• Bulletin of the Korean Chemical Society
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• v.16 no.2
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• pp.112-120
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• 1995

The conformational study on malonic acid, hydrogen malonate, malonate, malonyl methyl sulfide, and malonyl methyl sulfide anion, as the model compounds of malonyl-CoA, was carried out using the semiempirical MO methods (MNDO, AM1, and PM3) and hydration shell model. On the whole, the feasible conformations of malonic acid, hydrogen malonate, and malonate seem to be similar to each other. In malonic acid and malonate, two carboxyl groups are nearly perpendicular to the plane of the carbon skeleton, despite of different orientation of two carboxyl groups themselves. In particular, two carboxyl groups of hydrogen malonate are on the plane formed by carbon atoms with an intramolecular hydrogen bond. The calculated results on the geometry and conformation of three compounds are reasonably consistent with those of X-ray and spectroscopic experiments as well as the previous calculations. The orientation of two carbonyl groups of malonyl methyl sulfide is quite similar to that of malonic acid, but different from that of its anion. Especially, the computed probable conformations of the sulfide anion by the three methods are different from each other. The role of hydration seems not to be crucial in stabilizing the overall conformations of malonic acid, hydrogen malonate, malonate, and malonyl methyl sulfide. However, the probable conformations of the unhydrated sulfide anion obtained by the MNDO and AM1 methods become less stabilized by including hydration. The AM1 method seems to be appropriate for conformational study of malonyl-CoA and its model compounds because it does not result in the formation of too strong hydrogen bonds and significant change in conformational energy from one compound to another.

• Journal of the Korean Chemical Society
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• v.18 no.3
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• pp.215-220
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• 1974

Conformations and cofigurations were studied for some ${\alpha},{\beta}$-unsaturated phenylhydrazones which have similar structures to the stucture of butenedial bistosylhydrazone, a precursor of tetrahedrane, by the analysis of their nmr spectra. The chemical shift difference between two solvents, benzene and aliphatic solvents, was applied for the assigning syn and anti structures of phenylhydrazone isomers as a convenient method. In this work, it was found that the phenylhydrazones have syn configurations and also found that the dihedral angles of $CH_a-CH_b$ are around $150^{\circ}$ at room temperature from the the interpretation of the vicinal spin-spin coupling constants. These results were discussed in concerning with their conformations.

• Bulletin of the Korean Chemical Society
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• v.31 no.11
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• pp.3247-3251
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• 2010

Molecular structures of the various conformers for the four stereoisomers of tetra-t-butyl-tetra-O-methylsulfinylcalix[4]arene (1) were optimized using DFT BLYP and mPW1PW91/6-31G(d,p) (hybrid HF-DF) calculation methods. We have analyzed the total electronic and Gibbs free energies and normal vibrational frequencies of 16 different structures from four major conformations (cone (CONE), partial cone (PC), 1,2-alternate (1,2-A), 1,3-alternate (1,3-A)) of the four stereoisomers [1(rccc), 1(rcct), 1(rctt), 1(rtct)]. The mPW1PW91/6-31G(d,p) calculations suggested that the $1(rccc)_{CONE}$, $1(rcct)_{PC}$, $1(rctt)_{PC}$, and $1(rtct)_{1,3-A}$ were the most stable conformations of the respective stereoisomers. These outcomes are in accordance with the experimental structures obtained from X-ray crystallography. The electrostatic repulsion between the sulfinyl and methoxy groups is a primary factor for the relative stabilities of the four different conformations. The IR spectra of the most stable conformers [$1(rccc)_{CONE}$, $1(rcct)_{PC}$, $1(rctt)_{PC}$, $1(rtct)_{1,3-A}$] of each stereoisomer were compared to each other.

