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Research Progress of the Ion Activity Coefficient of Polyelectrolytes: A Review. Molecules 2023; 28:molecules28052042. [PMID: 36903289 PMCID: PMC10003794 DOI: 10.3390/molecules28052042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2023] [Revised: 02/15/2023] [Accepted: 02/20/2023] [Indexed: 02/25/2023] Open
Abstract
Polyelectrolyte has wide applications in biomedicine, agriculture and soft robotics. However, it is among one of the least understood physical systems because of the complex interplay of electrostatics and polymer nature. In this review, a comprehensive description is presented on experimental and theoretical studies of the activity coefficient, one of the most important thermodynamic properties of polyelectrolyte. Experimental methods to measure the activity coefficient were introduced, including direct potentiometric measurement and indirect methods such as isopiestic measurement and solubility measurement. Next, progress on the various theoretical approaches was presented, ranging from analytical, empirical and simulation methods. Finally, challenges for future development are proposed on this field.
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2
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Schmid F. Understanding and Modeling Polymers: The Challenge of Multiple Scales. ACS POLYMERS AU 2022. [DOI: 10.1021/acspolymersau.2c00049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Affiliation(s)
- Friederike Schmid
- Institut für Physik, Johannes Gutenberg-Universität Mainz, Staudingerweg 9, 55128Mainz, Germany
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3
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Mkandawire WD, Milner ST. Pulling simulation predicts mixing free energy for binary mixtures. SOFT MATTER 2022; 18:7998-8007. [PMID: 36222173 DOI: 10.1039/d2sm01065h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
Predicting the mixing free energy of mixing for binary mixtures using simulations is challenging. We present a novel molecular dynamics (MD) simulation method to extract the chemical potential μ(X) for mixtures of species A and B. Each molecule of species A and B is placed in equal and opposite harmonic potentials ±(1/2)Uex(x) centered at the middle of the simulation box, resulting in a nonuniform mole fraction profile X(z) in which A is concentrated at the center, and B at the periphery. Combining these, we obtain Uex(X), the exchange chemical potential required to induce a given deviation of the mole fraction from its average. Simulation results for Uex(X) can be fitted to simple free energy models to extract the interaction parameter χ for binary mixtures. To illustrate our method, we investigate benzene-pyridine mixtures, which provide a good example of regular solution behavior, using both TraPPE united-atom and OPLS all-atom potentials, both of which have been validated for pure fluid properties. χ values obtained with the new method are consistent with values from other recent simulation methods. However, the TraPPE-UA results differ substantially from the χ obtained from VLE experimental data, while the OPLS-AA results are in reasonable agreement with experiment, highlighting the importance of accurate potentials in correctly representing mixture behavior.
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Affiliation(s)
| | - Scott T Milner
- Pennsylvania State University, University Park, Pennsylvania, USA.
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4
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Vo P, Forsman J, Woodward CE. Boundary-Monte Carlo Method for Neutral and Charged Confined Fluids. J Chem Theory Comput 2022; 18:3766-3780. [PMID: 35575645 DOI: 10.1021/acs.jctc.1c01146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In this work, we describe a new Monte Carlo (MC) simulation method to investigate highly coupled fluids in confined geometries at a constant chemical potential. This method is based on so-called multi-scale Hamiltonian methods, wherein the chemical potential is determined using a more amenable Hamiltonian for a fluid in an "outer" region, which facilitates standard methods, such as grand canonical MC simulations or Widom's particle insertion method. The (inner region) fluid of interest is placed in diffusive contact with the simpler outer fluid via a boundary zone wherein the Hamiltonian is transformed. The current method utilizes an ideal fluid for the outer regions, which allows for implicit rather than explicit simulations. Only the boundary and inner region need explicit consideration; hence, the nomenclature used is boundary-Monte Carlo. We illustrate the utility of the method for simple neutral and charged fluids in cylindrical and planar pores. In the latter case, we use a dense room-temperature ionic liquid model and illustrate how the boundary zone establishes a proper Donnan equilibrium between inner and outer fluids in the presence of charged planar electrodes. Thus, the method allows direct calculation of properties such as the differential capacitance, without the need for additional difficult calculations of the requisite Donnan potential.
