• Bulletin of the Korean Chemical Society
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• v.10 no.2
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• pp.185-190
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• 1989

Geometries for a number of representative ${\beta}$ -lactam antibiotics (penams, cephems and monobactams) have been calculated by computer graphics/molecular mechanics energy minimization procedures using both MM2 and AMBER force fields. The calculated geometries have been found in reasonable agreement with the geometries reported in the X-ray crystal structures, especially in terms of the pyramidal character of the amide nitrogen in the ${\beta}$-lactam ring and the Cohen distance. Based on these calculations, it is suggested that the nitrogen atom in the monobactams may also have pyramidal geometries in the biologically active conformations.

• Bulletin of the Korean Chemical Society
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• v.11 no.4
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• pp.313-317
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• 1990

Geometries for several representative quinolone carboxylate type antibacterials have been calculated by computer graphics/molecular mechanics energy minimization procedures using both MM2 and AMBER force fields. The calculated geometries were found to be in reasonable agreements with the corresponding X-ray crystal structures. It has been pointed out that notwithstanding the weaknesses associated with calculating the resonance and hydrogen bonding contributions, the employed methods are capable of generating credible ring geometries and torsional angle dispositions of N(1)-ethyl and 3-carboxylate substituents of the quinolones.

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

• Journal of the Korea Computer Graphics Society
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• v.10 no.2
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• pp.1-9
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• 2004

본 논문에서는 바이러스와 같은 생화학 물질의 분자구조를 3 차원 모델로 시각화하여 관찰하고, 그 분자모델을 직관적인 방법으로 조작하기 위한 가상 현실 분자 모델링 시스템을 제안한다. 이 시스템을 사용하면, 입체영상 디스플레이 장치와 데이터 글러브 및 동작 추적 장치를 사용하여 3 차원 분자 모델을 실감나게 조작할 수 있어서 효율적으로 분자들을 관찰하고 결합, 분리하는 등의 분자 모델링 작업이 가능하다. 사용자들은 마우스나 키보드 등의 장비 대신에 자연스러운 몸 동작이나 손 동작을 이용하여 분자 모델링 작업을 위한 동작을 하게 된다. 분자들의 결합을 화학적으로 정확하게, 그리고 실시간으로 시뮬레이션 하기 위해서 에너지 계산 알고리즘을 구현하였으며 이러한 작업이 가능하도록 분자 구조를 표현하는 새로운 자료구조를 제안하였다. 본 연구에서 제안하는 동작 기반의 VR 분자 모델링 시스템의 타당성을 검증하기 위하여 HIV 바이러스 분자를 가지고 분자 모델링 작업을 수행하였고, 사용자 테스트를 실시하여 기존의 방식과 작업 성능 및 사용자 만족도를 비교하였다.

• Analytical Science and Technology
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• v.11 no.1
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• pp.8-12
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• 1998

The 2,2'-Biimidazole was synthesized by the reaction between glycol and ammonium solution. The correct solid structure of 2,2'-biimidazole in this method reported either trans ($C_{2h}$) or cis ($C_{2v}$) form. In this study, the correct structure of 2,2'-biimidazole was analysed by both FTIR and Raman spectroscopy using mutual exclusion properties of them. Also, it was analysed by $^1H$ and $^{13}C$ NMR and computer molecular modeling. The structure of 2,2'-biimidazole found to be trans ($C_{2h}$) than cis ($C_{2v}$) by comparison between FTIR and Raman Spectra. This results agree with computer molecular modeling and x-ray crystallography. This study provide good evidence for identifying structural orientation of the 2,2'-biimidazole containing pyridyl nitrogen.

• Journal of the Korea Computer Graphics Society
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• v.14 no.4
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• pp.35-39
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• 2008

A computer supported collaborative system provides with a shared virtual workspace over the Internet where its remote users cooperate in order to achieve their goals by overcoming problems caused by distance and time. VRMMS (Virtual Reality Molecular Modeling System) [1] is a VR based collaborative system where biologists can remotely participate in and exercise molecular modeling tasks such as viewing three dimensional structures of molecular models, confirming results of molecular simulations and providing with feedbacks for the next simulations. Biologists can utilize VRMMS in executing molecular simulations. However, first-time users and beginners need to spend some time for studying and practicing in order to skillfully manipulate molecular models and the system. The best way to resolve the problem is to have a face-to-face session of teaching and learning VRMMS. However, it is not practically recommended in the sense that the users are remotely located. It follows that the learning time could last longer than desired. In this paper, we propose to use Second Life [2] combining with VRMMS for removing the problem. It can be used in building a shared workplace over the Internet where molecular simulations using VRMMS can be exercised, taught, learned and practiced. Through the web, users can collaborate with each other using VRMMS. Their avatars and tools of molecular simulations can be remotely utilized in order to provide with senses of 'being there' to the remote users. The users can discuss, teach and learn over the Internet. The shared workspaces for discussion and education are designed and implemented in Second Life. Since the activities in Second Life and VRMMS are designed to realistic, the system is expected to help users in improving their learning and experimental performances.

