Quantum Kernels and Quantum Crystallography: Applications in Biochemistry

Quantum Biochemistry

Volumn , Issue , 2010, Pages 1-60

  Huang, Lulu ^a   Massa, Lou ^b   Karle, Jerome ^a  

^a NAVAL RESEARCH LABORATORY   (United States)

^b CITY UNIVERSITY OF NEW YORK   (United States)

Author keywords

Biomolecules; Kernel energy method; N representability; Quantum crystallography; Quantum kernels

Indexed keywords

EID: 84885514141     PISSN: None     EISSN: None     Source Type: Book    
DOI: 10.1002/9783527629213.ch1     Document Type: Chapter

References (108)

1. Von Neumann, J. (1927) Nachr. Ahad. Wiss. Gottigen, Math. Pysik. K1. II a. Math Physik. Chem. Abt., 245, 272-.
2. Dirac, P.A.M. (1931) Proc. Cambridge Phil. Soc., 27, 240-253.
3. Huisimi, K. (1940) Proc. Phys. - Math. Soc. Japan, 22, 264-314.
4. Mayer, J.E. (1955) Phys. Rev., 100, 1579-1586.
5. Tredgold, R.H. (1957) Phys. Rev., 105, 1421-1423.
6. Lowdin, P.O. (1955) Phys. Rev., 97, 1474-1489.
7. Coleman, J. (1963) Rev. Mod. Phys., 35, 668-686.
8. McWeeney, R. (1960) Rev. Mod. Phys., 32, 335-369.
9. Fano, K. (1957) Rev Mod. Phys., 29, 74-93.
10. Terhaar, D. (1976) Reduced Density Matrices in Quantum Chemistry, Academic Press, New York.
11. Davidson, E.R. (1976) Reduced Density Matrices in Quantum Chemistry, Theoretical Chemistry; A Series Of Monographs, vol. 6, Academic Press Inc., London.
12. Gilbert, T.L. (1975) Phys. Rev. B, 12, 2111-2120.
13. Frishberg, C.A. and Massa, L. (1981) Phys. Rev B, 24, 7018-7024.
14. Clinton, W.L., Galli, A., and Massa, L. (1969) Phys. Rev., 177, 7-13.
15. Massa, L., Goldberg, M., Frishberg, C.A., Boehme, R., and La Placa, S. (1985) Phys. Rev Lett., 55, 622-625.
16. Dovesi, R., Pisani, C., and Ricca, F. (1982) Phys. Rev B, 25, 3731-3739.
17. Chou, M.Y., Lam, P.K., and Cohen, M.L. (1983) Phys. Revs. B, 28, 4179-4185.
18. Huang, L., Massa, L., and Karle, J. (1999) Int. J. Quant. Chem., 73, 439-450.
19. Massa, L., Huang, L., and Karle, J. (1995) Int. J. Quant. Chem. Quant. Chem. Symp., 29, 371-384.
20. Huang, L., Massa, L., Karle, J., and Int, J. (1996) J. Quant. Chem. Quant. Chem. Symp., 30, 479-488.
21. Blessing, R. (ed.) (1990) Studies of Electron Distributions in Molecules and Crystals, Transactions of the American Crystallographic Association, vol. 26, Polycrystal Book Service, Dayton, OH.
22. Clinton, W.L., Galli, A.J., Henderson, G.A., Lamers, G.B., Massa, L.J., and Zarur, J. (1969) Phys. Rev., 177, 27-33.
23. Frishberg, C. (1986) Int. J. Quantum Chem., 30, 1-5.
24. Cohn, L., Frishberg, C., Lee, C., and Massa, L.J. (1985) Int. J. Quantum Chem. Symp., 19, 525-533.