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Affiliation(s)
- Phuong Vo
- School of Science, University of New South Wales, Canberra, Canberra ACT 2600, Australia
| | - Jan Forsman
- Department of Theoretical Chemistry, Chemical Centre, Lund University, Lund S-22100, Sweden
| | - Clifford E Woodward
- School of Science, University of New South Wales, Canberra, Canberra ACT 2600, Australia
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5
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Banerjee A, Sevilla M, Rudzinski JF, Cortes-Huerto R. Finite-size scaling and thermodynamics of model supercooled liquids: long-range concentration fluctuations and the role of attractive interactions. SOFT MATTER 2022; 18:2373-2382. [PMID: 35258066 DOI: 10.1039/d2sm00089j] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
We compute partial structure factors, Kirkwood-Buff integrals (KBIs) and chemical potentials of model supercooled liquids with and without attractive interactions. We aim at investigating whether relatively small differences in the tail of the radial distribution functions result in contrasting thermodynamic properties. Our results suggest that the attractive potential favours the nucleation of long-range structures. Indeed, upon decreasing temperature, Bathia-Thornton structure factors display anomalous behaviour in the k→0 limit. KBIs extrapolated to the thermodynamic limit confirm this picture, and excess coordination numbers identify the anomaly with long-range concentration fluctuations. By contrast, the purely repulsive system remains perfectly miscible for the same temperature interval and only reveals qualitatively similar concentration fluctuations in the crystalline state. Furthermore, differences in both isothermal compressibilities and chemical potentials show that thermodynamics is not entirely governed by the short-range repulsive part of the interaction potential, emphasising the nonperturbative role of attractive interactions. Finally, at higher density, where both systems display nearly identical dynamical properties and repulsive interactions become dominant, the anomaly disappears, and both systems also exhibit similar thermodynamic properties.
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Affiliation(s)
- Atreyee Banerjee
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany.
| | - Mauricio Sevilla
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany.
| | - Joseph F Rudzinski
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany.
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6
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Guardiani C, Cecconi F, Chiodo L, Cottone G, Malgaretti P, Maragliano L, Barabash ML, Camisasca G, Ceccarelli M, Corry B, Roth R, Giacomello A, Roux B. Computational methods and theory for ion channel research. ADVANCES IN PHYSICS: X 2022; 7:2080587. [PMID: 35874965 PMCID: PMC9302924 DOI: 10.1080/23746149.2022.2080587] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 05/15/2022] [Indexed: 06/15/2023] Open
Abstract
Ion channels are fundamental biological devices that act as gates in order to ensure selective ion transport across cellular membranes; their operation constitutes the molecular mechanism through which basic biological functions, such as nerve signal transmission and muscle contraction, are carried out. Here, we review recent results in the field of computational research on ion channels, covering theoretical advances, state-of-the-art simulation approaches, and frontline modeling techniques. We also report on few selected applications of continuum and atomistic methods to characterize the mechanisms of permeation, selectivity, and gating in biological and model channels.
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Affiliation(s)
- C. Guardiani
- Dipartimento di Ingegneria Meccanica e Aerospaziale, Sapienza Università di Roma, Rome, Italy
| | - F. Cecconi
- CNR - Istituto dei Sistemi Complessi, Rome, Italy and Istituto Nazionale di Fisica Nucleare, INFN, Roma1 section. 00185, Roma, Italy
| | - L. Chiodo
- Department of Engineering, Campus Bio-Medico University, Rome, Italy
| | - G. Cottone
- Department of Physics and Chemistry-Emilio Segrè, University of Palermo, Palermo, Italy
| | - P. Malgaretti
- Helmholtz Institute Erlangen-Nürnberg for Renewable Energy (IEK-11), Forschungszentrum Jülich, Erlangen, Germany
| | - L. Maragliano
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy, and Center for Synaptic Neuroscience and Technology, Istituto Italiano di Tecnologia, Genova, Italy
| | - M. L. Barabash
