References

The first eighteen references listed below provide general information about the algorithms used in Jaguar and some of their applications. Their titles are included in the listings, and copies of some of these references are available from Schrödinger upon request. The other listings in this section are referenced throughout this User's Guide.

1. R.A. Friesner, "Solution of Self-Consistent Field Electronic Structure Equations by a Pseudospectral Method," Chem. Phys. Lett. 116, 39 (1985).

2. R.A. Friesner, "Solution of the Hartree-Fock equations by a pseudospectral method: Application to diatomic molecules," J. Chem. Phys. 85, 1462 (1986).

3. R.A. Friesner, "Solution of the Hartree-Fock equations for polyatomic molecules by a pseudospectral method," J. Chem. Phys. 86, 3522 (1987).

4. R.A. Friesner, "An Automatic Grid Generation Scheme for Pseudospectral Self-Consistent Field Calculations on Polyatomic Molecules," J. Phys. Chem. 92, 3091 (1988).

5. M.N. Ringnalda, Y. Won, and R.A. Friesner, "Pseudospectral Hartree-Fock calculations on glycine," J. Chem. Phys. 92, 1163 (1990).

6. J.-M. Langlois, R.P. Muller, T.R. Coley, W.A. Goddard III, M.N. Ringnalda, Y. Won, and R.A. Friesner, "Pseudospectral generalized valence-bond calculations: Application to methylene, ethylene, and silylene," J. Chem. Phys. 92, 7488 (1990).

7. M.N. Ringnalda, M. Belhadj, and R.A. Friesner, "Pseudospectral Hartree-Fock theory: Applications and algorithmic improvements," J. Chem. Phys. 93, 3397 (1990).

8. Y. Won, J.-G. Lee, M.N. Ringnalda, and R.A. Friesner, "Pseudospectral Hartree-Fock gradient calculations," J. Chem. Phys. 94, 8152 (1991).

9. R.A. Friesner, "New Methods for Electronic Structure Calculations on Large Molecules," Ann. Rev. Phys. Chem. 42, 341 (1991).

10. W.T. Pollard and R.A. Friesner, "Efficient Fock matrix diagonalization by a Krylov-space method," J. Chem. Phys. 99, 6742 (1993).

11. R.P. Muller, J.-M. Langlois, M.N. Ringnalda, R.A. Friesner, and W.A. Goddard III, "A generalized direct inversion in the iterative subspace approach for generalized valence bond wave functions," J. Chem. Phys. 100, 1226 (1994).

12. R.B. Murphy, R.A. Friesner, M.N. Ringnalda, and W.A. Goddard III, "Pseudospectral Contracted Configuration Interaction From a Generalized Valence Bond Reference," J. Chem. Phys. 101, 2986 (1994).

13. B.H. Greeley, T.V. Russo, D.T. Mainz, R.A. Friesner, J.-M. Langlois, W.A. Goddard III, R.E. Donnelly, Jr., and M.N. Ringnalda, "New Pseudospectral Algorithms for Electronic Structure Calculations: Length Scale Separation and Analytical Two-Electron Integral Corrections," J. Chem. Phys. 101, 4028 (1994).

14. J.-M. Langlois, T. Yamasaki, R.P. Muller, and W.A. Goddard, "Rule Based Trial Wavefunctions for Generalized Valence Bond Theory," J. Phys. Chem. 98, 13498 (1994).

15. D.J. Tannor, B. Marten, R. Murphy, R.A. Friesner, D. Sitkoff, A. Nicholls, M. Ringnalda, W.A. Goddard III, and B. Honig, "Accurate First Principles Calculation of Molecular Charge Distributions and Solvation Energies from Ab Initio Quantum Mechanics and Continuum Dielectric Theory," J. Am. Chem. Soc. 116, 11875 (1994).

16. R.B. Murphy, M.D. Beachy, R.A. Friesner, and M.N. Ringnalda, "Pseudospectral Localized MP2 Methods: Theory and Calculation of Conformational Energies," J. Chem. Phys. 103, 1481 (1995).

