Abstract
This paper is a review of our recent computational studies of volumetric characteristics using computer models of dilute solutions. Partial molar volume (PMV) and its components are calculated for simple and complex molecules in water (methane, noble gases, surfactants, polypeptides). Advantages and disadvantages of various computational methods are discussed. It is proposed to use the Voronoi-Delaunay technique to determine the reasonable boundary between a solute molecule and solvent molecules and to identify the PMV components related to the molecule, the boundary layer, and the solvent. It is noted that the observed increase in PMV with temperature for large molecules is due to an increase in the volume of voids in the boundary layer, i.e., due to the “thermal volume.” In this case, the solvent gives a negative contribution to the PMV. In contrast, for simple molecules (methane), the contribution from the solvent is positive and is the main factor in the increase in the PMV, which is associated with a specific change in water structure around a spherical hydrophobic particle outside the boundary layer. For surfactant molecules, the contribution from the solvent changes sign (from negative to positive) with increasing temperature.
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References
T. V. Chalikian, Annu. Rev. Biophys. Biomol. Struct., 32, 207–235 (2003).
L. Mitra, N. Smolin, R. Ravindra, C. Royer, and R. Winter, Phys. Chem. Chem. Phys., 8, 1249–1265 (2006).
K. Akasaka, A. R. Latif, A. Nakamura, K. Matsuo, H. Tachibana, and K. Gekko, Biochemistry, 46, 10444–10450 (2007).
R. Ravindra, C. Royer, and R. Winter, Phys. Chem. Chem. Phys., 6, 1952–1961 (2004).
R. Filfil and T. V. Chalikian, J. Mol. Biol., 299, 827–842 (2000).
J. Rösgen and H. J. Hinz,, Biophys. Chem., 83, 61–71 (2000).
M. Haeckel, H.-J. Hinza, and G. R. Hedwig, Biophys. Chem., 82, 35–50 (1999).
T. Kamiyama and K. Gekko, Chem. Lett., 10, 1063/1064 (1997).
T. V. Chalikian, M. Totrov, T. Abagyan, and K. J. Breslauer, J. Mol. Biol., 260, 588–603 (1996).
E. A. Moelwyn-Hughes, Physical Chemistry, Book 2, Izd. Inostr. Lit., Moscow (1962).
A. Yu. Tsivadze (ed.), in: Theoretical and Experimental Methods of Solution Chemistry, (Problems of Solution Chemistry), Chapter 8, Densitometry of Solutions, 425–463, Prospekt, Moscow (2011).
M. Marchi, J. Phys. Chem. B, 107, 6598–6602 (2003).
C. Klofutar, J. Horvat, and D. Rudan-Tasič, Acta Chim. Slov., 53, 274–283 (2006).
I. Brovchenko, R. R. Burri, A. Krukau, A. Oleinikova, and R. Winter, J. Chem. Phys., 129, 195101 (2008).
V. P. Voloshin, N. N. Medvedev, M. N. Andrews, R. R. Burri, R. Winter, and A. Geiger, J. Phys. Chem. B, 115, 14217–14228 (2011).
T, Imai Cond. Matter Phys., 10, No. 3(51), 343–361 (2007).
R. A. Pierotti, J. Phys. Chem., 69, 281–288 (1965).
D. P. Kharakoz, J. Solut. Chem., 21, 569 (1992).
H. Reiss, H. L. Frisch, and J. L. Lebowitz, J. Chem. Phys., 31, 369 (1959).
F. H. Stillinger, J. Solut. Chem., 2, 141 (1973).
F. M. Richards, Methods Enzymol., 115, 440–646 (1985).
M. J. Connolly, J. Appl. Crystallogr., 16, 548–558 (1983).
M. L. Connolly, J. Am. Chem. Soc., 107, 1118–1124 (1985).
J. Liang, H. Edelsbrunner, P. Fu, P. V. Sudhakar, and S. Subramaniam, Proteins: Struct. Funct. Genet., 33, 1–17 (1998).
N. Patel, D. N. Dubins, R. Pomes, and T. V. Chalikian, J. Phys. Chem. B, 115, 4856–4862 (2011).
T. Imai, A. Kovalenko, and F. Hirata, J. Phys. Chem. B, 109, 6658–6665 (2005).
J. G. Kirkwood and F. P. Buff, J. Chem. Phys., 19, 774 (1951).
A. Ben-Naim, Molecular Theory of Solutions, Oxford University Press, Oxford (2006).
N. Matubayas and R. M. Levy, J. Phys. Chem., 100, 2681–2688 (1996).
M. S. Moghaddam and Hue Sun Chan., J. Chem. Phys., 126, 114507 (2007).
A. V. Sangwai and H. S. Ashbaugh, Ind. Eng. Chem. Res., 47, 5169–5174 (2008).
D. Chandler, J. Chem. Phys., 59, 2742–2747 (1973).
J.-P. Hansen, and I. R. McDonald, Theory of Simple Liquids, 3rd ed., Academic Press, London (2006).
Song-Ho Chong and F. Hirata, J. Phys. Chem. B, 101, 3209–3220 (1997).
