• Advances in nano research
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• 제1권3호
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• pp.133-151
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• 2013

The availability of advanced nanotechnological methodologies (experimental and theoretical) has widened the investigation of biological/organic matter in interaction with substrates. Minerals are good candidates as substrates because they may present a wide variety of physico-chemical properties and surface nanostructures that can be used to actively condense and manipulate the biomolecules. Scanning Probe Microscopy (SPM) is one of the best suited techniques used to investigate at a single molecule level the surface interactions. In addition, the recent availability of high performance computing has increased the possibility to study quantum mechanically the interaction phenomena extending the number of atoms involved in the simulation. In the present paper, firstly we will briefly introduce new SPM technological developments and applications to investigate mineral surfaces and mineral-biomolecule interaction, then we will present results on the specific RNA-mineral interaction and recent basics and applicative achievements in the field of the interactions between other fundamental biological molecules and mineral surfaces from both an experimental and theoretical point of view.

• EDISON SW 활용 경진대회 논문집
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• 제2회(2013년)
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• pp.294-298
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• 2013

A FeRh alloy is a well-known efficient magnetocaloric material and some experimental and theoretical studies of bulk FeRh have been reported already by several groups. In this study we report first-principles calculations on magnetic properties of different thickness FeRh thin films in order to investigate the possibility to enhance further the magnetocaloric efficiency. We used two methods of a Vienna Ab-initio Simulation Package (VASP) code and SIESTA package. We found that the FeRh thin films have quite different magnetic properties from the bulk when the thickness is thinner than 6-atomic-layers. While bulk FeRh has a G-type antiferromagnetic(AFM) state, thin films which are thinner than 6-atomic-layers have an A-type AFM state or a ferromagnetic (FM) state. We will discuss possibility of magnetic phase transitions of the FeRh thin films in the view point of a magnetocaloric effect. And we found 4-, 5-, 6-layers films with Fe surface and 7-layers film with Rh surface are FM and they have relatively small magnetocrystalline anisotropy (MCA) energy about less than 70 meV. The small MCA energy leads to reduction of the strength of magnetic field in operating a magnetic refrigerator.

• 한국전기전자재료학회:학술대회논문집
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• 한국전기전자재료학회 2005년도 하계학술대회 논문집 Vol.6
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• pp.172-173
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• 2005

The electronic state of ZnO doped with Y was calculated using the density functional theory. In this study, the program used for the calculation on theoretical structures of ZnO and doped ZnO was Vienna Ab-initio Simulation Package (VASP), which is a sort of pseudo potential method. The detail of electronic structure was obtained by the descrite variational $X\alpha$ (DV-$X\alpha$) method, which is a sort of molecular orbital full potential method. The optimized crystal structures obtained by calculations were compared to the measured structure. The density of state and energy levels of dopant elements was shown and discussed in association with optical properties.

• Bulletin of the Korean Chemical Society
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• 제20권1호
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• pp.42-48
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• 1999

We have performed a quantum-chemical investigation on the conformations and electronic properties of a variety of methoxy-substituted poly(p-phenylenevinylenes) (PPVs) to elucidate the effects of alkoxy substitution. Geometrical parameters for the polymers were fully optimized through Austin Model I (AM I) semi-empirical Hartree-Fock (HF) band calculations. Electronic properties of the polymers were obtained by applying the AM I optimized structures to the modified extended Huckel method. To confirm validity of the AM I conformational results, we also carried out ab initio HF calculations with the 6-31G (d) basis set for a variety of methoxy-substituted divinylbenzenes. It is found that the potential energy surfaces of alkoxy-substituted PPVs are quite shallow around the planar conformations, suggesting that the prepared films possess a variety of conformations with different torsion angle in the solid state, depending on the synthetic conditions. When two alkoxy groups are concurrently substituted at the adjacent sites in the phenylene ring, these groups are subject to rotating around the C(sp2)-O bonds by 70-80° to avoid the strong steric repulsion between them. Consequently, the overlap between the π-type p orbital of oxygen and the π molecular orbitals of the polymer decreases. This leads to a wide gap and a high oxidation potential for tetramethoxy-substituted PPV, compared to those of dialkoxy-substituted PPV.

