• Journal of the Korean Chemical Society
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• v.52 no.3
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• pp.322-327
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• 2008

The geometrical structure, binding energy and vibrational frequencies of HOOCl-H2O cluster were investigated with MP2/6-311G(d,p) and MP2/6-311G(2d,2p) methods. The most stable conformer is skew HOOCl-H2O cluster and the binding energy was 46~48kJ/mol. The trans HOOCl-H2O cluster is less stable than skew form, but the binding energy is big enough to stablize the complex. The vibrational frequencies of skew and trans HOOCl-H2O cluster were calculated and compared with the spectrum of HOOCl.

• BMB Reports
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• v.39 no.2
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• pp.167-170
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• 2006

Bovine adenosine deaminase undergoes a nondenaturational conformational change at $29^{\circ}C$ upon heating which is characterized by a large increase in heat capacity. We have determined the transition state thermodynamics of the conformational change using a novel application of differential scanning calorimetry (DSC) which employs very slow scan rates. DSC scans at the conventional, and arbitrary, scan rate of $1^{\circ}C/min$ show no evidence of the transition. Scan rates from 0.030 to $0.20^{\circ}C/min$ reveal the transition indicating it is under kinetic control. The transition temperature $T_t$ and the transition temperature interval ${\Delta}T$ increase with scan rate. A first order rate constant $k_1$ is calculated at each $T_t$ from $k_1\;=\;r_{scan}/{\Delta}T$, where $r_{scan}$ is the scan rate, and an Arrhenius plot is constructed. Standard transition state analysis reveals an activation free energy ${\Delta}G^{\neq}$ of 88.1 kJ/mole and suggests that the conformational change has an unfolding quality that appears to be on the direct path to the physiological-temperature conformer.

• Journal of the Korean Graphic Arts Communication Society
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• v.14 no.1
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• pp.47-54
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• 1996

Deuterium NMR studies have been carried out for two kinds of main- chain dimer liquid crystals $\alpha$.$\omega$-bis[(4,4`-cyanobipheny0oxy] alkane (CBA-n, n=9,100.The H-NMR spectra were recorded on a JEOP JNM-GSX-500 spectrometer by using deuterium labelled CBA-n at various temperatures. The RIS analysis of the NMR spectra was performed so as to elucidate the conformational characteristics of the spacer in the nematic phase. Following the previous treatment, the single-ordering-matrix model was adopted, in which the molecular axis was defined parallel to the line connecting the centers of the terminal mesogenic cores. Conformer fractions of the spacer were estimated by simulation so as to reproduce the observed NMR profile. The conformational entropy changes at both CN and NI interphases were estimated on the basis of the nematic conformations taken from the conformation map as well as those derived from the simulation. In these calculations the spacer was assumed th by in the all-trans conformation and in the random coil stats in the crystal and isotropic phases respectively. The esimated conformational entropy change values were then compared with the corresponding constant-volume entropies obtained from PVT measurements. The correspondence between both entropy values was found to be quite good in consideration of the uncertainties involved in both experiment and calculations.

• Bulletin of the Korean Chemical Society
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• v.35 no.12
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• pp.3514-3520
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• 2014

Molecular structures of the various conformers of para-bromocalix[4]aryl derivatives 1-4 were optimized using the DFT B3LYP calculation method. The total electronic and Gibbs free energies and normal vibrational frequencies of the different structures (CONE, partial cone (PACO), 1,2-Alternate(1,2-A) and 1,3-Alternate(1,3-A)) were calculated from the four kinds of para-bromocalix[4]aryl derivatives. The B3LYP/6-31G(d,p) calculations suggested the following: 1(PACO) is the most stable among four conformers of 1; 2(CONE) is the most stable among five conformers of 2; 3(PACO) is the most stable among four conformers of 3; 4(1,3-A) is the most stable among four conformers of 4. All the most stable structures optimized by the B3LYP calculation method were in accordance with the experimental crystal structures of 1-4. The calculated IR spectra of the various conformers (CONE, PACO, 1,2-A and 1,3-A) of 1-4 were compared.

• Bulletin of the Korean Chemical Society
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• v.31 no.1
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• pp.59-63
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• 2010

Calculations are presented for the $\gamma$-aminobutyric acid-$(H_2O)_n$ (n = 0-5) clusters in both canonical and zwitterionic forms. We examine the effects of microsolvation on the structures and transformation between the canonical and zwitterionic forms. The canonical forms are predicted to be more stable for n = 0-4. With five microsolvating water molecules, the two forms of $\gamma$-aminobutyric acid become quasidegenerate, with the energies of zwitterionic forms slightly (by 1 - 3 kcal/mol) higher. The lowest energy zwitterionic conformer of $\gamma$-aminobutyric acid-$(H_2O)_5$ cluster is calculated to isomerize to canonical form through a barrier-less proton transfer process and is thus predicted to be kinetically unstable. Therefore, we predict that the canonical conformers of $\gamma$-aminobutyric acid should be observed predominantly in the gas phase at low temperature in presence of up to five water molecules.

