• BMB Reports
• /
• v.29 no.4
• /
• pp.380-385
• /
• 1996

Ovomucoid third domain is a serine proteinase inhibitor protein which consists of 56 amino acid residues. A fifty picosecond molecular dynamics (MD) simulation was carried out for ovomucoid third domain protein with 5 $\AA$ layer of water molecules. A comparison of main chain atoms in the MD averaged structure with the crystal structure showed that most of the backbone structures are maintained during the simulation. Investigation of the intramolecular hydrogen bondings indicated that most of the interactions between main chain atoms were conserved, whereas those between side chains were reorganized for the period of the simulation. Especially, the side chain interactions around the scissile bond of reactive site P1 (Met18) were found to be more extensive for the MD structures. During the simulation, hydrogen bonds were maintained between the side chains of Glu19 and Arg21 as well as those of Thr17 and Glu19. Extensive side chain interactions observed in the MD structures may shed light on the question of why protein proteinase inhibitors are strong inhibitors for proteinases rather than good substrates.

• Bulletin of the Korean Chemical Society
• /
• v.33 no.4
• /
• pp.1264-1267
• /
• 2012

We rationally designed and synthesized metallopolymers with organic 1,4-benzenedicarboxylic acid (BDC) linkers with different lengths of oxyethylene side chains in order to examine the influence of side chains on the coordination characteristics. While in a previous report the BDC linkers with alkyl side chains were found to form three-dimensional (3D) isoreticular metal-organic framework (IRMOF) structures or one-dimensional (1D) coordination polymeric structures with short $-O(CH_2)_6CH_3$ or long $-O(CH_2)_9CH_3$ side chains, respectively, new BDC linkers with oxyethylene side chains of the same lengths, $-(OCH_2CH_2)_2CH_3$ and $-(OCH_2CH_2)_3CH_3$, form only 3D IRMOF structures. This result is attributed to the higher flexibility and smaller volume of oxyethylene side chains compared to alkyl side chains.

• Bulletin of the Korean Chemical Society
• /
• v.25 no.7
• /
• pp.1061-1064
• /
• 2004

Molecular visualization software has the common objective of manipulation and interpretation of data from numerical simulations. They visualize many complicated molecular structures with personal computer and workstation, to help analyze a large quantity of data produced by various computational methods. However, users are often discouraged from using these tools for visualization and analysis due to the difficult and complicated user interface. In this regard, we have developed an easy-to-use three-dimensional molecular visualization and analysis program named POSMOL. This has been developed on the Microsoft Windows platform for the easy and convenient user environment, as a compact program which reads outputs from various computational chemistry software without editing or changing data. The program animates vibration modes which are needed for locating minima and transition states in computational chemistry, draws two and three dimensional (2D and 3D) views of molecular orbitals (including their atomic orbital components and these partial sums) together with molecular systems, measures various geometrical parameters, and edits molecules and molecular structures.

• Elastomers and Composites
• /
• v.37 no.4
• /
• pp.234-243
• /
• 2002

A general scheme of a rubber structure is proposed. Using the thermomechanical method(TMA), some changes in the molecular and topological structures for uncured and cured, and unfilled and filled rubbers during processing are shown. In our investigations as region it is understood a complex structure, which is expressed at the thermomechanical curve(TMC) as a zone differed from others in thermal expansion properties. This zone is between the noticed temperatures of relaxation transitions, usually on the level like those determined by DMTA at 1Hz. These regions, which shares, are not stable, and differ in molecular-weight distribution(MWD) of chain fragments between the junctions. Differences in dynamics of the formation of the molecular and topological structures of a vulcanizate are dependent on the rubber formulation, mixing technology and curing time. Some of characteristics of these regions correlate with mechanical properties of vulcanizates what is shown for NR rubbers containing ENR or CPE as a polymeric additive. It is well known that the state of order influences diffusivity of low-molecular substances into the polymer matrix. Because of this, the two topological amorphous regions should influence the distribution of the ingredients and resulting in rubber compounds' heterogeneity, and related properties of cured rubber. Investigation of this problem is expected to be, in the future, one of the essential factors in determining further improvement of polymeric materials properties by compounding with additives and in reprocessing of rubber scrap.

• Proceedings of the Korean Society of Potoscience Conference
• /
• spring
• /
• pp.58-59
• /
• 1999

• Journal of The Korean Association For Science Education
• /
• v.27 no.6
• /
• pp.477-487
• /
• 2007

Previous studies show that students have difficulties in understanding and using molecular visualization tools. This study focuses on the ways in which first year chemistry undergraduates use ball-and-stick molecular models to explain the concept of addition reaction and the difficulties that they face using the models. Video recordings of interviews with undergraduates manipulating ball-and-stick models to solve problems related to reaction mechanisms are analysed to determine if they are able to elucidate their understanding with use of models. The results showed that students have difficulties with viewing the ball-and-stick models from the proper perspective and understanding the relationship between the various structures that they have created using the models. They also find the use of ball-and-stick models tedious and prefer drawing molecular structures on paper to explain their ideas. Implications for the teaching using ball-and-stick molecular models are discussed.

