• Genomics & Informatics
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• 제5권1호
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• pp.24-29
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• 2007

Computational virtual screening has become an essential platform of drug discovery for the efficient identification of active candidates. Moleculardocking, a key technology of receptor-centric virtual screening, is commonly used to predict the binding affinities of chemical compounds on target receptors. Despite the advancement and extensive application of these methods, substantial improvement is still required to increase their accuracy and time-efficiency. Here, we evaluate several advanced structure-based virtual screening approaches for elucidating the rank-order activity of chemical libraries, and the quantitative structureactivity relationship (QSAR). Our results show that the ensemble-average free energy estimation, including implicit solvation energy terms, significantly improves the hit enrichment of the virtual screening. We also demonstrate that the assignment of quantum mechanical-polarized (QM-polarized) partial charges to docked ligands contributes to the reproduction of the crystal pose of ligands in the docking and scoring procedure.

• 한국자기공명학회논문지
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• 제5권2호
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• pp.118-129
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• 2001

Binding interactions of cationic porphyrins, T4MPyP and TMAP with DNA oligomer d(CGCGAATTCGCG), were studied with NMR spectroscopy, W and CD spectroscopic method. Two porphyrins showed significant differences in NMR, UV and CD data upon binding to DNA. T4MPyP was considered to position more closely to DNA bases through partial intercalation as well as ionic intercalation between the positive charges of porphyrin and phosphate group of DNA at 5’-GC-3’steps. Contrast to this, TMAP was thought to bind to phosphate of DNA more or less outside of the groove.

• Journal of Pharmaceutical Investigation
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• 제26권3호
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• pp.155-168
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• 1996

The active site of cyclooxygenase was modeled by complementary receptor-cavity mapping procedure using 3D structures of the non-steroidal antiinflammatory drugs (NSAIDs). A total of 50 NSAIDs were chosen as data ligands which compete the same site on the enzyme. Partial atomic charges were estimated, and the energetic differences for various conformations were calculated so as to meet the need for a most efficient overlapping of the probably-equivalent functional groups of the ligand molecules. The structure activity relationships of the NSAIDs, if available, were fully considered throughout the modeling. The overall shape of the model obtained is similar to a boot-without-bottom. Most of inner surface of the cavity appeared as hydrophobic; two polar counterparts except the carboxyl-binding position were found. By this model, some clear explanations could be given on the experimental observations which were not satisfiably understood yet.

• 통합자연과학논문집
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• 제4권2호
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• pp.99-102
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• 2011

Effect of protonation and deprotonation of ionization compounds is an important application in Comparative molecular field analysis (CoMFA). There are enough information's were reported about different CoMFA applications such as Series design and selection of training set, Geometries and optimizations of molecules, Effect of partial atomic charges, bioactive conformations and alignment, Interaction energy fields, Effects of different grid spacing etc. However limited information's are available about the ionization of compounds. This study aimed at the critical review of about the effects of protonation of ionizable molecules and its impact on the predictability of CoMFA models. We also discussed about previous implications and the things needed to be considered to come for a final conclusion about its impact on CoMFA predictability.

• Bulletin of the Korean Chemical Society
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• 제34권8호
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• pp.2491-2494
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• 2013

The effect of additives in an electrolyte solution on the conversion efficiency of a dye sensitized solar cell was investigated. A density functional theory (DFT) method was used to examine the physical and chemical properties of nitrogen-containing additives adsorbed on a $TiO_2$ surface. Our results show that additives which cause lower partial charges, higher Fermi level shifts, and greater adsorption energies tend to improve the performance of DSSCs. Steric effects that prevent energy losses due to electron recombination were also found to have a positive effect on the conversion efficiency. In this work, 3-amino-5-methylthio-1H-1,2,4-triazole (AMT) has been suggested as a better additive than the most popular additive, TBP, and verified with experiments.

• 공업화학
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• 제8권6호
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• pp.914-919
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• 1997

본 연구에서는 Bratsch의 전기음성도 동등화 원리를 바탕으로 Pauling의 전기음성도 파라미터를 이용하여 음이온과 비이온 계면활성제의 전기음성도 동등화 및 그룹 전기음성도와 그룹 부분전하를 계산하여 계면활성제의 친수성기와 소수성기의 그룹 부분전하, 전기음성도와 CMC에 대한 특성을 조사하였다. 그 결과 계면활성제의 CMC는 친수성기와 소수성기의 그룹 부분전하와 그룹 전기음성도에 의존한다는 것을 알 수 있었다. 음이온 계면활성제인 경우 소수성기의 탄소수가 증가함에 따라 소수성기에도 음의 부분전하가 비편재화되어 전기음성도가 매우 큰 친수성 그룹의 음의 부분전하가 감소하여 친수성기간의 반발력이 상대적으로 줄어들기 때문에 CMC가 낮아짐을 알수 있다. 비이온 계면활성제의 경우에 소수성기의 탄소수가 증가하면 소수성기에서의 부분전하가 증가하게되며, 전기음성도의 증가가 친수성기의 전기음성도를 감소시켜 CMC가 낮아짐을 알수 있다. 그러나 친수성기의 반복단위가 증가하면 친수성기의 음의 부분전하가 증가하게 되고 따라서 수화능이 증가하기 때문에 계면활성제는 미셀로 존재하기 보다는 물속에 수화되기 때문에 CMC는 증가하게 된다.

