Theory on the molecular characteristic contour (II) - Molecular intrinsic characteristic contours of several typical organic molecules

Science in China, Series B: Chemistry

Volumn 48, Issue 2, 2005, Pages 89-100

  Gong, Lidong ^a   Zhao, Dongxia ^a   Yang, Zhongzhi ^a  

^a LIAONING NORMAL UNIVERSITY   (China)

Author keywords

Ab initio method; Electron density; Molecular intrinsic characteristic contour (MICC); Organic molecules; Potential acting on an electron in a molecule

Indexed keywords

CALCULATIONS; CONTOUR MEASUREMENT; ELECTRON DENSITY MEASUREMENT; METHANE; METHANOL;

AB INITIO METHOD; ATOMIC SIZE; ELECTRON DENSITY DISTRIBUTION; FORMIC ACID; MOLECULAR BOUNDARY; MOLECULAR CHEMICAL PROPERTIES; MOLECULAR INTRINSIC CHARACTERISTIC CONTOUR; ORGANIC MOLECULES;

MOLECULAR STRUCTURE;

EID: 19044364800     PISSN: 10069291     EISSN: None     Source Type: Journal    
DOI: 10.1360/04yb0127     Document Type: Article

References (46)

1. Mezey, P. G., Shape in Chemistry: An Introduction to Molecular Shape and Topology, New York: VCH, 1993.
2. Meyer, A. Y., The size of molecules, Chem. Soc. Rev., 1986, 15: 449-474.
3. Connolly, M. L., Solvent-accessible surface of proteins and nucleic acids, Science, 1983, 221: 709-713.
4. Mebane, R. C., Schanley, S. A., Rybolt, T. R. et al., The correlation of physical properties of organic molecules with computed molecular surface areas, J. Chem. Educ., 1999, 76: 688-693.
5. Jackson, R. M., Sternberg, M. J. E., Protein surface area defined, Nature, 1993, 366: 638.
6. Chothia, C., Structural invariants in protein folding, Nature, 1975, 254: 305-308.
7. Chothia, C., Janin, J., Principles of protein-protein recognition, Nature, 1975, 256: 705-708.
8. Leach, A. R., Molecular Modelling: Principles and Applications, 2nd edition, Harlow: Pearson Education Limited, 2001.
9. Bash, P. A., Pattabiraman, N., Huang, C. et al., van der Waals surface in molecular modeling: implementation with real-time computer graphics, Science, 1983, 222: 1325-1327.
10. Avnir, D., Farin, D., Molecular fractal surfaces, Nature, 1984, 308: 261-263.
11. Lee, B., Richards, F. M., The interpretation of protein structures: estimation of static accessibility, J. Mol. Biol., 1971, 55: 379-400.
12. Richards, F. M., Areas, volumes, packing and protein structure, Annu. Rev. Biophys. Bioeng., 1977, 6: 151-176.
13. Greer, J., Bush, B. L., Macromolecular shape and surface maps by solvent exclusion, Proc. Natl. Acad. Sci. USA, 1978, 75: 303-307.
14. Paci, E., Velikson, B., On the volume of macromolecules, Biopoly., 1997, 41: 785-797.
15. Randic, M., Krilov, G., On characterization of molecular surfaces, Int. I. Quantum Chem., 1997, 65: 1065-1076.
16. Laug, F., Borouchaki, H., Generation of finite element meshes on molecular surfaces, Int. I. Quantum Chem., 2003, 93: 131-138.
17. Lee, M. S., Feig, M., Salsbury, F. R. JR. et al., New analytic approximation to the standard molecular volume definition and its application to generalized Born calculations, J. Comput. Chem., 2003, 24: 1348-1356.
18. Pauling, L., The Nature of the Chemical Bond, 3rd edition, Ithaca, New York: Cornell University Press, 1960.
19. Bondi, A., van der Waals volumes and radii, J. Phys. Chem., 1964, 68: 441-451.
20. Gavezzotti, A., The calculation of molecular volumes and the use of volume analysis in the investigation of structured media and of solid-state organic reactivity, J. Am. Chem. Soc., 1983, 105: 5220-5225.
21. Boyd, R. J., The relative sizes of atoms, J. Phys., 1977, B10: 2283-2291.
22. Bader, R. F. W., Atoms in molecules-A Quantum Theory, New York: Oxford University Press, 1990.
