• Bulletin of the Korean Chemical Society
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• 제34권11호
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• pp.3327-3334
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• 2013

Infrared multiphoton dissociation (IRMPD) spectra of various protonated 1,2-diaminoethane-water clusters DAE-$H^+-(H_2O)_n$ (n = 1-6) were measured in the wavelength range of 3000-3800 $cm^{-1}$. The IRMPD spectra of the well separated ionic clusters were simulated by the MP2 method employing various basis sets. Comparison of the IRMPD spectra with the theory indicates that each cluster may exist as several low-lying conformers, and the sum spectra of the various conformers reveal almost one to one correspondence between theory and experiment. Free N-H and O-H stretches are observed in the ranges of 3400-3500 and 3600-3800 $cm^{-1}$, respectively. The $O-H{\cdots}N$ and $N-H{\cdots}O$ stretches are, however, observed in the broad region of 3000-3600 $cm^{-1}$. The theoretical calculations on DAE-$H^+-(H_2O)_n$ (n = 1-4) show gradual decrease of the average binding energy between DAE-$H^+$ and $H_2O$ as the cluster size increases, attaining the lowest value of 55 kJ/mol when n = 4. We found a low energy barrier of 21 kJ/mol to the isomerization converting the lowest energy cluster of DAE-$H^+-(H_2O)_n$ to the second lowest one.

• Restorative Dentistry and Endodontics
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• 제27권6호
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• pp.632-643
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• 2002

The purpose of this study was two-fold. First was to evaluate whether the molecular sieving model was appropriate for ionic dissociation experiment. Second was to compare the dissociation of calcium and hydroxyl ions from five types of calcium hydroxide pastes (Pure calcium hydroxide paste, DT temporary $dressing^{\circledR},{\;}Metapaste^{\circledR},{\;}Chidopex^{\circledR},{\;}Metapex^{\circledR}$) in three vehicles (aqueous, viscous and oily) and the antibacterial effect. Each calcium hydroxide pastes was placed into 0.65ml tube with cap and then 15% polyacrylamide gel was placed onto calcium hydroxide pastes. After the gel was hardened, the tubes were filled with tridistilled water (pH 7.14) and closed with cap. The tubes were stored in $37^{\circ}C$ 100% incubator The pH reading and the concentration of calcium ions were taken at 1, 4, 7. 10, and 14 days. The brain heart infusion agar plates with S. mutans and A. actinomycetemcomitans were used far antibacterial activity test. Middle of agar plate was filled with the calcium hydroxide pastes. The plates were incubated at $37^{\circ}C$ and observations were made to detect the zones of inhibition. These data were evaluated statistically by use of the analysis of variance and duncan test. The results were as follows. 1. In fresh mixing state, the pH of five types of calcium hydroxide pastes were measured between 12.5 and 12.8. 2. The pH was increased in all five types of calcium hydroxide pastes compared with control group. In 14 days, Pure calcium hydroxide paste (11.45) and DT temporary $dressing^{\circledR}$ (11.33) showed highest pH, followed by $Metapaste^{\circledR}$ (9.49), $Chidopex^{\circledR}$ (8.37) and $Metapex^{\circledR}$ (7.59) 3. Calcium was higher in all five types of calcium hydroxide pastes compared with control group. In 14 days, Pure calcium hydroxide paste (137.29 mg%) and DT temporary $dressing^{\circledR}$ (124.6 mg%) showed highest value, followed by $Metapaste^{\circledR}$ (116.74 mg%), $Chidopex^{\circledR}$ (111.84 mg%) and $Metapex^{\circledR}$ (60.22 mg%). 4. The zones of bacterial inhibition were seen around all five types of calcium hydroxide pastes. $Chidopex^{\circledR}{\;}and{\;}Metapex^{\circledR}$ groups which include iodoform were observed significantly larger zone of inhibition in A. actinomycetemcomitans compared with the other calcium hydroxide groups (p<0.05) However, $Metapex^{\circledR}$ showed the least antibacterial effect on S. mutans compared with other groups (p<0.05). The molecular sieving model was found to be acceptable in dissociation experiment of hydroxyl and calcium ions when compared with the previous tooth model study. But this model was not appropriate for the antibacterial test.

