• Bulletin of the Korean Chemical Society
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• v.18 no.4
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• pp.415-424
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• 1997

Conformational flexibilities of the GlcNAc(β1,3)Gal(β)OMe are investigated through NMR spectroscopy and molecular modeling. Adiabatic energy map generated with a dielectric constant of 50 contains three local minima. All of the molecular dynamics simulations on three local minimum energy structures show fluctuations between two low energy structures, N2 at φ=80° and ψ=60° and N3 at φ=60° and ψ=-40°. We have presented adequate evidences to state that GlcNAc(β1,3)Gal(β)OMe exists in two conformationally discrete forms. Two state model of N2 and N3 conformers with a population ratio of 40:60 is used to calculate the effective cross relaxation rate and reproduces the experimental NOEs very well. Molecular dynamics simulation in conjunction with two state model proves successfully the dynamic equilibrium existed in GlcNAc(β1,3)Gal(β)OMe and can be considered as a powerful method to analyze the motional properties in the structure of carbohydrate. This observation also cautions against the indiscriminate use of a rigid model to analyze NMR data.

• Bulletin of the Korean Chemical Society
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• v.18 no.10
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• pp.1076-1082
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• 1997

The infrared, Raman, and jet-cooled laser-induced fluorescence excitation spectra of 1,2,3,4-tetrahydronaphthalene have been recorded and analyzed. The observed vibrations have been assigned to understand the conformational behaviors in its electronic ground (S0) and excited (S1) states. Ab initio at the HF/6-31G** level and molecular mechanics (MM3) force field calculations have been carried out to generate the complete normal mode frequencies of the molecule in its S0 state. The vibrational frequencies calculated from the ab initio method show a better agreement with the observed infrared and Raman frequencies than those calculated from the MM3 method. In several cases, the normal mode calculations were very helpful to clarify some ambiguities of previous assignments. In addition, the ring inversion process between two twisted conformers of 1,2,3,4-tetrahydronaphthalene has been reexamined utilizing ab initio calculation. The results show that the ring inversion energy is in the range of 3.7-4.3 kcal/mol which is higher than the previously reported AM1 value of 2.1 kcal/mol.

• Bulletin of the Korean Chemical Society
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• v.20 no.10
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• pp.1145-1148
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• 1999

1H NMR spectra of methyl-, ethyl-, propyl-, isopropyl-, butyl-, N-methylethyl-, N-methylpropyl-, and N-methylisopropylamine coordinated to the paramagnetic 11-tungstocobalto(II)silicate anion (SiW11Co) in dimethylsulfoxide-d6 or dimethylformamide-d7 are reported. For these complexes the ligand exchange is slow on the NMR time scale and pure 1H NMR signals have been observed at room temperature. No complex is detected in D2O. From the pseudocontact shifts of the CH2 and CH3 groups in ethylamine the energy of the gauche conformers with respect to the anti conformer is estimated. Two diastereotopic protons in the CH2 group of N-methylethylamine have quite different chemical shifts especially at low temperatures (e.g. 48.5 vs. 19.4 ppm at -10℃). This may be attributed mainly to the different positions of the two protons in the most stable (gauche) conformer.

• Bulletin of the Korean Chemical Society
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• v.10 no.3
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• pp.227-230
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• 1989

The lowest excited state of styrylquinoxaline (StQx) has been studied by the SCF-MO-CI P-P-P and MM2 method. Results suggest that the lowest excited state is of a ${\pi},{\pi}^{\ast}(S_1$) nature with the n,${\pi}^{\ast}(S_2)$ state lying slightly above it. On the basis of these calculations the observed electronic spectra are discussed. The calculated absorption spectra are qualitatively similar to experimental ones with their characteristic visible bands. MM2 force field calculation suggested that the postulated conformers are different from each other in energy and planarity and are seperated by a barrier of about 4 Kcal/mole.

