• Journal of the Korean Magnetic Resonance Society
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• v.22 no.4
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• pp.139-143
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• 2018

Short antimicrobial peptide, A4W, have been studied by molecular dynamics (MD) simulation in an explicit dodecylphosphocholine (DPC) micelle. Peptide was aligned with DPC micelle and transferred new peptide-micelle coordinates within the same solvent box using specific micelle topology parameters. After initial energy minimization and equilibration, the conformation and orientation of the peptide were analyzed from trajectories obtained from the RMD (restrained molecular dynamics) or the subsequent free MD. Also, the information of solvation in the backbone and the side chain of the peptide, hydrogen bonding, and the properties of the dynamics were obtained. The results showed that the backbone residues of peptide are either solvated using water or in other case, they relate to hydrogen bonding. These properties could be a critical factor against the insertion mode of interaction. Most of the peptide-micelle interactions come from the hydrophobic interaction between the side chains of peptide and the structural interior of micelle system. The interaction of peptide-micelle, electrostatic potential and hydrogen bonding, between the terminal residues of peptide and the headgroups in micelle were observed. These interactions could be effect on the structure and flexibility of the peptide terminus.

• Journal of the Korean Chemical Society
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• v.19 no.1
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• pp.11-15
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• 1975

Kinetic study of halogen exchange for N,N-dimethylcarbamoyl chloride and N,N-diethylcarbamoyl chloride in acetone by using radioisotopic halide ions has been carried out at two temperatures as a part of studying the reactivity of carbonyl carbon atom. The order of nucleophilicity showed a similar tendency as that for alkyl chloroformate, but reaction rate is much slower than that for solvolysis and alkyl chloroformate. The activation parameters,${\Delta}H^*$and${\Delta}S^*$ were found to decrease in sequence $Cl^{\rightarrow}Br^{\rightarrow}I^-$ for N,N-dialkylcarbamoyl chlorides. The results are interpreted in terms of solvation effect, degree of bond-breaking and bond-formation and electronic requirements.

• Bulletin of the Korean Chemical Society
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• v.29 no.2
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• pp.431-437
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• 2008

The solvent effects on the relative free energies of binding of K+ and Na+ ions to 12-crown-4 and Dlog Ks (the difference of stability constant of binding) have been investigated by a Monte Carlo simulation of statistical perturbation theory (SPT) in several solvents. Comparing the relative free energies of binding of K+ and Na+ ions to 12-crown-4, in CH3OH of this study with experimental works, there is a good agreement among the studies. We have reported here the quantitative solvent-polarity relationships (QSPR) studied on the solvent effects the relative free energies of binding of K+ and Na+ ions to 12-crown-4. We noted that DN(donor number) dominates the differences in relative solvation Gibbs free energies of K+ and Na+ ions and DN dominates the negative values in differences in the stability constant (Dlog Ks) as well as the relative free energies of binding of K+ and Na+ ions to 12-crown-4 and p* (Kamlet-Tafts solvatochromic parameters) dominates the positive values in differences in the stability constant (Dlog Ks) as well as the relative free energies of binding of K+ and Na+ ions to 12-crown-4.

• Journal of Integrative Natural Science
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• v.3 no.4
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• pp.231-236
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• 2010

Partial charge is an important and fundamental concept which can explain many aspects of chemistry. Since a molecule can be regarded as neclei surrounded by electron cloud, there is no way to define a partial charge accurately. Nevertheless, there have been many attempts to define these seemingly impossible parameters, since they would facilitate the understanding of molecular properties such as molecular dipole moment, solvation, hydrogen bonding, molecular spectroscopy, chemical reaction, etc. Common methods are based on the charge equalization, orbital occupancy, charge density, and electric multipole moments, and electrostatic potential fitting. Methods based on the charge equalization using electronegativity are very fast, and therefore they have been used to study many compounds. Methods to subdivide orbital occupancy using basis set conversion, relies on the notion that molecular orbitals are composed of atomic orbitals. The main idea is to reduce overlap integral between two nuclei using converted orthogonal basis sets. Using some quantum mechanical observables like electrostatic potential or charge multipole moments. Using potential grids obtained from wavefunction, partial charges can be fitted. these charges are most useful to describe intermolecular electrostatic interactions. Methods to using dipole moment and its derivatives, seems to be sensitive the level of theory, Dividing electron density using density gradient being the most rigorous theoretically among various schemes, bears best potential to describe the charge the most adequately in the future.

