Coherent Effects in Charge Transport in Molecular Wires: Toward a Unifying Picture of Long-Range Hole Transfer in DNA

Arcsine laws for Brownian motion with Poissonian resetting

We analyze the equivalents of the celebrated arcsine laws for Brownian motion undergoing Poissonian resetting. We obtain closed-form formulas for the probability density functions of the corresponding random variables in the cases of the first and second arcsine law. Furthermore, we obtain numerical results for the third law.

Hole Transfer and the Resulting DNA Damage

In this review, we focus on the one-electron oxidation of DNA, which is a multipart event controlled by several competing factors. We will discuss the oxidation free energies of the four nucleobases and the electron detachment from DNA, influenced by specific interactions like hydrogen bonding and stacking interactions with neighboring sites in the double strand. The formation of a radical cation (hole) which can migrate through DNA (hole transport), depending on the sequence-specific effects and the allocation of the final oxidative damage, is also addressed. Particular attention is given to the one-electron oxidation of ds-ODN containing G:C pairs, including the complex mechanism of the deprotonation vs. hydration steps of a G:C•+ pair, as well as to the modes of formation of the two guanyl radical tautomers after deprotonation. Among the reactive oxygen species (ROS) generated in aerobic organisms by cellular metabolisms, several oxidants react with DNA. The mechanism of stable product formation and their use as biomarkers of guanine oxidation in DNA damage are also addressed.

Quantum Chemical Insights into DNA Nucleobase Oxidation: Bridging Theory and Experiment

The oxidation free energies of DNA nucleobases in aqueous solution are still matter of extensive discussion because of the contrasting results reported so far. With the aim of settling a longstanding debate about the oxidation potentials of DNA constituents, herein we report the results of state-of-the-art DFT-based molecular dynamics simulations, in which the whole solvent environment is modeled at the atomistic level, by using DFT supercell calculations, with periodic boundary conditions. Calculated vertical ionization energies are very close to those observed by photoelectron spectroscopy both in the gas phase and in solution. One-electron oxidation free energies in aqueous solution agree well with the results of differential pulse voltammetry measurements and with those inferred by photoelectron spectroscopy with the aid of theoretical computations to estimate vibrational relaxation.

Toward Efficient Modeling of Nonradiative Decay in Extended INVEST: Overcoming Computational Challenges in Quantum Dynamics Simulations

In recent years, an increasing number of fully organic molecules capable of thermally activated delayed fluorescence (TADF) have been reported, often with very small or even inverted singlet-triplet (INVEST) energy gaps. These molecules typically exhibit complex photophysics due to the close energy levels of multiple singlet and triplet states, which create various transition pathways toward emission. A predictive model for the rates of these transitions is thus essential for assessing the suitability of new materials for light-emitting devices. Quantum Dynamics (QD) calculations are ideal for this purpose, as they include quantum effects, without the limitations of first-order perturbative approaches, also allowing taking into account more than two electronic states at once. However, the huge computational demands of QD methodologies, especially for large molecules, currently limit their use as a standard tool. To address this problem, we here employ a strategy that allows us to include almost the whole set of the vibrational coordinates by selecting the key elements of the Hilbert space that significantly impact dynamics, thereby hugely reducing the computational burden. Application of this protocol to two relatively large INVEST molecules reveals that internal conversion in these systems is very fast, making indirect emissive pathways a possible channel for the population of the S1 state. More importantly, this study demonstrates that the dynamics can be accurately described even with a significantly reduced vibrational space, thus allowing quantum dynamics calculations that yield accurate transition rates in a few minutes of computational time.

