Skip to main content
SpringerLink
Log in

Effect of varying the 1–4 intramolecular scaling factor in atomistic simulations of long-chain N-alkanes with the OPLS-AA model

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

Abstract

A comprehensive molecular dynamics simulation study of n-alkanes using the optimized potential for liquid simulation with all-atoms (OPLS-AA) force field at ambient condition has been performed. Our results indicate that while simulations with the OPLS-AA force field accurately predict the liquid state mass density for n-alkanes with carbon number equal or less than 10, for n-alkanes with carbon number equal or exceeding 12, the OPLS-AA force field with the standard scaling factor for the 1–4 intramolecular Van der Waals and electrostatic interaction gives rise to a quasi-crystalline structure. We found that accurate predictions of the liquid state properties are obtained by successively reducing the aforementioned scaling factor for each increase of the carbon number beyond n-dodecane. To better understand the effects of reducing the scaling factor, its influence on the torsion potential profile, and the corresponding gauche-trans conformer distribution, heat of vaporization, melting point, and self-diffusion coefficient for n-dodecane were investigated. This relatively simple procedure enables more accurate predictions of the thermo-physical properties of longer n-alkanes.

 

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
Fig. 5
Fig. 6
Fig. 7
Fig. 8

Similar content being viewed by others

References

  1. MacKerell AD, Bashford D, Bellott M et al. (1998) J Phys Chem B 102:3586–3616

    Article  CAS  Google Scholar 

  2. 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 

  3. Jorgensen WL, TiradoRives J (1988) J Am Chem Soc 110:1657–1666

    Article  CAS  Google Scholar 

  4. Jorgensen WL, Maxwell DS, TiradoRives J (1996) J Am Chem Soc 118:11225–11236

    Article  CAS  Google Scholar 

  5. Weiner SJ, Kollman PA, Case DA, Singh UC, Ghio C, Alagona G, Profeta S, Weiner P (1984) J Am Chem Soc 106:765–784

    Article  CAS  Google Scholar 

  6. Thomas LL, Christakis TJ, Jorgensen WL (2006) J Phys Chem B 110:21198–21204

    Article  CAS  Google Scholar 

  7. Piringer OG, Baner AL (2008) Plastic packaging: interactions with food and pharmaceuticals, 2nd edn. Wiley-VCH, Weinheim

  8. Ungerer P, Nieto-Draghi C, Rousseau B, Ahunbay G, Lachet V (2007) J Mol Liq 134:71–89

    Article  CAS  Google Scholar 

  9. Firlej L, Kuchta B, Roth MW, Wexler C (2011) J Mol Model 17:811–816

    Article  CAS  Google Scholar 

  10. Bresme F, Chacon E, Tarazona P (2010) Mol Phys 108:1887–1898

    Article  CAS  Google Scholar 

  11. Siu SWI, Pluhackova K, Boeckmann RA (2012) J Chem Theor Comp 8:1459–1470. During the preparation of this manuscript, the paper by Siu et al. appeared that used a different approach to improve the performance of the OPLS-AA potential

    Article  CAS  Google Scholar 

  12. Plimpton S (1995) J Comp Phys 117:1–19. URL:http://lammps.sandia.gov/

    Google Scholar 

  13. Price ML, Ostrovsky D, Jorgensen WL (2001) J Comp Chem 22:1340–1352

    Article  CAS  Google Scholar 

  14. Darden T, York D, Pedersen D (1993) J Chem Phys 98:10089–10092

    Article  CAS  Google Scholar 

  15. Chandrasekhar S (1992) Liquid Crystals, 2nd edn. Cambridge University Press, Cambridge

    Book  Google Scholar 

  16. de Gennes PG, Prost J (1993) The Physics of Liquid Cyrstal, 2nd edn. Clarendon, Oxford

