• International Journal of Automotive Technology
• /
• v.7 no.2
• /
• pp.121-128
• /
• 2006

The interaction between adherent molecules and gas molecules was modeled in the molecular scale and simulated by the molecular dynamics method in order to understand evaporation and removal processes of adherent molecules on metallic surface using high temperature gas flow. Methanol molecules were chosen as adherent molecules to investigate effects of adhesion quantity and gas molecular collisions because the industrial oil has too complex structures of fatty acid. Effects of adherent quantity, gas temperature, surface temperature and adhesion strength for the evaporation rate of adherent molecules and the molecular removal mechanism were investigated and discussed in the present study. Evaporation and removal rates of adherent molecules from metallic surface calculated by the molecular dynamics method showed the similar dependence on the surface temperature shown in the experimental results.

• Macromolecular Research
• /
• v.16 no.8
• /
• pp.686-694
• /
• 2008

We studied the molecular shapes and structural characteristics of a 33-armed, star polystyrene (PS-33A) and two $3^{rd}$-generation, dendrimer-like, star-branched poly(methyl methacrylate)s with different architectures (pMMA-G3a and PMMA-3Gb) and 32 end-branches under good solvent and theta ($\Theta$) solvent conditions by using synchrotron small angle X-ray scattering (SAXS). The SAXS analyses were used to determine the structural details of the star PS and dendrimer-like, star-branched PMMA polymers. PS-33A had a fuzzy-spherical shape, whereas PMMA-G3a and PMMA-G3b had fuzzy-ellipsoidal shapes of similar size, despite their different chemical architectures. The star PS polymer's arms were more extended than those of linear polystyrene. Furthermore, the branches of the dendrimer-like, star-branched polymers were more extended than those of the star PS polymer, despite having almost the same number of branches as PS-33A. The differences between the internal chain structures of these materials was attributed to their different chemical architectures.

• Journal of Microbiology
• /
• v.39 no.3
• /
• pp.149-153
• /
• 2001

The electron transfer reaction is one of the most essential processes of life. Not only does it provide the means of transforming solar and chemical energy into a utilizable form for all living organisms, it also extends into a range of metabolic processes that support the life of a cell. Thus, it is of great interest to understand the physical basis of the rates and reduction potentials of these reactions. To identify the major determinants of reduction potentials in redox proteins, we have chosen the simplest electron transfer protein, rubredoxin, a small (52-54 residue) iron-sulfur protein family, widely distributed in bacteria and archaea. Rubredoxins can be grouped into two classes based on the correlation of their reduction potentials with the identity of residue 44; those with Ala44 (ex: Pyrococcus furiosus) have reduction potentials that are ∼50 mV higher than those with Va144 (ex: Clostridium pasteurianum). Based on the crystal structures of rubredoxins from C. pasteurianum and P. furiosus, we propose the identity of residue 44 alone determines the reduction potential by the orientation of the electric dipole moment of the peptide bond between 43 and 44. Based on 1.5 $\AA$ resolution crystal structures and molecular dynamics simulations of oxidized and reduced rubredoxins from C. pasteurianum, the structural rearrangements upon reduction suggest specific mechanisms by which electron transfer reactions of rubredoxin should be facilitated.

• Proceedings of the Korean Vacuum Society Conference
• /
• 2011.02a
• /
• pp.38-38
• /
• 2011

Covalently bonded halogen ligands possess unusual charge distributions, attracting both electrophilic and nucleophilic molecular ligands to form halogen bonds. In many biochemical systems, halogen bonds and hydrogen bonds coexist. The interplay between halogen and hydrogen bonds has been actively studied in various three-dimensional bulk molecular co-crystals. It was found that halogen bonds could be complementary to hydrogen bonds due to their similar bond strength and dissimilar directionality. In those ensemble-averaging approaches, however, it was not possible to extract local information such as individual bond configurations and nano-level domain structures, which is a crucial part of supramolecular studies. In this study, we directly visualize the individual molecular configuration of a brominated molecule and the role of halogen bonds on Au(111) using scanning tunneling microscopy. The precise arrangement of observed molecular structures was reproduced by first-principle studies and explained in the context of halogen and hydrogen bonds. We discuss the distances and the strengths of the observed halogen bonds and hydrogen bonds, which are consistent with previous bulk data.

• Polymer(Korea)
• /
• v.26 no.4
• /
• pp.508-515
• /
• 2002

The effects of the crosslinking caused by irradiation dose, molecular weights of the foaming materials, and various foaming processes on the foam structure of the polypropylene (PP) were investigated. The maximum gel content of the PP was 48% when the sheet was irradiated with 3.2 Mrad. This high gel content improved the cell structures by providing high thermal stability. The increase of both the gel content and structural development were stopped at the irradiation dose exceeding 3.2 Mrad. The increase of the molecular weights served to help produce a foam with particularly fine and even cell structures, along with improved thermal stability as well.

