Role of Atomic and Molecular Non-observable Properties in the Understanding and Description of Real Observables of the Chemical Systems. A Review

Conference paper
Part of the Learning and Analytics in Intelligent Systems book series (LAIS, volume 11)


Chemical species can be characterized by various observable features: mass, enthalpy of formation, charge (ions), dipole moment, magnetic susceptibility, electrical susceptibility, electromagnetic spectra, refraction index, polarizability, electron density distribution etc. But, on the other hand, the understanding of chemical an physical behavior is usually based on specific non-observable features - for example: electronegativity, partial atomic charges, nucleophilicity, atomic and molecular orbitals, aromaticity, hyperconjugation, … All non-observable features generally have no physical unit, and are not amenable to experimental measurements. For that reason the values ascribed to them are strongly dependent on the definition(s). For example, we know (and use) various electronegativity scales: Pauling’s, Mulliken’s, Alfred-Rochov’s [1, 2], Sanderson’s, Allen’s, and other. They are based on different theoretical assumptions, and produce (on many instances, significantly) different numerical values. On the other hand, all scales follow similar general trend, indicating that the values reflect some intrinsic chemical property.



Ministry of Education, Science, and Technological Development of the Republic of Serbia supported this work, Grant No. 172035. Author gratefully acknowledge the computational time provided on the PARADOX cluster at the Scientific Computing Laboratory of the Institute of Physics, Belgrade.