• Nuclear Engineering and Technology
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• v.52 no.2
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• pp.279-286
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• 2020

In this article, we develop a reactive distillation (RD) column configuration for the production of hydrogen. This RD column is in the HI decomposition section of the sulphur - iodine (SI) thermochemical cycle, in which HI decomposition and H₂ separation take place simultaneously. The section plays a major role in high hydrogen production efficiency (that depends on reaction conversion and separation efficiency) of the SI cycle. In the column simulation, the rigorous thermodynamic phase equilibrium and reaction kinetic model are used. The tuning parameters involved in phase equilibrium model are dependent on interactive components and system temperature. For kinetic model, parameter values are adopted from the Aspen flowsheet simulator. Interestingly, there is no side reaction (e.g., solvation reaction, electrolyte decomposition and polyiodide formation) considered aiming to make the proposed model simple that leads to a challenging prediction. The process parameters are determined on the basis of optimal hydrogen production as reflux ratio = 0.87, total number of stages = 19 and feeding point at 8th stage. With this, the column operates at a reasonably low pressure (i.e., 8 bar) and produces hydrogen in the distillate with a desired composition (H₂ = 9.18 mol%, H₂O = 88.27 mol% and HI = 2.54 mol%). Finally, the results are compared with other model simulations. It is observed that the proposed scheme leads to consume a reasonably low energy requirement of 327 MJ/kmol of H₂.

• Applied Chemistry for Engineering
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• v.10 no.5
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• pp.718-725
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• 1999

In order to investigate the interaction characteristics of poly(dimethylsiloxane) (PDMS) with various solvents such as water, ethanol, and iso-propanol, Inverse Gas Chromatography(IGC) at finite concentration, which is a very fast, accurate, and thus promising technique in thermodynamic study of polymer systems, is employed. By measuring the specific retention volumes of the probes, the interaction parameters are calculated by means of the Flory-Huggins equation. From the results, the interaction parameters of the probes are, as expected due to the hydrophobicity of the polymer, found to be of large positive values (2$2.0{\times}10^{-3}mol/g$. For the linear PDMS, interpretation of the space distribution of molecules is performed by the Kirkwood-Buff-Zimm(KBZ) integrals, which give intuitive information about physical properties. From the KBZ integrals, water does not show the tendency of preferential solvation with the PDMS but formed self-cluster. The larger solvent molecules show a stronger tendency to distribute more randomly in the mixture.

• Asian Pacific Journal of Cancer Prevention
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• v.14 no.12
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• pp.7473-7482
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• 2013

The G-protein coupled receptor 87 (GPR87) is a recently discovered orphan GPCR which means that the search of their endogenous ligands has been a novel challenge. GPR87 has been shown to be overexpressed in squamous cell carcinomas (SCCs) or adenocarcinomas in lungs and bladder. The 3D structure of GPR87 was here modeled using two templates (2VT4 and 2ZIY) by a threading method. Functional assignment of GPR87 by SVM revealed that along with transporter activity, various novel functions were predicted. The 3D structure was further validated by comparison with structural features of the templates through Verify-3D, ProSA and ERRAT for determining correct stereochemical parameters. The resulting model was evaluated by Ramachandran plot and good 3D structure compatibility was evidenced by DOPE score. Molecular dynamics simulation and solvation of protein were studied through explicit spherical boundaries with a harmonic restraint membrane water system. A DRY-motif (Asp-Arg-Tyr sequence) was found at the end of transmembrane helix3, where GPCR binds and thus activation of signals is transduced. In a search for better inhibitors of GPR87, in silico modification of some substrate ligands was carried out to form polar interactions with Arg115 and Lys296. Thus, this study provides early insights into the structure of a major drug target for SCCs.

