Kirkwood-Buff Analysis of Liquid Mixtures in an Open Boundary Simulation.

Using the adaptive resolution (AdResS) molecular dynamics scheme, we present a new approach to calculate the thermodynamic properties of liquid mixtures in an open boundary simulation. As a test case, we simulate methanol-water mixtures. We show that Kirkwood-Buff integrals (KBI), which directly connect global thermodynamic properties to microscopic molecular distributions, can be efficiently calculated over a wide range of methanol mole fractions by choosing only a very small (∼3% of total simulation domain) open boundary explicit (all atom) region and a surrounding coarse-grained reservoir that takes care of correct particle fluctuations.

[1]  Matej Praprotnik,et al.  Coupling different levels of resolution in molecular simulations. , 2009, The Journal of chemical physics.

[2]  H. Berendsen,et al.  Molecular dynamics with coupling to an external bath , 1984 .

[3]  K. Dill.  Dominant forces in protein folding. , 1990, Biochemistry.

[4]  W. Kauzmann.  Some factors in the interpretation of protein denaturation. , 1959, Advances in protein chemistry.

[5]  E. Ruckenstein,et al.  A protein molecule in a mixed solvent: the preferential binding parameter via the Kirkwood-Buff theory. , 2006, Biophysical journal.

[6]  J. Dzubiella,et al.  Structure-thermodynamics relation of electrolyte solutions. , 2009, The Journal of chemical physics.

[7]  J. Kirkwood,et al.  The Statistical Mechanical Theory of Solutions. I , 1951 .

[8]  C. Holm,et al.  Multiscale approaches and perspectives to modeling aqueous electrolytes and polyelectrolytes. , 2012, Topics in current chemistry.

[9]  Berk Hess,et al.  GROMACS 3.0: a package for molecular simulation and trajectory analysis , 2001 .

[10]  N. V. D. van der Vegt,et al.  A new force field for atomistic simulations of aqueous tertiary butanol solutions. , 2005, The Journal of chemical physics.

[11]  B. Hess,et al.  Ion pairing in aqueous electrolyte solutions with biologically relevant anions. , 2011, The journal of physical chemistry. B.

[12]  André Bardow,et al.  Calculating thermodynamic properties from fluctuations at small scales. , 2011, The journal of physical chemistry. B.

[13]  L Delle Site,et al.  Classical to path-integral adaptive resolution in molecular simulation: towards a smooth quantum-classical coupling. , 2010, Physical review letters.

[14]  W. F. van Gunsteren,et al.  Entropic Contributions in Cosolvent Binding to Hydrophobic Solutes in Water , 2004 .

[15]  P. Cremer,et al.  Interactions between macromolecules and ions: The Hofmeister series. , 2006, Current opinion in chemical biology.

[16]  J. Wyman,et al.  LINKED FUNCTIONS AND RECIPROCAL EFFECTS IN HEMOGLOBIN: A SECOND LOOK. , 1964, Advances in protein chemistry.

[17]  E. Ruckenstein,et al.  Effect of salts and organic additives on the solubility of proteins in aqueous solutions. , 2006, Advances in colloid and interface science.

[18]  Kurt Kremer,et al.  Comparative atomistic and coarse-grained study of water: What do we lose by coarse-graining? , 2009, The European physical journal. E, Soft matter.

[19]  S. Weerasinghe,et al.  A Kirkwood-Buff derived force field for methanol and aqueous methanol solutions. , 2005, The journal of physical chemistry. B.

[20]  K. Kremer,et al.  Adaptive resolution molecular-dynamics simulation: changing the degrees of freedom on the fly. , 2005, The Journal of chemical physics.

[21]  Kurt Kremer,et al.  Structure Formation of Toluene around C60: Implementation of the Adaptive Resolution Scheme (AdResS) into GROMACS. , 2012, Journal of chemical theory and computation.

[22]  P. Ball.  Water as an active constituent in cell biology. , 2008, Chemical reviews.

[23]  Paul E. Smith,et al.  A Kirkwood-Buff Derived Force Field for Aqueous Alkali Halides. , 2011, Journal of chemical theory and computation.

[24]  M. Record,et al.  Analysis of effects of salts and uncharged solutes on protein and nucleic acid equilibria and processes: a practical guide to recognizing and interpreting polyelectrolyte effects, Hofmeister effects, and osmotic effects of salts. , 1998, Advances in protein chemistry.

[25]  Alexander Lukyanov,et al.  Versatile Object-Oriented Toolkit for Coarse-Graining Applications. , 2009, Journal of chemical theory and computation.

[26]  J. Crain,et al.  Methanol-water solutions: a bi-percolating liquid mixture. , 2004, The Journal of chemical physics.

[27]  K Schulten,et al.  VMD: visual molecular dynamics. , 1996, Journal of molecular graphics.

[28]  Matej Praprotnik,et al.  Multiscale simulation of soft matter: from scale bridging to adaptive resolution. , 2008, Annual review of physical chemistry.

[29]  Q. Cui,et al.  Preferential interactions between small solutes and the protein backbone: a computational analysis. , 2010, Biochemistry.

[30]  G. Peters,et al.  Pair correlation function integrals: computation and use. , 2011, The Journal of chemical physics.

[31]  Cecilia Clementi,et al.  Communication: On the locality of hydrogen bond networks at hydrophobic interfaces. , 2010, The Journal of chemical physics.

[32]  Matej Praprotnik,et al.  Adaptive resolution simulation of liquid water , 2007 .

[33]  N. V. D. van der Vegt,et al.  Hofmeister ion interactions with model amide compounds. , 2011, The journal of physical chemistry. B.

[34]  W. Kunz.  Specific Ion Effects , 2009 .

[35]  Matej Praprotnik,et al.  Statistical Physics Problems in Adaptive Resolution Computer Simulations of Complex Fluids , 2011 .

[36]  B. Hess,et al.  Cation specific binding with protein surface charges , 2009, Proceedings of the National Academy of Sciences.

[37]  T. Straatsma,et al.  THE MISSING TERM IN EFFECTIVE PAIR POTENTIALS , 1987 .

[38]  Y. Marcus.  Preferential solvation in mixed solvents Part 8. Aqueous methanol from sub-ambient to elevated temperatures , 1999 .

[39]  A. Ben-Naim.  Solubility and thermodynamics of solution of argon in water-methanol system , 1967 .

[40]  Samantha Weerasinghe,et al.  Recent Applications of Kirkwood–Buff Theory to Biological Systems , 2007, Cell Biochemistry and Biophysics.