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

• 반도체디스플레이기술학회지
• /
• 제21권4호
• /
• pp.6-13
• /
• 2022

The electrostatic phenomenon seriously issued in extreme ultraviolet semiconductor cleaning was studied in junction with molecular dynamic aspect. It was understood that two lone pairs of electrons in water molecule were subtly different each other in molecular orbital symmetry, existed as two states of large energy difference, and became basis for water clustering through hydron bonds. It was deduced that when hydrogen bond formed by lone pair of higher energy state was broken, two types of [H₂O]⁺ and [H₂O]^- ions would be instantaneously generated, or that lone pair of higher energy state experiencing reactions such as friction with Teflon surface could cause electrostatic generation. It was specifically observed that, in case of electrolyzed cathode water, negative electrostatic charges by electrons were overlapped with negative oxidation reduction potentials without mutual reaction. Therefore, it seemed that negative electrostatic development could be minimized in cathode water by mutual repulsion of electrons and [OH]^- ions, which would be providing excellences on extreme ultraviolet cleaning and electrostatic control as well.

• 대한화학회지
• /
• 제41권6호
• /
• pp.277-283
• /
• 1997

질소를 포함한 평면형리간드가 배위된 백금(II)착물([$Pt(L)_2X_2$]; L=isoxazole(isox), 3,5-dimethylisoxazole(3,5-diMeisox), 3-methyl,5-phenylisoxazole(3-Me,5-Phisox), and 4-amino-3,5-dimethylisoxazole(4-ADI); X=Cl, Br)의 항암활성을 분자역학(MM2)법으로 최소에너지를 갖는 구조를 구한 후 확장분자궤도함수(Extended Huckel Molecular Orbital)법으로 조사하였다. X 원자의 알짜전하 값은 cis-, trans-이성체 모두 평면리간드의 N 원자보다 음의 값으로 크게 나타나서, N 원자보다 X 원자의 이탈이 용이함을 알 수가 있었고, ${\sigma}MO$에너지 준위로 비교한 결과도 $Pt(d_{x2-y2})-X(P_x)$의 ${\sigma}MO$에너지 준위$(E{\sigma}_{(Pt-X)})$가 $Pt(d_{x2-y2})-N(P_x)$의 ${\sigma}MO$에너지 준위$(E{\sigma}_{(Pt-N)})$보다 예외없이 높아서 Pt-N보다 Pt-X의 결합이 약함을 알 수 있었다. 또한 X 원자의 cis-, trans-이성체에서의 이탈 용이성을 비교하기 위하여 중심금속과 리간드사이의 ${\sigma}MO$에너지준위로 비교한 결과, trans-이성체에서 $Pt(d_{x2-y2})-N(P_x)$의 ${\sigma}MO$에너지준위$(E{\sigma}_{(Pt-X)})$가 cis-이성체에서 보다 예외없이 높아서 결합이 약함을 알 수 있었다. 아울러 같은 착물에서 cis-보다 trans-착물에서 Pt-X의 결합이 약함을 알 수 있었다, 따라서 $X^-$이온으로 떨어져 나가는 용이성과 그 구조변화가 항암활성과 관계가 있을 것으로 생각하였다. 즉, $E{\sigma}_{(P-N)}-E{\sigma}_{(P1-X)}$가 클수록 저해활성 계수 logIA값이 크게 나타나서 실험적 사실과 일치함을 알 수 있었다.

• Bulletin of the Korean Chemical Society
• /
• 제10권6호
• /
• pp.504-509
• /
• 1989

