Theoretical Chemistry Accounts

, Volume 130, Issue 4–6, pp 965–979 | Cite as

A quantum mechanical study of bioactive 3-chloro-2,5-dihydroxybenzyl alcohol through substitutions

  • Anoja Pushpamali Wickrama Arachchilage
  • Yong Wang
  • Feng Wang
Regular Article


Electronic structures, vibrational and ionization spectra of 3-chloro-2,5-dihydroxybenzyl alcohol (CHBA), a novel bioactive benzene derivative from marine fungi, are presented in this study using quantum mechanical methods such as density functional theory and outer valence Green function method. A number of related benzene derivatives such as chlorobenzene, 3-chlorobenzyl alcohol, hydroquinone and chlorohydroquinone are also studied, in order to assist our understanding of the structure, properties and interactions of CHBA. Vibrational spectra such as infrared (IR) and Raman spectra reveal signatures of the functional group substitutions and their hydrogen bond interactions in CHBA. Solvent effects on the IR spectra of CHBA with polar and non-polar solvents are simulated using the polarizable continuum model (PCM) and cause redshifts of some of the IR spectral frequencies with respect to the gas phase values at both ends of the 400–4,000 cm−1 region. The inner-shell ionization spectra, in particular the C–K spectra of the benzene derivatives, reveal detailed chemical environmental changes of the carbon and oxygen atoms due to the substitutions. The valence ionization energies of the highest occupied molecular orbital (HOMO) and the 3rd HOMO, (HOMO-2) of the benzene derivatives respond significantly to the substitutions, whereas the charge distributions of the HOMO and 2nd HOMO (HOMO-1) do not change significantly from their benzene counterparts. As a result, the 3rd HOMO changes significantly in both ionization energies and the charge distributions, which can serve as a signature of the substitutions among the benzene derivatives.


Density functional theory study Bioactive compounds 3-chloro-2,5-dihydroxybenzyl alcohol Benzene derivatives Electronic structures IR and Raman spectroscopy and ionization spectroscopy 



This paper is dedicated to Professor A. Imaruma on the occasion of his 77th birthday in 2011, which coincides with the International Year of Chemistry. FW would like to thank Prof. Y. Aoki for her kind invitation to contribute to this special issue. The project is supported by the Australian Research Council (ARC). National Computational Infrastructure (NCI) at the Australian National University for the award under the Merit Allocation Scheme, Victorian Partnership for Advanced Computing (VPAC) and Swinburne University Supercomputing Facilities are acknowledged. APWA acknowledges the Swinburne University Centenary Postgraduate Research Award.


