• Bulletin of the Korean Chemical Society
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• v.30 no.11
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• pp.2723-2728
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• 2009

The conformational properties of oligosaccharides are important to understand carbohydrate-protein interactions. A trimannoside, methyl 3,6-di-O-($\alpha$-D-Man)-$\alpha$-D-Man (TRIMAN) is a basic unit of N-linked oligosaccharides. This TRIMAN moiety was further modified by GlcNAc (BISECT), which is important to biological activity of N-glycan. To characterize the trimannoside and its bisecting one we performed a molecular dynamics simulation in water. The resulting models show the conformational transition with two major and minor conformations. The major conformational transition results from the $\omega$ angle transition; another minor transition is due to the $\psi$ angle transition of $\alpha$ (1 $\rightarrow$ 6) linkage. The introduction of bisecting GlcNAc on TRIMAN made the different population of the major and minor conformations of the TRIMAN moiety. Omega ($\omega$) angle distribution is largely changed and the population of gt conformation is increased in BISECT oligosaccharide. The inter-residue hydrogen bonds and water bridges via bisecting GlcNAc residue make alterations on the local and overall conformation of TRIMAN moiety. These changes of conformational distribution for TRIMAN moiety can affect the overall conformation of N-glycan and the biological activity of glycoprotein.

• Bulletin of the Korean Chemical Society
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• v.12 no.1
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• pp.61-67
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• 1991

Conformational free energy calculations using an empirical potential function and the hydration shell model (a program CONBIO) were carried out on the neutral L-ascorbic acid (AA) in the unhydrated and hydrated states. The conformational energy was minimized from starting conformations which included possible conformations of six torsion angles in the molecule. The conformational entropy of each low energy conformation in both states was computed using a harmonic approximation. From the analysis of conformational free energies for AA in both states, intramolecular hydrogen bonds (HBs) are proved to be an essential factor in stabilizing the overall conformations, and cause the conformations in both states to be quite different from those in crystal. In the case of hydrated AA, there is a competition between HBs and hydration, and the hydration around the two hydroxyl groups attached to the acyclic side chain forces the molecule to form less stable HBs. The hydration affects strongly the conformational energy surfaces of AA. Several feasible conformations obtained in this work indicate that there exists an ensemble of several conformations in aqueous solution. The calculated probable conformations for the rotation about the C5-C6 bond of the acyclic side chain are trans and gauche +, which are in good agreement with results of NMR experiment.

• Bulletin of the Korean Chemical Society
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• v.13 no.3
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• pp.230-235
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• 1992

The conformational analysis has been done for catecholamines (dopamine, norepinephrine, and epinephrine) in the cationic and di-anionic states. The species responsible for adsorption on silver metal surface is anionic deprotonated at hydroxyl groups of catechol moiety, i.e., di-anionic states of catecholamines. This was deduced from Fourier-transform Raman spectra of sodium salts of catecholamines. High resolution proton NMR (400 MHz) spectra of catecholamines in basic and neutral $D_2O$ solution show that the conformations of norepinephrine and epinephrine in the di-anionic states are preferred in gauche, but not for dopamine in the di-anionic state. However the energy difference between trans and gauche of catecholamines in the protonated cationic states is small enough to rotate freely through C-C bond in ethylamine moiety. The conformational calculations using an empirical potential function and the hydration shell model (a program CONBIO) show consistent with above experimental results. The calculations suggest that the species of catecholamines adsorbed on silver metal surface would be in favor of the gauche conformations.

• Bulletin of the Korean Chemical Society
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• v.6 no.5
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• pp.300-303
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• 1985

To understand the nature of the linkage between chromophore and apoprotein in the photoreceptor of Stentor coeruleus, a conformational analysis has been carried out on the dipeptide amides linked to the chromophore hypericin using an empirical potential function. The conformational energies for the dipeptide amides of Glu (OHyp)-X-NHMe, where X = Leu, Phe, Asp, and Tyr, have been calculated to investigate the influence of peptide residues in stabilizing conformers. It was found that the increase of acidity of hypericin upon photoexcitation may be facilitated by the formation of intramolecular hydrogen bonds between hydroxyl groups of hypericin and carbonyl groups of peptide backbone, and that the stabilities of dipeptide amides do not significantly depend on peptide residues directly linked to chromophore.

• Archives of Pharmacal Research
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• v.28 no.1
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• pp.16-21
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• 2005

We wanted to elucidate the reason why the trityloxymethyl substituent in $\gamma$-trityloxymethyl-$\gamma$­butyrolactone takes a sterically unfavorable specific conformation, and so we synthesized 5-trityloxymethyldihydrofuran-3-one, 3-(trityloxymethyl)-4-butanolide and 2-trityloxymethyl- tetrahy­drofuran and we then analyzed their conformation by $^{1}H-NMR$ analysis.

