Literature DB >> 18412453

A hybrid explicit/implicit solvation method for first-principle molecular dynamics simulations.

Giuseppe Brancato1, Nadia Rega, Vincenzo Barone.   

Abstract

In this work, we present a hybrid explicit/implicit solvation model, well suited for first-principles molecular dynamics simulations of solute-solvent systems. An effective procedure is presented that allows to reliably model a solute with a few explicit solvation shells, ensuring solvent bulk behavior at the boundary with the continuum. Such an approach is integrated with high-level ab initio methods using localized basis functions to perform first-principles or mixed quantum mechanics/molecular mechanics simulations within the extended-Lagrangian formalism. A careful validation of the model along with illustrative applications to solutions of acetone and glycine radical are presented, considering two solvents of different polarity, namely, water and chloroform. Results show that the present model describes dynamical and solvent effects with an accuracy at least comparable to that of conventional approaches based on periodic boundary conditions.

Entities:  

Year:  2008        PMID: 18412453     DOI: 10.1063/1.2897759

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


  10 in total

1.  Using DelPhi capabilities to mimic protein's conformational reorganization with amino acid specific dielectric constants.

Authors:  Lin Wang; Zhe Zhang; Walter Rocchia; Emil Alexov
Journal:  Commun Comput Phys       Date:  2013-01       Impact factor: 3.246

2.  DelPhi Web Server: A comprehensive online suite for electrostatic calculations of biological macromolecules and their complexes.

Authors:  Subhra Sarkar; Shawn Witham; Jie Zhang; Maxim Zhenirovskyy; Walter Rocchia; Emil Alexov
Journal:  Commun Comput Phys       Date:  2013-01       Impact factor: 3.246

3.  A smoothly decoupled particle interface: new methods for coupling explicit and implicit solvent.

Authors:  Jason A Wagoner; Vijay S Pande
Journal:  J Chem Phys       Date:  2011-06-07       Impact factor: 3.488

Review 4.  On the role of electrostatics in protein-protein interactions.

Authors:  Zhe Zhang; Shawn Witham; Emil Alexov
Journal:  Phys Biol       Date:  2011-05-13       Impact factor: 2.583

5.  Mapping the temperature-dependent and network site-specific onset of spectral diffusion at the surface of a water cluster cage.

Authors:  Nan Yang; Sean C Edington; Tae Hoon Choi; Elva V Henderson; Joseph P Heindel; Sotiris S Xantheas; Kenneth D Jordan; Mark A Johnson
Journal:  Proc Natl Acad Sci U S A       Date:  2020-10-06       Impact factor: 11.205

Review 6.  Implicit solvent methods for free energy estimation.

Authors:  Sergio Decherchi; Matteo Masetti; Ivan Vyalov; Walter Rocchia
Journal:  Eur J Med Chem       Date:  2014-08-25       Impact factor: 6.514

7.  Electronic and Vibrational Manifold of Tetracyanoethylene-Chloronaphthalene Charge Transfer Complex in Solution: Insights from TD-DFT and Ab Initio Molecular Dynamics.

Authors:  Federico Coppola; Paola Cimino; Fulvio Perrella; Luigi Crisci; Alessio Petrone; Nadia Rega
Journal:  J Phys Chem A       Date:  2022-09-29       Impact factor: 2.944

8.  Combining the Fluctuating Charge Method, Non-Periodic Boundary Conditions and Meta-Dynamics: Aqua Ions as case studies.

Authors:  Giordano Mancini; Giuseppe Brancato; Vincenzo Barone
Journal:  J Chem Theory Comput       Date:  2014-03-11       Impact factor: 6.006

9.  Modeling Excited-State Proton Transfer to Solvent: A Dynamics Study of a Super Photoacid with a Hybrid Implicit/Explicit Solvent Model.

Authors:  Umberto Raucci; Maria Gabriella Chiariello; Nadia Rega
Journal:  J Chem Theory Comput       Date:  2020-10-28       Impact factor: 6.006

10.  Time-Resolved Vibrational Analysis of Excited State Ab Initio Molecular Dynamics to Understand Photorelaxation: The Case of the Pyranine Photoacid in Aqueous Solution.

Authors:  Maria Gabriella Chiariello; Greta Donati; Nadia Rega
Journal:  J Chem Theory Comput       Date:  2020-10-02       Impact factor: 6.006

  10 in total

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