Absolute Rates of Hole Transfer in DNA

Current-driven mechanical motion of double stranded DNA results in structural instabilities and chiral-induced-spin-selectivity of electron transport

Chiral-induced-spin-selectivity of electron transport and its interplay with DNA's mechanical motion are explored in a double stranded DNA helix with spin-orbit-coupling. The mechanical degree of freedom is treated as a stochastic classical variable experiencing fluctuations and dissipation induced by the environment as well as force exerted by nonequilibrium, current-carrying electrons. Electronic degrees of freedom are described quantum mechanically using nonequilibrium Green's functions. Nonequilibrium Green's functions are computed along the trajectory for the classical variable taking into account dynamical, velocity dependent corrections. This mixed quantum-classical approach enables calculations of time-dependent spin-resolved currents. We showed that the electronic force may significantly modify the classical potential, which, at sufficient voltage, creates a bistable potential with a considerable effect on electronic transport. The DNA's mechanical motion has a profound effect on spin transport; it results in chiral-induced spin selectivity, increasing spin polarization of the current by 9% and also resulting in temperature-dependent current voltage characteristics. We demonstrate that the current noise measurement provides an accessible experimental means to monitor the emergence of mechanical instability in DNA motion. The spin resolved current noise also provides important dynamical information about the interplay between vibrational and spin degrees of freedom in DNA.

Two stage decoherence of optical phonons in long oligomers

Molecular vibrations are generally responsible for chemical energy transport and dissipation in molecular systems. This transport is fast and efficient if energy is transferred by optical phonons in periodic oligomers, but its efficiency is limited by decoherence emerging due to anharmonic interactions with acoustic phonons. Using a general theoretical model, we show that in the most common case of the optical phonon band being narrower than the acoustic bands, decoherence takes place in two stages. The faster stage involves optical phonon multiple forward scattering due to absorption and emission of transverse acoustic phonons, i.e., collective bending modes with a quadratic spectrum; the transport remains ballistic and the speed can be altered. The subsequent slower stage involves phonon backscattering in multiphonon processes involving two or more acoustic phonons resulting in a switch to diffusive transport. If the initially excited optical phonon possesses a relatively small group velocity, then it is accelerated in the first stage due to its transitions to states propagating faster. This theoretical expectation is consistent with the recent measurements of optical phonon transport velocity in alkane chains, increasing with increasing the chain length.

Rapid Estimation of the Intermolecular Electronic Couplings and Charge-Carrier Mobilities of Crystalline Molecular Organic Semiconductors through a Machine Learning Pipeline

Organic semiconductors (OSC) offer tremendous potential across a wide range of (opto)electronic applications. OSC development, however, is often limited by trial-and-error design, with computational modeling approaches deployed to evaluate and screen candidates through a suite of molecular and materials descriptors that generally require hours to days of computational time to accumulate. Such bottlenecks slow the pace and limit the exploration of the vast chemical space comprising OSC. When considering charge-carrier transport in OSC, a key parameter of interest is the intermolecular electronic coupling. Here, we introduce a machine learning (ML) model to predict intermolecular electronic couplings in organic crystalline materials from their three-dimensional (3D) molecular geometries. The ML predictions take only a few seconds of computing time compared to hours by density functional theory (DFT) methods. To demonstrate the utility of the ML predictions, we deploy the ML model in conjunction with mathematical formulations to rapidly screen the charge-carrier mobility anisotropy for more than 60,000 molecular crystal structures and compare the ML predictions to DFT benchmarks.

Unexpected large charge transfer rate mediated by adenine in twisted DNA structure

DNA exhibits remarkable charge transfer ability, which is crucial for its biological functions and potential electronic applications. The charge transfer process in DNA is widely recognized as primarily mediated by guanine, while the contribution of other nucleobases is negligible. Using the tight-binding models in conjunction with first-principles calculations, we investigated the charge transfer behavior of homogeneous GC and AT pairs. We found that the charge transfer rate of adenine significantly changes. With overstretching, the charge transfer rate of adenine can even surpass that of guanine, by as much as five orders of magnitude at a twist angle of around 26°. Further analysis reveals that it is attributed to the turnover of the relative coupling strength between homogeneous GC and AT base pairs, which is caused by the symmetry exchange between the two highest occupied molecular orbitals of base pairs occurring at different twist angles. Given the high degree of flexibility of DNA in vivo and in vitro conditions, these findings prompt us to reconsider the mechanism of biological functions concerning the charge transfer in DNA molecules and further open the potential of DNA as a biomaterial for electronic applications.

