• Bulletin of the Korean Chemical Society
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• v.21 no.10
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• pp.959-968
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• 2000

Direct reaction of elemental silicon with a mixture of (dichloromethyl)silanes 1 $[Cl_3-nMenSiCHCl_2:$ n = 0 (a), n = 1(b), n = 2(c), n = 3(d)] and hydrogen chloride has been studied in the presence of copper catalyst using a stirred bed reactor equ ipped with a spiral band agitator at various temperatures from $240^{\circ}C$ to $340^{\circ}C.$ Tris(si-lyl) methanes with Si-H bonds, 3a-d $[Cl_3-nMenSiCH(SiHCl_2)_2]$, and 4a-d $[Cl_3-nMenSiCH(SiHCl_2)(SiCl_3)]$, were obtained as the major products and tris(silyl)methanes having no Si-H bond, 5a-d $[Cl_3-nMenSiCH(SiCl_3)_2]$, as the minor product along with byproducts of bis(chlorosilyl)methanes, derived from the reaction of silicon with chloromethylsilane formed by the decomposition of 1. In addition to those products, trichlorosilane and tetra-chlorosilane were produced by the reaction of elemental silicon with hydrogen chloride. The decomposition of 1 was suppressed and the production of polymeric carbosilanes reduced by adding hydrogen chloride to 1. Cad-mium was a good promoter for and the optimum temperature for this direct synthesis was $280^{\circ}C$.

• Journal of the Korean Chemical Society
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• v.65 no.2
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• pp.106-112
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• 2021

12 kinds of (-)-catechin derivatives were designed and synthesized. The catechin derivatives were evaluated their antioxidant activities using DPPH method. Most of them showed good antioxidant activity, particularly compounds 1d, 1e and 1j exhibited more activity than butylated hydroxytoluene (BHT). Molecular docking studies for compounds 1d, 1e and 1j with STAT1 showed not only sufficent characteristics binding cavity but also agreement with the observed biological activity. Acording to docking results, the compounds showed greater than hydrogen bonding, hydrophobic interactions, electrostatic interactions, and Van der Waals interactions as compared to the reference compound. They formed hydrogen bonds with important residues such as Lys566, His568, Leu570, and Phe644. The compounds showed a novel hydrogen bonding interaction with Arg649, which was not reported previously. Our results might suggest the compounds could serve as a novel anti-oxidant agent.

• Journal of the Korean Chemical Society
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• v.63 no.1
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• pp.29-36
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• 2019

A potentially tetradentate Schiff base ligand, 2-((2-((pyridin-2-ylmethylene)amino)ethyl)amino)ethan-1-ol (PMAE), and its cadmium(II) complex, [$Cd(PMAE)I_2$] (1), were prepared and characterized by elemental analysis, FT-IR, Raman, $^1H$ and $^{13}C$ NMR spectroscopies and single-crystal X-ray diffraction. In the crystal structure of 1, the cadmium atom has a slightly distorted square-pyramidal geometry and a $CdN_3I_2$ environment in which the PMAE acts as an $N_3$-donor. In the crystal packing of the complex, the alcohol and amine groups of the coordinated ligands participate in hydrogen bonding with iodide ions and form $R^2{_2}(14)$ and $R^2{_2}(8)$ hydrogen bond motifs, respectively. In addition to the hydrogen bonds, the crystal network is stabilized by ${\pi}-{\pi}$ stacking interactions between pyridine rings. The thermodynamic stability of the isolated ligand and its cadmium complex along with their charge distribution patterns were studied by DFT and NBO analysis.

• Bulletin of the Korean Chemical Society
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• v.7 no.5
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• pp.331-334
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• 1986

The crystal structure of thiamin tetrahydrofurfuryl disulfide, one of the ring-opened derivatives of thiamin, has been determined by the X-ray diffraction methods. The crystal is monoclinic with cell dimensions of a = 8.704 (1), b = 11.207 (2), c = 21.260 (3) ${\AA}$ and ${\beta}$ = 92.44 (2)$^{circ}$, space group P2$_{1}$/c and Z = 4. The structure was solved by direct methods and refined to R = 0.076 for 1252 observed reflections measured on a diffractometer. The molecule assumes a folded conformation in which the pyrimidine and the tetrahydrofurfuryl rings are on the same side of the ethylenic plane. The pyrimidinyl, N-formyl and ethylenic planes are mutually perpendicular to each other and the N(3)-C(4) bond retains a single bond character. The structure is stabilized by an intramolecular N(4'${\alpha})-H{\cdots}O(2{\alpha}$) hydrogen bond. The molecules are connected via N(4'${\alpha}$)-H{\cdots}(N3')$ and O(5${\gamma})-H{\cdots}(N1')$ hydrogen bonds, forming a two-dimensional hydrogen-bonding network. The tetrahydrofurfuryl ring is dynamically disordered. The overall conformation as well as the packing mode is very similar to that of thiamin propyl disulfide.