  1. 1.
    Allred, A.L., Rochow, E.G.: A scale of electronegativity based on electrostatic force. J. Inorg. Nucl. Chem. 5(4), 264–268 (1958). Scholar
  2. 2.
    Ghosh, D.C., Chakraborty, T.: Gordy’s electrostatic scale of electronegativity revisited. J. Mol. Struct. (THOECHEM) 906, 87–93 (2009). Scholar
  3. 3.
    Pauling, L.: The nature of the chemical bond. IV. The energy of single bonds and the relative electronegativity of atoms. J. Am. Chem. Soc. 54, 3570–3582 (1932). Scholar
  4. 4.
    Mulliken, R.S.: New electroaffinity scale; together with data on valence states and on valence ionization potentials and electron affinities. J. Chem. Phys. 2, 782–793 (1934). Scholar
  5. 5.
    Hinze, J., Jaffé, H.H.: Electronegativity. I. Orbital electronegativity of neutral atoms. J. Am. Chem. Soc. 84, 540–546 (1962)CrossRefGoogle Scholar
  6. 6.
    Hinze, J., Whitehead, M.A., Jaffé, H.H.: Electronegativity. II. Bond and orbital electronegativities. J. Am. Chem. Soc. 85, 148–154 (1963)CrossRefGoogle Scholar
  7. 7.
    Hinze, J., Jaffé, H.H.: Electronegativity. III. Orbital electronegativities and electron affinities of transition metals. Can. J. Chem. 41, 1315–1328 (1963). Scholar
  8. 8.
    Hinze, J., Jaffé, H.H.: Electronegativity. IV. Orbital electronegativities of the neutral atoms of the periods three A and four A and of positive ions of periods one and two. J. Phys. Chem. 67, 1501–1506 (1963). Scholar
  9. 9.
    Iczkowski, R.P., Margrave, J.L.: Electronegativity. J. Am. Chem. Soc. 83, 3547–3551 (1961). Scholar
  10. 10.
    Coulson, C.A., Longuet-Higgins, H.C.: The electronic structure of conjugated systems. II. Unsaturated hydrocarbons and their hetero-derivatives. Proc. Roy. Soc. (London) A 192, 16–32 (1947). Scholar
  11. 11.
    Mulliken, R.S.: Electronic population analysis on LCAO-MO molecular wave functions. I. J. Chem. Phys. 23(10), 1833–1840 (1955). Scholar
  12. 12.
    Mayer, I.: Charge, bond order and valence in the AB initio SCF theory. Chem. Phys. Lett. 97(3), 270–274 (1983). Scholar
  13. 13.
    Mayer, I.: Charge, bond order and valence in the AB initio SCF theory. Chem. Phys. Lett. 117(4), 396 (1985). Scholar
  14. 14.
    Juranić, I.: Molecular descriptors as proxies for the modeling of the materials and their environmental impact. Mater. Prot. 57(3), 359–369 (2016). Scholar
  15. 15.
    Oliferenko, A.A., Palyulin, V.A., Pisarev, S.A., Neiman, A.V., Zefirov, N.S.: Novel point charge models: reliable instruments for molecular electrostatic. J. Phys. Org. Chem. 14, 355–369 (2001). Scholar
  16. 16.
    Abraham, R.J., Griffiths, L., Perez, M.: 1H NMR spectra. Part 30: 1H chemical shifts in amides and the magnetic anisotropy, electric field and steric effects of the amide group. Magn. Reson. Chem. 51(3), 143–155 (2013). Scholar
  17. 17.
    Abraham, R.J., Bardsley, B., Mobli, M., Smith, R.J.: 1H chemical shifts in NMR. Part 21–prediction of the 1H chemical shifts of molecules containing the ester group: a modelling and ab initio investigation. Magn. Reson. Chem. 43(1), 3–15 (2004). Scholar
  18. 18.
    Binev, Y., Aires-de-Sousa, J.: Structure-based predictions of 1H NMR chemical shifts using feed-forward neural networks. J. Chem. Inf. Comput. Sci. 44, 940–945 (2004). Scholar
  19. 19.
    Chis, V., Pîrnãu, A., Vasilescu, M., Varga, R.A., Oniga, O.: X-ray, 1H NMR and DFT study on 5-para-X-benzylidene-thiazolidine derivatives with X = Br, F. J. Mol. Struct. (THOECHEM) 851(1–3), 63–74 (2008). Scholar
  20. 20.
    Pazderski, L., Toušek, J., Sitkowski, J., Kozerski, L., Szłyk, E.: Experimental and quantum-chemical studies of 1H, 13C and 15N NMR coordination shifts in Pd(II) and Pt(II) chloride complexes with quinoline, isoquinoline, and 2,2 -biquinoline. Magn. Reson. Chem. 45(12), 1059–1071 (2007). Scholar
  21. 21.
    Shirts, R.B., Stolworthy, L.D.X.: Conformational sensitivity of polyether macrocycles to electrostatic potential: partial atomic charges, molecular mechanics, and conformational prediction. J. Inclusion Phenom. Mol. Recognit. Chem. 20(4), 297–321 (1994). Scholar
  22. 22.
    Wang, B., Truhlar, D.G.: Partial atomic charges and screened charge models of the electrostatic potential. J. Chem. Theory Comput. 8(6), 1989–1998 (2012). Scholar
  23. 23.
    Mehler, E.L., Solmajer, T.: Electrostatic effects in proteins: comparison of dielectric and charge models. Protein Eng. Des. Sel. 4(8), 903–910 (1991). Scholar
  24. 24.
    Bertonati, C., Honig, B., Alexov, E.: Poisson-Boltzmann calculations of nonspecific salt effects on protein-protein binding free energies. Biophys. J. 92(6), 1891–1899 (2007). Scholar
