Attila Bende

Structure of Polydopamine: A Never-Ending Story?

Polydopamine (PDA) formed by the oxidation of dopamine is an important polymer, in particular, for coating various surfaces. It is composed of dihydroxyindole, indoledione, and dopamine units, which are assumed to be covalently linked. Although PDA has been applied in a manifold way, its structure is still under discussion. Similarities have been observed in melanins/eumelanins as naturally occurring, deeply colored polymer pigments derived from L-DOPA. Recently, an alternative structure was proposed for PDA wherein dihydroxyindoline, indolinedione, and eventually dopamine units are not covalently linked to each other but are held together by hydrogen bonding between oxygen atoms or π stacking. In this study, we show that this structural proposal is very unlikely to occur taking into account unambiguous results obtained by different analytical methods, among them (13)C CPPI MAS NMR (cross-polarization polarization-inversion magic angle spinning NMR), (1)H MAS NMR (magic angle spinning NMR), and ES-HRMS (electrospray ionization high-resolution mass spectrometry) for the first time in addition to XPS (X-ray photoelectron spectroscopy) and FTIR spectroscopy. The results give rise to a verified structural assignment of PDA wherein dihydroxyindole and indoledione units with different degrees of (un)saturation are covalently linked by C-C bonds between their benzene rings. Furthermore, proof of open-chain (dopamine) monomer units in PDA is provided. Advanced DFT calculations imply the arrangements of several PDA chains preferably by quinone-hydroquinone-type interactions in a parallel or antiparallel manner. From all of these results, a number of hypotheses published before could be experimentally supported or were found to be contradictory, thus leading to a better understanding of the PDA structure.

A tri-atomic Renner-Teller system entangled with Jahn-Teller conical intersections

The present study concentrates on a situation where a Renner-Teller (RT) system is entangled with Jahn-Teller (JT) conical intersections. Studies of this type were performed in the past for contours that surround the RT seam located along the collinear axis [see, for instance, G. J. Halász, Á. Vibók, R. Baer, and M. Baer, J. Chem. Phys. 125, 094102 (2006)]. The present study is characterized by planar contours that intersect the collinear axis, thus, forming a unique type of RT-non-adiabatic coupling terms (NACT) expressed in terms of Dirac-δ functions. Consequently, to calculate the required adiabatic-to-diabatic (mixing) angles, a new approach is developed. During this study we revealed the existence of a novel molecular parameter, η, which yields the coupling between the RT and the JT NACTs. This parameter was found to be a pure number η = 22/π (and therefore independent of any particular molecular system) and is designated as Renner-Jahn coupling parameter. The present study also reveals an unexpected result of the following kind: It is well known that each (complete) group of states, responsible for either the JT-effect or the RT-effect, forms a Hilbert space of its own. However, the entanglement between these two effects forms a third effect, namely, the RT/JT effect and the states that take part in it form a different Hilbert space.

The electronic structure of the four nucleotide bases in DNA, of their stacks, and of their homopolynucleotides in the absence and presence of water.

