• Bulletin of the Korean Chemical Society
• /
• v.27 no.4
• /
• pp.495-502
• /
• 2006

Intramolecular energy flow and C-$H_{methyl}$ and C-$H_{ring}$ bond dissociations in vibrationally excited toluene in the collision with HF have been studied by use of classical trajectory procedures. The energy lost by the vibrationally excited toluene upon collision is not large and it increases slowly with increasing total vibrational energy content between 20,000 and 45,000 $cm ^{-1}$. Above the energy content of 45,000 $cm ^{-1}$, however, energy loss decreases. Furthermore, in the highly excited toluene, toluene gains energy from incident HF. The temperature dependence of energy loss is negligible between 200 and 400 K. Energy transfer to or from the excited methyl C-H bond occurs in strong collisions with HF transferring relatively large amount of its translational energy (>> $k_BT$) in a single step, whereas energy transfer to the ring C-H bond occurs in a series of small steps. When the total energy content $E_T$ of toluene is sufficiently high, either C-H bond can dissociate. The C-$H_{methyl}$ dissociation probability is higher than the C-$H_{ring}$ dissociation probability. The dissociation of the ring C-H bond is not the result of the intermolecular energy flow from the direct collision between the ring C-H and HF but the intramolecular flow of energy from the methyl group to the ring C-H stretch. The C-$H_{ring}$${\cdot}{\cdot}{\cdot}$HF interaction is not important in transferring energy and in turn bond dissociation.

• Korean Journal of Optics and Photonics
• /
• v.28 no.1
• /
• pp.9-15
• /
• 2017

We precisely measured and analyzed the dynamics of peptide-antibody interactions, using an ellipsometric biosensor based on a silicon substrate. To reduce the signal error due to the imperfect flatness of the substrate for extremely low concentrations of peptide, we fabricated the biosensor with a silicon substrate coated with Dextran SAM, instead of a glass prism coated with a thin metallic thin film. At an injection speed of $100{\mu}l/min$ of buffer liquid, we detected the dynamics of antibody-Dextran SAM or peptide-antibody fixed on biosensor, respectively. We detected the dynamics of antibody-Dextran SAM interactions down to a low concentration of 5 ng per liter, and we precisely measured the dynamics of association and dissociation of peptide and antibody down to 100 nM of peptide. We obtained the rate constants for association and dissociation from fitting the data by using deduced dynamical equation. As a result, we obtained an equilibrium constant for dissociation of 97 nM of peptide-antibody complex, which belongs to Class I.

• Bulletin of the Korean Chemical Society
• /
• v.33 no.11
• /
• pp.3618-3624
• /
• 2012

Photodissociation dynamics of propiolic acid ($HC{\equiv}C-COOH$) at 212 nm in the gas phase was investigated by measuring rotationally resolved laser-induced fluorescence spectra of OH ($^2{\Pi}$) radicals exclusively produced in the ground electronic state. From the spectra, internal energies of OH and total translational energy of products were determined. The electronic transition at 212 nm responsible for OH dissociation was assigned as the ${\pi}_{C{\equiv}C}{\rightarrow}{\pi}^*{_{C=O}}$ transition by time-dependent density functional theory calculations. Potential energy surfaces of both the ground and electronically excited states were obtained employing quantum chemical calculations. It was suggested that the dissociation of OH from propiolic acid excited at 212 nm should take place along the $S_1/T_1$ potential energy surfaces after internal conversion and/or intersystem crossing from the initially populated $S_2$ state based upon the potential energy calculations and model calculations for energy partitioning of the available energy among products.