25. Clinton, W.L. and Massa, L.J. (1972) Int. J. Quantum Chem., 6, 519-523.
26. Clinton, W.L. and Massa, L.J. (1972) Phys. Rev. Lett., 29, 1363-1366.
27. Clinton, W.L., Frishberg, C.A., Goldberg, M.J., Massa, L.J., and Oldfield, P.A. (1983) Int. J. Quantum. Chem. Symp., 17, 517-525.
28. Hammermesh, M. (1962) Group Theory, Addison-Wesley, Reading, MA.
29. Karle, I.L., Gibson, J.W., and Karle, J. (1970) J. Am. Chem. Soc., 92, 3755-3760.
30. Karle, I.L., Flippen-Anderson, J.L., Agarwalla, S., and Balaram, P. (1994) Biopolymers, 34, 721-735.
31. Frisch, M.J., Frisch, A., Foresman, J.B. et al. (1994) Gaussian 94, Gaussian, Inc., Pittsburgh, PA.
32. Huang, L., Massa, L., and Karle, J. (2005) Int. J. Quantum Chem., 103, 808-817.
33. Karle, I.L., Perozzo, M.A., Mishra, V.K., and Balaram, P. (1998) Proc. Natl. Acad. Sci. U.S.A., 95, 5501-5504.
34. Karle, I.L., Gopi, H.N., and Balaram, P. (2003) Proc. Natl. Acad. Sci. U.S.A., 100, 13946-13951.
35. Karle, I.L., Gopi, H.N., and Balaram, P. (2002) Proc. Natl. Acad. Sci. U.S.A., 99, 5160-5164.
36. Ravindra, G., Ranganayaki, R.S., Raghothama, S., Srinivasan, M., Gilardi, R.D., Karle, I.L., and Balaram, P. (2004) Chem. Biodiver., 1, 489-504.
37. Karle, I.L., Prasad, S., and Balaram, S. (2004) J. Peptide Res., 63, 175-180.
38. Gopi, H., Roy, R.S., Raghothama, S.R., and Karle, I. (2002) Helv. Chim. Acta, 85, 3313-3330.
39. Karle, I.L., Awasthi, S.K., and Balaram, P. (1996) Proc. Natl. Acad. Sci. U.S.A., 93, 8189-8193.
40. Karle, I., Gopi, H.N., and Balaram, P. (2001) Proc. Natl. Acad. Sci. U.S.A., 98, 3716-3719.
41. Karle, I.L., Das, C., and Balaram, P. (2000) Proc. Natl. Acad. Sci. U.S.A., 97, 3034-3037.
42. Vijayalakshmi, S., Rao, R.B., Karle, I.L., and Balaram, P. (2000) Biopolymers, 53, 84-98.
43. Huang, L., Massa, L., and Karle, J. (2006) Int. J. Quantum Chem., 106, 447-457.
44. Hehre, W.J., Stewart, R.F., and Pople, J.A. (1969) J. Chem. Phys., 51, 2657-2664.
45. Collins, J.B., Schleyer, P.v.R., Binkley, J.S., and Pople, J.A. (1976) J. Chem. Phys., 64, 5142-5151.
46. Binkley, J.S., Pople, J.A., and Hehre, W.J. (1980) J. Am. Chem. Soc., 102, 939-947.
47. Gordon, M.S., Binkley, J.S., Pople, J.A., Pietro, W.J., and Hehre, W.J. (1982) J. Am. Chem. Soc., 104, 2797-2803.
48. Pietro, W.J., Francl, M.M., Hehre, W.J., Defrees, D.J., Pople, J.A., and Binkley, J.S. (1982) J. Am. Chem. Soc., 104, 5039-5048.
49. Dobbs, K.D. and Hehre, W.J. (1986) J. Comput. Chem., 7, 359-378.
50. Dobbs, K.D. and Hehre, W.J. (1987) J. Comput. Chem., 8, 861-879.
51. Dobbs, K.D. and Hehre, W.J. (1987) J. Comput. Chem., 8, 880-893.
