How does ammonium dynamically interact with benzene in aqueous media? A first principle study using the Car-Parrinello molecular dynamics method

The Journal of Physical Chemistry. B
Rongjian SaHualiang Jiang

Abstract

The Car-Parrinello molecular dynamics (CPMD) method was used to study the dynamic characteristics of the cation-pi interaction between ammonium and benzene in gaseous and aqueous media. The results obtained from the CPMD calculation on the cation-pi complex in the gaseous state were very similar to those calculated from the Gaussian98 program with DFT and MP2 algorithms, demonstrating that CPMD is a valid approach for studying this system. Unlike the interaction in the gaseous state, our 12-ps CPMD simulation showed that the geometry of the complex in aqueous solution changes frequently in terms of the interaction angles and distances. Furthermore, the simulation revealed that the ammonium is constantly oscillating above the benzene plane in an aqueous environment and interacts with benzene mostly through three of its hydrogen atoms. In contrast, the interaction of the cation with the aromatic molecule in the gaseous state involves two hydrogen atoms. In addition, the free energy profile in aqueous solution was studied using constrained CPMD simulations, resulting in a calculated binding free energy of -5.75 kcal/mol at an optimum interaction distance of approximately 3.25 A, indicating that the cation-pi interaction between am...Continue Reading

References

Oct 1, 1993·Proceedings of the National Academy of Sciences of the United States of America·M HarelJ L Sussman
Mar 21, 1997·Journal of Molecular Biology·J Fernández-RecioJ Sancho
Mar 1, 1985·Physical Review A: General Physics·W G Hoover
Sep 15, 1988·Physical Review A: General Physics·A D Becke
Jan 15, 1991·Physical Review. B, Condensed Matter·N Troullier, J L Martins
Nov 25, 1985·Physical Review Letters·R Car, M Parrinello
Aug 18, 1999·Proceedings of the National Academy of Sciences of the United States of America·J P Gallivan, D A Dougherty
Aug 5, 1997·Chemical Reviews·Jennifer C. Ma, Dennis A. Dougherty
Apr 19, 2002·Journal of the American Chemical Society·Michael Bühl, Georges Wipff
Jun 19, 2002·Accounts of Chemical Research·Paolo CarloniMichele Parrinello
Jan 8, 2004·Journal of the American Chemical Society·Kevin Leung, Susan B Rempe

❮ Previous
Next ❯

Citations

Nov 14, 2012·Chemical Reviews·A Subha Mahadevi, G Narahari Sastry
Dec 3, 2014·Physical Chemistry Chemical Physics : PCCP·M Althaf HussainG Narahari Sastry
Feb 3, 2018·The Journal of Chemical Physics·Hythem SidkyJuan J de Pablo
Nov 8, 2012·Chemistry : a European Journal·Ainoa Rueda-ZubiaurreJosé Osío Barcina
Jul 1, 2008·Journal of Chemical Theory and Computation·Francesca CostanzoMichiel Sprik
Sep 17, 2008·The Journal of Physical Chemistry. B·Francesca Costanzo, Raffaele Guido Della Valle
Mar 2, 2012·The Journal of Physical Chemistry. a·M Albertí, N Faginas Lago
Jul 31, 2013·The Journal of Physical Chemistry. a·Pawel KadlubanskiJerzy Leszczynski
Oct 14, 2020·Journal of Chemical Theory and Computation·Aysegul TurupcuWilliam L Jorgensen
Jan 10, 2012·Journal of Chemical Theory and Computation·Esam A Orabi, Guillaume Lamoureux
May 29, 2012·Journal of the American Chemical Society·Shihao WangGuillaume Lamoureux
Feb 6, 2018·The Journal of Physical Chemistry. B·Esam A Orabi, Guillaume Lamoureux
Aug 9, 2013·The Journal of Physical Chemistry. B·Kay AnsorgBernd Engels
Jul 31, 2007·The Journal of Physical Chemistry. a·F Huarte-LarrañagaM Albertí

❮ Previous
Next ❯

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.