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Journal of Chemical Sciences

, Volume 129, Issue 5, pp 533–541 | Cite as

On the effect of external perturbation on amino acid salt bridge: a DFT study

  • Biswa Jyoti Dutta
  • Nabajit Sarmah
  • Pradip KR Bhattacharyya
Regular Article
  • 89 Downloads

Abstract

Effect of external perturbation (in terms of external electric field and solvents) on the stability of lysine-aspartic acid salt bridge was analyzed by density functional theory. Because of solvation, interaction energy in the aqueous phase is much lower as compared to gas phase. Interaction energy as well as stability (measured in terms of global hardness, HOMO energy and total electronic energy) are observed to be sensitive towards the strength and direction of the applied electric field. Gap between HOMO energy of the acids and salt bridge also points towards the feasibility of hydrogen bonding.

Graphical Abstract

Keywords

Salt bridge DFT DFRT Electric field PCM 

Notes

Acknowledgements

Authors thank the Department of Science and Technology (DST), India for the financial grant (No. SB/S1/PC-17/2014).

References

  1. 1.
    Kumar S and Nussinov R 1999 Salt bridge stability in monomeric proteins J. Mol. Biol. 93 1241CrossRefGoogle Scholar
  2. 2.
    Christie J M, Arvai A S, Baxter K J, Heilmann M, Pratt A J, O-Hara A, Kelly S M, Hothorn M, Smith B O, Hitomi K, Jenkins G I and Getzo E D 2012 Plant UVR8 photoreceptor senses UV-B by tryptophan-mediated disruption of cross-dimer salt bridges Science 335 1492CrossRefGoogle Scholar
  3. 3.
    Robert A 2000 In Copeland enzymes: A practical introduction to structure, mechanism, and data analysis (New York: Wiley-VCH)Google Scholar
  4. 4.
    Fersht A R 1984 Basis of biological specificity Biochem. Sci. 9 145Google Scholar
  5. 5.
    Honig B and Yang A S 1995 Free energy balance in protein folding Adv. Protein Chem. 46 27CrossRefGoogle Scholar
  6. 6.
    Gao J, Mammen M and Whitesides G M 1996 Evaluating electrostatic contributions to binding with the use of protein charge ladders Science 272 535CrossRefGoogle Scholar
  7. 7.
    Xu D, Lin S L and Nussinov R 1997 Protein binding versus protein folding: The role of hydrophilic bridges in protein associations J. Mol. Biol. 265 68CrossRefGoogle Scholar
  8. 8.
    Kohn W, Becke A D and Parr R G 1996 Density functional theory of electronic structure J. Phys. Chem. 100 12974CrossRefGoogle Scholar
  9. 9.
    Baerends E J and Gritsenko O V 1997 A quantum chemical view of density functional theory J. Phys. Chem. A 101 5383CrossRefGoogle Scholar
  10. 10.
    Chermette H 1998 Density functional theory: A powerful tool for theoretical studies in coordination chemistry Coord. Chem. Rev. 178 699CrossRefGoogle Scholar
  11. 11.
    Andrews L and Citra A 2002 Infrared spectra and density functional theory calculations on transition metal nitrosyls. Vibrational frequencies of unsaturated transition metal nitrosyls Chem. Rev. 102 885CrossRefGoogle Scholar
  12. 12.
    Ziegler T and Autschbach J 2005 Theoretical methods of potential use for studies of inorganic reaction mechanisms Chem. Rev. 105 2695CrossRefGoogle Scholar
  13. 13.
    Neese F 2009 Prediction of molecular properties and molecular spectroscopy with density functional theory: from fundamental theory to exchange-coupling Coord. Chem. Rev. 253 526CrossRefGoogle Scholar
  14. 14.
