• Bulletin of the Korean Chemical Society
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• 제31권4호
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• pp.895-900
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• 2010

In order to find a relationship between firefly luciferases structure and bioluminescence spectra, we focus on excited substrate geometries which may be affected by rigid luciferases. Density functional theory (DFT) and time dependent DFT (TDDFT) were employed. Changes in only six bond lengths of the excited substrate are important in determining the emission spectra. Analysis of these bonds suggests the mechanism whereby luciferases restrict more or less the excited substrate geometries and to produce multicolor bioluminescence.

• Bulletin of the Korean Chemical Society
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• 제32권4호
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• pp.1187-1194
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• 2011

The hydrogen abstraction reaction of $CF_3CH_2CHO$ + OH has been studied theoretically by dual-level direct dynamics method. Two stable conformers, trans- and cis-$CF_3CH_2CHO$, have been located, and there are four distinct OH hydrogen-abstraction channels from t-$CF_3CH_2CHO$ and two channels from c-$CF_3CH_2CHO$. The required potential energy surface information for the kinetic calculation was obtained at the MCG3-MPWB//M06-2X/aug-cc-pVDZ level. The rate constants, which were calculated using improved canonical transitionstate theory with small-curvature tunneling correction (ICVT/SCT) were fitted by a four-parameter Arrhenius equation. It is shown that the reaction proceeds predominantly via the H-abstraction from the -CHO group over the temperature range 200-2000 K. The calculated rate constants were in good agreement with the experimental data between 263 and 358 K.

• 한국생물정보학회:학술대회논문집
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• 한국생물정보시스템생물학회 2000년도 International Symposium on Bioinformatics
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• pp.32-34
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• 2000

Computational chemistry is a discipline using computational methods for the calculation of molecular structure, properties, and reaction or for the simulation of molecular behavior. Relating and turning the complexity of data from genomics, high-throughput screening, combinatorial chemical synthesis, gene-expression investigations, pharmacogenomics, and proteomics into useful information and knowledge is the primary goal of bioinformatics. In particular, the structure-based molecular design is one of essential fields in bioinformatics and it can be called as structural bioinformatics. Therefore, the conformational analysis for proteins and peptides using the techniques of computational chemistry is expected to play a role in structural bioinformatics. There are two major computational methods for conformational analysis of proteins and peptides; one is the molecular orbital (MO) method and the other is the force field (or empirical potential function) method. The MO method can be classified into ab initio and semiempirical methods, which have been applied to relatively small and large molecules, respectively. However, the improvement in computer hardwares and softwares enables us to use the ab initio MO method for relatively larger biomolecules with up to v100 atoms or ∼800 basis functions. In order to show how computational chemistry can be used in structural bioinformatics, 1 will present on (1) cis-trans isomerization of proline dipeptide and its derivatives, (2) positional preference of proline in ${\alpha}$-helices, and (3) conformations and activities of Arg-Gly-Asp-containing tetrapeptides.

• 인터넷정보학회논문지
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• 제21권5호
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• pp.97-107
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• 2020

This paper introduces an online experiment environment based on a computational science platform that can be used for various purposes ranging from basic education to quantum chemistry and professional quantum chemistry research. The simulation environment was constructed using a simulation workbench and simulation workflow, which are execution environment services of Science App provided by the computational science platform. We developed an environment in which learners can learn independently without an instructor by selecting experiment topics that can be used in various areas of chemistry, and offering the learning materials of the topics in a form of e-learning content that includes theory and simulation exercises. To verify the superiority of the proposed system, it was compared with WebMO, a state-of-the-art web-based quantum chemistry simulation service.

• 한국진공학회:학술대회논문집
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• 한국진공학회 2007년도 제33회 하계학술대회 초록집
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• pp.143-143
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• 2007

• 대한화학회지
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• 제55권3호
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• pp.354-363
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• 2011

3개의 적색 발광 Ir(III) 착물들인 $(fpmqx)_2Ir$(L) {fpmqx=2-(4-fluorophenyl)-3-methyl-quinoxaline; L=triazolylpyridine (trz) (1); L=picolinate (pic) (2) and L=acetylacetonate (acac) (3)}의 전자 구조, 흡수 및 인광 메커니즘, 전기 발광(EL) 특성을 양자화학적으로 연구하였다. 계산 결과에 따르면, 1의 HOMO는 강한 ${\eth}$-전자 받개 능력을 갖는 trz 부분에 편재되어 있으며, 2와 3의 HOMO는 Ir d-오비탈 과 페닐 고리 ${\pi}$-오비탈의 결합이라는 것을 나타내었다. 이 논문에서는 1-3사이의 인광 수득률과 차이에 대하여 연구하였으며, 1과 3보다 2의 EL 효율이 더 큰 이유를 합리적으로 설명하였다.

