• Journal of the Korean Magnetic Resonance Society
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• v.17 no.1
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• pp.19-23
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• 2013

The temperature dependences of the NMR spectrum and the spin-lattice relaxation times in $KH_2PO_4$ were investigated via single-crystal NMR and MAS NMR. The stretched-exponential relaxation that occurred because of the distribution of correlation times was indicative of the degree of the distribution of the double-well potential on the hydrogen bond. The behaviors responsible for the strong temperature dependences of the $^1H$ and $^{31}P$ spin-lattice relaxation times in the rotating frame $T_{1{\rho}}$ in $KH_2PO_4$ are likely related to the reorientational motion of the hydrogen-bond geometry and the $PO_4$ tetrahedral distortion.

• Bulletin of the Korean Chemical Society
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• v.17 no.2
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• pp.201-205
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• 1996

The crystal and molecular structure of thiourea dioxide, (NH2)2CSO2, was determined by x-ray single crystal diffraction techniques. Lattice constants are a=10.669(2), b=10.119(2), and c=3.9151(5) Å with the space group Pnma and Z=4. The thiourea portion of the molecule has a planar conformation. When the two oxygen atoms are included, the sulfur atom is at the apex of a trigonal pyramid formed with the two oxygen atoms and the carbon atom as the base. The crystal structure is stabilized by strong intermolecular hydrogen bonds. Ab initio calculations were performed to investigate the bonding features and reactivity of thiourea dioxide. The calculated bond order of S-C is only 0.481. The hydrogen bond energy was computed to be 22.3 kcal/mol for dimer. MEP analysis reveals that the sites on nucleophilic reactions are S and C atoms.

• BMB Reports
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• v.31 no.6
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• pp.590-594
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• 1998

X-ray crystallographic studies of the deoxy form of human adult hemoglobin (Hb A) have shown that ${\beta}99Asp$ is hydrogen bonded to both ${\alpha}42Tyr$ and ${\alpha}97Asn$ in the ${\alpha}_1{\beta}_2$ subunit interface, suggesting that the essential role of ${\beta}99Asp$ is to stabilize the deoxy-Hb by creating the intersubunit hydrogen bond. In particular, for Hb Kempsey (${\beta}99Asp{\rightarrow}Asn$), molecular dynamics simulation indicated that a new hydrogen bond involving ${\beta}99Asn$ can be induced by replacing ${\alpha}42Tyr$ with a strong hydrogen-bond acceptor such as Asp. Designed mutant recombinant (r) Hb (${\beta}99Asp{\rightarrow}Asn$, ${\alpha}42Tyr{\rightarrow}Asp$) have been produced in the Escherichia coli expression system and have shown that functional defects of Hb Kempsey could be compensated by the ${\alpha}42Tyr{\rightarrow}Asp$ substitution. However, as the ${\alpha}42 Tyr{\rightarrow}Asp$ mutation has never been reported before, it is still possible that the functional properties of r Hb (${\beta}99Asp{\rightarrow}Asn$, ${\alpha}42Tyr{\rightarrow}Asp$) may be due to the mutation itself. Thus, it is required to produce r Hb (${\alpha}42Tyr{\rightarrow}Asp$) and r Hb Kempsey (${\beta}99Asp{\rightarrow}AsnX$( as controls, and to compare their properties with those of r Hb (${\beta}99Asp{\rightarrow}Asn$, ${\alpha}42Tyr{\rightarrow}Asp$). r Hb (${\alpha}42Tyr{\rightarrow}Asp$) could not be purified because it is an unstable hemoglobin which forms Heinz bodies. r Hb Kempsey (${\beta}99Asp{\rightarrow}Asn$) exhibits very high oxygen affinity and greatly reduced cooperativity. Thus, r Hb (${\beta}99Asp{\rightarrow}Asn$) and r Hb (${\alpha}42Tyr{\rightarrow}Asp)$ compensate each other.

• 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.

• Journal of Electrochemical Science and Technology
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• v.7 no.3
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• pp.185-189
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• 2016

The coupled channel method via the Local Reflection (LORE) matrix is employed to investigate the quantum mechanical behavior of the sticking or adsorption and desorption of hydrogen (H) atom on bilayer graphene via the armchair edge. The sticking and desorption probabilities of H are calculated and are plotted against the initial translational energy of H. The sticking probability plot shows a barrierless reaction indicating that hydrogen is easily adsorbed on the armchair edge of graphene. The desorption probability plot, however, shows that desorption of H from the graphene sheets is an activated process with a barrier height of 4.19 eV suggesting that a strong bond exists between the adsorbed H atom and the edge carbon atom. Thus, temperatures higher than the operating temperatures (300 - 1500 K) of conventional fuel cells are necessary to release the adsorbed H atom from the armchair edge of graphene.