• Applied Chemistry for Engineering
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• v.5 no.1
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• pp.90-98
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• 1994

For elucidation of various parameters' effects on the reactive extraction of citric acids, citric-acetic-lactic acid system with various carriers, diluents, and modifiers were investigated. Carries used were secondary amines, tertiary amines, and solvation extract. Dileunts were n-butylacetate, methoisobutylketon(MIBK), kerosine, and xylene. Modifiers were TBP and isodecanol. The effects of temperature and pH in aquous phase were studied, and equilibrium constants for the reactive extraction were obtained. The re-extraction was performed by alkali solutions such as NaOH, $Na_2CO_3$, and $K_2HPO_4$. Based on the experiment Di-isotridecylamine(secondary amine ) gave higher degree of extraction and more selective than other extractants tested for the extraction of citric acid. N-butylacetate and TBP showed heigher performance for a diluent and modifier, repetitively. The degree of extraction was getting better with decreasing the pH in the aquous phase and the temperature of extraction system. The degree of re-extraction was getting higher with decreasing basicity in the stripping phase and the system temperature, and with increasing the concentration of alkali solution.

• Bulletin of the Korean Chemical Society
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• v.27 no.12
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• pp.2011-2018
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• 2006

We have investigated the solvent effects on $\Delta log\;K_s $(the difference of stability constant of binding) and the different free energies of binding of $Nd^{3+}$ and $Eu^{3+}$ ions to 18-crown-6, i.e., the selectivity of $Nd^{3+}$ and $Eu^{3+}$ ions to 18-crown-6 using a Monte Carlo simulation of statistical perturbation theory (SPT) in diverse solvents. The stability constant ($\Delta log\;K_s $) of binding of $Nd^{3+}$ and $Eu^{3+}$ ions to 18-crown-6, in $CH_3OH$ was calculated in this study as -1.06 agrees well with the different experimental results of -0.44~-0.6, respectively. We have reported here the quantitative solvent-polarity relationships (QSPR) studied on the solvent effects the relative free energies of binding of $Nd^{3+}$ and $Eu^{3+}$ ions to 18-crown-6. From the calculated coefficients of QSPR, we have noted that solvent polarity (ET) and Kamlet -Tafts solvatochromic parameters (b ) dominate the differences in relative solvation Gibbs free energies of $Nd^{3+}$ and $Eu^{3+}$ ions but basicity (Bj) dominates the negative values in differences in the stability constant ($\Delta log\;K_s $) as well as the relative free energies of binding of $Nd^{3+}$ and $Eu^{3+}$ ions to 18-crown-6 and acidity (Aj) dominates the positive values in differences in the stability constant ($\Delta log\;K_s $) as well as the relative free energies of binding of $Nd^{3+}$ and $Eu^{3+}$ ions to 18-crown-6.

• Journal of the Korean Chemical Society
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• v.40 no.5
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• pp.327-332
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• 1996

The rates of solvolylsis of methyl chloroformate, phenyl chloroformate and 1-adamantyl derivatives in binary solvent mixtures have been measured by conductometric method at various temperatures and pressures. The activation parameters were estimated from the rate constants. The activation volume (${\Delta}V_o^{\neq}$) and the activation entropy (${\Delta}S^{\neq}$) are both negative, but the activation enthalpy (${\Delta}H^{\neq}$) is positive. This behavior is discussed in terms of electrostriction of solvation. The reactivities of these reactions were also estimated from the correlation of the activation volumes with the activation entropies. From these results, it could be estimated that the solvolyses of 1-adamantyl fluoroformate (in aqueous TFE) and 1-adamantyl tosylate have pathway involving unimolecular reaction, while the reaction of methyl chloroformate, phenyl chloroformate and 1-adamantyl fluoroformate (in aqueous alcohol) proceed through a bimolecular reaction.