Ab initio molecular dynamics study of Se(iv) species in aqueous environment

Abstract

An ab initio molecular dynamics investigation is carried out on various water-borne Se(iv) species, HSeO, HSeO and SeO, in aqueous environment. Consistent with the reported acid dissociation constants, in neutral solution HSeO exchanges protons with the surrounding water molecules establishing a dynamic equilibrium with HSeO. The SeO species is found to be stable only in basic environment, which is emulated in the present simulation through introducing a hydroxide ion, OH, in the system. The hydration structure, hydrogen bonding and spectroscopic signatures of the species are comprehensively analyzed. The influence of the solute's hydration structure on the structural and dynamic response of the solvent is discussed. The correlation between the strength as well as the number of hydrogen bonds accepted by the solute on its vibrational properties are analyzed.

Ab initiomolecular dynamics studies of hydroxide coordination of alkaline earth metals and uranyl

“…While the former has been well documented in literature there is severely limited research on the later with literature focusing on gas phase [13][14][15] investigations, while the dynamics of hydrated hydroxide complexes have received limited attention. [16][17][18][19] This contribution aims to develop understanding of ion interactions with hydroxide in aqueous environments.…”

The Spermine Phosphate-Bound Cyclooctaoxygen Sodium Epigenetic Shell of Euchromatin DNA Is Destroyed by the Epigenetic Poison Glyphosate

“…Selenium is essential to mammalian physiology at nutritional levels, but supraphysiological intake of selenium is known to be toxic for mammals [5,7]. Sodium selenite (Na2SeO3), as hydrogen selenite HSeO3at pH 7.0 (selenious acid H2SeO3: pKa1 = 2.62, pKa2 = 8.32 [80]), binds to calf thymus genomic B-DNA at pH 7.0 [81], and…”

First-Principle Molecular Dynamics Investigation of Waterborne As-V Species

“…The Kohn–Sham orbitals are expanded in plane-wave basis up to a cutoff of 85 Ry. Simulations are carried out in NVT ensemble with the electronic as well as ionic degrees of freedom controlled using Nosé–Hoover thermostats. − The fictitious kinetic energy of electrons is maintained at 0.03 au, employing an electron mass of 600 au, for the necessary adiabatic separation of electronic and ionic degrees of freedom. ,− A time step of 0.1 fs is used for integration of equations of motion. The trajectories printed at every five MD steps, during the production phases, are subjected to a detailed analysis as discussed below.…”

“…The H bonds between different solute–solvent species are defined and analyzed in detail on the basis of the simultaneous fulfillment of the following criteria: (i) the donor–acceptor O···O distance is less than 3.5 Å, (ii) the hydrogen–acceptor H···O distance is less than 2.45 Å, and (iii) the hydrogen–donor–acceptor angle is less than 30°. This definition is widely employed for waters and similar systems in the literature. − ,− Lifetimes of different types of H bonds in the systems are computed using the continuous H-bond correlation function given by where h ( t ) = 1 if a tagged pair of donor–acceptor species is H-bonded at time t and h ( t ) = 0 otherwise. H ( t ) = 1 if the two species remain H-bonded (on the basis of all three criteria above) continually over a period t , else it equals 0.…”

“…Another time correlation function, C HB ( t ), known as intermittent H-bond correlation function, defined as which is not sensitive to the intermittent breaking of H bonds, gives a measure of structural relaxation through H bonds. In the above definitions, the angular brackets, ⟨···⟩, denote the statistical average over all pairs and time origins. ,,− …”