• 한국추진공학회지
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• 제19권6호
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• pp.54-63
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• 2015

본 연구에서는 고온/고압의 연소가스에 의해 야기되는 노즐목 삭마현상의 분자수준 메커니즘을 분자동역학 시뮬레이션을 이용하여 관찰한다. 노즐목은 두 개의 그래핀으로 구성된 그래파이트로 모델링하고 분자동역학 시뮬레이션은 충분한 속도를 가지고 그래파이트에 충돌하는 $H_2O$ 분자와 $CO_2$ 분자가 지속적으로 생성되는 과정과 평형상태의 시뮬레이션으로 구성된다. 반응을 모사할 수 있는 ReaxFF 포텐셜을 사용하며, 충돌에 의해 야기되는 $H_2O$ 및 $CO_2$ 분자의 해리와 화학적 삭마와의 관계에 중점을 두고 관찰하고자 하며, 거시적인 관찰결과들과 비교하고자 한다.

• Journal of Microbiology and Biotechnology
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• 제20권9호
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• pp.1283-1287
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• 2010

In eukaryotes, eRF3 participates in translation termination and belongs to the superfamily of GTPases. In this work, the dissociation constants for nucleosides bound to Euplotes octocarinatus eRF3 in the presence and absence of eRF1a were determined using fluorescence spectra methods. Furthermore, a GTP hydrolyzing assay of eRF3 was carried out using an HPLC method, and the kinetic parameters for GTP hydrolysis by eRF3 were determined. Consistent with data from humans, the results showed that eRF1a promoted the binding of GTP to eRF3 and the GTP hydrolyzing activity of eRF3. However, in contrast to the lack of GTP binding in the absence of eRF1 in human eRF3, the E. octocarinatus eRF3 was able to bind GTP by itself. The nucleotide binding affinity of the E. octocarinatus eRF3 also differed from the human data. A structure model and amino acid sequence alignment of potential G domains indicated that these differences may be due to valine 317 and glutamate 452 displacing the conserved glycine and lysine involved in GTP binding.

• Bulletin of the Korean Chemical Society
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• 제26권11호
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• pp.1682-1688
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• 2005

Using the ASED-MO (Atom Superposition and Electron Delocalization-Molecular Orbital) theory, we investigated carbon formation and carbon hydrogenation for $CO_2$ methanation on the Ni (111) surface. For carbon formation mechanism, we calculated the following activation energies, 1.27 eV for $CO_2$ dissociation, 2.97 eV for the CO, 1.93 eV for 2CO dissociation, respectively. For carbon methanation mechanism, we also calculated the following activation energies, 0.72 eV for methylidyne, 0.52 eV for methylene and 0.50 eV for methane, respectively. We found that the calculated activation energy of CO dissociation is higher than that of 2CO dissociation on the clean surface and base on these results that the CO dissociation step are the ratedetermining of the process. The C-H bond lengths of $CH_4$ the intermediate complex are 1.21 $\AA$, 1.31 $\AA$ for the C${\cdot}{\cdot}{\cdot}H_{(1)}$, and 2.82 $\AA$ for the height, with angles of 105${^{\circ}}$ for ∠ $H_{(1)}$CH and 98${^{\circ}}$ for $H_{(1)} CH _{(1)}$.

• BMB Reports
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• 제45권1호
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• pp.26-31
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• 2012

TRIM72 is known to play a critical role in skeletal muscle membrane repair. To better understand the molecular mechanisms of this protein, we carried out an in vitro binding study with TRIM72. Our study proved that TRIM72 binds various lipids with dissociation constants ($K_d$) ranging from 88.2 ${\pm}$ 9.9 nM to 550.5 ${\pm}$ 134.5 nM. In addition, the intrinsic fluorescence of TRIM72 exponentially decreased when the protein was diluted with stirring. The time-resolved fluorescence decay occurred in a concentration-independent manner. The fluorescence-decayed TRIM72 remained in its secondary structure, but its binding properties were significantly reduced. The dissociation constants ($K_d$) of fluorescence-decayed TRIM72 for palmitate and stearate were 159.1 ${\pm}$ 39.9 nM and 355.4 ${\pm}$ 106.0 nM, respectively. This study suggests that TRIM72 can be dynamically converted by various stimuli. The results of this study also provide insight into the role of TRIM72 in the repair of sarcolemma damage.

