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Natures of benzene-water and pyrrole-water interactions in the forms of σ and π types: theoretical studies from clusters to liquid mixture

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Abstract

A combined and sequential use of quantum mechanical (QM) calculations and classical molecular dynamics (MD) simulations was made to investigate the σ and π types of hydrogen bond (HB) in benzene-water and pyrrole-water as clusters and as their liquid mixture, respectively. This paper aims at analyzing similarities and differences of these HBs resulted from QM and MD on an equal footing. Based on the optimized geometry at ωb97xD/aug-cc-pVTZ level of theory, the nature and property of σ and π types of HBs are unveiled by means of atoms in molecules (AIM), natural bond orbital (NBO) and energy decomposition analysis (EDA). In light of the above findings, MD simulation with OPLS-AA and SPC model was applied to study the liquid mixture at different temperatures. The MD results further characterize the behavior and structural properties of σ and π types HBs, which are somewhat different but reasonable for the clusters by QM. Finally, we provide a reasonable explanation for the different solubility between benzene/water and pyrrole/water.

The σ and π types of hydrogen bond as benzene-water and pyrrole-water clusters in gas; Snapshot of benzene/water and pyrrole/water as 1:1 liquid mixture extracted from the MD simulations

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References

  1. Mata I, Alkorta I, Molins E, Espinosa E (2010) Chem Eur J 16:2442–2452

    Article  CAS  Google Scholar 

  2. Tsuzuki S, Uchimaru T (2006) Curr Org Chem 10:745–762

    Article  CAS  Google Scholar 

  3. Scheiner S, Kar T, Pattanayak J (2002) J Am Chem Soc 124:13257–13264

    Article  CAS  Google Scholar 

  4. Riley KE, Pitoňák M, Černý J, Hobza P (2010) J Chem Theory Comput 6:66–80

    Article  CAS  Google Scholar 

  5. Donoso-Tauda O, Jaque P, Santos JC (2011) Phys Chem Chem Phys 13:1552–1559

    Article  CAS  Google Scholar 

  6. Tsuzuki S, Fujii A (2008) Phys Chem Chem Phys 10:2584–2594

    Article  CAS  Google Scholar 

  7. Tsuzuki S, Honda K, Uchimaru T, Mikami M, Tanabe K (2000) J Am Chem Soc 122:11450–11458

    Article  CAS  Google Scholar 

  8. Meyer EA, Castellano RK, Diederich F (2003) Angew Chem Int Ed 42:1210–1250

    Article  CAS  Google Scholar 

  9. Hobza P, Müller-Dethlefs K (2010) Non-covalent interactions: theory and experiment. RSC, Cambridge

    Google Scholar 

  10. Carles S, Lecomte F, Schermann JP, Desfrançáois C (2000) J Phys Chem A 104:10662–10668

    Article  CAS  Google Scholar 

  11. Maris A, Melandri S, Miazzi M, Zerbetto F (2008) ChemPhysChem 9:1303–1308

    Article  CAS  Google Scholar 

  12. Crittenden DL (2009) J Phys Chem A 113:1663–1669

    Article  CAS  Google Scholar 

  13. Mishra BK, Sathyamurthy N (2007) J Phys Chem A 111:2139–2147

    Article  CAS  Google Scholar 

