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Theory on the molecular characteristic contou(II)

Molecular intrinsic characteristic contours of several typical organic molecules

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Abstract

The molecular intrinsic characteristic contour (MlCC) is defined based on the classical turning point of electron movement in a molecule. Three typical organic molecules, i.e. methane, methanol and formic acid, were employed as examples for detailed introduction of our method. Investigations on the cross-sections of MlCC provide important information about atomic size changing in the process of forming molecules. The electron density distributions on the MlCCs of these molecules were calculated and shown for the first time. Results showed that the electron density distribution on the MlCC correlates closely with molecular chemical properties, and it provides a new insight into molecular boundary.

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References

  1. Mezey, P. G., Shape in Chemistry: An Introduction to Molecular Shape and Topology, New York: VCH, 1993.

    Google Scholar 

  2. Meyer, A. Y., The size of molecules, Chem. Soc. Rev., 1986, 15: 449–474.

    Article  CAS  Google Scholar 

  3. Connolly, M. L., Solvent-accessible surface of proteins and nucleic acids, Science, 1983,221: 709–713.

    Article  CAS  Google Scholar 

  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.

    Article  CAS  Google Scholar 

  5. Jackson, R. M., Sternberg, M. J. E., Protein surface area defined, Nature, 1993, 366: 638.

    Article  Google Scholar 

  6. Chothia, C., Structural invariants in protein folding, Nature, 1975, 254: 305–308.

    Article  Google Scholar 

  7. Chothia, C., Janin, J., Principles of protein-protein recognition, Nature, 1975,256: 705–708.

    Article  CAS  Google Scholar 

  8. Leach, A. R., Molecular Modelling: Principles and Applications, 2nd edition, Harlow: Pearson Education Limited, 2001.

    Google Scholar 

  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.

    Article  CAS  Google Scholar 

  10. Avnir, D., Farin, D., Molecular fractal surfaces, Nature, 1984, 308: 261–263.

    Article  CAS  Google Scholar 

  11. Lee, B., Richards, F. M., The interpretation of protein structures: estimation of static accessibility, J. Mol. Biol., 1971, 55: 379–400.

    Article  CAS  Google Scholar 

  12. Richards, F. M., Areas, volumes, packing and protein structure, Annu. Rev. Biophys. Bioeng., 1977, 6: 151–176.

    Article  CAS  Google Scholar 

  13. Greer, J., Bush, B. L., Macromolecular shape and surface maps by solvent exclusion, Proc. Natl. Acad. Sci. USA, 1978, 75: 303–307.

    Article  CAS  Google Scholar 

  14. Paci, E., Velikson, B., On the volume of macromolecules, Biopoly., 1997,41: 785–797.

    Article  CAS  Google Scholar 

  15. Randic, M., Krilov, G., On characterization of molecular surfaces, Int. J. Quantum Chem., 1997,65: 1065–1076.

    Article  CAS  Google Scholar 

  16. Laug, F., Borouchaki, H., Generation of finite element meshes on molecular surfaces, Int. J. Quantum Chem., 2003, 93: 131–138.

    Article  CAS  Google Scholar 

  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.

    Article  CAS  Google Scholar 

  18. Pauling, L., The Nature of the Chemical Bond, 3rd edition, Ithaca, New York: Cornell University Press, 1960.

    Google Scholar 

  19. Bondi, A., van der Waals volumes and radii, J. Phys. Chem., 1964, 68:441–451.

    Article  CAS  Google Scholar 

  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.

    Article  CAS  Google Scholar 

  21. Boyd, R. J., The relative sizes of atoms, J. Phys., 1977, B10: 2283 -2291.

    Google Scholar 

  22. Bader, R. F. W., Atoms in molecules—A Quantum Theory, New York: Oxford University Press, 1990.

    Google Scholar 

  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.

    Article  CAS  Google Scholar 

  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.

    Article  CAS  Google Scholar 

  25. Murray, J. S., Sen, K. eds., Molecular Electrostatic Potentials: Concepts and Applications, Amsterdam: Elesevier, 1996.

    Google Scholar 

  26. Smith, B. J., Hall, N. E., Atomic radii: incorporation of solvation effects, J. Comput. Chem., 1998, 19: 1482–1493.

    Article  CAS  Google Scholar 

  27. Stefanovich, E. V., Tiwong, T. N., Optimized atomic radii for quantum dielectric continuum solvation models, Chem. Phys. Lett., 1995,244: 65–74.

    Article  CAS  Google Scholar 

  28. Yang, Z. Z., Niu, S. Y., A sort of radius to describe atomic size, Chin. Sci. Bull. (in Chinese), 1991, 36(2): 159.

    Google Scholar 

  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.

    CAS  Google Scholar 

  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.

    Article  CAS  Google Scholar 

  31. Yang, Z. Z., Tang, S. Q., Niu, S. Y., Boundary radii of cations, Acta Chim. Sinica (in Chinese), 1996, 54: 846–852.

    CAS  Google Scholar 

  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.

    Article  CAS  Google Scholar 

  33. Ayers, P. W., Strategies for computing chemical reactivity indices, Theor. Chem. Acc., 2001, 106: 271–279.

    Article  CAS  Google Scholar 

  34. Yang, Z. Z., Zhao, D. X., A characteristic molecular contour evaluated by a theoretical method, Chem. Phys. Lett., 1998, 292: 387–393.

    Article  CAS  Google Scholar 

  35. Zhao, D. X., Yang, Z. Z., Theory on the molecular characteristic contour (I).3-A new approach to defining molecular intrinsic characteristic contour, Sci. in China, Ser. B, 1999, 42(4): 391–399.

    Article  CAS  Google Scholar 

  36. Zhao, D. X., Yang, Z. Z., The changing features of the molecular intrinsic characteristic contours of H2 molecule in the ground and first excited states calculated by an ab initio method, J. Mol. Struct. (THEOCHEM), 2002, 579: 73–84.

    Article  CAS  Google Scholar 

  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.

    Article  CAS  Google Scholar 

  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.

    Article  CAS  Google Scholar 

  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.

    Article  CAS  Google Scholar 

  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.

    CAS  Google Scholar 

  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.

    Article  Google Scholar 

  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.

    Article  CAS  Google Scholar 

  43. Ghosh, S. K., Berkowitz, M., Parr, R. G., Transcription of groundstate density functional theory into a local thermodynamics. 5, Proc. Natl. Acad. Sci. USA, 1984, 81: 8028–8031.

    Article  CAS  Google Scholar 

  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.

    Article  CAS  Google Scholar 

  45. Davidson, E. R., MELD Program Description in MOTECC, New York: ESCOM, 1990, 553–592.

    Google Scholar 

  46. Lide, D. R., Frederikse, H. P. R., Eds., CRC Handbook of Chemistry and Physics, 76th edition, Boca Raton: CRC Press, 1995-1996.

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Correspondence to Zhongzhi Yang.

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Gong, L., Zhao, D. & Yang, Z. Theory on the molecular characteristic contou(II). Sc. China Ser. B-Chem. 48, 89–100 (2005). https://doi.org/10.1360/04yb0127

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