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The influence of carotenoid triplet states on the Qy electronic transitions of chlorophylls has been observed in experiments on light-harvesting complexes over the past three decades, but the interpretation of the resulting spectral feature in the triplet minus singlet (T–S) absorption spectra of photosystems is still debated, as the physical–chemical explanation of this feature has been elusive. Here, we resolve this debate, by explaining the T–S spectra of pigment complexes over the Qy-band spectral region through a comparative study of chlorophyll–carotenoid model dyads and larger pigment complexes from the main light harvesting complex of higher plants (LHCII). This goal is achieved by combining state-of-the-art time-dependent density functional theory with analysis of the relationship between electronic properties and nuclear structure, and by comparison to the experiment. We find that the special signature in the T–S spectra of both model and natural photosystems is determined by singlet-like triplet excitations that can be described as effective singlet excitations on chlorophylls influenced by a stable electronic triplet on the carotenoid. The comparison with earlier experiments on different light-harvesting complexes confirms our theoretical interpretation of the T–S spectra in the Qy spectral region. Our results indicate an important role for the chlorophyll–carotenoid electronic coupling, which is also responsible for the fast triplet–triplet energy transfer, suggesting a fast trapping of the triplet into the relaxed carotenoid structure. The gained understanding of the interplay between the electronic and nuclear structures is potentially informative for future studies of the mechanism of photoprotection by carotenoids. [ABSTRACT FROM AUTHOR]

The non-biological 2′-deoxy-2′-fluoro-arabinonucleic acid (2′F-ANA) may be used as a valid alternative to DNA in biomedical and electronic applications because of its higher resistance to hydrolysis and nuclease degradation. However, the advantage of using 2′F-ANA in such applications also depends on its charge-transfer properties compared to DNA. In this study, we compare the charge conduction properties of model 2′F-ANA and DNA double-strands, using structural snapshots from MD simulations to calculate the electronic couplings and reorganization energies associated with the hole transfer steps between adjacent nucleobase pairs. Inserting these charge-transfer parameters into a kinetic model for charge conduction, we find similar conductive properties for DNA and 2′F-ANA. Moreover, we find that 2′F-ANA's enhanced chemical stability does not correspond to a reduction in the nucleobase π-stack structural flexibility relevant to both electronic couplings and reorganization free energies. Our results promote the use of 2′F-ANA in applications that can be based on charge transport, such as biosensing and chip technology, where its chemical stability and conductivity can advantageously combine. [ABSTRACT FROM AUTHOR]

Using molecular dynamics simulations and electronic structure theory, we shed light on the charge dynamics that causes the differential interaction of tumor suppressor protein p53 with the p21 and Gadd45 genes in response to oxidative stress. We show that the sequence dependence of this selectivity results from competing charge transfer to the protein and through the DNA, with implications on the use of genome editing tools to influence the p53 regulatory function. [ABSTRACT FROM AUTHOR]

The non-biological nucleic acid 2′-deoxy-2′-fluoro-arabinonucleic acid (2′F-ANA) may be of use because of its higher chemical stability than DNA in terms of resistance to hydrolysis and nuclease degradation. In order to investigate the charge transfer characteristics of 2′F-ANA, of relevance to applications in nucleic acid-based biosensors and chip technologies, we compare the electronic couplings for hole transfer between stacked nucleobase pairs in DNA and 2′F-ANA by carrying out density functional theory (DFT) calculations on geometries taken from molecular dynamics simulations. We find similar averages and distribution widths of the base-pair couplings in the two systems. On the basis of this result, 2′F-ANA is expected to have charge transfer properties similar to those of DNA, while offering the advantage of enhanced chemical stability. As such, 2′F-ANA may serve as a possible alternative to DNA for use in a broad range of nanobiotechnological applications. Furthermore, we show that the (experimentally observed) enhanced chemical stability resulting from the backbone modifications does not cause reduced fluctuations of the base-pair electronic couplings around the values found for “ideal” B-DNA (with standard step parameter values). Our study also supports the use of a DFT implementation, with the M11 functional, of the wave function overlap method to compute effective electronic couplings in nucleic acid systems. [ABSTRACT FROM AUTHOR]

Using molecular dynamics simulations and electronic structure theory, we shed light on the charge dynamics that causes the differential interaction of tumor suppressor protein p53 with the p21 and Gadd45 genes in response to oxidative stress. We show that the sequence dependence of this selectivity results from competing charge transfer to the protein and through the DNA, with implications on the use of genome editing tools to influence the p53 regulatory function.

We consider a molecular conduction junction that comprises a redox molecule bridging between metal electrodes, in the limit of weak coupling and high temperature where electron transport is dominated by Marcus electron transfer kinetics. We address the correspondence between the Marcus description in terms of nuclear potential energy surfaces associated with different charging states of the molecular bridge, and the single electron description commonly used in theories of molecular conduction. The relationship between the energy gap, reorganization energy and activation energy parameters of the Marcus theory and the corresponding energy parameters in the single electron description is elucidated. We point out that while transport in the normal Marcus regime involves activated (therefore relatively slow) transitions between at least two charging states of the molecular bridge, deep in the inverted regime only one of these states is locally stable and transitions into this state are activationless. The relatively slow rates that characterize the normal Marcus transport regime manifest themselves in the appearance of hysteresis in the system transport behavior as a function of gate or bias potentials for relatively slow scan rates of these potentials, but not bistability in the junction conduction behavior. We also consider the limit of fast solvent reorganization that may reflect the response of the electronic environment (electronic polarization of a solvent and of the metal electrodes) to the changing charging state of the bridge. In this limit, environmental reorganization appears as renormalization of the bridge electronic energy levels. We show that the effect of this reorganization on the junction conduction properties is not universal and depends on the particular bridge charging states that are involved in the conduction process.