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

The Journal of Chemical Physics
Giuseppe BrancatoVincenzo 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.

References

Jul 1, 1983·Proceedings of the National Academy of Sciences of the United States of America·W F van GunsterenJ P Postma
Nov 25, 1985·Physical Review Letters·R Car, M Parrinello
Dec 26, 2001·Chemical Reviews·Modesto Orozco, F. Javier Luque
Jan 24, 2002·Proceedings of the National Academy of Sciences of the United States of America·Margaret S CheungJosé N Onuchic
Feb 19, 2002·Chemical Reviews·Christopher J. Cramer, Donald G. Truhlar
Apr 10, 2002·Journal of Computational Chemistry·Jean-Luc Fattebert, François Gygi
Jun 19, 2002·Accounts of Chemical Research·Vladimir MakarovMichael Feig
Apr 1, 2003·Journal of Computational Chemistry·Maurizio CossiVincenzo Barone
Apr 1, 2003·Journal of Computational Chemistry·Thom VrevenMichael J Frisch
Jun 11, 2005·The Journal of Chemical Physics·Giuseppe BrancatoAndrea Amadei
Jun 21, 2005·Journal of Computational Chemistry·Marek FreindorfJing Kong
Aug 12, 2005·Chemical Reviews·Jacopo TomasiRoberto Cammi
Aug 13, 2005·The Journal of Chemical Physics·Gabriele PetraglioMichele Parrinello
Dec 7, 2005·Chemphyschem : a European Journal of Chemical Physics and Physical Chemistry·Michele PavoneVincenzo Barone
Jan 19, 2006·Proceedings of the National Academy of Sciences of the United States of America·Viktor HornakCarlos Simmerling
Feb 24, 2006·The Journal of Physical Chemistry. B·Teodora TodorovaChristopher J Mundy
Feb 25, 2006·The Journal of Chemical Physics·Damián A ScherlisNicola Marzari
Mar 31, 2006·The Journal of Physical Chemistry. B·Demian RiccardiQiang Cui
May 4, 2006·Journal of the American Chemical Society·Orlando Acevedo, William L Jorgensen
Jun 16, 2006·The Journal of Chemical Physics·I Fdez GalvánM F Ruiz-López
Jun 16, 2006·The Journal of Chemical Physics·Giuseppe BrancatoVincenzo Barone
Jul 13, 2006·The Journal of Physical Chemistry. a·Kestutis AidasOve Christiansen
Jul 21, 2006·The Journal of Physical Chemistry. B·Carles CurutchetF Javier Luque
Oct 13, 2006·Biophysical Chemistry·B Roux, T Simonson

❮ Previous
Next ❯

Citations

Jul 9, 2010·Physical Chemistry Chemical Physics : PCCP·Giuseppe BrancatoVincenzo Barone
Jun 23, 2012·Physical Chemistry Chemical Physics : PCCP·Claudio A MorgadoJiří Šponer
Apr 24, 2013·Physical Chemistry Chemical Physics : PCCP·Hirofumi Sato
Dec 14, 2011·The Journal of Chemical Physics·Arvid Conrad IhrigDaniel Sebastiani
Jun 15, 2011·The Journal of Chemical Physics·Jason A Wagoner, Vijay S Pande
Nov 18, 2015·Journal of Chemical Theory and Computation·Alexander B KuhnLars V Schäfer
Sep 7, 2014·European Journal of Medicinal Chemistry·Sergio DecherchiWalter Rocchia
Oct 7, 2016·Physical Chemistry Chemical Physics : PCCP·Marina MacchiagodenaVincenzo Barone
Oct 12, 2018·Physical Chemistry Chemical Physics : PCCP·Maria Gabriella ChiarielloNadia Rega
May 8, 2009·Journal of Computational Chemistry·Roman I ZubatyukJerzy Leszczynski
May 17, 2011·Physical Biology·Zhe ZhangEmil Alexov
Jun 11, 2014·Journal of Computational Chemistry·Jiří Kessler, Petr Bouř
Jun 27, 2020·Physical Chemistry Chemical Physics : PCCP·Mattia BondanzaBenedetta Mennucci
Feb 8, 2018·Chemical Communications : Chem Comm·Dušan PetrovićShina Caroline Lynn Kamerlin
Mar 24, 2020·Journal of Physics. Condensed Matter : an Institute of Physics Journal·Cristina PuzzariniVincenzo Barone
Oct 8, 2020·Proceedings of the National Academy of Sciences of the United States of America·Nan YangMark A Johnson
Jun 9, 2009·Journal of Chemical Theory and Computation·Sittipong Komin, Daniel Sebastiani
Oct 14, 2008·Journal of Chemical Theory and Computation·Geoffrey P F WoodDavid M Smith
Mar 25, 2021·Journal of Physics. Condensed Matter : an Institute of Physics Journal·Laura P Granda-MarulandaMarc T M Koper
Apr 21, 2021·Physical Chemistry Chemical Physics : PCCP·Fabrizio SantoroRoberto Improta
Nov 18, 2020·Journal of Chemical Theory and Computation·Martí MunicoyVictor Guallar
Sep 23, 2014·Journal of the American Chemical Society·Alessio PetroneNadia Rega
Aug 13, 2013·Journal of Chemical Theory and Computation·Pandian SokkarYoung Min Rhee
Mar 11, 2014·Journal of Chemical Theory and Computation·Giordano ManciniVincenzo Barone
Nov 8, 2011·Journal of Chemical Theory and Computation·Filippo Lipparini, Vincenzo Barone
Mar 11, 2015·The Journal of Physical Chemistry. a·Balasubramanian ChandramouliGiuseppe Brancato
May 10, 2011·Journal of Chemical Theory and Computation·Christoph Schiffmann, Daniel Sebastiani
May 26, 2017·The Journal of Physical Chemistry. a·Kaiqiang Zhang, Stefan T Thynell
Nov 13, 2012·Journal of Chemical Theory and Computation·Filippo LippariniVincenzo Barone
Nov 13, 2012·Journal of Chemical Theory and Computation·Filippo LippariniVincenzo Barone

❮ Previous
Next ❯

Methods Mentioned

BETA
NMR

Software Mentioned

GLOB
N GLOB
ADMP
N07D
ONIOM
GAUSSIAN

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.