• Bulletin of the Korean Chemical Society
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• v.35 no.7
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• pp.2081-2085
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• 2014

Second-order rate constants ($k_N$) have been measured spectrophotometrically for the reactions of phenyl 2- pyridyl carbonate (6) with a series of cyclic secondary amines in MeCN at $25.0{\pm}0.1^{\circ}C$. The Br${\o}$nsted-type plot for the reaction of 6 is linear with ${\beta}_{nuc}$ = 0.54, which is typical for reactions reported previously to proceed through a concerted mechanism. Substrate 6 is over $10^3$ times more reactive than 2-pyridyl benzoate (5), although the reactions of 6 and 5 proceed through the same mechanism. A combination of steric hindrance, inductive effect and resonance contribution is responsible for the kinetic results. The reactions of 6 and 5 proceed through a cyclic transition state (TS) in which H-bonding interactions increase the nucleofugality of the leaving group (i.e., 2-pyridiniumoxide). The enhanced nucleofugality forces the reactions of 6 and 5 to proceed through a concerted mechanism. In contrast, the corresponding reaction of 4-nitrophenyl 2-pyridyl carbonate (7) proceeds through a stepwise mechanism with quantitative liberation of 4-nitrophenoxide ion as the leaving group, indicating that replacement of the 4-nitrophenoxy group in 7 by the PhO group in 6 changes the reaction mechanism (i.e., from a stepwise mechanism to a concerted pathway) as well as the leaving group (i.e., from 4-nitrophenoxide to 2-pyridiniumoxide). The strong electron-withdrawing ability of the 4-nitrophenoxy group in 7 inhibits formation of a H-bonded cyclic TS. The presence or absence of a H-bonded cyclic TS governs the reaction mechanism (i.e., a concerted or stepwise mechanism) as well as the leaving group (i.e., 2-pyridiniumoxide or 4-nitrophenoxide).

• Bulletin of the Korean Chemical Society
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• v.34 no.8
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• pp.2251-2255
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• 2013

Second-order rate constants ($k_{HOO^-}$) for the nucleophilic substitution reactions of Y-substituted-phenyl diphenylphosphinates (4a-4i) with $HOO^-$ in $H_2O$ have been measured spectrophotometrically. The ${\alpha}$-nucleophile $HOO^-$ is 10-70 times more reactive than the reference nucleophile $OH^-$ although the former is ca. $4pK_a$ units less basic than the latter, indicating the ${\alpha}$-effect is operative. The Bronsted-type plot for the reactions of 4a-4i with $HOO^-$ is linear with ${\beta}_{lg}=-0.51$, a typical ${\beta}_{lg}$ value for reactions which were reported to proceed through a concerted mechanism. The Yukawa-Tsuno plot is also linear with ${\rho}=1.40$ and r = 0.47, indicating that a negative charge develops partially on the O atom of the leaving group, which can be delocalized to the substituent Y through resonance interactions. Thus, the reactions have been proposed to proceed through a concerted mechanism. The magnitude of the ${\alpha}$-effect (i.e., the $k_{HOO^-}/k_{HO^-}$ ratio) decreases linearly as the leaving-group basicity increases. It has been concluded that solvation effect is not solely responsible for the ${\alpha}$-effect found in this study but the transition-state stabilization through an intramolecular H-bonding interaction is also responsible for the ${\alpha}$-effect.

• Journal of the Korean Chemical Society
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• v.39 no.8
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• pp.666-671
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• 1995

The conformational properties of poly(ethylene oxide) (PEO) in aqueous solutions are studied by viscometry with respect to the water structure perturbing capabilities of a series of urea solutes at $16^{\circ}C$, and experiments for the effect of amounts of urea and methylurea on PEO at 16 and $25^{\circ}C$ are also performed. The results show that the chain expansion, by ureas, of PEO of $1.0{\times}10^5$ molecular weight at $16^{\circ}C$ is similar to that of PEO of $8.0{\times}10^3$ molecular weight at $25^{\circ}C$ with respect to the water structure perturbation. Urea and methylurea make the PEO chain expand by the perturbation of water structure around PEO and by the hydrophobic interaction between methylurea and PEO, respectively. PEO of $1.0{\times}10^5$ molecular weight has hydrophobic sites on it, which are roughly classified into two parts; one is the inner hydrophobic groups which can interact between themselves (intramolecular hydrophobic interaction) and prevails at $16^{\circ}C$, and the other is the outer, exposed hydrophobic groups which can interact with the added hydrophobic solute (intermolecular hydrophobic interaction) and prevails at $25^{\circ}C.$

• Bulletin of the Korean Chemical Society
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• v.35 no.8
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• pp.2448-2452
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• 2014

