Atomic properties of selected biomolecules: Quantum topological atom types of hydrogen, oxygen, nitrogen and sulfur occurring in natural amino acids and their derivatives

Chemistry - A European Journal

Volumn 9, Issue 5, 2003, Pages 1207-1216

  Popelier, Paul L A ^a   Aicken, Fiòna M ^a  

^a UNIVERSITY OF MANCHESTER   (United Kingdom)

Author keywords

Amino acids; Density functional calculations; Electron density; Quantum chemical topology

Indexed keywords

CARRIER CONCENTRATION; CONFORMATIONS; DERIVATIVES; KINETIC ENERGY;

QUANTUM CHEMICAL TOPOLOGY (QCT);

AMINO ACIDS;

AMINO ACID; HYDROGEN; NITROGEN; OXYGEN; SULFUR;

ARTICLE; CHEMICAL STRUCTURE; CLUSTER ANALYSIS; ELECTRON; KINETICS; QUANTUM CHEMISTRY; QUANTUM MECHANICS;

AMINO ACIDS; HYDROGEN; MODELS, MOLECULAR; NITROGEN; OXYGEN; SULFUR;

EID: 0037416705     PISSN: 09476539     EISSN: None     Source Type: Journal    
DOI: 10.1002/chem.200390138     Document Type: Article

References (56)

