Consistent Acetonitrile Molecular Models for both Standard and Computationally Efficient Molecular Dynamics Studies
Keywords:
Acetonitrile, Three-site Models, Molecular Dynamics, Integration Time-step ScalabilityAbstract
Acetonitrile is widely utilized in scientific research, presenting an ideal solvent media for a large number of organic reactions. Its use at the industrial scale ranges from the production of molecules of pharmaceutical interest to photographic films. Additionally, certain enzyme based catalytic processes show great functionality in Acetonitrile media. Furthermore, numerous enzymes continue to act as efficient biocatalyzers in acetonitrile solution, showing in some cases significant changes in their original specificity and selectivity. Consequently, the study of the behavior of such proteins in this solvent by means of potent computational methods such as Molecular Dynamics results of great interest. Many molecular models for Acetonitrile have been developed for use in Molecular Dynamic studies. Nevertheless, all acetonitrile models developed up to date are only capable of performing reasonably when used with integration time-steps no greater than 2 femtoseconds (fs). We present two molecular models for acetonitrile which perform both efficiently and reliably with integration time steps of up to 4 fs. Furthermore, the optimization procedure used has enabled to achieve this performance improvement at no cost as regards the agreement between the experimental macroscopic data for Acetonitrile and the corresponding properties evaluated for the models here presented.
References
Bordusa, F., Proteases in Organic Synthesis. Chemical Reviews, 2002. 102(12): p. 4817-4868.
Morcelle, S.R., et al., Comparative behaviour of proteinases from the latex of Carica papaya and Funastrum clausum as catalysts for the synthesis of Z-Ala-Phe-OMe. Journal of Molecular Catalysis B: Enzymatic, 2006. 41(3-4): p. 117-124.
Morcelle, S.R., et al., Screening of plant peptidases for the synthesis of arginine-based surfactants. Journal of Molecular Catalysis B: Enzymatic, 2009. 57(1-4): p. 177-182.
Simon, L.M., Kotormán, M., Szabo, A., Nemcsók, J., Laczko I. (2007). The effects of organic solvent/water mixtures on the structure and catalytic activity of porcine pepsin. Proc Bioch, 42 : 909-912.
Simon, L.M., Lázló, K., Vértesi, A., Bagi, K., Szajáni, B. (1998). Stability of hydrolytic enzymes in water-organic solvent systems. J. Mol Catal B: Enzymatic, 4 : 41-45.
Szabó, A., Kotormán, M., Laczkó, I., Simon, L.M. (2006). Spectroscopic studies of stability of papain in aqueous organic solvents. J. Mol. Catal. B: Enzymatic, 41: 43-48.
Kijima, T., Yamamoto, S., Kise, H. (1996). Study on tryptophan fluorescence and catalytic activity of a-chymotrypsin in aqueous-organic media. Enzyme and Microbial Technology. 18 : 2-6.
C. R. Llerena-Suster, C. José, S. E. Collins, L. E. Briand, S. R. Morcelle. Investigation of the structure and proteolytic activity of papain in aqueous miscible organic media. Process biochemistry 47 (2012), 47-56.
Böhm, H.J., et al., Molecular motion in a model of liquid acetonitrile. Molecular Physics: An International Journal at the Interface Between Chemistry and Physics, 1984. 51(3): p. 761 - 777.
Nikitin, A.M. and A.P. Lyubartsev, New six-site acetonitrile model for simulations of liquid acetonitrile and its aqueous mixtures. Journal of Computational Chemistry, 2007. 28(12): p. 2020-2026.
Edwards, D.M.F., P.A. Madden, and I.R. McDonald, A computer simulation study of the dielectric properties of a model of methyl cyanide -- I. The rigid dipole case. Molecular Physics: An International Journal at the Interface Between Chemistry and Physics, 1984. 51(5): p. 1141 - 1161.
Jorgensen, W.L. and J.M. Briggs, Monte Carlo simulations of liquid acetonitrile with a three-site model. Molecular Physics: An International Journal at the Interface Between Chemistry and Physics, 1988. 63(4): p. 547 - 558.
Guà rdia, E., et al., Comparison of Different Three-site Interaction Potentials for Liquid Acetonitrile. Molecular Simulation, 2001. 26(4): p. 287 - 306.
Gee, P.J. and W.F. van Gunsteren, Acetonitrile revisited: a molecular dynamics study of the liquid phase. Molecular Physics: An International Journal at the Interface Between Chemistry and Physics, 2006. 104(3): p. 477 - 483.
Wick, C.D., et al., Transferable Potentials for Phase Equilibria. 7. Primary, Secondary, and Tertiary Amines, Nitroalkanes and Nitrobenzene, Nitriles, Amides, Pyridine, and Pyrimidine. The Journal of Physical Chemistry B, 2005. 109(40): p. 18974-18982.
Hirata, Y., Molecular Dynamics Simulation Study of the Rotational and Translational Motions of Liquid Acetonitrile. The Journal of Physical Chemistry A, 2002. 106(10): p. 2187-2191.
