• Bulletin of the Korean Chemical Society
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• 제34권11호
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• pp.3327-3334
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• 2013

Infrared multiphoton dissociation (IRMPD) spectra of various protonated 1,2-diaminoethane-water clusters DAE-$H^+-(H_2O)_n$ (n = 1-6) were measured in the wavelength range of 3000-3800 $cm^{-1}$. The IRMPD spectra of the well separated ionic clusters were simulated by the MP2 method employing various basis sets. Comparison of the IRMPD spectra with the theory indicates that each cluster may exist as several low-lying conformers, and the sum spectra of the various conformers reveal almost one to one correspondence between theory and experiment. Free N-H and O-H stretches are observed in the ranges of 3400-3500 and 3600-3800 $cm^{-1}$, respectively. The $O-H{\cdots}N$ and $N-H{\cdots}O$ stretches are, however, observed in the broad region of 3000-3600 $cm^{-1}$. The theoretical calculations on DAE-$H^+-(H_2O)_n$ (n = 1-4) show gradual decrease of the average binding energy between DAE-$H^+$ and $H_2O$ as the cluster size increases, attaining the lowest value of 55 kJ/mol when n = 4. We found a low energy barrier of 21 kJ/mol to the isomerization converting the lowest energy cluster of DAE-$H^+-(H_2O)_n$ to the second lowest one.

• Bulletin of the Korean Chemical Society
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• 제27권4호
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• pp.508-514
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• 2006

In this study, we have performed ab initio computer simulations to investigate the conformational and complexation characteristics of the trimethyl ether of p-tert-butylmonodeoxycalix[4]arene (6) with a potassium ion. The structures of different conformers of 6 and their potassium complexes were optimized by using ab initio RHF/6-31G and B3LYP/6-31G(d,p) methods. The relative stability of the various conformers of the uncomplexed 6 is in following order: cone (most stable) > 1-partial-cone ~ 2i-partial-cone > 2-partial-cone ~ 1,3-alternate > 3i-partial-cone. However, the relative stability of the conformational complexes of 6 with $K^+$ is in the following order: 2-partial cone ~ 1,3-alternate > cone > 3-partial cone > 1-partial cone (least stable). The highest binding strengths of 2-partial-cone and 1,3-alternate complexes originate from two strong cation-$\pi$ interactions and two strong cation-oxygen interactions in the complex of 6+$K^+$. Due to the cation-$\pi$ interactions, the calculated C-C bond distances in the arenes of the $K^+$-complexes are about 0.0048 $\AA$ longer than the values of their isolated hosts.

• 한국산학기술학회논문지
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• 제16권2호
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• pp.1563-1570
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• 2015

본 연구는 올리고펩티드의 연쇄성장 과정에서의 배좌의 변화를 조사하기 위하여 알라닌 올리고머 모델의 2량체 부터 5량체 까지 양자화학 계산(QCC)에 의한 구조최적화 계산을 하였다. 말단기의 영향을 확인하기 위하여 N말단 및 C말단이 공히 amide 구조를 갖는 "amide type" ($CH_3CONH-and-CONHCH_3$)과 N말단만이 methyl 구조를 갖는 "methyl type" ($CH_3NH-and-CONHCH_3$)의 2종류 모델을 준비하였다. 5량체 까지의 구조 최적화 계산 결과 3종류의 형태이성질체로 수렴이 되었다. 안정성이 높은 순서로 각각 ${\alpha}$ 나선형, PPII 유사형, ${\beta}$ 확장형으로 나타났으며, 사슬회전 방향이 서로 반대인 형태이성질체간의 에너지 값은 동일하게 나타났다 (5량체, "amide type" 좌 우회전형: ${\Delta}E=-1.05$, "methyl type" 좌 우회전형: ${\Delta}E=-1.62$). ${\alpha}$ 나선형의 모노머 단위당 에너지변화(${\Delta}E$)는 모노머의 증가와 함께 감소하였다.

• Bulletin of the Korean Chemical Society
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• 제21권3호
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• pp.281-290
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• 2000