• IMMUNE NETWORK
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• v.21 no.5
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• pp.34.1-34.16
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• 2021

Sjögren's syndrome (SS) is an autoimmune disease characterized by dryness of the mouth and eyes. The glandular dysfunction in SS involves not only T cell-mediated destruction of the glands but also autoantibodies against the type 3 muscarinic acetylcholine receptor or aquaporin 5 (AQP5) that interfere with the secretion process. Studies on the breakage of tolerance and induction of autoantibodies to these autoantigens could benefit SS patients. To break tolerance, we utilized a PmE-L peptide derived from the AQP5-homologous aquaporin of Prevotella melaninogenica (PmAqp) that contained both a B cell "E" epitope and a T cell epitope. Repeated subcutaneous immunization of C57BL/6 mice with the PmE-L peptide efficiently induced the production of Abs against the "E" epitope of mouse/human AQP5 (AQP5E), and we aimed to characterize the antigen specificity, the sequences of AQP5E-specific B cell receptors, and salivary gland phenotypes of these mice. Sera containing anti-AQP5E IgG not only stained mouse Aqp5 expressed in the submandibular glands but also detected PmApq and PmE-L by immunoblotting, suggesting molecular mimicry. Characterization of the AQP5E-specific autoantibodies selected from the screening of phage display Ab libraries and mapping of the B cell receptor repertoires revealed that the AQP5E-specific B cells acquired the ability to bind to the Ag through cumulative somatic hypermutation. Importantly, animals with anti-AQP5E Abs had decreased salivary flow rates without immune cell infiltration into the salivary glands. This model will be useful for investigating the role of anti-AQP5 autoantibodies in glandular dysfunction in SS and testing new therapeutics targeting autoantibody production.

• Current Photovoltaic Research
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• v.2 no.2
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• pp.48-52
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• 2014

A photovoltaic cell of CuPc:P3HT:PCBM was introduced to extend the light absorption in the visible wavelength between 300~500 and 550~800 nm. By fabricating the photovoltaic cells of ITO / PEDOT:PSS / CuPc:P3HT:PCBM / BCP / Al with small-molecular and polymer donating materials blended layer, we demonstrated a high PCE of 4.20% with high Jsc of $10.05mA/cm^2$. This performance of photovoltaic cell with the blended layer of small-molecular and polymer can be competitive with that of tandem cells.

• 한국정보디스플레이학회:학술대회논문집
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• 2009.10a
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• pp.607-609
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• 2009

We present a Brownian molecular dynamics computer simulation method for calculating the rotational viscosity of the liquid crystal mixture comprising pentylcyanobiphenol (5CB) and decylcyanobiphenol (10CB). Mean director of the ensemble has been used as a nematic director. Results show a good agreement with experimental ones [Sudeshna DasGupta et al., Physics Letters A 306(2003)235-242].

• Membrane Journal
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• v.30 no.4
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• pp.242-251
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• 2020

Computer simulation tools mainly used for polymer materials and polymeric membranes are divided into various fields depending on the size of the object to be simulated and the time to be simulated. The computer simulations introduced in this review are classified into three categories: Quantum mechanics (QM), molecular dynamics (MD), and mesoscale modeling, which are mainly used in computational material chemistry. The computer simulation used in polymer research has different research target for each kind of computational simulation. Quantum mechanics deals with microscopic phenomena such as molecules, atoms, and electrons to study small-sized phenomena, molecular dynamics calculates the movement of atoms and molecules calculated by Newton's equation of motion when a potential or force of is given, and mesoscale simulation is a study to determine macroscopically by reducing the computation time with large molecules by forming beads by grouping atoms together. In this review, various computer simulation programs mainly used for polymers and polymeric membranes divided into the three types classified above will be introduced according to each feature and field of use.