• Journal of the Korean Magnetic Resonance Society
• /
• v.18 no.1
• /
• pp.36-40
• /
• 2014

Predicting secondary structure of protein through assigned backbone chemical shifts has been used widely because of its convenience and flexibility. In spite of its usefulness, chemical shift based analysis has some defects including isotopic shifts and solvent interaction. Here, it is shown that corrected chemical shift analysis for secondary structure of protein. It is included chemical shift correction through consideration of deuterium isotopic effect and calculate chemical shift index using probability-based methods. Enhanced method was applied successfully to one of the proteins from Mycobacterium tuberculosis. It is suggested that correction of chemical shift analysis could increase accuracy of secondary structure prediction of protein and small molecule in solution.

• Journal of the Korean Chemical Society
• /
• v.38 no.5
• /
• pp.391-396
• /
• 1994

The hydrolysis of $\alpha-benzoxystyrene(1)$ in strong acidic solution has been investigated kinetically. In perchloric acid concentration lower than 5.5 M($H_o$ < -3.0), hydration paramer $\omega$ = + 7.6, and $\Phi$ = + 0.54 were obtained. The solvent isotope effect $k_{H_2O}/K_{D_2O}$ is 0.72. The substituent effect was found to conform to the Hammett $\sigma^+$ constant with $\rho$ = -0.60. On the basis of these results and other evidence, the hydrolysis of the enol ester proceeds by $A_{AL}$2 type mechanism. In concentration greater than 5.5 M($H_o$ > -3.0), isotope effect, $k_{H_2O}/_{D_2O}$ is 3.32, substituent effect, $\rho$ is -1.60 and the rate is linear with the acidity function, $H_o$. Thus, the mechanism changes one involving initial, and rate-determining olefin protonation.

• Bulletin of the Korean Chemical Society
• /
• v.32 no.12
• /
• pp.4185-4190
• /
• 2011

The nucleophilic substitution reactions of ethylene phosphorochloridate (1c) with substituted anilines ($XC_6H_4NH_2$) and deuterated anilines ($XC_6H_4ND_2$) are investigated kinetically in acetonitrile at $5.0^{\circ}C$. The anilinolysis rate of 1c involving a cyclic five-membered ring is four thousand times faster than its acyclic counterpart (1a: diethyl chlorophosphate) because of great positive value of the entropy of activation of 1c (${\Delta}S^{\neq}=+30\;cal\;mol^{-1}K^{-1}$ compared to negative value of 1a (${\Delta}S^{\neq}=-45\;cal\;mol^{-1}K^{-1}$) over considerably unfavorable enthalpy of activation of 1c (${\Delta}H^{\neq}=27.7\;kcal\;mol^{-1}$) compared to 1a (${\Delta}H^{\neq}=8.3\;kcal\;mol^{-1}$). Great enthalpy and positive entropy of activation are ascribed to sterically congested transition state (TS) and solvent structure breaking in the TS. The free energy correlations exhibit biphasic concave upwards for substituent X variations in the X-anilines with a break point at X = 3-Me. The deuterium kinetic isotope effects are secondary inverse ($k_H/k_D$ < 1) with the strongly basic anilines and primary normal ($k_H/k_D$ > 1) with the weakly basic anilines and rationalized by the TS variation from a dominant backside attack to a dominant frontside attack, respectively. A concerted $S_N2$ mechanism is proposed and the primary normal deuterium kinetic isotope effects are substantiated by a hydrogen bonded, four-center-type TS.

