• Journal of the Korean Chemical Society
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• v.27 no.6
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• pp.399-404
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• 1983

Raman spectra for the carbonyl stretching mode of the amides, and amide-solvent systems have been recorded to investigate the effect of alkyl substitutions at the carbonyl carbon and at the nitrogen on the amide hydrogen-bonding. The data have shown that the interaction affinities are in the order of amide-amide > amide-water > amide-alcohol in formamide system, and amide-water > amide-amide > amide-alcohol in acetamide and propionamide systems. The strength of the proton acceptor of the carbonyl oxygen is increased by the presence of alkyl group to the carbonyl carbon and the proton donorcity of the amide is decreased by the alkyl substitution at the nitrogen. The above results are in good agreement with the ab initio SCF MO calculation.

• Mass Spectrometry Letters
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• v.12 no.4
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• pp.131-136
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• 2021

Collision-induced dissociation of peptides involves a series of proton-transfer reactions in the activated peptide. To describe the kinetics of energy-variable dissociation, we considered the heat capacity of the peptide and the Marcus-theory-type proton-transfer rate. The peptide ion was activated to the high internal energy states by collision with a target gas in the collision cell. The mobile proton in the activated peptide then migrated from the most stable site to the amide oxygen and subsequently to the amide nitrogen (N-protonated) of the peptide bond to be broken. The N-protonated intermediate proceeded to the product-like complex that dissociated to products. Previous studies have suggested that the proton-transfer equilibria in the activated peptide affect the dissociation kinetics. To take the extent of collisional activation into account, we assumed a soft-sphere collision model, where the relative collision energy was fully available to the internal excitation of a collision complex. In addition, we employed a Marcus-theory-type rate equation to account for the proton-transfer equilibria. Herein, we present results from the integrated thermochemical approach using a tryptic peptide of ubiquitin.

• Bulletin of the Korean Chemical Society
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• v.12 no.6
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• pp.674-678
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• 1991

Methanolysis of a ${\beta}$-lactam ring of a cephalosporin was simulated with AM1 semiempirical quantum mechanical calculation. The tetrahedral intermediate TD1 from an O-protonated cephalosporin and a methanol transfers the proton intramolecularly to the C-4 carboxylate to generate an oxyanion, i.e., second tetrahedral intermediate TD2, which undergoes the amide bond cleavage without further protonation on the N-5. For this cleavage a low-energy barrier TS2 was located. According to the energy diagram, tetrahedral intermediates easily undergo ring cleavage even without the protonation on the amide nitrogen.

• Bulletin of the Korean Chemical Society
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• v.30 no.5
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• pp.1043-1046
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• 2009

Human protein tyrosine kinase-6 (PTK6) is a member of the non-receptor protein tyrosine kinase family and it is found in two-thirds of all breast tumors. Very recently, we proposed that the SH3 domain of PTK6 interacts with the linker region (Linker) between the SH2 and kinase domains, proving that the interaction between SH3 domain and Linker plays an important role in auto-inhibition mechanism. Residues from 1 to 191 corresponding region of SH3-SH2-Linker (SH32L) of PTK6 was cloned into the pET32a expression vector with Tobbaco etch virus (TEV) protease enzyme site by sequence homology and 3D structural model. The purified PTK6-SH32L was determined as a monomer conformation in solution. The amide proton resonances in the $^{15}N-^{1}H$ 2D-HSQC spectrum suggest that PTK6-SH32L possesses disordered structural region of the flexible/unstructured linker region. In addition, the backbone amide proton chemical shifts of the SH3 domain in the PTK6-SH32L differ from that of the independent domain, indicating that intra-molecular interaction between SH3 and Linker in the PTK6-SH32L is present.

• Journal of the Korean Magnetic Resonance Society
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• v.8 no.2
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• pp.127-138
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• 2004

We obtained the chemical shifts of amide protons (NHs) in helical peptides at various temperatures and trifluoroethanol (TFE) concentrations using 2-dimensional NMR spectroscopy. These NH chemical shifts and their temperature dependence exhibited characteristic periodicity of 3-4 residues per cycle along the helix, where downfield shifted NHs showed larger temperature dependence. In an attempt to understand these observations, we focused on hydrogen bonding changes in the peptides and examined the validity of two possible explanations: (1) changes in intermolecular hydrogen bonding caused by differential solvation of backbone carbonyl groups by TFE, and (2) changes in intramolecular hydrogen bonding due to disproportionate variations in the hydrogen bonding within the peptide helix. Interestingly, the slowly exchanging NHs, which were on the hydrophobic side of the helix, showed consistently larger temperature dependences. This could not be explained by the differential solvation assumption, because the slowly exchanging NHs would become more labile if the preceding carbonyl groups were preferentially solvated by TFE. We suggest that the disproportionate changes in intramolecular hydrogen bonding better explain both the temperature dependence and the exchange behavior observed in this study.