    Schultz N E, Zhao Y and Truhlar D G 2005 Density functionals for inorganometallic and organometallic chemistry J. Phys. Chem. A 109 11127CrossRefGoogle Scholar
  15. 15.
    Parr R G and Yang W 1989 Density functional theory of atoms and molecules (New York: Oxford University Press)Google Scholar
  16. 16.
    Chandra A K and Nguyen M T 2007 Use of DFT-based reactivity descriptors for rationalizing radical addition reactions: Applicability and difficulties Faraday Discuss. 135 191Google Scholar
  17. 17.
    Molteni G and Ponti A 2003 Arylazide Cycloaddition to Methyl Propiolate: DFT-Based Quantitative Prediction of Regioselectivity Chem. Eur. J. 9 2770CrossRefGoogle Scholar
  18. 18.
    Roy R K 2003 Nucleophilic substitution reaction of alkyl halides: a case study on density functional theory (DFT) based local reactivity descriptors J. Phys. Chem. A 107 397CrossRefGoogle Scholar
  19. 19.
    Nguyen H M T, Peeters J, Nguyen M T and Chandra A K 2004 Use of DFT-based reactivity descriptors for rationalizing radical reactions: A critical analysis J. Phys. Chem. A 108 484CrossRefGoogle Scholar
  20. 20.
    Melin J, Aparicio F, Subramanian V, Galvan M and Chattaraj P K 2004 Is the Fukui Function a Right Descriptor of Hard- Hard Interactions? J. Phys. Chem. A 108 2487CrossRefGoogle Scholar
  21. 21.
    Geerlings P, Proft F D and Langenaekar W 2003 Conceptual density functional theory Chem. Rev. 103 1793CrossRefGoogle Scholar
  22. 22.
    Chattaraj P K, Sarkar U and Roy D R 2006 Electrophilicity index Chem. Rev. 106 2065Google Scholar
  23. 23.
    Roy R K and Saha S 2010 Studies of regioselectivity of large molecular systems using DFT based reactivity descriptors Annu. Rep. Prog. Chem., Sect. C: Phys. Chem. 106 118CrossRefGoogle Scholar
  24. 24.
    Vijayaraj R, Subramanian V and Chattaraj P K 2009 Comparison of global reactivity descriptors calculated using various density functionals: A QSAR perspective J. Chem. Theor. Comput. 5 2744CrossRefGoogle Scholar
  25. 25.
    Putz M V, Mingos D and Michael P 2012 (Eds.) Applications of density functional theory to chemical reactivity (Berlin: Springer)Google Scholar
  26. 26.
    Cohen M H and Wasserman A 2007 On the foundations of chemical reactivity theory J. Phys. Chem. A  111 2229CrossRefGoogle Scholar
  27. 27.
    Ramya K R and Venkatnathan A 2012 Stability and reactivity of methane clathrate hydrates: insights from density functional theory J. Phys. Chem. A  116 7742CrossRefGoogle Scholar
  28. 28.
    Ross W 1993 Biological effects of electromagnetic fields J. Cell. Biochem. 51 410CrossRefGoogle Scholar
  29. 29.
    Neog B, Sarmah N and Bhattacharyya P K 2014 Effect of external electric field on drug-guanine adduct: A conceptual density functional theory study J. Ind. Chem. Soc. 91 95Google Scholar
  30. 30.
    Mazurkiewicz J and Tomasik P 2012 Effect of external electric field upon charge distribution, energy and dipole moment of selected monosaccharide molecules Natural Sci. 4 276CrossRefGoogle Scholar
  31. 31.
    Calvo F and Dugourd P 2008 Folding of gas-phase polyalanines in a static electric field: Alignment, deformations, and polarization effects Biophys. J. 1 18CrossRefGoogle Scholar
  32. 32.
    Kinosita K J and Tsong T Y 1977 Hemolysis of human erythrocytes by transient electric field Proc. Natl. Acad. Sci. USA 74 1923CrossRefGoogle Scholar
  33. 33.
