Comments on computational chemistry: From diatomic molecules to large biochemical systems

International Journal of Quantum Chemistry

Volumn 105, Issue 6, 2005, Pages 709-730

  Clementi, Enrico ^a   Corongiu, Giorgina ^b  

^a Università dell'Insubria ^*  (Italy)

^b UNIVERSITY OF INSUBRIA   (Italy)

Author keywords

Cellular automata; Cellular dynamics simulations; Computational chemistry; Hartree Fock; Heitler london; Molecular dynamics; microdynamics

Indexed keywords

APPROXIMATION THEORY; AUTOMATA THEORY; COMPUTATIONAL METHODS; MOLECULAR DYNAMICS; QUANTUM THEORY;

CELLULAR AUTOMATA; CELLULAR DYNAMICS SIMULATIONS; COMPUTATIONAL CHEMISTRY; HARTREE-FOCK; HEITLER-LONDON; MOLECULAR DYNAMICS; MICRODYNAMICS;

BIOCHEMISTRY;

EID: 30544452027     PISSN: 00207608     EISSN: None     Source Type: Journal    
DOI: 10.1002/qua.20656     Document Type: Conference Paper

References (110)

1. (a) Brändas, E. J.; Kryachko, E. S., Eds. Fundamental World of Quantum Chemistry; Kluwer/Academic: Boston, 2003;
2. (b) Dykstra, C. E.; Frenking, G.; Kim, K. S.; Scuseria, G. E., Eds. Theory and Application of Computational Chemistry: The First 40 Years; Elsevier: Amsterdam, 2005.
3. Clementi, E. In MOTECC: Modern Technique in Computational Chemistry; Clementi, E., Ed.; ESCOM: Leiden, 1990; p 1.
4. Clementi, E. Int J Quantum Chem 1992, 42, 524.
5. Gottfried, K.; Weisskopf, V. F. Concepts of Particle Physics; Oxford University Press: London, 1984.
6. Malli, G. L. Relativistic Effects in Atoms, Molecules and Solids; Plenum: New York, 1983.
7. Pykko, P. Relativistic Theory of Atoms and Molecules: A Bibliography. Lecture Notes in Chemistry; Springer-Verlag: New York, 1986; Vol 41.
8. Wilson, S., Ed. Relativistic Effects in Atoms and Molecules; Methods in Computational Chemistry; Plenum: New York, 1988; Vol 2.
9. Grant, I. P.; Quinei, H. M. Adv At Mol Phys 1988, 23, 37.
10. Okada, S.; Shinada, M.; Matsuoka, O. J Chem Phys 1989, 91, 4193.
11. Aerts, P. J. C.; Newport, W. C. Int J Quantum Chem 1986, 19, 267.
12. Hartmann, H.; Clementi, E. Phys Rev A 1964, 133, 1295;
13. see also Clementi, E. J. Mol Spect 1964, 12, 18.
14. Mohanty, A. K.; Parpia, F. A.; Clementi, E. In MOTECC-91; Clementi, E., Ed.; ESCOM: Leiden, 1991;
15. see also Mohanty, A. K.; Clementi, E. J Chem Phys 1990, 93, 1829.
16. Pisani, L.; André, J. M.; André, M. C.; Clementi, E. J Chem Educ 1993, 70, 894;
17. see also Pisani, L.; Clementi, E. J Chem Phys 1995, 103, 9321.
18. Heitler, W.; London, F. Z Phys 1927, 44, 455.
19. Slater, J. C. Phys Rev 1930, 35, 509;
20. Phys Rev 1931, 35, 1109;
21. Phys Rev 1932, 33, 255.
22. Wheland, G. W. Resonance in Organic Chemistry; Wiley: New York, 1955.
23. Pauling, L. J Am Chem Soc 1931, 53, 1357;
24. J Am Chem Soc 1932, 54, 998;
25. J Am Chem Soc 1932, 54, 3570.
26. Pauling, L. The Nature of the Chemical Bond; 3rd ed.; Cornell University Press: Ithaca, NY, 1960.
27. Bobrowic, F. B.; Goddard, W. A. In Methods of Electronic Structure Theory; Shaefer, H. F. III, Ed.; Plenum: New York, 1977; p 79.
28. Cooper, D. L.; Gerratt, J.; Raimondi, M. In Valence Bond Theory and Chemical Structure; Klein, D. J.; Trinajstic, N., Eds.; Elsevier: 1990; p 287.
29. McWeeny, R. Int J Quantum Chem 1999, 74, 87.
30. Nascimento, M. A. C.; Barbosa, A. G. H. Quantum Mechanics of Many-Electron System and Theories of Chemical Bond; Chapter in Vol. 1 of Ref. 1a.
