• 약학회지
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• 제33권6호
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• pp.350-360
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• 1989

The conformation and activity of the four benzenesulfonyl analogues of 4-aminobenzene-sulfonamide, 4-aminobenzenesulfonic acid, 4-methylbenzenesulfonamide, and 4-methylbenzenesulfonic acid with antibacterial activity on Staphylococcus aureus were studied using an empirical potential function (ECEPP/2) and the hydration shell model. The conformational energies were minimized from the starting conformations which included possible combinations of torsion angles in each molecule. To understand the hydration effect on the conformation of the molecule in aqueous solution, the hydration free energy of each group was calculated and compared each other. The conformational entropies of low-free-energy coformation of benzenesulfonly analogues were computed by a harmonic approximation. From the correlation of lowest-free-energy conformation of each compound and its antibacterial activity, it was found that the hydration of sulfonyl groups and the substituents are the decisive factors to show antibacterial activities.

• 통합자연과학논문집
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• 제4권2호
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• pp.99-102
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• 2011

Effect of protonation and deprotonation of ionization compounds is an important application in Comparative molecular field analysis (CoMFA). There are enough information's were reported about different CoMFA applications such as Series design and selection of training set, Geometries and optimizations of molecules, Effect of partial atomic charges, bioactive conformations and alignment, Interaction energy fields, Effects of different grid spacing etc. However limited information's are available about the ionization of compounds. This study aimed at the critical review of about the effects of protonation of ionizable molecules and its impact on the predictability of CoMFA models. We also discussed about previous implications and the things needed to be considered to come for a final conclusion about its impact on CoMFA predictability.

• ETRI Journal
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• 제18권3호
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• pp.195-206
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• 1996

Molecular conformations of stereoregular poly(methyl methacrylate) (PMMA) monolayers have been investigated by scanning probe microscopes. Isotactic and syndiotactic PMMAs were found to have right and left hand helical structures, respectively. On the contrary atactic PMMA showed rather random arrangement of the chains. It has been demonstrated that the PMMA Langmuir-Blodgett (LB) films can be utilized to form nanoscale patterns down to 50 nm and to forma geodesic lens. It has also been manifested that the quantum efficiency of a polymer electroluminescent device can be significantly enhanced by inserting the PMMA LB films between the emitting layer and the cathode. All the applications utilize the unique characteristics of the LB films to form thin and uniform films in the molecular level.

• 대한화학회지
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• 제34권6호
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• pp.539-547
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• 1990

DNA base인, Adenine, Guanine 그리고 Cytosine과 diaminecytosineplatinum(DCP)의 상호작용을 SC-MEH 방법에 의하여 계산한 결과, DNA base와 DCP 결합력의 크기는 guanine > adenine > cytosine임을 알 수 있었고, cis-백금(II)착물이 trans-백금(II) 착물보다 안정화에너지가 더 크게 나타남을 adenine-DCP 착물계에서 볼 수 있었다. DNA bases ring의 atomic charge는 백금(II)착물의 배위에 의해 많은 charge 변화가 있음을 관찰하였고, 이 효과에 의하여 백금(II)착물의 항암성 메카니즘을 설명할 수 있었다.

• Bulletin of the Korean Chemical Society
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• 제30권8호
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• pp.1845-1850
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• 2009

We have performed replica-exchange molecular dynamics (REMD) simulations on the dimer formation of fibrilforming segments of $\alpha$-Synuclein (residues 71 - 82) using implicit solvation models with two kinds of force fields- AMBER parm99SB and parm96. We observed spontaneous formation of dimers from the extensive simulations, demonstrating the self-aggregating and fibril forming properties of the peptides. Secondary structure profile and clustering analysis showed that dimers with antiparallel $\beta$-sheet conformations, stabilized by well-defined hydrogen boding, are major species corresponding to global free energy minimum. Parallel dimers with partial $\beta$-sheets are found to be off-pathway intermediates. The relative instability of the parallel arrangements is due to the repulsive interactions between bulky and polar side chains as well as weaker backbone hydrogen bonds.

