Related papers: Molecular Dynamics Study of Conformations of Beta-…
We report on extensive molecular dynamics atomistic simulations of a \textit{meta}-substituted \textit{poly}-phenylacetylene (pPA) foldamer dispersed in three solvents, water \ce{H2O}, cyclohexane \ce{cC6H12}, and \textit{n}-hexane…
We investigate the effects of solvent specificities on the stability of the native structure (NS) of a protein on the basis of our free-energy function (FEF). We use CPB-bromodomain (CBP-BD) and apoplastocyanin (apoPC) as representatives of…
Cyclodextrins (CDs) are cyclic oligosaccharides composed of glucopyranose units bonded together to form a truncated cone that can make inclusion complexes with guest molecules. The {\alpha}, \b{eta}, and {\gamma}-CDs, which respectively…
Cyclodextrins are a family of oligosaccharides with a toroid shape which exhibit a unique ability of entrapping guest molecules in their internal cavity. Water is the primary guest molecule and is omnipresent in the crystalline phases…
Cyclodextrins (CD) are a family of oligosaccharides with a toroid shape, which exhibit a remarkable ability to include guest molecules in their internal cavity providing a hydrophobic environment for poorly soluble molecules. Recently new…
We developed a novel pathway to highly efficiently synthesize the [60]Fullerene (C$_{60}$)-Cyclodextrin (CD) complex, which is termed as solvent-induced reversible recognition. Three kinds of typical complexes, namely,…
Using thermodynamics integration, we study the solvation free energy of 18 amino acid side chain equivalents in solvents with different polarity, ranging from the most polar water to the most non-polar cyclohexane. The amino acid side chain…
Understanding of the molecular interaction between asphaltenes and other molecules, which may act as its solvents, provides insights into the nature of its stability in petroleum fluids and its phase transitions. Molecular dynamics…
The current computational study investigates the changes in solvation dynamics of water when introducing hydrophobic side chains to the molecular probe N-methyl-6-oxyquinolinium betaine. High precision transient fluorescence and absorption…
Conformations of a single-component bottle-brush polymer with a fully flexible backbone under poor solvent conditions are studied by molecular-dynamics simulations, using a coarse-grained bead-spring model with side chains of up to N=40…
Small molecules are often found to exhibit extraordinarily diverse biological activities. Metformin is one of them. It is widely used as anti-diabetic drug for type-two diabetes. In addition to that, metformin hydrochloride shows…
Molecular dynamics simulations of diluted (~2.5 weight percent) aqueous solutions of two polyelectrolytes, namely sodium carboxy methyl cellulose (CMC) and sodium poly(acrylate) (PAA) have been performed. Water and counterions were taken…
Heavy metal pollution is a severe environmental problem affecting many water resources. The non-biodegradable nature of the heavy metals such as lead (Pb) causes severe human health issues, so their cost-effective, sensitive and rapid…
Solutions of {\it trans}$-$polyisoprene in cyclohexane are investigated in atomistic detail at different compositions at two different temperatures. We investigate the influence of polymer concentration on the dynamics of the solvent…
Two-dimensional materials have significant potential for the development of new devices. Here we report the electronic and structural properties of $\beta$-GeSe, a previously unreported polymorph of GeSe, with a unique crystal structure…
The molecular dynamics (MD) simulation study of solvation structure and free energetics in 1-ethyl-3-methylimidazolium chloride and 1-ethyl-3-methylimidazolium hexafluorophosphate using a probe solute in the preceding article [Y. Shim, M.…
Using molecular dynamics and thermodynamic integration, we report on the solvation process in water and in cyclohexane of seven polypeptides (GLY, ALA, ILE, ASN, LYS, ARG, GLU). The polypeptides are selected to cover the full hydrophobic…
Hydrotropes are substances consisting of amphiphilic molecules that are too small to self assemble in equilibrium structures in aqueous solutions, but can form dynamic molecular clusters H bonded with water molecules. Some hydrotropes, such…
The study of cyclic hydrocarbons is of utmost relevance in current astrochemical research, as they are considered to be among the most significant reservoirs of carbon in the interstellar medium. However, while unsaturated cyclic…
Molecular dynamics simulation is a prominent way of analyzing the dynamic properties of a system. The molecular dynamics simulation of diffusion, an important transport property, of dilute solution of cysteine in SPCE water at five…