Ab initio molecular dynamics investigation of structural, dynamic and spectroscopic aspects of Se(vi) species in the aqueous environment

2016 ◽  
Vol 18 (21) ◽  
pp. 14561-14568 ◽  
Author(s):  
Sangkha Borah ◽  
P. Padma Kumar
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Bonding ◽  
Ab Initio ◽  
Microscopic Investigation ◽  
Ab Initio Molecular Dynamics ◽  
Aqueous Environment ◽  
Structural Dynamic ◽  
Selenic Acid ◽  
Spectroscopic Signatures

Microscopic investigation of selenic acid in aqueous environment is carried out. Hydrogen bonding and spectroscopic signatures of HSeO4−and SeO42−species are discussed.

scholarly journals Solvent Effect on the Structure and Properties of RGD Peptide (1FUV) at Body Temperature (310 K) Using Ab Initio Molecular Dynamics

Polymers ◽  
2021 ◽  
Vol 13 (19) ◽  
pp. 3434
Author(s):  
Khagendra Baral ◽  
Puja Adhikari ◽  
Bahaa Jawad ◽  
Rudolf Podgornik ◽  
Wai-Yim Ching
Keyword(s):  
Molecular Dynamics ◽  
Body Temperature ◽  
Ab Initio ◽  
Density Functional ◽  
Density Functional Theory Calculations ◽  
Rgd Peptide ◽  
Ab Initio Molecular Dynamics ◽  
Quantum Mechanical ◽  
Aqueous Environment ◽  
Structure And Properties

The structure and properties of the arginine-glycine-aspartate (RGD) sequence of the 1FUV peptide at 0 K and body temperature (310 K) are systematically investigated in a dry and aqueous environment using more accurate ab initio molecular dynamics and density functional theory calculations. The fundamental properties, such as electronic structure, interatomic bonding, partial charge distribution, and dielectric response function at 0 and 310 K are analyzed, comparing them in dry and solvated models. These accurate microscopic parameters determined from highly reliable quantum mechanical calculations are useful to define the range and strength of complex molecular interactions occurring between the RGD peptide and the integrin receptor. The in-depth bonding picture analyzed using a novel quantum mechanical metric, the total bond order (TBO), quantifies the role played by hydrogen bonds in the internal cohesion of the simulated structures. The TBO at 310 K decreases in the dry model but increases in the solvated model. These differences are small but extremely important in the context of conditions prevalent in the human body and relevant for health issues. Our results provide a new level of understanding of the structure and properties of the 1FUV peptide and help in advancing the study of RGD containing other peptides.

Geometry of OH⋯O interactions in the liquid state of linear alcohols from ab initio molecular dynamics simulations

2020 ◽  
Vol 22 (12) ◽  
pp. 6690-6697 ◽  
Author(s):  
Aman Jindal ◽  
Sukumaran Vasudevan
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Bonding ◽  
Ab Initio ◽  
Molecular Dynamics Simulations ◽  
Liquid State ◽  
Crystalline State ◽  
Md Simulations ◽  
Ab Initio Molecular Dynamics ◽  
Linear Alcohols ◽  
Dynamics Simulations

Hydrogen bonding OH···O geometries in the liquid state of linear alcohols, derived from ab initio MD simulations, show no change from methanol to pentanol, in contrast to that observed in their crystalline state.

Dissolution of cellulose in ionic liquids: an ab initio molecular dynamics simulation study

2014 ◽  
Vol 16 (33) ◽  
pp. 17458-17465 ◽  
Author(s):  
Rajdeep Singh Payal ◽  
Sundaram Balasubramanian
Keyword(s):  
Molecular Dynamics ◽  
Hydrogen Bonding ◽  
Ionic Liquids ◽  
Molecular Dynamics Simulation ◽  
Ab Initio ◽  
Simulation Study ◽  
Molecular Hydrogen ◽  
Dynamics Simulation ◽  
Ab Initio Molecular Dynamics ◽  
Dynamics Simulations

Dissolution of cellulose in ionic liquids involves breaking of its inter- and intra-molecular hydrogen bonding network, as seen through ab initio molecular dynamics simulations.

scholarly journals Structural, dynamic, and electronic properties of liquid tin: An ab initio molecular dynamics study

2008 ◽  
Vol 129 (19) ◽  
pp. 194506 ◽  
Author(s):  
L. Calderín ◽  
D. J. González ◽  
L. E. González ◽  
J. M. López
Keyword(s):  
Molecular Dynamics ◽  
Ab Initio ◽  
Electronic Properties ◽  
Ab Initio Molecular Dynamics ◽  
Structural Dynamic ◽  
Liquid Tin

Vibrational mode frequencies of H4SiO4, D4SiO4, H6Si2O7, and H6Si3O9 in aqueous environment, obtained from ab initio molecular dynamics

2012 ◽  
Vol 137 (16) ◽  
pp. 164506 ◽  
Author(s):  
Georg Spiekermann ◽  
Matthew Steele-MacInnis ◽  
Piotr M. Kowalski ◽  
Christian Schmidt ◽  
Sandro Jahn
Keyword(s):  
Molecular Dynamics ◽  
Ab Initio ◽  
Vibrational Mode ◽  
Ab Initio Molecular Dynamics ◽  
Aqueous Environment

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

2016 ◽  
Vol 18 (38) ◽  
pp. 26755-26763 ◽  
Author(s):  
Sangkha Borah ◽  
P. Padma Kumar
Keyword(s):  
Molecular Dynamics ◽  
Ab Initio ◽  
Ab Initio Molecular Dynamics ◽  
Aqueous Environment ◽  
Water Borne

Anab initiomolecular dynamics investigation is carried out on various water-borne Se(iv) species, H2SeO3, HSeO3−and SeO32−, in aqueous environment.

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