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Rahbari A, Hens R, Ramdin M, Moultos OA, Dubbeldam D, Vlugt TJH. Recent advances in the continuous fractional component Monte Carlo methodology. MOLECULAR SIMULATION 2020. [DOI: 10.1080/08927022.2020.1828585] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- A. Rahbari
- Engineering Thermodynamics, Process & Energy Department, Faculty of Mechanical, Maritime and Materials Engineering, Delft University of Technology, Delft, Netherlands
| | - R. Hens
- Engineering Thermodynamics, Process & Energy Department, Faculty of Mechanical, Maritime and Materials Engineering, Delft University of Technology, Delft, Netherlands
| | - M. Ramdin
- Engineering Thermodynamics, Process & Energy Department, Faculty of Mechanical, Maritime and Materials Engineering, Delft University of Technology, Delft, Netherlands
| | - O. A. Moultos
- Engineering Thermodynamics, Process & Energy Department, Faculty of Mechanical, Maritime and Materials Engineering, Delft University of Technology, Delft, Netherlands
| | - D. Dubbeldam
- Van 't Hoff Institute for Molecular Sciences, University of Amsterdam, Amsterdam, Netherlands
| | - T. J. H. Vlugt
- Engineering Thermodynamics, Process & Energy Department, Faculty of Mechanical, Maritime and Materials Engineering, Delft University of Technology, Delft, Netherlands
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2
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Rathee VS, Sidky H, Sikora BJ, Whitmer JK. Explicit Ion Effects on the Charge and Conformation of Weak Polyelectrolytes. Polymers (Basel) 2019; 11:E183. [PMID: 30960167 PMCID: PMC6401944 DOI: 10.3390/polym11010183] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2018] [Revised: 01/03/2019] [Accepted: 01/09/2019] [Indexed: 12/28/2022] Open
Abstract
The titration behavior of weak polyelectrolytes is of high importance, due to their uses in new technologies including nanofiltration and drug delivery applications. A comprehensive picture of polyelectrolyte titration under relevant conditions is currently lacking, due to the complexity of systems involved in the process. One must contend with the inherent structural and solvation properties of the polymer, the presence of counterions, and local chemical equilibria enforced by background salt concentration and solution acidity. Moreover, for these cases, the systems of interest have locally high concentrations of monomers, induced by polymer connectivity or confinement, and thus deviate from ideal titration behavior. This work furthers knowledge in this limit utilizing hybrid Monte Carlo⁻Molecular Dynamics simulations to investigate the influence of salt concentration, pK a , pH, and counterion valence in determining the coil-to-globule transition of poorly solvated weak polyelectrolytes. We characterize this transition at a range of experimentally relevant salt concentrations and explicitly examine the role multivalent salts play in determining polyelectrolyte ionization behavior and conformations. These simulations serve as an essential starting point in understanding the complexation between weak polyelectrolytes and ion rejection of self-assembled copolymer membranes.
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Affiliation(s)
- Vikramjit S Rathee
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, IN 46556, USA.
| | - Hythem Sidky
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, IN 46556, USA.
| | - Benjamin J Sikora
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, IN 46556, USA.
| | - Jonathan K Whitmer
- Department of Chemical and Biomolecular Engineering, University of Notre Dame, Notre Dame, IN 46556, USA.