• Bulletin of the Korean Chemical Society
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• v.6 no.5
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• pp.300-303
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• 1985

To understand the nature of the linkage between chromophore and apoprotein in the photoreceptor of Stentor coeruleus, a conformational analysis has been carried out on the dipeptide amides linked to the chromophore hypericin using an empirical potential function. The conformational energies for the dipeptide amides of Glu (OHyp)-X-NHMe, where X = Leu, Phe, Asp, and Tyr, have been calculated to investigate the influence of peptide residues in stabilizing conformers. It was found that the increase of acidity of hypericin upon photoexcitation may be facilitated by the formation of intramolecular hydrogen bonds between hydroxyl groups of hypericin and carbonyl groups of peptide backbone, and that the stabilities of dipeptide amides do not significantly depend on peptide residues directly linked to chromophore.

• 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.

• Journal of the Korea Academia-Industrial cooperation Society
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• v.19 no.7
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• pp.95-104
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• 2018

The structures and energies of the anhydrate and hydrate (hydrate rate: h of 1) states of L-alanine (LA) and glycine (G) were calculated by quantum chemical calculations (QCCs) using B3LYP/6-31G(d,p) for four types of conformers (${\beta}$-extended: ${\Phi}/{\Psi}=t-/t+$, $PP_{II}$: g-/t+, $PP_{II}$-like: g-/g+, and ${\alpha}$-helix: g-/g-). In LA and G, which have an imino proton (NH), three conformation types of ${\beta}$-extended, $PP_{II}$-like, and ${\alpha}$-helix were obtained, and water molecules were inserted mainly between the intra-molecular hydrogen bond of $CO{\cdots}HN$ in $PP_{II}$-like and ${\alpha}$-helix, and attached to the CO group in ${\beta}$-extended. In LA and G, $PP_{II}$-like conformers were most stable in the anhydrate and hydrate states, and the result for LA was different from some experimental and theoretical results from other studies reporting that the main stable conformation of alanine oligopeptide was $PP_{II}$. The formation pattern and stability of the conformation of the oligopeptide was strongly dominated by the presence/absence of intra-molecular hydrogen bonding of $CO{\cdots}HN$, or the presence/absence of an $NH_2$ group in the starting amino acid.

• Journal of the Korean Chemical Society
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• v.53 no.5
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• pp.521-529
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• 2009

Molecular structures of the various conformers for the 1,3-dimethoxy-p-tert-butylthiacalix[4] crown-5-ether (3) were optimized by using DFT B3LYP/6 - 31 + G(d,p) and mPW1PW91/6 - 31 + G(d,p) (hybrid HF-DF) calculation methods. We have analyzed the energy differences and structures of eight in/out orientations (cone_oo, cone_oi, pc_oo, pc_io, pc_oi, pc_ii, 13a_oo, 13a_io) of two methoxy groups in three major conformations (cone, partial-cone and 1,3-alternate). The 13a_oo (out-out orientation of the 1,3-alternate conformer) is calculated to be the most stable among eight different conformations of 3, and in accord with the experimental result. The ordering of relative stability resulted from the mPW1PW91/6 - 31 + G(d,p) calculation method is following: 13a_oo > 13a_io$\sim$pc_io$\sim$cone_oo > cone_oi$\sim$pc_oo$\sim$pc_oi > pc_ii.

• 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 $1(rtct)_{CHAIR}$.

• Bulletin of the Korean Chemical Society
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• v.32 no.4
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• pp.1187-1194
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• 2011

The hydrogen abstraction reaction of $CF_3CH_2CHO$ + OH has been studied theoretically by dual-level direct dynamics method. Two stable conformers, trans- and cis-$CF_3CH_2CHO$, have been located, and there are four distinct OH hydrogen-abstraction channels from t-$CF_3CH_2CHO$ and two channels from c-$CF_3CH_2CHO$. The required potential energy surface information for the kinetic calculation was obtained at the MCG3-MPWB//M06-2X/aug-cc-pVDZ level. The rate constants, which were calculated using improved canonical transitionstate theory with small-curvature tunneling correction (ICVT/SCT) were fitted by a four-parameter Arrhenius equation. It is shown that the reaction proceeds predominantly via the H-abstraction from the -CHO group over the temperature range 200-2000 K. The calculated rate constants were in good agreement with the experimental data between 263 and 358 K.