    Alemani M, Peters M V, Hecht S, Rieder K H, Moresco F and Grill L 2006 Electric field-induced isomerization of azobenzene by STM J. Am. Chem. Soc. 128 14446CrossRefGoogle Scholar
  34. 34.
    Adey W R 1993 Biological effects of electromagnetic fields J. Cell. Biochem. 51 410CrossRefGoogle Scholar
  35. 35.
    Charles P and Elliots P 1995 In Handbook of biological effects of electromagnetic fields 2\(^{\rm nd}\) Ed. (USA: CRC press)Google Scholar
  36. 36.
    Parthasarathi R, Subramanian V and Chattaraj P K 2003 Effect of electric field on the global and local reactivity indices Chem. Phys. Lett. 382 48CrossRefGoogle Scholar
  37. 37.
    Kramer K H and Bernstein R B 1964 Sudden Approximation Applied to Rotational Excitation of Molecules by Atoms. I. Low-Angle Scattering J. Chem. Phys. 40 200CrossRefGoogle Scholar
  38. 38.
    Brooks P R and Jones M E 1966 Reactive scattering of K atoms from oriented CH3I molecules J. Chem. Phys. 45 3449Google Scholar
  39. 39.
    Kar R, Chandrakumar K R S and Pal S 2007 The Influence of electric field on the global and local reactivity descriptors: reactivity and stability of weakly bonded complexes J. Phys. Chem. A 111 375CrossRefGoogle Scholar
  40. 40.
    Kar R and Pal S 2008 Electric field response of molecular reactivity descriptors: A case study Theor. Chem. Acc. 120 375CrossRefGoogle Scholar
  41. 41.
    Kar R and Pal S 2010 Effect of solvents having different dielectric constants on reactivity: A conceptual DFT approach Int. J. Quant. Chem. 110 1642Google Scholar
  42. 42.
    Kar R and Pal S 2008 In External Field and Chemical Reactivity P K Chattaraj (Ed.) (Boca Raton: Taylor and Francis, CRC Press)Google Scholar
  43. 43.
    Ceróon-Carrasco J P, Cerezo J and Jacquemin D 2014 How DNA is damaged by external electric fields: selective mutation vs. random degradation Phys. Chem. Chem. Phys. 16 8243CrossRefGoogle Scholar
  44. 44.
    Jissy A K and Datta A 2010 Designing molecular switches based on DNA-base mispairing J. Phys. Chem. B 114 15311CrossRefGoogle Scholar
  45. 45.
    Cerón-Carrasco J P and Jacquemin D 2013 Electric-field induced mutation of DNA: A theoretical investigation of the GC base pair Phys. Chem. Chem. Phys. 15 4548CrossRefGoogle Scholar
  46. 46.
    Kanvah S, Joseph J, Schuster G B, Barnett R N, Cleveland C L and Landman U 2010 Oxidation of DNA: Damage to nucleobases Acc. Chem. Res. 43 280CrossRefGoogle Scholar
  47. 47.
    Parr R G and Pearson R G 1983 Absolute hardness: Companion parameter to absolute electronegativity J. Am. Chem. Soc. 105 7512CrossRefGoogle Scholar
  48. 48.
    Parr R G, Donnelly R A, Levy M and Palke W E 1978 Electronegativity: The density functional viewpoint J. Chem. Phys. 68 3801CrossRefGoogle Scholar
  49. 49.
    Koopmans T 1934 Über die Zuordnung von Wellenfunktionen und Eigenwerten zu den einzelnen Elektronen eines Atoms Physica 1 104CrossRefGoogle Scholar
  50. 50.
    Becke A D 1993 Density-functional thermochemistry. III. The role of exact exchange J. Chem. Phys. 98 5648CrossRefGoogle Scholar
  51. 51.
    Lee C, Yang W and Parr R G 1988 Development of the Colle-Salvetti correlation-energy formula into a functional of the electron density Phys. Rev. B 37 785CrossRefGoogle Scholar
  52. 52.
    Galano A and Alvarez-Idaboy J R 2006 A new approach to counterpoise correction to BSSE J. Comput. Chem. 27 1203CrossRefGoogle Scholar
  53. 53.