  1. 1.
    Chen Y-PP, Ivanova EP, Wang F, Carloni P (2010) Bioinformatics. In: Mander L, Lui H-W (eds) In comprehensive natural products II chemistry and biology, vol 9. Elsevier, Oxford, p 569Google Scholar
  2. 2.
    Butler MS (2005) Nat Prod Rep 22:162CrossRefGoogle Scholar
  3. 3.
    Chin Y-W, Balaunas MJ, Chai HB, Kinghorn AD (2006) AAPS J 8:E239Google Scholar
  4. 4.
    Harvey AL (2007) Curr Opin Chem Biol 11:480CrossRefGoogle Scholar
  5. 5.
    Kwong TF, Miao L, Li X, Qian PY (2006) Marine Biotechnol 8:634CrossRefGoogle Scholar
  6. 6.
    Sequin-Frey M, Tamm C (1971) Helv Chim Acta 54:84CrossRefGoogle Scholar
  7. 7.
    McCorkindale NJ, Roy TP, Hutchinson SA (1972) Tetrahedron 28:1107CrossRefGoogle Scholar
  8. 8.
    Sakamura S, Ito J, Sakai R (1971) Agr Biol Chem 35:105CrossRefGoogle Scholar
  9. 9.
    Zhang Y, Ahn EY, Jiang Y, Kim DK, Kang SG, Wu C, Kang SW, Park JS, Son BW, Jung JH (2007) Int J Oncol 31:1317Google Scholar
  10. 10.
    Zhang H, Xie H, Qiu SX, Xue J, Wei X (2008) Biosci Biotechnol Biochem 72:1746CrossRefGoogle Scholar
  11. 11.
    Wood EJ (2006) In: Crowe J, Bradshaw T, Monk P (eds) Chemistry for the biosciences: the essential concepts. Oxford University Press, Oxford, p 594Google Scholar
  12. 12.
    Hoffmann R, Imamura A, Hehre WJ (1968) J Am Chem Soc 90:1499CrossRefGoogle Scholar
  13. 13.
    Wickrama Arachchilage AP, Wang F, Feyer V, Plekan O, Prince KC (2010) J Chem Phys 133:174319CrossRefGoogle Scholar
  14. 14.
    Schmidt MW, Baldridge KK, Boatz JA, Elbert ST, Gordon MS, Jensen JH, Koseki S, Matsunaga N, Nguyen KA, Su SJ, Windus TL, Dupuis M, Montgomery JA (1993) J Comput Chem 14:1347CrossRefGoogle Scholar
  15. 15.
    Frisch MJ, Trucks GW, Schlegel HB, Scuseria GE, Robb MA, Cheeseman JR, Montgomery JJA, Vreven T, Kudin KN, Burant JC, Millam JM, Iyengar SS, Tomasi J, Barone V, Mennucci B, Cossi M, Scalmani G, Rega N, Petersson GA, Nakatsuji H, Hada M, Ehara M, Toyota K, Fukuda R, Hasegawa J, Ishida M, Nakajima T, Honda Y, Kitao O, Nakai H, Kelna M, Li X, Knox JE, Hratchian HP, Cross JB, Adamo C, Jaramillo J, Gomperts R, Stratmann RE, Yazyev O, Austin AJ, Cammi R, Pomelli C, Ochterski JW, Ayala PY, Morokuma K, Voth GA, Salvador P, Dannenberg JJ, Zakrzewski VG, Dapprich A, Daniels AD, Strain MC, Farkas O, Malick DK, Rabuck AD, Raghavachari K, Foresman JB, Ortiz JV, Cui Q, Baboul AG, Clifford S, Cioslowski J, Stefanov BB, Liu G, Liashenko A, Piskorz P, Komaromi I, Martin RL, Fox DJ, Keith T, Ak-Laham MA, Peng CY, Nanayakkara A, Challacombe M, Gill PMW, Johnson B, Chen W, Wong MW, Gonzalez C, Pople JA (2004) Gaussian03; Gaussian, Inc., WallingfordGoogle Scholar
  16. 16.
    Wickrama Arachchilage AP, Feyer V, Prince KC, Wang F (2011) Synchrotron sourced X-ray photoemission spectroscopy of dipeptide phenylalanylphenylalanine, to be submittedGoogle Scholar
  17. 17.
    Cossi M, Barone V, Cammi R, Tomasi J (1996) Chem Phys Lett 255:327CrossRefGoogle Scholar
  18. 18.
    Ayers P (2006) Theor Chem Acc 115:370CrossRefGoogle Scholar
  19. 19.
    Hirshfeld FL (1977) Theor Chim Acta 44:129CrossRefGoogle Scholar
  20. 20.
    Chong DP, van Lenthe E, van Gisbergen S, Baerends EJ (2004) J Comput Chem 25:1030CrossRefGoogle Scholar
  21. 21.
    van Leeuwen R, Baerends EJ (1994) Phys Rev A 49:2421CrossRefGoogle Scholar
  22. 22.
    Baerends EJ, Autschbach J, Bérces A, Bo C, Boerrigter PM, Cavallo L, Chong DP, Deng L, Dickson RM, Ellis DE, van Faassen M, Fan L, Fischer TH, Guerra CF, van Gisbergen SJA, Groeneveld JA, Gritsenko OV, Grüning M, Harris FE, van den Hoek P, Jacobsen H, Jensen L, van Kessel G, Kootstra F, van Lenthe E, McCormack D, Michalak A, Osinga VP, Patchkovskii S, Philipsen PHT, Post D, Pye CC, Ravenek W, Ros P, Schipper PRT, Schreckenbach G, Snijders JG, Solà M, Swart M, Swerhone D, te Velde G, Vernooijs P, Versluis L, Visser O, Wang F, van Wezenbeek E, Wiesenekker G, Wolff SK, Woo TK, Yakovlev A, Ziegler T (2006) Theo Chem ADF 2006.01, SCM; Vrije Universiteit, AmsterdamGoogle Scholar
  23. 23.
    Selvam L, Vasilyev V, Wang F (2009) J Phys Chem B 113:11496CrossRefGoogle Scholar