Chemical Repair of Radical Damage to the GC Base Pair by DNA-Bound Bisbenzimidazoles

The migration of an electron-loss center (hole) in calf thymus DNA to bisbenzimidazole ligands bound in the minor groove is followed by pulse radiolysis combined with time-resolved spectrophotometry. The initially observed absorption spectrum upon oxidation of DNA by the selenite radical is consistent with spin on cytosine (C), as the GC• pair neutral radical, followed by the spectra of oxidized ligands. The rate of oxidation of bound ligands increased with an increase in the ratio (r) ligands per base pair from 0.005 to 0.04. Both the rate of ligand oxidation and the estimated range of hole transfer (up to 30 DNA base pairs) decrease with the decrease in one-electron reduction potential between the GC• pair neutral radical of ca. 1.54 V and that of the ligand radicals (E0', 0.90-0.99 V). Linear plots of log of the rate of hole transfer versus r give a common intercept at r = 0 and a free energy change of 12.2 ± 0.3 kcal mol-1, ascribed to the GC• pair neutral radical undergoing a structural change, which is in competition to the observed hole transfer along DNA. The rate of hole transfer to the ligands at distance, R, from the GC• pair radical, k2, is described by the relationship k2 = k0 exp(constant/R), where k0 includes the rate constant for surmounting a small barrier.

Charge transport in a double-stranded DNA: Effects of helical symmetry and long-range hopping

Within a tight-binding framework, we examine conformation-dependent charge transport properties of the DNA double-helix, including helical symmetry and the possibility of multiple charge conduction pathways. Using techniques based on the Green's function method, we inspect changes in the localization properties of DNA in the presence of long-range hopping, with varying disorder strength. We study three characteristic DNA sequences, two periodic and one random. We observe that, in all cases, due to disorder-induced delocalization, the localization length variation is similar. We also investigate the effect of backbone energetics on current-voltage (I-V) responses, using the Landauer-Büttiker formalism. We find that, in the presence of helical symmetry and long-range hopping, due to environmental effects, DNA can undergo a phase transition from semiconductor to insulator.

Charge transport through DNA with energy-dependent decoherence

Modeling charge transport in DNA is essential to understand and control the electrical properties and develop DNA-based nanoelectronics. DNA is a fluctuating molecule that exists in a solvent environment, which makes the electron susceptible to decoherence. While knowledge of the Hamiltonian responsible for decoherence will provide a microscopic description, the interactions are complex and methods to calculate decoherence are unclear. One prominent phenomenological model to include decoherence is through fictitious probes that depend on spatially variant scattering rates. However, the built-in energy independence of the decoherence (E-indep) model overestimates the transmission in the bandgap and washes out distinct features inside the valence or conduction bands. In this study, we introduce a related model where the decoherence rate is energy-dependent (E-dep). This decoherence rate is maximum at energy levels and decays away from these energies. Our results show that the E-dep model allows for exponential transmission decay with the DNA length and maintains features within the bands' transmission spectra. We further demonstrate that we can obtain DNA conductance values within the experimental range. Our model can help study and design nanoelectronics devices that utilize weakly coupled molecular structures such as DNA.

Spin-selectivity effect of G-quadruplex DNA molecules

Chirality-induced spin selectivity has been attracting extensive interest in recent years and is demonstrated in a variety of chiral molecules, all of which arise from inherent molecular chirality. Here, we first propose a theoretical model to study the spin-dependent electron transport along guanine-quadruplex (G4) DNA molecules, connected to two nonmagnetic electrodes, by considering the molecule-electrode contact and weak spin-orbit coupling. Our results indicate that the G4-DNA molecular junctions exhibit pronounced spin-selectivity effect, and the asymmetric contact-induced external chirality, instead of the inherent molecular chirality, dominates their spin filtration efficiency. Furthermore, the spin-selectivity effect is robust against the disorder and hold in a wide range of model parameters. These results could be checked by charge transport measurements and provide an alternative way to improve the spin-selectivity effect of chiral nanodevices.

Towards the description of charge transfer states in solubilised LHCII using subsystem DFT

Light harvesting complex II (LHCII) in plants and green algae have been shown to adapt their absorption properties, depending on the concentration of sunlight, switching between a light harvesting and a non-harvesting or quenched state. In a recent work, combining classical molecular dynamics (MD) simulations with quantum chemical calculations (Liguori et al. in Sci Rep 5:15661, 2015) on LHCII, it was shown that the Chl611-Chl612 cluster of the terminal emitter domain can play an important role in modifying the spectral properties of the complex. In that work the importance of charge transfer (CT) effects was highlighted, in re-shaping the absorption intensity of the chlorophyll dimer. Here in this work, we investigate the combined effect of the local excited (LE) and CT states in shaping the energy landscape of the chlorophyll dimer. Using subsystem Density Functional Theory over the classical [Formula: see text]s MD trajectory we look explicitly into the excitation energies of the LE and the CT states of the dimer and their corresponding couplings. Upon doing so, we observe a drop in the excitation energies of the CT states, accompanied by an increase in the couplings between the LE/LE and the LE/CT states facilitated by a shorter interchromophoric distance upon equilibration. Both these changes in conjunction, effectively produces a red-shift of the low-lying mixed exciton/CT states of the supramolecular chromophore pair.