    Miertus S, Scrocco E and Tomasi J 1981 Electrostatic interaction of a solute with a continuum. A direct utilizaion of AB initio molecular potentials for the prevision of solvent effects J. Chem. Phys. 55 117Google Scholar
  54. 54.
    Mennucci B and Tomasi J 1997 Continuum solvation models: A new approach to the problem of solute’s charge distribution and cavity boundaries J. Chem. Phys. 106 5151Google Scholar
  55. 55.
    Cammi R, Mennucci B and Tomasi J 2000 Fast evaluation of geometries and properties of excited molecules in solution: A Tamm-Dancoff model with application to 4-dimethylaminobenzonitrile J. Phys. Chem. A 104 5631CrossRefGoogle Scholar
  56. 56.
    Frisch M J et al. 2010 Gaussian 09, Revision B.01, Gaussian, Inc., Wallingford, CT.Google Scholar
  57. 57.
    Arabi A A and Matta C F 2011 Effects of external electric fields on double proton transfer kinetics in the formic acid dimer Phys. Chem. Chem. Phys. 13 13738CrossRefGoogle Scholar
  58. 58.
    Sarmah N, Neog B and Bhattacharyya P K 2011 Affinity of aziridinium ion towards different nucleophiles: A density functional study Comput. Theor. Chem. 976 30CrossRefGoogle Scholar
  59. 59.
    Parr R G and Chattaraj P K 1991 Principle of maximum hardness J. Am. Chem. Soc113 1854CrossRefGoogle Scholar
  60. 60.
    Chamorro E, Chattaraj P K and Fuentealba P 2003 Variation of the electrophilicity index along the reaction path J. Phys. Chem. A  107 7068CrossRefGoogle Scholar
  61. 61.
    Sinha S and Bhattacharyya P K 2014 Alkylation of guanine by formononetin nitrogen mustard derivatives: A DFT study Comput. Theor. Chem. 1027 135CrossRefGoogle Scholar
  62. 62.
    Parthasarathi R, Padmanabhan J, Subramanian V, Maiti B and Chattaraj P K 2003 Chemical reactivity profiles of two selected polychlorinated biphenyls J. Phys. Chem. A 107 10346CrossRefGoogle Scholar
  63. 63.
    Bhattacharyya P K 2015 Reactivity, aromaticity and absorption spectra of pillar [5] arene conformers: A DFT study Comput. Theor. Chem. 1066 20Google Scholar
  64. 64.
    Ash S, Beg H, Mazumdar P, Salgado-Morán G and Misra A 2014 Polarizability, hardness and electrophilicity as global descriptors for intramolecular proton transfer reaction path Comput. Theor. Chem. 1031 50CrossRefGoogle Scholar
  65. 65.
    Chattaraj P K and Poddar A 1998 A density functional treatment of chemical reactivity and the associated electronic structure principles in the excited electronic states J. Phys. Chem. A 102 9944CrossRefGoogle Scholar
  66. 66.
    Bhattacharyya P K and Kar R 2011 Does structural variation in the aziridinium ion facilitate alkylation? Comput. Theor. Chem. 967 5CrossRefGoogle Scholar
  67. 67.
    Jayakumar N and Kolandaivel P 2000 Studies of isomer stability using the maximum hardness principle (MHP) Int. J. Quant. Chem. 76 648CrossRefGoogle Scholar
  68. 68.
    Neog B, Sarmah N, Kar R and Bhattacharyya P K 2011 Effect of external electric field on aziridinium ion intermediate: A DFT study Comput. Theor. Chem. 967 60CrossRefGoogle Scholar
  69. 69.
    Sarma R, Bhattacharyya P K and Baruah J B 2011 Short range interactions in molecular complexes of 1, 4-benzenediboronic acid with aromatic N-oxides Comput. Theor. Chem. 963 141CrossRefGoogle Scholar

Copyright information

© Indian Academy of Sciences 2017

Authors and Affiliations

  • Biswa Jyoti Dutta
    • 1
  • Nabajit Sarmah
    • 1
  • Pradip KR Bhattacharyya
    • 1
  1. 1.Department of ChemistryArya Vidyapeeth CollegeGuwahatiIndia

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