23. Rellick, L. M., Becktel, W. J., Comparison of van der Waals and semiempirical calculations of the molecular volumes of small molecules and proteins, Biopoly., 1997, 42: 191-202.
24. Politzer, P., Murray, J. S., Concha, M. C., The complementary roles of molecular surface electrostatic potentials and average local ionization energies with respect to electrophilic processes, Int. J. Quantum Chem., 2002, 88: 19-27.
25. Murray, J. S., Sen, K. eds., Molecular Electrostatic Potentials: Concepts and Applications, Amsterdam: Elsevier, 1996.
26. Smith, B. J., Hall, N. E., Atomic radii: incorporation of solvation effects, J. Comput. Chem., 1998, 19: 1482-1493.
27. Stefanovich, E. V., Tiwong, T. N., Optimized atomic radii for quantum dielectric continuum solvation models, Chem. Phys. Lett, 1995, 244: 65-74.
28. Yang, Z. Z., Niu, S. Y, A sort of radius to describe atomic size, Chin. Sci. Bull, (in Chinese), 1991, 36(2): 159.
29. Niu, S. Y, Yang, Z. Z., A new scale of atomic size-atomic boundary radius, Acta Chim. Sinica (in Chinese), 1994, 52: 551-555.
30. Yang, Z. Z., Davidson, E. R., Evaluation of a characteristic atomic radius by an ab initio method, Int. J. Quantum Chem, 1997, 62: 47-53.
31. Yang, Z. Z., Tang, S. Q., Niu, S. Y, Boundary radii of cations, Acta Chim. Sinica (in Chinese), 1996, 54: 846-852.
32. Yang, Z. Z., Li, G. H., Zhao, D. X. et al., Theoretical study on characteristic ionic radii, Chin. Sci. Bull., 1998, 43(17): 1452-1455.
33. Ayers, P. W., Strategies for computing chemical reactivity indices, Theor. Chem. Ace., 2001, 106: 271-279.
34. Yang, Z. Z., Zhao, D. X., A characteristic molecular contour evaluated by a theoretical method, Chem. Phys. Lett., 1998, 292: 387-393.
35. Zhao, D. X., Yang, Z. Z., Theory on the molecular characteristic contour (I)-A new approach to defining molecular intrinsic characteristic contour, Sci. in China, Ser. B, 1999, 42(4): 391-399.
36. 2 molecule in the ground and first excited states calculated by an ab initio method, J. Mol. Struct. (THEOCHEM), 2002, 579: 73-84.
37. Yang, Z. Z., Zhao, D. X., Wu, Y, Polarization and bonding of the intrinsic characteristic contours of hydrogen and fluorine atoms of forming a hydrogen fluoride molecule based on an ab initio study, J. Chem. Phys., 2004, 121(8): 3452-3462.
38. Gong, L. D., Zhao, D. X., Yang, Z. Z., The molecular intrinsic characteristic contours (MICCs) of some small organic molecules, J. Mol. Struct. (THEOCHEM), 2003, 636: 57-70.
39. Gong, L. D., Zhao, D. X., Yang, Z. Z., Molecular intrinsic characteristic contours of small organic molecules containing oxygen atom, Chin. Sci. Bull., 2003, 48(18): 1943-1946.
40. Zhao, D. X., Gong, L. D., Yang, Z. Z., Theoretical study of the potential felt by a single electron within a molecule, Chem. J. Chin. Univ. (in Chinese), 2001, 22: 1893-1895.
41. Zhao, D. X., Gong, L. D., Yang, Z. Z., Exploration of the potential acting on an electron within diatomic molecules, Chin. Sci. Bull., 2001, 47(8): 635-640.
42. Yang, Z. Z., Liu, S. B., Wang, Y. A., Uniqueness and asymptotic behavior of the local kinetic energy, Chem. Phys. Lett., 1996, 258: 30-36.
43. Ghosh, S. K., Berkowitz, M., Parr, R. G., Transcription of ground-state density functional theory into a local thermodynamics. 5, Proc. Natl. Acad. Sci. USA, 1984, 81: 8028-8031.
44. Ayers, P. W., Parr, R. G, Nagy, A., Local kinetic energy and local temperature in the density-functional theory of electronic structure, Int. J. Quantum Chem., 2002, 90: 309-326.
45. Davidson, E. R., MELD Program Description in MOTECC, New York: ESCOM, 1990, 553-592.
46. Lide, D. R., Frederikse, H. P. R., Eds., CRC Handbook of Chemistry and Physics, 76th edition, Boca Raton: CRC Press, 1995-1996.