• Bulletin of the Korean Chemical Society
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• v.35 no.8
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• pp.2311-2316
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• 2014

Conformations and vibrational frequencies of the racemic (2RS,3RS)-5-amino-3-(4-phenylpiperazin-1-yl)-1,2,3,4-tetrahydronaphthalen-2-ol-(I) [(2RS,3RS)-(I)], a precursor of benzovesamicol analogues, have been carried out using various DFT methods (M06-2X, B3LYP, B3PW91, PBEPBE, LSDA, and B3P86) with basis sets of 6-31G(d), 6-31+G(d,p), 6-311+G(d,p), 6-311++G(d,p), cc-pVTZ, and TZVP. The LSDA/6-31G(d) level of theory shows the best performance in reproducing the X-ray powder structure. However, the PBEPBE/cc-pVTZ level of theory is the best method to predict the vibrational frequencies of (2RS,3RS)-(I). The potential energy surfaces of racemic pairs (2RS,3RS)-(I) and -(II) are obtained at the LSDA/6-31G(d) level of theory in the gas phase and in water. The results indicate that (2RS,3RS)-(I) are more stable by ~0.75 kcal/mol in energy than (2RS,3RS)-(II) in water, whereas conformer AIIg and BIIg are more stable by ~0.04 kcal/mol than AIg in gas phase. In particular, the hydrogen bond distances between the N of piperazine and the OH of tetrahydronaphthalen become longer in gas, compared with those in the water phase. Vibrational frequencies calculated at the PBEPBE/cc-pVTZ level of theory in the gas phase are larger than those in water, whereas their intensities in the gas phase are weaker than those in water.

• Journal of the Korean Chemical Society
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• v.51 no.1
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• pp.7-13
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• 2007

The oxazole plays an important role in the binding of lexitropsin to the guanine-cytosine base pair from minor groove of DNA. The geometry optimization is performed with DFT calculations for the two possible conformations of the protonated oxazole. The proton affinities are calculated at B3LYP level of theory with 6-31G* basis set for the optimized geometry. It is found that the proton affinites of the conformations in which the oxazole nitrogen is the protonation center are greater than that of the conformations in which the oxazole oxygen is the protonation center. This result is in good agreement with molecular electrostatic potential (MEP) contour map. The proton affinities are also studied for various substituted oxazoles with the electron-donating and -withdrawing groups to estimate substitutent effect on the proton affinity at the hydrogen bonding site of the oxazoles. it is shown that the electron-donating substituents increase the proton affinity of oxazole, while the electron-withdrawing substituents decrease it.

• CELLMED
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• v.2 no.2
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• pp.15.1-15.3
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• 2012

Kampo medicine, a Japanese traditional herbal medicine, has been used in clinical practice in Japan. The most appropriate Kampo formula should be chosen for each individual by the four diagnostic procedures. Fuku shin, the abdominal exam, is one of the most important approaches in the procedures. There are several abdominal conformations (signs) when administering Fuku shin. In Kampo medicine, psychiatric illness-marked by depression and anxiety-has been shown to be related with an abdominal conformation, Shin ka hi koh (Epigastric Obstructive Hardness). The aim was to see the occurrence of abdominal conformations in each level of depression and anxiety symptoms. Two hundred fifteen patients were assigned to high-, moderate-, or low-level psychiatric comorbidity based on the Hospital Anxiety and Depression Scale and were studied regarding the occurrence of major abdominal conformations. Moderate and high psychopathological groups showed the higher occurrence of Shin ka hi koh [Low, 21%; Moderate, 67%; High, 74%] ($p$ < 0.0001). In conclusion, moderate and high psychopathological patients showed the higher occurrence of a specific abdominal sign.

• Proceeding of EDISON Challenge
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• 2014.03a
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• pp.63-74
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• 2014

Predicting protein loop structures is an important modeling problem since protein loops are often involved in diverse biological functions by participating in enzyme active sites, ligand binding sites, etc. However, loop structure prediction is difficult even when structures of homologous proteins are known due to large sequence and structure variability among loops of homologous proteins. Therefore, an ab initio approach is necessary to solve loop modeling problems. One of the difficulties in the development of ab initio loop modeling method is to derive an accurate scoring function that closely approximates the true free energy function. In particular, entropy as well as energy contribution have to be considered adequately for loops because loops tend to be flexible compared to other parts of protein. In this study, the contribution of conformational entropy is considered in scoring loop conformations by employing "colony energy" which was previously proposed to estimate the free energy for an ensemble of conformations. Loop conformations were generated by using two EDISON_Chem programs GalaxyFill and GalaxySC, and colony energy was designed for this sampling by tuning relevant parameters. On a test set of 40 loops, the accuracy of predicted loop structure improved on average by scoring with the colony energy compared to scoring by energy alone. In addition, high correlation between colony energy and deviation from the native structure suggested that more extensive sampling can further improve the prediction accuracy. In another test on 6 ligand-binding loops that show conformational changes by ligand binding, both ligand-free and ligand-bound states could be identified by using colony energy when no information on the ligand-bound conformation is used.

• Journal of the Korean Chemical Society
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• v.36 no.4
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• pp.523-535
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• 1992

The conformations of hexapeptides, their complexation with alkali cations and the inhibition of the cation transport by 5,5-diphenylhydantoin(DPH) were studied theoretically using ECEPP/2 and MM2 force field. Several low energy conformations of uncomplexed cyclic hexapepides are obtained, and they adopt compact conformations in which most amide hydrogens form intramolecular hydrogen bond to amide carbonyl oxygens. The complexation energy of the peptide with $Na^+$ ion and DPH is -60 kcaal/mol and -18 kcal/mol, respectively. However, no suitable cavity to bind metal cation exists for the local minima of the peptide, and the internal energy of the uncomplexed hexapeptide having cavity is higher than that of the uncomplexed global minimum of this work by 10 kcal/mol. Also, one of the most important amino acid residue to bind DPH is Glycine, and this can explain experimental observation that the replacement of Gly by Sarcosine (N-methyl Glycine) reduce the inhibition ability of the cation transport.