Second-order rate constants ($k_N$) have been measured spectrophotometrically for $S_NAr$ reactions of Y-substituted-phenoxy-2,4-dinitrobenzenes (1a-1g) with hydrazine and glycylglycine in 80 mol % $H_2O$/20 mol % DMSO at $25.0{\pm}0.1^{\circ}C$. Hydrazine is 14.6-23.4 times more reactive than glycylglycine. The magnitude of the ${\alpha}$-effect increases linearly as the substituent Y becomes a stronger electron-withdrawing group (EWG). The Br${\o}$nsted-type plots for the reactions with hydrazine and glycylglycine are linear with ${\beta}_{lg}=-0.21$ and -0.14, respectively, which is typical for reactions reported previously to proceed through a stepwise mechanism with expulsion of the leaving group occurring after rate-determining step (RDS). The Hammett plots correlated with ${\sigma}^{\circ}$ constants result in much better linear correlations than ${\sigma}^-$ constants, indicating that expulsion of the leaving group is not advanced in the transition state (TS). The reaction of 1a-1g with hydrazine has been proposed to proceed through a five-membered cyclic intermediate ($T_{III}$), which is structurally not possible for the reaction with glycylglycine. Stabilization of the intermediate $T_{III}$ through intramolecular H-bonding interaction has been suggested as an origin of the ${\alpha}$-effect exhibited by hydrazine.

• Journal of the Korean Chemical Society
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• v.22 no.2
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• pp.86-94
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• 1978

The crystal and molecular structure of theophylline hydrochloride has been determined from X-ray data by Patterson techniques. The structure has been refined by block-diagonal least-squares and Fourier synthesis on three dimensional data. The unit cell is orthorhombic, space group $P_{na21}$, with a = 14.01, b = 11.49, c = 6.77${\AA}$, and contains four molecules. The final R value based on 743 observed reflexions is 12.2%. The intramolecular distances are similar to those in other compounds containing a purine or pyrimidine group. The molecules are nearly planar and are stacked in layers parallel to the (001)plane. The chlorine atom is coordinated to N(1) atom at a distance of 3.06${\AA}$. The structure is stabilized mainly by van der Waals interactions; however, a short N${\cdot}{\cdot}{\cdot}$Cl contact of length $3.06\AA$, which is slightly less than the expected van der Waals separation, suggest that weak charge transfer interaction may be present. The relationship between this structure and the known structures of theophylline monohydrate and caffeine monohydrate are discussed.

• Polymer(Korea)
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• v.26 no.1
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• pp.18-27
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• 2002

Poly(ο-hydroxyamide)s as polybenzoxazoles precursors were synthesized by polycondensation from 2,2'-bis(3-amino-4-hydroxyphenyl) hexafluoropropane and various bis-acids. And the polymers were modified to acid-sensitive polyamides by introducing tetrahydropyran in order to impart photosensitivity. A study of optical transmittance at 365 nm, according to the chemical structure of bis-acid, revealed that the polymer derived from 4,4'-oxydibenzoic acid showed better optical transparency than those from other bis-acids. This tendency of optical transmittance could be explained by formation of charge transfer complex. In case of the polymer derived from 4,4'-oxydibenzoic acid, the electron accepting characteristic of bis-acid is reduced by introduction of electron donating group, -O-. Thus, optical transmittance increased due to the diminished formation of intramolecular charge transfer complex. In addition, the optical transmittance increased with increasing the THP content in the polymer. This is attributed to the reduced intermolecular interaction by the loosening of the packing density of the polymer chain.

• Bulletin of the Korean Chemical Society
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• v.34 no.4
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• pp.1115-1119
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• 2013

A kinetic study is reported for nucleophilic substitution reactions of benzyl 2-pyridyl thionocarbonate (5b) and t-butyl 2-pyridyl thionocarbonate (6b) with a series of alicyclic secondary amines in $H_2O$ at $25.0^{\circ}C$. General-base catalysis, which has often been reported to occur for aminolysis of esters possessing a C=S electrophilic center, is absent for the reactions of 5b and 6b. The Br${\o}$nsted-type plots for the reactions of 5b and 6b are linear with ${\beta}_{nuc}$ = 0.29 and 0.43, respectively, indicating that the reactions of 5b proceed through a stepwise mechanism with formation of a zwitterionic tetrahedral intermediate ($T^{\pm}$) being the rate-determining step while those of 6b proceed through a concerted mechanism. The reactivity of 5b and 6b is similar to that of their oxygen analogues (i.e., benzyl 2-pyridyl carbonate 5a and t-butyl 2-pyridyl carbonate 6a, respectively), indicating that the effect of modification of the electrophilic center from C=O to C=S (i.e., from 5a to 5b and from 6a to 6b) on reactivity is insignificant. In contrast, 6b is much less reactive than 5b, indicating that the replacement of the $PhCH_2$ in 5b by the t-Bu in 6b results in a significant decrease in reactivity as well as a change in the reaction mechanism (i.e., from a stepwise mechanism to a concerted pathway). It has been concluded that the contrasting reactivity and reaction mechanism for the reactions of 5b and 6b are not due to the electronic effects of $PhCH_2$ and t-Bu but are caused by the large steric hindrance exerted by the bulky t-Bu in 6b.