• Proceedings of the Korean Institute of Electrical and Electronic Material Engineers Conference
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• 2007.11a
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• pp.426-427
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• 2007

Here we describe the formation of a self-assembled film of thin multiwalled carbon Nanotubes(t-MWNT) modified with hydroxy groups through hydrogen peroxide treatment. Morphologies of t-MWNT films could be controlled by the various coating method, such as filtering, drop casting, spraying method, etc. The results show that on densification of the CNT suspension during drying, multiple hydroxy group-modified MWNTs can be self-assembled through strong surface hydrogen bond interaction while MWNTs usually exist an entangled state in the film. The interaction between t-MWNT was illustrated from Raman spectrum of spray coated films.

• BMB Reports
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• v.29 no.4
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• pp.380-385
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• 1996

Ovomucoid third domain is a serine proteinase inhibitor protein which consists of 56 amino acid residues. A fifty picosecond molecular dynamics (MD) simulation was carried out for ovomucoid third domain protein with 5 $\AA$ layer of water molecules. A comparison of main chain atoms in the MD averaged structure with the crystal structure showed that most of the backbone structures are maintained during the simulation. Investigation of the intramolecular hydrogen bondings indicated that most of the interactions between main chain atoms were conserved, whereas those between side chains were reorganized for the period of the simulation. Especially, the side chain interactions around the scissile bond of reactive site P1 (Met18) were found to be more extensive for the MD structures. During the simulation, hydrogen bonds were maintained between the side chains of Glu19 and Arg21 as well as those of Thr17 and Glu19. Extensive side chain interactions observed in the MD structures may shed light on the question of why protein proteinase inhibitors are strong inhibitors for proteinases rather than good substrates.

• Bulletin of the Korean Chemical Society
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• v.18 no.1
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• pp.18-23
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• 1997

Data from structure/activity studies in vir gene induction system have led to evaluate the working hypothesis of interaction between phenolic inducers and phenol binding proteins. The primary specificity in the association of a phenolic inducer with its receptor in our system is hypothesized to be the hydrogen bonding interactions through the ortho methoxy substituents as well as the proton transfer between the inducer and the binding protein. In this paper the proposed working model for phenol-mediating signal transduction was evaluated in several ways. The importance of the general acid-base catalysis was first addressed by the presence of an acidic residue and a basic residue in the phenol binding protein. Series of compounds were tested for vir gene expression activity to confirm the generation of a strong nucleophile by an acidic residue and an involvement of a basic residue as a proton acceptor. An attempt was made to correlate the pKa values of the phenolic compounds with vir gene induction activities as inducers to further support the proposed proton transfer mechanism. Finally, it was also observed that the regioselectively attached methoxy group on phenol compounds is required as the proper hydrogen bond acceptor.

• Bulletin of the Korean Chemical Society
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• v.7 no.2
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• pp.124-129
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• 1986

The effects of molecular attraction and orientations for the energy mismatch variance, vibrational energy level and double-quantum transition, in the vibration-vibration energy exchange, have been considered. The contribution of molecular attraction increases the exchange rate of the purely repulsive interaction, in general, significantly, but which becomes smaller as the temperature is increased. As the energy mismatch is increased, its contribution is also increased, but which is small. However, its contribution for the double-quantum transition is very paramount. At each orientation, the exchange rate constants have been calculated and compared with the results for rotational average, and it is found that the exchange rate is a strong function of the orientation angles of colliding molecules. We have also discussed about the system having the strong interaction such as the hydrogen bond, and it is found that for this system the preferred orientation should be considered in order to calculate the exchange rates.

• Bulletin of the Korean Chemical Society
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• v.16 no.2
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• pp.112-120
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• 1995

The conformational study on malonic acid, hydrogen malonate, malonate, malonyl methyl sulfide, and malonyl methyl sulfide anion, as the model compounds of malonyl-CoA, was carried out using the semiempirical MO methods (MNDO, AM1, and PM3) and hydration shell model. On the whole, the feasible conformations of malonic acid, hydrogen malonate, and malonate seem to be similar to each other. In malonic acid and malonate, two carboxyl groups are nearly perpendicular to the plane of the carbon skeleton, despite of different orientation of two carboxyl groups themselves. In particular, two carboxyl groups of hydrogen malonate are on the plane formed by carbon atoms with an intramolecular hydrogen bond. The calculated results on the geometry and conformation of three compounds are reasonably consistent with those of X-ray and spectroscopic experiments as well as the previous calculations. The orientation of two carbonyl groups of malonyl methyl sulfide is quite similar to that of malonic acid, but different from that of its anion. Especially, the computed probable conformations of the sulfide anion by the three methods are different from each other. The role of hydration seems not to be crucial in stabilizing the overall conformations of malonic acid, hydrogen malonate, malonate, and malonyl methyl sulfide. However, the probable conformations of the unhydrated sulfide anion obtained by the MNDO and AM1 methods become less stabilized by including hydration. The AM1 method seems to be appropriate for conformational study of malonyl-CoA and its model compounds because it does not result in the formation of too strong hydrogen bonds and significant change in conformational energy from one compound to another.