• Bulletin of the Korean Chemical Society
• /
• v.25 no.2
• /
• pp.198-202
• /
• 2004

Hydrogen bond is an important factor in the structures of carbohydrates. Because of great strength, short range, and strong angular dependence, hydrogen bonding is an important factor stabilizing the structure of carbohydrate. In this study, conformational properties and the hydrogen bonds in GlcNAc( ${\beta}$1,3)Gal(${\beta}$)OMe in DMSO are investigated through NMR spectroscopy and molecular dynamics simulation. Lowest energy structure in the adiabatic energy map was utilized as an initial structure for the molecular dynamics simulations in DMSO. NOEs, temperature coefficients, SIMPLE NMR data, and molecular dynamics simulations proved that there is a strong intramolecular hydrogen bond between O7' and HO3' in GlcNAc( ${\beta}$1,3)Gal(${\beta}$)OMe in DMSO. In aqueous solution, water molecule makes intermolecular hydrogen bonds with the disaccharides and there was no intramolecular hydrogen bonds in water. Since DMSO molecule is too big to be inserted deep into GlcNAc(${\beta}$1,3)Gal(${\beta}$)OMe, DMSO can not make strong intermolecular hydrogen bonding with carbohydrate and increases the ability of O7' in GlcNAc(${\beta}$1,3)Gal(${\beta}$)OMe to participate in intramolecular hydrogen bonding. Molecular dynamics simulation in conjunction with NMR experiments proves to be efficient way to investigate the intramolecular hydrogen bonding existed in carbohydrate.

• Archives of Pharmacal Research
• /
• v.13 no.3
• /
• pp.246-251
• /
• 1990

Intermolecular interaction between barbiturates and membrane components such as phospholipid and cholesterol were investigated on $^1$H-NMR spectra and infrared spectra. According to previous reports, barbiturates interacted with phospholipid through intermolecular hydrogen bonds. We also investigated thi observation using dipalmitoyl-phosphatidylcholine (DPPC) as phospholipid in deuterochloroform, and characterized quantitatively. Also, the observed drug could interact with cholesterol which is one of the major components of biomembranes through hydrogen bonds. It was the carbonyl groups of barbiturate and the hydroxyl group of cholesterol that formed hydrogen bond complex. In addition to spectroscopic studies, we investigated the direct effect of phenobarbital on lipid multibilayer vesicles, whose compositions were varied, by calorimetric method. Phenobarbital caused a reduction in the temperature of phase transition of vesicles. These studies may provided a basis for interpreting the mode of action of barbiturates.

• Bulletin of the Korean Chemical Society
• /
• v.33 no.1
• /
• pp.95-99
• /
• 2012

Two novel copper(II) complexes, [Cu(dmamhp)$(H_2O)_2(SO_4)]_n$ (1) and [Cu(dmamhp)$(NO_3)_2(H_2O)]{\cdot}H_2O$ (2) [dmamhp = 2-dimethylaminomethyl-3-hydroxypyridine] have been synthesized and structurally characterized by single crystal X-ray diffraction analysis. Compound 1 displays a double one-dimensional chains structure, in which each chain is constituted with the distorted octahedral copper(II) complex bridged through bidentate sulfate ligands resulting in a coordination polymer. The bifurcated hydrogen bonds and $\pi-\pi$ interactions play important roles in the formation of the double chains structure. On the other hand, compound 2 adopts a distorted square pyramidal geometry around copper(II) ion and exists as a discrete monomer. There are intermolecular bifurcated hydrogen bonds and $\pi-\pi$ stacking interactions between the monomeric units. The magnetic properties revealed that the paramagnetic behaviors are dominantly manifested and there are no intermolecular magnetic interactions in both compound 1 and 2.

• Proceedings of the Korean Vacuum Society Conference
• /
• 2011.02a
• /
• pp.38-38
• /
• 2011

Covalently bonded halogen ligands possess unusual charge distributions, attracting both electrophilic and nucleophilic molecular ligands to form halogen bonds. In many biochemical systems, halogen bonds and hydrogen bonds coexist. The interplay between halogen and hydrogen bonds has been actively studied in various three-dimensional bulk molecular co-crystals. It was found that halogen bonds could be complementary to hydrogen bonds due to their similar bond strength and dissimilar directionality. In those ensemble-averaging approaches, however, it was not possible to extract local information such as individual bond configurations and nano-level domain structures, which is a crucial part of supramolecular studies. In this study, we directly visualize the individual molecular configuration of a brominated molecule and the role of halogen bonds on Au(111) using scanning tunneling microscopy. The precise arrangement of observed molecular structures was reproduced by first-principle studies and explained in the context of halogen and hydrogen bonds. We discuss the distances and the strengths of the observed halogen bonds and hydrogen bonds, which are consistent with previous bulk data.

