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Journal of Computer-Aided Molecular Design

, Volume 33, Issue 10, pp 905–912 | Cite as

Application of the 3D-RISM-KH molecular solvation theory for DMSO as solvent

  • Dipankar Roy
  • Andriy KovalenkoEmail author
Article
  • 77 Downloads

Abstract

The molecular solvation theory in the form of the Three-Dimensional Reference Interaction Site Model (3D-RISM) with Kovalenko–Hirata (KH) closure relation is benchmarked for use with dimethyl sulfoxide (DMSO) as solvent for (bio)-chemical simulation within the framework of integral equation formalism. Several force field parameters have been tested to correctly reproduce solvation free energy in DMSO, ion solvation in DMSO, and DMSO coordination prediction. Our findings establish a united atom (UA) type parameterization as the best model of DMSO for use in 3D-RISM-KH theory based calculations.

Keywords

DMSO 3D-RISM-KH Solvation free energy Force field validation Solvent coordination Ion coordination 

Notes

Acknowledgements

This work was financially supported by the NSERC Discovery Grant (RES0029477), and the Alberta Prion Research Institute Explorations VII Research Grant (RES0039402). Generous computing time provided by WestGrid (www.westgrid.ca) and Compute Canada/Calcul Canada (www.computecanada.ca) is acknowledged.

Compliance with ethical standards

Conflict of interest

The authors declare that they have no conflict of interest.

Supplementary material

10822_2019_238_MOESM1_ESM.docx (6.5 mb)
Supplementary file1 (DOCX 6664 kb)

