• 통합자연과학논문집
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• 제6권1호
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• pp.8-11
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• 2013

In this manuscript, we report a protocol to determine most of the lowest energy conformations from the ensemble of conformations. 12-crown-4 was taken as study compound to get the most of energy minima conformations. Molecular dynamic (MD) simulation for 1 nanosecond (ns) was performed at 300, 500, 700, 900 and 1100 K temperature. At particular interval conformations were sampled. Then Gaussian program was used to minimize compounds using PM6 energy levels. Duplicates were removed by checking energy as well as mirror image conformations, and only unique conformations were retained for the next $6-31+G^*$ level minimization. It was observed that upto certain increment in temperature the number of unique conformations were increased, but afterword it decreased.

• Bulletin of the Korean Chemical Society
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• 제12권1호
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• pp.61-67
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• 1991

Conformational free energy calculations using an empirical potential function and the hydration shell model (a program CONBIO) were carried out on the neutral L-ascorbic acid (AA) in the unhydrated and hydrated states. The conformational energy was minimized from starting conformations which included possible conformations of six torsion angles in the molecule. The conformational entropy of each low energy conformation in both states was computed using a harmonic approximation. From the analysis of conformational free energies for AA in both states, intramolecular hydrogen bonds (HBs) are proved to be an essential factor in stabilizing the overall conformations, and cause the conformations in both states to be quite different from those in crystal. In the case of hydrated AA, there is a competition between HBs and hydration, and the hydration around the two hydroxyl groups attached to the acyclic side chain forces the molecule to form less stable HBs. The hydration affects strongly the conformational energy surfaces of AA. Several feasible conformations obtained in this work indicate that there exists an ensemble of several conformations in aqueous solution. The calculated probable conformations for the rotation about the C5-C6 bond of the acyclic side chain are trans and gauche +, which are in good agreement with results of NMR experiment.

• 약학회지
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• 제39권3호
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• pp.329-336
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• 1995

Conformational free energy calculations using an empirical potential function and a hydration shell model(program CONBIO) were carried out on hypoglycemic agent acetohexamide and tolazamide in the unhydrated and hydrated states. The initial geometry of sulfonylureas was obtained from X-ray crystallographieal data and homologous molecular fragments. In both states, the feasible conformations were obtained from the calculations of conformational energy, conformational entropy, and hydration free energy by varying all the torsion angles of the molecules. From the calculation results, it is known that the conformations] entropy is the major contribution to stabflize the low-free-energy conformations of two sulfonylureas in both states. But, in hydrated state, the hydration does not directly affect each conformations. The intramolecular hydrogen bonding of sulfonylurea hydrogen and 7-membered nitrogen appeared to the conformations of tolazamide in both states. It is thought that the hydrogen bonding decrease steric hindrance on the receptor binding direction. The substitution of alicyclic or N-heterocyclic ring than that of carbons chain of urea moiety may be properly interaction between sulfonylureas and the putative pancreatic receptor.

• Bulletin of the Korean Chemical Society
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• 제12권2호
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• pp.143-148
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• 1991

In the unhydrated and hydrated states, conformational free energies of L-ascorbic acid anion (AAA) were computed with an empirical potential function and the hydration shell model (a program CONBIO). The conformational energy was minimized from possible starting conformations expressed with five torsion angles of the molecule. The conformational entropy of each low energy conformation in both states was computed using a harmonic approximation. As found in L-ascorbic acid (AA), intramolecular hydrogen bonds (HBs) are proved to be of significant importance in stabilizing the overall conformations of AAA in both states, and give the folded conformations, which are quite different from those in crystal. There are competitions between HBs and hydration around O3 atom of the lactone ring and hydroxyls of the acyclic side chain. Especially, the whole conformation of AAA is strongly dependent on the water-accessibility of O3 atom. Though there is a significant effect of the hydration on conformational surface, the lowest energy conformation of the unhydrated AAA is conserved. The different patterns of HBs and hydration result in the conformations of AAA in both states being different from those of AA. It can be drawn by several feasible conformations obtained in the hydrated state that there exists an ensemble of several conformations in aqueous solution.

• 한국생물물리학회:학술대회논문집
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• 한국생물물리학회 2003년도 정기총회 및 학술발표회
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• pp.75-75
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• 2003

We report here the results on N-acetyl-N'-dimethylamide of proline (Ac-Pro-NM $e_2$) calculated using the ab initio molecular orbital method with the self-consistent reaction field (SCRF) theory at the HF level with the 6-31+G(d) basis set to investigate the conformational preference of polyproline depending on the cis/trans peptide bonds and down/up puckerings along the backbone torsion angle $\square$ in the gas phase, chloroform, and water. In the gas phase, Ac-Pro-NM $e_2$ has seven local minima of tFd, tFu, cFd, cFu, cAu, tAu, and cAd conformations. In particular, polyproline conformations tFd, tFu, cFd, and cFu are found to be more stable than $\square$-helical conformations cAu, tAu, and cAd. In contrast, Ac-Pro-NHMe has seven local minima of tCd, tCu, cBd, cAu, tAu, cFd, and cFu conformations. Conformations tCd and tCu are found to be most stable, which is ascribed to the intramolecular hydrogen bond between C=O of acetyl group and $N^{~}$ H of N'-methyl amide group. The stability of the cFd conformation (i.e., the polyproline I structure) in chloroform is somewhat increased, relative to that in water, although tFd and tFu conformations (i.e., the polyproline II structure) are dominate both in chloroform and water. The population of backbone conformations feasible in chloroform and water is consistent with the experiments. This work is supported by a Korea Research Foundation Grant (KRF-2002-041-C00129).

