• ETRI Journal
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• v.46 no.2
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• pp.290-306
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• 2024

To treat the novel COronaVIrus Disease (COVID), comparatively fewer medicines have been approved. Due to the global pandemic status of COVID, several medicines are being developed to treat patients. The modern COVID medicines development process has various challenges, including predicting and detecting hazardous COVID medicine responses. Moreover, correctly predicting harmful COVID medicine reactions is essential for health safety. Significant developments in computational models in medicine development can make it possible to identify adverse COVID medicine reactions. Since the beginning of the COVID pandemic, there has been significant demand for developing COVID medicines. Therefore, this paper presents the transferlearning methodology and a multilabel convolutional neural network for COVID (MLCNN-COV) medicines development model to identify negative responses of COVID medicines. For analysis, a framework is proposed with five multilabel transfer-learning models, namely, MobileNetv2, ResNet50, VGG19, DenseNet201, and Inceptionv3, and an MLCNN-COV model is designed with an image augmentation (IA) technique and validated through experiments on the image of three-dimensional chemical conformer of 17 number of COVID medicines. The RGB color channel is utilized to represent the feature of the image, and image features are extracted by employing the Convolution2D and MaxPooling2D layer. The findings of the current MLCNN-COV are promising, and it can identify individual adverse reactions of medicines, with the accuracy ranging from 88.24% to 100%, which outperformed the transfer-learning model's performance. It shows that three-dimensional conformers adequately identify negative COVID medicine responses.

• Bulletin of the Korean Chemical Society
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• v.33 no.5
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• pp.1561-1565
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• 2012

The structures of the four lowest alanine conformers, along with their radical cations and the effect of ionization on the intramolecular proton transfer process, are studied using the density functional theory and MP2 method. The energy order of the radical cations of alanine differs from that of the corresponding neutral conformers due to changes in the basicity of the $NH_2$ group upon ionization. Ionization favors the intramolecular proton transfer process, leading to a proton-transferred radical-cation structure, [$NH_3{^+}-CHCH_3-COO{\bullet}$], which contrasts with the fact that a proton-transferred zwitterionic conformer is not stable for a neutral alanine in the gas phase. The energy barrier during the proton transfer process is calculated to be about 6 kcal/mol.

• Bulletin of the Korean Chemical Society
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• v.29 no.10
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• pp.1893-1897
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• 2008

We have performed DFT calculations to investigate the conformational characteristics and hydrogen bonds of the p-tert-butylcalix[5]arene (1) and p-tert-butylcalix[4]arene (2). The structures of different conformers of 1 were optimized by using B3LYP/6-31+G(d,p) method. The relative stability of the various conformers of 1 is in the following order: cone (most stable) > 1,2-alternate > partial-cone > 1,3-alternate. The relative stability of four conformers of 2 is in the following order: cone (most stable) > partial-cone > 1,2-alternate > 1,3-alternate. The primary factor affecting the relative stabilities of the various conformers of the 1 and 2 are the number and strength of the intramolecular hydrogen bonds. The hydrogen-bond distances are discussed based on different calculation methods.

• Coupled systems mechanics
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• v.6 no.3
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• pp.369-376
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• 2017

Intermolecular interaction energies and conformer geometries of the hydrogen bonded acrylamide dimers have been studied by using the second-order Møller-Plesset (MP2) perturbation theory and the density functional theory (DFT) with 17 density functionals. Dunning's correlation consistent basis sets (up to aug-cc-pVTZ) have been used to study the basis set effects. The DFT calculated interaction energies are compared to the reference energy data calculated by the MP2 method and the coupled cluster method at the complete basis set (CCSD(T)/CBS) limit in order to determine the relative performance of the studied density functionals. Overall, dispersion-energy-corrected density functionals outperform uncorrected ones. The ${\omega}B97XD$ density functional is particularly effective in terms of both accuracy and computational cost in estimating the reference energy values using small basis sets and is highly recommended for similar calculations for larger systems.

• Journal of Photoscience
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• v.6 no.4
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• pp.157-158
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• 1999

The conformational studies of glycinemethylester have been carried out by the ab initio method. We have optimized the geometries of glycinemethylester at various levels of sophisticated for electron exchange and correlation within MP2 level. The scale factors of glycinemethylester were used to obtain the scaled ab initio force field of the minimum energy conformer of it, which was used to predict the vibrational frequencies and their potential energy distribution. The Raman spectra of the glycinemethylester were compared with the observed one and the other calculated with HF/6-3IG level.

