• Journal of the Semiconductor & Display Technology
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• v.8 no.2
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• pp.55-58
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• 2009

Density functional theory was used to investigate the adsorption and reaction of $HfCl_4$ with two hydroxyls on Si (001)-$2{\times}1$ surface in atomic layer deposition (ALD) process. We prepared a reasonable Si substrate which consisted of six inter-dimer dissociated $H_2O$ molecules and two intra-dimer dissociated $H_2O$ molecules. The $HfCl_4$must react with two hydroxyls to be a bulk-like structure. When $HfCl_4$ was adsorbed on a hydroxyl, there was energy benefit of -0.55 eV. Though there was energy loss for $HfCl_4$ to react with H of hydroxyl, thermal energy of ALD chamber would be enough to pass the energy barriers. There were five reaction pathways for $HfCl_4$ to react with two hydroxyls; inter-dimer, intra-dimer, cross-dimer, inter-row, and cross-row. Inter-row, inter-dimer and intra-dimer were relatively favorable among the five reaction pathways based on the energy difference. The electron densities between O and Hf in these three reactions were higher than the others and they had shorter Hf-O and O-O bond lengths than the other two reaction pathways.

• Bulletin of the Korean Chemical Society
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• v.31 no.6
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• pp.1681-1688
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• 2010

Density functional theory was adopted to study the various surface products and their reaction channels focusing on the on-dimer configuration which has not been suggested before. Energetic results show that the most stable on-dimer configuration is the 6,6-[2+2] structure which resembles the typical [2+2] cycloaddition product. The 6,6-[2+2] product is also more stable than any other possible surface structures of inter-dimer configuration further suggesting its existence. Potential energy surface scan along various possible initial surface reactions show that some of the possible on-dimer surface products require virtually no reaction barrier indicating that initial population of on-dimer surface products is thermodynamically determined. Various surface isomerization reaction channels exist further facilitating thermal redistribution of the initial surface products.

• Bulletin of the Korean Chemical Society
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• v.31 no.12
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• pp.3579-3582
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• 2010

We studied the reaction of tri-methylaluminum (TMA) on hydroxyl (OH)-terminated Si (001) surfaces for the initial growth of aluminum oxide thin-films using density functional theory. TMA was adsorbed on the oxygen atom of OH due to the oxygen atom’s lone pair electrons. The adsorbed TMA reacted with the hydrogen atom of OH to produce a di-methylaluminum group (DMA) and methane with an energy barrier of 0.50 eV. Low energy barriers in the range of 0 - 0.11 eV were required for DMA migration to the inter-dimer, intra-dimer, and inter-row sites on the surface. A unimethylaluminum group (UMA) was generated at each site with low energy barriers in the range of 0.21 - 0.25 eV. Among the three sites, the inter-dimer site was the most probable for UMA formation.

• Transactions on Electrical and Electronic Materials
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• v.11 no.1
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• pp.11-14
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• 2010

The interaction of -$Al(CH_3)_2$ with -OH on a fully OH-terminated Si (001) surface was studied using density functional theory. Two sites for $Al(CH_3)_3$ to react with the -OH on the surface were identified. The $-Al(CH_3)_2$ product energetically favored the dimer-row site rather than the inter-row site because the Al atom of $-Al(CH_3)_2$ at the dimer-row site was attracted by the lone pair electrons of the O atom in the neighboring -OH. The energy barrier for the transfer of the $-Al(CH_3)_2$ between the two sites was 0.11 eV, and therefore, the $-Al(CH_3)_2$ at the inter-row site can easily transfer to the dimer-row site at room temperature.

• Korean Journal of Materials Research
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• v.20 no.9
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• pp.457-462
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• 2010

Adsorption of a water molecule on a Si (001) surface and its dissociation were studied using density functional theory to study the distribution of -OH fragments on the Si surface. The Si (001) surface was composed of Si dimers, which buckle in a zigzag pattern below the order-disorder transition temperature to reduce the surface energy. When a water molecule approached the Si surface, the O atom of the water molecule favored the down-buckled Si atom, and the H atom of the water molecule favored the up-buckled Si atom. This is explained by the attractions between the negatively charged O of the water and the positively charged down-buckled Si atom and between the positively charged H of the water and the negatively charged up-buckled Si atom. Following the adsorption of the first water molecule on the surface, a second water molecule adsorbed on either the inter-dimer or intra-dimer site of the Si dimer. The dipole-dipole interaction of the two adsorbed water molecules led to the formation of the water dimer, and the dissociation of the water molecules occurred easily below the order-disorder transition temperature. Therefore, the 1/2 monolayer of -OH on the water-terminated Si (001) surface shows a regular distribution. The results shed light on the atomic layer deposition process of alternate gate dielectric materials, such as $HfO_2$.