• Bulletin of the Korean Chemical Society
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• 제32권5호
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• pp.1604-1612
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• 2011

We developed three-dimensional quantitative structure activity relationship (3D-QASR) models for 17 adamantyl derivatives as P-glycoprotein (P-gp) inhibitors. Eighteen different partial charge calculation methods were tested to check the feasibility of the 3D-QSAR models. Best predictive comparative molecular field analysis (CoMFA) model was obtained with the Austin Model 1-Bond Charge Correction (AM1-BCC) atomic charge. The 3D-QSAR models were derived with CoMFA and comparative molecular similarity indices analysis (CoMSIA). The final CoMFA model ($q^2$ = 0.764, $r^2$ = 0.988) was calculated with an AM1-BCC charge and electrostatic parameter, whereas the CoMSIA model ($q^2$ = 0.655, $r^2$ = 0.964) was derived with an AM1-BCC charge and combined steric, electrostatic, hydrophobic and HB-acceptor parameters. Leave-five-out (LFO) cross-validation was also performed, which yielded good correlation coefficient for both CoMFA (0.801) and CoMSIA (0.656) models. Robustness of the developed models was checked further with 1000 run bootstrapping analyses, which gave an acceptable correlation coefficient for CoMFA (BS-$r^2$ = 0.997, BS-SD = 0.003) and CoMSIA (BS-$r^2$ = 0.996, BS-SD = 0.018).

• JSTS:Journal of Semiconductor Technology and Science
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• 제1권2호
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• pp.95-102
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• 2001

Hafnium oxide thin films for gate dielectric were deposited at $300^{\circ}C$ on p-type Si (100) substrates by plasma enhanced chemical vapor deposition (PECVD) and annealed in $O_2$ and $N_2$ ambient at various temperatures. The effect of hydrogen treatment in 4% $H_2$ at $350^{\circ}C$ for 30 min on the electrical properties of $HfO_2$for gate dielectric was investigated. The flat-band voltage shifts of $HfO_2$capacitors annealed in $O_2$ambient are larger than those in $N_2$ambient because samples annealed in high oxygen partial pressure produces the effective negative charges in films. The oxygen loss in $HfO_2$films was expected in forming gas annealed samples and decreased the excessive oxygen contents in films as-deposited and annealed in $O_2$ or $N_2$ambient. The CET of films after hydrogen forming gas anneal almost did not vary compared with that before hydrogen gas anneal. Hysteresis of $HfO_2$films abruptly decreased by hydrogen forming gas anneal because hysteresis in C-V characteristics depends on the bulk effect rather than $HfO_2$/Si interface. The lower trap densities of films annealed in $O_2$ambient than those in $N_2$were due to the composition of interfacial layer becoming closer to $SiO_2$with increasing oxygen partial pressure. Hydrogen forming gas anneal at $350^{\circ}C$ for samples annealed at various temperatures in $O_2$and $N_2$ambient plays critical role in decreasing interface trap densities at the Si/$SiO_2$ interface. However, effect of forming gas anneal was almost disappeared for samples annealed at high temperature (about $800^{\circ}C$) in $O_2$ or $N_2$ambient.

• Bulletin of the Korean Chemical Society
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• 제31권10호
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• pp.2903-2908
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• 2010

Protein S-nitrosation is common in cells under nitrosative stress. In order to model proteins with S-nitrosocysteine (CysSNO) residues, we first developed an Amber force field for S-nitrosoethanethiol (EtSNO) and then transferred it to CysSNO. Partial atomic charges for EtSNO and CysSNO were obtained by a restrained electrostatic potential approach to be compatible with the Amber-99 force field. The force field parameters for bonds and angles in EtSNO were obtained from a generalized Amber force field (GAFF) by running the Antechamber module of the Amber software package. The GAFF parameters for the CC-SN and CS-NO dihedrals were not accurate and thus determined anew. The CC-SN and CS-NO torsional energy profiles of EtSNO were calculated quantum mechanically at the level of B3LYP/cc-pVTZ//HF/6-$31G^*$. Torsional force constants were obtained by fitting the theoretical torsional energies with those obtained from molecular mechanics energy minimization. These parameters for EtSNO reproduced, to a reasonable accuracy, the corresponding torsional energy profiles of the capped tripeptide ACE-CysSNO-NME as well as their structures obtained from quantum mechanical geometry optimization. A molecular dynamics simulation of myoglobin with a CysSNO residue produced a well-behaved trajectory demonstrating that the parameters may be used in modeling other S-nitrosated proteins.

• Bulletin of the Korean Chemical Society
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• 제28권11호
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• pp.2003-2008
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• 2007

The aminolysis of diphenyl thiophosphinic chloride (2) with substituted anilines in acetonitrile at 55.0 oC is investigated kinetically. Kinetic results yield large Hammett ρX (ρnuc = ?3.97) and Bronsted βX (βnuc = 1.40) values. A concerted mechanism involving a partial frontside nucleophilic attack through a hydrogen-bonded, four-center type transition state is proposed on the basis of the primary normal kinetic isotope effects (kH/kD = 1.0-1.1) with deuterated aniline (XC6H4ND2) nucleophiles. The natural bond order charges on P and the degrees of distortion of 42 compounds: chlorophosphates [(R1O)(R2O)P(=O)Cl], chlorothiophosphates [(R1O)(R2O)P(=S)Cl], phosphonochloridates [(R1O)R2P(=O)Cl], phosphonochlorothioates [(R1O)R2P(=S)Cl], chlorophosphinates [R1R2P(=O)Cl], and chlorothiophosphinates [R1R2P(=S)Cl] are calculated at the B3LYP/ 6-311+G(d,p) level in the gas phase.