• 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.74-74
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• 2003

We report here the results on N-acetyl-N'-methylamide of oxazolidine (Ac-Oxa-NHMe) calculated using the ab initio molecular orbital method with the self-consistent reaction field (SCRF) theory at the HF level of theory with the 6-3l+G(d) basis set. The displacement of the $\square$-CH$_2$ group in proline ring by oxygen atom has affected the structure of proline, cis$\^$∼/ trans equilibrium, and rotational barrier. The up-puckered structure is found to be prevalent for the trans conformers of the Oxa amide. The higher cis populations of the Oxa amide can be interpreted due to the longer distance between the acetyl methyl group and the 5-methylene group of the ring for the trans conformer of the Oxa amide than that of the Pro amide. The changes in charge of the prolyl nitrogen and the decrease in electron overlap of the C$\^$∼/ N bond for TS structures seem to play a role in lowering rotational barriers of the Oxa amide compared to that of the Pro amide. The calculated preferences for cis conformers in the order of Oxa > Pro amides and for trans-to-cis rotational barriers in the order of Pro > Oxa amide in water are consistent with experimental results on Oxa-containing peptides. The pertinent distance between the prolyl nitrogen and the N$\^$∼/ H amide group to form a hydrogen bond might indicate that this intramolecular hydrogen bond could contribute in stabilizing the TS structures of Oxa and Pro amides and play a role in prolyl isomerization.

• Journal of the Korean Chemical Society
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• v.50 no.1
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• pp.7-13
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• 2006

infrared(IR) absorption spectra were calculated for the ethyl ester of p-tert-butylcalix[4]arene (1) in the cone conformer and its alkali-metal-ion complex. The vibrational spectra were obtained by restricted Hartree-Fock (RHF) calculations with the 6-31G basis set. The characteristic vibrational frequencies of various C-O and C=O stretching motions of the complexes show that the structure of 1+K+ complex is almost of C4v symmetry compared to 1+Na+ (C2v) analogue. The theoretical results for the host molecule 1 and complex (1+Na+) were compared with the experimental results, and the calculated vibrational frequencies agree well with the features of the experimental spectra.

• Bulletin of the Korean Chemical Society
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• v.32 no.1
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• pp.100-104
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• 2011

The structures of the conformers for 1,3-di-t-butyl-2,4-dinitro-tetramethoxysulfonylcalix[4]arene (1) and 1,2-di-t-butyl-3,4-dinitro-tetramethoxysulfonylcalix[4]arene (2) 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 the differences between the various conformations (cone, partial-cone (PC), 1,2-alternate, and 1,3-alternate) of 1 and 2. For both compounds, the 1,3-alternate (1,3-A) conformers were calculated to be the most stable, which correlate very well with the experimental results. The orderings of the relative stability of 1 and 2 that resulted from the mPW1PW91/6-31G(d,p) calculations are the following: 1: 1,3-A (syn) > PC (syn) > PC (anti) > 1,2-A (anti) > CONE (syn); 2: 1,3-A (anti) > PC (anti) > PC (syn) > 1,2-A (anti) > 1,2-A (syn) > CONE (syn). The BLYP/6-31G(d) calculated IR spectra of the most stable 1,3-A conformers of 1 and 2 are compared.

• Bulletin of the Korean Chemical Society
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• v.30 no.4
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• pp.837-845
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• 2009

We have performed DFT calculations to investigate the conformational characteristics and hydrogen bonds of the calix[6]arene (1) and p-tert-butylcalix[6]arene (2). The structures of various conformers of 1 were optimized by using the B3LYP/6-31G(d,p) and /6-31+G(d,p) methods followed by single point calculation of MPW1PW91/ 6-31G(d,p). The relative stability of the conformers of 1 is in the following order: cone (pinched: most stable) > partial-cone > cone (winged) $\sim$ 1,2-alternate $\sim$ 1,2,3-alternate > 1,4-alternate > 1,3-alternate > 1,3,5-alternate. The structures of different conformers of 2 were optimized by using the B3LYP/6-31G(d,p) method followed by single point calculation of MPW1PW91/6-31G(d,p). The relative stability of the conformers of 2 is in the following order: cone (pinched) > 1,2-alternate > cone (winged) > 1,4-alternate $\sim$ partial-cone > 1,2,3-alternate > 1,3,5alternate > 1,3-alternate. One of the important factors affecting the relative stabilities of the various conformers of the 1 and 2 is the number and strength of the intramolecular hydrogen bonds.