• Bulletin of the Korean Chemical Society
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• 제32권2호
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• pp.510-514
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• 2011

Photodissociation dynamics of allyl alcohol ($H_2C$=CH-$CH_2OH$) has been investigated at 205 - 213 nm along the UV absorption band by measuring rotationally-resolved laser-induced fluorescence spectra of OH radicals. Observed energy partitioning of the available energy among products at all photon energies investigated was similar and the barrier energy for OH production is about 574.7 kJ/mol from the OH yield measurements. The potential energy surfaces for the $S_0$, $T_1$, and $S_1$ excited states along the dissociation coordinate were obtained by ab initio quantum chemical calculations. The observed energy partitioning was successfully modeled by the "barrier-impulsive model" with the reverse barrier and the geometry obtained by the calculated potential energy surfaces. The dissociation takes place on the $T_1$ excited state potential energy surface with an energy barrier in the exit channel and a large portion of the photon energy is distributed in the internal degrees of freedom of the polyatomic products.

• BMB Reports
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• 제29권4호
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• pp.286-293
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• 1996

Association of antigenic peptide with class I MHC is believed to be crucial for maintaining stable conformation of class I molecules. T2 cells that are defective in TAP gene function mainly express class I molecules with an unstable conformation due to little or no association with antigenic peptides, whereas T1 cells that are normal in TAP gene function mainly express the stable form of class I molecules. In this work, attempts were made to determine the molecular stability of stable and unstable class I molecules. Dissociation of HLA-A2 molecules on T1 and T2 cells was monitored by flow cytometry using anti-HLA-A2 antibody after the cells were treated with brefeldin A to shut down the transport of newly-assembled HLA-A2. Estimated dissociation rate constants for the stable and unstable forms of HLA-A2 were 0.076 $h^{-1}$ and 0.66 $h^{-1}$, respectively. It appeared that both T1 and T2 cells express stable and unstable class I complex, but with different ratios of the two forms. Furthermore, $interferon-{\gamma}$ treatment of T1 cells appeared to induce the expression of both the stable and unstable class I molecules. These results demonstrate that class I MHC molecules can be divided into two groups in terms of structural stability and that they exist on the cell surface in both forms in a certain ratio.

• Bulletin of the Korean Chemical Society
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• 제30권7호
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• pp.1470-1474
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• 2009

Thermal and photochemistry of methyl iodide ($CH_3I)\;adsorbed\;on\;D_2O$ ice film on Cu(111) at 100 K were studied using temperature-programmed desorption (TPD) time-of-flight mass spectrometry (TOF-MS), X-ray and ultraviolet photoelectron spectroscopies. On the basis of TPD, multilayer and monolayer $CH_3I$ molecules desorb from $D_2O$ ice layer at 120 and 130 K, respectively. Photo-irradiation at 100 K exhibits dramatic changes in the TPD and I $3d_{5/2}\;XPS\;of\;CH_3I$ on ice film, due to a dramatic dissociation of $CH_3I$. The dissociation is likely activated by solvated electrons transferred from the metal substrate during photo-irradiation. No other photo-initiated reaction products were found within our instrumental detection limit. During photo-irradiation, the $CH_3I$, $CH_3$ and I could be trapped (or solvated) in ice film by rearrangement (and self-diffusion) of water molecules. A newly appeared parent molecular desorption peak at 145 K is attributed to trapped $CH_3I$. In addition, the $CH_3$ and I may diffuse through ice and chemisorb on Cu(111), indicated by TPD and I $d_{5/2}$ XPS taken with photo-irradiation time, respectively. No molecular ejection was found during photo-irradiation at 100 K. The work functions for $CH_3I/Cu(111),\;D_2O/Cu(111)\;and\;CH_3I/D_2$O/Cu(111) were all measured to be about 3.9 eV, 1.0 eV downward shift from that of clean Cu(111).

• Bulletin of the Korean Chemical Society
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• 제27권3호
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• pp.389-394
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• 2006

Fragmentation efficiencies of various ‘activated-ion’ electron capture dissociation (AI-ECD) methods are compared for a model system of bovine ubiquitin 7+ cations. In AI-ECD studies, sufficient internal energy was given to protein cations prior to ECD application using IR laser radiation, collisions, blackbody radiation, or in-beam collisions, in turn. The added energy was utilized in increasing the population of the precursor ions with less intra-molecular noncovalent bonds or enhancing thermal fluctuations of the protein cations. Removal of noncovalent bonds resulted in extended structures, which are ECD friendly. Under their best conditions, a variety of activation methods showed a similar effectiveness in ECD fragmentation. In terms of the number of fragmented inter-residue bonds, IR laser/blackbody infrared radiation and ‘in-beam’ activation were almost equally efficient with ~70% sequence coverage, while collisions were less productive. In particular, ‘in-beam’ activation showed an excellent effectiveness in characterizing a pre-fractionated single kind of protein species. However, its inherent procedure did not allow for isolation of the protein cations of interest.