394
Views
18
CrossRef citations to date
0
Altmetric
Articles

Overview of MedeA®-GIBBS capabilities for thermodynamic property calculation and VLE behaviour description of pure compounds and mixtures: application to polar compounds generated from ligno-cellulosic biomass

, , , &
Pages 1165-1211 | Received 09 Apr 2013, Accepted 25 Jul 2013, Published online: 14 Oct 2013

REFERENCES

  • van SpeybroeckV, GaniR, MeierRJ. The calculation of thermodynamic properties of molecules. Chem Soc Rev. 2010;39:1764–1779.
  • MackieAD, TavitianB, BoutinA, FuchsAH. Vapor–liquid equilibria predictions of methane–alkane mixtures by Monte Carlo simulation. Mol Simul. 1997;19:1–15.
  • JorgensenWL, MaxwellDS, Tirado-RivesJ. Development and testing of the opls all-atom force field on conformational energetics and properties of organic liquids. J Am Chem Soc. 1996;118:11225–11236.
  • ReiherIIIWE. Theoretical studies of hydrogen bonding [PhD thesis]. Cambridge, MA: Department of Univesity, Harvard University; 1985.
  • MacKerellAD, BashfordD, BellottM, DunbrackRL, EvanseckJD, FieldMJ, FischerS, GaoJ, GuoH, HaS, Joseph-McCarthyD, KuchnirL, KuczeraK, LauFTK, MattosC, MichnickS, NgoT, NguyenDT, ProdhomB, ReiherWE, RouxB, SchlenkrichM, SmithJC, StoteR, StraubJ, WatanabeM, Wiórkiewicz-KuczeraJ, YinD, KarplusM. All-atom empirical potential for molecular modeling and dynamics studies of proteins. J Phys Chem B. 1998;102:3586–3616.
  • MacKerellAD, FeigM, BrooksCL. Extending the treatment of backbone energetics in protein force fields: limitations of gas-phase quantum mechanics in reproducing protein conformational distributions in molecular dynamics simulations. J Comput Chem. 2004;25:1400–1415.
  • CornellWD, CieplakP, BaylyCI, GouldIR, MerzKM, FergusonDM, SpellmeyerDC, FoxT, CaldwellJW, KollmanPA. A second generation force field for the simulation of proteins, nucleic acids, and organic molecules. J Am Chem Soc. 1995;117:5179–5197.
  • FrenkelD, SmitB. Understanding molecular simulation. San Diego, LA: Academic Press; 1996.
  • AllenMP, TildesleyDJ. Computer simulation of liquids. Oxford: Oxford Science Publications; 1987.
  • MetropolisN, RosenbluthAW, RosenbluthMN, TellerAH, TellerE. Equation of state calculations by fast computing machines. J Chem Phys. 1953;21:1087–1092.
  • de PabloJJ, LasoM, SuterUW. Simulation of polyethylene above and below the melting point. J Chem Phys. 1992;96:2395–2403.
  • NicholsonD, ParsonageNG. Computer simulation and the statistical mechanics of adsorption. New York: Academic Press; 1982.
  • PanagiotopoulosAZ. Direct determination of phase coexistence properties of fluids by Monte Carlo simulation in a new ensemble. Mol Phys. 1987;61:813–826.
  • PlimptonS. Fast parallel algorithms for short-range molecular dynamics. J Comput Phys. 1995;117:1–19.
  • TheodorouDN. Understanding and predicting structure property relations in polymeric materials throught molecular simulations. Mol Phys. 2004;102:147–166.
  • ChandrasekharJ, SpellmeyerD, JorgensenWL. Energy component analysis for dilute aqueous solutions of Li+, Na+, F−  and Cl−  ions. J Am Chem Soc. 1984;106:903–910.
  • CournoyerME, JorgensenWL. Solvent effects on the relative energies of carbonium ions. Solvation and internal rotation for the allyl cation in liquid hydrogen fluoride. J Am Chem Soc. 1984;106:5104–5112.
  • JorgensenWL, MaduraJD, SwensonCJ. Optimized intermolecular potential functions for liquid hydrocarbons. J Am Chem Soc. 1984;106:6638–6646.
  • JorgensenWL, SwensonCJ. Optimized intermolecular potential functions for amides and peptides. Structure and properties of liquid amides. J Am Chem Soc. 1985;107:569–578.
  • JorgensenWL. Optimized intermolecular potential functions for liquid alcohols. J Phys Chem. 1986;90:1276–1284.
  • JorgensenWL. Intermolecular potential functions and Monte Carlo simulations for liquid sulfur compounds. J Phys Chem. 1986;90:6379–6388.
  • JorgensenWL, BriggsJM. Monte Carlo simulations of liquid acetonitrile with a three-site model. Mol Phys. 1988;63:547–558.
