• Bulletin of the Korean Chemical Society
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• v.32 no.12
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• pp.4195-4198
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• 2011

Intramolecular ${\pi}-{\pi}$ and ${\sigma}-{\pi}$ interactions are omnipresent for numerous energetic and structural phenomena in nature, and the exact description of these nonbonding interactions plays an important role in the accurate prediction of the three-dimensional structures for numerous interesting molecular systems such as protein folding and polymer shaping. We have selected two prototype molecular systems for benchmarking calculations of intramolecular ${\pi}-{\pi}$ and ${\sigma}-{\pi}$ interactions. Accurately describing conformational energy of such systems requires highly elaborate but very expensive ab initio methods such as coupled cluster singles, doubles, and (triples) (CCSD(T)). Our calculations reveal a double hybrid density functional incorporating dispersion correction (B2PLYP-D) that agrees excellently with the CCSD(T) results, indicating that B2PLYP-D can serve as a practical method of choice.

• Bulletin of the Korean Chemical Society
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• v.35 no.9
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• pp.2679-2683
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• 2014

Mechanisms underlying the impacts of interactions between carbon nanoparticles (CNPs) and ionic liquids (ILs) on the physicochemical behavior of CNPs need to be more full worked out. This manuscript describes a theoretical investigation at multiple levels on the interactions of fullerene $C_{60}$ with 21 imidazolium-based ILs of varying alkyl side chain lengths and anionic types and their impacts on $C_{60}$ dispersion behavior. Results show that ${\pi}$-cation interaction contributed to mechanism of the $C_{60}$-IL interaction more than ${\pi}$-anion interaction. The calculated interaction energy ($E_{INT}$) indicates that $C_{60}$ can form stable complex with each IL molecule. Moreover, the direction of charge transfer occurred from IL to $C_{60}$ during the $C_{60}$-IL interaction. Quantitative models were developed to evaluate the self-diffusion coefficient of $C_{60}$ ($D_{fullerene}$) in bulk ILs. Three interpretative molecular descriptors (heat of formation, $E_{INT}$, and charge) that describe the $C_{60}$-IL interactions and the alkyl side chain length were found to be determinants affecting $D_{fullerene}$.

• Journal of the Korean Magnetic Resonance Society
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• v.2 no.2
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• pp.152-157
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• 1998

The diversity of RNA functions ranges from storage and propagation of genetic information to enzymatic activity during RNA processing and protein synthesis. This diversity of functions requires an equally diverse arrays of structures, and, very often, the formation of functional RNA-protein complexes. Recognition of specific RNA signals by RNA-binding proteins is central to all aspects of post-transcriptional regulation of gene expression. We will describe how NMR is being used to understand at the atomic level how these important biological processes occur.

• Bulletin of the Korean Chemical Society
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• v.32 no.1
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• pp.347-349
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• 2011

• YAKHAK HOEJI
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• v.35 no.6
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• pp.461-465
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• 1991

Silica-based gel filtration chromatography has been used to characterize molecular weight of proteins. However, the molecular weight measured by this method was distorted by protein-silica interactions like hydrophobic and electrostatic forces. Therefore, we characterized protein-silica interaction using two forms of phytochrome (124 kDa) having different hydrophobicity and surface charge. PH and ionic strength affected the retention time of phytochrome suggesting that electrostatic force is the major interaction between protein and silica surface.

• Proceedings of the KSME Conference
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• 2004.04a
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• pp.537-541
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• 2004

Molecular dynamics simulation of nanolithography by AFM is conducted to study nucleation of various defects, and their subsequent development and interactions as well. During nanolithography via AFM, dislocation loops are emitted along the top surface, and resourceful defect interactions such as, formation of voids chain via the motion of a jog, and creations of extended nodes and Lomer-Cottrell Lock are observed.

• Bulletin of the Korean Chemical Society
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• v.32 no.1
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• pp.162-168
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• 2011

Many ligands have been experimentally designed and tested for their activities as inhibitors against bacterial enoyl-ACP reductase (FabI), ENR. Here the binding energies of the reported ligands with the E. coli ENR-$NAD^+$ were calculated, analyzed and compared, and their molecular dynamics (MD) simulation study was performed. IDN, ZAM and AYM ligands were calculated to have larger binding energies than TCL and IDN has the largest binding energy among the considered ligands (TCL, S54, E26, ZAM, AYM and IDN). The contribution of residues to the ligand binding energy is larger in E. coli ENR-NAD+-IDN than in E. coli ENR-$NAD^+$-TCL, while the contribution of $NAD^+$ is smaller for IDN than for TCL. The large-size ligands having considerable interactions with residues and $NAD^+$ have many effective functional groups such as aromatic $\pi$ rings, acidic hydroxyl groups, and polarizable amide carbonyl groups in common. The cation-$\pi$ interactions have large binding energies, positively charged residues strongly interact with polarisable amide carbonyl group, and the acidic phenoxyl group has strong H-bond interactions. The residues which have strong interactions with the ligands in common are Y146, Y156, M159 and K163. This study of the reported inhibitor candidates is expected to assist the design of feasible ENR inhibitors.

• Bulletin of the Korean Chemical Society
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• v.31 no.3
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• pp.595-598
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• 2010

Ab initio and DFT molecular orbital calculations predict that acetyl radical reacts with acetylene through interactions primarily involving the SOMO of the radical and the in-plane ${\pi}$-bond of acetylene. An energy barrier (${\Delta}E_1$) of 39.6 kJ $mol^{-1}$ is predicted for the preferred anti arrangement of reactants at the CCSD(T)/cc-pVDZ//BHandHLYP/cc-pVDZ level of theory. NBO analysis reveals additional interactions between the radical SOMO and the nearby C-H ${\sigma}$-bond in acetylene worth about 10% of the total transition state interaction energy. This type of orbital interaction has not previously been observed in radical addition reactions involving C-C ${\pi}$-bonds.

• Biotechnology and Bioprocess Engineering:BBE
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• v.11 no.4
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• pp.357-363
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• 2006

Monolithic molecularly imprinted columns were designed and prepared by an in-situ thermal-initiated copolymerization technique for rapid separation of tryptophan and N- CBZ-phenylalanine enantiomers. The influence of polymerization conditions and separation conditions on the specific molecular recognition ability for enantiomers and diastereomers was investigated. The specious molecular recognition was found to be dependent on the stereo structures and the arrangement of functional groups of the imprinted molecule and the cavities in the molecularly imprinted polymer (MIP). Moreover, hydrogen bonding interactions and hydrophobic interactions played an important role in the retention and separation. Compared to conventional MIP preparation procedures, the present method is very simple, and its macroporous structure has excellent separation properties.

• BMB Reports
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• v.43 no.6
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• pp.389-399
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• 2010

Fertilization is a complex process comprised of numerous steps. During fertilization, two highly specialized and differentiated cells (sperm and egg) fuse and subsequently trigger the development of an embryo from a quiescent, arrested oocyte. Molecular interactions between the sperm and egg are necessary for regulating the developmental potential of an oocyte, and precise coordination and regulation of gene expression and protein function are critical for proper embryonic development. The nematode Caenorhabditis elegans has emerged as a valuable model system for identifying genes involved in fertilization and the oocyte-to-embryo transition as well as for understanding the molecular mechanisms that govern these processes. In this review, we will address current knowledge of the molecular underpinnings of gamete interactions during fertilization and the oocyte-to-embryo transition in C. elegans. We will also compare our knowledge of these processes in C. elegans to what is known about similar processes in mammalian, specifically mouse, model systems.