Skip to main content
SpringerLink
Log in

A model of atomic compressibility and its application in QSAR domain for toxicological property prediction

  • Original Paper
  • Published:
Journal of Molecular Modeling Aims and scope Submit manuscript

Abstract

A model for computing the atomic compressibility (β) based on two periodic descriptors, namely, absolute radius (r) and atomic electrophilicity index (ω), is proposed as

$$ \beta \propto \left({r}^2/\omega \right) $$

The ansatz is invoked to compute compressibilities of atoms of 57 elements of the periodic table. The computed atomic data exhibits all sine qua non of periodic properties. Further, the concept group compressibility (Gβ) is also established invoking additivity property using some molecules with different functional groups and consequently utilized in correlating with molecular polarizability. Since toxicity prediction is an imperative need of the hour, chemical reactivity descriptors are of paramount importance in the study of toxicological behaviour along with a lot of other molecular reactivity studies within a Quantitative Structure–Activity Relationship (QSAR) context. Hence, this quantity is applied in the modelling of toxicological property through QSAR and a comprehensive study is performed in an effort to investigate and validate the application of compressibility in determining its toxicological power. Consequently, varied 209 organic molecules are selected for studying the toxic effect on Tetrahymena pyriformis. A QSAR model is constructed in terms of compressibility which offers a superior prediction of toxicity independently without adopting additional descriptors or properties as in some other QSAR studies.

Graphical abstract

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig. 1
Fig. 2
Fig. 3
Fig. 4

Similar content being viewed by others

References

  1. Bonin KD, Kresin VV (1997) Electric-dipole polarizabilities of atoms, Molecules and Clusters, World Scientific, Singapore

  2. Connerade JP, Kengkan P, Lakshmi PA, Semaoune R (2000) Scaling laws for atomic compressibility. J Phys B Atomic Mol Phys 33:L847

    CAS  Google Scholar 

  3. Connerade JP, Semaoune R (2000) Atomic compressibility and reversible insertion of atoms into solids. J Phys B Atomic Mol Phys 33:3467

    CAS  Google Scholar 

  4. Chattaraj PK, Sarkar U (2003) Chemical reactivity of the spherically confined atoms. Chem Phys Lett 372:805–809

    CAS  Google Scholar 

  5. Noorizadeh S, Parhizgar M (2005) The atomic and group compressibility. J Mol Struct THEOCHEM 725:23–26

    CAS  Google Scholar 

  6. Chattaraj PK, Sengupta S (1996) Popular electronic structure principles in a dynamical context. J Phys Chem 100:16126–16130

    CAS  Google Scholar 

  7. Parr RG, Pearson RG (1983) Absolute hardness: companion parameter to absolute electronegativity. J Am Chem Soc 105:7512–7516

    CAS  Google Scholar 

  8. Donald KJ (2006) Electronic compressibility and polarizability: origins of a correlation. J Phys Chem A 110:2283–2289

    CAS  PubMed  Google Scholar 

  9. Mullay J (1987) In: Sen KD, Jorgensen CK (eds) Structural bonding: electronegativity. Berlin, Springer-Verlag

    Google Scholar 

  10. Parr RG, Ayers PW, Nalewajski RF (2005) What is an atom in a molecule? J Phys Chem A 109:3957–3959

    CAS  PubMed  Google Scholar 

  11. Chakraborty T, Gazi K, Ghosh DC (2010) Computation of the atomic radii through the conjoint action of the effective nuclear charge and the ionization energy. Mol Phys 108:2081–2092

    CAS  Google Scholar 

  12. Tandon H, Chakraborty T, Suhag V (2019) A new scale of electrophilicity index invoking force concept and its application in computing internuclear bond distance. Journal of Structural Chemistry (Accepted)

  13. Fahrmeir L, Kneib T, Lang S, Marx B (2013) Regression: models, methods and applications, Springer Science & Buisness Media, Berlin, Heidelberg

  14. Minitab 17 Statistical Software (2010) [Computer software] State College, PA: Minitab, Inc. (www.minitab.com)

  15. Thole BT (1981) Molecular polarizabilities calculated with a modified dipole interaction. Chem Phys 59:3413–3450

    Google Scholar 

  16. Korchowiec J, Nalewajski RF (1992) Group electronegativity and Fukui function studies of the substituent effects in aromatic and inorganic systems. Int J Quantum Chem 44:1027–1040

    CAS  Google Scholar 

  17. Huheey JE (1965) The electronegativity of groups. J Phys Chem 69:3284–3291

    CAS  Google Scholar 

  18. Reed LH, Allen LC (1992) Bond polarity index: application to group electronegativity. J Phys Chem 96:157–164

    CAS  Google Scholar 

  19. Smith DW (1998) Group electronegativities from electronegativity equilibration applications to organic thermochemistry. J Chem Soc Faraday Trans 94:201–205