• Bulletin of the Korean Chemical Society
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• v.24 no.3
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• pp.357-362
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• 2003

The pathway producing imide ring closure during the thermal imidization of poly(amic acid) (PAA) was investigated in detail using a new analytical method, two-dimensional (2D) Raman correlation spectroscopy. The signs of the cross peaks in synchronous spectra provided evidence of the thermal imidization of PAA into PI as the heating temperature increased. The signs of the cross peaks in asynchronous spectra suggested that the imide-related modes changed prior to the amide or carboxylic mode, which indicates that cyclization occurred before the amide proton was abstracted.

• Investigative Magnetic Resonance Imaging
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• v.21 no.2
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• pp.65-70
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• 2017

Purpose: To optimize the saturation time and maximizing the pH-weighted difference between the normal and ischemic brain regions, on 3-tesla amide proton transfer (APT) imaging using an in vivo rat model. Materials and Methods: Three male Wistar rats underwent middle cerebral artery occlusion, and were examined in a 3-tesla magnetic resonance imaging (MRI) scanner. APT imaging acquisition was performed with 3-dimensional turbo spin-echo imaging, using a 32-channel head coil and 2-channel parallel radiofrequency transmission. An off-resonance radiofrequency pulse was applied with a Sinc-Gauss pulse at a $B_{1,rms}$ amplitude of $1.2{\mu}T$ using a 2-channel parallel transmission. Saturation times of 3, 4, or 5 s were tested. The APT effect was quantified using the magnetization-transfer-ratio asymmetry at 3.5 ppm with respect to the water resonance (APT-weighted signal), and compared with the normal and ischemic regions. The result was then applied to an acute stroke patient to evaluate feasibility. Results: Visual detection of ischemic regions was achieved with the 3-, 4-, and 5-s protocols. Among the different saturation times at $1.2{\mu}T$ power, 4 s showed the maximum difference between the ischemic and normal regions (-0.95%, P = 0.029). The APTw signal difference for 3 and 5 s was -0.9% and -0.7%, respectively. The 4-s saturation time protocol also successfully depicted the pH-weighted differences in an acute stroke patient. Conclusion: For 3-tesla turbo spin-echo APT imaging, the maximal pH-weighted difference achieved when using the $1.2{\mu}T$ power, was with the 4 s saturation time. This protocol will be helpful to depict pH-weighted difference in stroke patients in clinical settings.

• Bulletin of the Korean Chemical Society
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• v.19 no.1
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• pp.110-114
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• 1998

The hydrogen-bonding interactions between thioacetamide (TA) and urea derivatives such as tetramethylurea (TMU) and dimethyldiphenylurea (DMDPU) have been studied using near-infrared absorption spectroscopy. Thermodynamic parameters for the interactions between TA and urea derivatives were determined by analyzing the $v^{as}_{N-H}$+Amide Ⅱ combination band of TA at 1970 nm. The ΔH° values, indicating the intrinsic strength of hydrogen bonding, are - 23.0 kJ/mole and - 19.8 kJ/mol for TMU and DMDPU, respectively. This is well explained by the inductive effects of substituents. Ab initio molecular orbital calculations for the proton affinity of TMU, N,N-dimethylformamide (DMF), and N,N-dimethylacetamide (DMA) in gas phase have been carried out at HF/3-21G ad HF/6-31G(d) levels, showing that the proton affinity of TMU is larger than that of DMA, which agrees well the experimental results.

• Bulletin of the Korean Chemical Society
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• v.31 no.8
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• pp.2351-2356
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• 2010

Various dienamide derivatives were synthesized in reasonable yields from benzonitriles having an amide moiety at the ortho-position, via the sequential (i) In-mediated allylation of nitrile moiety to form an imine intermediate, (ii) intramolecular quenching of an acyl group by the imine intermediate, and (iii) a proton transfer to dienamide.

• Bulletin of the Korean Chemical Society
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• v.16 no.9
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• pp.864-869
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• 1995

Investigation of the structures of the gangliosides has proven to be very important in the understanding of their biological roles such as regulation of differentiation and growth of cells. We used nuclear magnetic resonance spectros-copy in order to investigate the structure of GA1. In order to do this, the assignment of spectra is a prerequisite. Since GA1 does not have polar sialic acid, the spectral overlap is severe. In order to solve this problem, we use 2D NMR spectroscopy and heteronuclear 1H/13C correlated spectroscopy in this study. Here, we report the complete assignment of the proton and the carbon spectra of the GA1 in DMSO-d6-D20 (98:2, v/v). These assignments will be useful for interpreting 1H and 13C NMR data from uncharacterized oligosaccharides and for determining the linkage position, the number of sugar rings, and the sequence of new ganglioside. Amide proton in ring Ⅲ shows many interring nOes and has intramolecular hydrogen bonding. This appears to be an important factor in tertiary folding of GA1. Based on this assignment, determination of three dimensional structure of GA1 will be carried out. Studies on the conformational properties of GA1 may lead to a better understanding of the molecular basis of its functions.