T. Imai, M. Kinoshita, and F. Hirata, J. Chem. Phys., 112, 9469 (2000).
I. Brovchenko, M. N. Andrews, and A. Oleinikova, Phys. Chem. Chem. Phys., 12, 4233–4238 (2010).
I. Yu, T. Tasaki, K. Nakada, and M. Nagaoka, J. Phys. Chem. B, 114, 12392–12397 (2010).
H. S. Ashbaugh, L. Liu, and L. N. Surampudi, J. Chem. Phys., 135, 054510 (2011).
A. C. Moskalev, Bachelor’s Diploma: Investigation of Hydration Shells of Molecules of Noble Gases in Aqueous Solutions, Novosibirsk State University (2012).
M. N. Andrews and R. Winter, Biophys. Chem., 156, 43–50 (2011).
N. V. Plyasunova, A. V. Plyasunov, and E. L. Shock, Intern. J. Thermophys., 25, 351–360 (2004).
A. S. Moskalev, A. V. Anikeenko, N. N. Medvedev, and A. Geiger, Book of Abstracts. EMLG-JMLG Annual Meeting (2013).
J. L. F. Abascal and C. Vega, J. Chem. Phys., 123, 234505 (2005).
H. L. Pi, J. L. Aragones, C. Vega, E. G. Noya, J. L. F. Abascal, M. A. Gonzalez, and C. McBride, Mol. Phys., 107, 365–374 (2009).
S. K. Pal, J. Peon, and A. H. Zewail, PNAS, 99, 1763–1768 (2002).
A. Ben-Naim, J. Chem. Phys., 128, 234501 (2008).
F. Hirata, Molecular Theory of Solvation (Understanding Chemical Reactivity), Kluwer Academic Publishers, Boston (2003).
J. Liang, Computational Methods for Protein Structure Prediction and Modeling. Biological and Medical Physics Biomedical Engineering, Springer, New York (2007), pp. 181–206.
V. P. Voloshin, A. V. Anikeenko, N. N. Medvedev, and A. Geiger, Proc. 9th Int. Symp. on Voronoi Diagrams in Science and Engineering (ISVD 2011), June 28th–30th, Qingdao, China (2011), pp. 170–176.
F. Cazals, H. Kanhere, and S. Loriot, ACM Trans. Math. Softw. (2011), p. 3.
A. V. Kim, N. N. Medvedev, and A. Geiger, J. Mol. Liq., 189, 74–80 (2013).
Computational Geometry Algorithms Library (CGAL). http://www.cgal.org
A. Okabe, B. Boots, K. Sugihara, and S. Chiu, Spatial Tessellations — Concepts and Applications of Voronoi Diagrams. Wiley, New York (2000).
N. N. Medvedev, Voronoi-Delaunay Method in Studies of Non-Crystalline Systems, Izd. SO RAN, Novosibirsk (2000).
V. P. Voloshin, A. V. Anikeenko, N. N. Medvedev, A. Geiger, and D. Stoyan, Proc.7th Int. Symp. on Voronoi Diagrams in Science and Engineering, Quebec, 28–30. Quebec, Canada (2010), pp. 254–259.
G. F. Voronoi, J. Reine Angew Math., 136, 67 (1909).
B. N. Delaunay, Proc. Int. Math. Congress, Toronto, August 11–16 (1924); University of Toronto, Press: Toronto (1928); pp. 695–700.
S. V. Anishchik and N. N. Medvedev, Phys. Rev. Lett., 75, 4314–4317 (1995).
M. G. Alinchenko, A. V. Anikeenko, N. N. Medvedev, V. P. Voloshin, M. Mezei, and P. Jedlovszky, J. Phys. Chem. B, 108, 19056–19067 (2004).
N. N. Medvedev, V. P. Voloshin, V. A. Luchnikov, and M. L. Gavrilova, J. Comput. Chem., 27, 1676–1692 (2006).
D.-S. Kim, Y. Cho, and K. Sugihara, Computer-Aided Design, 42, No. 10, 874–888 (2010).
F. Aurenhammer, SIAM J. Comput., 16, 78–96 (1987).
P. Procacci and R. Scateni, Int. J. Quantum Chem., 42, 1515–1528 (1992).
E. Paci and M. Marchi, PNAS, 93, 11609–11614 (1996).
V. Lounnas and B. M. Pettitt, Proteins: Struct., Funct., Genet., 18, 133–147 (1994).
A. V. Kim, V. P. Voloshin, N. N. Medvedev, and A. Geiger, Proc. Int. Symp. on Voronoi Diagrams in Science and Engineering, Rutgers University, USA. June 27–29, 2012, p. 95–102.
A. V. Kim, V. P. Voloshin, N. N. Medvedev, and A. Geiger, Trans. Comp. Sci. J.i, Springer (2013).
V. P. Voloshin and N. N. Medvedev, Proc. Int. Symp. on Voronoi Diagrams in Science and Enginering, St. Petersburg, Russia, July 8–10 (2013) (in preparation).
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Original Russian Text © 2013 N. N. Medvedev, V. P. Voloshin, A. V. Kim, A. V. Anikeenko, A. Geiger.
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Translated from Zhurnal Strukturnoi Khimii, Vol. 54, Supplement 2, pp. S276–S293, 2013.
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Medvedev, N.N., Voloshin, V.P., Kim, A.V. et al. Culation of partial molar volume and its components for molecular dynamics models of dilute solutions. J Struct Chem 54 (Suppl 2), 271–288 (2013). https://doi.org/10.1134/S0022476613080088
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DOI: https://doi.org/10.1134/S0022476613080088