  • JorgensenWL, BriggsJM, ContrerasML. Relative partition coefficients for organic solutes from fluid simulations. J Phys Chem. 1990;94:1683–1686.
  • PranataJ, WierschkeSG, JorgensenWL. OPLS potential functions for nucleotide bases. Relative association constants of hydrogen-bonded base pairs in chloroform. J Am Chem Soc. 1991;113:2810–2819.
  • MartinMG, SiepmannJI. Transferable potentials for phase equilibria. 1. United-atom description of n-alkanes. J Phys Chem B. 1998;103:2569–2577.
  • MartinMG, SiepmannJI. Novel configurational-bias Monte Carlo method for branched molecules. Transferable potentials for phase equilibria. 2. United-atom description of branched alkanes. J Phys Chem B. 1999;103:4508–4517.
  • ChenB, SiepmannJI. Transferable potentials for phase equilibria. 3. Explicit-hydrogen description of n-alkanes. J Phys Chem B. 1999;103:5370–5379.
  • WickCD, MartinMG, SiepmannJI. Transferable potentials for phase equilibria. 4. United-atom description of linear and branched alkenes and of alkylbenzenes. J Phys Chem B. 2000;104:8008–8016.
  • ChenB, PotoffJJ, SiepmannJI. Monte Carlo calculations for alcohols and their mixtures with alkanes. Transferable potentials for phase equilibria. 5. United-atom description of primary, secondary and tertiary alcohols. J Phys Chem B. 2001;105:3093–3104.
  • StubbsJM, PotoffJJ, SiepmannJI. Transferable potentials for phase equilibria. 6. United-atom description for ethers, glycols, ketones and aldehydes. J Phys Chem B. 2004;108:17596–17605.
  • WickCD, StubbsJM, SiepmannJI. Transferable potentials for phase equilibria. 7. United-atom description for nitrogen, amines, amides, nitriles, pyridine and pyrimidine. J Phys Chem B. 2005;109(4):18974–18992.
  • LubnaN, KamathG, PotoffJJ, RaiN, SiepmannJI. Transferable potentials for phase equilibria. 8. United-atom description for thiols, sulfides, disulfides, and thiophene. J Phys Chem B. 2005;109:24100–24107.
  • RaiN, SiepmannJI. Transferable potentials for phase equilibria. 9. Explicit-hydrogen description of benzene and 5-membered and 6-membered heterocyclic aromatic compounds. J Phys Chem B. 2007;111:10790–10799.
  • KeaslerSJ, CharanSM, WickCD, EconomouIG, SiepmannJI. Transferable potentials for phase equilibria-united atom description of five- and six-membered cyclic alkanes and ethers. J Phys Chem B. 2012;116:11234–11246.
  • UngererP, BeauvaisC, DelhommelleJ, BoutinA, RousseauB, FuchsAH. Optimization of the anisotropic united atoms intermolecular potential for n-alkanes. J Chem Phys. 2000;112(12):5499–5510.
  • BourasseauE, HaboudouM, BoutinA, FuchsAH, UngererP. New optimization method for intermolecular potentials: optimization of a new anisotropic united atoms potential for olefins: prediction of equilibrium properties. J Chem Phys. 2003;118:3020–3034.
  • Contreras-CamachoRO, UngererP, BoutinA, MackieAD. Optimized intermolecular potential for aromatic hydrocarbons based on anisotropic united atoms. i. benzene. J Phys Chem B. 2004;108:14109–14114.
  • Contreras-CamachoRO, UngererP, AhunbayMG, LachetV, Perez-PelliteroJ, MackieAD. Optimized intermolecular potential for aromatic hydrocarbons based on anisotropic united atoms. ii. Alkylbenzenes and styrene. J Phys Chem B. 2004;108:14115–14123.
  • FerrandoN, LachetV, Perez-PelliteroJ, MackieAD, MalfreytP, BoutinA. A transferable force field to predict phase equilibria and surface tension of ethers and glycol ethers. J Phys Chem B. 2011;115:10654–10664.
  • FerrandoN, LachetV, TeulerJ-M, BoutinA. Transferable force field for alcohols and polyalcohols. J Phys Chem B. 2009;113:5985–5995.
  • BourasseauE, UngererP, BoutinA, FuchsAH. Monte Carlo simulation of branched alkanes and long chain n-alkanes with anisotropic united atoms intermolecular potential. Mol Simul. 2002;28:317–336.
  • MedeA® 2.13. Santa Fe, NM: Materials Desing, Inc., 2013.
  • SmitB, KaraborniS, SiepmannJI. Computer simulation of vapor–liquid phase equilibria of n-alkanes. J Chem Phys. 1995;102:2126–2140.