  25. 25.
    Schröder, C.: Comparing reduced partial charge models with polarizable simulations of ionic liquids. Phys. Chem. Chem. Phys. 14(9), 3089 (2012). Scholar
  26. 26.
    Tsiper, E.V., Soos, Z.G.: Electronic polarization in pentacene crystals and thin films. Phys. Rev. B 68(8), 085201-10 (2003). Scholar
  27. 27.
    Tsiper, E.V., Soos, Z.G., Gao, W., Kahn, A.: Electronic polarization at surfaces and thin films of organic molecular crystals: PTCDA. Chem. Phys. Lett. 360(1–2), 47–52 (2002). Scholar
  28. 28.
    Anker, L.S., Jurs, P.C., Edwards, P.A.: Quantitative structure-retention relationship studies of odor-active aliphatic compounds with oxygen-containing functional groups. Anal. Chem. 62(24), 2676–2684 (1990). Scholar
  29. 29.
    Stanton, D.T., Jurs, P.C.: Development and use of charged partial surface area structural descriptors in computer-assisted quantitative structure-property relationship studies. Anal. Chem. 62(21), 2323–2329 (1990). Scholar
  30. 30.
    Katritzky, A.R., Mu, L., Lobanov, V.S.: Correlation of boiling points with molecular structure. 1. A training set of 298 diverse organics and a test set of 9 simple inorganics. J. Phys. Chem. 100, 10400–10407 (1996). Scholar
  31. 31.
    Ghatee, M.H., Zolghadr, A.R., Moosavi, F., Ansari, Y.: Studies of structural, dynamical, and interfacial properties of 1-alkyl-3-methylimidazolium iodide ionic liquids by molecular dynamics simulation. J. Chem. Phys. 136, 124706-14 (2012). Scholar
  32. 32.
    Knight, J.L., Yesselman, J.D., Brooks III, C.L.: Assessing the quality of absolute hydration free energies among CHARMM-compatible ligand parameterization schemes. J. Comput. Chem. 34, 893–903 (2013). Scholar
  33. 33.
    Lísal, M., Chval, Z., Storch, J., Izák, P.: Towards molecular dynamics simulations of chiral room-temperature ionic liquids. J. Mol. Liq. 189, 85–94 (2014). Scholar
  34. 34.
    Bhatta, R.S., Yimer, Y.Y., Perry, D.S., Tsige, M.: Improved force field for molecular modeling of poly(3hexylthiophene). J. Phys. Chem. B 117, 10035–10045 (2013). Scholar
  35. 35.
    Núnez-Rojas, E., García-Melgarejo, V., de la Luz, A.P., Alejandre, J.: Systematic parameterization procedure to develop force fields for molecular fluids using explicit water. Fluid Phase Equilib. 490, 1–12 (2019). Scholar
  36. 36.
    Vitnik, Ž.J., Vitnik, V.D., Pokorni, S.V., Juranić, I.O.: Correlation of pKa values for series of benzoic acids with the theoretically calculated atomic charges. In: Physical Chemistry 2012, 11th International Conference on Fundamental and Applied Aspects of Physical Chemistry, Belgrade, September 2012, Proceedings, A-9-P, pp. 61–63 (2012)Google Scholar
  37. 37.
    Wang, H., Ulander, J.: High-throughput pKa screening and prediction amenable for ADME profiling. Expert Opin. Drug Metabol. Toxicol. 2, 139–155 (2006)CrossRefGoogle Scholar
  38. 38.
    Grierson, L., Perkins, M.J., Rzepa, H.S.: A comparison of the MNDO and AM1 SCF-MO methods for dipolar cycloaddition and the claisen reaction. J. Chem. Soc. Chem. Commun. 1779 (1987)Google Scholar
  39. 39.
    Rzepa, H.: Cheletropic elimination reactions. A comparison of the MNDO, AM1 and ab initio SCF-MO methods. J. Chem. Res. 224 (1988)Google Scholar
  40. 40.
    Juranic, I., Rzepa, H.S., Yi, M-Y.: Molecular orbital studies of molecular exciplexes. Part 1: AM1 and PM3 calculations of the ammonia-oxygen complex and its solvation by water. J. Chem. Soc. Perkin Trans. 877 (1990)Google Scholar
  41. 41.
    Pfendt, L., Dražić, B., Popović, G., Drakulić, B., Vitnik, Ž., Juranić, I.: Determination of all pKa values of some di- and tri-carboxylic unsaturated and epoxy acids and their polylinear correlation with the carboxylic group atomic charges. J. Chem. Res. (S) 2003, 247 (2003)CrossRefGoogle Scholar
  42. 42.
    Vitnik, Ž.: Correlations between physical and chemical properties of carboxylic acids with a calculated atomic charges. Ph.D. thesis, University of Belgrade, 12 December 2011Google Scholar
  43. 43.
    Juranić, I.: Simple method for the estimation of pKa of amines. Croat. Chem. Acta 87(4), 343–347 (2014). Scholar
  44. 44.
    Jovanović, B., Juranić, I., Mišić-Vuković, M., Brkić, D., Vitnik, Ž.: Kinetics and mechanism of the reaction of substituted 4-pyrimidine carboxylic acids with diazodiphenylmethane in dimethylformamide. J. Chem. Res. (S) 2000, 506–507 (2000)CrossRefGoogle Scholar

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Authors and Affiliations

  1. 1.University of Belgrade, IChTM, Centre for ChemistryBelgradeSerbia

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