    Google Scholar 

  17. Cui ST, Gupta SA, Cummings PT, Cochran HD (1996) J Chem Phys 105:1214–1220

    Article  CAS  Google Scholar 

  18. Menger FM, D’Angelo LL (1988) J Am Chem Soc 110:8241–8244

    Article  CAS  Google Scholar 

  19. Casal HL, Yang PW, Mantsch HH (1986) Can J Chem 64:1544–1547

    Article  CAS  Google Scholar 

  20. Casal HL, Mantsch HH (1989) J Mol Struct 192:41–45

    Article  CAS  Google Scholar 

  21. Casal HL, Mantsch HH (1989) J Mol Struct 213:328–328

    Article  CAS  Google Scholar 

  22. Holler F, Callis JB (1989) J Phys Chem 93:2053–2058

    Article  CAS  Google Scholar 

  23. Deleuze MS, Pang WN, Salam A, Shang RC (2001) J Am Chem Soc 123:4049–4061

    Article  CAS  Google Scholar 

  24. Compton DAC, Montero S, Murphy WF (1980) J Phys Chem 84:3587–3591

    Article  CAS  Google Scholar 

  25. Balabin RM (2009) J Phys Chem A 113:1012–1019

    Article  CAS  Google Scholar 

  26. Riddick JA, Bunger WB, Sakano TK (1986) Techniques of Chemistry, Vol. II, 4th edn, Organic Solvents, Physical Properties and Methods of Purification. Wiley, New York

    Google Scholar 

  27. Tofts PS, Lloyd D, Clark CA, Barker GJ, Parker GJM, McConville P, Baldock C, Pope JM (2000) Magn Reson Med 43:368–374

    Article  CAS  Google Scholar 

  28. Heyes DM, Cass MJ, Powles JG, Evans WAB (2007) J Phys Chem B 111:1455–1464

    Article  CAS  Google Scholar 

  29. Yeh IC, Hummer G (2004) J Phys Chem B 108:15873–15879

    Article  CAS  Google Scholar 

Download references

Acknowledgments

This work was supported by the US Department of Energy, Office of Nuclear Energy under the Nuclear Energy University Program (DOE-NEUP), contract number: DE-AC07-051D14517. Computing resources used at the Center for Advanced Modeling and Simulation at the Idaho National Laboratory through a collaboration with the Nuclear Energy Advanced Modeling and Simulation program of the Nuclear Energy Office of DOE are greatly appreciated. The Oak Ridge National Laboratory is managed by UT-Battelle, LLC for the DOE under contract No. DE-AC05-00OR22725.

Author information

Authors and Affiliations

  1. Materials Research and Innovative Laboratory (MRAIL), Department of Chemical and Biomolecular Engineering, University of Tennessee, Knoxville, TN, 37996, USA

    Xianggui Ye, Shengting Cui & Bamin Khomami

  2. Sustainable Energy and Research Center, University of Tennessee, Knoxville, TN, 37996, USA

    Bamin Khomami

  3. Oak Ridge National Laboratory, Oak Ridge, TN, 37831-6181, USA

    Valmor F. de Almeida

Authors
  1. Xianggui Ye
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Shengting Cui
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Valmor F. de Almeida
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Bamin Khomami
    View author publications

    You can also search for this author in PubMed Google Scholar

Corresponding authors

Correspondence to Shengting Cui or Bamin Khomami.

Electronic supplementary material

Below is the link to the electronic supplementary material.

ESM 1

See supplementary material for mass density, and end-to-end distance for n-decane, n-tetradecane, and n-hexadecane for various scaling factors corresponding to crystalline and disordered state, and comparison of torsion potential profile for n-dodecane for the terminal dihedral: CH3-CH2-CH2-CH2 in gas phase for varying 1–4 intramolecular scaling factor. (DOC 951 kb)

Rights and permissions

Reprints and permissions

About this article

Cite this article

Ye, X., Cui, S., de Almeida, V.F. et al. Effect of varying the 1–4 intramolecular scaling factor in atomistic simulations of long-chain N-alkanes with the OPLS-AA model. J Mol Model 19, 1251–1258 (2013). https://doi.org/10.1007/s00894-012-1651-5

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s00894-012-1651-5

Keywords

Search

Navigation