52. Schaefer, A., Horn, H., and Ahlrichs, R. (1992) J. Chem. Phys., 97, 2571-2577.
53. Schaefer, A., Huber, C., and Ahlrichs, R. (1994) J. Chem. Phys., 100, 5829-5835.
54. Ditchfield, R., Hehre, W.J., and Pople, J.A. (1971) J. Chem. Phys., 54, 724-728.
55. Hehre, W.J., Ditchfield, R., and Pople, J.A. (1972) J. Chem. Phys., 56, 2257-2261.
56. Hariharan, P.C. and Pople, J.A. (1974) Mol. Phys., 27, 209-214.
57. Gordon, M.S. (1980) Chem. Phys. Lett., 76, 163-168.
58. Hariharan, P.C. and Pople, J.A. (1973) Theo. Chim. Acta, 28, 213-222.
59. Blaudeau, J.P., McGrath, M.P., Curtiss, L.A., and Radom, L. (1997) J. Chem. Phys., 107, 5016-5021.
60. Francl, M.M., Pietro, W.J., Hehre, W.J., Binkley, J.S., DeFrees, D.J., Pople, J.A., and Gordon, M.S. (1982) J. Chem. Phys., 77, 3654-3665.
61. Binning, R.C. Jr. and Curtiss, L.A. (1990) J. Comput. Chem., 11, 1206-1216.
62. Rassolov, V.A., Pople, J.A., Ratner, M.A., and Windus, T.L. (1998) J. Chem. Phys., 109, 1223-1229.
63. Rassolov, V.A., Ratner, M.A., Pople, J.A., Redfern, P.C., and Curtiss, L.A. (2001) J. Comput. Chem., 22, 976-984.
64. Dunning, T.H. Jr. and Hay, P.J. (1976) Modern Theoretical Chemistry III, vol. 3 (ed. H.F. Schaefer), Plenum, New York, pp. 1-28.
65. Petersson, G.A. and Al-Laham, M.A. (1991) J. Chem. Phys., 94, 6081-6090.
66. Petersson, G.A., Bennett, A., Tensfeldt, T.G., Al-Laham, M.A., Shirley, W.A., and Mantzaris, J. (1988) J. Chem. Phys., 89, 2193-2218.
67. Woon, D.E. and Dunning, T.H. Jr. (1993) J. Chem. Phys., 98, 1358-1371.
68. Kendall, R.A., Dunning, T.H. Jr., and Harrison, R.J. (1992) J. Chem. Phys., 96, 6796-6806.
69. Dunning, T.H. Jr. (1989) J. Chem. Phys., 90, 1007-1023.
70. Peterson, K.A., Woon, D.E., and Dunning, T.H. Jr. (1994) J. Chem. Phys., 100, 7410-7415.
71. Wilson, A., Mourik, T.v., and Dunning, T.H. Jr. (1997) J. Mol. Struct. (Theochem), 388, 339-350.
72. Dewar, M. and Thiel, W. (1977) J. Am. Chem. Soc., 99, 4499-4450.
73. James, J.P. (2001) A major enhancement in computational chemistry accuracy: MOPAC 2002, Stewart Computational Chemistry, Fujitsu Computational Chemistry Seminars.
74. Roothan, C.C.J. (1951) Rev. Mod. Phys., 23, 69-89.
75. Kohn, W. and Sham, L.J. (1965) Phys. Rev., 140, A1133-A1138.
76. Pople, J.A., Seeger, R., and Krishnan, R. (1977) Int.J. Quantum Chem. Symp., 11, 149-163.
77. Moller, C. and Plesset, M.S. (1934) Phys. Rev., 46, 618-622.
78. Bartlett, R.J. and Purvis, G.D. (1978) Int.J. Quantum Chem., 14, 561-581.
79. Sanger, F. and Tuppy, H. (1951) Biochem. J., 49, 463-481.
80. Hodgkin, D. (1970) Verh. Schweiz. Naturforsch. Ges., 150, 93-101.
81. Gursky, O., Badger, J., Li, Y, and Caspar, D. (1992) Biophys.J., 63, 1210-1220.
