A pseudobond approach to combining quantum mechanical and molecular mechanical methods
10.1063/1.478083
Crossref journal-article
AIP Publishing
The Journal of Chemical Physics (317)
Abstract

A major challenge for combined quantum mechanical and molecular mechanical methods (QM/MM) to study large molecules is how to treat the QM/MM boundary that bisects some covalent bonds. Here a pseudobond approach has been developed to solve this problem for ab initio QM/MM calculations: a one-free-valence atom with an effective core potential is constructed to replace the boundary atom of the environment part and to form a pseudobond with the boundary atom of the active part. This pseudobond, which is described only by the QM method, is designed to mimic the original bond with similar bond length and strength, and similar effects on the rest of the active part. With this pseudobond approach, some well-known deficiencies of the link atom approach have been circumvented and a well-defined potential energy surface of the whole QM/MM system has been provided. The construction of the effective core potential for the pseudobond is independent of the molecular mechanical force field and the same effective core potential is applicable to both Hartree–Fock and density functional methods. Tests on a series of molecules yield very good structural, electronic, and energetic results in comparison with the corresponding full ab initio quantum mechanical calculations.

Bibliography

Zhang, Y., Lee, T.-S., & Yang, W. (1999). A pseudobond approach to combining quantum mechanical and molecular mechanical methods. The Journal of Chemical Physics, 110(1), 46–54.

Authors 3
  1. Yingkai Zhang (first)
  2. Tai-Sung Lee (additional)
  3. Weitao Yang (additional)
References 53 Referenced 443
  1. {'key': '2024021017482378700_r1'}
  2. {'key': '2024021017482378700_r2'}
  3. 10.1103/PhysRevLett.66.1438 / Phys. Rev. Lett. (1991)
  4. 10.1209/0295-5075/17/6/012 / Europhys. Lett. (1992)
  5. 10.1103/PhysRevLett.73.122 / Phys. Rev. Lett. (1994)
  6. 10.1103/PhysRevB.47.10891 / Phys. Rev. B (1993)
  7. 10.1103/PhysRevB.47.10895 / Phys. Rev. B (1993)
  8. {'key': '2024021017482378700_r8', 'first-page': '10157', 'volume': '51', 'year': '1994', 'journal-title': 'Phys. Rev. B'} / Phys. Rev. B (1994)
  9. 10.1103/PhysRevLett.76.3168 / Phys. Rev. Lett. (1996)
  10. 10.1063/1.473579 / J. Chem. Phys. (1997)
  11. 10.1063/1.474404 / J. Chem. Phys. (1997)
  12. 10.1103/PhysRevB.47.9973 / Phys. Rev. B (1993)
  13. {'key': '2024021017482378700_r13', 'first-page': '1640', 'volume': '52', 'year': '1995', 'journal-title': 'Phys. Rev. B'} / Phys. Rev. B (1995)
  14. 10.1103/PhysRevB.48.14646 / Phys. Rev. B (1993)
  15. 10.1103/PhysRevB.53.R10441 / Phys. Rev. B (1996)
  16. 10.1103/PhysRevB.50.17811 / Phys. Rev. B (1994)
  17. 10.1103/PhysRevLett.70.3631 / Phys. Rev. Lett. (1993)
  18. 10.1002/(SICI)1097-461X(1996)58:2<133::AID-QUA2>3.0.CO;2-Z / Int. J. Quantum Chem. (1996)
  19. {'key': '2024021017482378700_r19'}
  20. 10.1063/1.470549 / J. Chem. Phys. (1995)
  21. 10.1063/1.472136 / J. Chem. Phys. (1996)
  22. 10.1021/ja973522w / J. Am. Chem. Soc. (1998)
  23. 10.1021/ja961937w / J. Am. Chem. Soc. (1996)
  24. 10.1103/PhysRevLett.80.5011 / Phys. Rev. Lett. (1998)
  25. 10.1063/1.471382 / J. Chem. Phys. (1996)
  26. 10.1016/0009-2614(96)00490-3 / Chem. Phys. Lett. (1996)
  27. {'key': '2024021017482378700_r27'}
  28. {'key': '2024021017482378700_r28'}
  29. 10.1016/0022-2836(76)90311-9 / J. Mol. Biol. (1976)
  30. 10.1002/jcc.540070604 / J. Comput. Chem. (1986)
  31. 10.1002/jcc.540110605 / J. Comput. Chem. (1990)
  32. 10.1126/science.1411573 / Science (1992)
  33. 10.1021/j100148a005 / J. Phys. Chem. (1993)
  34. 10.1002/jcc.540150303 / J. Comput. Chem. (1994)
  35. 10.1002/jcc.540160911 / J. Comput. Chem. (1995)
  36. 10.1002/(SICI)1097-461X(1996)60:6<1189::AID-QUA7>3.0.CO;2-W / Int. J. Quantum Chem. (1996)
  37. 10.1021/jp9536514 / J. Phys. Chem. (1996)
  38. {'key': '2024021017482378700_r38', 'first-page': '1051', 'volume': '63', 'year': '1997', 'journal-title': 'Int. J. Quantum Chem.'} / Int. J. Quantum Chem. (1997)
  39. 10.1021/jp9809890 / J. Phys. Chem. A (1998)
  40. 10.1063/1.463928 / J. Chem. Phys. (1992)
  41. {'key': '2024021017482378700_r41'}
  42. 10.1002/(SICI)1097-461X(1996)58:2<153::AID-QUA4>3.0.CO;2-X / Int. J. Quantum Chem. (1996)
  43. 10.1016/S0009-2614(96)01165-7 / Chem. Phys. Lett. (1996)
  44. 10.1021/jp973084f / J. Phys. Chem. B (1998)
  45. 10.1021/ja00124a002 / J. Am. Chem. Soc. (1995)
  46. {'key': '2024021017482378700_r46', 'first-page': '6016', 'volume': '81', 'year': '1984', 'journal-title': 'J. Chem. Phys.'} / J. Chem. Phys. (1984)
  47. {'key': '2024021017482378700_r47'}
  48. 10.1063/1.464913 / J. Chem. Phys. (1993)
  49. 10.1103/PhysRevA.38.3098 / Phys. Rev. A (1988)
  50. 10.1103/PhysRevB.37.785 / Phys. Rev. B (1988)
  51. 10.1073/pnas.84.19.6611 / Pro. Natl. Acad. Sci. (1987)
  52. 10.1103/PhysRevLett.80.1357 / Phys. Rev. Lett. (1998)
  53. {'key': '2024021017482378700_r53'}
Dates
Type When
Created 23 years, 1 month ago (July 26, 2002, 8:17 a.m.)
Deposited 1 year, 6 months ago (Feb. 10, 2024, 1:17 p.m.)
Indexed 1 month, 3 weeks ago (July 8, 2025, 3:44 a.m.)
Issued 26 years, 7 months ago (Jan. 1, 1999)
Published 26 years, 7 months ago (Jan. 1, 1999)
Published Print 26 years, 7 months ago (Jan. 1, 1999)
Funders 0

None

@article{Zhang_1999, title={A pseudobond approach to combining quantum mechanical and molecular mechanical methods}, volume={110}, ISSN={1089-7690}, url={http://dx.doi.org/10.1063/1.478083}, DOI={10.1063/1.478083}, number={1}, journal={The Journal of Chemical Physics}, publisher={AIP Publishing}, author={Zhang, Yingkai and Lee, Tai-Sung and Yang, Weitao}, year={1999}, month=jan, pages={46–54} }