• Bulletin of the Korean Chemical Society
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• 제34권1호
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• pp.299-302
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• 2013

• 약학회지
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• 제60권2호
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• pp.78-84
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• 2016

N-Phenylthiourea derivatives and catechol oxidase receptor complex was studied using molecular mechanics method. The starting structure was adopted from the protein databank and the calculation of energy minimization and molecular dynamics was performed with AMBER package. The molecular dynamics showed that the simulation time span of 20 ns was long enough to observe the interaction profile and stationary ligand-receptor configuration in the complex. The conformation of the ligand was related to the interaction to the receptor and the efficacy was also interpreted in this context.

• 대한기계학회논문집A
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• 제38권2호
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• pp.121-127
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• 2014

단층 그래핀 시트(Single layer graphene sheet, SLGS)의 찢어짐 모드(모드 III) 파괴 예측을 위한 원자 기반 미세결합요소모델이 개발되었다. 이 모델은 그래핀 시트의 최대 변형률 관계를 예측하기 위해 수정된 모스포텐셜을 사용한다. 면외 전단하중 조건에서 그래핀의 모드 III 파괴를 광범위한 분자역학(Molecular mechanics, MM) 시뮬레이션으로 조사하였다. 분자역학은 원자의 균열선단 근처 원자의 변위를 설명하기 위해 사용되었고, 선형탄성파괴역학은 이 영역 바깥의 영역을 설명하기 위해 사용되었다. 해석 결과 분자역학 방법이 SLGS의 전단 물성 계산뿐만 아니라 armchair 및 zigzag 방향 모드 III 파괴인성 연구에도 단순하면서도 신뢰할만하다는 것을 보여준다. SLGS 의 모드 III 파괴인성은 zigzag 방향에 대해 $0.86MPa{\sqrt{m}}$, armchair 방향에 대해 $0.93MPa{\sqrt{m}}$로 예측되었다.

• Macromolecular Research
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• 제8권5호
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• pp.224-230
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• 2000

Molecular mechanics technique has been used for finding energy-minimized conformation to understand the mechanism of yielding of glassy polymers in atomistic level. As a model polymer, amor- phous isotactic polypropylene (iPP) was generated by molecular mechanics and molecular dynamics methods. The stress-strain cone was successfully obtained by using molecular mechanics technique. The torsional angle distribution showed no significant change during extension, although the torsional angles of certain bonds in polymer backbone changed more largely than other bonds. No significant change in the van der Waals interaction is observed at yielding point, whereas the torsional angle energy starts to decrease at yield strain.

• Bulletin of the Korean Chemical Society
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• 제21권5호
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• pp.465-470
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• 2000

The conformations and energies of p-tert-butylcalix[4] crown-6-ether (1) and its alkyl ammonium complexes have been simulated by AM1 semi-empirical quantum mechanics and molecular mechanics calculations using a variety of forcefields (MM2, MM+, CVFF). We performed molecular dynamics calculations to simulate the behavior of these coplexes primartily focusing on the three representative conformations (cone, partial cone, 1,3-alternate) of host molecule 1. When we performed AM1 semi-empirical and molecular mechanics calculations, the one conformation was generally found to be most stable for all the employed calculation methods. The primary binding site of host 1 for the recognition of alkyl ammonium guests was confirmed to be the central part of the crown moiety. The complexation enthalpy calculations revealed that the alkyl amonium cations having smaller and linear alkyl group showed the better complexation efficiencies when combined with p-tert-butylcalix[4]crown-6-ether, that is in satisfactory agreement with the experimental results.