    CAS  Google Scholar 

  20. Van Lier G, Safi B, Geerlings P (1997) Acidity of substituted hydrofullerenes: an ab initio quantum-chemical study. J Phys Chem Solids 58:1719–1727

    Google Scholar 

  21. Langenaeker W, Demel K, Geerlings P (1991) Quantum-chemical study of the Fukui function as a reactivity index1: part 2. Electrophilic substitution on mono-substituted benzenes. Journal of Molecular Structure: THEOCHEM 234:329–342

    Google Scholar 

  22. De Proft F, Langenaeker W, Geerlings P (1993) Ab initio determination of substituent constants in a density functional theory formalism: calculation of intrinsic group electronegativity, hardness, and softness. J Phys Chem 97:1826–1831

    Google Scholar 

  23. De Proft F, Amira S, Choho K, Geerlings P (1994) Quantum-chemical study of the acidity of substituted acetic acids with density functional theory based descriptors. J Phys Chem 98:5227–5233

    Google Scholar 

  24. De Proft F, Langenaeker W, Geerlings P (1995) Acidity of first-and second-row hydrides: effects of electronegativity and hardness. Int J Quantum Chem 55:459–468

    Google Scholar 

  25. De Proft F, Langenaeker W, Geerlings P (1995) Acidity of alkyl substituted alcohols: are alkyl groups electron-donating or electron-withdrawing? Tetrahedron. 51:4021–4032

    Google Scholar 

  26. Krishnamurty S, Pal S (2000) Intermolecular reactivity trends using the concept of group softness. J Phys Chem A 104:7639–7645

    CAS  Google Scholar 

  27. Pérez P, Toro-Labbé A (2000) Characterization of keto-enol tautomerism of acetyl derivatives from the analysis of energy, chemical potential, and hardness. J Phys Chem A 104:1557–1562

    Google Scholar 

  28. Jaque P, Toro-Labbe A (2000) Theoretical study of the double proton transfer in the CHX− XH⊙⊙⊙ CHX− XH (X= O, S) complexes. J Phys Chem A 104:995–1003

    CAS  Google Scholar 

  29. Cárdenas-Jirón GI, Toro-Labbé A (1997) Fragment chemistry of the hydrogen thioperoxide molecule; energy, chemical potential and hardness. J Mol Struct THEOCHEM 390:79–89

    Google Scholar 

  30. Van Duijnen PT, Swart M (1998) Molecular and atomic polarizabilities: Thole’s model revisited. J Phys Chem A 102:2399–2407

    Google Scholar 

  31. Mekenyan OG, Veith GD (1993) Relationships between descriptors for hydrophobicity and soft electrophilicity in predicting toxicity. SAR QSAR Environ Res 1:335–344

    CAS  PubMed  Google Scholar 

  32. Comporti M (1989) Three models of free radical-induced cell injury. Chem Biol Interact 72:1–56

    CAS  PubMed  Google Scholar 

  33. Mikolajczyk A, Gajewicz A, Rasulev B, Schaeublin N, Maurer-Gardner E, Hussain S, Leszczynski J, Puzyn T (2015) Zeta potential for metal oxide nanoparticles: a predictive model developed by a nano-quantitative structure–property relationship approach. Chem Mater 27:2400–2407

    CAS  Google Scholar 

  34. Mikolajczyk A, Sizochenko N, Mulkiewicz E, Malankowska A, Nischk M, Jurczak P, Hirano S, Nowaczyk G, Zaleska-Medynska A, Leszczynski J, Gajewicz A (2017) Evaluating the toxicity of TiO2-based nanoparticles to Chinese hamster ovary cells and Escherichia coli: a complementary experimental and computational approach. Beilstein J Nanotechnol 8:2171–2180

    CAS  PubMed  PubMed Central  Google Scholar 

  35. Mikolajczyk A, Gajewicz A, Mulkiewicz E, Rasulev B, Marchelek M, Diak M, Hirano S, Zaleska-Medynska A, Puzyn T (2018) Nano-QSAR modeling for ecosafe design of heterogeneous TiO 2-based nano-photocatalysts. Environ Sci Nano 5:1150–1160

    CAS  Google Scholar 

  36. Mikolajczyk A, Sizochenko N, Mulkiewicz E, Malankowska A, Rasulev B, Puzyn T (2019) A chemoinformatics approach for characterization of hybrid nanomaterials: safer and efficient design perspective. Nanoscale 11:1808–11818