17. D. Lu, B. Marten, Y. Cao, M.N. Ringnalda, R.A. Friesner, and W.A. Goddard III, "ab initio Predictions of Large Hyperpolarizability Push-Pull Polymers: Julolidinyl-n-isoxazolone and Julolidinyl-n-N,N'-diethylthiobarbituric acid," Chem. Phys. Lett. 242, 543 (1995).

18. R.B. Murphy, W.T. Pollard, and R.A. Friesner, "Pseudospectral localized generalized Møller-Plesset methods with a generalized valence bond reference wave function: Theory and calculation of conformational energies," J. Chem. Phys. 106, 5073 (1997).

19. G. Vacek, J.K. Perry, and J.-M. Langlois, Chem. Phys. Lett. 310, 189 (1999).

20. F.W. Bobrowicz and W.A. Goddard III, in Modern Theoretical Chemistry: Methods of Electronic Structure Theory, H.F. Schaefer III, ed., 3, Chapter 4 (Plenum, New York, 1977).

21. BIOGRAF manual.

22. MacroModel manual.

23. M.J. Frisch, G.W. Trucks, M. Head-Gordon, P.M.W. Gill, M.W. Wong, J.B. Foresman, B.G. Johnson, H.B. Schlegel, M.A. Robb, E.S. Replogle, R. Gomperts, J.L. Andres, K. Raghavachari, J.S. Binkley, C. Gonzalez, R.L. Martin, D.J. Fox, D.J. DeFrees, J. Baker, J.J.P. Stewart, and J.A. Pople, Gaussian 92 (Gaussian, Inc., Pittsburgh, PA, 1992).

24. Babel version 1.3, copyright (©) 1992-96 W. Patrick Walters and Matthew T. Stahl, All Rights Reserved. (Permission of authors granted to incorporate Babel into Jaguar.)

25. A.D. Becke, J. Chem. Phys. 98, 1372 (1993).

26. A.D. Becke, J. Chem. Phys. 98, 5648 (1993).

27. J.C. Slater, Quantum Theory of Molecules and Solids, Vol. 4: The Self-Consistent Field for Molecules and Solids (McGraw-Hill, New York, 1974).

28. S.H. Vosko, L. Wilk, and M. Nusair, Can. J. Phys. 58, 1200 (1980). (The VWN correlation functional is described in the paragraph below equation [4.4] on p. 1207, while the VWN5 functional is described in the caption of Table 5 and on p. 1209.)

29. J.P. Perdew, in Electronic Structure Theory of Solids, P. Ziesche and H. Eschrig, eds. (Akademie Verlag, Berlin, 1991); J.P. Perdew, J.A. Chevary, S.H. Vosko, K.A. Jackson, M.R. Pederson, D.J. Singh, and C. Fiolhais, Phys. Rev. B 46, 6671 (1992).

30. A.D. Becke, Phys. Rev. A 38, 3098 (1988).

31. C. Lee, W. Yang, and R.G. Parr, Phys. Rev. B 37, 785 (1988); implemented as described in B. Miehlich, A. Savin, H. Stoll, and H. Preuss, Chem. Phys. Lett. 157, 200 (1989).