• Proceedings of the KSME Conference
• /
• 2007.05a
• /
• pp.502-505
• /
• 2007

PMMA has been extensively adopted in Nano Imprint Lithography(NIL). PMMA nano-structures experience severe mechanical load and deformation during NIL process, and understanding its mechanical behavior is very important in designing and optimizing NIL process. One of the most promising techniques for characterizing the mechanical behavior of nano structures is nano pillar compression test. In this study, the mechanical behaviors of PMMA pillars during compression test are analyzed using Molecular Dynamics. Two methods for simulation of PMMA nano pillars are proposed. The stress-strain relationship of nano-scale PMMA structure is obtained based on CVFF(Covalent Valence Force Fields) potential and the dependency of the applied strain rate on the stress-strain relationship is analyzed. The obtained stress-strain relationships can be useful in simulating nano-scale PMMA structures using Finite Element Method(FEM) and understanding the experimental results obtained by compression test of PMMA nano pillars.

• Journal of Pharmaceutical Investigation
• /
• v.12 no.3
• /
• pp.64-73
• /
• 1982

Molecular structures of ${\omega}-Amino$ acids, ${\omega}-Aminosulfonic$ acids and their ${\beta}-hydroxy$ substituted compounds were determined by X-ray diffraction method, and the similarities and differences between their molecular structures or between related compounds were discussed.

• BMB Reports
• /
• v.37 no.3
• /
• pp.304-313
• /
• 2004

Three-dimensional (3D) models for the 65-kDa activated Cry4A and Cry4B $\delta$-endotoxins from Bacillus thuringiensis subsp. israelensis that are specifically toxic to mosquito-larvae were constructed by homology modeling, based on atomic coordinates of the Cry1Aa and Cry3Aa crystal structures. They were structurally similar to the known structures, both derived 3D models displayed a three-domain organization: the N-terminal domain (I) is a seven-helix bundle, while the middle and C-terminal domains are primarily comprise of anti-parallel $\beta$-sheets. Circular dichroism spectroscopy confirmed the secondary structural contents of the two homology-based Cry4 structures. A structural analysis of both Cry4 models revealed the following: (a) Residues Arg-235 and Arg-203 are located in the interhelical 5/6 loop within the domain I of Cry4A and Cry4B, respectively. Both are solvent exposed. This suggests that they are susceptible to tryptic cleavage. (b) The unique disulphide bond, together with a proline-rich region within the long loop connecting ${\alpha}4$ and ${\alpha}5$ of Cry4A, were identified. This implies their functional significance for membrane insertion. (c) Significant structural differences between both models were found within domain II that may reflect their different activity spectra. Structural insights from this molecular modeling study would therefore increase our understanding of the mechanic aspects of these two closely related mosquito-larvicidal proteins.

• Asian-Australasian Journal of Animal Sciences
• /
• v.30 no.11
• /
• pp.1575-1589
• /
• 2017

Objective: This study was conducted to determine molecular structures related to carbohydrates and lipid in alfalfa hay cut at early bud, late bud and early flower and in the afternoon and next morning using Fourier transform infrared spectroscopy (FT/IR) and to determine their relationship with alfalfa hay nutrient profile and availability in ruminants. Methods: Chemical composition analysis, carbohydrate fractionation, in situ ruminal degradability, and DVE/OEB model were used to measure nutrient profile and availability of alfalfa hay. Univariate analysis, hierarchical cluster analysis (CLA) and principal components analysis (PCA) were conducted to identify FT/IR spectra differences. Results: The FT/IR non-structural carbohydrate (NSCHO) to total carbohydrates and NSCHO to structural carbohydrate ratios decreased (p<0.05), while lignin to NSCHO and lipid CH3 symmetric to CH2 symmetric ratios increased with advancing maturity (p<0.05). The FT/IR spectra related to structural carbohydrates, lignin and lipids were distinguished for alfalfa hay at three maturities by PCA and CLA, while FT/IR molecular structures related to carbohydrates and lipids were similar between alfalfa hay cut in the morning and afternoon when analyzed by PCA and CLA analysis. Positive correlations were found for FT/IR NSCHO to total carbohydrate and NSCHO to structural carbohydrate ratios with non-fiber carbohydrate (by wet chemistry), ruminal fast and intermediately degradable carbohydrate fractions and total ruminal degradability of carbohydrates and predicted intestinal nutrient availability in dairy cows ($r{\geq}0.60$; p<0.05) whereas FT/IR lignin to NSCHO and CH3 to CH2 symmetric stretching ratio had negative correlation with predicted ruminal and intestinal nutrient availability of alfalfa hay in dairy cows ($r{\geq}-0.60$; p<0.05). Conclusion: FT/IR carbohydrate and lipid molecular structures in alfalfa hay changed with advancing maturity from early bud to early flower, but not during the day, and these molecular structures correlated with predicted nutrient supply of alfalfa hay in ruminants.