1. R. F. W. Bader, Encyclopedia of Computational Chemistry, Vol. 1 (Ed.: P. von R. Schleyer), Wiley, Chichester, 1998, p. 64.
2. R. F. W. Bader, Atoms in Molecules. A Quantum Theory, Oxford University Press, Oxford (UK), 1990.
3. P. L. A. Popelier, Atoms in Molecules. An Introduction, Pearson Education, London (UK), 2000.
4. R. F. W. Bader, T. T. Nguyen-Dang, Adv. Quantum Chem. 1981, 14, 63-124.
5. R. F. W. Bader, Pure Appl. Chem. 1988, 60, 145-155.
6. R. F. W. Bader, P. L. A. Popelier, Int. J. Quantum Chem. 1993, 45, 189-207.
7. P. L. A. Popelier, F. M. Aicken, J. Am. Chem. Soc. 2003, 125, in press.
8. C. F. Matta, R. F. W. Bader, Proteins: Struct. Funct. Genet. 2000, 40, 310-329.
9. C. F. Matta, R. F. W. Bader, Proteins: Struct. Funct. Genet. 2002, 48, 519-538.
10. A. M. Graña, R. A. Mosquera, J. Chem. Phys. 2000, 113, 1492-1500.
11. A. Vila, R. A. Mosquera, J. Chem. Phys. 2001, 115, 1264-1273.
12. M. Mandado, A. M. Graña, R. A. Mosquera, J. Mol. Struct. Theochem. 2002, 584, 221-234.
13. J. L. Lopez, M. Mandado, A. M. Graña, R. A. Mosquera, Int. J. Quantum Chem. 2002, 86, 190-198.
14. R. F. W. Bader, D. Bayles, J. Phys. Chem. A 2000, 104, 5579-5589.
15. C. M. Breneman, T. R. Thompson, M. Rhem, M. Dung, Comput. Chem. 1995, 19, 161-179.
16. S. L. Price, A. J. Stone, J. Chem. Soc. Faraday Trans. 1992, 88, 1755-1763.
17. C. Chipot, J. G. Angyan, B. Maigret, H. A. Scheraga, J. Phys. Chem. 1993, 97, 9788-9796.
18. C. H. Faerman, S. L. Price, J. Am. Chem. Soc. 1990, 112, 4915-4926.
19. P. D. Walker, P. G. Mezey, J. Am. Chem. Soc. 1994, 116, 12022-12032.
20. P. L. A. Popelier, Mol. Phys. 1996, 87, 1169-1187.
21. P. L. A. Popelier, Comput. Phys. Commun. 1998, 108, 180-190.
22. F. M. Aicken, P. L. A. Popelier, Can. J. Chem. 2000, 78, 415-426.
23. P. L. A. Popelier, F. M. Aicken, S. E. O'Brien, in "Chemical Modelling: Applications and Theory", Vol. 1 (Ed.: A. Hinchliffe), Royal Society of Chemistry Specialist, Periodical Report, Chapter 3, pp. 143-198, 2000.
24. P. L. A. Popelier, P. J. Smith, in "Chemical Modelling: Applications and Theory", Vol. 2 (Ed.: A. Hinchliffe), Royal Society of Chemistry Specialist Periodical Report, Chapter 8, pp. 391-448, 2002.
25. B. Silvi, A. Savin, Nature 1994, 371, 683-686.
26. A. D. Becke, K. E. Edgecombe, J. Chem. Phys. 1990, 92. 5397-5403.
27. R. J. Gillespie, P. L. A. Popelier, Chemical Bonding and Molecular Geometry from Lewis to Electron Densities, Oxford University Press, New York, USA, 2001.
28. R. N. Zare, Angular Momentum, Wiley Interscience, 1988.
29. D. S. Kosov, P. L. A. Popelier, J. Chem. Phys. 2000, 113, 3969-3974.
30. D. S. Kosov, P. L. A. Popelier, J. Phys. Chem. A 2000, 104, 7339-7345.
31. P. L. A. Popelier, L. Joubert, D. S. Kosov, J. Phys. Chem. A 2001, 105, 8254-8261.
32. L. Joubert, P. L. A. Popelier, Phys. Chem. Chem. Phys. 2002, 4, 4353-4359.
33. P. L. A. Popelier, M. Devereux, unpublished results.
34. R. F. W. Bader, M. T. Carroll, J. R. Cheeseman, C. Chang, J. Am. Chem. Soc. 1987, 109, 7968-7979.
35. B. S. Everitt, Cluster Analysis, 3rd ed., Edward Arnold, London (GB), 1993.
36. M. R. Anderberg, Cluster Analysis for Applications, Academic Press, New York (USA), 1973.
37. L. Livingstone, Data Analysis for Chemists, 1st, ed., Oxford University Press, Oxford (UK), 1995.
38. D. Wishart, ClustanGraphics Primer "A Guide to Cluster Analysis", Clustan, Edinburgh (UK), 1999.
39. G. Schaftenaar, J. H. Noordik, J. Comput. Aided Mol. Design 2000, 14, 123-134.
40. GAUSSIAN94, M. J. Frisch, G. W. Trucks, H. B. Schlegel, P. M. W. Gill, B. G. Johnson, M. A. Robb, J. R. Cheeseman, T. Keith, G. A. Petersson, J. A. Montgomery, K. Raghavachari, M. A. Al-Laham, V. G. Zakrzewski, J. V. Ortiz, J. B. Foresman, J. Cioslowski, B. B. Stefanov, A. Nanayakkara, M. Challacombe, C. Y. Peng, P. Y. Ayala, W. Chen. M. W. Wong, J. L. Andres, E. S. Replogle, R. Gomperts, R. L. Martin, D. J. Fox, J. S. Binkley, D. J. Defrees, J. Baker, J. P. Stewart, M. Head-Gordon, C. Gonzalez, and J. A. Pople, Gaussian, Inc., Pittsburgh PA. 1995.
41. C. Lee, W. Yang, R. G. Parr, Phys. Rev. 1988, B37, 785-789.
42. A. D. Becke, J. Chem. Phys. 1993, 98, 5648-5652.
43. P. C. Hariharan, J. A. Pople, Theor. Chim. Acta 1973, 28, 213.
44. J. B. Foresman, A. Frisch, Exploring Chemistry with Electronic Structure Methods, 2nd ed., Gaussian, Pittsburgh, USA, 1996.
45. S. E. O'Brien, P. L. A. Popelier, Can. J. Chem. 1999, 77, 28-36.
46. F. M. Aicken, UMIST (Manchester), 2000.
47. MORPHY98, a program written by P. L. A. Popelier with a contribution from R. G. A. Bone, UMIST, Manchester (UK), 1998, see http://morphy.ch.umist.ac.uk/1998.
48. P. L. A. Popelier, Mol. Phys. 1996, 87, 1169-1187.
49. D. Wishart, Edinburgh, Scotland (UK), 1999.
50. SPSS Inc., version 10.0.7. Chicago (USA), 2000, http://www.spss.com.
51. U. Koch, P. L. A. Popelier, J. Phys. Chem. 1995, 99, 9747-9754.
52. A. Korolkovas, Essentials of Molecular Pharmacology: Background for Drug Design, Wiley, New York, 1970.
53. A. Burger, Medicinal Chemistry, 3rd ed., Wiley, New York, 1970.
54. L. R. Murphy, T. L. Meek, A. L. Allred, L. C. Allen, J. Phys. Chem. A 2000, 104, 5867-5871, claim that this is a misreading of Pauling's definition, as if electronegativity is an intrinsic, in situ, molecular property.
55. This coefficient is defined as equation presented where x and y are atomic properties, and x̄ and ȳ their respective means. The sum runs over the number of clusters (i.e., atom types). The value of r lies within [0,1] M. R. Spiegel, Theory and Problems of Statistics, McGraw-Hill, New York (USA), 1972.
56. T. Slee, A. Larouche, R. F. W. Bader, J. Phys. Chem. 1988, 92, 6219-6227.