• Journal of the Korean Chemical Society
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• v.20 no.1
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• pp.3-14
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• 1976

The crystal structure of alicylaldehyde-4-piperidinothiosemicarbazone, $C_{13}H_{l7}N_3OS$, has been determined by single crystal X-ray analysis. The crystals are orthorhombic, space group $P2_12_12_1$, with unit cell dimensions a = 6.52(2), b = 13.42(4), c = 14.92(4)${\AA}$. There are four formular units in a unit cell. The structure was solved by the heavy atom method and refined by isotropic block diagonal least-squares methods to a final R value of 0.10 for 1019 observed reflections. The oxygen atom of the hydroxyl group is involved in two hydrogen bonds, one as donor in the intramolecular O-H${\cdots}$N hydrogen bond and the other as acceptor in the intermolecular N-H${\cdots}$O hydrogen bond, the distances of the hydrogen bonds 2.56 and 3.00${\AA}$ respectively.The molecules are joined into infinite columns by the N-H${\cdots}o$O hydrogen bonds which form spirals along the two fold screw axis parallel to the a axis. The molecular columns are held together by van der Waals forces.

• Journal of the Korean Chemical Society
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• v.55 no.3
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• pp.385-391
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• 2011

The time-dependent density functional theory (TDDFT) method has been carried out to investigate the excitedstate hydrogen-bonding dynamics of phenol-$(H_2O)_2$ complex. The geometric structures and infrared (IR) spectra in ground state and different electronically excited states ($S_1$ and $T_1$) of the hydrogen-bonded complex have been calculated using the density functional theory (DFT) and TDDFT method. A ring of three hydrogen bonds is formed between phenol and two water molecules. We have demonstrated that the intermolecular hydrogen bond $O_1-H_2{\cdots}O_3-H$ of the three hydrogen bonds is strengthened in $S_1$ and $T_1$ states. In contrast, the hydrogen bond $O_5-H_6{\cdots}O_1-H$ is weakened in $S_1$ and $T_1$ states. These results are obtained by theoretically monitoring the changes of the bond lengths of the hydrogen bonds and hydrogen-bonding groups in different electronic states. The hydrogen bond $O_1-H_2{\cdots}O_3-H$ strengthening in both the $S_1$ and $T_1$ states is confirmed by the calculated stretching vibrational mode of O-H (phenol) being red-shifted upon photoexcitation. The hydrogen bond strengthening and weakening behavior in electronically excited states may exist in other ring structures of phenol-$(H_2O)_n$.

• Bulletin of the Korean Chemical Society
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• v.23 no.11
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• pp.1527-1530
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• 2002

1,12-diazacyclodocosane-2,11-dione was first isolated from a plant Phyllanthus niruri Linn. Its structure has been determined by means of spectroscopy methods and X-ray crystallography. Two peptide groups in the big ring (lactam) are the main factors influencing intermolecular contacts. The hydrogen-bond interaction of these hydrophilic groups is observed in the crystal structure. Meanwhile, C-H···O hydrogen bonds in molecules contribute to the formation of the whole crystal. These two kinds of hydrogen-bond form six- member rings among molecules. This compound crystallizes in the triclinic space group P-1 with a= 9.588(1) $\AA$, b= $9.850(1)\AA$, c = $11.810(1)\AA$, $\alpha=$ 68.18(1)$^{\circ}C$ , $\beta=$ 84.98(1), $\gamma$ = 86.03(1)$^{\circ}C$ , V = $1030.66(17)\AA3$ , Z = 2. A disorder of five-member carbon chain in the whole ring is observed in the title compound. The bond angle 105.8(4) is determined for a extreme configuration C(14)-C(15)-C(16), and 117.7(10) for another extreme configuration C(14')-C(15')-C(16'). In this crystal, two molecules are tied each other by short intermolecular hydrogen bonds, the oxygen atom being tied by hydrogen bond to nitrogen atom of another two molecules. The NMR and IR spectral data coincides to the structure of the compound.

• Journal of the Korean Chemical Society
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• v.47 no.4
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• pp.334-338
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• 2003

The crystal structure of $[Co(phen)_2(Cl)(H_2O)] Clㆍ2H_2O$(phen=1,10-phenanthroline) has been determined by X-ray crystallography. It crystallizes in the triclinic system, space group P1, with lattice parameters a=9.662(2), b=11.445(1), c=13.037(2)${\AA}$ ${\alpha}$=64.02(1), ${\beta}$=86.364(9), ${\gamma}=78.58(2)^°$, and Z=2. The coordinated cations contain a six-coordinated cobalt atom chelated by two phen ligands and one chloride anion and one water ligand in cis arrangement. In addition to the chloride coordinated to the cobalt, there are one chloride ion and four water molecules which complete the crystal structure. In the solid state, the title compound forms three dimensional network structure through hydrogen bonds, within which exists the strongest hydrogen bond (O(3)-O(4)=2.33${\AA}$). The intermolecular hydrogen bonds connect the $[Co(phen)_2(Cl)(H_2O)]1+,\;H_2O$ moieties and chloride ion.

• Archives of Pharmacal Research
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• v.2 no.2
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• pp.99-110
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• 1979

The crystal structure of sulfapyridine, $C_{11}H_{11}N_{3}O_{2}S$, has been determined by X-ray diffraction method. The compound crystallizees in the monoclinic space group C2/c with a = 12, 80(4), b= 11.72(4), $c= 15.36(5){\AA}, {\beta}= 94(3)^{\circ}$and Z = 8. A total of 1133 observed reflections were collected by the Weissenberg method with CuKaradiation. Structure was solved by the heavy atom method and refined by isostropic block-diagonal least-squares method to the R value of 0.14. The nitrogen in the pyridine ring of sulfapyridine is associated with an extra-annular hydrogen. The C (benzene ring) S-N-C (pyridine ring) group adopts the gauche form with a fonformational angle of $71^{\circ}$. The benzene ring are inclined at angle of $84^{\circ}.to the pyridine ring plane. Sulfapyridine shows three different hydrogen bonding in the crystal. They are two N-H...O hydrogen bonds with the distance of 2.90 and 2.98${\AA}$ respectively, and on N-H...N with the distance of 3.06 ${\AA}$.