31. Hartree, D. R. Proc Roy Soc A 1933, 141, 282.
32. Fock, V. Z Phys 1930, 62, 795.
33. Hund, F. R. Z Phys 1927, 40, 742;
34. Z Phys 1927, 42, 93;
35. Z Phys 1928, 51, 759.
36. See references in Herzberg, G. Spectra of Diatomic Molecules; D. Van Nostrand: Princeton, NJ, 1951.
37. Mulliken, R. S. Phys Rev 1928, 32, 186;
38. Phys Rev 1928, 32, 761;
39. Phys Rev 1929, 33, 730;
40. Phys Rev 1932, 40, 55.
41. Roothaan, C. C. J. Rev Mod Phys 1951, 23, 69.
42. Roothaan, C. C. J. Rev Mod Phys 1960, 32, 179.
43. Boys, S. F. Proc Roy Soc A 1950, 200, 542;
44. see, in addition, McWeeny, R. F. Proc Roy Soc A 1946, 196, 215.
45. Shavitt, I. Methods of Computational Physics; Academic Press: New York, 1963; Vol II.
46. Schaefer, H. F. III, Ed. Methods of Electronic Structure Theory; Plenum: New York, 1977.
47. Hartree, D. R.; Hartree, W.; Swirles, B. Trans R Soc 1939, 299, 238.
48. Clementi, E.; Veillard, A. J Chem Phys 1969, 44, 3050.
49. Veillard, A.; Clementi, E. Theor Chim Acta 1967, 7, 133.
50. See for example references in Hinze, J. J Chem Phys 1973, 50, 6424.
51. Helgaker, T.; Jensen, H. J.; Jørgensen, P.; Olsen, J.; Ruud, K.; Ågren, H.; Anderson, T.; Bak, K. L.; Bakken, V.; Christiansen, O.; Dahle, P.; Dalskov, E. K.; Enevoldsen, T.; Fernandez, B.; Heiberg, H.; Hettema, H.; Jonsson, D.; Kirpekar, S.; Kobayashi, R.; Koch, H.; Mikkelsen, K. V.; Norman, P.; Packer, M. J.; Saue, T.; Taylor, P. R.; Vahtras, O. DALTON, an Ab Initio Electronic Structure Program; Release 1.0; 1977.
52. Roos, B. O.; Karlstom, G.; Malmquist, P.-A.; Sadley, A. J.; Widmark, P.-O. In MOTECC-91; Clementi, E., Ed.; ESCOM: Leiden, 1991. See also Chapters in Ref. la, and 1b.
53. Corongiu, G. to be submitted.
54. Lie, G. C.; Clementi, E. J Chem Phys 1974, 60, 1275;
55. J Chem Phys 1974, 60, 1288.
56. (a) Huber, K. P.; Herzberg, G. Molecular Spectra and Molecular Structure. IV. Constants of Diatomic Molecules; Van Nostrand Reinhold: New York, 1979;
57. (b) Kołos, W.; Szalewicz, K. J Chem Phys 1986, 84, 7278.
58. Clementi, E. Attempting to Simulate Large Molecular Systems; Chapter in Ref. 1b.
59. Clementi, E.; Corongiu, G. Int J Quantum Chem 1997, 62, 571.
60. Clementi, E.; Corongiu, G. Chem Phys Lett 1998, 282, 335.
61. Clementi, E.; Corongiu, G. J Mol Struct (Theochem) 1999, 493, 1.
62. Clementi, E.; Corongiu, G. J Mol Struct (Theochem) 2001, 543, 39.
63. Clementi, E. In Fundamental World of Quantum Chemistry; Brändas, E. J.; Kryachko, E. S., Eds.; Kluwer/Academic: Boston, 2003; Vol 1, p 601.
64. Clementi, E. J Chem Phys 1962, 36, 33.
65. Slater, J. C. Electronic Structure of Atoms and Molecules; Technical Report No 3, Solid State and Molecular Theory Group; Massachusetts Institute of Technology: Cambridge, MA, 1953.
66. Lowdin, P.-O. Adv Chem Phys 1959, 2, 207.
67. Corongiu, G. (in preparation).
68. Clementi, E.; Pitzer, K. S. J Chem Phys 1960, 32, 656.
69. Clementi, E.; Mehl, J. Jerusalem Symposia in Quantum Chemistry and Biochemistry; Academic Press: New York, 1974; Vol VI; p 137.
70. Clementi, E. IBM J Res Dev 1965, 9, 2.
71. Alder, B. J.; Wainwright, T. E. Phys Rev A 1970, 1, 18.
72. Löwdin, P.-O. In Structure and Dynamics. Nucleic Acids and Proteins; Clementi, E.; Sharma, R. H., Eds.; Adenine: New York, 1983.