    Google Scholar 

  37. Shalini A, Tandon H, Chakraborty T (2017) Molecular electrophilicity index - A promising descriptor for predicting toxicological property. J Bioequiv Availab 9:518–527

  38. Singh PP, Srivastava HK, Pasha FA (2004) DFT-based QSAR study of testosterone and its derivatives. Bioorg Med Chem 12:171–177

    CAS  PubMed  Google Scholar 

  39. Pasha FA, Srivastava HK, Singh PP (2005) Comparative QSAR study of phenol derivatives with the help of density functional theory. Bioorg Med Chem 13:6823–6829

    CAS  PubMed  Google Scholar 

  40. Srivastava HK, Pasha FA, Singh PP (2005) Atomic softness-based QSAR study of testosterone. Int J Quantum Chem 103:237–245

    CAS  Google Scholar 

  41. Chakraborty T, Ghosh DC (2013) Correlation of the drug activities of some anti-tubercular chalcone derivatives in terms of the quantum mechanical reactivity descriptors. In: Haghi AK (ed) Methodologies and applications for chemoinformatics and chemical engineering. IGI Global, Hershey, PA, pp 155–168

    Google Scholar 

  42. Parr RG, Yang W (1989) Density functional theory of atoms and molecules. Oxford University Press, New York

    Google Scholar 

  43. Mikolajczyk A, Malankowska A, Nowaczyk G, Gajewicz A, Hirano S, Jurga S, Zaleska-Medynska A, Puzyn T (2016) Combined experimental and computational approach to developing efficient photocatalysts based on Au/Pd-TiO2 nanoparticles. Environ Sci Nano 3:1425–1435

    CAS  Google Scholar 

  44. Chermette H (1999) Chemical reactivity indexes in density functional theory. J Comput Chem 20:129–154

    CAS  Google Scholar 

  45. Geerlings P, De Proft F, Langenaeker W (2003) Conceptual density functional theory. Chem Rev 103:1793–1874

    CAS  PubMed  Google Scholar 

  46. Chattaraj PK, Nath S, Maiti B (2004) Reactivity descriptors. In: Bultinck P, Winter HD, Langenaeker W, Tollenaere JP (eds) Computational medicinal chemistry for drug discovery. Marcel Dekker, New York, USA, pp 295–322

    Google Scholar 

  47. Parr RG (1983) Density functional theory. Annu Rev Phys Chem 34:631–656

    CAS  Google Scholar 

  48. Chattaraj PK, Maiti B, Sarkar U (2003) Philicity: a unified treatment of chemical reactivity and selectivity. J Phys Chem A 107:4973–4975

    CAS  Google Scholar 

  49. Chattaraj PK, Roy DR (2005) Local descriptors around a transition state: a link between chemical bonding and reactivity. J Phys Chem A 109:3771–3772

    CAS  PubMed  Google Scholar 

  50. Tandon H, Chakraborty T, Suhag V (2019) A new model of atomic nucleophilicity index and its application in the field of QSAR. International Journal of Quantitative Structure-Property Relationships 4:99–117

    Google Scholar 

  51. Tandon H, Shalini, Ranjan P, Suhag V, Chakraborty T (2019) A review of a computational study of carbon nanotubes. In: Vakhrushev AV, Kodolov VI, Haghi AK, Ameta SC (eds) Carbon nanotubes and nanoparticles: current and potential applications. Apple Academic Press, Toronto; New Jersey, pp 25–38

    Google Scholar 

  52. Thanikaivelan P, Subramanian V, Rao JR, Nair BU (2000) Application of quantum chemical descriptor in quantitative structure activity and structure property relationship. Chem Phys Lett 323:59–70

    CAS  Google Scholar 

  53. Parthasarathi R, Subramanian V, Roy DR, Chattaraj PK (2004) Electrophilicity index as a possible descriptor of biological activity. Bioorg Med Chem 12:5533–5543

    CAS  PubMed  Google Scholar 

  54. Roy DR, Sarkar U, Chattaraj PK, Mitra A, Padmanabhan J, Parthasarathi R, Subramanian V, Van Damme S, Bultinck P (2006) Analyzing toxicity through electrophilicity. Mol Divers 10:119–131

    CAS  PubMed  Google Scholar 

  55. Akers KS, Sinks GD, Schultz TW (1999) Structure–toxicity relationships for selected halogenated aliphatic chemicals. Environ Toxicol Pharmacol 7:33–39

    CAS  PubMed  Google Scholar 

  56. Schultz TW (1997) TETRATOX: Tetrahymena pyriformis population growth impairment endpointa surrogate for fish lethality. Toxicology methods 7:289–309