• 대한화학회지
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• 제21권1호
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• pp.32-37
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• 1977

EHT 분자궤도함수법 계산으로 9가지 furan, thiophene 및 pyrrole의 2-치환체의 우세한 형태를 구명하였다. 계산 결과는 furan 유도체의 우세한 형태는 trans형인데 이것은 주로 정전기적 상호작용에 의하여 안정화되어 있으며 thiophene에서는 hetero 고리의 S원자와 카르보닐 산소와의 전자적 콘쥬게이션이, 그리고 pyrrole에서는 정전기적 및 콘쥬게이션 효과가 안정한 형태를 결정하는데 작용하고 있다. EHT계산 결과는 실험결과와도 잘 일치된다.

• Bulletin of the Korean Chemical Society
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• 제11권2호
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• pp.144-149
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• 1990

Conformational free energy calculations using an empirical potential function (ECEPP/2) and the hydration shell model were carried out on the sulfonylurea herbicides of bensulfuron methyl (Londax) and metsulfuron methyl (Ally). The conformational energy was minimized from starting conformations which included possible combinations of torsion angles in the molecule. The conformational entropy of each conformation was computed using a harmonic approximation. To understand the hydration effect on the conformation of the molecule in aqueous solution, the hydration free energy of each group was calculated and compared each other. It was found that the low-free-energy conformations of two molecules in aqueous solution prefer the overall folded structure, in which an interaction between the carbonyl group of ester in aryl ring and the first amido group of urea bridge plays an important role. From the analysis of total free energy, the hydration and conformational entropy are known to be essential in stabilizing low-free-energy conformations of Londax, whereas the conformational energy is proved to be a major contribution to the total free energy of low-free-energy conformations of Ally.

• 약학회지
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• 제36권6호
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• pp.518-528
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• 1992

To determine the optimal conformation of sulfonylureas, the correlation between conformation and hypoglycemic activity of the two sulfonylureas of tolbutamide and chlorpropamide as hypoglycemic agent was studied using an empirical potential function (ECEPP/2) and the hydration shell model in the unhydrated and hydrated states. The conformational energy was minimized from several starting conformations with possible torsion angles in each molecule. The conformational entropy change of each conformation was computed using a harmonic approximation. To understand the hydration effect on the conformation of the molecules in aqueous solution, the contribution of water-accessible volume of each group or atom in the lowest-free-energy conformation was calculated and compared each other. From comparison of the computed lowest-free-energy conformations of two sulfonylureas, it could be suggested that the hydration of sulfonylurea moiety is related to increase the hypoglycemic activity. From the calculation results, it was known that the conformational entropy is the major contribution to stabilize the low-free-energy conformations of two sulfonylureas in unhydrated state. Whereas, in hydrated state, the hydration free energy largely contributes to the total free energies of low-free-energy conformations of tolbutamide and conformational entropy contributes to stabilize the low-free-energy conformations of chlorpropamide. The torsion angles from phenyl ring to urea moiety of the low-free-energy conformations of the two sulfonylureas were shown the nearly regular trend. On the basis of these results, the conformation exhibiting the optimal hypoglycemic activity of sulfonylureas and the binding direction to pancreatic receptor site A could be predicted. Also, according to the side chain lengthening of urea moiety, tolbutamide showed various conformational change. Therefore, steric effect may be important factor in the interaction between sulfonylureas and the putative pancreatic receptor.

• BMB Reports
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• 제30권5호
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• pp.352-355
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• 1997

The surface adsorbed protein conformations onto the vaccine adjuvants were observed with a Raman spectroscopy by using the maximum adsorption conditions described previously. The adsorbed state Raman vibrational spectra and subsequent spectral analysis display no conformational changes for BSA or IgG relative to their native species in solution.

• 정보처리학회논문지:컴퓨터 및 통신 시스템
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• 제4권1호
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• pp.1-4
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• 2015

본 논문에서는 주어진 채널이 변형될 때, 아미노산들의 유효한 사이드 체인 배치(side chain conformation)를 찾는 알고리즘을 제시한다. 제안된 알고리즘은 아미노산의 유연성에 근거하여 사이드 체인 유연성을 가진 단백질 분자를 구현하고, 채널 변화에 영향을 주는 인접 아미노산(adjacent amino acid)을 추출한다. 인접 아미노산과 이웃(neighbor) 아미노산의 충돌 검사를 수행하여 유효하지 않은 사이드 체인 배치를 제거한 후, 회전각 조합 트리(rotation angle combination Tree)를 구성하여 사이드 체인 배치 중 유효한 것들만을 추출한다.