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Affiliation(s)
- Braden Kelly
- Department of Mathematics and Statistics, University of Guelph, Guelph, Canada
| | - William R. Smith
- Department of Mathematics and Statistics, University of Guelph, Guelph, Canada
- Department of Chemistry, University of Guelph, Guelph, Canada
- Department of Chemical Engineering, University of Waterloo, Waterloo, Canada
- Faculty of Science, University of Ontario Institute of Technology, Oshawa Canada
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Rathee VS, Sidky H, Sikora BJ, Whitmer JK. Role of Associative Charging in the Entropy-Energy Balance of Polyelectrolyte Complexes. J Am Chem Soc 2018; 140:15319-15328. [PMID: 30351015 DOI: 10.1021/jacs.8b08649] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Polyelectrolytes may be classified into two primary categories (strong and weak) depending on how their charge state responds to the local environment. Both of these find use in many applications, including drug delivery, gene therapy, layer-by-layer films, and fabrication of ion filtration membranes. The mechanism of polyelectrolyte complexation is, however, still not completely understood, though experimental investigations suggest that entropy gain due to release of counterions is the key driving force for strong polyelectrolyte complexation. Here we perform a comprehensive thermodynamic investigation through coarse-grained molecular simulations permitting us to calculate the free energy of complex formation. Importantly, our expanded-ensemble methods permit the explicit separation of energetic and entropic contributions to the free energy. Our investigations indicate that entropic contributions indeed dominate the free energy of complex formation for strong polyelectrolytes, but are less important than energetic contributions when weak electrostatic coupling or weak polyelectrolytes are present. Our results provide a new view of the free energy of polyelectrolyte complex formation driven by polymer association, which should also arise in systems with large charge spacings or bulky counterions, both of which act to weaken ion-polymer binding.
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Affiliation(s)
- Vikramjit S Rathee
- Department of Chemical and Biomolecular Engineering , University of Notre Dame , Notre Dame , Indiana 46556 , United States
| | - Hythem Sidky
- Department of Chemical and Biomolecular Engineering , University of Notre Dame , Notre Dame , Indiana 46556 , United States
| | - Benjamin J Sikora
- Department of Chemical and Biomolecular Engineering , University of Notre Dame , Notre Dame , Indiana 46556 , United States
| | - Jonathan K Whitmer
- Department of Chemical and Biomolecular Engineering , University of Notre Dame , Notre Dame , Indiana 46556 , United States
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Smith WR, Qi W. Molecular Simulation of Chemical Reaction Equilibrium by Computationally Efficient Free Energy Minimization. ACS CENTRAL SCIENCE 2018; 4:1185-1193. [PMID: 30276252 PMCID: PMC6161046 DOI: 10.1021/acscentsci.8b00361] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Indexed: 05/25/2023]
Abstract
The molecular simulation of chemical reaction equilibrium (CRE) is a challenging and important problem of broad applicability in chemistry and chemical engineering. The primary molecular-based approach for solving this problem has been the reaction ensemble Monte Carlo (REMC) algorithm [Turner et al. Molec. Simulation2008, 34, (2), 119-146], based on classical force-field methodology. In spite of the vast improvements in computer hardware and software since its original development almost 25 years ago, its more widespread application is impeded by its computational inefficiency. A fundamental problem is that its MC basis inhibits the implementation of significant parallelization, and its successful implementation often requires system-specific tailoring and the incorporation of special MC approaches such as replica exchange, expanded ensemble, umbrella sampling, configurational bias, and continuous fractional component methodologies. We describe herein a novel CRE algorithm (reaction ensemble molecular dynamics, ReMD) that exploits modern computer hardware and software capabilities, and which can be straightforwardly implemented for systems of arbitrary size and complexity by exploiting the parallel computing methodology incorporated within many MD software packages (herein, we use GROMACS for illustrative purposes). The ReMD algorithm utilizes these features in the context of a macroscopically inspired and generally applicable free energy minimization approach based on the iterative approximation of the system Gibbs free energy function by a mathematically simple convex ideal solution model using the composition at each iteration as a reference state. Finally, we additionally describe a simple and computationally efficient a posteriori method to estimate the equilibrium concentrations of species present in very small amounts relative to others in the primary calculation. To demonstrate the algorithm, we show its application to two classic example systems considered previously in the literature: the N2-O2-NO system and the ammonia synthesis system.