• Proceedings of the Korean Biophysical Society Conference
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• 2003.06a
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• pp.69-69
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• 2003

Human CD99 is a ubiquitous 32-kDa transmembrane protein encoded by the mic2 gene. The major cellular functions of CD99 protein are related to homotypic cell adhension, apoptosis, vesicular protein transport, and differentiation of thymocytes or T cells. Recently it has been reported that expression of a splice variant of CD99 transmembrane protein (Type I and Type II) increases invasive ability of human breast cancer cells. To understand structural basis for cellular functions of CD99 (Type I), we have initiated studies on hCD99$^{TMcytoI}$ and hCD99$^{cytoI}$ using circular dichroism (CD) and multi-dimensional NMR spectroscopy. CD spectrum of hCD99$^{TMcytoI}$ in the presence of 200mM DPC and CHAPS displayed an existence $\alpha$-helical conformation. The solution structure of hCD99$^{cytoI}$ determined by NMR is composed of one N-terminal $\alpha$-helix, $\alpha$A, two C-terminal short $\alpha$-helix segments, $\alpha$B and $\alpha$C. While $\alpha$A and $\alpha$B are connected by the long flexible loop, $\alpha$B and $\alpha$C connected by type III$\beta$-turn. Although it has been rarely figured out the correlation between structure and functional mechanism of hCD99$^{TMcytoI}$ and hCD99$^{cytoI}$, there is possibility of dimerization or oligomerization. In addition, the feasible mechanism of hCD99$^{cytoI}$ is that it could have intramolecular interaction between the N- and C- terminal domain through large flexible AB loop.

• Journal of the Korean Chemical Society
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• v.40 no.3
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• pp.187-195
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• 1996

Ab initio SCF calculations have been carried out for the five conceivable trimers formed between one hydrogen cyanide and two hydrogen fluorides using a basis set of TZ＋P quality. Several ground state properties of these trimeric complexes have been evaluated, and compared with those of isolated monomers and appropriate dimers. Computed equilibrium geometries, stabilization energies, and dipole moments are given in order to suppliment the available experimental data. At this level of approximation, intramolecular bond distances are consistently shorter than experimental ones. However, intermolecular distances upon complex formation, and dipole moments are overestimated compared with experimental ones. HCN$(HF)_2$ trimer appears to be the most favourable among the five kinds of trimer complex, and also more stable than $(HCN)_2HF$. The typical features of the non-additivity of intermolecular interaction are relatively strong in the HCN$(HF)_2$ trimer.

• Proceedings of the Botanical Society of Korea Conference
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• 1987.07a
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• pp.149-155
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• 1987

Growth and development of a higher plant, or any living organism for that matter, could be defined as an orderly expression of the genome in time and space in close interaction with the environment. During differentiation and development of a tissue or organ a group of genes must be selectively turned on or turned off mainly by trans-acting regulators. In this general concept of regulation of regulation of gene expression, a DNA molecule is recognized at a specific nucleotide sequence by DNA-binding factors. Molecular biology of the regulatory factors such as hormones, and their receptors, target DNA sequences and DNA-binding proteins are well advanced. What is not clearly understood is the molecular basis of the interactions between DNA and binding factors, expecially of the usages of the dyad symmetry of the target DNA sequences and the dimeric nature of the DNA-binding proteins. A unique 3-dimensional structure of DNA has been proposed that may play an important role in the orderly expression of the gene. A foldback intercoil (FBI) DNA configuration which was originally found by electron microscopy among mtDNA molecules from pearl millet has some unique features. The FBI configuration of DNA is believed to be formed when a flexible double helix folds back and interwines in the widened major grooves resulting in a four stranded, intercoil DNA whose thickness is the same as that of double stranded DNA. More recently, the FBI structure of DNA has been also induced in vitro by a novel enzyme which was purified from pearl millet mitochondria. It has been proposed that the FBI DNA could be utillized in intramolecular recombination which leads to inversion or deletion, and in intermolecular recombination which can lead to either site-specific recombination, genetic recombination via single strand invasion, or cross strand recombination. The structure and function of DNA in 3-dimensional aspect is emphasized for better understanding orderly expression of genes during growth and development.