/PCM method suffered 70% or larger deviations from the calorimetry data. Results are discussed in terms of the molecular models used for guest-host complexation and the quality of the intermolecular potentials.