• Advances in nano research
• /
• 제9권2호
• /
• pp.83-90
• /
• 2020

This research investigates the effect of single walled carbon nanotubes (SWCNTs) dimensions in terms of diameter on the mechanical properties (longitudinal and transverse Young's modulus) of the simulated nanocomposites by molecular dynamics (MDs) method. MDs utilized to create nanocomposite models consisting of five case studies of SWCNTs with different chiralities (5, 0), (10, 0), (15, 0), (20, 0) and (25, 0) as the reinforcement and using polymethyl methacrylate (PMMA) as the common matrix. The results show that with increasing of SWCNTs diameter, the mechanical and physical properties increase. It is important that with the increasing of SWCNTs diameter, density, longitudinal and transverse Young's modulus, shear modulus, poisson's ratio, and bulk modulus of simulated nanocomposite from (5, 0) to (25, 0) approximately becomes 1.54, 3, 2, 1.43, 1.11 and 1.75 times more than (5, 0), respectively. Then to validate the results, the stiffness matrix is obtained by Materials studio software.

• Bulletin of the Korean Chemical Society
• /
• 제35권6호
• /
• pp.1769-1776
• /
• 2014

Binding modes of a series of catechol derivatives such as protein tyrosine phosphatase 1B (PTP1B) inhibitors were identified by molecular modeling techniques. Docking, molecular dynamics simulations and free energy calculations were employed to determine the modes of these new inhibitors. Binding free energies were calculated by involving different energy components using the Molecular Mechanics-Poisson-Boltzmann Surface Area and Generalized Born Surface Area methods. Relatively larger binding energies were obtained for the catechol derivatives compared to one of the PTP1B inhibitors already in use. The Molecular Mechanics/Generalized Born Surface Area (MM/GBSA) free energy decomposition analysis indicated that the hydroxyl functional groups and biphenyl ring system had favorable interactions with Met258, Tyr46, Gln262 and Phe182 residues of PTP1B. The results of hydrogen bound analysis indicated that catechol derivatives, in addition to hydrogen bonding interactions, Val49, Ile219, Gln266, Asp181 and amino acid residues of PTP1B are responsible for governing the inhibitor potency of the compounds. The information generated from the present study should be useful for the design of more potent PTP1B inhibitors as anti-diabetic agents.

• 한국광물학회지
• /
• 제27권4호
• /
• pp.271-281
• /
• 2014

점토광물의 물리화학적 특성에 대한 분자 또는 원자 스케일의 연구 중요성이 강조되고 있다. 그러나 실험만으로는 광물의 미시적 현상을 이해하기 어려운 경우가 많다. 특히 2:1 점토광물 팔면체에 존재하는 수산기(hydroxyl)가 금속 양이온 흡착과정에 큰 역할을 한다는 가정은 X-ray를 이용하는 실험만으로는 명확하게 테스트하기 어렵다. 이번 논문에서는 점토광물 내의 수산기 연구에 대한 전산광물학(computational mineralogy) 이용 가능성에 대하여 조사하였다. 점토광물의 기본구조인 팔면체 층만으로 구성된 광물, 1:1 구조를 갖는 광물, 2:1 구조를 갖는 광물 중 대표적인 이팔면체 및 삼팔면체 층상규산염 광물을 선별하여 구조최적화를 실시하였다. 분자역학적(molecular mechanics) 계산과 양자역학적(quantum mechanical) 계산 모두 실험값의 격자상수(lattice parameters)를 잘 재현할 수 있었다. 그러나, 사면체층과 팔면체의 구조적 뒤틀림(structural distortion) 등 광물 내부구조를 기존 실험결과와 비교했을 때, 양자역학적 계산결과가 분자역학적 방법을 이용한 결과 보다 더 낮은 오차를 보였다. 파이로필라이트(pyrophyllite) 수산기가 (001)면과 이루는 각은, 수산기의 H(proton)과 사면체의 Si 양이온 간의 척력으로 결정되는데, 양자역학적 방법은 약 $25-26^{\circ}$로 예측하였고, 분자역학적 방법은 약 $35^{\circ}$ 정도로 양자역학계산 결과와 무려 $10^{\circ}$의 큰 차이를 보였다. 전산광물학은 점토광물 구조연구에 신뢰성이 매우 높은 연구방법으로 양이온 흡착과정 중 수산기의 역할 규명에 사용될 수 있다.

• 전산구조공학
• /
• 제18권2호
• /
• pp.25-33
• /
• 2005

• Bulletin of the Korean Chemical Society
• /
• 제10권2호
• /
• pp.216-218
• /
• 1989

• Macromolecular Research
• /
• 제14권4호
• /
• pp.430-437
• /
• 2006

The ultra-drawing process of an ultra high molecular weight polyethylene (UHMWPE) gel film was examined by incorporating linear low-density polyethylene (LLDPE) and $BaTiO_3$ nanoparticles. The effects of LLDPE and the draw ratios on the morphological development and mechanical properties of the nanocomposite membrane systems were investigated. By incorporating $BaTiO_3$ nanoparticles in the UHMWPE/LLDPE blend systems, the ultra-drawing process provided a highly extended, fibril structure of UHMWPE chains to form highly porous, composite membranes with well-dispersed nanoparticles. The ultra-drawing process of UHMWPE/LLDPE dry-gel films desirably dispersed the highly loaded $BaTiO_3$ nanoparticles in the porous membrane, which could be used to form multi-layered structures for electronic applications in various embedded, printed circuit board (PCB) systems.