• 대한화학회지
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• 제67권5호
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• pp.333-338
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• 2023

In this study, the H₂O reaction with SiO clusters was investigated using ab initio Monte Carlo simulations and density functional theory calculations. Three chemistry models, PBE1/DGDZVP (Model 1), PBE1/DGDZVP (Si atom), and aug-cc-pVDZ (O and H atoms), (Model 2) and PBE1/aug-cc-pVDZ (Model 3), were used. The average bond lengths, as well as the relative and reaction energies, were calculated using Models 1, 2, and 3. The average bond lengths of Si-O and O-H are 1.67-1.75 Å and 0.96-0.97 Å, respectively, using Models 1, 2, and 3. The most stable structures were formed by the H transfer from an H₂O molecule except for Si₃O₃-H₂O-1 cluster. The Si₃O₃ cluster with H₂O exhibited the lowest reaction energy. In addition, the Bader charge distributions of the Si_nO_n and (SiO)_n-H₂O clusters with n = 1-7 were calculated using Model 1. We determined that the reaction sites between H₂O and the SiO clusters possessed the highest fraction of electrons.

• Genomics & Informatics
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• 제21권3호
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• pp.41.1-41.11
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• 2023

The Dengue virus M protein is a 75 amino acid polypeptide with two helical transmembranes (TM). The TM domain oligomerizes to form an ion channel, facilitating viral release from the host cells. The M protein has a critical role in the virus entry and life cycle, making it a potent drug target. The oligomerization of the monomeric protein was studied using ab initio modeling and molecular dynamics simulation in an implicit membrane environment. The representative structures obtained showed pentamer as the most stable oligomeric state, resembling an ion channel. Glutamic acid, threonine, serine, tryptophan, alanine, isoleucine form the pore-lining residues of the pentameric channel, conferring an overall negative charge to the channel with approximate length of 51.9 Å. Residue interaction analysis for M protein shows that Ala94, Leu95, Ser112, Glu124, and Phe155 are the central hub residues representing the physicochemical interactions between domains. The virtual screening with 165 different ion channel inhibitors from the ion channel library shows monovalent ion channel blockers, namely lumacaftor, glipizide, gliquidone, glisoxepide, and azelnidipine to be the inhibitors with high docking scores. Understanding the three-dimensional structure of M protein will help design therapeutics and vaccines for Dengue infection.

• Bulletin of the Korean Chemical Society
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• 제34권12호
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• pp.3690-3694
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• 2013

The $H_2Ge=Ge:$ and its derivatives ($X_2Ge=Ge:$, X = H, Me, F, Cl, Br, Ph, Ar${\ldots}{\ldots}$) is a new species. Its cycloaddition reactions is a new area for the study of germylene chemistry. The mechanism of the cycloaddition reaction between singlet state Cl2Ge=Ge: and formaldehyde has been investigated with CCSD(T)//MP2/$6-31G^*$ method. From the potential energy profile, it could be predicted that the reaction has only one dominant reaction pathway. The reaction rule presented is that the two reactants first form a fourmembered Ge-heterocyclic ring germylene through the [2+2] cycloaddition reaction. Because of the 4p unoccupied orbital of Ge: atom in the four-membered Ge-heterocyclic ring germylene and the ${\pi}$ orbital of formaldehyde forming a ${\pi}{\rightarrow}p$ donor-acceptor bond, the four-membered Ge-heterocyclic ring germylene further combines with formaldehyde to form an intermediate. Because the Ge: atom in intermediate hybridizes to an $sp^3$ hybrid orbital after transition state, then, intermediate isomerizes to a spiro-Ge-heterocyclic ring compound via a transition state. The research result indicates the laws of cycloaddition reaction between $H_2Ge=Ge:$ and formaldehyde, and laid the theory foundation of the cycloaddition reaction between $H_2Ge=Ge:$ and its derivatives ($X_2Ge=Ge:$, X = H, Me, F, Cl, Br, Ph, Ar${\ldots}{\ldots}$) and asymmetric ${\pi}$-bonded compounds, which is significant for the synthesis of small-ring and spiro-Ge-heterocyclic compounds. The study extends research area and enriches the research content of germylene chemistry.