32. J.P. Perdew and A. Zunger, Phys. Rev. B 23, 5048 (1981).

33. J.P. Perdew, Phys. Rev. B 33, 8822 (1986), and Erratum, J.P. Perdew, Phys. Rev. B 34, 7406 (1986).

34. C. Møller and M.S. Plesset, Phys. Rev. 46, 618 (1934).

35. S. Sæbø and P. Pulay, Theor. Chim. Acta 69, 357 (1986).

36. S. Sæbø and P. Pulay, Ann. Rev. Phys. Chem. 44, 213 (1993).

37. S. Sæbø, W. Tong, and P. Pulay, J. Chem. Phys. 98, 2170 (1993).

38. J.M. Foster and S.F. Boys, Rev. Mod. Phys. 32, 300 (1960).

39. J. Pipek and P.G. Mezey, J. Chem. Phys. 90, 4916 (1989).

40. L.B. Harding and W.A. Goddard III, J. Am. Chem. Soc. 97, 6293 (1975).

41. E.A. Carter and W.A. Goddard III, J. Chem. Phys. 86, 862 (1987).

42. T.H. Fischer and J. Almlöf, J. Phys. Chem. 96, 9768 (1992).

43. H.B. Schlegel, Theor. Chim. Acta 66, 333 (1984).

44. CRC Handbook of Chemistry and Physics, R.C. Weast, ed., 60th edition (CRC Press, Boca Raton, FL, 1979). Dielectric constants for 20 deg. C were used.

45. Water's probe radius is set to 1.40 to reproduce solvation energies properly. All other probe radii are calculated from (1024 A3/cm3), where r is the solvent probe radius in Angstroms, m is the molecular mass obtained by dividing the molecular weight given in ref. [44] in grams per mole by 6.02 x 1023, Dr is the density in g/cm3 at 20 deg. C obtained from ref. [44]. Finding the actual Drequire a detailed knowledge of the structure of the liquid. Currently, all D(For FCC lattices, D is 0.7405, and for BCC lattices, D is 0.6802.)

46. A.K. Rappé, C.J. Casewit, K.S. Colwell, W.A. Goddard, and W.M. Skiff, J. Am. Chem. Soc. 114, 10024 (1992).

47. L.E. Chirlian and M.M. Francl, J. Comput. Chem. 8, 894 (1987); R. J. Woods, M. Khalil, W. Pell, S.H. Moffat, and V.H. Smith, Jr., J. Comput. Chem. 11, 297 (1990).

48. C.M. Breneman and K.B. Wiberg, J. Comput. Chem. 11, 361 (1990).

49. S.L. Mayo, B.D. Olafson, and W.A. Goddard III, J. Phys. Chem. 94, 8897 (1990).

50. R.S. Mulliken, J. Chem. Phys. 23, 1833 (1955).

51. NBO 4.0, E.D. Glendening, J.K. Badenhoop, A.E. Reed, J.E. Carpenter, and F. Weinhold, Theoretical Chemistry Institute, University of Wisconsin, Madison, WI, 1996.

52. J. Baker, A.A. Jarzecki, and P. Pulay, J. Phys. Chem A 102, 1412 (1998).

53. A.P. Scott and L. Radom, J. Phys.Chem. 100, 16502 (1996).

54. W.J. Hehre, R.F. Stewart, and J.A. Pople, J. Chem. Phys. 51, 2657 (1969).

55. W.J. Hehre, R. Ditchfield, R.F. Stewart, and J.A. Pople, J. Chem. Phys. 52, 2769 (1970).

56. W.J. Pietro, B.A. Levi, W.J. Hehre, and R.F. Stewart, Inorg. Chem. 19, 2225 (1980).

57. W.J. Pietro, E.S. Blurock, R.F. Hout, Jr., W.J. Hehre, D.J. DeFrees, and R.F. Stewart, Inorg. Chem. 20, 3650 (1980).

58. J.B. Collins, P. von R. Schleyer, J.S. Binkley, and J.A. Pople, J. Chem. Phys. 64, 5142 (1976).

59. J.S. Binkley, J.A. Pople, and W.J. Hehre, J. Am. Chem. Soc. 102, 939 (1980).

60. M.S. Gordon, J.S. Binkley, J.A. Pople, W.J. Pietro, and W.J. Hehre, J. Am. Chem. Soc. 104, 2797 (1982).

61. W.J. Pietro, M.M. Francl, W.J. Hehre, D.J. DeFrees, J.A. Pople, and J.S. Binkley, J. Am. Chem. Soc. 104, 5039 (1982).

