• Journal of the Korean Chemical Society
• /
• v.40 no.7
• /
• pp.509-514
• /
• 1996

The three-dimensional metal complex inclusion compound $Cd(pn)Ni(CN)_4{\cdot}0.5NO_2C_6H_5$(pn: 1,2-diaminopropane=propylenediamine) crystallizes in the orthorhombic space group, $Pn2_1$a, (a=13.868(5), b=26.591(4), c=7.840(1)${\AA}$, V=2891(1)${\AA}^3$, Z=4), R=0.054 for 2800 independent reflections. The host structure of the inclusion compound appears the same one(T-type) of inclusion compound with branched aliphatic-guest molecule. The nitrobenzeneguest molecule attains the stable position in the nodal channel of T-type by placing the polar nitro group between the pn-amino groups at the node and the bulky aromatic ring in the antinodal zone of the channel. The substituted aromatic guest molecule is accommodated in the host structure of metal complex $Cd(pn)Ni(CN)_4$ with channel cavity.

• 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.

• Biotechnology and Bioprocess Engineering:BBE
• /
• v.10 no.3
• /
• pp.212-217
• /
• 2005

Desorption/ionization on silicon mass spectrometry (DIOS-MS) is a relatively new laser desorption/ionization technique for mass spectrometry without employing an organic matrix. This present study was carried to survey the experimental factors to improve the efficiency of DIOS-MS through electrochemical etching condition in structure and morphological properties of the porous silicon. The porous structure of silicon structure and its properties are crucial for the better performance of DIOS-MS and they can be controlled by the suitable selection of electrochemical conditions. The fabrication of porous silicon and ion signals on DIOS-MS were examined as a function of silicon orientation, etching time, etchant, current flux, irradiation, pore size, and pore depth. We have also examined the effect of pre- and post-etching conditions for their effect on DIOS-MS. Finally, we could optimize the electrochemical conditions for the efficient performance of DIOS-MS in the analysis of small molecule such as amino acid, drug and peptides without any unknown noise or fragmentation.

• Journal of the Korean Magnetics Society
• /
• v.26 no.4
• /
• pp.119-123
• /
• 2016

We have studied electronic and magnetic structure of cubane-type Cu magnetic molecule using density functional method. The calculated density of states show that Cu has 3d $x^2-y^2$ hole orbital because of short distances between Cu atom and in-plane 4 ligand atoms. The calculated total energy with in-plane antiferromagnetic spin configuration is lower than those of ferromagnetic configurations. The calculated exchange interaction J between in-plane Cu atoms is much larger than those between out-plane Cu atoms, since the $x^2-y^2$ hole orbital ordering of Cu 3d orbitals induces strong super-exchange interaction between in-plane Cu atoms.

• Bulletin of the Korean Chemical Society
• /
• v.24 no.6
• /
• pp.805-808
• /
• 2003

Fundamental ideas of the free energy gradient method are briefly reviewed with three applications: the stable structures of glycine and ammonia-water molecule pair in aqueous solution and the transition state (TS) structure of a Menshutkin reaction $NH_3 + CH_3Cl → CH_3NH_3^+ + Cl^-$ in aqueous solution, which is the first example of full TS optimization of all internal degrees of freedom.

• Bulletin of the Korean Chemical Society
• /
• v.34 no.12
• /
• pp.3749-3754
• /
• 2013

Two 3D isomorphous and isostructural complexes, namely, $[Zn(BDOA)(bpy)(H_2O)_2]_n$ (1) and $[Cd(BDOA)-(bpy)(H_2O)_2]_n$ (2); (BDOA = Benzene-1,4-dioxyacetic acid, bpy = 4,4'-bipyridine) were synthesized under hydrothermal conditions and characterized by means of elemental analyses, thermogravimetric (TG), infrared spectrometry, and single crystal X-ray diffraction. Complexes 1 and 2 crystallize in the triclinic system, space group P-1 and each metal ion in the complexes are six-coordinated with the same coordination environment. In the as-synthesized complexes, $BDOA^{2-}$ anions link central metal ions to form a 1D zigzag chain $[-BDOA^{2-}-Zn(Cd)-BDOA^{2-}-Zn(Cd)-]_{\infty}$, whereas bpy pillars connect metal ions to generate a 1D linear chain $[-bpy-Zn(Cd)-bpy-Zn(Cd)-]_{\infty}$. Both infinite chains are interweaved into 2D grid-like layers which are further constructed into a 3D open framework, where hydrogen bonds play as the bridges between the adjacent 2D layers. Luminescent properties of complex 1 showed selectivity for $Hg^{2+}$ ion.