• Bulletin of the Korean Chemical Society
• /
• v.19 no.9
• /
• pp.968-973
• /
• 1998

Solvolyses of para-substituted phenyl chloroformates in water, $D_2O,\;CH_3OD$, 50% $D_2O-CH_3OD$, and in aqueous binary mixtures of acetone, ethanol, methanol are investigated at 25.0 ℃. Product selectivities are reported for a wide range of ethanol-water and methanol-water solvent compositions. These data are interpreted using the Grunwald-Winstein relationship, Hammett equation, and quantum mechanical model. Grunwald-Winstein plots of the first-order rate constants for phenyl chloroformates with $Y_{Cl}$ (based on 1-adamantyl chloride) show marked dispersions into three separate curves for the three aqueous mixtures with a small m value and a rate maximum for aqueous alcohol solvents. To account for these results, third-order rate constants, $k_{ww},\;k_{aw},\;k_{wa}$, and $k_{aa}$ were calculated from the observed $k_{ww}\;and\;k_{aa}$ values together with $k_{aw}\;and\;k_{wa}$ calculated from the computer fit. The kinetic solvent isotope effects determined in water and methanol are consistent with the proposed mechanism of the general base catalyzed carbonyl addition-elimination for para-substituted phenyl chloroformates solvolyses based on mass law and stoichiometric salvation effect studies. This study has shown that the quantum mechanical model predicts transition state variation correctly for $S_N2\;like\;S_AN$ reaction mechanism of para-substituted phenyl chloroformates.

• Animal cells and systems
• /
• v.2 no.2
• /
• pp.243-248
• /
• 1998

We have partially sequenced glutaminyl cyclases from several mammalian and one avian species and found that the two cysteine residues of the human glutaminyl cyclase are completely conserved. The mammalian glutaminyl cyclase has been reported to possess reactive thiols (Busby, Jr, et aI., 1987, J BioI Chern 262, 8532-8536). Mutagenesis of these cysteine residues, however, resulted in only a slight decrease in enzyme activity. Likewise, the recombinant human enzyme was completely resistant to attempted chemical modification of the putative reactive thiols. Although the human glutaminyl cyclase did not appear to have reactive thiols, it was sensitive to diethylpyrocarbonate and acetylimidazole, indicating the presence of functionally important histidine and tyrosine residues which could act as acid/base catalysts. Almost identical deuterium solvent isotope effect (1.2 vs 1.3) upon the reaction by the human and papaya enzymes, respectively, provides an evidence both animal and plant glutaminyl cyclases catalyze pyroglutamyl-peptide formation by intramolecular cyclization.

• Bulletin of the Korean Chemical Society
• /
• v.21 no.10
• /
• pp.955-956
• /
• 2000

Solvolyses of methanesulfonyl chloride in water, $D^2O$, $CH^3OD$, and in aqueous binary mixtures of acetone, eth-anol and methanol are investigated at 25, 35 and $45^{\circ}C.$ The Grunwald-Winstein plot of first-order rate con-stants for the solvolytic react ion of methanesulfonyl chloride with YCl (based on 2-adamantyl chloride) shows marked dispersions into three separate lines for three aqueous mixtures with a small m value (m < 0.30), and shows a rate maximum for aqueous alcoholic solvents. Stoichiometric third-order rate constants, kww and kaa were calculated from the observed first-order rate constants and (kaw + kwa) was calculated from the kww and kaa values. The kinetic solvent isotope effects determined in water and methanol are consistent with the proposed mechanism of the general base catalyzed and/or SAN/SN2 reaction mechanism for methanesulfonyl chloride solvolyses based on mass law and stoichiometric solvation effect studies.

• Journal of Life Science
• /
• v.12 no.1
• /
• pp.32-42
• /
• 2002

It was researched to react horse serum-BChE with hefanoylthiocholine chosen among choline esters. According as number of carbon of acyl group in choline esters was increased, reactivity was decreased but strength of ES complex was increased (Km=0,140mM). The pH-V/K profile for BChE-catalyzed hydrolysis of hexanoylthiocholine yields a p $K_{a}$ =4.974$\pm$0.028. This value is equal to recent literature that shows systematic shift from dependence of activity on the basic form fo a residue that huts a p $K_{a}$ =6.2~6.4 to catalysis by a residue or residues that has a p $K_{a}$ =4.7~5.0. The resulting kinetic solvent isotope effect of hexanoylthiocholine is $^{D/V}$K=1.18. The magnitude of the isotope effect suggests that proton transfer is not an element of transition-state stabilization.n.