62. P. Pulay, G. Fogarasi, F. Pang, and J.E. Boggs, J. Am. Chem. Soc. 101, 2550 (1979).

63. J.D. Dill and J.A. Pople, J. Chem. Phys. 62, 2921 (1975).

64. R. Ditchfield, W.J. Hehre, and J.A. Pople, J. Chem. Phys. 54, 724 (1971).

65. W.J. Hehre and J.A. Pople, J. Chem. Phys. 56, 4233 (1972).

66. J.S. Binkley and J.A. Pople, J. Chem. Phys. 66, 879 (1977).

67. P.C. Hariharan and J.A. Pople, Theor. Chim. Acta 28, 213 (1973).

68. W.J. Hehre, R. Ditchfield, and J.A. Pople, J. Chem. Phys. 56, 2257 (1972).

69. M.M. Francl, W.J. Pietro, W.J. Hehre, J.S. Binkley, M.S. Gordon, D.J. DeFrees, and J.A. Pople, J. Chem. Phys. 77, 3654 (1982).

70. V.A. Rassolov, J.A. Pople, M.A. Ratner, and T.L. Windus, J. Chem. Phys. 109, 1223 (1998).

71. T. Clark, J. Chandrasekhar, G.W. Spitznagel, and P. von R. Schleyer, J. Comput. Chem. 4, 294 (1983).

72. M.J. Frisch, J.A. Pople, and J.S. Binkley, J. Chem. Phys. 80, 3265 (1984).

73. R. Krishnan, J.S. Binkley, R. Seeger, and J.A. Pople, J. Chem. Phys. 72, 650 (1980).

74. A.D. McLean and G.S. Chandler, J. Chem. Phys. 72, 5639 (1980).

75. T.H. Dunning, Jr. and P.J. Hay, in Modern Theoretical Chemistry: Methods of Electronic Structure Theory, H.F. Schaefer III, ed., 3, Chapter 1 (Plenum, New York, 1977).

76. A.K. Rappé and W.A. Goddard, unpublished.

77. T.H. Dunning, Jr., J. Chem. Phys. 90, 1007 (1989).

78. R.A. Kendall, T.H. Dunning, Jr., and R.J. Harrison, J. Chem. Phys. 96, 6796 (1992).

79. D.E. Woon and T.H. Dunning, Jr., J. Chem. Phys. 98, 1358 (1993).

80. D.E. Woon, K. A. Peterson, and T.H. Dunning, Jr., unpublished.

81. P.J. Hay and W.R. Wadt, J. Chem. Phys. 82, 270 (1985).

82. P.J. Hay and W.R. Wadt, J. Chem. Phys. 82, 284 (1985).

83. P.J. Hay and W.R. Wadt, J. Chem. Phys. 82, 299 (1985).

84. The LACV3P basis set is a triple-zeta contraction of the LACVP basis set developed and tested at Schrödinger, Inc.

85. T.R. Cundari and W.J. Stevens, J. Chem. Phys. 98, 5555 (1993).

86. T.P. Hamilton and P. Pulay, J. Chem. Phys. 84, 5728 (1986); P. Pulay, J. Comput. Chem. 3, 556 (1982); P. Pulay, Chem. Phys. Lett. 73, 393 (1980).

87. S. Obara and A. Saika, J. Chem. Phys. 84, 3963 (1986).

88. P.M.W. Gill, M. Head-Gordon, and J.A. Pople, J. Chem. Phys. 94, 5564 (1990); P.M.W. Gill, M. Head-Gordon, and J.A. Pople, Int. J. Quantum Chem. S23, 269 (1989); M. Head-Gordon and J.A. Pople, J. Chem. Phys. 89, 5777 (1988).