DNA-Based Complexes and Composites: A Review of Fabrication Methods, Properties, and Applications

Deoxyribonucleic acid (DNA), a macromolecule that stores genetic information in organisms, has recently been gradually developed into a building block for new materials due to its stable chemical structure and excellent biocompatibility. The efficient preparation and functional integration of various molecular complexes and composite materials based on nucleic acid skeletons have been successfully achieved. These versatile materials possess excellent physical and chemical properties inherent to certain inorganic or organic molecules but are endowed with specific physiological functions by nucleic acids, demonstrating unique advantages and potential applications in materials science, nanotechnology, and biomedical engineering in recent years. However, issues such as the production cost, biological stability, and potential immunogenicity of DNA have presented some unprecedented challenges to the application of these materials in the field. This review summarizes the cutting-edge manufacturing techniques and unique properties of DNA-based complexes and composites and discusses the trends, challenges, and opportunities for the future development of nucleic acid-based materials.

Electron Localization and Mobility in Monolayer Fullerene Networks

The novel 2D quasi-hexagonal phase of covalently bonded fullerene molecules (qHP C60), the so-called graphullerene, has displayed far superior electron mobilities, if compared to the parent van der Waals three-dimensional crystal (vdW C60). Herein, we present a comparative study of the electronic properties of vdW and qHP C60 using state-of-the-art electronic-structure calculations and a full quantum-mechanical treatment of electron transfer. We show that both materials entail polaronic localization of electrons with similar binding energies (≈0.1 eV) and, therefore, they share the same charge transport via polaron hopping. In fact, we quantitatively reproduce the sizable increment of the electron mobility measured for qHP C60 and identify its origin in the increased electronic coupling between C60 units.

Simulation of polymeric mixed ionic and electronic conductors with a combined classical and quantum mechanical model

In organic polymeric materials with mixed ionic and electronic conduction (OMIEC), the excess charge in doped polymers is very mobile and the dynamics of the polymer chain cannot be accurately described with a model including only fixed point charges. Ions and polymer are comparatively slower and a methodology to capture the correlated motions of excess charge and ions is currently unavailable. Considering a prototypical interface encountered in this type of materials, we constructed a scheme based on the combination of MD and QM/MM to evaluate the classical dynamics of polymer, water and ions, while allowing the excess charge of the polymer chains to rearrange following the external electrostatic potential. We find that the location of the excess charge varies substantially between chains. The excess charge changes across multiple timescales as a result of fast structural fluctuations and slow rearrangement of the polymeric chains. Our results indicate that such effects are likely important to describe the phenomenology of OMIEC, but additional features should be added to the model to enable the study of processes such as electrochemical doping.

Charge transport properties of ideal and natural DNA segments, as mutation detectors

DNA sequences of ideal and natural geometries are examined, studying their charge transport properties as mutation detectors. Ideal means textbook geometry. Natural means naturally distorted sequences; geometry taken from available databases. A tight-binding (TB) wire model at the base-pair level is recruited, together with a transfer matrix technique. The relevant TB parameters are obtained using a linear combination of all valence orbitals of all atoms, using geometry, either ideal or natural, as the only input. The investigated DNA sequences contain: (i) point substitution mutations - specifically, the transitions guanine (G) ↔ adenine (A) - and (ii) sequences extracted from human chromosomes, modified by expanding the cytosine-adenine-guanine triplet [(CAG)_n repeats] to mimic the following diseases: (a) Huntington's disease, (b) Kennedy's disease, (c) Spinocerebellar ataxia 6, (d) Spinocerebellar ataxia 7. Quantities such as eigenspectra, density of states, transmission coefficients, and the - more experimentally relevant - current-voltage (I-V) curves are studied, intending to find adequate features to recognize mutations. To this end, the normalised deviation of the I-V curve from the origin (NDIV) is also defined. The features of the NDIV seem to provide a clearer picture, being sensitive to the number of point mutations and allowing to characterise the degree of danger of developing the aforementioned diseases.

Sol-Gel Dipping Devices for H2S Visualization

In this contribution we report the synthesis and full characterization, via a combination of different spectroscopies (e.g., ¹H NMR, UV-vis, fluorescence, MALDI), of a new family of fluorescent zinc complexes with extended π-conjugated systems, with the final aim of setting up higher performance H₂S sensing devices. Immobilization of the systems into a polymeric matrix for use in a solid-state portable device was also explored. The results provided proof-of-principle that the title complexes could be successfully implemented in a fast, simple and cost-effective H₂S sensing device.