- Department of Materials Science and Nanoengineering, Rice University, Houston, TX 77005, USA
| | - G. Camisasca
- Dipartimento di Ingegneria Meccanica e Aerospaziale, Sapienza Università di Roma, Rome, Italy
- Dipartimento di Fisica, Università Roma Tre, Rome, Italy
| | - M. Ceccarelli
- Department of Physics and CNR-IOM, University of Cagliari, Monserrato 09042-IT, Italy
| | - B. Corry
- Research School of Biology, The Australian National University, Canberra, ACT 2600, Australia
| | - R. Roth
- Institut Für Theoretische Physik, Eberhard Karls Universität Tübingen, Tübingen, Germany
| | - A. Giacomello
- Dipartimento di Ingegneria Meccanica e Aerospaziale, Sapienza Università di Roma, Rome, Italy
| | - B. Roux
- Department of Biochemistry & Molecular Biology, University of Chicago, Chicago IL, USA
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7
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Lucco Castello F, Tolias P. Bridge functions of classical one-component plasmas. Phys Rev E 2022; 105:015208. [PMID: 35193199 DOI: 10.1103/physreve.105.015208] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2021] [Accepted: 01/10/2022] [Indexed: 06/14/2023]
Abstract
In a recent paper, Lucco Castello et al. [arXiv:2107.03537] performed systematic extractions of classical one-component plasma bridge functions from molecular dynamics simulations and provided an accurate parametrization that was incorporated in their isomorph-based empirically modified hypernetted chain approach for Yukawa one-component plasmas. Here the extraction technique and parametrization strategy are described in detail, while the deficiencies of earlier efforts are discussed. The structural and thermodynamic predictions of the updated version of the integral equation theory approach are compared with extensive available simulation results revealing a truly unprecedented level of accuracy in the entire dense liquid region of the Yukawa phase diagram.
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Affiliation(s)
- F Lucco Castello
- Space and Plasma Physics, Royal Institute of Technology, Stockholm SE-100 44, Sweden
| | - P Tolias
- Space and Plasma Physics, Royal Institute of Technology, Stockholm SE-100 44, Sweden
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8
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Sundar S, Sandilya AA, Priya MH. Unraveling the Influence of Osmolytes on Water Hydrogen-Bond Network: From Local Structure to Graph Theory Analysis. J Chem Inf Model 2021; 61:3927-3944. [PMID: 34379415 DOI: 10.1021/acs.jcim.1c00527] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Water structure in aqueous osmolyte solutions, deduced from the slight alteration in the water-water radial distribution function, the decrease in water-water hydrogen bonding, and tetrahedral ordering based only on the orientation of nearest water molecules derived from the molecular dynamics simulations, appears to have been perturbed. A careful analysis, however, reveals that the hydrogen bonding and the tetrahedral ordering around a water molecule in binary solutions remain intact as in neat water when the contribution of osmolyte-water interactions is appropriately incorporated. Furthermore, the distribution of the water binding energies and the water excess chemical potential of solvation in solutions are also pretty much the same as in neat water. Osmolytes are, therefore, well integrated into the hydrogen-bond network of water. Indeed, osmolytes tend to preferentially hydrogen bond with water molecules and their interaction energies are strongly correlated to their hydrogen-bonding capability. The graph network analysis, further, illustrates that osmolytes act as hubs in the percolated hydrogen-bond network of solutions. The degree of hydrogen bonding of osmolytes predominantly determines all of the network properties. Osmolytes like ethanol that form fewer hydrogen bonds than a water molecule disrupt the water hydrogen-bond network, while other osmolytes that form more hydrogen bonds effectively increase the connectivity among water molecules. Our observation of minimal variation in the local structure and the vitality of osmolyte-water hydrogen bonds on the solution network properties clearly imply that the direct interaction between protein and osmolytes is solely responsible for the protein stability. Further, the relevance of hydrogen bonds on solution properties suggests that the hydrogen-bonding interaction among protein, water, and osmolyte could be the key determinant of the protein conformation in solutions.