References

  1. 1.
    Papich MG (2016) Saunders handbook of veterinary drugs, 4th edn. Elsevier, St. LouisGoogle Scholar
  2. 2.
    Babij NR, McCusker EO, Whiteker GT, Canturk B, Choy N, Creemer LC, De Amicis CV, Hewlwtt NM, Johnson PL, Knobelsdorf JA, Li F, Lorsbach BA, Nugent BM, Ryan SJ, Smith MR, Yang Q (2016) Org Proc Res Dev 20:661–667Google Scholar
  3. 3.
    Zhou B, Zhao L, Shen M, Zhao J, Shi X (2017) J Mater Chem B 5:1542–1550Google Scholar
  4. 4.
    Clark T, Murray JS, Lane P, Politzer P (2008) J Mol Model 14:689–697PubMedGoogle Scholar
  5. 5.
    Marren K (2011) Physician Sportsmed 39:75–82Google Scholar
  6. 6.
    Soper AK, Luzar A (1992) J Chem Phys 97:1320Google Scholar
  7. 7.
    Pekary AE (1974) J Phys Chem 78:1744–1746Google Scholar
  8. 8.
    Higashigaki Y, Christensen DH, Wang CH (1981) J Phys Chem 85:2531–2535Google Scholar
  9. 9.
    Onthong U, Megyes T, Bako I, Radnai T, Grosz T, Hermansson K, Probst M (2004) Phys Chem Chem Phys 9:2136–2144Google Scholar
  10. 10.
    Rao BG, Singh UC (1990) J Am Chem Soc 112:3803–3811Google Scholar
  11. 11.
    Luzar A, Soper AK, Chandler D (1993) J Chem Phys 99:6836–6847Google Scholar
  12. 12.
    Liu H, Müeller-Plathe F, van Gunsteren WF (1995) J Am Chem Soc 117:4363Google Scholar
  13. 13.
    Bordat P, Sacristan J, Reith D, Girard S, Glättli A, Müller-Plathe F (2003) Chem Phys Lett 374:201–205Google Scholar
  14. 14.
    Zheng Y-J, Ornstein RL (1996) J Am Chem Soc 118:4175–4180Google Scholar
  15. 15.
    Vishnyakov A, Lyubartsev AP, Laaksonen A (2001) J Phys Chem A 105:1702–1710Google Scholar
  16. 16.
    Geerke DP, Oostenbrink C, van der Vegt NFA, van Gunsteren WF (2004) J Phys Chem B 108:1436–1445Google Scholar
  17. 17.
    Chalaris M, Marinakis S, Dellis D (2008) Fluid Phase Equilib 267:47–60Google Scholar
  18. 18.
    Strader ML, Feller SE (2002) J Phys Chem A 106:1074–1080Google Scholar
  19. 19.
    Mrázková E, Hobza P (2003) J Phys Chem A 107:71032–71039Google Scholar
  20. 20.
    Skaf MS, Vechi SM (2003) J Chem Phys 119:2181Google Scholar
  21. 21.
    Venkataramanan NS, Suvitha A (2018) J Mol Graph Model 81:50–59PubMedGoogle Scholar
  22. 22.
    Chandler D, McCoy JD, Singer SJ (1986) J Chem Phys 85:5971–5976Google Scholar
  23. 23.
    Chandler D, McCoy JD, Singer SJ (1986) J Chem Phys 85:5977–5982Google Scholar
  24. 24.
    Lowden LJ, Chandler D (1973) J Chem Phys 59:6587–6595Google Scholar
  25. 25.
    Johnson J, Case DA, Yamazaki T, Gusarov S, Kovalenko A, Luchko T (2016) J Phys Condens Matter 28:344002PubMedPubMedCentralGoogle Scholar
  26. 26.
    Luchko T, Blinov N, Limon GC, Joyce KP, Kovalenko A (2016) J Comput Aided Mol Des 30:1115–1127PubMedGoogle Scholar
  27. 27.
    Kovalenko A, Hirata F (2005) Phys Chem Chem Phys 7:1785–1793PubMedGoogle Scholar
  28. 28.
    Kovalenko A (2015) Condens Matter Phys 18:32601Google Scholar
  29. 29.
    Tsednee T, Luchko T (2019) Phys Rev B 99:032130Google Scholar
  30. 30.
    Palmer DS, Frolov A, Ratkova EL, Fedorov MV (2010) J Phys Condens Matter 22:492101PubMedGoogle Scholar
  31. 31.
    Kovalenko A (2017) Multiscale modeling of solvation. In: Breitkopf C, Swider-Lyons K (eds) Springer handbook of electrochemical energy. Springer, Berlin, pp 95–139Google Scholar
  32. 32.
    Roy D, Kovalenko A (2019) J Phys Chem A 123:4087–4093PubMedGoogle Scholar
  33. 33.
    Misin M, Fedorov MV, Palmer DS (2015) J Chem Phys 142:091105PubMedGoogle Scholar
  34. 34.
    Roy D, Blinov N, Kovalenko A (2017) J Phys Chem B 121:9268–9273PubMedGoogle Scholar
  35. 35.
    Hinge VK, Roy D, Kovalenko A (2019) J Comput Aided Mol Des 33:605–611PubMedGoogle Scholar
  36. 36.
    Roy D, Hinge VK, Kovalenko A (2019) ACS Omega 4:3055–3060Google Scholar
  37. 37.
    Heil J, Tomazic D, Egbers S, Kast SM (2014) J Mol Model 20:2161PubMedGoogle Scholar
  38. 38.
