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Research Article

Application of the 2PT model to understanding entropy change in molecular coarse-graining

ORCID Icon, & ORCID Icon
Pages 274-289 | Received 14 Nov 2019, Accepted 22 Feb 2020, Published online: 09 Mar 2020

References

  • Müller-Plathe, F. Coarse-Graining in Polymer Simulation: From the Atomistic to the Mesoscopic Scale and Back. ChemPhysChem. 2002, 3, 754–769. DOI:10.1002/1439-7641(20020916)3:9<754::AID-CPHC754>3.0.CO;2-U.
  • Noid, W. G. Perspective: Coarse-grained Models for Biomolecular Systems. J. Chem. Phys. 2013, 139, 090901. DOI:10.1063/1.4818908.
  • Saunders, M. G.; Voth, G. A. Coarse-Graining Methods for Computational Biology. Annu. Rev. Biophys. 2013, 42, 73–93. DOI:10.1146/annurev-biophys-083012-130348.
  • Brini, E.; Algaer, E. A.; Ganguly, P.; Li, C.; Rodríguez-Ropero, F.; van der Vegt, N. F. A. Systematic Coarse-graining Methods for Soft Matter Simulations – A Review. Soft Matter. 2013, 9, 2108–2119. DOI:10.1039/C2SM27201F.
  • Lin, S.-T.; Blanco, M.; Iii, W. A. G. The Two-phase Model for Calculating Thermodynamic Properties of Liquids from Molecular Dynamics: Validation for the Phase Diagram of Lennard-Jones Fluids. J. Chem. Phys. 2003, 119, 11792–11805. DOI:10.1063/1.1624057.
  • Fritz, D.; Koschke, K.; Harmandaris, V. A.; van der Vegt, N. F. A.; Kremer, K. Multiscale Modeling of Soft Matter: Scaling of Dynamics. Phys. Chem. Chem. Phys. 2011, 13, 10412–10420. DOI:10.1039/c1cp20247b.
  • Füchslin, R. M.; Fellermann, H.; Eriksson, A.; Ziock, H.-J. Coarse Graining and Scaling in Dissipative Particle Dynamics. J. Chem. Phys. 2009, 130, 214102. DOI:10.1063/1.3143976.
  • Izvekov, S.; Rice, B. M. Multi-scale Coarse-graining of Non-conservative Interactions in Molecular Liquids. J. Chem. Phys. 2014, 140, 104104. DOI:10.1063/1.4866142.
  • Trément, S.; Schnell, B.; Petitjean, L.; Couty, M.; Rousseau, B. Conservative and Dissipative Force Field for Simulation of Coarse-grained Alkane Molecules: A Bottom-up Approach. J. Chem. Phys. 2014, 140, 134113. DOI:10.1063/1.4870394.
  • Deichmann, G.; Van der Vegt, N. F. A. Bottom-up Approach to Represent Dynamic Properties in Coarse-grained Molecular Simulations. J. Chem. Phys. 2018, 149, 244114. DOI:10.1063/1.5064369.
  • Rudzinski, J. F. Recent Progress Towards Chemically-Specific Coarse-Grained Simulation Models with Consistent Dynamical Properties. Computation. 2019, 7, 42. DOI: 10.3390/computation7030042.
  • Rosenfeld, Y. Relation between the Transport Coefficients and the Internal Entropy of Simple Systems. Phys. Rev. A. 1977, 15, 2545–2549. DOI:10.1103/PhysRevA.15.2545.
  • Mittal, J.; Errington, J. R.; Truskett, T. M. Relationships between Self- Diffusivity, Packing Fraction, and Excess Entropy in Simple Bulk and Confined Fluids. J. Phys. Chem. B. 2007, 111, 10054–10063. DOI:10.1021/jp071369e.
  • Rondina, G. G.; Böhm, M. C.; Müller-Plathe, F. Predicting the Mobility Increase of Coarse-Grained Polymer Models from Excess Entropy Differences. J. Chem. Theory Comput. 2020. DOI:10.1021/acs.jctc.9b01088.