• Archives of Pharmacal Research
• /
• v.7 no.2
• /
• pp.137-139
• /
• 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 $\beta$ = $93.9^{\circ}$

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

• Bulletin of the Korean Chemical Society
• /
• v.29 no.10
• /
• pp.1951-1959
• /
• 2008

Pentamer cluster of azodicarbonamide (ADA) based on the crystalline structure was investigated for the equilibrium structure, the stabilization energies, and the vibrational properties at various levels of the density functional theory. Stretching force constants of N${\cdot}{\cdot}{\cdot}$H or O${\cdot}{\cdot}{\cdot}$H, and angle-bending force constants of N-H${\cdot}{\cdot}{\cdot}$N or N-H${\cdot}{\cdot}{\cdot}$O for intermolecular hydrogen bonds in the pentamer cluster were obtained in 0.2-0.5 mdyn/$\AA$ and 1.6-2.0 mdyn$\AA$, respectively. The geometry of central ADA molecule fully hydrogen bonded with other four molecules shows good coincidence to the crystalline structure except the bond distances of N-H. Calculated Raman and infrared spectra of central ADA molecule in cluster represent well the experimental spectra of ADA obtained in the solid state compared to a single molecule. Detailed structural and vibrational properties of central ADA molecule in the pentamer cluster are presented.

• Proceedings of the Korean Vacuum Society Conference
• /
• 2011.08a
• /
• pp.107-107
• /
• 2011

Supramolecular structures of anthraquinone molecules on a metallic surface are studied using scanning tunneling microscope (STM) under ultrahigh-vacuum conditions. When we deposited anthraquinone molecules on Au(111) substrate, the molecules formed three different phases (Chevron type, tetragon type and disordered type) on the surface. Based on our STM measurements, we proposed models for the observed molecular structures. Chevrons are consisted of several molecular chains, which make well-ordered two-dimensional islands by some weak interrow interactions and we could observe tetragon structures which make array of (111) metallic surface. each molecular rows in the chevrons are stabilized by two parallel O-H hydrogen bonds and disordered structures are observed 1-dimensional phase with hydrogen bond. First-principles calculations based on density functional theory are performed to reproduce the proposed models. Distances and energy gains for each intermolecular bond are estimated. In this presentation, we explain possible origins of these molecular structures in terms of hydrogen bonds, Van der Waals interactions and molecule-substrate interactions.

• Bulletin of the Korean Chemical Society
• /
• v.31 no.10
• /
• pp.2897-2902
• /
• 2010

Seven fully optimized geometries of 3,6-dihydrazino-1,2,4,5-tetrazine (DHT) dimers have been obtained with density functional theory (DFT) method at the B3LYP/$6-311++G^{**}$ level. The intermolecular interaction energy was calculated with zero point energy (ZPE) correction and basis set superposition error (BSSE) correction. The greatest corrected intermolecular interaction energy of the dimers is $-23.69\;kJ{\cdot}mol^{-1}$. Natural bond orbital (NBO) analysis is performed to reveal the origin of the interaction. Based on the vibrational analysis, the changes of thermodynamic properties from the monomers to dimer with the temperature ranging from 200.0 K to 800.0 K have been obtained using the statistical thermodynamic method. It was found that the hydrogen bonds dominantly contribute to the dimers, while the binding energies are not only determined by hydrogen bonding. The dimerization process can not occur spontaneously at given temperatures.

• Bulletin of the Korean Chemical Society
• /
• v.31 no.4
• /
• pp.881-886
• /
• 2010

A novel Schiff base N-(2,4-dinitro-phenyl)-N'-(1-phenyl-ethylidene)-hydrazine has been synthesized and structurally characterized by X-ray single crystal diffraction, elemental analysis, IR spectra and UV-vis spectrum. The crystal belongs to monoclinic with space group P21/n. The molecules are connected via intermolecular O-$H{\cdots}O$ hydrogen bonds into 1D infinite chains. The crystal structure is consolidated by the intramolecular N-$H{\cdots}O$ hydrogen bonds. weak intermolecular C-$H{\cdots}O$ hydrogen bonds link the molecules into intriguing 3D framework. Furthermore, Density functional theory (DFT) calculations of the structure, stabilities, orbital energies, composition characteristics of some frontier molecular orbitals and Mulliken charge distributions of the title compound were performed by means of Gaussian 03W package and taking B3LYP/6-31G(d) basis set. The time-dependent DFT calculations have been employed to calculate the electronic spectrum of the title compound, and the UV-vis spectra has been discussed on this basis. The results show that DFT method at B3LYP/6-31G(d) level can well reproduce the structure of the title compound.