• Bulletin of the Korean Chemical Society
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• 제26권11호
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• pp.1795-1802
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• 2005

Potential energy curves and internuclear (M-X) distance variations for dissociation reactions of $[MX_4]^{2-}$ into ($[MX_3]^-$ + $X^-$) have been calculated using ab initio Hartree-Fock (HF), second order M$\ddot{o}$ller-Plesset perturbation (MP2), and Density Functional Theory (DFT) methods with a triple zeta plus polarization (TZP) basis set. The equilibrium geometrical structures of $[MX_4]^{2-}$ are optimized to tetrahedral geometry for $[NiX_4]^{2-}$ and square planar geometry for ($[PdX_4]^{2-}$ and $[PtX_4]^{2-}$). The bond (M-X) distances of $[NiCl_4]^{2-}$, $[NiBr_4]^{2-}$, $[PdCl_4]^{2-}$, $[PdBr_4]^{2-}$, $[PtCl_4]^{2-}$, and $[PtBr_4]^{2-}$ at the DFT level are 2.258, 2.332, 2.351, 2.476, 2.367, and 2.493 $\AA$, respectively. The dissociation energies for the bond dissociation of ($[MX_3]^-$${\cdot}{\cdot}{\cdot}$$X^-$) at the DFT level are found to be 4.73 eV for $[NiCl_4]^{2-}$, 4.89 eV for $[NiBr_4]^{2-}$, 4.93 eV for $[PdCl_4]^{2-}$, 5.57 eV for $[PdBr_4]^{2-}$, 5.44 eV for $[PtCl_4]^{2-}$, and 5.87 eV for $[PtBr_4]^{2-}$. As the (M${\cdot}{\cdot}{\cdot}$X) distance of ($[MX_3]^-$${\cdot}{\cdot}{\cdot}$$X^-$) increases, the distance variation (Rt) of trans (M-X) bond at the trans-position is shorter than those (Rc) of two cis (M-X) bonds at the cisposition. Simultaneously the atomic charge variation of trans-X atom is more positive than those of equilibrium $[MX_4]^{2-}$ structures, while the variation of leaving X group is more positive.

• 대한화학회지
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• 제59권5호
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• pp.387-396
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• 2015

HOOO-(H₂O)_n (n=1~5) 클러스터에 대해서 다양한 기저집합과 밀도 범함수 이론(DFT) 및 순 이론(ab initio) 방법을 사용하여 가능한 여러 구조를 최적화하고 결합에너지와 조화진동수를 계산하였다. HOOO 단량체의 경우에는 CCSD(T) 이론 수준에서 trans 구조가 cis 구조보다 열역학적으로 더 안정한 것으로 계산되었다. HOOO-(H₂O)_n 클러스터에 대해서는 B3LYP/aug-cc-pVTZ와 CAM-B3LYP/aug-cc-pVTZ 이론 수준에서 분자 구조를 최적화하고 열역학적으로 가장 안정한 분자구조를 예측하였다. HOOO-H₂O 클러스터의 결합에너지는 MP2//CAM-B3LYP 한 점 에너지 계산에서 영점 진동에너지(ZPVE)와 바탕 집합 중첩에러(BSSE)까지 모두 보정한 후 6.05 kcal/mol로 계산되었으며, n=2-5의 경우에는 물 분자의 수가 증가 할수록 물분자 1개 당 평균 결합에너지는 증가하여 약 7.2 kcal/mol의 값으로 수렴하였다.

• 한국생물정보학회:학술대회논문집
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• 한국생물정보시스템생물학회 2004년도 The 3rd Annual Conference for The Korean Society for Bioinformatics Association of Asian Societies for Bioinformatics 2004 Symposium
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• pp.250-261
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• 2004

A novel method for ab initio prediction of protein tertiary structures, PROFESY (PROFile Enumerating SYstem), is introduced. This method utilizes secondary structure prediction information and fragment assembly. The secondary structure prediction of proteins is performed with the PREDICT method which uses PSI-BLAST to generate profiles and a distance measure in the pattern space. In order to predict the tertiary structure of a protein sequence, we assemble fragments in the fragment library constructed as a byproduct of PREDICT. The tertiary structure is obtained by minimizing the potential energy using the conformational space annealing method which enables one to sample diverse low lying minima of the energy function. We apply PROFESY for prediction of some proteins with known structures, which shows good performances. We also participated in CASP5 and applied PROFESY to new fold targets for blind predictions. The results were quite promising, despite the fact that PROFESY was in its early stage of development. In particular, the PROFESY result is the best for the hardest target T0161.