  • Mukherjee, B.; Peter, C.; Kremer, K. Single Molecule Translocation in Smectics Illustrates the Challenge for Time-mapping in Simulations on Multiple Scales. J. Chem. Phys. 2017, 147, 114501. DOI:10.1063/1.5001482.
  • Jin, J.; Han, Y.; Voth, G. A. Coarse-graining Involving Virtual Sites: Centers of Symmetry Coarse-graining. J. Chem. Phys. 2019, 150, 154103. DOI:10.1063/1.5067274.
  • Tschöp, W.; Kremer, K.; Batoulis, J.; Bürger, T.; Hahn, O. Simulation of Polymer Melts. I. Coarse-Graining Procedure for Polycarbonates. Acta Polym. 1998, 49, 61–74. DOI:10.1002/()1521-4044.
  • Fritz, D.; Harmandaris, V. A.; Kremer, K.; Van der Vegt, N. F. A. Coarse- Grained Polymer Melts Based on Isolated Atomistic Chains: Simulation of Polystyrene of Different Tacticities. Macromolecules. 2009, 42, 7579–7588.
  • Foley, T. T.; Shell, M. S.; Noid, W. G. The Impact of Resolution upon Entropy and Information in Coarse-grained Models. J. Chem. Phys. 2015, 143, 243104. DOI:10.1063/1.4929836.
  • Rudzinski, J. F.; Bereau, T. Structural-kinetic-thermodynamic Relationships Identified from Physics-based Molecular Simulation Models. J. Chem. Phys. 2018, 148, 204111. DOI: 10.1063/1.5025125.
  • Lin, S.-T.; Maiti, P. K.; Goddard, W. A. Two-Phase Thermodynamic Model for Efficient and Accurate Absolute Entropy of Water from Molecular Dynamics Simulations. J. Phys. Chem. B. 2010, 114, 8191–8198. DOI: 10.1021/jp103120q.
  • Baron, R.; de Vries, A. H.; Hünenberger, P. H.; van Gunsteren, W. F. Comparison of Atomic-Level and Coarse-Grained Models for Liquid Hydrocarbons from Molecular Dynamics Configurational Entropy Estimates. J. Phys. Chem. B. 2006, 110, 8464–8473. DOI:10.1021/jp055888y.
  • Chaimovich, A.; Shell, M. S. Anomalous Waterlike Behavior in Spherically- Symmetric Water Models Optimized with the Relative Entropy. Phys. Chem. Chem. Phys. 2009, 11, 1901–1915. DOI: 10.1039/b818512c.
  • Riniker, S.; Allison, J. R.; van Gunsteren, W. F. On Developing Coarse-grained Models for Biomolecular Simulation: A Review. Phys. Chem. Chem. Phys. 2012, 14, 12423–12430. DOI:10.1039/c2cp40934h.
  • Das, A.; Andersen, H. C. The Multiscale Coarse-graining Method. V. Isothermal- Isobaric Ensemble. J. Chem. Phys. 2010, 132, 164106. DOI:10.1063/1.3394862.
  • Kmiecik, S.; Gront, D.; Kolinski, M.; Wieteska, L.; Dawid, A. E.; Kolinski, A. Coarse-Grained Protein Models and Their Applications. Chem. Rev. 2016, 116, 7898–7936. DOI:10.1021/acs.chemrev.6b00163.
  • Baron, R.; de Vries, A. H.; Hünenberger, P. H.; van Gunsteren, W. F. Configurational Entropies of Lipids in Pure and Mixed Bilayers from Atomic-Level and Coarse-Grained Molecular Dynamics Simulations. J. Phys. Chem. B. 2006, 110, 15602–15614. DOI:10.1021/jp061627s.
  • Shell, M. S. The Relative Entropy Is Fundamental to Multiscale and Inverse Thermodynamic Problems. J. Chem. Phys. 2008, 129, 144108. DOI:10.1063/1.2992060.