82. Huang, L., Massa, L., and Karle, J. (2005) Proc. Natl. Acad. Sci. U.S.A., 102, 12690-12693.
83. Wahl, M.C., Rao, S.T., and Sundaralingam, M. (1996) Biophys.J., 70, 2857-2866.
84. Leonard, G.A., Hambley, T.W., and Mcauleyhecht, K. (1993) Acta Crystallogr., Sect. D: Biol. Crystallogr, 49, 458-467.
85. Soler-Lopez, M., Malinina, L., Tereshko, V., Zarytova, V., and Subirana, J.A. (2002) J. Biol. Inorg. Chem., 7, 533-538.
86. Vargason, J.M., Henderson, K., and Ho, P.S. (2001) Proc. Natl. Acad. Sci. U.S.A., 98, 7265-7270.
87. Tari, L.W. and Secco, A.S. (1995) Nucleic Acids Res., 23, 2065-2073.
88. Valls, N., Uson, I., and Subiriana, C.J.A. (2004) J.Am. Chem. Soc., 126, 7812-7816.
89. Qiu, H., Dewan, J.C., and Seeman, N.C. (1997) J. Mol. Biol., 267, 881-898.
90. Rozenberg, H., Rabinovich, D., Frolow, F., and Hegde, R.S. (1998) Proc. Natl. Acad. Sci. U.S.A., 95, 15194-15199.
91. Nunn, C.M. and Neidle, S.J. (1995) Med. Chem., 38, 2317-2325.
92. Egli, M., Williams, L.D., Gao, Q., and Rich, A. (1991) Biochemistry, 30, 11388-11402.
93. Shakked, Z., Rabinovich, D., Kennard, O., Cruse, W.B., Salisbury, S.A., and Viswamitra, M.A. (1983) J. Mol. Biol., 166, 183-201.
94. Huang, L., Massa, L., and Karle, J. (2005) Biochemistry, 44, 16747-16752.
95. Basavappa, R. and Sigler, P.B. (1991) EMBOJ, 10, 3105-3111.
96. Huang, L., Massa, L., and Karle, J. (2006) Proc. Natl. Acad. Sci. U.S.A., 103, 1233-1237.
97. Russell, R., Murray, J., Lentzen, G., Haddad, J., and Mobashery, S. (2003) J. Am. Chem. Soc., 125, 3410-3411.
98. Huang, L., Massa, L., and Karle, J. (2007) Proc. Natl. Acad. Sci. U.S.A., 104, 4261-4266.
99. Delacoux, F., Fichard, A., Geourjon, C., Garrone, R., and Ruggiero, F. (1998) J. Biol. Chem., 273, 15069.
100. Huang, L., Massa, L., and Karle, J. (2007) J. Chem. Theory Comput., 3, 1337-1341.
101. Huang, L., Massa, L., and Karle, J. (2008) Proc. Natl. Acad. Sci. U.S.A., 105, 1849-1854.
102. Frisch, M.J., Trucks, G.W., Schlegel, H.B. et al. (2003) Gaussian 03, Gaussian, Inc., Pittsburgh, PA.
103. Zhang, X., Green, T.J., Tsao, J., Qiu, S., and Luo, M. (2008) J. Virol., 82, 674-682.
104. Zhang, X., Green, T.J., Tsao, J., Qiu, S., and Luo, M. (2007) HyperChem 8.0.3 for Windows, Hypercube, Inc, Gainesville, FL.
105. Huang, L., Massa, L., and Karle, J. (2009) Proc. Natl. Acad. Sci. U.S.A., 106, 1731-1736.
106. Stillinger, F.H. et al. (1995) Mathematical Challenges from Theoretical/Computational Chemistry, National Academy Press, Washington.
107. Lipscomb, W.N. (1972) Trans. Am. Cryst. Assoc., 8, 79-92.
108. Provenzano, A. (2009) Oncol. Times, 31, 3-4.