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Affiliation(s)
- Smrithi Sundar
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
| | - Avilasha A Sandilya
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
| | - M Hamsa Priya
- Department of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
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9
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Baptista LA, Dutta RC, Sevilla M, Heidari M, Potestio R, Kremer K, Cortes-Huerto R. Density-functional-theory approach to the Hamiltonian adaptive resolution simulation method. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2021; 33:184003. [PMID: 33690194 DOI: 10.1088/1361-648x/abed1d] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Accepted: 03/09/2021] [Indexed: 06/12/2023]
Abstract
In the Hamiltonian adaptive resolution simulation method (H-AdResS) it is possible to simulate coexisting atomistic (AT) and ideal gas representations of a physical system that belong to different subdomains within the simulation box. The Hamiltonian includes a field that bridges both models by smoothly switching on (off) the intermolecular potential as particles enter (leave) the AT region. In practice, external one-body forces are calculated and applied to enforce a reference density throughout the simulation box, and the resulting external potential adds up to the Hamiltonian. This procedure suggests an apparent dependence of the final Hamiltonian on the system's thermodynamic state that challenges the method's statistical mechanics consistency. In this paper, we explicitly include an external potential that depends on the switching function. Hence, we build a grand canonical potential for this inhomogeneous system to find the equivalence between H-AdResS and density functional theory (DFT). We thus verify that the external potential inducing a constant density profile is equal to the system's excess chemical potential. Given DFT's one-to-one correspondence between external potential and equilibrium density, we find that a Hamiltonian description of the system is compatible with the numerical implementation based on enforcing the reference density across the simulation box. In the second part of the manuscript, we focus on assessing our approach's convergence and computing efficiency concerning various model parameters, including sample size and solute concentrations. To this aim, we compute the excess chemical potential of water, aqueous urea solutions and Lennard-Jones (LJ) mixtures. The results' convergence and accuracy are convincing in all cases, thus emphasising the method's robustness and capabilities.
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Affiliation(s)
- L A Baptista
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
| | - R C Dutta
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
| | - M Sevilla
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
| | - M Heidari
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
| | - R Potestio
- Physics Department, University of Trento, via Sommarive, 14 I-38123 Trento, Italy
- INFN-TIFPA, Trento Institute for Fundamental Physics and Applications, I-38123 Trento, Italy
| | - K Kremer
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
| | - R Cortes-Huerto
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128, Mainz, Germany
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10
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Cortes-Huerto R, Praprotnik M, Kremer K, Delle Site L. From adaptive resolution to molecular dynamics of open systems. THE EUROPEAN PHYSICAL JOURNAL. B 2021; 94:189. [PMID: 34720711 PMCID: PMC8547219 DOI: 10.1140/epjb/s10051-021-00193-w] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 08/31/2021] [Indexed: 05/14/2023]
Abstract
ABSTRACT We provide an overview of the Adaptive Resolution Simulation method (AdResS) based on discussing its basic principles and presenting its current numerical and theoretical developments. Examples of applications to systems of interest to soft matter, chemical physics, and condensed matter illustrate the method's advantages and limitations in its practical use and thus settle the challenge for further future numerical and theoretical developments.
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Affiliation(s)
| | - Matej Praprotnik
- Laboratory for Molecular Modeling, National Institute of Chemistry, Ljubljana, Slovenia and Department of Physics, Faculty of Mathematics and Physics, University of Ljubljana, Ljubljana, Slovenia
| | - Kurt Kremer
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Luigi Delle Site
- Department of Mathematics and Computer Science, Institute for Mathematics, Freie Universität Berlin, Berlin, Germany
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11
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Sandilya A, Natarajan U, Priya MH. Molecular View into the Cyclodextrin Cavity: Structure and Hydration. ACS OMEGA 2020; 5:25655-25667. [PMID: 33073091 PMCID: PMC7557249 DOI: 10.1021/acsomega.0c02760] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2020] [Accepted: 08/14/2020] [Indexed: 05/21/2023]
Abstract
We find, through atomistic molecular dynamics simulation of native cyclodextrins (CDs) in water, that although the outer surface of a CD appears like a truncated cone, the inner cavity resembles a conical hourglass because of the inward protrusion of the glycosidic oxygens. Furthermore, the conformations of the constituent α-glucose molecules are found to differ significantly from a free monomeric α-glucose molecule. This is the first computational study that maps the conformational change to the preferential hydrogen bond donating capacity of one of the secondary hydroxyl groups of CD, in consensus with an NMR experiment. We have developed a simple and novel geometry-based technique to identify water molecules occupying the nonspherical CD cavity, and the computed water occupancies are in close agreement with the experimental and density functional theory studies. Our analysis reveals that a water molecule in CD cavity loses out about two hydrogen bonds and remains energetically frustrated but possesses higher orientational degree of freedom compared to bulk water. In the context of CD-drug complexation, these imply a nonclassical, that is, enthalpically driven hydrophobic association of a drug in CD cavity.