• Korean Journal of Pharmacognosy
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• v.19 no.3
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• pp.153-169
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• 1988

The combined use of the J-modulated selective INEPT and CSCM 1DNMR techniques is described for the structure elucidation of several new classes of compound including prionitin, the loureirins and larreantin, and for the regiosubstitution of the furanonaphthoquinones. Spectroscopic studies on the conformation of the cytotoxic agent savinin are also described, together with the NMR assignments and preliminary biosynthetic experiments on the antitumor antibiotic staurosporine.

• YAKHAK HOEJI
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• v.36 no.6
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• pp.518-528
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• 1992

To determine the optimal conformation of sulfonylureas, the correlation between conformation and hypoglycemic activity of the two sulfonylureas of tolbutamide and chlorpropamide as hypoglycemic agent was studied using an empirical potential function (ECEPP/2) and the hydration shell model in the unhydrated and hydrated states. The conformational energy was minimized from several starting conformations with possible torsion angles in each molecule. The conformational entropy change of each conformation was computed using a harmonic approximation. To understand the hydration effect on the conformation of the molecules in aqueous solution, the contribution of water-accessible volume of each group or atom in the lowest-free-energy conformation was calculated and compared each other. From comparison of the computed lowest-free-energy conformations of two sulfonylureas, it could be suggested that the hydration of sulfonylurea moiety is related to increase the hypoglycemic activity. From the calculation results, it was known that the conformational entropy is the major contribution to stabilize the low-free-energy conformations of two sulfonylureas in unhydrated state. Whereas, in hydrated state, the hydration free energy largely contributes to the total free energies of low-free-energy conformations of tolbutamide and conformational entropy contributes to stabilize the low-free-energy conformations of chlorpropamide. The torsion angles from phenyl ring to urea moiety of the low-free-energy conformations of the two sulfonylureas were shown the nearly regular trend. On the basis of these results, the conformation exhibiting the optimal hypoglycemic activity of sulfonylureas and the binding direction to pancreatic receptor site A could be predicted. Also, according to the side chain lengthening of urea moiety, tolbutamide showed various conformational change. Therefore, steric effect may be important factor in the interaction between sulfonylureas and the putative pancreatic receptor.

• Bulletin of the Korean Chemical Society
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• v.33 no.3
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• pp.917-924
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• 2012

The conformational study of glycerol has been carried out using the M06-2X/cc-pVTZ level of theory in the gas phase and the SMD M06-2X/cc-pVTZ level of theory in water in order to understand its conformational preferences and solvation effects. Most of the preferred conformers of glycerol have two $C_5$ hydrogen bonds in the gas phase, as found by the analysis of calorimetric data. It has been known that the solvation drove the hydrogen bonds of glycerol to be weaker and its potential surface to be fatter and that glycerol exists as an ensemble of many feasible local minima in water. The calculated populations of glycerol in the gas phase and in water are consistent with the observed values, which are better than the previously calculated ones at the G2(MP2), CBS-QB3, and SM5.42 HF/6-31G(d) levels of theory.

• Journal of Sericultural and Entomological Science
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• v.42 no.2
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• pp.114-119
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• 2000

Effects of ethanlo treatment on the structural and thermal characteristics of regenerated Antheraea pernyi silk fibroin (RSF) were investigated. Infrared spectroscopy and X-ray diffractometry showed that the conformational transition of RSF might be affected by concentration of ethanol and its treatment time. The structure of RSF was rapidly changed from random coil to $\beta$-sheet conformation when RSF was treated with les than 75% ethanol concentration. However, RSF treated with ethanol(100%) did not show conformational change. Differential scanning calorimetry showed that exotherm at 232$\^{C}$ disappeared and the intensity of endotherm at 228$\^{C}$ decreased with treatment of 75% ethanol. Dynamic thermal analysis showed that loss modulus (E") and tan $\delta$$\_$E/ of RSF treated with aqueous ethanol was broaden and shifted to higher temperature in comparison with those of untreated RSF.

• Bulletin of the Korean Chemical Society
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• v.10 no.6
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• pp.554-559
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• 1989

The electronic structure, conformational preferences, and rotational barriers have been studied for transition metal indenyl allyl complexes by means of extended Huckel calculations. After geometrical optimization the exo conformation of allyl moiety is favored over the endo. The rotational barrier of indenyl ring in (Indenyl)Mo(CO)_2(Allyl)$ is computed to be 3.8 kcal/mol. Population analysis is applied to account for the conformational preferences and rotational barriers. A series of substituted allyl complexes has been also optimized. It shows steric hindrance plays a crucial role in setting the allyl orientation.