The effect of oxygen-deficiency on the charge distributions and orbital energies for small copper oxide clusters representing the superconducting materials $YBa_2Cu_3O_x (6{\leq}x{\leq}7)$ were investigated by the extended Huckel molecular orbital (EHMO) method with the tight-binding model. Our calculations show +3 oxidation state of Cu(1) in the $CuO_3$ chain and +2 or +1 of Cu(2) in the $CuO_2$ layers for $YBa_2Cu_3O_7$ with the nominal charge of $Cu_3$ = +7 (or +5), while for $YBa_2Cu_3O_6$ +1 oxidation state of Cu(1) and +3 (or +2) of Cu(2) in the $CuO_2$ layers with the nominal charge of $Cu_3$ = +7 (or +5). For $Cu_3O_{12}$ cluster representing $YBa_2Cu_3O_7$ with the nominal charge of $Cu_3$ = +7 the Cu(2) $d_{{x^2}-{y^2}}$ orbitals in the $CuO_2$ layers is a typical Jahn-Teller $d^9$ system with the partial hole and the Cu(1) $d_{{_z2}-{_y2}}$ orbital in the $CuO_3$ chain contains hole occupancy. For $Cu_3O_{10}$ cluster representing $YBa_2Cu_3O_6$ with the nominal charge of Cu = +5 the orbital character of the highest partially occupied MO (HPOMO) and the lowest completely unoccupied MO (LCUMO) of $Cu_3O_{12}$ representing $YBa_2Cu_3O_7$ with the nominal charge of $Cu_3$ = +7 is reversed, and the character of Cu(1) $d{{x^2}-{y^2}}$ orbital of LCUMO of the $Cu_3O_{12} $cluster is vanished. It is suggested that the local crystal field environment of Cu(1) by the oxygens in the Cu(1) chain may play a vital role in conductivity and superconductivity, either alone or through cooperative electronic coupling with the Cu(2) layers in $YBa_2Cu_3O_7.$.

• 한국진공학회:학술대회논문집
• /
• 한국진공학회 2014년도 제46회 동계 정기학술대회 초록집
• /
• pp.415.1-415.1
• /
• 2014

Carrying out first-principles calculations, we study N-doped capped carbon nanotube (CNT) electrodes applied to DNA sequencing. While we obtain for the face-on nucleobase junction configurations a conventional conductance ordering where the largest signal results from guanine according to its high highest occupied molecular orbital (HOMO) level, we extract for the edge-on counterparts a distinct conductance ordering where the low-HOMO thymine provides the largest signal. The edge-on mode is shown to operate based on a novel molecular sensing mechanism that reflects the chemical connectivity between N-doped CNT caps that can act both as electron donors and electron acceptors and DNA functional groups that include the hyperconjugated thymine methyl group[1].

• 대한화학회지
• /
• 제20권6호
• /
• pp.507-513
• /
• 1976

새로 合成한 cis-2-butenedialdioxime의 立體構造를 NMR, 攫張分子軌道法(EHT) 및 非等方性效果에 대한 Pople의 model을 사용하여 그 形態를 決定하였다. 이 物質의 두개의 炭素-炭素 單一結合이 炭素-炭素 二重結合의 여섯 $sp^2$ 混成軌道가 이루는 平面에서 같은 方向으로 25˚回轉된 形態임을 알았다.

• Bulletin of the Korean Chemical Society
• /
• 제15권6호
• /
• pp.453-455
• /
• 1994

Semiempirical MO calculations are applied to estimate the substituent effects on acylations of the nonfused N-vinyl-2-amino $\beta-lactams$ having frameworks analogous to 3-cephems. The stabilization energy for the reaction intermediate of the nucleophilic attack by the hydroxide ion is selected as the reactivity index and calculated by AM1 and PM3 methods for the model $\beta-lactams$ with substituents at the C1 and N-vinyl terminal positions. The reactivities are larger for -SH connected to the C1 and strong $\pi-acceptors$ at the N-vinyl terminal implying the large reactivity for known active cephalosporins. Quantum chemical calculation of stabilization energy could be useful in correlating antibiotic activities of many compounds obtained as derivatives of a lead compound.