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Affiliation(s)
- Avilasha
A. Sandilya
- Department
of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
| | - Upendra Natarajan
- Department
of Chemical Engineering, Indian Institute
of Technology Madras, Chennai 600036, India
| | - M. Hamsa Priya
- Department
of Biotechnology, Bhupat and Jyoti Mehta School of Biosciences, Indian Institute of Technology Madras, Chennai 600036, India
- . Phone: +91-44-22574132
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12
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Fiorentini R, Kremer K, Potestio R. Ligand-protein interactions in lysozyme investigated through a dual-resolution model. Proteins 2020; 88:1351-1360. [PMID: 32525263 PMCID: PMC7497117 DOI: 10.1002/prot.25954] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2020] [Revised: 05/04/2020] [Accepted: 05/16/2020] [Indexed: 12/12/2022]
Abstract
A fully atomistic (AT) modeling of biological macromolecules at relevant length- and time-scales is often cumbersome or not even desirable, both in terms of computational effort required and a posteriori analysis. This difficulty can be overcome with the use of multiresolution models, in which different regions of the same system are concurrently described at different levels of detail. In enzymes, computationally expensive AT detail is crucial in the modeling of the active site in order to capture, for example, the chemically subtle process of ligand binding. In contrast, important yet more collective properties of the remainder of the protein can be reproduced with a coarser description. In the present work, we demonstrate the effectiveness of this approach through the calculation of the binding free energy of hen egg white lysozyme with the inhibitor di-N-acetylchitotriose. Particular attention is payed to the impact of the mapping, that is, the selection of AT and coarse-grained residues, on the binding free energy. It is shown that, in spite of small variations of the binding free energy with respect to the active site resolution, the separate contributions coming from different energetic terms (such as electrostatic and van der Waals interactions) manifest a stronger dependence on the mapping, thus pointing to the existence of an optimal level of intermediate resolution.
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Affiliation(s)
| | - Kurt Kremer
- Max Planck Institute for Polymer Research, Mainz, Germany
| | - Raffaello Potestio
- Physics Department, University of Trento, Trento, Italy.,INFN-TIFPA, Trento Institute for Fundamental Physics and Applications, Trento, Italy
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13
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Heidari M, Kremer K, Golestanian R, Potestio R, Cortes-Huerto R. Open-boundary Hamiltonian adaptive resolution. From grand canonical to non-equilibrium molecular dynamics simulations. J Chem Phys 2020; 152:194104. [DOI: 10.1063/1.5143268] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Affiliation(s)
- Maziar Heidari
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Kurt Kremer
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | - Ramin Golestanian
- Max Planck Institute for Dynamics and Self-Organization (MPIDS), 37077 Göttingen, Germany
- Rudolf Peierls Centre for Theoretical Physics, University of Oxford, Oxford OX1 3PU, United Kingdom
| | - Raffaello Potestio
- Physics Department, University of Trento, Via Sommarive, 14, I-38123 Trento, Italy
- INFN-TIFPA, Trento Institute for Fundamental Physics and Applications, I-38123 Trento, Italy
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14
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Rogers TR, Wang F. Comparing Alchemical Free Energy Estimates to Experimental Values Based on the Ben-Naim Formula: How Much Agreement Can We Expect? J Phys Chem B 2020; 124:840-847. [PMID: 31922746 DOI: 10.1021/acs.jpcb.9b08965] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The solvation free energy (SFE) plays a key role in thermodynamics. One well-established method for computing the SFE is through an alchemical transformation. However, experimental SFEs are generally determined according to the Ben-Naim equations relying on vapor pressure or density ratios. It is important to establish whether, or to what extent, typical alchemical-based free energy computations provide results comparable to experimental SFEs. In this work, we mimic experimental measurements by simulating the liquid-vapor coexistence of water without alchemical operations. The SFEs measured through vapor pressure and density ratios are used to validate the SFEs obtained through alchemical transformations. It is shown that proper consideration of the nonideal behavior of the vapor is important to ensure that the alchemical SFEs are consistent with the Ben-Naim SFEs. Alchemical transformations in the vapor phase should be performed in addition to solution phase transformations for strongly interacting solutes, such as those with low boiling temperatures and large second virial coefficients. A formula based on the virial expansion of pressure is proposed to provide a better estimate of the true SFE from the simulated vapor pressures. The proposed formula is also applicable to experimental determinations of SFE when the pressure-based route is used.
