Ab initio studies on the tri- and diphosphate fragments of adenosine triphosphate

Biophysical Chemistry

Volumn 119, Issue 2, 2006, Pages 127-136

  Hansia, Priti ^a   Guruprasad, Nandini ^a   Vishveshwara, Saraswathi ^a  

^a INDIAN INSTITUTE OF SCIENCE   (India)

Author keywords

"High energy" of pyrophosphates; Delocalized molecular orbitals; Frequencies of polyphosphates; Hydrolysis of P O P linkage

Indexed keywords

ADENOSINE TRIPHOSPHATE; METHYL DIPHOSPHATE; METHYL TRIPHOSPHATE; PYROPHOSPHORIC ACID DERIVATIVE; UNCLASSIFIED DRUG;

AB INITIO CALCULATION; ARTICLE; CHEMICAL MODEL; GEOMETRY; HIGH ENERGY PHOSPHATE; HYDROLYSIS; PRIORITY JOURNAL; PROTON TRANSPORT; QUANTUM CHEMISTRY; VIBRATION;

ADENOSINE TRIPHOSPHATE; HYDROLYSIS; MODELS, CHEMICAL; PHOSPHATES; QUANTUM THEORY; SENSITIVITY AND SPECIFICITY; SPECTROSCOPY, FOURIER TRANSFORM INFRARED; THERMODYNAMICS; VIBRATION;

EID: 30844433744     PISSN: 03014622     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.bpc.2005.07.011     Document Type: Article

References (31)