• Bulletin of the Korean Chemical Society
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• 제25권12호
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• pp.1911-1916
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• 2004

The conformational preference of tetrahomodioxacalix[4]arenes with three different para substituents on the phenolic ring has been investigated by using ab initio molecular orbital theory (RHF/6-31$G^{\ast}$) and density functional theory (B3LYP/6-31$G^{\ast}$). The stability order is predicted to be cone > C-1,2-alternate > partial cone > 1,3-alternate > COC-1,2-alternate. The distorted cone conformation is found to be most stable in a gas phase and the calculated results are in agreement with the reported $^1$H NMR and X-ray experimental observations. The substitution of methylene with dimethyleneoxa bridges increases the size of the annulus of the molecule, its conformational mobility, and the number of hydrogen bonding patterns. The thermodynamic stability and the conformational characteristics of tetrahomodioxacalix[4]arenes are discussed in regards of the number of phenolic hydrogen bonding patterns and the polarity of a molecule. The substituent effects on the para position of the phenolic ring are also introduced.

• 한국생물물리학회:학술대회논문집
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• 한국생물물리학회 2001년도 학술 발표회 진행표 및 논문초록
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• pp.35-35
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• 2001

The conformational study on cyclic Ac-Cys-Pro-Xaa-Cys-NHMe (Ac-CPXC-NHMe; X = Ala, Val, Leu, Aib, Gly, His, Phe, Tyr, Asn, and Ser) peptides has been carried out using the ECEPP/3 force field and the hydration shell model in the unhydrated and hydrated states. This work has been undertaken to investigate structural implications of the CPXC sequence as the chain reversal for the initiation of protein folding and as the motif for active site of disulfide oxidoreductases.(omitted)

• 대한화학회지
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• 제24권2호
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• pp.101-107
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• 1980

비결합 효과를 기초로 하여 상대적인 이성질체의 안정도를 예측하는 복합파이구조 분석법을 제안하였다. 우선 각 이성질체내의 모든 고리구조를 찾아내고, 이들을 $(n{\pi}/m)$형의 약호로 나타낸 다음 간단한 규칙과 가감율을 사용하여 안정도 순위를 결정한다. 이 분석절차의 예를 여러가지 들어 해설하였다.

• Macromolecular Research
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• 제10권6호
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• pp.297-303
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• 2002

We have investigated the microstructural properties of a weakly charged polyelectrolyte modeled with both Hookean spring and Debye-Huckel potential, by employing a novel hybrid scheme of molecular dynamics (MD) and Monte Carlo (MC) simulations. Although the off-lattice pivot step facilitates the earlier computations stage, it gives rise to oscillations and hinders the stable equilibrium state. In order to overcome this problem, we adopt the MC off-lattice pivot step in early stage only, and then switch the computation to a pure MD step. The result shows that the computational speed-up compared to the previous method is entirely above 10 to 50, without loss of the accuracy. We examined the conformations of polyelectrolyte in solvents in terms of the end-to-end distance, radius of gyration, and structure factor with variations of the screening effects of solvent and the monomer charges. The emphasis can favorably be given on the elongation behavior of a polyelectrolyte chain, with observing the simultaneous snapshots.

• The Plant Pathology Journal
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• 제31권4호
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• pp.323-333
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• 2015

As sessile organisms, plants are exposed to persistently changing stresses and have to be able to interpret and respond to them. The stresses, drought, salinity, chemicals, cold and hot temperatures, and various pathogen attacks have interconnected effects on plants, resulting in the disruption of protein homeostasis. Maintenance of proteins in their functional native conformations and preventing aggregation of non-native proteins are important for cell survival under stress. Heat shock proteins (HSPs) functioning as molecular chaperones are the key components responsible for protein folding, assembly, translocation, and degradation under stress conditions and in many normal cellular processes. Plants respond to pathogen invasion using two different innate immune responses mediated by pattern recognition receptors (PRRs) or resistance (R) proteins. HSPs play an indispensable role as molecular chaperones in the quality control of plasma membrane-resident PRRs and intracellular R proteins against potential invaders. Here, we specifically discuss the functional involvement of cytosolic and endoplasmic reticulum (ER) HSPs/chaperones in plant immunity to obtain an integrated understanding of the immune responses in plant cells.