Electron Transfer Rates in Solution: Toward a Predictive First Principle Approach

Using a very recently proposed theoretical model, electron transfer rates in solution are calculated from first principles for different donor-acceptor pairs in tetrahydrofuran. We show that this approach, which integrates tunneling effects into a classical treatment of solvent motion, is able to provide reliable rate constants and their temperature dependence, even in the case of highly exergonic reactions, where Marcus’ theory usually fails.

Duplex DNA Retains the Conformational Features of Single Strands: Perspectives from MD Simulations and Quantum Chemical Computations

Molecular dynamics simulations and geometry optimizations carried out at the quantum level as well as by quantum mechanical/molecular mechanics methods predict that short, single-stranded DNA oligonucleotides adopt conformations very similar to those observed in crystallographic double-stranded B-DNA, with rise coordinates close to ≈3.3 Å. In agreement with the experimental evidence, the computational results show that DNA single strands rich in adjacent purine nucleobases assume more regular arrangements than poly-thymine. The preliminary results suggest that single-stranded poly-cytosine DNA should also retain a substantial helical order in solution. A comparison of the structures of single and double helices confirms that the B-DNA motif is a favorable arrangement also for single strands. Indeed, the optimal geometry of the complementary single helices is changed to a very small extent in the formation of the duplex.

Modeling Charge Transfer Reactions by Hopping between Electronic Ground State Minima: Application to Hole Transfer between DNA Bases

In this paper, we extend the previously described general model for charge transfer reactions, introducing specific changes to treat the hopping between energy minima of the electronic ground state (i.e., transitions between the corresponding vibrational ground states). We applied the theoretical-computational model to the charge transfer reactions in DNA molecules which still represent a challenge for a rational full understanding of their mechanism. Results show that the presented model can provide a valid, relatively simple, approach to quantitatively study such reactions shedding light on several important aspects of the reaction mechanism.

Electron Transfer Rates in Polar and Non-Polar Environments: a Generalization of Marcus' Theory to Include an Effective Treatment of Tunneling Effects

A multistep kinetic model in which solvent motion is treated in the framework of Marcus theory and the rates of the elementary electron transfer step are evaluated at full quantum mechanical level is proposed and applied to the calculation of the rates of intramolecular electron transfer reactions in rigidly spaced D-Br-A (D = 1,1'-biphenyl radical anion, Br = androstane) compounds, for five acceptors (A) in three organic solvents with different polarity. The calculated rates agree well with experimental ones, and their temperature dependence is almost quantitatively reproduced.

Remote Photodamaging of DNA by Photoinduced Energy Transport

Local DNA photodamaging by light is well-studied and leads to a number of structurally identified direct damage, in particular cyclobutane pyrimidine dimers, and indirect oxidatively generated damage, such as 8-oxo-7,8-hydroxyguanine. Similar damages have now been found at remote sites, at least more than 105 Å (30 base pairs) away from the site of photoexcitation. In contrast to the established mechanisms of local DNA photodamaging, the processes of remote photodamage are only partially understood. Known pathways include those to remote oxidatively generated DNA photodamages, which were elucidated by studying electron hole transport through the DNA about 20 years ago. Recent studies with DNA photosensitizers and mechanistic proposals on photoinduced DNA-mediated energy transport are summarized in this minireview. These new mechanisms to a new type of remote DNA photodamaging provide an important extension to our general understanding to light-induced DNA damage and their mutations.

The Time Scale of Electronic Resonance in Oxidized DNA as Modulated by Solvent Response: An MD/QM-MM Study

The time needed to establish electronic resonant conditions for charge transfer in oxidized DNA has been evaluated by molecular dynamics simulations followed by QM/MM computations which include counterions and a realistic solvation shell. The solvent response is predicted to take ca. 800-1000 ps to bring two guanine sites into resonance, a range of values in reasonable agreement with the estimate previously obtained by a kinetic model able to correctly reproduce the observed yield ratios of oxidative damage for several sequences of oxidized DNA.