• 한국재료학회지
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• 제17권12호
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• pp.637-641
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• 2007

The total energy and strength of Mg alloy doped with Al, Ca and Zn, were calculated using the density functional theory. The calculations was performed by two programs; the discrete variational $X{\alpha}\;(DV-X{\alpha})$ method, which is a sort of molecular orbital full potential method; Vienna Ab-initio Simulation Package (VASP), which is a sort of pseudo potential method. The fundamental mixed orbital structure in each energy level near the Fermi level was investigated with simple model using $DV-X{\alpha}$. The optimized crystal structures calculated by VASP were compared to the measured structure. The density of state and the energy levels of dopant elements was discussed in association with properties. When the lattice parameter obtained from this study was compared, it was slightly different from the theoretical value but it was similar to Mk, and we obtained the reliability of data. A parameter Mk obtained by the $DV-X{\alpha}$ method was proportional to electronegativity and inversely proportional to ionic radii. We can predict the mechanical properties because $\Delta{\overline{Mk}}$is proportional to hardness.

• 반도체디스플레이기술학회지
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• 제7권3호
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• pp.35-39
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• 2008

We study the interaction of acetone molecule $[(CH_3)_2CO]$ on Si(001) surface using density functional theory. An acetone molecule is adsorbed on a Si atom of the Si dimer of the Si(001) surface. The adsorption of the acetone molecule on the Si atom at lower height between the two Si atoms of the dimer is more favorable than that on the Si atoms at upper height. Then we calculate an energy variation of dissociation and four-membered ring structures of the acetone molecule adsorbed on the Si surface. Total energy difference between the two structures is about 0.05 eV, indicating that the two structures are almost equally stable. Energy barrier exists when a hydrogen atom is dissociated and adsorbed on the other Si atom of the dimer, while energy barrier does not exist when the adsorbed acetone molecule changes to four-membered ring structure, except for the rotation of the acetone molecule along z-direction. Therefore, four-membered ring structure is kinetically more favorable than the dissociation structure when the acetone molecule is adsorbed on the Si(001) surface.

• 한국진공학회:학술대회논문집
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• 한국진공학회 2014년도 제46회 동계 정기학술대회 초록집
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• pp.180.2-180.2
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• 2014

Opening a bandgap by forming graphene nanoribbons (GNRs) and tailoring their properties via doping is a promising direction to achieve graphene-based advanced electronic devices. Applying a first-principles computational approach combining density functional theory (DFT) and DFT-based non-equilibrium Green's function (NEGF) calculation, we herein study the structural, electronic, and charge transport properties of boron-nitrogen binary edge doped GNRs and show that it can achieve novel doping effects that are absent for the single B or N doping. For the armchair GNRs, we find that the B-N edge co-doping almost perfectly recovers the conductance of pristine GNRs. For the zigzag GNRs, it is found to support spatially and energetically spin-polarized currents in the absence of magnetic electrodes or external gate fields: The spin-up (spin-down) currents along the B-N undoped edge and in the valence (conduction) band edge region. This may lead to a novel scheme of graphene band engineering and benefit the design of graphene-based spintronic devices.

