Journal of Molecular Modeling

, 25:370 | Cite as

Evolution of diffusion and structure of six n-alkanes in carbon dioxide at infinite dilution over wide temperature and pressure ranges: a molecular dynamics study

  • Huajie Feng
  • Wei Gao
  • Li Su
  • Yanchun Liu
  • Zhenfan Sun
  • Liuping ChenEmail author
Original Paper


Over wide temperature and pressure ranges, the molecular dynamics simulation is performed to study the mass transfer of six n-alkanes from n-C5H12 to n-C10H22 in CO2 at infinite dilution by calculating the diffusion coefficients, which have not yet been measured by experiment. Meanwhile, the structural properties of these systems are explored. It is found that under different temperature and pressure conditions, the variation trends of the radial distribution functions of n-alkanes are quite different, while the variation trends of the average coordination number of n-alkanes can be divided into three types. The radius of gyration and the solvent accessible surface area are both affected by temperature and carbon chain length, but their variation trends are different, and it could explain the abnormal variation trends of the radial distribution functions and the average coordination number.

Graphical abstract

Over wide temperature and pressure ranges, the variation trends of the average coordination number of n-alkanes can be divided into three types.


Flexibility Solvent accessible surface area Radius of gyration Alkane 


Funding information

This work was supported by Hainan Provincial Science and Technology Project (No. ZDYF2019160), the Program of Hainan Association for Science and Technology Plans to Youth R & D Innovation (No. HAST201621), the Natural Science Foundation of Hainan Province (No. 20162027), the Natural Science Foundation of Guangdong Province (No. 2015A030310176), and the Medical Science Research Foundation of Guangdong Province (No. A2015607).