• Bulletin of the Korean Chemical Society
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• v.30 no.4
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• pp.837-845
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• 2009

We have performed DFT calculations to investigate the conformational characteristics and hydrogen bonds of the calix[6]arene (1) and p-tert-butylcalix[6]arene (2). The structures of various conformers of 1 were optimized by using the B3LYP/6-31G(d,p) and /6-31+G(d,p) methods followed by single point calculation of MPW1PW91/ 6-31G(d,p). The relative stability of the conformers of 1 is in the following order: cone (pinched: most stable) > partial-cone > cone (winged) $\sim$ 1,2-alternate $\sim$ 1,2,3-alternate > 1,4-alternate > 1,3-alternate > 1,3,5-alternate. The structures of different conformers of 2 were optimized by using the B3LYP/6-31G(d,p) method followed by single point calculation of MPW1PW91/6-31G(d,p). The relative stability of the conformers of 2 is in the following order: cone (pinched) > 1,2-alternate > cone (winged) > 1,4-alternate $\sim$ partial-cone > 1,2,3-alternate > 1,3,5alternate > 1,3-alternate. One of the important factors affecting the relative stabilities of the various conformers of the 1 and 2 is the number and strength of the intramolecular hydrogen bonds.

• Journal of Sericultural and Entomological Science
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• v.39 no.1
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• pp.44-55
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• 1997

This study was carried out to find out the relationship between qualities and contraction phenomenon of silk fibers by treatment of concentrated neutral salts. The contraction effects of silk fibers showed the critical point on the treatment conditions of concentration, temperature and time, among three kinds of neutral salts such as calcium nitrate, calcium chloride and lithium bromide. But, The silk fibers, pretreated with bromide and/or formaldehyde, did not show the contraction upon treating with calcium nitrate. This indicates that tyrosine and serine can be correlated with the contraction reaction because of coupling these amino acids with bromide and formaldehyde. In conclusion, a mechanism for the contraction of silk fiber with highly concentrated calcium nitrate solution is supposed as follows. At the initial stage of ration, the water was penetrated into the amorphous regions and fibers swollen, therefore, the contraction took place mainly in amorphous regions, which have plenty of functional groups with hydroxyl residues. Then, as the calcium nitrate is penetrated into the microfibril, the gydrogen bonds of tyrosine and serine residues and broken and crystalline regions are more and more influenced by increasing concentration of calcium nitrate solution. Microgibrils of crystalline regions become entangled, contracted to linear direction and rearranged to form new stable hydrogen bonds.

• Bulletin of the Korean Chemical Society
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• v.32 no.4
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• pp.1228-1230
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• 2011

A new amine receptor 2 utilizing anthracene and nitrophenyl group as signaling group was designed and synthesized. The receptor 2 only utilizes four amine N-H's and 9-anthracenyl hydrogen to bind anions. The receptor 2 can bind anions through hydrogen bonds with a selectivity of $CH_3CO_2^-$ > $H_2PO_4^-$ > $F^-$ > $C_6H_5CO_2^-$ > $Cl^-$ in highly polar solvent such as DMSO without protonation of amine.

• Bulletin of the Korean Chemical Society
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• v.29 no.9
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• pp.1717-1722
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• 2008

The 70 kDa heat-shock protein (Hsp70) involved in various cellular functions, such as protein folding, translocation and degradation, regulates apoptosis in cancer cells. Recently, it has been reported that the green tea flavonoid (−)-epigallocatechin 3-gallate (EGCG) induces apoptosis in numerous cancer cell lines and could inhibit the anti-apoptotic effect of human Hsp70 ATPase domain (hATPase). In the present study, docking model between EGCG and hATPase was determined using automated docking study. Epi-gallo moiety in EGCG participated in hydrogen bonds with side chain of K71 and T204, and has metal chelating interaction with hATPase. Hydroxyl group of catechin moiety also participated in metal chelating hydrogen bond. Gallate moiety had two hydrogen bondings with side chains of E268 and K271, and hydrophobic interaction with Y15. Based on this docking model, we determined two pharmacophore maps consisted of six or seven features, including three or four hydrogen bonding acceptors, two hydrogen bonding donors, and one lipophilic. We searched a flavonoid database including 23 naturally occurring flavonoids and 10 polyphenolic flavonoids with two maps, and myricetin and GC were hit by map I. Three hydroxyl groups of B-ring in myricetin and gallo moiety of GC formed important hydrogen bonds with hATPase. 7-OH of A-ring in myricetin and OH group of catechin moiety in GC are hydrogen bond donors similar to gallate moiety in EGCG. From these results, it can be proposed that myricetin and GC can be potent inhibitors of hATPase. This study will be helpful to understand the mechanism of inhibition of hATPase by EGCG and give insights to develop potent inhibitors of hATPase.

• Archives of Pharmacal Research
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• v.7 no.2
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• pp.137-139
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• 1984

The molecular structure of (+)-6-Me hoxy-.alpha.-methyl-2-naphthaleneacetic acid (Naproxen), $C_{14}H_{14}O_{ 3}$, was determined by X-Ray diffraction technique. Naproxen crystallized in $P2_1$ with two molecules on the unit cell of dimensions a = 7.855, b = 5.783, c = 13.347$\AA$ and $\beta$ = $93.9^{\circ}$