• Current Optics and Photonics
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• v.6 no.3
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• pp.337-343
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• 2022

Microfluidic chips are new devices that can manipulate liquids at the micrometer level, and terahertz (THz) time-domain spectroscopy has good applicability in biochemical detection. The combination of these two technologies can shorten the distance between sample and THz wave, reduce THz wave absorption by water, and more effectively analyze the kinetics of biochemical reactions in aqueous solutions. This study investigates the effects of different external magnetic field intensities on the THz transmission characteristics of deionized water, CuSO₄, CuCl₂, (CH₃COO)₂Cu, Na₂SO₄, NaCl, and CH₃COONa; the THz spectral intensity of the sample solutions decrease with increasing intensity of the applied magnetic field. Analysis shows that the magnetic field leads to a change in the dipole moment of water molecules in water and electrolyte solutions, which enhances not only the hydrogen-bond networking ability of water but also the hydration around ions in electrolyte solutions, increasing the number of hydrogen bonds. Increasing the intensity of this magnetic field further promotes the hydrogen-bond association between water molecules, weakening the THz transmission intensity of the solution.

• Journal of the Korean Chemical Society
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• v.21 no.5
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• pp.330-338
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• 1977

In order to elucidate the plastic deformation of solids, the following assumptions were made: (1) the plastic deformation of solids is classified into two main types, the one which is caused by dislocation movement and the other caused by grain boundary movement, each movement being restricted on a different shear surface, (2) the dislocation movement is expressed by a mechanical model of a parallel connection of various kinds of Maxwell dislocation flow units whereas the grain boundary movement is also expressed by a parallel connection of various kinds of Maxwell grain boundary flow units; the parallel connection in each type of movements indicates that all the flow units on each shear surface flow with the same shear rate, (3) the latter model for grain boundary movement is connected in series to the former for dislocation movement, this means physically that the applied stress distributes homogeneously in the flow system while the total strain rate distributes heterogeneously on the two types of shear planes (dislocation or grain boundary shear plane), (4) the movement of dislocation flow units and grain boundary units becomes possible when the atoms or molecules near the obstacles, which hinder the movement of flow units, diffuse away from the obstacles.Using the above assumptions in conjunction with the theory of rate processes, generalized equations of shear stress and shear rate for plastic deformation were derived. In this paper, four cases important in practice were considered.ted N${\cdot}{\cdot}{\cdot}$O hydrogen bond and the second of two normal N${\cdot}{\cdot}{\cdot}$O hydrogen bonds, both of which exist between the amino group and the perchlorate, groups. A p-phenylenediamine group is approximately planar within an experimental error and bonded to twelve perchlorates: ten perchlorates forming hydrogen bonds and two being contacted with the van der Waals forces. A perchlorate group is surrounded by six p-phenylenediamines and four perchlorates; among the six p-phenylenediamines, five of them are hydrogen-bonded, and the rest contacted with the van der Waals force.

• Journal of the Korean Chemical Society
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• v.25 no.6
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• pp.343-350
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• 1981

The crystal and molecular structure of P-aminobenzaldehyde cyclohexylthiosemicarbazone, C14H20N4S, has been determined from 2712 integrated intensities measured on a computer controlled four circle diffractometer with monochromated $CuK_{\alpha}$, X-ray radiation. The crystals are monoclinic, space group C2/c with eight molecules in a unit cell of dimensions, a = 12.488(2), b = 12.276(4), c = 19.997(6)${\AA}$ and ${\beta}=103.55(3)^{\circ}$. The structure was solved by Patterson and Fourier method and refined by a full-matrix least squares method to a final R value of 0.058 for all reflections. The C(8)-S bond is trans to N(2)-N(3) and C(8)-N(1) is cis to N(2)-N(3) bond. The cyclohexane ring has chair conformation and makes an angle of $40.7^{\circ}$ with the benzene ring. The molecules are linked by N(2)H…S hydrogen bonds into dimer-like units which are held together by $N-H{\ldots}N$ hydrogen bonds. Sulfur accepts second rather weak hydrogen bond from N(4). An intramolecular hydrogen bond exists between N(1) and N(3) atoms.