Using the ab initio Hartree-Fock crystal orbital method in its linear combination of atomic orbital form, the energy band structure of the four homo-DNA-base stacks and those of poly(adenilic acid), polythymidine, and polycytidine were calculated both in the absence and presence of their surrounding water molecules. For these computations Clementis double zeta basis set was applied. To facilitate the interpretation of the results, the calculations were supplemented by the calculations of the six narrow bands above the conduction band of poly(guanilic acid) with water. Further, the sugar-phosphate chain as well as the water structures around poly(adenilic acid) and polythymidine, respectively, were computed. Three important features have emerged from these calculations. (1) The nonbase-type or water-type bands in the fundamental gap are all close to the corresponding conduction bands. (2) The very broad conduction band (1.70 eV) of the guanine stack is split off to seven narrow bands in the case of poly(guanilic acid) (both without and with water) showing that in the energy range of the originally guanine-stack-type conduction band, states belonging to the sugar, to PO(4)(-), to Na(+), and to water mix with the guanine-type states. (3) It is apparent that at the homopolynucleotides with water in three cases the valence bands are very similar (polycytidine, because it has a very narrow valence band, does not fall into this category). We have supplemented these calculations by the computation of correlation effects on the band structures of the base stacks by solving the inverse Dyson equation in its diagonal approximation taken for the self-energy the MP2 many body perturbation theory expression. In all cases the too large fundamental gap decreased by 2-3 eV. In most cases the widths of the valence and conduction bands, respectively, decreased (but not in all cases). This unusual behavior is most probably due to the rather large complexity of the systems. From all this emerges the following picture for the charge transport in DNA: There is a possibility in short segments of the DNA helix of a Bloch-type conduction of holes through the nucleotide base stacks of DNA combined with hopping (and in a lesser degree with tunneling). The motivation of this large scale computation was that recently in Zurich (ETH) they have performed high resolution x-ray diffraction experiments on the structure of the nucleosomes. The 8 nucleohistones in them are wrapped around by a DNA superhelix of 147 base pairs in the DNA B form. The most recent investigations have shown that between the DNA superhelix (mostly from its PO(4) (-) groups) there is a charge transfer to the positively charged side chains (first of all arginines and lysines) of the histones at 120 sites of the superhelix. This would cause a hole conduction in DNA and an electronic one in the proteins.

Molecular Modeling of Phenothiazine Derivatives: Self-Assembling Properties

This study aims to present a detailed theoretical investigation of noncovalent intermolecular interactions between different π-π stacking phenothiazine derivatives and between different alkane chains varying from propane to decane. Second-order Møller-Plesset perturbation (MP2), coupled cluster (CC), and density functional (DFT) theories were the quantum chemistry methods used in our calculation. For MP2 and CC methods, the density-fitting and local approximations were taken into account, while in the case of DFT, the M06 and M06-2x hybrid meta-GGA exchange-correlation functionals as well as the semiempirical correction to the DFT functional for dispersion (BLYP-D) was considered. The results obtained with the aforementioned methods were compared with the potential energy curve given by the DF-SCSN-LMP2 theory considered as benchmark. For all these calculations, the correlation-consistent basis sets of cc-pVNZ (where N = D, T, Q) were used. In addition, potential energy curves built using the semiempirical PM6-D2 and the MM3 molecular force field methods were also compared with the benchmark curve and their efficiency was discussed. As the next step, several geometry conformations were investigated for both phenothiazine derivatives and alkane chain dimers. It was found that the conformational stability of these molecular systems is exclusively given by the dispersion-type electron correlation effects. The density functional tight-binding (DFTB) method applied for dimer structures was compared with the results obtained by the higher level local perturbation theory method, and based on these conclusions larger phenothiazine derivative oligomers structures were investigated. Finally, the optimal configuration of the complex molecular systems built by phenothiazine derivative, alkane chain fragments, and thiol groups was determined, and their self-assembling properties were discussed.

Calculation of the band structure of polyguanilic acid in the presence of water and Na+ ions

Using the Hartree-Fock crystal orbital method with a combined symmetry (helix) operation, the band structure of polyguanilic acid was calculated in the presence of water and Na(+) ions. The water structure was optimized with the help of molecular mechanics. The obtained band structure shows that both the valence and conduction bands are purely guanine type. The three impurity bands in the 10.66 eV large gap are close to the conduction band and therefore cannot play any role in the assumed hole conduction of the system. Namely, according to detailed x-ray diffraction investigations of the nucleosomes in chromatin, there are possibilities of charge transfer from the negative sites of DNA to the positive ones in histones. Therefore most probably there is a hole conduction in DNA and an electronic one in the histone proteins.