  24. 24.
    Ahemd M, Ganesan A, Wang F, Prince K, Feyer V, Plekan O (2011) Determination of X-ray photoelectron spectra of β-lactam: core and valence, to be submittedGoogle Scholar
  25. 25.
    Noorizadeh S, Dardab M (2010) Chem Phys Lett 493:376CrossRefGoogle Scholar
  26. 26.
    Cederbaum LS (1975) J Phys B At Mol Phys 8:290CrossRefGoogle Scholar
  27. 27.
    Cederbaum LS, Domcke W (1977) Adv Chem Phys 36:205CrossRefGoogle Scholar
  28. 28.
    von Niessen W, Schirmer J, Cederbaum LS (1984) Comput Phys Rep 1:57CrossRefGoogle Scholar
  29. 29.
    Zakrzewski VG, von Niessen W (1993) J Comput Chem 14:13CrossRefGoogle Scholar
  30. 30.
    Zakrzewski VG, Ortiz JV (1995) Int J Quantum Chem 53:583CrossRefGoogle Scholar
  31. 31.
    Wang F, Downton M, Kidwani N (2005) J Theor Comp Chem 4:247CrossRefGoogle Scholar
  32. 32.
    Ganesan A, Wang F (2009) J Chem Phys 131:044321CrossRefGoogle Scholar
  33. 33.
    NIST Mass Spec Data Center, S.E. Stein, director, “Infrared Spectra” in NIST Chemistry WebBook, NIST Standard Reference Database Number 69. PJ Linstrom and WG Mallard (eds), National Institute of Standards and Technology, Gaithersburg MD, 20899, (retrieved October 28, 2009)
  34. 34.
    Scott AP, Radom L (1996) J Phys Chem 100:16502CrossRefGoogle Scholar
  35. 35.
    Huang Z, Yu W, Lin Z (2006) J Mole Struc Theochem 758:195CrossRefGoogle Scholar
  36. 36.
    Zhang G, Musgrave CB (2007) J Phys Chem A 111:1554CrossRefGoogle Scholar
  37. 37.
    Wang F, Pang W, Duffy P (2011) Mol Sim (in press)Google Scholar
  38. 38.
    Akai N, Kudoh S, Takayanagi M, Nakata M (2002) Chem Phys Lett 356:133CrossRefGoogle Scholar
  39. 39.
    Wilson HW (1974) Spectrochimica Acta A 30:2141CrossRefGoogle Scholar
  40. 40.
    Akai N, Kudoh S, Nakata M (2005) J Photochem Photobiol A Chem 169:47CrossRefGoogle Scholar
  41. 41.
    Huang Z, Yu W, Lin Z (2006) J Mol Struct THEOCHEM 758:195CrossRefGoogle Scholar
  42. 42.
    Selvam L, Chen F, Wang F (2010) Chem Phys Lett 500:327CrossRefGoogle Scholar
  43. 43.
    Jalkanen KJ, Degtyarenko IM, Nieminen RM, Cao X, Nafie LA, Zhu F, Barron LD (2008) Theor Chem Acc 119:191CrossRefGoogle Scholar
  44. 44.
    Gristsenko OV, van Leeuwen R, Baerends EJ (1995) Phys Rev A 52:1870CrossRefGoogle Scholar
  45. 45.
    Wang F (2005) J Mol Struct THEOCHEM 728:31CrossRefGoogle Scholar
  46. 46.
    Clark DT, Kilcast D, Adams DB, Musgrave WKR (1975) J Electron Spectrosc Rel Phenom 6:117CrossRefGoogle Scholar
  47. 47.
    Xie Y, Sherwood MA (1991) Chem Mater 3:164CrossRefGoogle Scholar
  48. 48.
    Fukui K, Yonezawa T, Shingu H (1952) J Chem Phys 20:722CrossRefGoogle Scholar
  49. 49.
    Stener M, Fronzoni G, Decleva P (2005) J Chem Phys 122:234301CrossRefGoogle Scholar
  50. 50.
    Fujisawa S, Ohno K, Masuda S, Harada Y (1986) J Am Chem Soc 108:6505CrossRefGoogle Scholar
  51. 51.
    Ballard RE, Jones J, Sutherland E, Read D, Inchley A (1986) Chem Phys Lett 126:311CrossRefGoogle Scholar
  52. 52.
    Duflot D, Flament JP, Heinesch J, Hubin-Franskin MJ (2000) J Electron Spectrosc Relat Phenom 113:79CrossRefGoogle Scholar
  53. 53.
    Cradock S, Muir JM, Rankin DWH (1990) J Mol Struct 220:205CrossRefGoogle Scholar
  54. 54.
    Onda M, Ohashi O, Yamaguchi I (1976) J Mol Struct 31:203CrossRefGoogle Scholar
  55. 55.
    Spinrad B (1946) J Am Chem Soc 68:617CrossRefGoogle Scholar
  56. 56.
    Caminati W, Melandri S, Favero LB (1994) J Chem Phys 100:8569CrossRefGoogle Scholar
  57. 57.
    McQuaidae BH, Banna MS (1988) Can J Chem 66:1919Google Scholar
  58. 58.
    Naves De Brito A, Svensson S, Keane MP, Karlsson L, Ågren H, Correia N (1992) Europhys Lett 20:205CrossRefGoogle Scholar

Copyright information

© Springer-Verlag 2011

Authors and Affiliations

  • Anoja Pushpamali Wickrama Arachchilage
    • 1
  • Yong Wang
    • 2
  • Feng Wang
    • 1
  1. 1.Faculty of Life and Social SciencesSwinburne University of TechnologyHawthorn, MelbourneAustralia
  2. 2.Chongqing Institute for Drug ControlChongqingPeople’s Republic of China

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