• Journal of Photoscience
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• 제9권2호
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• pp.51-54
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• 2002

We propose a novel mechanism (Twist Sharing Mechanism) for the cis-trans photoisomerization of rhodopsin, based on the molecular dynamics (MD) simulation study. New things devised in our simulations are (1) the adoption of Mt. Fuji potentials in the excited state for twisting of the three bonds C9=C10, C11=C12 and C13=14 which are modeled using the detailed ab initio quantum chemical calculations and (2) to use the rhodopsin structure which was resolved recently by the X-ray crystallographic study. As a result, we found the followings: Due to the intramolecular steric hindrance between 20-methyl and 10-H in the retinal chromophore, the C12-C13 and C10-C11 bonds are considerably twisted counterclockwise in rhodopsin, allowing only counterclockwise rotation of the C11 =C12 in the excited state. The movement of 19-methyl in rhodopsin is blocked by the surrounding three amino acids, Thr 118, Met 207 and Tyr 268, prohibiting the rotation of C9=C10. As a result only all-trans form of the chromophore is obtainable as a photoproduct. At the 90$^{\circ}$ twisting of C11=C12 in the course of photoisomerization, twisting energies of the other bonds amount to about 20 kcal/mol. If the transition state for the thermal isomerization is assumed to be similar to this structure, the activation energy for the thermal isomerization around C11=C12'in rhodopsin is elevated by about 20 kcal/mol and the thermal isomerization rate is decelerated by 10$\^$-14/ times than that of the retinal chromophore in solution, protecting photosignal from the thermal noise.

• 새물리
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• 제68권12호
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• pp.1288-1292
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• 2018

반도체 특성을 가지는 이차원 전이금속 칼코겐 화합물 $MoS_2$와 강자성이면서 금속성을 가지는 $VS_2$로 이루어진 수평접합 구조를 기반으로 해서, 0%부터 10%까지 2% 간격으로 변형에 따른 쇼트키 장벽(Schottky Barrier) 변화를 밀도 범함수 이론 계산을 통해 연구하였다. 그 결과, 홀의 쇼트키 장벽이 전자의 쇼트키 장벽에 비해 훨씬 작고, 홀의 쇼트키 장벽 높이가 변형에 따라 선형적으로 감소함을 발견하였다. 특히, 8% 이후의 변형에서 홀의 스핀 업 쇼트키 장벽의 높이가 0에 가까워지는 임계 변형값이 존재함을 발견하였고, 이 임계 변형값 이상에서는 스핀 업 성분의 홀이 $MoS_2/VS_2$ 수평접합구조를 통해 쇼트키 장벽 없이 쉽게 흐르게 됨을 알게 되었다. 이러한 연구 결과는 향후, 변형을 통한 이차원 전이금속 칼코겐 수평 접합구조 기반 소자 특성 최적화에 중요한 기초자료로 이용될 것으로 기대한다.

• 대한화학회지
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• 제55권5호
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• pp.733-740
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• 2011

Multiple regression analysis was used for the calculation of pKa values of 15 substituted benzaldoximes by using various types of descriptors as parameters. These descriptors are based on quantum mechanical treatments. They were derived by employing semi-empirical calculation represented by the PM3 model and an Abinitio method expressed by Hartree-Fock(HF) model performed at the 6-311 G(d, p) level of theory. The parameters tested for their ability to represent the variations observed in the experimental pKa(s) are atomic and structural properties including Muliken charges on the atoms of hydroxyl group and C=N bond, the angle $C_6-C_1-C_7$, and length of O-H bond. Molecular properties are also used like energies of HOMO and LUMO, hardness(${\eta}$), chemical potential(${\mu}$), total energy(TE), dipole of molecule(DM), and electrophilicity index(W). The relation between pKa values and each of these parameters of the studied compounds is investigated. Depending on these relations, two sets of parameters were constructed for comparison between the PM3 and HF methods. The results obtained favor the Abinitio method for such applications although both models proved to have high predictive power and have sufficient reliability to describe the effect of substituents on pKa values of benzaldoxime compounds under consideration which is clear from the values of correlation coefficient $R^2$ obtained and the consistency between the experimental and the calculated values.