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Affiliation(s)
- William R. Smith
- Department
of Mathematics and Statistics, University
of Guelph, Guelph, Ontario N1G 2W1, Canada
- Department
of Chemistry, University of Guelph, Guelph, Ontario N1G 2W1, Canada
- Department
of Chemical Engineering, University of Waterloo, Waterloo, Ontario N2L 3G1, Canada
- Faculty
of Science, University of Ontario Institute
of Technology, Oshawa, Ontario L1H 7K4, Canada
| | - Weikai Qi
- Department
of Mathematics and Statistics, University
of Guelph, Guelph, Ontario N1G 2W1, Canada
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Mullen RG, Maginn EJ. Reaction Ensemble Monte Carlo Simulation of Xylene Isomerization in Bulk Phases and under Confinement. J Chem Theory Comput 2017; 13:4054-4062. [DOI: 10.1021/acs.jctc.7b00498] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ryan Gotchy Mullen
- Department of Chemical and
Biomolecular Engineering, University of Notre Dame, Notre Dame, Indiana, United States
| | - Edward J. Maginn
- Department of Chemical and
Biomolecular Engineering, University of Notre Dame, Notre Dame, Indiana, United States
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Yang X, Rees RJ, Conway W, Puxty G, Yang Q, Winkler DA. Computational Modeling and Simulation of CO2 Capture by Aqueous Amines. Chem Rev 2017; 117:9524-9593. [PMID: 28517929 DOI: 10.1021/acs.chemrev.6b00662] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Xin Yang
- CSIRO Manufacturing, Bayview Avenue, Clayton 3169, Australia
- College
of Chemistry, Key Lab of Green Chemistry and Technology in Ministry
of Education, Sichuan University, Chengdu 610064, People’s Republic of China
| | - Robert J. Rees
- Data61
- CSIRO, Door 34 Goods
Shed, Village Street, Docklands VIC 3008, Australia
| | | | | | - Qi Yang
- CSIRO Manufacturing, Bayview Avenue, Clayton 3169, Australia
| | - David A. Winkler
- CSIRO Manufacturing, Bayview Avenue, Clayton 3169, Australia
- Monash Institute of Pharmaceutical Sciences, 392 Royal Parade, Parkville 3052, Australia
- Latrobe Institute for Molecular Science, Bundoora 3046, Australia
- School
of
Chemical and Physical Science, Flinders University, Bedford Park 5042, Australia
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Jalink T, Farrand T, Herdes C. Towards EMIC rational design: setting the molecular simulation toolbox for enantiopure molecularly imprinted catalysts. Chem Cent J 2016; 10:66. [PMID: 27822298 PMCID: PMC5078882 DOI: 10.1186/s13065-016-0215-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2016] [Accepted: 10/20/2016] [Indexed: 11/23/2022] Open
Abstract
A critical appraisal of the current strategies for the synthesis of enantiopure drugs is presented, along with a systematic background for the computational design of stereoselective porous polymers. These materials aim to achieve the enantiomeric excess of any chiral drug, avoiding the racemic separation. Particular emphasis is given to link statistical mechanics methods to the description of each one of the experimental stages within the catalyst’s synthesis, setting a framework for the fundamental study of the emerging field of molecularly imprinted catalysts.The envisaged modelling tools in the EMIC toolbox: quantum mechanics (QM), molecular dynamics and Monte Carlo (in the NPT and NVT ensembles), grand canonical Monte Carlo (GCMC) and kinetic Monte Carlo (kMC), for the synthesis of an enantiopure drug via our proposed EMIC catalyst. ![]()
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Affiliation(s)
- Tessa Jalink
- Department of Chemical Engineering, University of Bath, Bath, BA2 7AY UK
| | - Tom Farrand
- Department of Chemical Engineering, University of Bath, Bath, BA2 7AY UK
| | - Carmelo Herdes
- Department of Chemical Engineering, University of Bath, Bath, BA2 7AY UK
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9
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Leiding J, Coe JD. Reactive Monte Carlo sampling with an ab initio potential. J Chem Phys 2016; 144:174109. [DOI: 10.1063/1.4948303] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Jeff Leiding
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
| | - Joshua D. Coe
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
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Loeffler TD, Sepehri A, Chen B. Improved Monte Carlo Scheme for Efficient Particle Transfer in Heterogeneous Systems in the Grand Canonical Ensemble: Application to Vapor–Liquid Nucleation. J Chem Theory Comput 2015; 11:4023-32. [DOI: 10.1021/acs.jctc.5b00466] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Troy D. Loeffler