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Affiliation(s)
- T Ryan Rogers
- Department of Chemistry and Biochemistry , University of Arkansas , Fayetteville , Arkansas 72703 , United States
| | - Feng Wang
- Department of Chemistry and Biochemistry , University of Arkansas , Fayetteville , Arkansas 72703 , United States
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15
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Hunkler S, Lemke T, Peter C, Kukharenko O. Back-mapping based sampling: Coarse grained free energy landscapes as a guideline for atomistic exploration. J Chem Phys 2019; 151:154102. [DOI: 10.1063/1.5115398] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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16
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Heidari M, Cortes-Huerto R, Potestio R, Kremer K. Steering a solute between coexisting solvation states: Revisiting nonequilibrium work relations and the calculation of free energy differences. J Chem Phys 2019; 151:144105. [PMID: 31615249 DOI: 10.1063/1.5117780] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
By analogy with single-molecule pulling experiments, we present a computational framework to obtain free energy differences between complex solvation states. To illustrate our approach, we focus on the calculation of solvation free energies (SFEs). However, the method can be readily extended to cases involving more complex solutes and solvation conditions as well as to the calculation of binding free energies. The main idea is to drag the solute across the simulation box where atomistic and ideal gas representations of the solvent coexist at constant temperature and chemical potential. At finite pulling speeds, the resulting work allows one to extract SFEs via nonequilibrium relations, whereas at infinitely slow pulling speeds, this process becomes equivalent to the thermodynamic integration method. Results for small molecules well agree with literature data and pave the way to systematic studies of arbitrarily large and complex molecules.
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Affiliation(s)
- Maziar Heidari
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
| | | | - Raffaello Potestio
- Physics Department, University of Trento, Via Sommarive, 14, I-38123 Trento, Italy
| | - Kurt Kremer
- Max Planck Institute for Polymer Research, Ackermannweg 10, 55128 Mainz, Germany
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17
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Zhuang L, Wang R, Lindberg GE, Hu H, Li XZ, Wang F. From a Liquid to a Crystal without Going through a First-Order Phase Transition: Determining the Free Energy of Melting with Glassy Intermediates. J Phys Chem B 2019; 123:7740-7747. [DOI: 10.1021/acs.jpcb.9b06840] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Lin Zhuang
- State Key Laboratory for Artificial Microstructure and Mesoscopic Physics, and School of Physics, Peking University, Beijing 100871, People’s Republic of China
| | - Rui Wang
- International Center for Quantum Materials, School of Physics, Peking University, Beijing 100871, People’s Republic of China
| | - Gerrick E. Lindberg
- Department of Chemistry and Biochemistry, and Department of Applied Physics and Materials Science, Northern Arizona University, 700 South Osborne Drive, Flagstaff, Arizona 86011, United States
| | - Hongyi Hu
- Department of Chemistry and Biochemistry, University of Arkansas, 119 Chemistry Building, Fayetteville, Arkansas 72701, United States
| | - Xin-Zheng Li
- State Key Laboratory for Artificial Microstructure and Mesoscopic Physics, and School of Physics, Peking University, Beijing 100871, People’s Republic of China
- Collaborative Innovation Center of Quantum Matter, Peking University, Beijing 100871, People’s Republic of China
| | - Feng Wang
- Department of Chemistry and Biochemistry, University of Arkansas, 119 Chemistry Building, Fayetteville, Arkansas 72701, United States
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18
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Roese SN, Margulis GV, Schmidt AJ, Uzat CB, Heintz JD, Paluch AS. A Simple Method to Predict and Interpret the Formation of Azeotropes in Binary Systems Using Conventional Solvation Free Energy Calculations. Ind Eng Chem Res 2019. [DOI: 10.1021/acs.iecr.9b03694] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Sydnee N. Roese
- Department of Chemical, Paper, and Biomedical Engineering, Miami University, Oxford, Ohio 45056, United States
| | - Griffin V. Margulis
- Department of Chemical, Paper, and Biomedical Engineering, Miami University, Oxford, Ohio 45056, United States
| | - Alexa J. Schmidt
- Department of Chemical and Environmental Engineering, Yale University, New Haven, Connecticut 06520, United States