• Molecules and Cells
• /
• v.37 no.8
• /
• pp.592-597
• /
• 2014

The cell membrane provides critical cellular functions that rely on its elaborate structure and organization. The structure of turtle membranes is an important part of an ongoing study of erythrocyte membranes. Using a combination of atomic force microscopy and single-molecule force spectroscopy, we characterized the turtle erythrocyte membrane structure with molecular resolution in a quasi-native state. High-resolution images both leaflets of turtle erythrocyte membranes revealed a smooth outer membrane leaflet and a protein covered inner membrane leaflet. This asymmetry was verified by single-molecule force spectroscopy, which detects numerous exposed amino groups of membrane proteins in the inner membrane leaflet but much fewer in the outer leaflet. The asymmetric membrane structure of turtle erythrocytes is consistent with the semi-mosaic model of human, chicken and fish erythrocyte membrane structure, making the semi-mosaic model more widely applicable. From the perspective of biological evolution, this result may support the universality of the semi-mosaic model.

• Proceedings of the Korean Vacuum Society Conference
• /
• 2013.02a
• /
• pp.280-280
• /
• 2013

Using both experimentaland theoretical methods, we have investigated the structural and electronic properties of self-assembled two-dimensional organic molecule (hexaaza-triphenylene-hexacarbonitrile, HATCN), which is used as an efficient OLED hole injection material, on Au(111) surfaces. Low-temperature scanning tunneling microscope (STM) measurements revealed that self-assembled linear and hexagonal porous structures are formed at atomic steps and terraces of Au(111), respectively. We also found that the hexagonal porous structure have chirality and forms only small (＜1,000 nm2) phase-separated chiral domains that can easily change their chiral phase in subsequence STM images at 80 K. To explain these observations, we calculated the molecular-molecular and molecule-surface interaction energies by using first-principles density functional theory method. We found that the change of their chiral phase resulted from the competition between the two energies. These results have not only verified our experimental observations, but also revealed the delicate balance between different interactions that caused the self-assembed structures at the surface.

• Bulletin of the Korean Chemical Society
• /
• v.12 no.2
• /
• pp.178-181
• /
• 1991

The crystal structure of dehydrated fully $Cd^{2+}$-exchanged zeolite A evacuated at $2{\times}10^{-6}$ Torr and $450^{\circ}C (a = 12.225(2){\AA})$ and of its ethylene sorption complex (a = 12.219(2) ${\AA}$) have been determined by single crystal X-ray diffraction techniques in the cubic space group Pm3m at $21(1)^{\circ}$. The structures were refined to final error indices, $R_1$ = 0.063 and $R_2$ = 0.065 with 266 reflections and $R_1$ = 0.055 and $R_2$ = 0.062 with 260 reflections, respectively, for which $I{\gg}3{\sigma}(I)$. In both structures, six $Cd^{2+}$ ions lie at two distinguished three-fold axes of unit cell. Dehydrated $Cd_6$-A sorbs 4 ethylene molecules per unit cell at $25^{\circ}C$ (vapor pressure of ethylene is ca. 100 Torr). Each $Cd^{2+}$ ion forms a lateral ${pi}$ complex with an ethylene molecule. Four $Cd^{2+}$ ions exist in a nearly tetrahedral environment, 2.210(7)${\AA}$ apart from three framework oxygen ions (considering ethylene molecule as a monodentate ligand) and $2.67(6){\AA}$ from each carbon atom of ethylene molecule.

• Proceedings of the Korean Society for Technology of Plasticity Conference
• /
• 1999.03b
• /
• pp.173-178
• /
• 1999

In this study MD simulations have been performed to observe the behavior of a grain boundary in an a-Fe plate under 2-dimensional loading. In MD simulation the acceleration of every molecule can be achieved from the potential energy and the force interacting between each molecule and the integration of the motion equation by using Verlet method gives the displacement of each molecule. Initially four a-Fe rectangular plates having different misorientation angles of grain boundary were modeled by using the Johnson potential and Morse potential We compared the potential energy of the grain boundary system with that of the perfect structure model. Also we could obtain the width of the grain boundary by investigating the local potential energy distribution. The tensile loading for each grain boundary models was applied and the behavior of grin boundary was studied. From this study it was clarified that in the case using Johnson potential the obvious fracture mechanism occurs along the grain boundary in the case of Morse potential the diffusion of the grain boundary appears instead of the grain boundary fracture.