  14. Schwartz CP, Uejio JS, Duffin AM, England AH, Prendergast D, Saykally RJ (2009) J Chem Phys 131:114509

    Google Scholar 

  15. Nagy PI, Durant GJ, Smith DA (1993) J Am Chem Soc 115:2912–2922

    Article  CAS  Google Scholar 

  16. Janjić GV, Veljković DŽ, Zarić SD (2011) Cryst Growth Des 11:2680–2683

    Article  CAS  Google Scholar 

  17. Suzuki S, Green PG, Bumgarner RE, Dasgupta S, Goddard WA III, Blake GA (1992) Science 257:942–945

    Article  CAS  Google Scholar 

  18. Augspurger JD, Dykstra CE, Zwier TS (1993) J Phys Chem 97:980–984

    Article  CAS  Google Scholar 

  19. Tarakeshwar P, Choi HS, Lee SJ, Lee JY, Kim KS, Ha T-K, Jang JH, Lee JG, Lee H (1999) J Chem Phys 111:5838–5850

    Article  CAS  Google Scholar 

  20. Prakash M, Samy KG, Subramanian V (2009) J Phys Chem A 113:13845–13852

    Article  CAS  Google Scholar 

  21. Feller D (1999) J Phys Chem A 103:7558–7561

    Article  CAS  Google Scholar 

  22. Ma J, Alfè D, Michaelides A, Wang E (2009) J Chem Phys 130:154303

    Article  CAS  Google Scholar 

  23. Li S, Cooper VR, Thonhauser T, Puzder A, Langreth DC (2008) J Phys Chem A 112:9031–9036

    Article  CAS  Google Scholar 

  24. Slipchenko LV, Gordon MS (2009) J Phys Chem A 113:2092–2102

    Article  CAS  Google Scholar 

  25. Gierszal KP, Davis JG, Hands MD, Wilcox DS, Slipchenko LV, Ben-Amotz DJ (2011) J Phys Chem Lett 2:2930–2933

    Article  CAS  Google Scholar 

  26. Raschke TM, Levitt M (2004) J Phys Chem B 108:13492–13500

    Article  CAS  Google Scholar 

  27. Keresztúri Á, Jedlovszky P (2005) J Phys Chem B 109:16782–16793

    Article  CAS  Google Scholar 

  28. Ikawa S-I (2005) J Chem Phys 123:244507

    Article  CAS  Google Scholar 

  29. Gamieldien MR, Strümpfer J, Naidoo KJ (2012) J Phys Chem B 116:324–331

    Article  CAS  Google Scholar 

  30. Allesch M, Lightstone FC, Schwegler E, Galli G (2008) J Chem Phys 128:014501

    Article  CAS  Google Scholar 

  31. Allesch M, Schwegler E, Galli G (2007) J Phys Chem B 111:1081–1089

    Article  CAS  Google Scholar 

  32. Urahata S, Canuto S (1999) Chem Phys Lett 313:235–240

    Article  CAS  Google Scholar 

  33. Tubergen MJ, Andrews AM, Kuczkowski RL (1993) J Phys Chem 97:7451–7457

    Article  CAS  Google Scholar 

  34. Matsumoto Y, Honma K (2009) J Chem Phys 130:054311

    Article  CAS  Google Scholar 

  35. Li Y, Liu X-H, Wang X-Y, Lou N-Q (1999) J Phys Chem A 103:2572–2579

    Article  CAS  Google Scholar 

  36. Kumar A, Kołaski M, Kim KS (2008) J Chem Phys 128:034304

    Article  CAS  Google Scholar 

  37. Sobolewski AL, Domcke W (2000) Chem Phys Lett 321:479–484

    Article  CAS  Google Scholar 

  38. Frank I, Damianos K (2008) Chem Phys 343:347–352

    Article  CAS  Google Scholar 

  39. Riley KE, Pitoňák M, Jurečka P, Hobza P (2010) Chem Rev 110:5023–5063

    Article  CAS  Google Scholar 

  40. Hohenstein EG, Sherrill CD (2009) J Phys Chem A 113:878–886

    Article  CAS  Google Scholar 

