• Nuclear Engineering and Technology
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• v.38 no.3
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• pp.201-210
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• 2006

This article presents a brief overview of an important area of neutron scattering: the general principles and techniques of elastic, quasielastic and inelastic scattering from a system composed predominately of incoherent scatterers. The methodology is then applied to the study of water, specifically when it is confined in nanometer-scale environments. The confined water exhibits uniquely anomalous properties in the supercooled state. It also nourishes biological functions, and supports essential chemical reactions in living systems. We focus on recent investigations of water encapsulated in nanoporous silica and carbon nanotubes, hydrated water in proteins and water or hydroxyl species incorporated in nanostructured minerals. Through these scientific examples, we demonstrate the advantages derived from the high sensitivity of incoherent neutron spectroscopy to hydrogen atom motions and hydrogen-bond dynamics, aided by rigorous data interpretation method using molecular dynamics simulations or theoretical modelling. This enables us to probe the inter-/intramolecular vibrations and relaxation/diffusion processes of water molecules in a complex environment.

• Journal of the Korean Chemical Society
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• v.27 no.1
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• pp.1-8
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• 1983

Solvent effects on nucleophilic substitution reaction of naphthalene sulfonyl chlorides with pyridine in protic and aprotic solvent have been studied by means of conductometry. Results showed that the rate constants increased with dielectric constants for protic solvents, while they decreased with dielectric constants for aprotic solvents, except for acetonitrile which has a higher dielectric constant but had also greater rate constant. The rate constants were shown to be more susceptible to polarity-polarizability parameter, , than to hydrogen bond donor acidity parameter, ${\alpha}$, indicating that the pulling effect of hydrogen bonding solvent.

• Bulletin of the Korean Chemical Society
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• v.31 no.8
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• pp.2147-2150
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• 2010

c-Jun N-terminal kinase 1 (JNK1) is involved in apoptosis, cell differentiation and proliferation. It has been reported that a flavonol, quercetin, induces cell apoptosis and JNK inhibition. In order to understand the interactions of quercetin and JNK1, we performed receptor-oriented pharmacophore based in silico screening and determined a binding model of human JNK1 and quercetin at the ATP binding site of JNK1. 5-OH of A-ring and carbonyl oxygen of C-ring of quercetin participated in hydrogen bonding interactions with backbone of E109 and M111. Additionally, 3'-OH of quercetin formed a hydrogen bond with backbone of I32. One hydrophobic interaction is related on the binding of quercetin to JNK1 with I32, N114, and V158. Based on this model, we conducted a docking study with other 8 flavonols to find possible flavonoids inhibitors of JNK1. We proposed that one flavonols, rhamnetin, can be a potent inhibitor of JNK and 5-OH of A-ring and 3'-OH of B-ring of flavonols are the essential features for JNK1 inhibition.

• Bulletin of the Korean Chemical Society
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• v.35 no.11
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• pp.3169-3174
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• 2014

Numerous studies have examined the role of flavonoids in modulating inflammatory responses in vitro. In this study, we found a novel flavonoid, 3,6,3'-trihydroxyflavone (1), with anti-inflammatory effects. Anti-inflammatory activity and mechanism of action were examined in mouse macrophages stimulated with lipopolysaccharide (LPS). Our results showed that the anti-inflammatory effects of 1 are mediated via p38 mitogen-activated protein kinase (p38 MAPK), Jun-N terminal kinase (JNK), and the extracellular-signal-regulated kinase (ERK) pathway in lipopolysaccharide (LPS)-stimulated RAW264.7 cells. Binding studies revealed that 1 had a high binding affinity to JNK1 ($1.568{\times}10^8M^{-1}$) and that the 3- and 6-hydroxyl groups of the C-ring and A-ring of 1 participated in hydrogen bonding interactions with the side chains of Asn114 and Lys55, respectively. The oxygen at the 3' position of the B-ring formed a hydrogen bond with side chain of Met111. Therefore, 1 could be a potential inhibitor of JNKs, with potent anti-inflammatory activity.

• Journal of Environmental Health Sciences
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• v.38 no.4
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• pp.351-359
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• 2012

Objectives: This study was conducted in order to investigate the specific correlation between physicochemical properties and bioactivity in ecdysteroids found in living organisms. Methods: The examined steroidal compounds were classified into three groups according to their relevance to ecdysone activity. Each compound molecule was completely drawn to automatically calculate its physicochemical parameters and docked against 20-hydroxyecdysone to calculate the total distance. Electronic charge distribution was also observed for each molecule. All procedures were conducted using a computational chemistry program. Results: Ecdysone agonists showed different ranges of parameter values, such as log P, hydrophilic-lipophilic balance (HLB), solubility parameter (SP), hydrophilic surface (HPS), hydrogen bond (HB) and Kappa 2, when compared with antagonists and steroids without ecdysone activity. They also showed a similar electronic charge distribution that is significantly different from the electron charge distribution of antagonists and steroids without ecdysone activity. The total distance values of agonists, estimated by docking them with 20-hydroxyecdysone, were relatively small but showed no correlation with binding affinity with receptor ligand. Conclusions: These results suggest that physicochemical properties such as steric and electronic effects, hydrophobicity and hydrogen bonding may operate in combination to determine the binding activity of ecdysteroids to the receptor protein.

