Literature DB >> 25877568

Molecular dynamics simulations of solutions at constant chemical potential.

C Perego1, M Salvalaglio2, M Parrinello1.   

Abstract

Molecular dynamics studies of chemical processes in solution are of great value in a wide spectrum of applications, which range from nano-technology to pharmaceutical chemistry. However, these calculations are affected by severe finite-size effects, such as the solution being depleted as the chemical process proceeds, which influence the outcome of the simulations. To overcome these limitations, one must allow the system to exchange molecules with a macroscopic reservoir, thus sampling a grand-canonical ensemble. Despite the fact that different remedies have been proposed, this still represents a key challenge in molecular simulations. In the present work, we propose the Constant Chemical Potential Molecular Dynamics (CμMD) method, which introduces an external force that controls the environment of the chemical process of interest. This external force, drawing molecules from a finite reservoir, maintains the chemical potential constant in the region where the process takes place. We have applied the CμMD method to the paradigmatic case of urea crystallization in aqueous solution. As a result, we have been able to study crystal growth dynamics under constant supersaturation conditions and to extract growth rates and free-energy barriers.

Entities:  

Year:  2015        PMID: 25877568     DOI: 10.1063/1.4917200

Source DB:  PubMed          Journal:  J Chem Phys        ISSN: 0021-9606            Impact factor:   3.488


  7 in total

1.  Crystal Nucleation in Liquids: Open Questions and Future Challenges in Molecular Dynamics Simulations.

Authors:  Gabriele C Sosso; Ji Chen; Stephen J Cox; Martin Fitzner; Philipp Pedevilla; Andrea Zen; Angelos Michaelides
Journal:  Chem Rev       Date:  2016-05-26       Impact factor: 60.622

Review 2.  RNA Structural Dynamics As Captured by Molecular Simulations: A Comprehensive Overview.

Authors:  Jiří Šponer; Giovanni Bussi; Miroslav Krepl; Pavel Banáš; Sandro Bottaro; Richard A Cunha; Alejandro Gil-Ley; Giovanni Pinamonti; Simón Poblete; Petr Jurečka; Nils G Walter; Michal Otyepka
Journal:  Chem Rev       Date:  2018-01-03       Impact factor: 60.622

3.  The role of molecular modelling and simulation in the discovery and deployment of metal-organic frameworks for gas storage and separation.

Authors:  Arni Sturluson; Melanie T Huynh; Alec R Kaija; Caleb Laird; Sunghyun Yoon; Feier Hou; Zhenxing Feng; Christopher E Wilmer; Yamil J Colón; Yongchul G Chung; Daniel W Siderius; Cory M Simon
Journal:  Mol Simul       Date:  2019       Impact factor: 2.178

4.  Unraveling Mg2+-RNA binding with atomistic molecular dynamics.

Authors:  Richard A Cunha; Giovanni Bussi
Journal:  RNA       Date:  2017-02-01       Impact factor: 4.942

5.  Solubility of Organic Salts in Solvent-Antisolvent Mixtures: A Combined Experimental and Molecular Dynamics Simulations Approach.

Authors:  Zoran Bjelobrk; Ashwin Kumar Rajagopalan; Dan Mendels; Tarak Karmakar; Michele Parrinello; Marco Mazzotti
Journal:  J Chem Theory Comput       Date:  2022-07-14       Impact factor: 6.578

6.  Concentration gradient driven molecular dynamics: a new method for simulations of membrane permeation and separation.

Authors:  Aydin Ozcan; Claudio Perego; Matteo Salvalaglio; Michele Parrinello; Ozgur Yazaydin
Journal:  Chem Sci       Date:  2017-03-20       Impact factor: 9.825

7.  Modeling of Gas Transport through Polymer/MOF Interfaces: A Microsecond-Scale Concentration Gradient-Driven Molecular Dynamics Study.

Authors:  Aydin Ozcan; Rocio Semino; Guillaume Maurin; A Ozgur Yazaydin
Journal:  Chem Mater       Date:  2020-01-07       Impact factor: 9.811

  7 in total

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