• 한국진공학회:학술대회논문집
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• 한국진공학회 2014년도 제46회 동계 정기학술대회 초록집
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• pp.210.1-210.1
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• 2014

The hexagonal boron nitride (h-BN) sheet, a 2D material like graphene sheet, is comprised of boron and nitrogen atoms. Similar to graphene, h-BN sheet has attractive mechanical properties while it has a wide band gap unlike graphene. Recently, many experimental groups studied the growth of single BN layer by chemical vapor deposition (CVD) method on the copper substrate. To study the initial stage of h-BN growth on the copper surface, we have performed density functional theory calculations. We investigate several adsorption sites of a boron or nitride atom on the Cu surfaces. Then, by increasing the number of adsorbed B and N atoms, we study formation behaviors of the BN flakes on the surface. Several types of BN flakes atoms such as triangular, linear, and hexagonal shapes are considered on the copper surface. We find that the formation of the BN flake in triangular shape is most favorable on the surface. On the basis of the theoretical results, we discuss the growth mechanism of h-BN layer on the copper surfaces in terms of its shapes in the initial stage of growth.

• Mass Spectrometry Letters
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• 제5권4호
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• pp.120-123
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• 2014

The interference of water vapor on the chemical ionization (CI) of hydroxyl radicals (OH) by sulfur hexafluoride ion ($SF_6{^-}$) was investigated using a flow tube system coupled to a high-pressure CI mass spectrometer. Water vapor, which is required to study heterogeneous reactions of OH under real tropospheric conditions, transforms the reagent ion $SF_6{^-}$ into $SF_4O^-$ and $F^-(HF)_n$, resulting in a substantial loss in CI sensitivity. Therefore, under humid conditions, peaks corresponding to OH are drastically diminished, while those corresponding to OH-water complex ions ($[OH(H_2O)_n]^-$) are enhanced. $[OH(H_2O)_3]^-$ was observed as the major OH species. The obsercation of $[OH(H_2O)_n]^-$ by isolating humid conditions to the CI region and preliminary ab initio calculations suggested that $[OH(H_2O)_n]^-$ ions were produced from reactions between OH ions ($OH^-$) and water molecules. An additional helium buffer flow introduced into the CI region reduced loss of the reagent ion and resulted in a partial recovery of OH peak intensities under humid conditions.

• Bulletin of the Korean Chemical Society
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• 제30권10호
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• pp.2233-2239
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• 2009

In the present study, firstly, the variations of the geometric parameters induced by different substituents on boroxine skeleton (symmetrically H, $CH_3$, Cl, F, $NO_2$ substituted boroxines) are investigated by using B3LYP/6-31G(d,p), RHF/6-31G(d,p), and MP2/6-31G(d,p) levels of the theory. The second objective is to estimate the substituent effect on the molecular aromaticity of boroxine derivatives using energetic and NICS criteria. Moreover, the effects of different theoretical levels on NICS values have been investigated in a systematic approach. Lastly, a rotational analysis has been performed to investigate the effect of rotation around the B-Me and B-$NO_2$ bonds on total energy of the system. It has been found that electron withdrawing substituents contribute the aromaticity of boroxine affirmatively. Conversely, electron donors make the system less aromatic. Also, the theoretical vibrational spectra for these boroxine derivatives are presented and compared with the experimental data from the literature.

• Bulletin of the Korean Chemical Society
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• 제33권6호
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• pp.1998-2004
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• 2012

We carried out DFT calculations for monohydrated sulfuric and phosphoric acids. We are interested in clusters which differ in orientation of hydrogen atoms only. Such molecular complexes are close in energy, since they lie in the vicinity of the global minimum energy structure on the flat potential energy surface. For monohydrated sulfuric acid we identified four different isomers. The monohydrated phosphoric acid forms five different conformers. These systems are difficult to study from the theoretical point of view, since binding energy differences in several cases are very small. For each structure, we calculated harmonic vibrational frequencies to be sure that if the optimized structures are at the local or global minima on the potential energy surface. The analysis of calculated -OH vibrational frequencies is useful in interpretation of infrared photodissociation spectroscopy experiments. We employed four different DFT functionals in our calculations. For each structure, we calculated binding energies, thermodynamic properties, and harmonic vibrational frequencies. Our analysis clearly shows that DFT approach is suitable for studying monohydrated inorganic acids with different hydrogen atom orientations. We carried out MP2 calculations with aug-cc-pVDZ basis set for both monohydrated acids. MP2 results serve as a benchmark for DFT calculations.