• Smart Structures and Systems
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• 제13권4호
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• pp.685-709
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• 2014

Carbon nanotubes are due to their outstanding mechanical properties destined for a wide range of possible applications. Since the knowledge of the material behavior is vital regarding the possible applications, experimental and theoretical studies have been conducted to investigate the properties of this promising material. The aim of the present research is the calculation of mechanical properties and of the mechanical behavior of single wall carbon nanotubes (SWCNTs). The numerical simulation was performed on basis of a molecular mechanics approach. Within this approach two different issues were taken into account: (i) the nanotube geometry and (ii) the modeling of the covalent bond. The nanotube geometry is captured by two different approaches, the roll-up and the exact polyhedral model. The covalent bond is modeled by a structural molecular mechanics approach according to Li and Chou. After a short introduction in the applied modeling techniques, the results for the Young's modulus for several SWCNTs are presented and are discussed extensively. The obtained numerical results are compared to results available in literature and show an excellent agreement. Furthermore, deviations in the geometry stemming from the different models are given and the resulting differences in the numerical findings are shown. Within the investigation of the deformation mechanisms occurring in SWCNTs, the basic contributions of each individual covalent bond are considered. The presented results of this decomposition provide a deeper understanding of the governing deformation mechanisms in SWCNTs.

• Bulletin of the Korean Chemical Society
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• 제18권2호
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• pp.143-149
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• 1997

We have investigated a relationship between conformational preferences of various substituents in monosubstituted cyclohexanes and pertinent torsional parameter values in molecular mechanics calculations. We have manipulated torsional parameters to supply a certain energy difference between gauche and anti conformers, and applied those parameters to monosubstituted cyclohexanes. After investigating 6 different substituents, namely Me, SiH3, F, Cl, Br, and I, MM3 calculations show that (1) the MM3 calculated A values with the current torsional parameters reproduce the available experimental values well, (2) the conformational energy difference between axial and equatorial conformations (the A value) correlates perfectly with the gauche/anti energy differences of the corresponding butane-like fragment (correlation coefficient=l.000), and (3) the A values are essentially twice as the gauche/anti energy differences (slopes=1.86-2.00). On the basis of our analysis, the A values as well as the gauche/anti energy differences are easily calibrated by an adjustment of the relevant torsional parameter. Thus, our technique for tuning the torsional parameters may be of great use in updating molecular mechanics results about conformational preferences whenever a further refinement is necessary.

• Coupled systems mechanics
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• 제4권2호
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• pp.137-155
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• 2015

This paper presents a simple procedure to obtain a substitute, homogenized mechanical response of single layer graphene sheet. The procedure is based on the judicious combination of molecular mechanics simulation results and homogenization method. Moreover, a series of virtual experiments are performed on the representative graphene lattice. Following these results, the constitutive model development is based on the well-established continuum mechanics framework, that is, the non-linear membrane theory which includes the hyperelastic model in terms of principal stretches. A proof-of-concept and performance is shown on a simple model problem where the hyperelastic strain energy density function is chosen in polynomial form.

• 약학회지
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• 제54권1호
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• pp.62-66
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• 2010

Benzopyrene is known to be one of the most powerful carcinogens which can build intercalated motif between base pairs in damaged DNA. The dimension of benzopyrene itself is much bigger than any of the DNA bases and thus the question whether the lesion of some base pair by insertion of benzopyrene can happen with or without a dramatic distortion of the helical structure is a highly interesting theme. In this work we used a molecular mechanics simulation using AMBER program package to go into the conformational characteristics. The condition of the insertion process of the benzopyrene motif from minor groove of the starting structure between the base pairs in the internal area of double helix was investigated using the molecular dynamics simulation at elevated temperature.

• 약학회지
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• 제54권1호
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• pp.67-74
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• 2010

Some of the benzopyrene (BP)-DNA adduct are known to build intercalated motif between flanking base pairs in damaged DNA depending on the structural condition. The size of benzopyrene itself is definitely not comparable with any of the DNA bases and thus the question whether the lesion of some base pair by insertion of benzopyrene can happen with or without a dramatic distortion of the helical structure is a highly interesting theme. In this work we used a molecular dynamics simulation based on the theory of molecular mechanics. The specific consequences about the structural properties of the intercalated structures and benzopyrene motif in minor groove of the double helix are deduced after 5 ns simulation time.