73. Clementi, E. Determination of Liquid Water Structure, Coordination Numbers for Ion and Solvation for Biological Molecules; Springer-Verlag: Berlin, 1976; Vol 2.
74. Clementi, E. Computational Aspects for Large Chemical Systems; Springer-Verlag: Berlin, 1980; Vol 19.
75. Wojcik, M.; Clementi, E. J Chem Phys 1986, 85, 6085.
76. Detrich, J. H.; Corongiu, G.; Clementi, E. Chem Phys Lett 1984, 112, 426.
77. Corongiu, G.; Aida, M.; Pas, M. F.; Clementi, E. In MOTECC-91; Clementi, E., Ed.; ESCOM: Leiden, 1991; p 847.
78. Parrinello, M. In MOTECC-91; Clementi, E., Ed.; ESCOM: Leiden, 1991; p 833.
79. Bolis, G.; Ragazzi, M.; Salvaderi, D.; Ferro, D. R.; Clementi, E. Int J Quantum Chem 1978, 14, 815.
80. Ermak, D. L.; McCammon, J. A. J Chem Phys 1978, 69, 1352.
81. Alison, S.; Austin, R.; Hogan, M. J Chem Phys 1989, 90, 3843.
82. Sharp, K.; Fine, R.; Honig, B. Science 1987, 236, 1460.
83. Ciccotti, G. C.; Ferrario, M.; Ryckaert, J. P. Mol Phys 1982, 46, 875.
84. van Gusteren, W. F.; Berendsen, H. J. C. Mol Sim 1988, 1, 173.
85. Bhattacharya, D. K.; Xue, W.; Clementi, E. In MOTECC-91; Clementi, E., Ed.; ESCOM: Leiden, 1991; p 921.
86. Ciccotti, G.; Hoover, W., Eds. Molecular Dynamics Simulation of Statistical Mechanical Systems; Clarendon: London, 1987.
87. Bhattacharya, D. K.; Lie, G. C.; Clementi, E. In MOTECC-91; Clementi, E., Ed.; ESCOM: Leiden, 1991; p 939.
88. Hannon, L.; Lie, G. C.; Clementi, E. J Sci Comput 1986, 1, 145.
89. Hannon, L.; Lie, G. C.; Clementi, E. J Stat Phys 1988, 51, 965.
90. Rapaport, D. C.; Clementi, E. Phys Rev Lett 1986, 57, 695.
91. Mareschal, M.; Kestemont, E. Nature 1986, 329, 427.
92. Hannon, L.; Lie, G. C.; Clementi, E. Phys Lett A 1986, 119, 174.
93. Givens, J.; Clementi, E. J Chem Phys 1989, 90, 7376.
94. Neumann, L. Theory of Self Reproducing Automata; University of Illinois Press: Urbana, IL, 1966.
95. Kardanoff, L. P.; Swift, J. Phys Rev 1968, 165, 310.
96. Hardy, J.; de Pazzis, O.; Pomeau, Y. Phys Rev A 1976, 13, 1949.
97. Frisch, U.; Hasslacher, B.; Pomeau, Y. Phys Rev Lett 1986, 56, 1505.
98. Panda, R.; Sonnad, V. J.; Clementi, E. In MOTECC-91; Clementi, E., Ed.; ESCOM: Leiden, 1991; p 1017.
99. Scimomura, T.; Doolen, G. D.; Hasslacher, B.; Fu, C. Los Alamos Sci (Spec Issue) 1987, 15, 201.
100. Succi, S.; Benzi, R.; Cancelliere, A.; Higuera, F.; Vergassola, M. In MOTECC-91; Clementi, E., Ed.; ESCOM: Leiden, 1991; p 1031.
101. Maximow, A. A.; Bloom, W. A. Textbook of Histology; W. B. Saunders: London, 1957.
102. de Duve, C. Life Evolving; Oxford University Press: London, 2002.
103. Garfinkel, D. In Metabolie Compartmentation in Brain; Balazs, R.; Cremer, J. E., Eds.; John Wiley & Sons: London, 1972; p 121.
104. Kuffler, S. W.; Nicholl, J. G. From Neuron to Brain; Sinauer Associates: Sunderland, MA, 1976.
105. Katz, B. Nerve, Muscle, and Synapse; McGraw-Hill: New York, 1966.
106. Clementi, E.; Chin, S., Eds.; Structure and Dynamics of Nucleic Acids, Protein and Membranes; Plenum: New York, 1986.
107. Fox, S. The Emergence of Life; Basic Books: New York, 1988.
108. Sackmann, E.; Duwe, H. P.; Zeman, K.; Zilker, A. In Structure and Dynamics of Nucleic Acids, Proteins and Membranes; Clementi, E.; Chin, S.; Eds. ; Plenum: New York, 1986; p 251.
109. Jackson, P. Introduction to Expert Systems; Addison-Wesley: 1986.
110. Waterman, D. A Guide to Expert Systems; Addison-Wesley: Reading, MA, 1986.