Molecular Structure of 9H-Adenine Tautomer: Gas-Phase Electron Diffraction and Quantum-Chemical Studies

The role of intramolecular and intermolecular hydrogen bonding effect for adenine-containing polyimide films

A series of adenine-containing polyimides (APIs) with intramolecular hydrogen bonding (HB) were prepared from N 1 -(9-(4-aminophenyl)- 9H-purin-6-yl)-2-methoxybenzene-1,4-diamine (b-H-MeO-APA) and commercial dianhydrides. And a systematic comparison between intramolecular and intermolecular HB effects was made using APIs with (b-H-MeO-APIs) and without (b-H-H-API) methoxy group. FTIR indicated that the occurrence of intramolecular HB originated from the side MeO group ortho to -NH-. XRD indicated that the introduction of side group MeO and corresponding intramolecular HB could destroy the orderly stacking of b-H-H-APIs. Birefringence and polarized ATR FTIR studies showed that the groups and chains in b-H-MeO-APIs films could also be simultaneously self-arranged in the in-plane direction. In contrast, the orientation degree in the in-plane direction is generally lower than that of b-H-H-APIs. The b-H-MeO-APIs films showed lower water absorption, higher Tg, and lower CTE compared to b-H-H-APIs films, which indicates that the introduction of intramolecular HB may have some positive influence in controlling water absorption, Tg, and CTE.

Metal nanoparticle alters adenine induced charge transfer kinetics of vitamin K3 in magnetic field

In this article, we highlight the alterations in the photoinduced electron transfer (ET) and hydrogen atom transfer (HAT) pathways between an anti-tumor drug vitamin-K3 (MQ) and a nucleobase adenine (ADN) in the presence of gold (Au) and iron (Fe) nanoparticles (NPs). Inside the confined micellar media, with laser flash photolysis corroborated with an external magnetic field (MF), we have detected the transient geminate radicals of MQ and ADN, photo-generated through ET and HAT. We observe that the presence of AuNP on the MQ-ADN complex (^AuMQ-ADN) assists HAT by limiting the ET channel, on the other hand, FeNP on the MQ-ADN complex (^FeMQ-ADN) mostly favors a facile PET. We hypothesize that through selective interactions of the ADN molecules with AuNP and MQ molecules with FeNP, a preferential HAT and PET process is eased. The enhanced HAT and PET have been confirmed by the escape yields of radical intermediates by time-resolved transient absorption spectroscopy in the presence of MF.

Geometric and energetic consequences of prototropy for adenine and its structural models – a review

Prototropy for adenine and its convenient models causes parallel changes of geometric (HOMED) and energetic (ΔE) parameters for neutral tautomers.

Quantum chemical and spectroscopic investigations of 3-methyladenine

FTIR, FT-Raman and UV-Vis spectra of 3-methyladenine have been recorded and investigated using quantum chemical calculations. The molecular geometry and vibrational spectra of 3-methyladenine in the ground state are computed by using HF and DFT methods with 6-311G(d,p) basis set. VSCF, CC-VSCF methods based on 2MR-QFF and PT2 (Barone method) have been utilized for computing anharmonic vibrational frequencies. These methods yield results that are in remarkable agreement with the experimental data. The magnitudes of coupling between pair of modes have been also computed. Vibrational modes are assigned with the help of visual inspection of atomic displacements. The electronic spectra, simulated at TD-B3LYP/6-311++G(d,p) level of theory, are compared to the experiment. The global quantities: electronic chemical potential, electrophilicity index, chemical hardness and softness based on HOMO and LUMO energy eigenvalues are also computed at B3LYP/6-311++G(d,p) level of theory.

Geometric consequences of electron delocalization for adenine tautomers in aqueous solution

Geometric consequences of electron delocalization were studied for all possible adenine tautomers in aqueous solution by means of ab initio methods {PCM(water)//DFT(B3LYP)/6-311+G(d,p)} and compared to those in the gas phase {DFT(B3LYP)/6-311+G(d,p)}. To measure the consequences of any type of resonance conjugation (π-π, n-π, and σ-π), the geometry-based harmonic oscillator model of electron delocalization (HOMED) index, recently extended to the isolated (DFT) and hydrated (PCM//DFT) molecules, was applied to the molecular fragments (imidazole, pyrimidine, 4-aminopyrimidine, and purine) and also to the whole tautomeric system. For individual tautomers, the resonance conjugations and consequently the bond lengths strongly depend on the position of the labile protons. The HOMED indices are larger for tautomers (or their fragments) possessing the labile proton(s) at the N rather than C atom. Solvent interactions with adenine tautomers slightly increase the resonance conjugations. Consequently, they slightly shorten the single bonds and lengthen the double bonds. When going from the gas phase to water solution, the HOMED indices increase (by less than 0.15 units). There is a good relation between the HOMED indices estimated in water solution and those in the gas phase for the neutral and ionized forms of adenine. Subtle effects, being a consequence of intramolecular interactions between the neighboring groups, are so strongly reduced by solvent that the relation between the HOMED indices and the relative energies for the neutral adenine tautomers seems to be better in water solution than in the gas phase.

Interplay of experiment and theory: determination of an accurate equilibrium structure of 1-methyluracil by the gas electron diffraction method and coupled-cluster computations

As far as fundamental knowledge is concerned, the methyl derivatives of uracil can be considered as the simplest objects for studying the structural effects due to the substitution in the pyrimidyne nucleobases. From this point of view, 1-methyluracil is of special importance in biochemistry because uracil attaches ribose in ribonucleic acid (RNA) just precisely at the N1 atom. The semi-experimental equilibrium structure (r(e)(se)) of 1-methyluracil has been determined for the first time by the gas electron diffraction (GED) method taking into account rovibrational corrections to the thermal-average internuclear distances calculated with harmonic and anharmonic (cubic) MP2/cc-pVTZ force constants with consideration of the methyl torsion as a large-amplitude motion. For the first time, the structure of the molecule has been optimized by the very time-consuming coupled-cluster method with single and double excitations and perturbative treatment of connected triples using the correlation-consistent polarized weighted core-valence triple-ζ basis set with all electrons being correlated (CCSD(T)(all)/cc-pwCVTZ) and extrapolated to the complete basis set (CBS) with the help of the MP2 calculations. Small differences between similar bond lengths of equilibrium configurations were assumed in the GED analysis at the CCSD(T)(all)/CBS values. A remarkable agreement between the semi-experimental and computed equilibrium structures points out the high accuracy of both the GED determination and the coupled-cluster computations. The effect of methylation on the structure of uracil has been analyzed.