• Archives of Pharmacal Research
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• v.15 no.1
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• pp.52-57
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• 1992

The molecular structure of a natural compound was determined by single crystal X-ray diffraction analysis. The compound was isolated by methanol extraction and repeated chromatography from the stem of Paulownia tomentosa. Yellow prismatic crystals of the compound, which were recrystallized from tetrahydrofuran, are triclinic, with a = 7.310 (6), b = 10.753(6), c = 11.586(5) ${\AA}.\;\alpha= 93.30(6),\;\beta=105.62(10),\;\gamma=109.49(7)^\circ,\;D_x=1.514,\;D_m=1.51 g/cm^3$, space group P1 and Z = 2. The structure was solved by direct method, and refined by least-squares procedure to the final R-value of 0.032 for 1271 independent reflections $(F\le3\sigma{(F))}$. The compound is one of new furanquinone analogue. The molecule has a nearly planar conformation with an intramolecular hydrogen bond. In the crystal, the planar molecules are arranged as a prallel sheet-like pattern, and these stackings are stabilized by the O-H...O type intermolecular hydrogen bonds. The other intermolecular contacts appear to be the normal van der Waals interactions.

• Bulletin of the Korean Chemical Society
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• v.26 no.1
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• pp.57-62
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• 2005

The potentiometric responses for various anions are investigated with membrane electrode (membrane 1) based on 1,3-diethyl-1,3-dihydroxy-1,3-bis(2-dimethylaminomethyl ferrocenyl) disiloxane. The nitrate ion-selective electrode based on compound 1 gave a good Nernstian response of 58.18 mV per decade for nitrate with the detection limit of −e5.66 of log [NO3−e]. Compound 1 has all those functional groups and the other two compounds have less functional group of ferrocenyl or ferrocenyl and hydroxide, respectively. Even though, potentiometric response to anions was excellent at pH 5, the selectivity pattern for all three membrane electrode based on series of disiloxane is almost like Hofmeister sequence at pH 5. However, the membrane electrode 1-3 exhibited very different response to anions at pH 7. In this pH, NH2 is not protonated and ionophore may act as neutral carrier. Hydrogen bond may enhance the responsibility to hydrogen acceptors and intramolecular electro-active site may increase the permeability of analyte to ionophore in membrane.

• Archives of Pharmacal Research
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• v.3 no.1
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• pp.37-49
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• 1980

Chlorpropamide, $C_{10}H_{13}N_{2}O_{3}SCI$, forms orthofombic crystals of space group $P_{2}_{ 1}2_{1}2_{1}$ with a 9.066 $\pm$ 0.004, b = 5.218 $\pm$ 0.003, c = 26, 604 $\pm$, 0.008 $\AA$, and four molecules per cell. Three dimensional photographic data were collected with Mo-K$\alpha$ radiation. The structure was determined using Patterson, Fourier and Difference syntheses methods and refined by the block-diagonal least-squares methods with anisotropic thermal parameters for all nonhydrogen atoms and isotropic thermal parameters for all hydrogen atomes. The final R value was 0.10 for the 1823 observed independent reflections. The dihedral angle between the planes through the benzene ring and the urea goup is 99$^{\circ}$. The conformational angle formed by the projection of the S-C(1) with that of N(1)-C(7) when the projection is taken along the S-N(1) bond is 76$^{\circ}$. The molecule appears to form with neighbouring molecules two hydrogen bonds, N(1)..H...O(3) and N(2)-H...0(2) of lengths 2.774 and 2.954$\AA$ respectively related by screw diads parallel to the a axis. Adjacent molecules parallel to b and c axis are bound together by van der Wasls forces.

• Journal of the Korean Chemical Society
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• v.19 no.3
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• pp.149-155
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• 1975

Pivalic acid, which has a globular shape and is a plastic crystal, has been examined by means of temperature-dependent with-line proton magnetic resonance spectroscopy. Results of temperature-dependent line width, second moment, and spin-lattice relaxation time studies of pivalic acid were interpreted in terms of dynamic behavior and hydrogen bonding. The dynamic behavior consists of superimposed reorientation of the methyl groups about their three-fold axes$(C_3) and of the molecule about the central C-C bond(C_3'),$ general molecular reorientation about the center of gravity, and molecular self-diffusion. Activation energies for the motional processes have been obtained from line width measurements using the modified Bloembergen, Purcell, and Pound theory and from spin-lattice relaxation time measurements. The results were compared with the Pople-Karasz theory of fusion and the agreement was found to be poor. The discrepancy was interpreted in terms of hydrogen bonding in this molecule.

• Bulletin of the Korean Chemical Society
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• v.30 no.2
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• pp.409-414
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• 2009

Novel binol aldehydes derivatized at 2' hydroxy position with both uryl and acetamide groups (2), and diuryl groups (3) have been synthesized. Both were designed for streospecific binding and chirality conversion of general dipeptides with support of multiple hydrogen bonding donor sites in the receptors. The receptors, 2 and 3, converted the chirality of N-terminal amino acids of peptides such as Ala-Gly, Met-Gly, Leu-Gly and His-Gly with stereoselectivity on D-form over L-form. The stereoselectivity ratios were in the range of 5-11, somewhat higher than those of the binol receptor with mono uryl group (1). The DFT calculation at the B3LYP/6-31G$^*$//MPWB1K/6-31G$^*$ level revealed that 3-D-Ala-Gly was 2.2 kcal/mol more stable than 3-L-Ala-Gly. The considerable steric hindrance between the methyl group of the alanine and the imine CH moiety of the receptor seems to be the main contributing factor for the thermodynamic preference.