  • DoddLR, BooneTD, TheodorouDN. A concerted rotation algorithm for atomistic Monte Carlo simulation of polymer melts and glasses. Mol Phys. 1993;78:961–996.
  • UngererP, TavitianB, BoutinA. Applications of molecular simulation in the oil and gas industry – Monte Carlo methods. Paris: Editions Technip; 2005.
  • ErringtonJR, PanagiotopoulosAZ. New intermolecular potential models for benzene and cyclohexane. J Chem Phys. 1999;111:9731.
  • MacedoniaMD, MaginnEJ. A biased grand canonical Monte Carlo method for simulating adsorption using all-atom and branched united atom models. Mol Phys. 1999;96:1375–1390.
  • WidomB. Some topics in the theory of fluids. J Chem Phys. 1963;39:2808–2812.
  • SmitB. Grand canonical Monte Carlo simulations of chain molecules: adsorption isotherms of alkanes in zeolites. Mol Phys. 1995;85:153–172.
  • CracknellRF, NicholsonD, ParsonageNG. Rotational insertion bias: a novel method for simulating dense phases of structured particles, with particular application to water. Mol Phys. 1990;71:931–943.
  • JeffroyM, BoutinA, FuchsAH. Understanding the equilibrium ion exchange properties in faujasite zeolite from Monte Carlo Simulations. J Phys Chem B. 2011;115:15059–15066.
  • ChemB, MartinMG, SiepmannJI. Thermodynamic properties of the Williams, OPLS-AA, and MMFF94 All-atom force fields for normal alkanes. J Phys Chem B. 1998;102:2578–2586.
  • ToxvaerdS. Molecular dynamics calculation of the equation of state of alkanes. J Chem Phys. 1997;107:5197–5204.
  • PadillaP, ToxvaerdS. Self-diffusion in n-alkane fluid models. J Chem Phys. 1991;94:5650–5654.
  • MoellerD, OprzynskiJ. Prediction of thermodynamic properties of fluid mixtures by molecular dynamics simulations: methane–ethane. Mol Phys. 1992;75:363–378.
  • HarrisJG, YungKH. Carbon dioxide's liquid–vapor coexistence curve and critical properties as predicted by a simple molecular model. J Phys Chem. 1995;99:12021–12024.
  • MerkerT, EnginC, VrabecJ, HasseH. Molecular model for carbon dioxide optimized to vapor–liquid equilibria. J Chem Phys. 2010;132:234512.
  • JorgensenWL, ChandrasekharJ, MaduraJD, ImpeyRW. Comparison of simple potential functions for simualting liquid water. J Chem Phys. 1983;79:926–935.
  • HornHW, SwopeWC, PiteraJW, MaduraJD, DickTJ, HuraGL, Head-GordonT. Development of an improved four-site water model for biomolecular simulations: Tip4p-ew. J Chem Phys. 2004;120:9665–9678.
  • BerendsenHJC, PostmaJPM, van GunsterenWF, HermansJ. Interaction models for water in relation to protein hydration. In: PullmanB, editor. Intermolecular forces. Dordrecht: Reidel; 1981. p. 331–342.
  • KristofT, LisziJ. Effective intermolecular potential for fluid hydrogen sulfide. J Phys Chem B. 1997;101:5480–5483.
  • DelhommelleJ. Etablissement de potentiels dinteraction pour la simulation moleculaire-application a la prediction des equilibrews liquide–vapeur de melanges binaires alcane-molecule multipolaire [PhD thesis]. Orsay, France: Universite de Paris XI; 2000.
  • VrabecJ, StollJ, HasseH. A set of molecular models for symmetric quadrupolar fluids. J Phys Chem B. 2001;105:12126–12133.
  • DarkrimF, VermesseJ, MalbrunotP, LevesqueD. Monte Carlo simulations of nitrogen and hydrogen physisorption at high pressures and room temperature. Comparison with experiments. J Chem Phys. 1999;110:4020–4027.
  • El AhmarE, CretonB, ValtzA, CoqueletC, LachetV, RichonD, UngererP. Thermodynamic study of binary systems containing sulphur dioxide: measurements and molecular modeling. Fluid Phase Equilib. 2011;304:21–34.
  • LagacheM, UngererP, BoutinA, FuchsAH. Prediction of thermodynamic derivative properties of fluids by Monte Carlo Simulation. Phys Chem Chem Phys. 2001;3:4333–4339.
  • MaerzkeKA, SchultzNE, RossRB, SiepmannI. TraPPE-UA force field for acrylates and Monte Carlo simulations for their mixtures with alkanes and alcohols. J Phys Chem B. 2009;113:6415–6425.
  • WildingN. Critical point and coexistence curve properties of the Lennard-Jones fluid: a finite-size scaling study. Phys Rev E. 1995;53:926–934.