  • Rudzinski, J. F.; Noid, W. G. Coarse-graining Entropy, Forces, and Structures. J. Chem. Phys. 2011, 135, 214101. DOI: 10.1063/1.3663709.
  • Guenza, M. G. Structural and Thermodynamic Consistency in Coarse-grained Models of Macromolecules. J. Phys. Conf. Ser. 2015, 640, 012009.
  • Jin, J.; Pak, A. J.; Voth, G. A. Understanding Missing Entropy in Coarse- Grained Systems: Addressing Issues of Representability and Transferability. J. Phys. Chem. Lett. 2019, 10, 4549–4557. DOI:10.1021/acs.jpclett.9b01228.
  • Shell, M. S.;. Coarse-Graining with the Relative Entropy. In Advances in Chemical Physics; 2016; 395–441; Rice, S. A.; Dinner, A. R., Eds.; John Wiley & Sons, Ltd.
  • Brini, E.; Marcon, V.; van der Vegt, N. F. A. Conditional Reversible Work Method for Molecular Coarse Graining Applications. Phys. Chem. Chem. Phys. 2011, 13, 10468–10474. DOI:10.1039/c0cp02888f.
  • Deichmann, G.; Van der Vegt, N. F. A. Conditional Reversible Work Coarse- Grained Models of Molecular Liquids with Coulomb Electrostatics – A Proof of Concept Study on Weakly Polar Organic Molecules. J. Chem. Theory Comput. 2017, 13, 6158–6166. DOI:10.1021/acs.jctc.7b00611.
  • Pascal, T. A.; Goddard, W. A.; Jung, Y. Entropy and the Driving Force for the Filling of Carbon Nanotubes with Water. Proc. National Academy Sci. 2011, 108, 11794–11798. DOI:10.1073/pnas.1108073108.
  • Pascal, T. A.; Lin, S.-T.; Iii, W. A. G. Thermodynamics of Liquids: Standard Molar Entropies and Heat Capacities of Common Solvents from 2PT Molecular Dynamics. Phys. Chem. Chem. Phys. 2010, 13, 169–181. DOI:10.1039/C0CP01549K.
  • Carnahan, N. F.; Starling, K. E. Equation of State for Nonattracting Rigid Spheres. J. Chem. Phys. 1969, 51, 635–636. DOI:10.1063/1.1672048.
  • Lai, P.-K.; Lin, S.-T. Rapid Determination of Entropy for Flexible Molecules in Condensed Phase from the Two-phase Thermodynamic Model. RSC Adv. 2014, 4, 9522–9533. DOI:10.1039/c3ra47071g.
  • Huang, S.-N.; Pascal, T. A.; Goddard, W. A.; Maiti, P. K.; Lin, S.-T. Absolute Entropy and Energy of Carbon Dioxide Using the Two-Phase Thermodynamic Model. J. Chem. Theory Comput. 2011, 7, 1893–1901. DOI:10.1021/ct200211b.
  • Caro, M. A.; Laurila, T.; Lopez-Acevedo, O. Accurate Schemes for Calculation of Thermodynamic Properties of Liquid Mixtures from Molecular Dynamics Simulations. J. Chem. Phys. 2016, 145, 244504. DOI:10.1063/1.4973001.
  • Bernhardt, M. Solvation Thermodynamic Properties from Molecular Dynamics on the Terahertz Time Scale. MA thesis, TU Darmstadt, Dec 2016.
  • Eckart, C. Some Studies Concerning Rotating Axes and Polyatomic Molecules. ?phys. Rev. 1935, 47, 552–558. DOI:10.1103/PhysRev.47.552.
  • Louck, J. D.; Galbraith, H. W. Eckart Vectors, Eckart Frames, and Polyatomic Molecules. Rev. Mod. Phys. 1976, 48, 69–106. DOI:10.1103/RevModPhys.48.69.
