Ab Initio Molecular Dynamics Simulation of the Phosphate Ion in Water: Insights into Solvation Shell Structure, Dynamics, and Kosmotropic Activity

The Journal of Physical Chemistry. B
Bikramjit Sharma, Amalendu Chandra

Abstract

The structure and dynamics of solvation shells of the phosphate ion in deuterated water are studied by means of Born-Oppenheimer molecular dynamics simulation. The total number of molecules in the first and second solvation shells is found to be close to the effective hydration number reported experimentally. The OD bonds that are hydrogen bonded to the phosphate ion are found to be red shifted as compared to bulk water, which is consistent with experimental results. However, the two OD bonds of the same water molecule in the first hydration shell are found to be vibrationally distinct, which can be attributed to different strengths of the ion-water and water-water hydrogen bonds near the ion. Also, the hydrogen bonds formed by the second solvation shell OD bonds are somewhat stronger than the bulk. This finding shows a long ranged effect of the phosphate ion on water and also gives insights into the water structure making property of this anion. The dynamics of water in the first solvation shell is found to be significantly slower than that of the bulk. We have investigated the origin of the orientational slowing down of the first solvation shell water molecules and made connections to similar results observed experimentally.

References

Mar 6, 1987·Science·F H Westheimer
Sep 15, 1988·Physical Review A: General Physics·A D Becke
Jul 19, 2003·Science·Anne Willem OmtaHuib J Bakker
Jan 31, 2004·Science·I-Feng W Kuo, Christopher J Mundy
Jan 11, 2005·The Journal of Chemical Physics·Joost VandeVondeleMichele Parrinello
Aug 5, 2005·Chemphyschem : a European Journal of Chemical Physics and Physical Chemistry·Matthew J McGrathMatthias Krack
Jul 18, 2006·Spectrochimica Acta. Part A, Molecular and Biomolecular Spectroscopy·S A BrandánA Ben Altabef
Sep 7, 2006·Journal of Computational Chemistry·Stefan Grimme
Oct 13, 2006·Current Opinion in Chemical Biology·Yanjie Zhang, Paul S Cremer
Jan 11, 2007·The Journal of Chemical Physics·Giovanni BussiMichele Parrinello
May 5, 2007·The Journal of Chemical Physics·Hee-Seung Lee, Mark E Tuckerman
Jun 7, 2007·Physical Chemistry Chemical Physics : PCCP·R MancinelliA K Soper
Jun 8, 2007·The Journal of Chemical Physics·R KumarJ L Skinner
Nov 9, 2007·The Journal of Physical Chemistry. B·R MancinelliA K Soper
May 14, 2008·Journal of Computational Chemistry·Andreas B PribilBernd M Rode
May 22, 2008·The Journal of Physical Chemistry. a·Bhabani S MallikAmalendu Chandra
May 6, 2009·The Journal of Physical Chemistry. B·Maciej SmiechowskiJanusz Stangret
Jun 4, 2010·Journal of the American Chemical Society·Jeremy T O'BrienEvan R Williams
Dec 2, 2010·The Journal of Physical Chemistry. B·Kathrin M LangeEmad F Aziz
Jan 12, 2011·Annual Review of Physical Chemistry·Damien LaageJames T Hynes
Aug 4, 2011·Journal of the American Chemical Society·Nicholas M LevinsonSteven G Boxer
Sep 29, 2011·The Journal of Chemical Physics·Debashree Chakraborty, Amalendu Chandra
Oct 28, 2011·The Journal of Chemical Physics·Romain JonchiereRodolphe Vuilleumier
Nov 30, 2011·Journal of the American Chemical Society·Stefan FunknerMartina Havenith
Feb 23, 2012·The Journal of Physical Chemistry. a·Joost VandeVondeleGerald Mathias
Apr 7, 2012·The Journal of Physical Chemistry. B·N Galamba
May 9, 2012·The Journal of Chemical Physics·Zhang PanQing Ji
Jul 20, 2013·Journal of the American Chemical Society·Guillaume StirnemannDamien Laage
Dec 5, 2013·The Journal of Physical Chemistry. B·Mohammed AhmedSisir K Sarkar
Jan 30, 2015·Physical Chemistry Chemical Physics : PCCP·Chen ChenAnders Nilsson
Apr 1, 2015·The Journal of Physical Chemistry. B·Andreas EiberweiserRichard Buchner
Jun 8, 2015·The Journal of Chemical Physics·Rene CostardThomas Elsaesser
Oct 22, 2015·Physical Chemistry Chemical Physics : PCCP·Rene CostardBenjamin P Fingerhut
Dec 3, 2015·The Journal of Chemical Physics·Pujarini BanerjeeTapas Chakraborty

❮ Previous
Next ❯

Citations

Apr 2, 2019·Physical Chemistry Chemical Physics : PCCP·Giuseppe CassoneJiri Sponer
Jul 22, 2019·The Journal of Chemical Physics·Anjali S NairBiman Bagchi
Sep 1, 2019·Journal of Molecular Modeling·Agata Paneth, Piotr Paneth
Jun 3, 2020·The Journal of Physical Chemistry. B·Sangkha Borah
May 29, 2020·Inorganic Chemistry·Maciej Śmiechowski, Ingmar Persson

❮ 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.