  • BoutardY, UngererP, TeulerJM, AhunbayMG, SabaterSF, Perez-PelliteroJ, MackieAD, BourasseauE. Extension of the anisotropic united atoms intermolecular potential to amines, amides and alkanols. Application to the problems of the 2004 fluid simulation challenge. Fluid Phase Equilib. 2005;236:25–41.
  • Perez-PelliteroJ, BourasseauE, DemachyI, RihardJ, UngererP, MackieAD. Anisotropic united-atoms (AUA) potential for alcohols. J Phys Chem B. 2008;112:9853–9863.
  • WildingWV, RowleyRL, OscarsonJL. Dippr project 801 evaluated process design data. Fluid Phase Equilib. 1998;150–151:413–420.
  • NIST TRC. Gaithersburgh, MD: NIST; 2011.
  • RowleyRL, WildingmWV, OscarsonJL, YangY, ZundelNA, DaubertTE, DannerRP. DIPPR data compilation of pure compounds properties. New York, NY: Design Institute for Physical Properties, AIChE; 2003.
  • OnkenU, GmehlingJ. The Dortmund Data Bank: a computerized system for retrieval, correlation, and prediction of thermodynamic properties of mixtures. Int J Thermophys. 1989;10:739–747.
  • HarveyGG. Fourier analysis of liquid methyl alcohol. J Chem Phys. 1938;6:111–114.
  • WertzDL, KruhRK. Reinvestigation of the structures of ethanol and methanol at room temperature. J Chem Phys. 1967;47:388–390.
  • NartenAH, SandlerSI. X-ray diffraction study of liquid tertiary butyl alcohol at 26 °C. J Chem Phys. 1979;71:2069–2073.
  • YamaguchiT, HidakaK, SoperAK. X-ray diffraction study of liquid tertiary butyl alcohol at 26 °C. Mol Phys. 1999;97:603–605.
  • LinK, ZhouXG, LuoY, LiuSL. The structure of liquid methanol revisited: a neutron diffraction experiment at − 80 °C and +25 °C. J Phys Chem B. 2010;114:3567–3573.
  • JorgnesenWL. Quantum and statistical mechanical studies of liquids. 7. Structure and properties of liquid methanol. J Am Chem Soc. 1980;102:543–549.
  • JorgnesenWL. Quantum and statistical mechanical studies of liquids. 12. Simulation of liquid ethanol including internal rotation. J Am Chem Soc. 1981;103:345–350.
  • SchnabelT, SrivastavaA, VrabecJ, HasseH. Hydrogen bonding of methanol in supercritical CO2: comparison between 1H NMR spectroscopic data and molecular simulation results. J Phys Chem B. 2007;111:9871–9878.
  • FerrandoN, LachetV, BoutinA. Monte Carlo simulations of mixtures involving ketones and aldehydes by a direct bubble pressure calculation. J Phys Chem B. 2010;114:8680–8688.
  • McLainSE, SoperAK, LuzarA. Orientational correlations in liquid acetone and dimethyl sulfoxide: a comparative study. J Chem Phys. 2006;124:074502.
  • BrunnerE, HöltenschmidtW, SchlichthärleG. Fluid mixtures at high pressures IV. isothermal phase equlibria in binary mixtures consisting of (methanol+hydrogen or nitrogen or methane or carbon monoxide or carbon dioxide). J Chem Thermodyn. 1987;19:273–291.
  • BrunnerE, HöltenschmidtW. Fluid mixtures at high pressures VIII. isothermal phase equlibria in the binary mixtures: (ethanol+hydrogen or methane or ehtane). J Chem Thermodyn. 1990;22:73–84.
  • JonassonA, PersonO, RasmussenP. High-pressure solubility of hydrogen in dimethyl ether. J Chem Eng Data. 1995;40:1209–1210.
  • AmdahlG. Validity of the single processor approach to achieving large-scale computing capabilities. Proceedings of the April 18–20, 1967, Spring Joint Computer Conference, AFIPS '67 (Spring), Atlantic City, NJ, USA. New York: ACM; 1967. p. 483–485. doi: 10.1145/1465482.1465560.
  • WolffU. High precision simulations with fast algorithms. In: Gausterer H, Lang CB, editors. Computational methods in field theory. Vol. 409, Lecture notes in physics; 1992. p. 127–158.
  • Perez-PelliteroJ, UngererP, MackieAD. Effective critical point location: application to thiophenes. Mol Simul. 2007;3:777–785.
  • GarridoNM, QueimadaAJ, JorgeM, EconomouIG, MacedoEA. Molecular simulation of absolute hydration Gibbs energies of polar compounds. Fluid Phase Equilib. 2010;296:110–115.
  • DuaneS, KennedyAD, PendletonBJ, RowethD. Hybrid Monte Carlo. Phys Lett B. 1987;195:216–222.

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.