• Bulletin of the Korean Chemical Society
• /
• v.33 no.11
• /
• pp.3544-3550
• /
• 2012

Cetrizine dihydrochloride (CTZH) is widely used as an anti-allergic drug. Sodium N-bromo-p-toluenesulfonamide or bromamine-T (BAT) is the bromine analogue of chloramine-T (CAT) and is found to be a better oxidizing agent than CAT. In the present research, the kinetics of oxidation of CTZH with BAT in acid and alkaline media was studied at 313 K. The experimental rate laws obtained are: -d[BAT]/dt=$k[BAT][CTZH]^{0.80}[H^+]^{-0.48}$ in acid medium and -d[BAT]/dt=$k[BAT][CTZH]^{0.48}[OH^-]^{0.52}[PTS]^{-0.40}$ in alkaline medium where PTS is p-toluenesulfonamide. Activation parameters and reaction constants were evaluated. The solvent isotope effect was studied using $D_2O$. The dielectric effect is positive. The stoichiometry of the reaction was found to be 1:1 and the oxidation products were identified as 4-chlorobenzophenone and (2-piperazin-1-yl-ethoxy)-acetic acid in both media. The rate of oxidation of CTZH is faster in acid medium. Suitable mechanisms and related rate laws have been worked out.

• Bulletin of the Korean Chemical Society
• /
• v.26 no.12
• /
• pp.2001-2006
• /
• 2005

Glycoproteins and glycolipids play key roles in intracellular reactions between cells and their environments at the membrane surface. For better understanding of the nature of these events, it is necessary to know threedimensional structures of those carbohydrates, involved in them. Since carbohydrates contain many hydroxyl groups which can serve both as hydrogen bond donors and acceptors, hydrogen bond is an important factor stabilizing the structure of carbohydrate. DMSO is an aprotic solvent frequently used for the study of carbohydrates because it gives detailed insight into the intramolecular hydrogen bond network. In this study, conformational properties and the hydrogen bonds in $\beta$-lactose in DMSO are investigated by NMR spectroscopy and molecular dynamics simulations. NOEs, temperature coefficients, deuterium isotope effect, and molecular dynamics simulations proved that there is a strong intramolecular hydrogen bond between O3 and HO2' in $\beta$-lactose and also OH3 in $\beta$-lactose may form an intermolecular hydrogen bond with DMSO.

• Bulletin of the Korean Chemical Society
• /
• v.30 no.9
• /
• pp.1939-1945
• /
• 2009

Kinetic investigations on the oxidation of pyrazine and four 2-substituted pyrazines viz., 2-methylpyrazine, 2-ethylpyrazine, 2-methoxypyrazine and 2-aminopyrazine by bromamine-B (BAB) to the respective N-oxides have been studied in HCl$O_4$ medium at 303 K. The reactions show identical kinetics being first-order each in $[BAB]_o\;and\;[pyrazine]_o$, and a fractional- order dependence on $[H^+]$. Effect of ionic strength of the medium and addition of benzenesulfonamide or halide ions showed no significant effect on the reaction rate. The dielectric effect is positive. The solvent isotope effect was studied using $D_2$O. The reaction has been studied at different temperatures and activation parameters for the composite reaction have been evaluated from the Arrhenius plots. The reaction showed 1:1 stoichiometry and the oxidation products of pyrazines were characterized as their respective N-oxides. Under comparable experimental conditions, the oxidation rate of pyrazines increased in the order: 2-aminopyrazine > 2-methoxypyrazine > 2-ethylpyrazine > 2-methylpyrazine > pyrazine. The rates correlate with the Hammett $\sigma$ relationship and the reaction constant $\rho$ was found to be -0.8, indicating that electron donating centres enhance the rate of reaction. An isokinetic temperature of $\beta$ = 333 K, indicated that the reaction was enthalpy controlled. A mechanism consistent with the experimental results has been proposed in which the rate determining step is the formation of an intermediate complex between the substrate and the diprotonated species of the oxidant. The related rate law in consistent with observed results has been deduced.