  41. Grimme S, Antony J, Ehrlich S, Krieg H (2010) J Chem Phys 132:154104

    Article  CAS  Google Scholar 

  42. Goerigk L, Grimme S (2011) Phys Chem Chem Phys 13:6670–6688

    Article  CAS  Google Scholar 

  43. Grimme S (2011) WIREs Comput Mol Sci 1:211–228

    Article  CAS  Google Scholar 

  44. Burns LA, Vázquez-Mayagoitia Á, Sumpter BG, Sherrill CD (2011) J Chem Phys 134:084107

    Article  CAS  Google Scholar 

  45. Chai J-D, Head-Gordon M (2008) Phys Chem Chem Phys 10:6615–6620

    Article  CAS  Google Scholar 

  46. Chai J-D, Head-Gordon M (2008) J Chem Phys 128:084106

    Article  CAS  Google Scholar 

  47. Tian B, Eriksson ESE, Eriksson LA (2010) J Chem Theory Comput 6:2086–2094

    Article  CAS  Google Scholar 

  48. Kang YK, Byun BJ (2010) J Comput Chem 31:2915–2923

    Article  CAS  Google Scholar 

  49. Simon S, Duran M (1996) J Chem Phys 105:11024–11031

    Article  CAS  Google Scholar 

  50. Boys SF, Bernardi F (1970) Mol Phys 19:553–566

    Article  CAS  Google Scholar 

  51. Frisch MJ, Trucks GW, Schlegel HB, Scuseria GE, Robb MA, Cheeseman JR et al. (2010) Gaussian 09 C01. Gaussian Inc, Wallingford, CT. <http://www.gaussian.com>

  52. Schwabe T, Grimme S (2007) Phys Chem Chem Phys 9:3397–3406

    Article  CAS  Google Scholar 

  53. Zhao Y, Truhlar DG (2008) Acc Chem Res 41:157–167

    Article  CAS  Google Scholar 

  54. Bader RFW (1991) Chem Rev 91:893–928

    Article  CAS  Google Scholar 

  55. Bader RFW (1990) Atoms in molecules: a quantum theory. Clarendon, Oxford

    Google Scholar 

  56. Grabowski SJ, Ugalde JM (2010) J Phys Chem A 114:7223–7229

    Article  CAS  Google Scholar 

  57. Keith TA, AIMAll, Version 10.03.25, <http://aim.tkgristmill.com>

  58. Lu T, Chen F (2012) J Comput Chem 33:580–592

    Article  CAS  Google Scholar 

  59. Lu T. Multiwfn, Version 2.3.3, <http://multiwfn.codeplex.com>

  60. Reed AE, Curtiss LA, Weinhold F (1988) Chem Rev 88:899–926

    Article  CAS  Google Scholar 

  61. Morokuma K (1971) J Chem Phys 55:1236–1244

    Article  CAS  Google Scholar 

  62. Ziegler T, Rauk A (1977) Theor Chim Acta 46:1–10

    CAS  Google Scholar 

  63. Mitoraj MP, Michalak A, Ziegler T (2009) J Chem Theory Comput 5:962–975

    Article  CAS  Google Scholar 

  64. Grimme S, Antony J, Schwabe T, Mück-Lichtenfeld C (2007) Org Biomol Chem 5:741–758

    Article  CAS  Google Scholar 

  65. Baerends EJ, Autschbach J, Bashford D, Bérces A, Bickelhaupt FM, Bo C et al (2012) ADF version 2012.01, SCM, Theoretical Chemistry, Vrije Universiteit, Amsterdam, The Netherlands.<http://www.scm.com>

  66. te Velde G, Bickelhaupt FM, Baerends EJ, Fonseca Guerra C, van Gisbergen SJA, Snijders JG, Ziegler T (2001) J Comput Chem 22:931–967

    Article  Google Scholar 

  67. Bickelhaupt FM, Baerends EJ (2000) Kohn-Sham density functional theory: predicting and understanding chemistry. In: Lipkowitz KB, Boyd DB (eds) vol. 15 Rev Comput Chem. Wiley-VCH, New York, pp 1–86 doi:10.1002/9780470125922.ch1