We varied recombination method of fenetic algorithm (GA), i.e., crossover step, to compare efficiency of these methods, and to find more optimum GA method. In one method (A), we select two conformations(parents) to be recombined by systematic combination of lowest energy conformations, and in the other (B), we select them in a ratio proportional to the energy of the conformation. Second variation lies in how to select crossover point. First, we select it randomly(1). Second, we select range of residues where internal energy of the molecule does not vary for more than two residues, select randomly among such regions, and we select either thr first (2a) or the second residue (2b) from the N-terminal side, or the first (2c) or the second residue (2d) from the C-terminal side in the selected region for crossover point. Third, we select longest such hregion, and select such residue(as cases 2) (3a, 3b, 3c or 3d) of the region. These methods were tested in a 2-dimensionl lattice system for 8 different sequences (the same ones used by Unger and Moult., 1993). Results show that compared to Unger and Moult's result(UM) which corresponds to B-1 case, our B-1 case performed similarly in overall. There are many cases where our new methods performed better than UM for some different sequences. When cooling factor affecting higher energy conformation to be accepted in Monte Carlo step was reduced, our B-1 and other cases performed better than UM; we found lower energy conformers, and found same energy conformers in a smaller steps. We discuss importance of cooling factor variation in Monte Carlo simulations of protein folding for different proteins. (A) method tends to find the minimum conformer faster than (B) method, and (3) method is superior or at least equal to (1) method.

• ETRI Journal
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• 제46권2호
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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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• 제32권11호
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• pp.3855-3860
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• 2011

The competitive solvent extractions of alkali and alkaline earth metals by di-ionizable calix[4]arene nano-baskets were studied using nine conformers of calix[4]arene nano-baskets. The objective of this work is to assess the variation of macrocycle conformation, orientation and position of pendant moieties upon the extraction parameters (efficiency, selectivity and $pH_{1/2}$) of the complexes. The results revealed that alternation of ring conformation in calixarene scaffold affects the solvent extraction parameters towards alkali and alkaline earth metals, while changing the orientation of pendant moieties from ortho- to para- as well as cis- to trans-analogues depicted no changes in those extraction parameters.

• Bulletin of the Korean Chemical Society
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• 제33권3호
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• pp.917-924
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• 2012

The conformational study of glycerol has been carried out using the M06-2X/cc-pVTZ level of theory in the gas phase and the SMD M06-2X/cc-pVTZ level of theory in water in order to understand its conformational preferences and solvation effects. Most of the preferred conformers of glycerol have two $C_5$ hydrogen bonds in the gas phase, as found by the analysis of calorimetric data. It has been known that the solvation drove the hydrogen bonds of glycerol to be weaker and its potential surface to be fatter and that glycerol exists as an ensemble of many feasible local minima in water. The calculated populations of glycerol in the gas phase and in water are consistent with the observed values, which are better than the previously calculated ones at the G2(MP2), CBS-QB3, and SM5.42 HF/6-31G(d) levels of theory.

• 대한약학회:학술대회논문집
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• 대한약학회 2002년도 Proceedings of the Convention of the Pharmaceutical Society of Korea Vol.2
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• pp.363.3-364
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• 2002

Unmodified nucleosides exist in either S-type or N-type conformation, but due to the low energy barrier between this two dominating conformers a fast equilibrium between them exists in solution state. Therefore. many approaches to lock the puckering of the furanose ring in N-type or S-type have been made since HIV-1 reverse transciptase is able to discriminate between two conformationally locked carbocyclic AZT triphosphate analogues. (omitted)

• 약학회지
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• 제41권3호
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• pp.298-304
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• 1997

Molecular mechanics and conformation search methods were carried oyt to investigate the relationship between conformations and thromboxane synthetase ingibitory activities of om ega-pyridylalkenoic acids. The initial geometries of ${\omega}$-pyridylalkenoic acids and heme part of cytochrome P-450 were obtained from MM+ geometry optimization. The bond lenths and angles were not varied by step during the conformation searching. Stable conformers of some ${\omega}$-pyridylalkenoic acids were obtained by comformational search method. The distances were 8.5~10.8 ${\AA}$- between N atom at 3-position of pyridine ring and C atom at carboxylic group of stable ${\omega}$-pyridylalkenoic acids. The conformations of ${\omega}$-pyridylalkenoic acids and heme part complex were determined by same method. In theses structures, benzene ring and ethylene group in ${\omega}$-pyridylalkenoic acids are making the structure more rigid and increase inhbitory activity. The electron donating groups in C atom shich is connected to pyridine ring also increase activity.

• 자연과학논문집
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• 제16권1호
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• pp.129-141
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• 2005

The equilibrium geometry, adiabatic electron affinity, harmonic vibrational frequencies, and infrared intensities of 1,4,6,9-Tetra chlorinated dibenzo-$\rho$-dioxin anion have been studied using B3LYP method. The local minimum conformation is found to be twisted form with $D_2$ symmetry. The predicted adiabatic electron affinity is 0.54 eV. The predicted inversion barrier between twisted and planar conformers was 0.9 kcal/mol, thus we expect that experimentally observed structure seems to be planar. the characteristic IR band of 1,4,6,9-TCDD anion appears at 1510 $cm^4$, which is a benzene ring skeleton vibration mode related with CaCb and C2C3 bond. this characteristic band could be sued for identication of 1,4,6,9-TCDD anion.