• Bulletin of the Korean Chemical Society
• /
• 제31권9호
• /
• pp.2581-2587
• /
• 2010

Nitration of tyrosine and tryptophan residues is common in cells under nitrative stress. However, physiological consequences of protein nitration are not well characterized on a molecular level due to limited availability of the 3D structures of nitrated proteins. Molecular dynamics (MD) simulation can be an alternative tool to probe the structural perturbations induced by nitration. In this study we developed molecular mechanics parameters for 3-nitrotyrosine (NIY) and 6-nitrotryptophan (NIW) that are compatible with the AMBER-99 force field. Partial atomic charges were derived by using a multi-conformational restrained electrostatic potential (RESP) methodology that included the geometry optimized structures of both $\alpha$- and $\beta$-conformers of a capped tripeptide ACE-NIY-NME or ACE-NIW-NME. Force constants for bonds and angles were adopted from the generalized AMBER force field. Torsional force constants for the proper dihedral C-C-N-O and improper dihedral C-O-N-O of the nitro group in NIY were determined by fitting the torsional energy profiles obtained from quantum mechanical (QM) geometry optimization with those from molecular mechanical (MM) energy minimization. Force field parameters obtained for NIY were transferable to NIW so that they reproduced the QM torsional energy profiles of ACE-NIW-NME accurately. Moreover, the QM optimized structures of the tripeptides containing NIY and NIW were almost identical to the corresponding structures obtained from MM energy minimization, attesting the validity of the current parameter set. Molecular dynamics simulations of thioredoxin nitrated at the single tyrosine and tryptophan yielded well-behaved trajectories suggesting that the parameters are suitable for molecular dynamics simulations of a nitrated protein.

• 소성∙가공
• /
• 제10권6호
• /
• pp.449-456
• /
• 2001

The concept of stress wave was introduced through the quantized kinetic energy which is related to the potentional energy change of atom, molecular bond energy. Differentiated molecular bond energy $\varphi$() by the lst order displacement u becomes force F(F = d$\varphi$($u_i$)/du), if resversely stated, causing physically atomic displacement $u_i$. Such physical phenomena lead stress(force/area of applied force) can be expressed by wave equation of linearly quantized physical property. Through the stress wave concept, formation of dislocation, which could not explained easily from a theory of continuum mechanics, can be explained. Moreover, this linearly quantized stress wave equation with a stress concept for grains in a crystalline solid was applied to three typical metallic microstructures and a simple shape. The result appears to be a product from well treated equations of a quantized stress wave. From this result, it can be expected to answer the reason why the defect free and very fine diameters of long crystalline shapes exhibit ideal tensile strength of materials.

• Bulletin of the Korean Chemical Society
• /
• 제23권1호
• /
• pp.48-52
• /
• 2002

Using several molecular modeling programs we have performed computer simulations to investigate the complexation behaviors of an ester derivative of p-tert-butylcalix[5]arene (1e) toward a variety of butylammonium ions. Semi-empirical AM1 method was used for calculating the binding energies and the formation enthalpies. MM and CVFF forcefields for molecular mechanics calculations were adapted to express the complexation energies of the host. Molecular dynamics were performed to the calculated complex systems to simulate the ionophoric behavior of the host-guest complexes. The absolute Gibbs free energies of the host (1e) complexed with four kinds of butylammonium ions have been calculated using the Finite Difference Thermodynamic Integration (FDTI) method in Discover. Calculation results show that the trend in complex formation is n-$BuNH_3^+$ > iso-$BuNH_3^+$ >> sec-$BuNH_3^+$ > tert-$BuNH_3^+$, which is in good agreement with the experimental results.

• Bulletin of the Korean Chemical Society
• /
• 제33권3호
• /
• pp.862-868
• /
• 2012

Based on the recently derived general expression for the rates of diffusion-controlled reactions, we calculate the rates of dismutation of the superoxide anion radical catalyzed by Cu/Zn superoxide dismutases (SOD). This is the first attempt to calculate the absolute rates of diffusion-controlled enzyme reactions based on the atomiclevel molecular dynamics simulations. All solvent molecules are included explicitly and the effects of the structural flexibility of enzyme, especially those of side chain motions near the active site, are included in the present calculation. In addition, the actual mobility of the substrate molecule is taken into account, which may change as the molecule approaches the active site of enzyme from the bulk solution. The absolute value of the rate constant for the wild type SOD reaction obtained from MD simulation is shown to be in good agreement with the experimental value. The calculated reactivity of a mutant SOD is also in agreement with the experimental result.