Ultrafast Vibrational Spectroscopy of Aqueous Solution of Methylamine from First Principles MD Simulations

2017 ◽  
Vol 2 (1) ◽  
pp. 74-83 ◽  
Author(s):  
Sohag Biswas ◽  
Bhabani S. Mallik
Keyword(s):  
Aqueous Solution ◽  
Vibrational Spectroscopy ◽  
First Principles ◽  
Md Simulations ◽  
Ultrafast Vibrational Spectroscopy

scholarly journals Trimethylamine-N-oxide: its hydration structure, surface activity, and biological function, viewed by vibrational spectroscopy and molecular dynamics simulations

2017 ◽  
Vol 19 (10) ◽  
pp. 6909-6920 ◽  
Author(s):  
Tatsuhiko Ohto ◽  
Johannes Hunger ◽  
Ellen H. G. Backus ◽  
Wataru Mizukami ◽  
Mischa Bonn ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Aqueous Solution ◽  
Molecular Dynamics Simulations ◽  
Surface Activity ◽  
Vibrational Spectroscopy ◽  
Biological Function ◽  
Molecular Simulations ◽  
Structure Surface ◽  
Dynamics Simulations ◽  
Hydrophilicity And Hydrophobicity

Vibrational spectroscopy and molecular simulations revealed the hydrophilicity and hydrophobicity of TMAO in aqueous solution.

Ultrafast vibrational spectroscopy (2D-IR) of CO2 in ionic liquids: Carbon capture from carbon dioxide’s point of view

2015 ◽  
Vol 142 (21) ◽  
pp. 212425 ◽  
Author(s):  
Thomas Brinzer ◽  
Eric J. Berquist ◽  
Samrat Dutta ◽  
Clinton A. Johnson ◽  
Cullen S. Krisher ◽  
...  
Keyword(s):  
Ionic Liquids ◽  
Vibrational Spectroscopy ◽  
Carbon Capture ◽  
Point Of View ◽  
2D Ir ◽  
Ultrafast Vibrational Spectroscopy

scholarly journals Succinic acid in aqueous solution: connecting microscopic surface composition and macroscopic surface tension

2014 ◽  
Vol 16 (39) ◽  
pp. 21486-21495 ◽  
Author(s):  
Josephina Werner ◽  
Jan Julin ◽  
Maryam Dalirian ◽  
Nønne L. Prisle ◽  
Gunnar Öhrwall ◽  
...  
Keyword(s):  
Aqueous Solution ◽  
Surface Tension ◽  
Succinic Acid ◽  
Photoelectron Spectroscopy ◽  
Surface Composition ◽  
Md Simulations ◽  
Vapor Interface ◽  
X Ray ◽  
Ph Values ◽  
Microscopic Surface

The water–vapor interface of aqueous solutions of succinic acid, where pH values and bulk concentrations were varied, has been studied using surface sensitive X-ray photoelectron spectroscopy (XPS) and molecular dynamics (MD) simulations.

MD Simulations and first principles to evaluate the role of binary Fe–V alloys layer on the radiation resistance in the alpha-iron

2018 ◽  
Vol 45 (3) ◽  
pp. 178-185 ◽  
Author(s):  
Meng Zhang ◽  
Xinkai Ding ◽  
Weixiang Peng ◽  
Hongliang Zhang ◽  
Bingjie Wu ◽  
...  
Keyword(s):  
First Principles ◽  
Radiation Resistance ◽  
Md Simulations ◽  
Alpha Iron

Two-dimensional ultrafast vibrational spectroscopy of azides in ionic liquids reveals solute-specific solvation

2015 ◽  
Vol 17 (40) ◽  
pp. 26575-26579 ◽  
Author(s):  
Samrat Dutta ◽  
Zhe Ren ◽  
Thomas Brinzer ◽  
Sean Garrett-Roe
Keyword(s):  
Ionic Liquids ◽  
Vibrational Spectroscopy ◽  
Two Dimensional ◽  
Specific Solvation ◽  
2D Ir ◽  
Ir Studies ◽  
Ultrafast Vibrational Spectroscopy

2D-IR studies of organic and inorganic azides dissolved in ionic liquids show different solvation structures and picosecond dynamics.

scholarly journals Identification of rare Lewis oligosaccharide conformers in aqueous solution using enhanced sampling molecular dynamics

2017 ◽  
Author(s):  
Irfan Alibay ◽  
Kepa K. Burusco ◽  
Neil J. Bruce ◽  
Richard A. Bryce
Keyword(s):  
Molecular Dynamics ◽  
Aqueous Solution ◽  
Md Simulations ◽  
Umbrella Sampling ◽  
Biological Action ◽  
Sialyl Lewis X ◽  
Enhanced Sampling ◽  
Sialyl Lewis ◽  
Aqueous Solvent ◽  
A Minor

<p>Determining the conformations accessible to carbohydrate ligands in aqueous solution is important for understanding their biological action. In this work, we evaluate the conformational free energy surfaces of Lewis oligosaccharides in explicit aqueous solvent using a multidimensional variant of the swarm-enhanced sampling molecular dynamics (msesMD) method; we compare with multi-microsecond unbiased MD simulations, umbrella sampling and accelerated MD approaches. For the sialyl Lewis A tetrasaccharide, msesMD simulations in aqueous solution predict conformer landscapes in general agreement with the other biased methods and with triplicate unbiased 10 ms trajectories; these simulations find a predominance of closed conformer and a range of low occupancy open forms. The msesMD simulations also suggest closed-to-open transitions in the tetrasaccharide are facilitated by changes in ring puckering of its GlcNAc residue away from the <sup>4</sup>C<sub>1</sub> form, in line with previous work. For sialyl Lewis X tetrasaccharide, msesMD simulations predict a minor population of an open form in solution, corresponding to a rare lectin-bound pose observed crystallographically. Overall, from comparison with biased MD calculations, we find that triplicate 10 ms unbiased MD simulations may not be enough to fully sample glycan conformations in aqueous solution. However, the computational efficiency and intuitive approach of the msesMD method suggest potential for its application in glycomics as a tool for analysis of oligosaccharide conformation.</p>

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