Molecular Design of Ionization-Induced Proton Switching Element Based on Fluorinated DNA Base Pair

Hydrogen Storage Mechanism in Sodium-Based Graphene Nanoflakes: A Density Functional Theory Study

Carbon materials, such as graphene nanoflakes, carbon nanotubes, and fullerene, can be widely used to store hydrogen, and doping these materials with lithium (Li) generally increases their H2-storage densities. Unfortunately, Li is expensive; therefore, alternative metals are required to realize a hydrogen-based society. Sodium (Na) is an inexpensive element with chemical properties that are similar to those of lithium. In this study, we used density functional theory to systematically investigate how hydrogen molecules interact with Na-doped graphene nanoflakes. A graphene nanoflake (GR) was modeled by a large polycyclic aromatic hydrocarbon composed of 37 benzene rings, with GR-Na-(H2)n and GR-Na+-(H2)n (n = 0–12) clusters used as hydrogen storage systems. Data obtained for the Na system were compared with those of the Li system. The single-H2 GR-Li and GR-Na systems (n = 1) exhibited binding energies (per H2 molecule) of 3.83 and 2.72 kcal/mol, respectively, revealing that the Li system has a high hydrogen-storage ability. This relationship is reversed from n = 4 onwards; the Na systems exhibited larger or similar binding energies for n = 4–12 than the Li-systems. The present study strongly suggests that Na can be used as an alternative metal to Li in H2-storage applications. The H2-storage mechanism in the Na system is also discussed based on the calculated results.

A theoretical study on the excited-state deactivation paths for the A-5FU dimer

The photostability of DNA plays a key role in the normal function of organisms. A-5FU is a base pair derivative of the A-T dimer where the methyl group is replaced by a F atom. Here, accurate static TDDFT calculations and non-adiabatic dynamic simulations are used to systematically investigate the excited-state decay paths of the A-5FU dimer related to the proton transfer and the out-of-plane twisting deformation motion of A and 5FU in the 1ππ* and 1nπ* states. CC2 is used to check the accuracy of the current TDDFT calculations. Our results show that the deformation of the C[double bond, length as m-dash]C or C[double bond, length as m-dash]N double bond in A and 5FU provides an efficient pathway for the depopulation of the lowest excited states, which can compete with the excited-state proton transfer paths in the dimer. This finding indicates that monomer-like decay paths could be important for the photostability of weakly hydrogen-bonded DNA base pairs and provide a new insight into the excited-state decay paths in base pairs and their analogues.

Proton Transfer vs Complex Formation Channels in Ionized Formic Acid Dimer: A Direct Ab Initio Molecular Dynamics Study

Photoirradiation to a hydrogen-bonded system plays an important role in the initial DNA and enzyme damage processes. The formic acid (FA) dimer is a model compound of double proton transfer systems, such as DNA base pairs. In the present study, the reactions of the FA dimer cation, formed upon ionization of the neutral dimer, have been investigated by the direct ab initio molecular dynamics method. Two reaction channels were identified for the FA dimer cation: complex formation and proton transfer (PT). In the complex formation channel, the carbonyl oxygen atoms of the two FA monomers were bound symmetrically, and a face-to-face complex was formed. In the PT channel, the proton of FA⁺ was transferred to FA, forming the H⁺(HCOOH)--HCO₂ radical cation as product. At low temperature, the complex channel was dominant, whereas the PT channel increased with increasing temperature. The asymmetric spin distribution on the FA dimer cation exhibited a strong correlation with the PT channel.

Intramolecular Reactions in Ionized Ammonia Clusters: A Direct Ab Initio Molecular Dynamics Study

Ammonia cluster cations are a chemical species that has recently attracted considerable research attention as an ion-molecule reaction species in the planetary atmosphere, surface reaction species in materials chemistry, and super-alkali species. Reactions of the radical cation of an ammonia cluster, [(NH₃)_n]⁺ (n = 2-6), following the ionization of the parent neutral cluster, were investigated using direct ab initio molecular dynamics to elucidate the reactions of the ammonia cluster cation under astrochemical conditions. The calculations showed that two competing reaction channels-proton transfer (PT) channel and complex formation channel-operate after the ionization of neutral clusters. In the PT channel, a proton of NH₃⁺ was transferred to a neighboring ammonia molecule. The PT channel was found in all clusters (n = 2-6). Reaction via the PT channel became faster with increasing cluster size and saturated around n = 5-6. In the complex formation channel, a face-to-face complex having a H₃N-NH₃⁺ structure (with a N-N bond) was formed. This channel was found only in larger clusters (n = 5-6). Time scales of PT and complex formation channels were calculated to be 20-30 and 40-50 fs, respectively. The reaction mechanism was discussed based on the results of theoretical calculations.

Theoretical analyses and experimental validation of the effects caused by the fluorinated substituent modification of DNA

Halogen-modified nucleic acid molecules, such as trifluorothymidine (FTD) and 5-fluorouracil, are widely used in medical science and clinical site. These compounds have a very similar nucleobase structure. It is reported that both of these compounds could be incorporated into DNA. The incorporation of FTD produces highly anti-tumor effect. However, it is not known whether to occur a significant effect by the incorporation of 5-fluorouracil. Nobody knows why such a difference will occur. To understand the reason why there is large differences between trifluorothymidine and 5-fluorouracil, we have performed the molecular dynamics simulations and molecular orbital calculations. Although the active interaction energy between Halogen-modified nucleic acids or and complementary adenine was increased, in only FTD incorporated DNA, more strongly dispersion force interactions with an adjacent base were detected in many thermodynamic DNA conformations. As the results, the conformational changes occur even if it is in internal body temperature. Then the break of hydrogen bonding between FTD and complementary adenine base occur more frequently. The double helix structural destabilization of DNA with FTD is resulted from autoagglutination caused by the bonding via halogen orbitals such as halogen bonding and the general van der Waals interactions such as CH–\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$${\rm{\pi }}$$\end{document}π, lone pair (LP)–\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$${\rm{\pi }}$$\end{document}π, and \documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$${\rm{\pi }}$$\end{document}π–\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$${\rm{\pi }}$$\end{document}π interactions. Therefore, it is strongly speculated that such structural changes caused by trifluoromethyl group is important for the anti-tumor effect of FTD alone.

Deciphering the excited state intramolecular charge-coupled double proton transfer in an asymmetric quinoline–benzimidazole system

Asymmetrical H-bonding responsible for charge coupled-excited state intramolecular double proton transfer.