| | - Cole B. Uzat
- Department of Chemical, Paper, and Biomedical Engineering, Miami University, Oxford, Ohio 45056, United States
| | - Justin D. Heintz
- Department of Chemical, Paper, and Biomedical Engineering, Miami University, Oxford, Ohio 45056, United States
| | - Andrew S. Paluch
- Department of Chemical, Paper, and Biomedical Engineering, Miami University, Oxford, Ohio 45056, United States
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Ciccotti G, Delle Site L. The physics of open systems for the simulation of complex molecular environments in soft matter. SOFT MATTER 2019; 15:2114-2124. [PMID: 30761396 DOI: 10.1039/c8sm02523a] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Molecular dynamics (MD) has become one of the most powerful tools of investigation in soft matter. Despite such success, simulations of large molecular environments are mostly run using the approximation of closed systems without the possibility of exchange of matter. Due to the molecular complexity of soft matter systems, an optimal simulation strategy would require the application of concurrent multiscale resolution approaches such that each part of a large system can be considered as an open subsystem at a high resolution embedded in a large coarser reservoir of energy and particles. This paper discusses the current capability and the future perspectives of multiscale adaptive resolution MD methods to satisfy the conceptual principles of open systems and to perform simulations of complex molecular environments in soft matter.
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Affiliation(s)
- Giovanni Ciccotti
- Instituto per le Applicazioni del Calcolo, Consiglio Nazionale delle Ricerche, and Universita' La Sapienza, Rome, Italy.
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20
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Long GE, Dhakal P, Redeker BN, Paluch AS. Using limiting activity coefficients to efficiently evaluate the ability of fixed-charge force fields to model miscible water plus cosolvent mixtures. MOLECULAR SIMULATION 2018. [DOI: 10.1080/08927022.2018.1531399] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Garrett E. Long
- Department of Chemical, Paper and Biomedical Engineering, Miami University, Oxford, OH, USA
| | - Pratik Dhakal
- Department of Chemical, Paper and Biomedical Engineering, Miami University, Oxford, OH, USA
| | - Bryce N. Redeker
- Department of Chemical, Paper and Biomedical Engineering, Miami University, Oxford, OH, USA
| | - Andrew S. Paluch
- Department of Chemical, Paper and Biomedical Engineering, Miami University, Oxford, OH, USA
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21
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Belloni L. Finite-size corrections in numerical simulation of liquid water. J Chem Phys 2018; 149:094111. [DOI: 10.1063/1.5046835] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Luc Belloni
- LIONS, NIMBE, CEA, CNRS, Université Paris-Saclay, 91191 Gif-sur-Yvette, France
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22
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Fluctuations, Finite-Size Effects and the Thermodynamic Limit in Computer Simulations: Revisiting the Spatial Block Analysis Method. ENTROPY 2018; 20:e20040222. [PMID: 33265313 PMCID: PMC7512739 DOI: 10.3390/e20040222] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2018] [Revised: 03/21/2018] [Accepted: 03/22/2018] [Indexed: 12/04/2022]
Abstract
The spatial block analysis (SBA) method has been introduced to efficiently extrapolate thermodynamic quantities from finite-size computer simulations of a large variety of physical systems. In the particular case of simple liquids and liquid mixtures, by subdividing the simulation box into blocks of increasing size and calculating volume-dependent fluctuations of the number of particles, it is possible to extrapolate the bulk isothermal compressibility and Kirkwood–Buff integrals in the thermodynamic limit. Only by explicitly including finite-size effects, ubiquitous in computer simulations, into the SBA method, the extrapolation to the thermodynamic limit can be achieved. In this review, we discuss two of these finite-size effects in the context of the SBA method due to (i) the statistical ensemble and (ii) the finite integration domains used in computer simulations. To illustrate the method, we consider prototypical liquids and liquid mixtures described by truncated and shifted Lennard–Jones (TSLJ) potentials. Furthermore, we show some of the most recent developments of the SBA method, in particular its use to calculate chemical potentials of liquids in a wide range of density/concentration conditions.
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