• YAKHAK HOEJI
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• v.41 no.6
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• pp.765-772
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• 1997

Conformational analyses on thromboxane $A_2$ (Tx$A_2$) and thromboxane $A_2$ receptor antagonists (TxRA) were carried out by molecular mechanics method. Based on the assumption that active conformer is the nonintrahydrogen bonding and more stable former of Tx$A_2$ and TxRA, the molecular structural requirements for potent TxA2 receptor antagonists are like below: 1) The distance is 5.0-5.6${\AA}$ between C atom of carboxyl group and S atom of sulfonyl group or C atom which is bonded to hydroxyl group in the active conformers. 2) The putative active conformers of Tx$A_2$and TxRAs are hairpin-like forms.

• Bulletin of the Korean Chemical Society
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• v.21 no.3
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• pp.300-304
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• 2000

The B3LYP method based on the density functional theory(DFT) is shown to be much better than the ab initio MP2 method for structural determination of diphosphadithiatetrazocine systems having transannular S--S bonding. The presence of bonding between the two sulfur atoms across the cyclic ring is theoretically confirmed in the case of the neutral diphosphadithiatetrazocine. The S--S dobding disappears in the ionized species. The planarity of the dicationic heterocyclic ring system turns out to be closely associated with the $\pi-electron$ delocalization over the entire ring as well as the N-S-N bonds, which become stiffened upon ionizaiton. In the case of dianionic species, the chair-boat and chair conformers are nearly degenerate and far more stable than the crown conformer.

• Bulletin of the Korean Chemical Society
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• v.9 no.3
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• pp.171-175
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• 1988

The spectral properties of piroxicam in different solvents are similar to those of its skeletal precursor, HMBDC. The maximum absorption and emission wavelengths strongly depend on the hydrogen bonding ability of the solvent, and it is shown that intramolecular hydrogen bonding between the -OH and the ortho carbonyl group of the parent benzothiazine ring plays an important role in the solvent-dependence of their spectroscopic properties. The fluorescence spectra in aprotic nonpolar solvent exhibit abnormally large Stokes-shifted (${\sim}9,000cm^{-1}$) emission bands in contrast to the spectra in water. In ethanol, dual emission bands with two different fractional components of lifetimes have been observed. These results suggest that the abnormally red-shifted emission is attributed to the proton transferred form of an intramolecularly hydrogen-bonded closed conformer.

• Bulletin of the Korean Chemical Society
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• v.32 no.11
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• pp.3979-3990
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• 2011

Eight ionizable nano-baskets of cone 25,26-di(carboxymethoxy)calix[4]arene-crown-3,4,5,6 were synthesized and were verified by $^1H$ and $^{13}C$ NMR spectroscopy, IR spectroscopy and elemental analysis. The competitive solvent extractions of alkali and alkaline earth metal cations were studied using such nano-baskets. The novelty of this study is including three binding units of calixarene's bowl, crown ether's ring and electron-donor ionizable moieties in a unique scaffold to assess the binding tendency towards the cations. The objective of this work is to study the extraction efficiency, selectivity and $pH_{1/2}$ of such complexes. The result of solvent extraction experiments indicated that these compounds were effective extractants of alkali and alkaline earth metal cations. Their selectivities were greatly influenced by the acidity of solution and the conformations of the calixcrown. One conformer was selective to $Na^+$ in pH ${\geq}$ 4, while the other was highly selective to $Ba^{2+}$ in pH 6 and upper.

• Bulletin of the Korean Chemical Society
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• v.35 no.5
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• pp.1323-1328
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• 2014

Molecular structures of the various conformational stereoisomers of 2,8,14,20-cyanophenyl pyrogallol[4]arenes 1 were optimized using the mPW1PW91 (hybrid Hartree-Fock density functional) calculation method. The total electronic and Gibbs free energies and the normal vibrational frequencies of the different structures from three major conformations (CHAIR, TABLE, and 1,2-Alternate) of the four stereoisomers [1(rccc), 1(rcct), 1(rctt), and 1(rtct)] were analyzed. The mPW1PW91/6-31G(d,p) calculations suggested that $1(rcct)_{1,2-A}$, 1(rctt)CHAIR, and $1(rtct)_{CHAIR}$ were the more stable conformations of the respective stereoisomers. Hydrogen bonding is the primary factor for the relative stabilities of the various conformational isomers, and maximizing the ${\pi}-{\pi}$ interaction between the cyanophenyl rings is the secondary factor. The calculated IR spectra of the more stable conformers [$1(rctt)_{CHAIR}$, $1(rcct)_{1,2-A}$, $1(rtct)_{CHAIR}$] were compared with the experimental IR spectrum of $1(rtct)_{CHAIR}$.