  • Sablić, J.; Delgado-Buscalioni, R.; Praprotnik, M. Application of the Eckart Frame to Soft Matter: Rotation of Star Polymers under Shear Flow. Soft Matter. 2017, 13, 6988–7000. DOI:10.1039/C7SM00616K.
  • Rhee, Y. M.; Kim, M. S. Mode-specific Energy Analysis for Rotating-vibrating Triatomic Molecules in Classical Trajectory Simulation. J. Chem. Phys. 1997, 107, 1394–1402. DOI:10.1063/1.474493.
  • Heidelbach, C.; Vikhrenko, V. S.; Schwarzer, D.; Schroeder, J. Molecular Dynamics Simulation of Vibrational Relaxation of Highly Excited Molecules in Fluids. II. Nonequilibrium Simulation of Azulene in CO2 and Xe. J. Chem. Phys. 1999, 110, 5286–5299. DOI:10.1063/1.478423.
  • Jorgensen, W. L.; Madura, J. D.; Swenson, C. J. Optimized Intermolecular Potential Functions for Liquid Hydrocarbons. J. Am. Chem. Soc. 1984, 106, 6638–6646. DOI: 10.1021/ja00334a030.
  • Price, M. L. P.; Ostrovsky, D.; Jorgensen, W. L. Gas-phase and Liquid-state Properties of Esters, Nitriles, and Nitro Compounds with the OPLS-AA Force Field. J. Comput. Chem. 2001, 22, 1340–1352. DOI:10.1002/jcc.1092.
  • Allen, M. P.; Tildesley, D. J. Computer Simulation of Liquids; Oxford: Clarendon Press, 1989.
  • Darden, T.; York, D.; Pedersen, L. Particle Mesh Ewald: An N·log(N) Method for Ewald Sums in Large Systems. J. Chem. Phys. 1993, 98, 10089. DOI:10.1063/1.464397.
  • Essmann, U.; Perera, L.; Berkowitz, M. L.; Darden, T.; Lee, H.; Pedersen, L. G. A Smooth Particle Mesh Ewald Method. J. Chem. Phys. 1995, 103, 8577–8593. DOI:10.1063/1.470117.
  • Abraham, M. J.; Murtola, T.; Schulz, R.; Páll, S.; Smith, J. C.; Hess, B.; Lindahl, E. GROMACS: High Performance Molecular Simulations through Multi- Level Parallelism from Laptops to Supercomputers. SoftwareX. 2015, 1–2, 19–25. DOI:10.1016/j.softx.2015.06.001.
  • Nosé, S. A Unified Formulation of the Constant Temperature Molecular Dynamics Methods. J. Chem. Phys. 1984, 81, 511–519. DOI:10.1063/1.447334.
  • Parrinello, M.; Rahman, A. Polymorphic Transitions in Single Crystals: A New Molecular Dynamics Method. J. Appl. Phys. 1981, 52, 7182–7190. DOI:10.1063/1.328693.
  • Deichmann, G.; Marcon, V.; Van der Vegt, N. F. A. Bottom-up Derivation of Conservative and Dissipative Interactions for Coarse-grained Molecular Liquids with the Conditional Reversible Work Method. J. Chem. Phys. 2014, 141, 224109. DOI:10.1063/1.4903454.
  • Brini, E.; van der Vegt, N. F. A. Chemically Transferable Coarse-grained Potentials from Conditional Reversible Work Calculations. J. Chem. Phys. 2012, 137, 154113. DOI: 10.1063/1.4758936.
  • Ardham, V. R.; Deichmann, G.; Van der Vegt, N. F. A.; Leroy, F. Solid-liquid Work of Adhesion of Coarse-grained Models of N-hexane on Graphene Layers Derived from the Conditional Reversible Work Method. J. Chem. Phys. 2015, 143, 243135. DOI: 10.1063/1.4936253.
  • Plimpton, S.;. Fast Parallel Algorithms for Short-Range Molecular Dynamics. J. Comput. Phys. 1995, 117, 1–19. DOI: 10.1006/jcph.1995.1039.