• Bulletin of the Korean Chemical Society
• /
• v.28 no.9
• /
• pp.1472-1476
• /
• 2007

Artificial neural networks (ANNs) are successfully developed for the modeling and prediction of normalized polarity parameter (ETN) of 216 various solvents with diverse chemical structures using a quantitative-structure property relationship. ANN with architecture 5-9-1 is generated using five molecular descriptors appearing in the multi-parameter linear regression (MLR) model. The most positive charge of a hydrogen atom (q+), total charge in molecule (qt), molecular volume of solvent (Vm), dipole moment (μ) and polarizability term (πI) are input descriptors and its output is ETN. It is found that properly selected and trained neural network with 192 solvents could fairly represent the dependence of normalized polarity parameter on molecular descriptors. For evaluation of the predictive power of the generated ANN, an optimized network is applied for prediction of the ETN values of 24 solvents in the prediction set, which are not used in the optimization procedure. Correlation coefficient (R) and root mean square error (RMSE) of 0.903 and 0.0887 for prediction set by MLR model should be compared with the values of 0.985 and 0.0375 by ANN model. These improvements are due to the fact that the ETN of solvents shows non-linear correlations with the molecular descriptors.

• Bulletin of the Korean Chemical Society
• /
• v.34 no.4
• /
• pp.1089-1095
• /
• 2013

The tumor necrosis factor-receptor 1 (TNFR1)-associated death domain protein (TRADD) contains an N-terminal TRAF binding domain and a C-terminal death domain. TRADD is known to interact directly with TNF receptor 2 (TNFR2) and the Fas-associated death domain protein (FADD), which are signal transducers that activate NF-${\kappa}B$ and induce apoptosis, respectively. To date, there has been no structural information on the TRADD and FADD death domain (DDs) complex. In this study, the death domains of TRADD and FADD were co-expressed and purified from Escherichia coli for structural characterization. We found that human TRADD (hTRADD) interacted strongly with mouse FADD (mFADD) via their DDs and interacted weakly with human FADD (hFADD)-DD. Moreover, the structures of the TRADD-DD:FADD-DD complexes were separately modeled from predicted structures in the protein data bank (PDB). The results of this study will have important applications in human diseases such as cancer, AIDS, degenerative and autoimmune diseases, and infectious diseases.

• Bulletin of the Korean Chemical Society
• /
• v.24 no.1
• /
• pp.75-80
• /
• 2003

The structures and complexation energies of penta-O-alkylated 1b and penta-O-tert-butyl ester 1e of p-tert-butylcalix[5]arene and their simplified structures (2b and 2e) toward a series of alkyl ammonium guests have been calculated by a semi-empirical AM1 method. For AM1 calculations, complexation efficiencies of the simplified host 2e are very similar to the values of host 1e. The complexes of simplified host 2e with alkyl ammonium ions also have been optimized by ab initio HF/6-31G method. The calculated complexation efficiencies for 2e by ab initio method have been found to be bigger in magnitude than the values obtained by AM1 calculations for linear alkyl ammonium guests. Calculation results show that all of the calix[5]aryl derivatives investigated in this study have much better complexation ability toward ammonium cation without alkyl group compared with other alkyl ammonium guests. Ab initio calculations also well duplicate the molecular discriminating behaviors of calix[5]arene derivative 2e between butyl ammonium ions: $n-BuNH_3^+\;>\;iso-BuNH_3^+\;>\;sec-BuNH_3^+\;>\;tert-BuNH_3^+$.

• Molecules and Cells
• /
• v.41 no.6
• /
• pp.515-522
• /
• 2018

Patients with head and neck cancer are treated with therapeutic irradiation, which can result in irreversible salivary gland dysfunction. Because there is no complete cure for such patients, stem cell therapy is an emerging alternative for functional restoration of salivary glands. In this study, we investigated in vitro characteristics of primarily isolated epithelial cells from human salivary gland (Epi-SGs) and in vivo formation of acini-like structures by Epi-SGs. Primarily isolated Epi-SGs showed typical epithelial cell-like morphology and expressed E-cadherin but not N-cadherin. Epi-SGs expressed epithelial stem cell (EpiSC) and embryonic stem cell (ESC) markers. During long-term culture, the expression of EpiSC and ESC markers was highly detected and maintained within the core population with small size and low cytoplasmic complexity. The core population expressed cytokeratin 7 and cytokeratin 14, known as duct markers indicating that Epi-SGs might be originated from the duct. When Epi-SGs were transplanted in vivo with Matrigel, acini-like structures were readily formed at 4 days after transplantation and they were maintained at 7 days after transplantation. Taken together, our data suggested that Epi-SGs might contain stem cells which were positive for EpiSC and ESC markers, and Epi-SGs might contribute to the regeneration of acini-like structures in vivo. We expect that Epi-SGs will be useful source for the functional restoration of damaged salivary gland.

• Journal of the Korea Institute of Military Science and Technology
• /
• v.6 no.3
• /
• pp.86-102
• /
• 2003

Polynitrogen molecules are of great interest as potential high energy-density materials, and hence such structures of various isomers of nitrogen clusters have been calculated using molecular modeling techniques by the researchers from various sectors of scientific institutions. In this article, the predicted meta-stable structures of these hypothetical molecules have been thoroughly reviewed.