    Marenich AV, Kelly CP, Thompson JD, Hawkins GD, Chambers CC, Giesen DJ, Winget P, Cramer CJ, Truhlar DG (2012) Minnesota solvation database—version 2012. University of Minnesota, MinneapolisGoogle Scholar
  39. 39.
    Inada Y, Hayashi H, Sugimoto K, Funahashi S (1999) J Phys Chem A 103:1401–1406Google Scholar
  40. 40.
    Case DA, Ben-Shalom IY, Brozell SR, Cerutti DS, Cheatham TE III, Cruzeiro VWD, Darden TA, Duke RE, Ghoreishi D, Gilson MK, Gohlke H, Goetz AW, Greene D, Harris R, Homeyer N, Izadi S, Kovalenko A, Kurtzman T, Lee TS, LeGrand S, Li P, Lin C, Liu J, Luchko T, Luo R, Mermelstein DJ, Merz KM, Miao Y, Monard G, Nguyen C, Nguyen H, Omelyan I, Onufriev A, Pan F, Qi R, Roe DR, Roitberg A, Sagui C, Schott-Verdugo S, Shen J, Simmerling CL, Smith J, Salomon-Ferrer R, Swails J, Walker RC, Wang J, Wei H, Wolf RM, Wu X, Xiao L, York DM, Kollman PA (2018) AMBER 2018. University of California, San FranciscoGoogle Scholar
  41. 41.
    Hirata F, Pettitt BM, Rossky PJ (1982) J Chem Phys 77:509Google Scholar
  42. 42.
    Zhao Y, Truhlar DG (2008) Theor Chem Acc 120:215Google Scholar
  43. 43.
    McLean AD, Handler GS (1980) J Chem Phys 72:5639Google Scholar
  44. 44.
    Raghavachari K, Binkley JS, Seeger R, Pople JA (1980) J Chem Phys 72:650Google Scholar
  45. 45.
    Frisch MJ, Trucks GW, Schlegel HB, Scuseria GE, Robb MA, Cheeseman JR, Scalmani G, Barone V, Petersson GA, Nakatsuji H, Li X, Caricato M, Marenich AV, Bloino J, Janesko BG, Gomperts R, Mennucci B, Hratchian HP, Ortiz JV, Izmaylov AF, Sonnenberg JL, Williams-Young D, Ding F, Lipparini F, Egidi F, Goings J, Peng B, Petrone A, Henderson T, Ranasinghe D, Zakrzewski VG, Gao J, Rega N, Zheng G, Liang W, Hada M, Ehara M, Toyota K, Fukuda R, Hasegawa J, Ishida M, Nakajima T, Honda Y, Kitao O, Nakai H, Vreven T, Throssell K, Montgomery JA Jr, Peralta JE, Ogliaro F, Bearpark MJ, Heyd JJ, Brothers EN, Kudin KN, Staroverov VN, Keith TA, Kobayashi R, Normand J, Raghavachari K, Rendell AP, Burant JC, Iyengar SS, Tomasi J, Cossi M, Millam JM, Klene M, Adamo C, Cammi R, Ochterski JW, Martin RL, Morokuma K, Farkas O, Foresman JB, Fox DJ (2016) Gaussian 16, revision B.01. Gaussian Inc, WallingfordGoogle Scholar
  46. 46.
    O’Boyle NM, Banck M, James CA, Morley C, Vandermeersch T, Hutchison GR (2011) J Cheminform 3:33PubMedPubMedCentralGoogle Scholar
  47. 47.
    Rappe AK, Casewit CJ, Colwell KS, Goddard WA, Skiff WM (1992) J Am Chem Soc 114:10024–10035Google Scholar
  48. 48.
    Dewar MJS, Zoebisch EG, Healy EF, Stewart JJP (1985) J Am Chem Soc 107:3902–3909Google Scholar
  49. 49.
    MOPAC (2016) Stewart JJP. Stewart Computational Chemistry, Colorado SpringsGoogle Scholar
  50. 50.
    Chai J-D, Head-Gordon M (2008) Phys Chem Chem Phys 10:6615–6620PubMedGoogle Scholar
  51. 51.
    Weigend F (2006) Phys Chem Chem Phys 8:1057–1065PubMedGoogle Scholar
  52. 52.
    Chan EJ, Cox BG, Harrowfield JM, Ogden MI, Skelton BW, White AH (2004) Inorg Chim Acta 357:2365Google Scholar
  53. 53.
    Persson I, Persson P, Sandstrom A, Ullstrom A-S (2002) J Chem Soc Dalton Trans 7:1256Google Scholar
  54. 54.
    Glatz M, Schroffenegger M, Weil M, Kirchner K (2016) Acta Crystallogr E 72:904Google Scholar
  55. 55.
    Tzou J-R, Mullaney M, Norman RE (1995) Acta Crystallogr C 51:2249–2252Google Scholar
  56. 56.
    Borin IA, Skaff MS (1999) J Chem Phys 110:6412Google Scholar
  57. 57.
    LeBel RG, Goring DAI (1962) J Chem Eng Data 7:100–101Google Scholar
  58. 58.
    Chaban VV (2018) Phys Chem Chem Phys 20:23754–23761PubMedGoogle Scholar
  59. 59.
    Perera A, Lovrincevic B (2018) Mol Phys 116:21–22Google Scholar

Copyright information

© Springer Nature Switzerland AG 2019

Authors and Affiliations

  1. 1.Department of Mechanical Engineering, 10-203 Donadeo Innovation Centre for EngineeringUniversity of AlbertaEdmontonCanada
  2. 2.Nanotechnology Research CentreEdmontonCanada

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