• Bulletin of the Korean Chemical Society
• /
• v.18 no.12
• /
• pp.1274-1280
• /
• 1997

The photodissociation dynamics of CH2I2 has been studied at 304 nm by state-selective photofragment translational spectroscopy. Velocity distributions, anisotropy parameters, and relative quantum yields are obtained for the ground I(2P3/2) and spin-orbit excited state I*(2P1/2) iodine atoms, which are produced from photodissociation of CH2I2 at this wavelength. These processes are found to occur via B1 ← A1 type electronic transitions. The quantum yield of I*(2P1/2) is determined to be 0.25, indicating that the formation of ground state iodine is clearly the favored dissociation channel in the 304 nm wavelength region. From the angular distribution of dissociation products, the anisotropy parameters are determined to be β(I)=0.4 for the I(2P3/2) and β(I*)=0.55 for the I*(2P1/2) which substantially differ from the limiting value of 1.13. The positive values of anisotropy parameter, however, show that the primary processes for I and I* formation channels proceed dominantly via a transition which is parallel to I-I axis. The above results are interpreted in terms of dual path formation of iodine atoms from two different excited states, i.e., a direct and an indirect dissociation via curve crossing between these states. The translational energy distributions of recoil fragments reveal that a large fraction of the available energy goes into the internal excitation of the CH2I photofragment; < Eint > /Eavl=0.80 and 0.82 for the I and I* formation channels, respectively. The quantitative analysis for the energy partitioning of available energy into the photofragments is used to compare the experimental results with the prediction of direct impulsive model for photodissociation dynamics.

• Bulletin of the Korean Chemical Society
• /
• v.27 no.10
• /
• pp.1641-1647
• /
• 2006

Vibrational relaxation and competitive C-$H_{methyl}$ and C-$H_{ring}$ bond dissociations in vibrationally excited methylpyrazine in the collision with HF have been studied by use of classical trajectory procedures. The energy lost by the vibrationally excited methylpyrazine upon collision is not large and it increases slowly with increasing total vibrational energy content between 20,000 and 45,000 $cm^{-1}$. Above the energy content of 45,000 $cm^{-1}$, however, energy loss decreases. The temperature dependence of energy loss is negligible between 200 and 400 K, but above 45,000 $cm^{-1}$ the energy loss increases as the temperature is raised. Energy transfer to or from the excited methyl C-H bond occurs in strong collisions with HF, that is, relatively large amount of translational energy is transferred in a single step. On the other hand, energy transfer to the ring C-H bond occurs in a series of small steps. When the total energy content ET of methylpyrazine is sufficiently high, either or both C-H bonds can dissociate. The C-$H_{methyl}$ dissociation probability is higher than the C-$H_{ring}$ dissociation probability. The dissociation of the ring C-H bond is not the result of the direct intermolecular energy flow from the direct collision between the ring C-H and HF but the result of the intramolecular flow of energy from the methyl group to the ring C-H stretch.

• Bulletin of the Korean Chemical Society
• /
• v.31 no.1
• /
• pp.92-99
• /
• 2010

Photoexcitation of a precursor ion inside a cell floated at high voltage installed in a tandem time-of-flight (TOF) mass spectrometer provides triple tandem mass spectrometric information and allows kinetic and mechanistic studies. In this work, the factors affecting, or downgrading, the performance of the technique were identified. Ion-optical and computational analyses showed that an optimum instrument could be designed by utilizing a reflectron with linear-plus-quadratic potential inside. Theoretical predictions were confirmed by tests with instruments built with different ion-optical layout. With optimized instruments, masses of intermediate ions in the consecutive dissociation of a precursor ion could be determined with the maximum error of $\pm5$ Da. We also observed excellent agreement in dynamical parameters (critical energy and entropy) for the dissociation of a model peptide ion determined by instruments with different ion-optical layout operated under optimum conditions. This suggests that these parameters can be determined reliably by the kinetic method developed previously when properly designed and operated tandem TOF instruments are used.

