• Bulletin of the Korean Chemical Society
• /
• v.35 no.12
• /
• pp.3532-3534
• /
• 2014

In theoretical simulations of proton transfer in DNA, environmental factors nearly have not been considered. In our calculations, using QM/MM method on the basis of CP2K, proton transfer on adenine-thymine base pair is studied in water, at wide scope temperature, and under the external electric field. Our results indicate that the external electric field induces the proton transfer at room temperature, and its intensity and temperature have some effect on hole localization and proton transfer.

• Bulletin of the Korean Chemical Society
• /
• v.34 no.7
• /
• pp.1961-1966
• /
• 2013

Theoretical investigations have been performed for the ground state ($S_0$) and the first excited state ($S_1$) of the hydrogen bonded green fluorescent protein (GFP) model. The potential energy surface (PESs) of $S_0$ was obtained by B3LYP method and that of $S_1$ was obtained by CIS method. Based on the relative stabilities of species and the energy barriers for the proton transfer, it was found that proton transfer could take place both under the ground state and the first excited state. As determined by the proton motions along the reaction coordinate, both the ground state proton transfer (GSPT) and the excited state proton transfer (ESPT) are considered as a concerted and asynchronous process.

• Bulletin of the Korean Chemical Society
• /
• v.25 no.10
• /
• pp.1538-1544
• /
• 2004

Fragmentations and proton transfer reactions of mono-, di-, and triethanolamines were studied using FTMS. It was found that the most abundant fragment ion was $[M-CH_2OH]^+$. The $[M-CH_2OH-H_2O]^+$ was observed in the mass spectra of diethanolamine and triethanolamine. By increasing the ion trapping time in the ICR cell, the $[M+H]^+$ and $[M+H-H_2O]^+$ ions were notably increased for all the samples while the $[M+H-2H_2O]^+$ was observed in the mass spectra of diethanolamine and triethanolamine. The proton transfer reactions between the fragment ions and neutral molecules occurred predominantly by increasing the ion trapping time. The rate constants for the proton transfer reactions were calculated from experimental results. The proton transfer reaction of $CHO^+$ was the fastest one, which is consistent with the heats of reaction. The rate constants for proton transfer reactions of triethanolamine were much slower than those of ethanolamine and diethanolamine because of the steric hindered structure of triethanolamine. The plausible structures of observed ions and heats of reaction for proton transfer were calculated with AM1 semiempirical method.

• Bulletin of the Korean Chemical Society
• /
• v.12 no.4
• /
• pp.441-444
• /
• 1991

The intramolecular proton transfers of 2-hydroxy-4,5-naphthotropone in room temperature solutions are studied using static and time-resolved absorption and emission spectroscopy. Dual normal and tautomer fluorescence is observed in ethanol solution, while only the tautomer fluorescence is observed in cyclohexane solution. The fluorescence lifetimes and quantum yields in ethanol and cyclohexane solutions indicate that in hydrocarbon solvents, rapid intersystem crossing competes with proton transfer in the first excited singlet state. Transient absorption spectra and kinetics indicate that proton transfer also undergoes in the first triplet state with a transfer time of ∼ 3 ns. No transient absorption from the tautomer ground state indicates a rapid back proton transfer in the ground state.

• Bulletin of the Korean Chemical Society
• /
• v.33 no.5
• /
• pp.1561-1565
• /
• 2012

The structures of the four lowest alanine conformers, along with their radical cations and the effect of ionization on the intramolecular proton transfer process, are studied using the density functional theory and MP2 method. The energy order of the radical cations of alanine differs from that of the corresponding neutral conformers due to changes in the basicity of the $NH_2$ group upon ionization. Ionization favors the intramolecular proton transfer process, leading to a proton-transferred radical-cation structure, [$NH_3{^+}-CHCH_3-COO{\bullet}$], which contrasts with the fact that a proton-transferred zwitterionic conformer is not stable for a neutral alanine in the gas phase. The energy barrier during the proton transfer process is calculated to be about 6 kcal/mol.