  1. 1.
    Zarabadi AS, Pawliszyn J (2015) Accurate determination of the diffusion coefficient of proteins by Fourier analysis with whole column imaging detection. Anal Chem 87(4):2100–2106PubMedCrossRefGoogle Scholar
  2. 2.
    Zheng S, Li HA, Sun H, Yang D (2016) Determination of diffusion coefficient for alkane solvent–CO2 mixtures in heavy oil with consideration of swelling effect. Ind Eng Chem Res 55(6):1533–1549CrossRefGoogle Scholar
  3. 3.
    Ehrl A, Landesfeind J, Wall WA, Gasteiger HA (2017) Determination of transport parameters in liquid binary lithium ion battery electrolytes: I. Diffusion coefficient. J Electrochem Soc 164(4):A826–A836CrossRefGoogle Scholar
  4. 4.
    Chen LP, Gross T, Lüdemann HD (1999) The density dependence of self-diffusion in some simple amines. Phys Chem Chem Phys 1(15):3503–3508CrossRefGoogle Scholar
  5. 5.
    Chen LP, Groß T, Krienke H, Lüdemann HD (2001) T, p-Dependence of the self-diffusion and spin lattice relaxation in fluid hydrogen and deuterium. Phys Chem Chem Phys 3(11):2025–2030CrossRefGoogle Scholar
  6. 6.
    Groß T, Chen L, Buchhauser J, Lüdemann H-D (2001) T,p-Dependence of intradiffusion in binary fluid mixtures with ammonia as one component. Phys Chem Chem Phys 3(17):3701–3706CrossRefGoogle Scholar
  7. 7.
    Feng H, Liu X, Gao W, Chen X, Wang J, Chen L, Lüdemann H-D (2010) Evolution of self-diffusion and local structure in some amines over a wide temperature range at high pressures: a molecular dynamics simulation study. Phys Chem Chem Phys 12(45):15007–15017PubMedCrossRefGoogle Scholar
  8. 8.
    Gao W, Feng H, Xuan X, Chen L (2012) A theoretical study of N–H · π H-bond interaction of pyrrole: from clusters to the liquid. Mol Phys 110(18):2151–2161CrossRefGoogle Scholar
  9. 9.
    Feng H, Gao W, Nie J, Wang J, Chen X, Chen L, Liu X, Lüdemann H-D, Sun Z (2013) MD simulation of self-diffusion and structure in some n-alkanes over a wide temperature range at high pressures. J Mol Model 19(1):73–82PubMedCrossRefGoogle Scholar
  10. 10.
    Feng H, Gao W, Sun Z, Chen L, Lüdemann H-D, Lei B, Li G (2014) The self-diffusion and hydrogen bond interaction in neat liquid alkanols: a molecular dynamic simulation study. Mol Simulat 40(13):1074–1084CrossRefGoogle Scholar
  11. 11.
    Zhong H, Lai S, Wang J, Qiu W, Lüdemann H-D, Chen L (2015) Molecular dynamics simulation of transport and structural properties of CO2 using different molecular models. J Chem Eng Data 60(8):2188–2196CrossRefGoogle Scholar
  12. 12.
    Chockalingam R, Natarajan U (2015) Dynamics of conformations, hydrogen bonds and translational diffusion of poly(methacrylic acid) in aqueous solution and the concentration transition in MD simulations. Mol Phys 113(21):3370–3382CrossRefGoogle Scholar
  13. 13.
    Che X, Zhang J, Zhu Y, Yang L, Quan H, Gao YQ (2016) Structural flexibility and conformation features of cyclic dinucleotides in aqueous solutions. J Phys Chem B 120(10):2670–2680PubMedCrossRefGoogle Scholar
  14. 14.
    Wang J, Zhong H, Liang C, Chen X, Chen L (2016) Molecular dynamics simulation of diffusion and structure of n-alkane/n-alkanol mixtures at infinite dilution. J Mol Liq 223:489–496CrossRefGoogle Scholar
  15. 15.
    Garcia MT, Kaczerewska O, Ribosa I, Brycki B, Materna P, Drgas M (2017) Hydrophilicity and flexibility of the spacer as critical parameters on the aggregation behavior of long alkyl chain cationic gemini surfactants in aqueous solution. J Mol Liq 230:453–460CrossRefGoogle Scholar
  16. 16.
    Roszak K, Katrusiak A, Dega-Szafran Z, Komasa A, Kowalczyk I, Szafran M (2017) Conformational flexibility and pseudosymmetric aggregation in a betainium salt hydrate. Struct Chem 28(3):859–865CrossRefGoogle Scholar
  17. 17.
    Guruge I, Taherzadeh G, Zhan J, Zhou Y, Yang Y (2018) B-factor profile prediction for RNA flexibility using support vector machines. J Comput Chem 39(8):407–411PubMedCrossRefGoogle Scholar
  18. 18.
    Bennett TD, Cheetham AK, Fuchs AH, Coudert F-X (2016) Interplay between defects, disorder and flexibility in metal-organic frameworks. Nat Chem 9(1):11–16PubMedCrossRefPubMedCentralGoogle Scholar
  19. 19.
    Liu Y, Lin D, Yuen PY, Liu K, Xie J, Dauskardt RH, Cui Y (2017) An artificial solid electrolyte interphase with high li-ion conductivity, mechanical strength, and flexibility for stable lithium metal anodes. Adv Mater 29(10):1605531CrossRefGoogle Scholar
  20. 20.
    Che X, Du X-X, Cai X, Zhang J, Xie WJ, Long Z, Ye Z-Y, Zhang H, Yang L, Su X-D, Gao YQ (2017) Single mutations reshape the structural correlation network of the DMXAA–Human STING complex. J Phys Chem B 121(9):2073–2082PubMedCrossRefGoogle Scholar
  21. 21.
    Eckert CA (1996) Supercritical fluids as solvents for chemical and materials processing. Nature 383:313–318CrossRefGoogle Scholar
  22. 22.
    Johnston KP, Shah PS (2004) Making nanoscale materials with supercritical fluids. Science 303(5657):482–483PubMedCrossRefGoogle Scholar
  23. 23.
    Moisan S, Martinez V, Weisbecker P, Cansell F, Mecking S, Aymonier C (2007) General approach for the synthesis of organic−inorganic hybrid nanoparticles mediated by supercritical CO2. J Am Chem Soc 129(34):10602–10606PubMedCrossRefGoogle Scholar
  24. 24.
    Sui R, Charpentier P (2012) Synthesis of metal oxide nanostructures by direct sol–gel chemistry in supercritical fluids. Chem Rev 112(6):3057–3082PubMedCrossRefGoogle Scholar
  25. 25.