• Bulletin of the Korean Chemical Society
• /
• v.34 no.5
• /
• pp.1401-1406
• /
• 2013

This study tested the feasibility of observing H/D exchange of intact protein by top-down electron capture dissociation (ECD) mass spectrometry for the investigation of protein structure. Ubiquitin is selected as a model system. Local structural information was obtained from the deuteration levels of c and $z^{\cdot}$ ions generated from ECD. Our results showed that ${\alpha}$-helix region has the lowest deuteration level and the C-terminal fraction containing a highly mobile tail has the highest deuteration level, which correlates well with previous X-Ray and HDX/NMR analyses. We studied site-specific H/D exchange kinetics by monitoring H/D exchange rate of several structural motives of ubiquitin. Two hydrogen bonded ${\beta}$-strands showed similar HDX rates. However, the outer ${\beta}$-strand always has higher deuteration level than the inner ${\beta}$-strand. The HDX rate of the turn structure (residues 8-11) is lower than that of ${\beta}$-strands (residues 1-7 and residues 12-17) it connects. Although isotopic distribution gets broader after H/D exchange which results in a limited number of backbone cleavage sites detected, our results demonstrate that this method can provide valuable detailed structural information of proteins. This approach should also be suitable for the structural investigation of other unknown proteins, protein conformational changes, as well as protein-protein interactions and dynamics.

• Mass Spectrometry Letters
• /
• v.12 no.4
• /
• pp.126-130
• /
• 2021

The mass spectrometry (MS) provides the mass-to-charge ratios of atoms, molecules, stable/metastable complexes, and their fragments. I have taken a long journey with MS to address outstanding issues and problems by experiments and theory and gain insights into underlying principles in chemistry. By looking through the mass-to-charge ratio, I have studied thermochemical problems in silicon chemistry, the infrared multiphoton dissociation spectroscopy of organometallic intermediates, unimolecular dissociations of halotoluene radical cations, and the kinetics of association/dissociation of alkali halide triple ions with Lewis bases. Various MS platforms have been used to characterize non-covalent interactions between porphyrins and fullerenes and those between the group IIB ions and trioctylchalcogenides, and to examine the binding of the group IA, IIA and porphyrin ions to G-quadruplex DNA. Recently, I have focused on mass-balanced H/D isotope dipeptide tags for MS-based quantitative proteomics, a simple chemical modification method for MS-based lipase assay, and the kinetics and dynamics of energy-variable collision-induced dissociation of chemically modified peptides. Now, I see an important role of MS in global issues in the post-COVID era, as the society demands high standards for indoor air quality to contain the airborne-pathogen transmission as well as in-situ monitoring and tracking of carbon emissions to reduce global warming.

• Proceeding of EDISON Challenge
• /
• 2017.03a
• /
• pp.32-38
• /
• 2017

Prion is a group of the proteins known for its infection mechanisms of Creutzfeldt-Jakob disease (CJD) and other diseases. Solved structures and proven biological roles of fungal prions add tremendous potential to conducting computational simulations. Our research focuses on the binding dynamics of HET-s(218-289), one of the heterokaryon fungal prion originated from Podospora anserina, by calculating the binding free energy using umbrella sampling at 300 K. The binding free energy calculated was $-54.5kcal\;mol^{-1}$, relatively similar to the binding energy of other amyloid fibrils. The simulation result suggests the thermodynamic properties of ${\beta}$-solenoid of HET-s prion and its similarity in dissociation pathways compared to amyloids.

• Interaction and multiscale mechanics
• /
• v.1 no.4
• /
• pp.437-448
• /
• 2008

This paper examined the stability of high-dense dislocation substructures (HDDSs) associated with martensite laths in High Cr steels supposed to be used for FBR, based on a series of dislocation dynamics (DD) simulations. The DD simulations considered interactions of dislocations with impurity atoms and precipitates which substantially stabilize the structure. For simulating the dissociation processes, a point defect model is developed and implemented into a discrete DD code. Wall structure composed of high dense dislocations with and without small precipitates were artificially constructed in a simulation cell, and the stability/instability conditions of the walls were systematically investigated in the light of experimentally observed coarsening behavior of the precipitates, i.e., stress dependency of the coarsening rate and the effect of external stress. The effect of stress-dependent coarsening of the precipitates together with application of external stress on the subsequent behavior of initially stabilized dislocation structures was examined.