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | - Aliasghar Sepehri
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | - Bin Chen
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, United States
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11
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Punnathanam SN. A Gibbs-ensemble based technique for Monte Carlo simulation of electric double layer capacitors (EDLC) at constant voltage. J Chem Phys 2014; 140:174110. [DOI: 10.1063/1.4873707] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
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Bourasseau E, Maillet JB, Desbiens N, Stoltz G. Microscopic Calculations of Hugoniot Curves of Neat Triaminotrinitrobenzene (TATB) and of Its Detonation Products. J Phys Chem A 2011; 115:10729-37. [DOI: 10.1021/jp2047739] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Emeric Bourasseau
- Commissariat à l’Energie Atomique, DAM, DIF, F-91297 Arpajon, France
| | | | - Nicolas Desbiens
- Commissariat à l’Energie Atomique, DAM, DIF, F-91297 Arpajon, France
| | - Gabriel Stoltz
- Université Paris Est, CERMICS, MICMAC Project-team, INRIA-Ecole des Ponts ParisTech, 6 et 8 Av. Blaise Pascal, 77455 Marne-la-Vallée Cedex 2, France
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Bourasseau E, Maillet JB. Coupling microscopic and mesoscopic scales to simulate chemical equilibrium between a nanometric carbon cluster and detonation products fluid. Phys Chem Chem Phys 2011; 13:7060-70. [DOI: 10.1039/c0cp02622k] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Hervouët A, Desbiens N, Bourasseau E, Maillet JB. Microscopic Approaches to Liquid Nitromethane Detonation Properties. J Phys Chem B 2008; 112:5070-8. [DOI: 10.1021/jp077250n] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Anaïs Hervouët
- CEA, Centre DAM - Ile de France, Département de Physique Théorique et Appliquée, Bruyères-le-Chatel, 91297 Arpajon Cedex, France
| | - Nicolas Desbiens
- CEA, Centre DAM - Ile de France, Département de Physique Théorique et Appliquée, Bruyères-le-Chatel, 91297 Arpajon Cedex, France
| | - Emeric Bourasseau
- CEA, Centre DAM - Ile de France, Département de Physique Théorique et Appliquée, Bruyères-le-Chatel, 91297 Arpajon Cedex, France
| | - Jean-Bernard Maillet
- CEA, Centre DAM - Ile de France, Département de Physique Théorique et Appliquée, Bruyères-le-Chatel, 91297 Arpajon Cedex, France
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Heath Turner C, Brennan JK, Lísal M, Smith WR, Karl Johnson J, Gubbins KE. Simulation of chemical reaction equilibria by the reaction ensemble Monte Carlo method: a review†. MOLECULAR SIMULATION 2008. [DOI: 10.1080/08927020801986564] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Bourasseau E, Dubois V, Desbiens N, Maillet JB. Molecular simulations of Hugoniots of detonation product mixtures at chemical equilibrium: Microscopic calculation of the Chapman-Jouguet state. J Chem Phys 2007; 127:084513. [PMID: 17764275 DOI: 10.1063/1.2766939] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
In this work, we used simultaneously the reaction ensemble Monte Carlo (ReMC) method and the adaptive Erpenbeck equation of state (AE-EOS) method to directly calculate the thermodynamic and chemical equilibria of mixtures of detonation products on the Hugoniot curve. The ReMC method [W. R. Smith and B. Triska, J. Chem. Phys. 100, 3019 (1994)] allows us to reach the chemical equilibrium of a reacting mixture, and the AE-EOS method [J. J. Erpenbeck, Phys. Rev. A 46, 6406 (1992)] constrains the system to satisfy the Hugoniot relation. Once the Hugoniot curve of the detonation product mixture is established, the Chapman-Jouguet (CJ) state of the explosive can be determined. A NPT simulation at P(CJ) and T(CJ) is then performed in order to calculate direct thermodynamic properties and the following derivative properties of the system using a fluctuation method: calorific capacities, sound velocity, and Gruneisen coefficient. As the chemical composition fluctuates, and the number of particles is not necessarily constant in this ensemble, a fluctuation formula has been developed to take into account the fluctuations of mole number and composition. This type of calculation has been applied to several usual energetic materials: nitromethane, tetranitromethane, hexanitroethane, PETN, and RDX.
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Affiliation(s)
- Emeric Bourasseau
- CEA, Département de Physique Théorique et Appliquée, BP 12, 91680 Bruyères-le-Châtel, France.
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