C.C. Huang, A. Chatterji, G. Sutmann, G. Gompper, R.G. Winkler, Cell-level canonical sampling by velocity scaling for multiparticle collision dynamics simulations. J. Comput. Phys. 229(1): 168-177, 2010.
Berendsen, H. J. C., Postma, J. P. M., DiNola, A., Haak, J. R. Molecular dynamics with coupling to an external bath. J. Chem. Phys. 81:3684–3690, 1984.
M. P. Allen and D. J. Tildesley, Oxford Science Publications, Clarendon Press, Oxford (1987).
W F. van Gunsteren and H. J. C. Berendsen, Mol. Phys., 34, 1311 (1977).
J. C. Berendsen and W F. van Gunsteren, in Molecular Liquids: Dynamics and Interactions; J. Barnes et al. Eds., NATO ASI Series, C135, 475; Reidel, Dordrecht (1984).
M. Levitt, J. Mol. Biol., 168, 595 (1983).
An, X.-W. and M. MÃ¥nsson, Enthalpies of combustion and formation of acetonitrile. The Journal of Chemical Thermodynamics, 1983. 15(3): p. 287-293.
Spoel, D.v.d., P.J.v. Maaren, and H.J.C. Berendsen, A systematic study of water models for molecular simulation: Derivation of water models optimized for use with a reaction field. Vol. 108. 1998: AIP. 10220-10230.
Barthel, J., M. Kleebauer, and R. Buchner, Dielectric relaxation of electrolyte solutions in acetonitrile. Journal of Solution Chemistry, 1995. 24(1): p. 1-17.
Allen, M.P. and D.J. Tildesley, Computer Simulation of Liquids. 1989: Oxford University Press, USA.
Palmer, B.J., Transverse-current autocorrelation-function calculations of the shear viscosity for molecular liquids. Physical Review E, 1994. 49(1): p. 359.
Gallant, R. W., Physical properties of hydrocarbons. XXXVI. Nitriles, Hydrocarbon Process., 1969. 48, 135.
An, X.-W. and M. MÃ¥nsson, Enthalpies of combustion and formation of acetonitrile. The Journal of Chemical Thermodynamics, 1983. 15(3): p. 287-293.
Wagman, D.D., et al., The NBS tables of chemical thermodynamic properties : selected values for inorganic and C1 and C2 organic substances in SI units. 1982. 11(1).
Cunningham, G.P., G.A. Vidulich, and R.L. Kay, Several properties of acetonitrile-water, acetonitrile-methanol, and ethylene carbonate-water systems. Journal of Chemical & Engineering Data, 1967. 12(3): p. 336-337.
Kovacs, H., et al., Multinuclear relaxation and NMR self-diffusion study of the molecular dynamics in acetonitrile-chloroform liquid mixtures. The Journal of Physical Chemistry, 1989. 93(2): p. 962-969.
Narayanaswamy, G., G. Dharmaraju, and G.K. Raman, Excess volumes and isentropic compressibilities of acetonitrile +n-propanol, +i-propanol, +n-butanol, +i-butanol, and +cyclohexanol at 303.15 K. The Journal of Chemical Thermodynamics, 1981. 13(4): p. 327-331.
Grant-Taylor, D.F. and D.D. Macdonald, Thermal pressure and energy–volume coefficients for the acetonitrile + water system. Canadian Journal of Chemistry, 1976. 54(17): p. 2813-2819.
Yuan, P. and M. Schwartz, Molecular reorientation in acetonitrile. A comparison of diffusion coefficients from Raman bandshapes and nuclear magnetic resonance relaxation times. Journal of the Chemical Society, Faraday Transactions, 1990. 86(4): p. 593-596.
Downloads
Published
Issue
Section
License
- Papers must be submitted on the understanding that they have not been published elsewhere (except in the form of an abstract or as part of a published lecture, review, or thesis) and are not currently under consideration by another journal published by any other publisher.
- It is also the authors responsibility to ensure that the articles emanating from a particular source are submitted with the necessary approval.
- The authors warrant that the paper is original and that he/she is the author of the paper, except for material that is clearly identified as to its original source, with permission notices from the copyright owners where required.
- The authors ensure that all the references carefully and they are accurate in the text as well as in the list of references (and vice versa).
- Authors retain copyright and grant the journal right of first publication with the work simultaneously licensed under a Attribution-NonCommercial 4.0 International that allows others to share the work with an acknowledgement of the work's authorship and initial publication in this journal.
- Authors are able to enter into separate, additional contractual arrangements for the non-exclusive distribution of the journal's published version of the work (e.g., post it to an institutional repository or publish it in a book), with an acknowledgement of its initial publication in this journal.
- Authors are permitted and encouraged to post their work online (e.g., in institutional repositories or on their website) prior to and during the submission process, as it can lead to productive exchanges, as well as earlier and greater citation of published work (See The Effect of Open Access).
- The journal/publisher is not responsible for subsequent uses of the work. It is the author's responsibility to bring an infringement action if so desired by the author.
