• Bulletin of the Korean Chemical Society
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• v.31 no.4
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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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• v.32 no.4
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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.

• Proceedings of the Korean Society for Bioinformatics Conference
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• 2000.11a
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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.

• Journal of Internet Computing and Services
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• v.21 no.5
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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.

• Proceedings of the Korean Vacuum Society Conference
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• 2007.08a
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• pp.143-143
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• 2007

• Journal of the Korean Chemical Society
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• v.55 no.3
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• pp.354-363
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• 2011

Quantum-chemistry study was explored to investigate the electronic structures, absorption and phosphorescence mechanism, as well as electroluminescence (EL) properties of three red-emitting Ir(III) complexes, $(fpmqx)_2Ir$(L) {fpmqx=2-(4-fluorophenyl)-3-methyl-quinoxaline; L=triazolylpyridine (trz) (1); L=picolinate (pic) (2) and L=acetylacetonate (acac) (3)}. The calculated results show that the HOMO distribution for 1 is mainly localized on trz moiety due to its stronger ${\pi}$-electron acceptor ability, and HOMO for 2 and 3 is the combination of Ir d- and phenyl ring ${\pi}$-orbital. The higher phosphorescence yields and differences among 1-3 are investigated in this paper. In addition, the reasons of higher EL efficiency of 2 than 1 and 3 have been rationalized.

• Bulletin of the Korean Chemical Society
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• v.33 no.9
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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.

• The Journal of Korean Institute for Practical Engineering Education
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• v.3 no.2
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• pp.18-26
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• 2011

Computational chemistry is one of the chemistry fields that deals with the theoretical chemistry problem using computer calculations and can be described as the chemistry lab moved on computer space. In line with recent enhancement of processing capability of computers, utilization of high performance computer cannot be overemphasized in the field of computational chemistry in performing complex calculation of huge molecular structure and simulation. While they have to use commands and consoles for high performance computer to execute complex calculation of huge molecular structure and simulation, most of students in natural science and engineering, who are not experts in computer technically, are likely to be unaware of UNIX. Under the circumstances, web-based educational support system for computational chemistry is needed to enable them to practice computational chemistry, even not knowing UNIX command. In this study, e-Chem, one of such educational support systems, is developed by using Liferay portal platform, which is a Java open source more oriented to standard and outstanding in its content management and collaboration function than other web portals. By using this system, even students who are not familiar with computer, are expected to take part in lab classes and save time learning Unix command and also enhance the learning efficiency by using familiar interface.

• 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.

• Bulletin of the Korean Chemical Society
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• v.29 no.2
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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.