  • Martyna, G. J.; Tobias, D. J.; Klein, M. L. Constant Pressure Molecular Dynamics Algorithms. J. Chem. Phys. 1994, 101, 4177–4189. DOI: 10.1063/1.467468.
  • Tuckerman, M. E.; Alejandre, J.; López-Rendón, R.; Jochim, A. L.; Martyna, G. J. A Liouville-operator Derived Measure-preserving Integrator for Molecular Dynamics Simulations in the Isothermal–isobaric Ensemble. J. Phys. A Math. Theor. 2006, 39, 5629–5651. DOI: 10.1088/0305-4470/39/19/S18.
  • Hockney, R. W.; Eastwood, J. W. Computer Simulation Using Particles; Hilger: Bristol, 1988.
  • Karimi-Varzaneh, H. A.; van der Vegt, N. F. A.; Müller-Plathe, F.; Carbone, P. How Good are Coarse-Grained Polymer Models? A Comparison for Atactic Polystyrene. ChemPhysChem. 2012, 13, 3428–3439. DOI: 10.1002/cphc.201200111.
  • Rühle, V.; Junghans, C.; Lukyanov, A.; Kremer, K.; Andrienko, D. Versatile Object-Oriented Toolkit for Coarse-Graining Applications. J. Chem. Theory Comput. 2009, 5, 3211–3223. DOI:10.1021/ct900369w.
  • Li, Z.; Bian, X.; Li, X.; Karniadakis, G. E. Incorporation of Memory Effects in Coarse-grained Modeling via the Mori-Zwanzig Formalism. J. Chem. Phys. 2015, 143, 243128. DOI:10.1063/1.4935490.
  • Dyre, J. C. Perspective: Excess-entropy Scaling. J. Chem. Phys. 2018, 149, 210901. DOI:10.1063/1.5055064.
  • Armstrong, J. A.; Chakravarty, C.; Ballone, P. Statistical Mechanics of Coarse Graining: Estimating Dynamical Speedups from Excess Entropies. J. Chem. Phys. 2012, 136, 124503. DOI: 10.1063/1.3697383.
  • Shell, M. S. Systematic Coarse-graining of Potential Energy Landscapes and Dynamics in Liquids. J. Chem. Phys. 2012, 137, 084503. DOI:10.1063/1.4746391.
  • Sackur, O. Die Anwendung der kinetischen Theorie der Gase auf chemische Probleme. Annalen der Physik. 1911, 341, 958–980. DOI:10.1002/()1521-3889.
  • Nettleton, R. E.; Green, M. S. Expression in Terms of Molecular Distribution Functions for the Entropy Density in an Infinite System. J. Chem. Phys. 1958, 29, 1365–1370. DOI:10.1063/1.1744724.
  • Voyiatzis, E.; Müller-Plathe, F.; Böhm, M. C. Do Transport Properties of Entangled Linear Polymers Scale with Excess Entropy? Macromolecules. 2013, 46, 8710–8723. DOI:10.1021/ma401617z.
  • Jakse, N.; Pasturel, A. Excess Entropy Scaling Law for Diffusivity in Liquid Metals. Sci. Rep. 2016, 6. DOI:10.1038/srep20689.
  • Chopra, R.; Truskett, T. M.; Errington, J. R. On the Use of Excess Entropy Scaling to Describe Single-Molecule and Collective Dynamic Properties of Hydrocarbon Isomer Fluids. J. Phys. Chem. B. 2010, 114, 16487–16493. DOI:10.1021/jp107878u.
  • Domalski, E. S.; Hearing, E. D. Condensed Phase Heat Capacity Data, NIST Chemistry WebBook, NIST Standard Reference Database Number 69, P.J. Linstrom and W.G. Mallard Eds.; Gaithersburg MD: National Institute of Standards and Technology, 20899, DOI:10.18434/T4D303, (retrieved January 09, 2019)

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