• Bulletin of the Korean Chemical Society
• /
• v.27 no.7
• /
• pp.1009-1014
• /
• 2006

Density functional theory calculations are applied to investigate the intramolecular proton transfer in the tautomers of thymine radical cation and its hydrated complexes with one water molecule. The optimized structures and energies for 6 tautomers and 6 transition states of thymine radical cation are calculated at the B3LYP/6-311++G(d,p) level. It is predicted that the order of relative stability for the keto and enol tautomers of thymine radical cation is the same with that of the neutral thymine tautomers, though the enol tautomers are more stabilized with respect to the di-keto form in the radical cation than in the neutral state. A new channel of proton transfer from >C5-$CH_{3}$ of thymine is found to open and have the lowest energy barrier of other proton transfer processes in thymine radical cation. The roles of hydration are also investigated with thymine-water 1 : 1 complex ions. The presence of water significantly lowers the barrier of the proton transfer, which clearly shows the assisting role of hydration even with one water molecule

• Bulletin of the Korean Chemical Society
• /
• v.26 no.12
• /
• pp.1953-1961
• /
• 2005

We have performed high-level quantum mechanical calculation for multiple proton transfer in HOCl + HCl and $H_2O$ + $ClONO_2$ on water clusters, which can be used as a model of the reactions on ice surface in stratospheric clouds. Multiple proton transfer on ice surface plays crucial role in these reactions. The structures of the clusters with 0-3 water molecules and the transition state structures for the multiple proton transfer have been calculated. The energies and barrier heights of the proton transfer were calculated at various levels of theory including multi-coefficient correlated quantum mechanical methods (MCCM) that have recently been developed. The transition state structures and the predicted reaction mechanism depend very much on the level of theory. In particular, the HF level can not correctly predict the TS structure and barrier heights, so the electron correlation should be considered appropriately.

• Bulletin of the Korean Chemical Society
• /
• v.13 no.2
• /
• pp.140-145
• /
• 1992

The excited state intramolecular proton transfer and physical properties of 7-hydroxyquinoline are studied in various solutions and heterogeneous systems by measuring steady state and time-resolved fluorescence, reflection and NMR spectra. Proton transfer is observed only in protic solvents owing to its requirement of hydrogen-bonded solvent bridge for proton relay transfer. The activation energies of the proton transfer are 2.3 and 5.4 kJ/mol in $CH_3OH$ and in $CH_3OD$, respectively. Dimers of normal molecules are stable in microcrystalline powder form and undergo an extremely fast concerted double proton transfer upon absorption of a photon, consequently forming dimers of tautomer molecules. In the supercage of zeolite NaY, its tautomeric form is stable in the ground state and does not show any proton transfer.

• Bulletin of the Korean Chemical Society
• /
• v.16 no.5
• /
• pp.410-416
• /
• 1995

The proton transfer energies of gas phase glycine and alanine and those of hydrated glycine and alanine were calculated both with Hartree-Fock and $M{\Phi}ller-Plesset$ ab initio molecular orbital (MO) calculations with 6-31G** basis set. The transition states of the proton transfer of gas phase glycine was also investigated. For zwitterions, both for glycine and alanine, the water bound to -NH3+ site stabilize the complex more compared with the water bound to -CO2-. The proton transfer energy, ΔEpt, of glycine, alanine, mono-hydrated glycine, mono-hydrated alanine, di-hydrated glycine and di-hydrated alanine were obtained as 30.78 (MP2: 22.57), 31.43, 23.99 (MP2: 17.00), 24.98, 22.87, and 25.63 kcal/mol, respectively. The activation energy for proton transfer from neutral (Nt) glycine to zwitterion (Zw) glycine, Ea, was obtained as 16.13 kcal/mol and that for reverse process, Ear, was obtained as 0.85 kcal/mol. Since the transition state of the proton transfer of gas phase glycine locate near the glycine zwitterion on the potential energy surface and the shape of the potential well of the zwitterion is shallow, the zwitterion easily changed to neutral glycine through the proton transfer.

• Bulletin of the Korean Chemical Society
• /
• v.10 no.6
• /
• pp.488-491
• /
• 1989

Theoretical studies on the proton transfer reaction in a formamide dimer have been done by Ab initio SCF calculation. In this study, we have shown several effects on the potential energy profile of the proton transfer in a formamide dimer, such as the effect of a basis set, the effect of a geometry optimization, and the effect of a distance between proton-donor and proton-acceptor.