• Journal of the Korean Chemical Society
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• v.18 no.5
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• pp.329-340
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• 1974

Sulfadiazine, $C_{10}H_{10}N_4O_2S$, forms monoclinic crystals of space group $P21}c$ from a mixture of acetone and ethanol with $a=13.71{\pm}0.04,\;b=5.84{\pm}0.03,\;c=15.11{\pm}0.05{\AA},\;{\beta}=115.0{\pm}0.3^{\circ}$, and four molecules per cell. Three dimensional photographic data were collected with $CuK\alpha$ radiation. The structure was determined using Patterson and Fourier synthesis methods and refined by block diagonal least-squares methods with isotropic thermal parameter for all non-hydrogen atoms. The final R value was 0.15 for the 1517 observed independent reflections. The dihedral angle between the planes through the benzene ring and the pyrimidine ring is $76^{\circ}$. The conformational angle formed by the projection of the S-C(5) bond with that of N(1)-C(1) where the projection is taken along the S-N(1) bond is $77^{\circ}$. The imino nitrogen atom, N(1), and pyrimidine nitrogen atom, N(3), form intermolecular $N-H{\cdots}N$ hydrogen bond between the molecules related by center of symmetry. Amino nitrogen atom, N(4), forms two intermolecular $N-H{\cdots}O$ hydrogen bonds, with O(1) and O(2) atoms of different molecules separated by b. A two dimensional network of hydrogen bonds form infinite molecular sheets parallel to the (100) plane. Adjacent sheets are bound together by van der Waals forces.

• Journal of the Korean Chemical Society
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• v.57 no.4
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• pp.447-454
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• 2013

In this research, two new complexes of N-(2-aminoethyl)-1,3-propanediamine (aepn), $[Cd(aepn)_2]I_2$ (1) and $[Cd(aepn)_2]Cl_2{\cdots}H_2O$ (2), were prepared and identified by elemental analysis, FT-IR, Raman spectroscopy and single-crystal X-ray diffraction. Geometry around the cadmium atom in two complexes by coordination of six nitrogen atoms of two aepn is distorted octahedral. If distortion in the mer-$[Cd(aepn)_2]^{2+}$ cation is disregarded, it has a $C_2$ axis and $C_2$ symmetry. The cyclic voltammetry experiments were carried out to study the complexation process. Two structural surveys on coordination modes and complexes of aepn are presented. A study was carried out using CSD data to estimate the averages of bond lengths for different types of the Cd-N bonds. It was found that the intermolecular $N-H{\cdots}I$, $C-H{\cdots}I$ hydrogen bonds in 1 and $N-H{\cdots}Cl$, $N-H{\cdots}O$, $C-H{\cdots}O$, $O-H{\cdots}Cl$ in 2 stabilized the crystal networks.

• International Journal of Control, Automation, and Systems
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• v.4 no.3
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• pp.382-393
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• 2006

Mechanical system dynamics plays an important role in the area of computational structural biology. Elastic network models (ENMs) for macromolecules (e.g., polymers, proteins, and nucleic acids such as DNA and RNA) have been developed to understand the relationship between their structure and biological function. For example. a protein, which is basically a folded polypeptide chain, can be simply modeled as a mass-spring system from the mechanical viewpoint. Since the conformational flexibility of a protein is dominantly subject to its chemical bond interactions (e.g., covalent bonds, salt bridges, and hydrogen bonds), these constraints can be modeled as linear spring connections between spatially proximal representatives in a variety of coarse-grained ENMs. Coarse-graining approaches enable one to simulate harmonic and anharmonic motions of large macromolecules in a PC, while all-atom based molecular dynamics (MD) simulation has been conventionally performed with an aid of supercomputer. A harmonic analysis of a macroscopic mechanical system, called normal mode analysis, has been adopted to analyze thermal fluctuations of a microscopic biological system around its equilibrium state. Furthermore, a structure-based system optimization, called elastic network interpolation, has been developed to predict nonlinear transition (or folding) pathways between two different functional states of a same macromolecule. The good agreement of simulation and experiment allows the employment of coarse-grained ENMs as a versatile tool for the study of macromolecular dynamics.