  68. Liu Z (2009) J Phys Chem A 113:6410–6414

    Article  CAS  Google Scholar 

  69. Allen MP, Tildesley DJ (1987) Computer simulation of liquids. Clarendon, Oxford

    Google Scholar 

  70. Jorgensen WL, Maxwell DS, Tirado-Rives J (1996) J Am Chem Soc 117:11225–11236

    Article  Google Scholar 

  71. Ponder JW. Tinker, version 4.2, <http://dasher.wustl.edu/tinker>

  72. Mark P, Nilsson L (2001) J Phys Chem A 105:9954–9960

    Article  CAS  Google Scholar 

  73. Berweger CD, van Gunsteren WF, Müller-Plathe F (1995) Chem Phys Lett 232:429–436

    Article  CAS  Google Scholar 

  74. McDonald NA, Jorgensen WL (1998) J Phys Chem B 102:8049–8059

    Article  CAS  Google Scholar 

  75. Cornell WD, Cieplak P, Bayly CI, Gould IR, Merz KM, Ferguson DM, Spellmeyer DC, Fox T, Caldwell JW, Kollman PA (1995) J Am Chem Soc 117:5179–5197

    Article  CAS  Google Scholar 

  76. Joseph J, Jemmis ED (2007) J Am Chem Soc 129:4620–4632

    Article  CAS  Google Scholar 

  77. Pluhácková K, Hobza P (2007) ChemPhysChem 8:1352–1356

    Article  CAS  Google Scholar 

  78. Koch U, Popelier PLA (1995) J Phys Chem 99:9747–9754

    Article  CAS  Google Scholar 

  79. Lipkowski P, Grabowski SJ, Robinson TL, Leszczynski J (2004) J Phys Chem A 108:10865–10872

    Article  CAS  Google Scholar 

  80. Johnson ER, Keinan S, Mori-Sánchez P, Contreras-García J, Cohen AJ, Yang W (2010) J Am Chem Soc 132:6498–6506

    Google Scholar 

  81. Chocholoušová J, Špirko V, Hobza P (2004) Phys Chem Chem Phys 6:37–41

    Article  CAS  Google Scholar 

  82. Alabugin IV, Manoharan M, Peabody S, Weinhold F (2003) J Am Chem Soc 125:5973–5987

    Article  CAS  Google Scholar 

  83. Zhou P-P, Qiu W-Y (2009) J Phys Chem A 113:10306–10320

    Article  CAS  Google Scholar 

  84. Rozas I (2007) Phys Chem Chem Phys 9:2782–2790

    Article  CAS  Google Scholar 

  85. Raschke TM, Levitt M (2005) Proc Natl Acad Sci U S A 102:6777–6782

    Article  CAS  Google Scholar 

  86. Chandler D (2005) Nature 437:640–647

    Article  CAS  Google Scholar 

  87. Lide DR (ed) (2010) CRC handbook of chemistry and physics, 90th edn., (internet version 2010). CRC Press/Taylor and Francis, Boca Raton

    Google Scholar 

Download references

Acknowledgments

Financial support by the National Natural Science Foundation of China (No. 21173069) as well as the Science and Technology Foundation of Guangdong Province, China (2010B060900084) are acknowledged. Authors also thank Dr. Tian Lu at the Institute of Chemical and Biological Technology, University of Science and Technology Beijing for helpful discussion. The computation of the Gaussian is supported by the School of Chemical and Environmental Sciences, Henan Normal University.

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Authors and Affiliations

  1. KLGHEI of Environment and Energy Chemistry, School of Chemistry and Chemical Engineering, Sun Yat-sen University, Guangzhou, 510275, China

    Wei Gao, Jiqing Jiao, Huajie Feng & Liuping Chen

  2. College of Pharmacy, Guangdong Pharmaceutical University, Guangzhou, 510006, China

    Wei Gao

  3. School of Chemical and Environmental Sciences, Key Laboratory of Green Chemical Media and Reactions, Ministry of Education, Henan Normal University, Xinxiang, Henan, 453007, China

    Xiaopeng Xuan

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  1. Wei Gao
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Correspondence to Liuping Chen.

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Gao, W., Jiao, J., Feng, H. et al. Natures of benzene-water and pyrrole-water interactions in the forms of σ and π types: theoretical studies from clusters to liquid mixture. J Mol Model 19, 1273–1283 (2013). https://doi.org/10.1007/s00894-012-1659-x

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