• Bulletin of the Korean Chemical Society
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• 제33권9호
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• pp.2937-2942
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• 2012

We have theoretically investigated the magnetic properties of N-confused porphyrin (NCP), tetraphenyl-N-confused porphyrin (TPNCP) and their substituted derivatives with O, S and Se heteroatoms (2ONCP, 2STPNCP, 2SeNCP, 2OTPNCP, etc.) by using DFT method. In the minimum energy structures of the 2OTPNCP, the two couples opposite phenyl substitutes are staggered. In the case of TPNCP, 2STPNCP and 2SeTPNCP, two phenyls being respectively close to or opposite to N-confused pyrrole are found to be pointed the same direction, whilst others are in the opposite direction. Based on the equilibrium structures, the $^1H$ chemical shifts and nucleus-independent chemical shifts (NICS) are calculated in this paper. The ${\pi}$ current density being induced by the tridimensional perpendicular magnetic field transmits the inner section of the pyrrole segments for NCP and TPNCP. As for their substituted derivatives with O, S and Se atoms, the current path passes through the outer section of the two heterorings. The NICS values at the ring critical points of the heterorings are much lower (in absolute value) than those of which is at the center of an isolated pyrrole molecule. The $^1H$ NMR for ${\beta}H$ atoms of the heterorings decreases from O, S to with Se.

• 한국실천공학교육학회논문지
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• 제3권2호
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• pp.18-26
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• 2011

계산화학이란 컴퓨터를 이용한 계산을 통하여 이론 화학의 문제를 다루는 화학의 한 분야로 화학실험실을 컴퓨터로 옮겨 놓은 것이라고 말할 수 있다. 컴퓨터 처리 능력이 향상됨에 따라 거대 분자 구조의 복잡한 계산과 시뮬레이션을 수행하여야 하는 계산화학분야에서의 고성능 컴퓨터 활용은 매우 중요하다. 분자 구조 계산과 시뮬레이션 등의 작업을 위하여 고성능 컴퓨터를 이용하려면 Unix 명령어와 콘솔을 활용하여야 하는데 화학과목을 배우는 이공계 학생들 대부분은 컴퓨터 비전공자로서 Unix에 관하여 모르는 경우가 대부분이다. 그래서 Unix 명령어를 모르더라도 계산화학 실습이 가능한 웹 기반 계산화학 실습 교육 지원 시스템이 필요하다. 본 논문에서 개발한 웹 기반 계산화학 실습 교육 지원 시스템(e-Chem)은 다른 웹 포털 플랫폼보다 표준 지향적이고 콘텐츠 관리 및 협업 기능이 뛰어난 자바 오픈소스인 Liferay 포털 플랫폼을 활용하여 개발하였다. 본 시스템을 활용하면 컴퓨터 비전공자들도 쉽게 계산화학 실습 수업에 참여할 수 있고, Unix 명령어 등을 배우는 시간을 절약할 수 있으며, 친숙한 웹 인터페이스로 학습 효과도 높아질 것으로 기대된다.

• Bulletin of the Korean Chemical Society
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• 제25권7호
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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.

• Bulletin of the Korean Chemical Society
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• 제29권2호
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• pp.305-308
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• 2008

We performed coupled-cluster calculations to determine the intermolecular interaction energy between two TiAu4 clusters. Our ab initio calculations predict that the binding energy is 2.89 eV, which is somewhat larger than the known binding energy of 2.0 eV for TiH4-TiH4. The intermolecular binding energy is relatively high, despite TiAu4 having all the attributes of a magic cluster. The favorable orbital interaction between occupied Au(6s) and unoccupied Ti(3d) orbitals leads to the strong dimeric interaction for TiAu4-TiAu4.