• Bulletin of the Korean Chemical Society
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• v.14 no.2
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• pp.200-206
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• 1993

Structures of two polymorphs of ${\alpha},{\alpha}$-trehalose octaacetate monohydrate, $C_{28}H_{38}O_{19}\;{\cdot}\;H_2O$, have been studied by X-ray diffraction method. ${\alpha},{\alpha}$-trehalose (${\alpha}$-D-glucopyranosyl ${\alpha}$-D-glucopyranoside) is a nonreducing disaccharide. The polymorph I belongs to the monoclinic $P2_1$, and has unit cell parameters of a=10.725(l), b=15.110(4), c=11.199(5) ${\AA}$, ${\beta}=108.16(2)^{\circ}$ and Z=2. The polymorph II is orthorhombic $P2_12_12_1$, with a=13.684(4), b=15.802(4), c=17.990(9) ${\AA}$ and Z=4. The final R and R$_w$ values for monoclinic polymorph I are 0.043 and 0.048 and for orthorhombic polymorph II are 0.116 and 0.118, respectively. Those R values of polymorph II are high because the large thermal motions of acetyl groups and the poor quality of the crystal. The molecular conformations in the two polymorphs are similar. Both D-glucopyranosyl rings have chair $^4C_1$ conformations and atoms of glycosidic chain ${\alpha}(1{\rightarrow}1)$ linkage are coplanar. The primary acetate groups of the pyranose residues assume both gauche-trans conformations. The molecules of two polymorphs have pseudo-C$_2$ symmetry at glycosidic O(1) atom. The bond lengths and angles are normal compared with those in other acetylated sugar compounds. The molecules in the monoclinic crystal are held by the hydrogen bonds with the water molecules and by van der Waals forces.

• Bulletin of the Korean Chemical Society
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• v.25 no.5
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• pp.601-602
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• 2004

• Bulletin of the Korean Chemical Society
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• v.35 no.5
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• pp.1323-1328
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• 2014

Molecular structures of the various conformational stereoisomers of 2,8,14,20-cyanophenyl pyrogallol[4]arenes 1 were optimized using the mPW1PW91 (hybrid Hartree-Fock density functional) calculation method. The total electronic and Gibbs free energies and the normal vibrational frequencies of the different structures from three major conformations (CHAIR, TABLE, and 1,2-Alternate) of the four stereoisomers [1(rccc), 1(rcct), 1(rctt), and 1(rtct)] were analyzed. The mPW1PW91/6-31G(d,p) calculations suggested that $1(rcct)_{1,2-A}$, 1(rctt)CHAIR, and $1(rtct)_{CHAIR}$ were the more stable conformations of the respective stereoisomers. Hydrogen bonding is the primary factor for the relative stabilities of the various conformational isomers, and maximizing the ${\pi}-{\pi}$ interaction between the cyanophenyl rings is the secondary factor. The calculated IR spectra of the more stable conformers [$1(rctt)_{CHAIR}$, $1(rcct)_{1,2-A}$, $1(rtct)_{CHAIR}$] were compared with the experimental IR spectrum of $1(rtct)_{CHAIR}$.

• Bulletin of the Korean Chemical Society
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• v.34 no.3
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• pp.899-906
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• 2013

Using generated conformations from docking analysis by Gold algorithm, some 3D-QSAR models; CoMFA and CoMSIA have been created on 39 N-benzoylated phenoxazines and phenothiazines, including their S-oxidized analogues. These molecules inhibit the polymerization of tubulin into microtubules and thus they have been studied for the development of antitumor drugs. Training set for the CoMFA and CoMSIA models using 30 docked conformations gives $q^2$ Leave one out (LOO) values of 0.756 and 0.617, and $r^2$ ncv values of 0.988 and 0.956, respectively. The ability of prediction and robustness of the models were evaluated by test set, cross validation (leave-one-out and leave-ten-out), bootstrapping, and progressive scrambling approaches. The all-orientation search (AOS) was used to achieve the best orientation to minimize the effect of initial orientation of the structures. The docking results confirmed CoMFA and CoMSIA contour maps. The docking and 3D-QSAR studies were thoroughly interpreted and discussed and confirmed the experimental $pIC_{50}$ values.

• YAKHAK HOEJI
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• v.40 no.6
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• pp.632-639
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• 1996

Most stable conformers of some antiinflammatory fenamates were obtained by conformational free energy change calculations. Conformational energies for the molecules as unhydrate d state were estimated first, and those as hydrated state were calculated then to simulate the molecules in aqueous solution using a hydration shell model. The initial geometries of the molecules were obtained either from X-ray crystallographic data or from homologous molecular fragments. The bond lengths and angles were not varied, but all the torsion angles were varied step by step during the conformational free energy surface searching. The results show that there are several feasible conformations for a compound. And the molecules are somewhat stabilized by hydration (-${\delta}G_{hyd}{\cong}$13 to 16kcal/mole), but the conformations were not changed significantly by the hydration itself. There seems to be a strong tendency of intramolecular hydrogen bonding between imino hydrogen and carboxyl oxygen of the compounds. As a result, the carboxyl group cannot be rotated freely, and the rotation of the second aromatic ring is the main reason for the conformational variations of the compounds. The ECEPP force fields via the program CONBIO were used throughout this study.