Omega Polynomial in Diamond-like Networks

Design of diamond-like lattices can be achieved by using some net operations. Hypothetical networks, thus obtained, can be characterized in their topology by various counting polynomials and topological indices from which they are derived. The repeat units of the proposed network are derived from adamantane, the constructive unit of diamond, and proved to be extremely stable, as shown by computed total energy. Their topology is described in terms of Omega polynomial.

H-bond-driven supramolecular architectures of the syn and anti isomers of the dioxime of bicyclo[3.3.1]nonane-3,7-dione.

The formation and high stability of the H-bond-driven supramolecular architectures of the syn and anti isomers of the dioxime of bicyclo[3.3.1]nonane-3,7-dione were investigated by single crystal X-ray diffraction, NMR, FTIR, and molecular modeling. Self-assembly of the achiral syn isomer into a cyclic trimer (supramolecular wheel) and of the chiral anti isomer into homochiral cyclic dimers was observed.

Tautomerism and proton transfer in photoionized acetaldehyde and acetaldehyde–water clusters

Understanding the gas-phase chemistry of acetaldehyde can be challenging because the molecule can assume several tautomeric forms, namely keto, enol and carbene. The two last forms are the most stable ionic forms. Here, insight into the gas-phase cluster ion chemistry of homogeneous acetaldehyde and mixed water-acetaldehyde clusters is provided by mass spectrometry/vacuum ultraviolet photoionization combined with density functional theory calculations. (AA)nH(+) clusters (AA = acetaldehyde) and mixed (AA)nH3O(+) clusters were detected using tunable vacuum ultraviolet photoionization. Barrierless proton transfers were observed during the geometry optimization of the most stable dimer structures and helped to explain the cluster ion chemistry induced by photoionization, namely the formation of deprotonated tautomers and protonated keto tautomers. Water was found to catalyze the keto-enol and keto-carbene isomerizations and facilitate the proton transfer from the ionized enol or carbene part of the cluster to the neutral keto part, resulting in protonated keto structures. The production of protonated keto structures was identified to be the main fragmentation channel following ionization of the homogeneous acetaldehyde cluster and a channel for ionized mixed clusters as well. These findings are significant for a broad range of fields, including current atmospheric models, because acetaldehyde is one of the most prominent organic species in the troposphere and ions play a crucial role in aerosol formation.

Dressed adiabatic and diabatic potentials for the Renner-Teller/Jahn-Teller F + H2 system.

We follow a suggestion by Lipoff and Herschbach (Mol. Phys. 2010, 108, 1133) and compare dressed potentials to get insight regarding the low-energy dynamics (e.g., cold reaction) taking place in molecular systems. In this particular case we are interested in studying the effect of topological effects on the interacting atoms. For this purpose we consider dressed adiabatic and adiabatic-via-dressed diabatic potentials in the entrance channel of reactive systems. In a recent study of this kind for the F + H2 system (J. Chem. Phys. 2012, 136, 054104), we revealed that a single Jahn-Teller conical intersection is expected to have only a mild effect on the dynamics. This fact implies that the Born-Oppenheimer approximation is expected to be valid for this system at least for low enough energies. In the present article this study is extended to include also the Renner-Teller effect as produced by the two lower degenerate Π states. As a result we consider three electronic states which enforce the use of the adiabatic-to-diabatic transformation (ADT) matrix A. The results indicate that the topological effects as produced by the extended Renner/Teller-Jahn/Teller system are strong to the level that, most likely, abolishes the Born-Oppenheimer approximation for this system, all this in contrast to our previous findings (see above publication).

Localization and anharmonicity of the vibrational modes for GC Watson–Crick and Hoogsteen base pairs

We present an ab initio study of the vibrational properties of cytosine and guanine in the Watson–Crick and Hoogsteen base pair configurations. The results are obtained by using two different implementations of the DFT method. We assign the vibrational frequencies to cytosine or to guanine using the vibrational density of states. Next, we investigate the importance of anharmonic corrections for the vibrational modes. In particular, the unusual anharmonic effect of the H+ vibration in the case of the Hoogsteen base pair configuration is discussed.