1. M. Baltscheffsky, and P. Nyren L. Ernster Bioenergetics 1984 Elsvier Amsterdam
2. M. Baltscheffsky, and H. Baltscheffsky L. Ernster Molecular Mechanism in Bioenergetics 1992 Elsvier Amsterdam
3. Y. Sugawara, N. Kamiya, H. Isawaki, T. Ito, and Y. Satow Humidity-controlled reversible structure transition of disodium adenosine 5′-triphosphate between dihydrate and trihydrate in a single crystal state J. Am. Chem. Soc. 113 1991 5440 5445
4. F. Lipmann Metabolic generation and utilization of phosphate bond energy Adv. Enzymol. 1 1941 99 162
5. J.C. Sowden, and H.O.L. Fischer The chemistry and metabolism of the compounds of phosphorus Ann. Rev. Biochem. 11 1942 203 216
6. H.M. Kalckar The nature of energetic coupling in biological syntheses Chem. Rev. 28 1941 71 178
7. P. Oesper Sources of the high energy content in energy-rich phosphates Arch. Biochem. Biophys. 27 1950 255 270
8. T.L. Hill, and M.F. Morales On "High Energy Phosphate Bonds" of biochemical interest J. Am. Chem. Soc. 73 1951 1656 1660
9. K. Laki, M. Seel, and J. Ladik Conformation of triphosphate and lysine-triphosphate-arginine complex J. Theor. Biol. 67 1977 489 498
10. W. Saenger, B.S. Reddy, K. Mühlegger, and G. Weimann X-ray study of the lithium complex of NAD Nature 267 1977 225 229
11. D.M. Hayes, G.L. Kenyon, and P.A. Kollman Theoretical calculations of the hydrolysis energies of some "High-Energy" molecules: 2. A survey of some biologically important hydrolytic reactions J. Am. Chem. Soc. 100 1978 4331 4340
12. M. O'keeffe, B. Domenges, and G.V. Gibbs Ab initio molecular orbital calculations on phosphates: comparison with silicates J. Phys. Chem. 89 1985 2304 2309
13. 2n - 1 for n = 1 to 4 J. Am. Chem. Soc. 110 1988 79 86
14. H. Saint-Martin, I. Ortega-Blake, A. Leś, and L. Adamowicz Ab initio calculations of the pyrophosphate hydrolysis reaction Biochim. Biophys. Acta. 1080 1991 205 214
15. B. Ma, C. Meredith, and H.F. Schaefer III Pyrophosphate structures and reactions: evaluation of electrostatic effects on the pyrophosphates with and without alkali cations J. Phys. Chem. 98 1994 8216 8223
16. M.E. Colvin, E. Evleth, and Y. Akacem Quantum chemical studies of pyrophosphate hydrolysis J. Am. Chem. Soc. 117 1995 4357 4362
17. M. Hwang, P. Chu, J. Chen, and I. Chao Conformational analysis of three pyrophosphate model species: diphosphate, methyl diphosphate and triphosphate J. Comput. Chem. 20 1999 1702 1715
18. C. Allin, M.R. Ahmadian, A. Wittinghofer, and K. Gerwert Monitoring the GAP analyzed H-Ras GTPase reaction at atomic resolution in real time Proc. Natl. Acad. Sci. U. S. A. 98 2001 7754 7759
19. A. Omoike, J. Chorover, K.D. Kwon, and J.D. Kubicki Adhesion of bacterial exopolymers to α-FeOOH: inner-sphere complexation of phosphodiester groups Langmuir 20 2004 11108 11114
20. P.C. Hariharan, and J.A. Pople The influence of polarization functions on molecular orbital hydrogenation energies Theor. Chim. Acta 28 1973 213 222
21. G.A. Petersson, A. Bennett, T.G. Tensfeldt, M.A. Al-Laham, W.A. Shirley, and J. Mantzaris A complete basis set model chemistry: I. The total energies of closed-shell atoms and hydrides of the first-row elements J. Chem. Phys. 89 1988 2193 2218
22. Gaussian 03, Revision C.02, M.J. Frisch, G.W. Trucks, H.B. Schlegel, G.E. Scuseria, M.A. Robb, J.R. Cheeseman, J.A. Montgomery Jr., T. Vreven, K.N. Kudin, J.C. Burant, J.M. Millam, S.S. Iyengar, J. Tomasi, V. Barone, B. Mennucci, M. Cossi, G. Scalmani, N. Rega, G. Petersson, H. Nakatsuji, M. Hada, M. Ehara, K. Toyota, R. Fukuda, J. Hasegawa, M. Ishida, T. Nakajima, Y. Honda, O. Kitao, H. Nakai, M. Klene, X. Li, J.E. Knox, H.P. Hratchian, J.B. Cross, V. Bakken, C. Adamo, J. Jaramillo, R. Gomperts, R.E. Stratmann, O. Yazyev, A.J. Austin, R. Cammi, C. Pomelli, J.W. Ochterski, P.Y. Ayala, K. Morokuma, G.A. Voth, P. Salvador, J.J. Dannenberg, V.G. Zakrzewski, S. Dapprich, A.D. Daniels, M.C. Strain, O. Farkas, D.K. Malick, A.D. Rabuck, K. Raghavachari, J.B. Foresman, J.V. Ortiz, Q. Cui, A.G. Baboul, S. Clifford, J. Cioslowski, B.B. Stefanov, G. Liu, A. Liashenko, P. Piskorz, I. Komaromi, R.L. Martin, D.J. Fox, T. Keith, M.A. Al-Laham, C.Y. Peng, A. Nanayakkara, M. Challacombe, P.M.W. Gill, B. Johnson, W. Chen, M.W. Wong, C. Gonzalez, J.A. Pople, Gaussian, Inc., Wallingford CT, 2004.
23. A.D. Becke Density functional thermochemistry: III. The role of exact exchange J. Chem. Phys. 98 1993 5648 5652
24. M. Head-Gordon, J.A. Pople, and M.J. Frisch MP2 energy evaluation by direct methods Chem. Phys. Lett. 153 1988 503 506
25. G. Schaftenaar, and J.H. Noordik Molden: a pre- and post-processing program for molecular and electronic structures J. Comput. Aided. Mol. Des. 14 2000 123 134
26. G.A. Jaffrey, J.A. Pople, J.S. Binkley, and S. Vishveshwara Application of ab initio molecular orbital calculations to the structural moieties of carbohydrates. 3 J. Am. Chem. Soc. 100 1978 373 379
27. D.G. Gorenstein Conformation and dynamics of DNA and protein-DNA complexes by 31P NMR Chem. Rev. 94 1994 1315 1338
28. D.G. Gorenstein, J.B. Findlay, B.A. Luxon, and D. Kar Stereoelectronic control in carbon-oxygen and phosphorus-oxygen bond breaking processes. Ab initio calculations and speculations on the mechanism of action of ribonuclease A, staphylococcal nuclease, and lysozyme J. Am. Chem. Soc. 99 1977 3473 3479
29. W. Förner, and H.M. Badawi Ab initio calculations of vibrational frequencies, potential functions of internal rotations and vibrational infrared and Raman spectra for 3,3,3-trifluoropropanal J. Mol. Model 6 2000 99 111
30. W. Li, Q. Wu, Q.Y. Ye, M. Luo, D. Shi, and J. Hu Density functional and ab initio studies of the molecular structure and vibrational spectra of novel O,O'-diethyl-N-(alpha-aryloxyacetyl)thiophosphoryl hydrazine herbicides J. Raman Spectrosc. 34 2003 892 901
31. A.P. Scott, and L. Radom Harmonic vibrational frequencies: an evaluation of Hartree-Fock, Moller-Plesset, quadratic configuration interaction, density functional theory, and semiempirical scale factors J. Phys. Chem. 100 1996 16502 16513