• Applied Biological Chemistry
• /
• 제38권1호
• /
• pp.90-94
• /
• 1995

벼(Oryza sativa L.)를 위시하여 논잡초인 피(Echinochloa crus-galli)와 물달개비(Monochoria vaginalis Presl)에 대한 phenylvinylsulfone유도체(S)들의 제초활성을 측정 한 바, 발아 전후에 벼(Oryza sativa L.)이외의 잡초에 대하여 현저하게 속효성이고 선택적인 제초활성을 나타내었다. (S)의 phenyl기에 X-치환기가 변화함에 따른, 구조와 제초활성과의 관계(SAR)를 양자 약리학적 방법으로 분석한 바, 피의 경우에는 ${\pi}$상수가 클수록(${\pi}$<0) 그리고 LUMO가 음의 값으로 증가할수록 제초활성이 증가 하였다. 한편, 물달개비의 경우에는 ${\pi}$상수의 적정값(optimal value)이 1.10이었으므로 이 값에 가까울수록 제초활성이 클 것이며 HOMO에 의존적임을 알 수 있었다. 따라서 X-치환기로 전자끌게가 치환됨으로써 ${\pi}$상수가 크고(${\pi}$<01.10) 음의 값으로 HOMO와 LUMO가 클수록 고활성을 나타낼 수 있는 화합물의 조건들에 대하여 검토되었으며 실험사실을 합리적으로 설명할 수 있는 제초활성 작용기작(mode of action)을 가정 하였다.

• Journal of Photoscience
• /
• 제4권2호
• /
• pp.61-67
• /
• 1997

The model based on the idea that the p$_y$-orbital of the carbonyl oxygen is responsible to receiving hydrogen was devised for simulation of intramolecular hydrogen transfer. A Monte Carlo method was applied to free rotation of a molecular chain performed by changing the dihedral angles, and a "hit" was defined as the case when the migrating hydrogen comes within the region defined as the p$_y$-orbital and satisfies all the geometrical requirements for abstraction. A set of parameters was employed for defining the region and the requirements; $\tau$ was defined as the angle formed between O...H vector and its projection on the mean plane of the carbonyl group (- 43$\circ$ < $\tau$ < + 43$\circ$), $\Delta$ as the C=O...H angle (90 -15$\circ$ < $\Delta$ < 90 + 15$\circ$), $\theta$ as the O...H - C angle ( 180 - 80$\circ$< 0 < 180 + 80$\circ$), d as the distance from the center of the lobe of the p$_y$-orbital to hydrogen (0 < d < 1.04 ${\AA}$). The minimum value for the distance between carbonyl oxygen (O$_1$) and the migrating hydrogen (H$_i$) and for that between non-bonded atoms except the pair of O$_1$ and H$_i$ were assumed to be 0.52 ${\AA}$ and 1.54 ${\AA}$, respectively. The apphcation of this model to intramolecular $\beta$-, $\gamma$-, $\delta$-, $\epsilon$-, and $\zeta$-hydrogen abstraction in ketones and $\eta$- and $\theta$- proton transfer in oxoesters gave good results reflecting their photochemical behavior. The model was also used for prediction of photoreactivities of 2-(N,N-dibenzylamino)ethyl 2-, 3- and 4-benzoylbenzoate (1a - c). (1a - c).

• 한국염색가공학회지
• /
• 제28권2호
• /
• pp.57-62
• /
• 2016

We have synthesized five novel phthaloperinone dyes via a condensation reaction to be applied as yellow colorants for liquid crystal display(LCD) color filters. The reaction between 1,8-naphthalic anhydride(1a), 4-chloro-1,8-naphthalic anhydride(1b), 4-bromo-1,8-naphthalic anhydride(1c), 3-nitro-1,8-naphthalic anhydride(1d), 4-nitro-1,8-naphthalic anhydride(1e) and 1,2-diaminoanthraquinone(2) proceeded readily giving a product in 72-88% yields. The synthesized dyes were characterized by UV-Vis, mass spectrometry and elemental analysis. The spectral properties and thermal stability of the dyes were examined. The dyes absorb at around 400-450nm. All five dyes showed satisfactory thermal stability: the dyes retain 99-100% of its original weight at $300^{\circ}C$, 98-100% at $350^{\circ}C$, 92-98% at $400^{\circ}C$, and 84-92% at $450^{\circ}C$. We have quantitatively evaluated the reaction mechanism and reactivity of dye molecules by means of Pariser-Parr-Pople Molecular Orbital Method(PPP-MO).