• Progress in Medical Physics
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• v.33 no.4
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• pp.80-87
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• 2022

Purpose: Proton therapy has different relative biological effectiveness (RBE) compared with X-ray treatment, which is the standard in radiation therapy, and the fixed RBE value of 1.1 is widely used. However, RBE depends on a charged particle's linear energy transfer (LET); therefore, measuring LET is important. We have developed a LET measurement method using the inefficiency characteristic of an EBT3 film on a proton beam's Bragg peak (BP) region. Methods: A Gafchromic EBT3 film was used to measure the proton beam LET. It measured the dose at a 10-cm pristine BP proton beam in water to determine the quenching factor of the EBT3 film as a reference beam condition. Monte Carlo (MC) calculations of dose-averaged LET (LET_d) were used to determine the quenching factor and validation. The dose-averaged LETs at the 12-, 16-, and 20-cm pristine BP proton beam in water were calculated with the quenching factor. Results: Using the passive scattering proton beam nozzle of the National Cancer Center in Korea, the LET_d was measured for each beam range. The quenching factor was determined to be 26.15 with 0.3% uncertainty under the reference beam condition. The dose-averaged LETs were measured for each test beam condition. Conclusions: We developed a method for measuring the proton beam LET using an EBT3 film. This study showed that the magnitude of the quenching effect can be estimated using only one beam range, and the quenching factor determined under the reference condition can be applied to any therapeutic proton beam range.

• 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.27 no.4
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• pp.539-544
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• 2006

Proton transfer reactions and ion-molecule reactions of bifunctional ethanes of $H_2NCH_2CH_2NH_2$, $H_2NCH_2CH_2OH$, and $HOCH_2CH_2OH$ were studied using Fourier transform mass spectrometry (FTMS). The rate constants for proton transfer reactions between the fragment ions and neutral molecules were obtained from the temporal variation of the ion abundances. The rate constants were consistent with the heats of reaction. The fastest proton transfer reactions were the reactions of $CH_2N^+$, $CHO^+$, and $CH_3O^+$ for $H_2NCH_2CH_2NH_2$, $H_2NCH_2CH_2OH$, and $HOCH_2CH_2OH$, respectively. The $[M+13]^+$ ion was formed by the ion-molecule reaction between $H_2C=NH_2 ^+$ or $H_2C=OH^+$ and the neutral molecule. The major product ions generated from the ion-molecule reactions between the protonated molecule and neutral molecule were $[2M+H]^+$, $[M+27]^+$, and $[M+15]^+$.

• Bulletin of the Korean Chemical Society
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• v.32 no.4
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• pp.1117-1124
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• 2011

We present a brief review for theoretical/computational studies of proton transfer processes of some simple biomolecules promoted by microsolvating water molecules. Focus is given on the relative stability of the canonical vs. zwitterionic forms of amino acids, tautomeric forms of the DNA base adenine, and the biologically active vs. inactive forms of nicotine. The biochemical implications of these findings are also discussed.

• Bulletin of the Korean Chemical Society
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• v.27 no.11
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• pp.1903-1906
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• 2006

• Bulletin of the Korean Chemical Society
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• v.32 no.10
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• pp.3634-3640
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• 2011

We have performed quantum mechanical calculations to study the geometries and binding energies of biologically important, cyclic hydrogen-bonded complexes, such as formic acid + $H_2O$, formamidine + $H_2O$, formamide + $H_2O$, formic acid dimer, formamidine dimer, formamide dimer, formic acid + formamide, formic acid + formamidine, formamide + formamidine, and barrier heights for the double proton transfer in these complexes. Various ab initio, density functional theory, multilevel methods have been used. Geometries and energies depend very much on the level of theory. In particular, the transition state symmetry of the proton transfer in formamidine dimer varies greatly depending on the level of theory, so very high level of theory must be used to get any reasonable results.

• Bulletin of the Korean Chemical Society
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• v.22 no.12
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• pp.1407-1409
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• 2001

• Bulletin of the Korean Chemical Society
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• v.28 no.12
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• pp.2343-2353
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• 2007

We report the application of time-dependent density functional theory (TDDFT) to the calculation of potential energy profile relevant to the excited state intramolecular proton transfer (ESIPT) processes in title molecules. The TDDFT single point energy calculations along the reaction path have been performed using the CIS optimized structure in the excited state. In addition to the Stokes shifts, the transition energies including absorption, fluorescence, and 0-0 transition are estimated from the TDDFT potential energy profiles along the proton transfer coordinate. The excited state TDDFT potential energy profile of SA and 3ASA resulted in very flat function of the OH distance in the range ROH = 1.0-1.6 A, in contrast to the relatively deep single minimum function in the ground state. Furthermore, we obtained very shallow double minima in the excited state potential energy profile of SA and 3ASA in contrast to the single minimum observed in the previous work. The change of potential energy profile along the reaction path induced by the substitution of electron donating groups (-NH2 and -OCH3) at different sites has been investigated. Substitution at para position with respect to the phenolic OH group showed strong suppression of excited state proton dislocation compared with unsubstitued SA, while substitution at ortho position hardly affected the shape of the ESIPT curve. The TDDFT results are discussed in comparison with those of CASPT2 method.

• Bulletin of the Korean Chemical Society
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• v.34 no.2
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• pp.465-469
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• 2013

Proton transfer reaction is one of the most fundamental processes in chemistry and life science. Excited state intramolecular proton transfer (ESIPT) has been studied as a model system of the proton transfer, since it can be conveniently initiated by light. We report ESIPT reaction dynamic of 1-hydroxy-anthraquione (1-HAQ) in solution by highly time-resolved fluorescence. ESIPT time of 1-HAQ is determined to be $45{\pm}10$ fs directly from decay of the reactant fluorescence and rise of the product fluorescence. High time resolution allows observation of the coherent vibrational wave packet motion in the excited state of the reaction product tautomer. The coherently excited vibrational mode involves large displacement of the atoms, which shortens the distance between the proton donor and the acceptor. With the theoretical analysis, we propose that the ESIPT of 1-HAQ proceeds barrierlessly with assistance of the skeletal vibration, which in turn becomes excited coherently by the ESIPT reaction.

• Bulletin of the Korean Chemical Society
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• v.24 no.11
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• pp.1675-1679
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• 2003

The photodynamics of excited-state intramolecular proton transfer reaction of 1-hydroxyanthraquinone (1-HAQ) and 1-deuterioanthraquinone was investigated in toluene with time-resolved emission and femtosecond transient transmittance techniques at room temperature. The temporal profiles of transient transmittance of 1-HAQ could be well described with multi-decaying time constants. The ultrafast time constant within ca. 260 fs reflects the dynamics of proton transfer. The decay component of 2 ps is assigned to an additional proton translocation process induced by the intramolecular vibrational relaxation, whereas the decay component of 18 ps is assigned to the vibrational cooling process, while the long component (200 ps) can be explained in terms of the relaxation from excited-state keto-tautomer to its ground state. Time-resolved anisotropy decay dynamics and isotope effects on the photodynamics reveals that the ESIPT from enol-tautomer to keto-one of 1-HAQ is barrierless reaction and coupled to a vibrational relaxation process.