    Rahmawati A, Pang D, Ju Y-H, Soetaredjo FE, Ki OL, Ismadji S (2015) Supercritical CO2 extraction of phytochemical compounds from Mimosa pudica Linn. Chem Eng Commun 202(8):1011–1017CrossRefGoogle Scholar
  26. 26.
    Iwai Y, Higashi H, Uchida H, Arai Y (1997) Molecular dynamics simulation of diffusion coefficients of naphthalene and 2-naphthol in supercritical carbon dioxide. Fluid Phase Equilibr 127(1–2):251–261CrossRefGoogle Scholar
  27. 27.
    Higashi H, Iwai Y, Uchida H, Arai Y (1998) Diffusion coefficients of aromatic compounds in supercritical carbon dioxide using molecular dynamics simulation. J Supercrit Fluid 13(1–3):93–97Google Scholar
  28. 28.
    Higashi H, Iwai Y, Arai Y (2000) Calculation of self-diffusion and tracer diffusion coefficients near the critical point of carbon dioxide using molecular dynamics simulation. Ind Eng Chem Res 39(12):4567–4570CrossRefGoogle Scholar
  29. 29.
    Skarmoutsos I, Samios J (2006) Local intermolecular structure and dynamics in binary supercritical solutions. A molecular dynamics simulation study of methane in carbon dioxide. J Mol Liq 125(2–3):181–186CrossRefGoogle Scholar
  30. 30.
    Zabala D, Nieto-Draghi C, de Hemptinne JC, López de Ramos AL (2008) Diffusion coefficients in CO2/n-alkane binary liquid mixtures by molecular simulation. J Phys Chem B 112(51):16610–16618PubMedCrossRefGoogle Scholar
  31. 31.
    Vaz RV, Gomes JRB, Silva CM (2016) Molecular dynamics simulation of diffusion coefficients and structural properties of ketones in supercritical CO2 at infinite dilution. J Supercrit Fluids 107:630–638CrossRefGoogle Scholar
  32. 32.
    Feng H, Gao W, Sun Z, Lei B, Li G, Chen L (2013) Molecular dynamics simulation of diffusion and structure of some n-alkanes in near critical and supercritical carbon dioxide at infinite dilution. J Phys Chem B 117(41):12525–12534PubMedCrossRefGoogle Scholar
  33. 33.
    Umezawa S, Nagashima A (1992) Measurement of the diffusion coefficients of acetone, benzene, and alkane in supercritical CO2 by the Taylor dispersion method. J Supercrit Fluids 5(4):242–250CrossRefGoogle Scholar
  34. 34.
    Wang J, Zhong H, Feng H, Qiu W, Chen L (2014) Molecular dynamics simulation of diffusion coefficients and structural properties of some alkylbenzenes in supercritical carbon dioxide at infinite dilution. J Chem Phys 140(10):429–435Google Scholar
  35. 35.
    Feng H, Gao W, Su L, Sun Z, Chen L (2017) MD simulation study of the diffusion and local structure of n-alkanes in liquid and supercritical methanol at infinite dilution. J Mol Model 23(6):195PubMedCrossRefPubMedCentralGoogle Scholar
  36. 36.
    Hess B, Kutzner C, van der Spoel D, Lindahl E (2008) Gromacs 4: Algorithms for highly efficient, load-balanced, and scalable molecular simulation. J Chem Theory Comput 4(3):435–447PubMedCrossRefPubMedCentralGoogle Scholar
  37. 37.
    Jorgensen WL, Madura JD, Swenson CJ (1984) Optimized intermolecular potential functions for liquid hydrocarbons. J Am Chem Soc 106(22):6638–6646CrossRefGoogle Scholar
  38. 38.
    Harris JG, Yung KH (1995) Carbon dioxide’s liquid-vapor coexistence curve and critical properties as predicted by a simple molecular model. J Phys Chem 99(31):12021–12024CrossRefGoogle Scholar
  39. 39.
    Nieto-Draghi C, de Bruin T, Pérez-Pellitero J, Avalos JB, Mackie AD (2007) Thermodynamic and transport properties of carbon dioxide from molecular simulation. J Chem Phys 126(6):064509PubMedCrossRefPubMedCentralGoogle Scholar
  40. 40.
    Hockney RW, Goel SP, Eastwood JW (1974) Quiet high-resolution computer models of a plasma. J Comput Phys 14(2):148–158CrossRefGoogle Scholar
  41. 41.
    Bussi G, Donadio D, Parrinello M (2007) Canonical sampling through velocity rescaling. J Chem Phys 126(1):014101PubMedCrossRefGoogle Scholar
  42. 42.
    Darden T, York D, Pedersen L (1993) Particle mesh Ewald: An N·log(N) method for Ewald sums in large systems. J Chem Phys 98(12):10089–10092CrossRefGoogle Scholar
  43. 43.
    Essmann U, Perera L, Berkowitz ML, Darden T, Lee H, Pedersen LG (1995) A smooth particle mesh Ewald method. J Chem Phys 103(19):8577–8593CrossRefGoogle Scholar
  44. 44.
    Lemmon EW, McLinden MO, Friend DG (2009) Thermophysical properties of fluid systems. In NIST Chemistry WebBook, NIST Standard Reference Database Number 69, Eds. National Institute of Standards and Technology, Gaithersburg.
  45. 45.
    Bondi A (1964) van der Waals Volumes and Radii. J Phys Chem 68(3):441–451CrossRefGoogle Scholar
  46. 46.
    Badenhoop JK, Weinhold F (1997) Natural steric analysis: Ab initio van der Waals radii of atoms and ions. J Chem Phys 107(14):5422–5432CrossRefGoogle Scholar
  47. 47.
    Gross T, Buchhauser J, Lüdemann HD (1998) Self-diffusion in fluid carbon dioxide at high pressures. J Chem Phys 109(11):4518–4522CrossRefGoogle Scholar

Copyright information

© Springer-Verlag GmbH Germany, part of Springer Nature 2019

Authors and Affiliations

  • Huajie Feng
    • 1
  • Wei Gao
    • 2
  • Li Su
    • 3
  • Yanchun Liu
    • 1
  • Zhenfan Sun
    • 1
  • Liuping Chen
    • 4
    Email author
  1. 1.School of Chemistry and Chemical EngineeringHainan Normal UniversityHaikouPeople’s Republic of China
  2. 2.School of PharmacyGuangdong Pharmaceutical UniversityGuangzhouPeople’s Republic of China
  3. 3.Hainan Entry-Exit Inspection and Quarantine Technology CenterHaikouPeople’s Republic of China
  4. 4.KLGHEI of Environment and Energy Chemistry, School of ChemistrySun Yat-sen UniversityGuangzhouPeople’s Republic of China

Personalised recommendations