• Bulletin of the Korean Chemical Society
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• v.29 no.1
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• pp.122-126
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• 2008

The magnetic properties of the organic/inorganic hybrid copper-methylenediphosphonate, Cu2(O3PCH2PO3) were examined by performing the spin dimer analysis based on the extended Hckel tight binding method. In Cu2(O3PCH2PO3) the CuO3 chains made up of edge-sharing CuO5 square pyramidal units are inter-linked by O-P-O bridges. The Cu-O-Cu superexchange interactions of the CuO3 chains are negligibly weak compared with the Cu-O…O-Cu super-superexchange interactions that occur between the CuO3 chains. The spin exchange interactions of Cu2(O3PCH2PO3) are dominated by three super-superexchange interactions, which leads to a three-dimensional antiferromagnetic spin lattice. The strongest spin exchange interactions form isolated spin dimers, which suggests that, to a first approximation, the magnetic properties can be described in terms of an isolated spin dimer model.

• Journal of the Korean Chemical Society
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• v.48 no.3
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• pp.229-235
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• 2004

For the study of hydrogen bonding phenomenon of high energetic compounds, we have been carried out a theoretical calculations for the nitromethane with the program Gaussian-98. The calculations at levels of restricted BLYP/6-311++G(d,p), B3LYP/6-311++G(d,p) and MP2/6-311++G have been performed to obtain molecular structures, hydrogen bonding effects and vibrational spectra of nitromethane monomer and dimer. The results show nitromethane is favored to make two hydrogen bonds between molecules and the nitromethane dimer is more stable than the monomer about 15.2, 19.4 and 32.6 kJ/mol for the BLYP, B3LYP, and MP2 level calculations, respectively.

• Proceedings of the Korean Magnetic Resonance Society Conference
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• 2002.08a
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• pp.90-90
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• 2002

Syndecans, transmembrane heparan sulfate proteoglycans, are coreceptors with integrin in cell adhesion process. It forms a ternary signaling complex with protein kinase C and phosphatidylinositol 4,5 bisphosphate (PIP2) for integrin signaling. NMR data indicates that cytoplasmic domain of syndecan-4 (4L) undergoes a conformational transition in the presence of PIP2, forming oligomeric conformation. The structure based on NMR data demonstrated that syndecan-4L itself forms a compact intertwined symmetric dimer with an unusual clamp shape for residues Leu$^{186}$ -Ala$^{195}$ . The molecular surface of the syndecan-4L dimer is highly positively charged. In addition, no inter-subunit NOEs in membrane proximal amino acid resides (Cl region) has been observed, demonstrating that the Cl region is mostly unstructured in syndecan-4L dimmer. However, the complex structure in the presence of PIP2 induced a high order multimeric conformation in solution. In addition, phosphorylation of cytoplasmic domain induces conformational change of syndecan-4, resulting inhibition of PKC signaling. The NMR structural data strongly suggest that PIP2 promotes oligomerization of syndecan-4 cytoplasmic domain for PKC activation and further induces structural reorganization of syndecan for mediating signaling network in cell adhesion procedure.

• Journal of Microbiology and Biotechnology
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• v.22 no.12
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• pp.1724-1730
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• 2012

An ${\alpha}$-L-arabinofuranosidase (TmAFase) from Thermotoga maritima MSB8 is a highly thermostable exo-acting hemicellulase that exhibits a relatively higher activity towards arabinan and arabinoxylan, compared with other glycoside hydrolase 51 family enzymes. In the present study, we carried out the enzymatic characterization and structural analysis of TmAFase. Tight domain associations found in TmAFase, such as an inter-domain disulfide bond (Cys306 and Cys476) in each monomer, a novel extended arm (amino acids 374-385) at the dimer interface, and total 12 salt bridges in the hexamer, may account for the thermostability of the enzyme. One of the xylan binding determinants (Trp96) was identified in the active site, and a region of amino acids (374-385) protrudes out forming an obvious wall at the substrate-binding groove to generate a cavity. The altered cavity shape with a strong negative electrostatic distribution is likely related to the unique substrate preference of TmAFase towards branched polymeric substrates.