• Proceedings of the Korean Biophysical Society Conference
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• 2003.06a
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• pp.76-76
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• 2003

We report here the results on N-acetyl-N'-methylamide of 4-fluoroproline (Ac-Flp-NHMe) 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 stereoelectronic effects on the conformational preference of proline 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, all potential energy surfaces for Ac-Flp-NHMe are quite similar to those of Ac-Pro-NHMe, except that up-puckered conformations are more stabilized than down-puckered ones. In chloroform and water, polyproline structures become dominant, whose populations are larger than those of Ac-Pro-NHMe. In chloroform and water, the populations of polyproline II (i.e., tF conformations) are quite similar to each other, but those of polyproline I (i.e., cF conformations) are larger by 5％ in water than in chloroform. In particular, all cis populations for Ac-Flp-NHMe in the gas phase, chloroform, and water are decreased than those of Ac-Pro-NHMe.

• Proceedings of the PSK Conference
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• 2005.11a
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• pp.103-103
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• 2005

• Proceedings of the PSK Conference
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• 2000.10a
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• pp.201.1-201.1
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• 2000

• Bulletin of the Korean Chemical Society
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• v.35 no.5
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• pp.1403-1408
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• 2014

The cycloaddition reactions of the N-heterocyclic carbene boryl azide with methyl acrylate, butenone, and hexafluoropropene have been investigated theoretically. Solvent effects on these reactions have been explored by calculation that included a polarizable continuum model (PCM) for the solvent (C6H6). The title reaction could produce 4- and 5-substituted 1,2,3-triazolines, respectively. The reaction systems have the higher chemical reactivity with the low barriers and could be favored. Yet the smaller differences have been found to occur in energetics, and the cycloaddition reactions occur for s-trans conformations over s-cis conformations. The calculations indicated that the cycloaddition reaction of the alkenes have certain regioselectivity.

• Applied Biological Chemistry
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• v.41 no.8
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• pp.568-571
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• 1998

The conformations of human insulin precursors, proinsulin and preproinsulin, are described in terms of molecular dynamics simulations. Despite the presence of the C-peptide and/or the signal peptide, molecular dynamics calculations utilizing the hydration shell model over a period of 500 ps indicate that the native conformations of the A and B chains are well conserved in both cases. These results further support the NMR spectroscopy results that the C-peptide is relatively disordered and does not influence the overall conformation of the native structure. The robustness of the native structure as demonstrated by experiment and simulation will permit future protein engineering applications, whereby the expression or purification yields can be improved upon sequence modification of the C-peptide and/or the signal peptide.

• Bulletin of the Korean Chemical Society
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• v.28 no.12
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• pp.2310-2314
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• 2007

Stable molecular conformations were calculated for the p-tert-butylcalix[4]arene crown ether bridged at the lower rim with pyridyl unit (1) in the various conformers and their potassium-ion complexes. The structures of three distinct conformations have been optimized using DFT B3LYP/6-31G(d,p) method. Relative stability of free host 1 is in following order: cone (most stable) > partial-cone > 1,3-alternate conformer. For two different kinds of complexation mode, the potassium cation in the crown-ether moiety (cr) has much better complexation efficiency than in the benzene-rings (bz) pocket for all three kinds of conformation of host molecule 1. The relative stability of complex (1+K+) in the cr-binding mode is in following order: partial-cone (most stable) ~ cone > 1,3-alternate conformer.

• Korean Journal of Crystallography
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• v.10 no.1
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• pp.66-70
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• 1999

The calix[4]arene molecule adopting the 1,3-alternate conformation forms a square cavity, and two pair phenyl rings lying above and below a least-square plane defined by the four bridging methylene groups in the calix[4]arene are widened upwards and downwards, respectively, from central axis, which leads to O1-O4=4.064 and O2-O3=3.864 . Two propyloxy groups are stabilized with all trans conformations, but the rather short azacrown ether chain with two oxygen atoms includes cis/trans conformations with O1-C35=2.906 . Therefore the cavity does not seem to be big enough to form a host-guest complex.