Junsu Kim

The effect of salt on the dynamics of water molecules follows the Hofmeister series. For some "structure-making" salts, the self-diffusion coefficient of the water molecules, D, decreases with increasing salt concentration. For other "structure-breaking" salts, D increases with increasing salt concentration. In this work, the concentration and temperature dependence of the self-diffusion of water in electrolyte solutions is studied using molecular dynamics simulations and pulsed-field-gradient N

A new podand-type dioxaoctanediamide-based chemosensor having two pyrene moieties was prepared, and its fluoroionophoric behaviors toward transition-metal ions were investigated. Pyrene-appended dioxaoctanediamide 1 showed a selective fluorescence quenching toward Hg2+ ions over other transition-metal ions in an aqueous methanol solution. Unique responses in pyrene monomer and excimer emissions allowed selective ratiometric determination of Hg2+ ions in aqueous environments, and the detection li

A visible-light-induced synthesis of N -H carbazoles from easily accessible 2,2′-diaminobiaryls in the absence of any external photosensitizer is reported. The process only requires t BuONO and natural resources, visible light, and molecular oxygen for the synthesis of N -H carbazoles. Experimental and computational studies support that the in situ formation of a visible-light-absorbing photosensitizing intermediate, benzocinnoline N -imide, is responsible for the activation of triplet molecular

The effect of added salt (NaCl) on the melting of ice is studied using molecular dynamics simulations. The equilibrium freezing point depression observed in the simulations is in good agreement with experimental data. The kinetic aspects of melting are investigated in terms of the exchange of water molecules between ice and the liquid phase. The ice/liquid equilibrium is a highly dynamic process with frequent exchange of water molecules between ice and the liquid phase. The balance is disturbed

We present molecular dynamics (MD) simulations of a single poly(N-isopropylacrylamide) (PNIPAM) chain in explicit water at temperatures between 270 and 320 K near the lower critical solution temperature (LCST). The force-fields of OPLS-AA and TIP4P/2005 are used for a PNIPAM chain and water molecules, respectively. Three independent simulations with durations of 1 μs are performed at each temperature for a 30-mer PNIPAM chain starting with three distinct conformations: extended, loosely collapse

We investigate structural alterations of random-loop polymers due to changes in the crowding condition, as a model to study environmental effects on the structure of chromosome subcompartments. The polymer structure is changed in a nonmonotonic fashion with an increasing density of crowders: condensed at small volume fractions; decondensed at high crowding volume fractions. The nonmonotonic behavior is a manifestation of the nontrivial distance dependence of the depletion interactions. We also s

The well-established molecular dynamics simulation methods for constant- NPT ensemble systems such as the Andersen-Nosé-Hoover method and their variants may alter the dynamic properties of the molecules under consideration, because their equations of motion are modified by the coupling with thermostat or barostat. To circumvent this artifact, we propose a new molecular dynamics simulation algorithm, by which only the molecules near the wall of the simulation box are coupled to the thermostat and

The effect of peptides on the growth of ice crystals are studied using molecular dynamics simulations. The growth of the ice crystal is simulated at a supercooling of 14 K, and the effect of a single tetrapeptide on the growth rate is calculated. For pure ice the simulated crystal grows at a rate comparable to experiment. When a peptide molecule is added near the interface, the growth rate is diminished significantly, by up to a factor of 5 for Gly-Pro-Ala-Gly and a factor of 3 for Gly-Gly-Ala-G

Molecular dynamics simulations are presented for the self-diffusion coefficient of water in aqueous sodium chloride solutions. At temperatures above the freezing point of pure water, the self-diffusion coefficient is a monotonically decreasing function of salt concentration. Below the freezing point of pure water, however, the self-diffusion coefficient is a non-monotonic function of salt concentration, showing a maximum at approximately one molal salt. This suggests that sodium chloride, which

The cell cytoplasm is a dense environment where the presence of inert cosolutes can significantly alter the rates of protein folding and protein association reactions. Most theoretical studies focus on hard sphere crowding agents and quantify the effect of excluded volume on reaction rates. In this work the effect of interactions between the crowding agents on the thermodynamics of protein association is studied using computer simulation. Three cases are considered, where the crowding agents are

In this paper, separation possibilities of light rare-earths (LREs), Ce, La, Nd, and Pr with three acidic organophosphorus extractants such as TOPS 99 (an equivalent of di-2-ethylhexyl phosphoric acid, D2EHPA), PC 88A(2-ethylhexylphosphonic acid mono-2-ethylhexyl ester), and Cyanex 272 (Bis(2,4,4-trimethylpentyl)phosphinic acid) from synthetic chloride solutions of monazite at three initial pH values has been investigated. The composition of synthetic leach liquor is Ce − 5.4 g/L, La − 3.12 g/L,

Our study shows that among aza-heterocycles of various ring sizes, including aziridines, azetidines, pyrrolidines, and piperidines, only N-alkyl pyrrolidines undergo competitive reaction pathways with chloroformates to yield N-dealkylated pyrrolidines and 4-chlorobutyl carbamates. The pathway taken depends on the substituent on the nitrogen, i.e., ring-opening with methyl and ethyl substituents and dealkylation with a benzyl substituent. Computational calculations support the substituent-depende