    CAS  Google Scholar 

  57. Dimitrov SD, Mekenyan OG, Sinks GD, Schultz TW (2003) Global modeling of narcotic chemicals: ciliate and fish toxicity. J Mol Struct THEOCHEM 622:63–70

    CAS  Google Scholar 

  58. Roy DR, Parthasarathi R, Maiti B, Subramanian V, Chattaraj PK (2005) Electrophilicity as a possible descriptor for toxicity prediction. Bioorg Med Chem 13:3405–3412

    CAS  PubMed  Google Scholar 

  59. SAS Institute Inc. (1989) SAS/STAT® user’s guide, version 6 (4th edition), Volume 2, Cary NC: SAS Institute Inc.

  60. Finney DJ (1971) Probit analysis. Cambridge University Press, Cambridge, UK

    Google Scholar 

  61. Bridgman PW (1926) The five alkali metals under high pressure. Phys Rev 27:68–86

    CAS  Google Scholar 

  62. Grosse AV (1964) The compressibility of solid noble gases and the alkali metals at 0° K. J Inorg Nucl Chem 26:1801–1809

    CAS  Google Scholar 

  63. Smeyers YG, Bouniam L, Smeyers NJ, Ezzamarty A, Hernandez-Laguna A, Sainz-Diaz CI (1998) Quantum mechanical and QSAR study of some α-arylpropionic acids as anti-inflammatory agents. Eur J Med Chem 33:103–112

    CAS  Google Scholar 

  64. Karabunarliev S, Mekenyan OG, Karcher W, Russom CL, Bradbury SP (1996) Quantum-chemical descriptors for estimating the acute toxicity of electrophiles to the fathed minnow (Pimephales promelas): an analysis based on molecular mechanisms. Quant Struct Act Relat 15:302–310

    CAS  Google Scholar 

  65. Lipnick RL (1991) Outliers: their origin and use in the classification of molecular mechanisms of toxicity. Sci Total Environ 109:131–153

    PubMed  Google Scholar 

  66. Gawley RE (1976) The Robinson annelation and related reactions. Synthesis 1976:777–794

    Google Scholar 

  67. Netzeva TI, Schultz TW, Aptula AO, Cronin MT (2003) Partial least squares modelling of the acute toxicity of aliphatic compounds to Tetrahymena pyriformis. SAR QSAR Environ Res 14:265–283

    CAS  PubMed  Google Scholar 

  68. Schultz TW, Cronin MT, Netzeva TI, Aptula AO (2002) Structure–toxicity relationships for aliphatic chemicals evaluated with tetrahymena pyriformis. Chem Res Toxicol 15:1602–1609

    CAS  PubMed  Google Scholar 

  69. Toropov AA, Benfenati E (2004) QSAR modelling of aldehyde toxicity against a protozoan, Tetrahymena pyriformis by optimization of correlation weights of nearest neighboring codes. J Mol Struct THEOCHEM 679:225–228

    CAS  Google Scholar 

  70. Castro EA, Toropov AA, Nesterova AI, Nazarov AU (2003) QSAR study of the toxic action of aliphatic compounds to the bacteria Vibrio fisheri based on correlation weighting of local graph invariants. J Mol Struct THEOCHEM 639:129–135

    CAS  Google Scholar 

Download references

Acknowledgements

The authors are thankful to Manipal University Jaipur for providing computational and research facility.

Author information

Authors and Affiliations

  1. Department of Chemistry, Manipal University Jaipur, Jaipur-Ajmer Express Highway, Dehmi Kalan, Near GVK Toll Plaza, Jaipur, Rajasthan, 303007, India

    Hiteshi Tandon & Tanmoy Chakraborty

  2. Department of Applied Sciences, BML Munjal University, National Highway 8, 67 KM Milestone, Gurugram, Haryana, 122413, India

    Vandana Suhag

Authors
  1. Hiteshi Tandon
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Tanmoy Chakraborty
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Vandana Suhag
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding author

Correspondence to Tanmoy Chakraborty.

Ethics declarations

Conflict of interest

The authors declare that they have no conflict of interest.

Additional information

Publisher’s note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Rights and permissions

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Tandon, H., Chakraborty, T. & Suhag, V. A model of atomic compressibility and its application in QSAR domain for toxicological property prediction. J Mol Model 25, 303 (2019). https://doi.org/10.1007/s00894-019-4199-9

Download citation

  • Received:

  • Accepted:

  • Published:

  • DOI: https://doi.org/10.1007/s00894-019-4199-9

Keywords

Search

Navigation