89. R.B. Murphy and R.P. Messmer, J. Chem. Phys. 98, 10102 (1993).

90. For information on Molden, please see the Molden web site http://www.caos.kun.nl/~schaft/molden/molden.html.

91. MOPAC 6, J.J.P. Stewart, QCPE #455.

92. P. Hohenberg and W. Kohn, Phys. Rev. B 136, 864 (1964).

93. W. Kohn and L.J. Sham, Phys. Rev. A 140, 1133 (1965).

94. R.G. Parr and W. Yang, Density-Functional Theory of Atoms and Molecules (Oxford, New York, 1989).

95. J.K. Labanowski and J.W. Andzelm, eds., Density Functional Methods in Chemistry (Springer-Verlag, Berlin, 1991).

96. R. Colle and O. Salvetti, J. Chem. Phys. 93, 534 (1990).

97. E. Kraka, Chem. Phys. 161, 149 (1992).

98. G. Audi and A.H. Wapstra, Nuclear Phys. A595 4, 409 (1995).

99. P. Császár and P. Pulay, J. Mol. Struct. 114, 31 (1984).

100. H.B. Schlegel, J. Comput. Chem. 3, 214 (1982).

101. M.J.D. Powell, Math. Prog. 1, 26 (1971).

102. J.M. Bofill, J. Comp. Chem. 15, 1 (1994).

103. B.A. Murtagh and R.W.H. Sargent, Comp. J. 13, 185 (1972).

104. R. Fletcher, in Practical Methods of Optimization (Wiley, New York, 1987).

105. A. Banerjee, N. Adams, J. Simons, and R. Shepard, J. Phys. Chem. 89, 52 (1985).

106. P. Culot, G. Dive, V.H. Nguyen, and J.M. Ghuysen, Theor. Chim. Acta 82, 189 (1992).

107. J. Simons, P. Jorgensen, H. Taylor, and J. Ozment, J. Phys. Chem. 87, 2745 (1983).

108. M. Häser and R. Ahlrichs, J. Comput. Chem. 10, 104 (1989); D. Cremer and J. Gauss, J. Comput. Chem. 7, 274 (1986); J. Almlöf, K. Faegri, Jr., and K. Korsell, J. Comput. Chem. 3, 385 (1982).

109. C.I. Bayly, P. Cieplak, W.D. Cornell, and P.A. Kollman, J. Phys. Chem. 97, 10269 (1993).

110. A.H. Stroud, Approximate Calculation of Multiple Integrals (Prentice-Hall, 1971).

111. V.I. Lebedev, Zh. vychisl. Mat. mat. Fiz. 15, 48-54 (1975).

112. V.I. Lebedev, Zh. vychisl. Mat. mat. Fiz. 16, 293-306 (1976).

113. V.I. Lebedev, Sibirsk. Mat. Zh. 18, 132-142 (1977).

114. V.I. Lebedev, in Theory of Cubature Formula and Numerical Mathematics (in Russian), S.L Sobolev, ed. ("Nauka" Sibirsk, Otdel., Novosibirsk, 1980), pages 110-114.

115. C.J. Cramer and D.G. Truhlar, J. Comp. Aided Mol. Design 6, 629 (1992).

116. B. Marten, K. Kim, C. Cortis, R.A.Friesner, R.B. Murphy, M.N. Ringnalda, D. Sitkoff, and B. Honig, "New Model for Calculation of Solvation Free Energies: Correction of Self-Consistent Reaction Field Continuum Dielectric Theory for Short-Range Hydrogen-Bonding Effects," J. Phys. Chem. 100, 11775 (1996).

117. D. Chasman, M.D. Beachy, L. Wang, and R.A. Friesner, "Parallel Pseudospectral Electronic Structure. I. Hartree-Fock Calculations," J. Comp. Chem. 19, 1017-1029 (1998).

118. M. D. Beachy, D. Chasman, R.B. Murphy, and R.A. Friesner, "Parallel Pseudospectral Electronic Structure. II. Localized Mëëëëëëëëëëëëëëëëëëëëëëëëëëëëëëëëëëëëëëëëëëëëëëëëëëëëëëëëëëëøller-Plesset Calculations, J. Comp. Chem. 19, 1030-1038 (1998).

119. Y. H. Jang, L. C. Sowers, T. Cagin, and W. A. Goddard III, J. Phys. Chem. A 105, 274-280 (2001).

Schrödinger, Inc. http://www.schrodinger.com Voice: (503) 299-1150 Fax: (503) 299-4532 help@schrodinger.com Last updated: Thu Oct 11 19:11:25 2001