Chiral-Induced Spin Selectivity in Photon-Coupled Achiral Matters

Chiral-induced spin selectivity is a phenomenon in which electron spins are polarized as they are transported through chiral molecules, and the spin polarization depends on the handedness of the chiral molecule. In this study, we show that spin selectivity can be realized in achiral materials by strongly coupling electrons to a circularly polarized mode of an optical cavity or waveguide. Through the investigation of spin-dependent electron transport in a two-terminal setup using the nonequilibrium Green's function approach, it is found that a large spin polarization can be obtained if the rate of dephasing is sufficiently small and the average chemical potential of the two leads is within an appropriate range of values, which is narrow because of the high frequency of the optical mode. To obtain a wider range of energies for a large spin polarization, chiral molecules can be combined with light-matter interactions. To demonstrate this, the spin polarization of electrons transported through a helical molecule strongly coupled to a circularly polarized optical mode is evaluated.

Shedding light on the physical nature of ion pair interactions involving carba-closo-dodecaborate anions. Insights from computation

closo-Carboranes are structures that have been studied for many decades due to their vast applicability in medicine, catalysis, and energy storage. In order to go deeper into the physics behind the interactions of oppositely charged ions, which have potential applications in electrical energy storage and conversion devices, the present work aims to shed light on the physical nature of the interactions involving (R-CB₁₁H₁₁^-, R = H, F, CH₃, CF₃) and M^q+ = Li⁺, Na⁺, Mg²⁺, Zn²⁺ ions. The bonding situations are evaluated in light of both canonical Kohn-Sham energy decomposition, EDA-NOCV, and local energy decomposition, LED, analyses. Electron and hole transports are also evaluated through charge transfer integrals. The findings reveal that such complexes present not only more significant electrostatic, but also non-negligible orbital contributions. Both energy decomposition analyses EDA-NOCV and DLPNO-LED confirm that the strength of ionic pair interactions (R-CB₁₁H₁₁^- ↔ M^q+) is much more dependent on the nature of the cation employed than on the substituent R used. The results also reveal that charge transfers are not significant in such interacting systems.

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.

A 300-fold conductivity increase in microbial cytochrome nanowires due to temperature-induced restructuring of hydrogen bonding networks

Although proteins are considered as nonconductors that transfer electrons only up to 1 to 2 nanometers via tunneling, Geobacter sulfurreducens transports respiratory electrons over micrometers, to insoluble acceptors or syntrophic partner cells, via nanowires composed of polymerized cytochrome OmcS. However, the mechanism enabling this long-range conduction is unclear. Here, we demonstrate that individual nanowires exhibit theoretically predicted hopping conductance, at rate (>10¹⁰ s^-1) comparable to synthetic molecular wires, with negligible carrier loss over micrometers. Unexpectedly, nanowires show a 300-fold increase in their intrinsic conductance upon cooling, which vanishes upon deuteration. Computations show that cooling causes a massive rearrangement of hydrogen bonding networks in nanowires. Cooling makes hemes more planar, as revealed by Raman spectroscopy and simulations, and lowers their reduction potential. We find that the protein surrounding the hemes acts as a temperature-sensitive switch that controls charge transport by sensing environmental perturbations. Rational engineering of heme environments could enable systematic tuning of extracellular respiration.

Prediction and comparative analysis of CTCF binding sites based on a first principle approach

We calculated the patterns for the CCCTC transcription factor (CTCF) binding sites across many genomes on a first principle approach. The validation of the first principle method was done on the human as well as on the mouse genome. The predicted human CTCF binding sites are consistent with the consensus sequence, ChIP-seq data for the K562 cell, nucleosome positions for IMR90 cell as well as the CTCF binding sites in the mouse HOXA gene. The analysis of Homo sapiens, Mus musculus, Sus scrofa, Capra hircus and Drosophila melanogaster whole genomes shows: binding sites are organized in cluster-like groups, where two consecutive sites obey a power-law with coefficient ranging from to 0.3292 0.0068 to 0.5409 0.0064; the distance between these groups varies from 18.08 0.52kbp to 42.1 2.0kbp. The genome of Aedes aegypti does not show a power law, but 19.9% of binding sites are 144 4 and 287 5bp distant of each other. We run negative tests, confirming the under-representation of CTCF binding sites in Caenorhabditis elegans, Plasmodium falciparum and Arabidopsis thaliana complete genomes.

Modified fullerenes as acceptors in bulk heterojunction organic solar cells - a theoretical study

In the present study, electronic structure calculations were used to provide strategies for designing poly(3-hexylthiophene) (P3HT)-fullerene-derivative-based donor-acceptor materials for use in high-efficiency bulk heterojunction organic solar cells (BHJ OSCs). The work systematically analyses the impact of electron-donating and -withdrawing substituents on the opto-electronic properties of the fullerene structures. Parameters relating to the absorption spectra, orbital distributions, and energy ordering of the frontier molecular orbitals (FMO), the interactions between P3HT and the fullerene derivatives, and charge transfer across the interface were investigated. We found that substitution with the electron-withdrawing group NO₂ enhances the electronic coupling between the fullerene and P3HT; however, it reduces the open-circuit voltage (V_OC) of the OSC through lowering the LUMO energy level. Furthermore, the results show that substitution with an electron-withdrawing group (NO₂) and electron-donating group (OCH₃) can improve the power conversion efficiency (PCE) of the OSC, since this slightly improves the photon absorption abilities and charge transfer coupling at the interface without overly compromising V_OC relative to PC₆₁BM. Our study shows that alkyl chain modification in the PC₆₁BM acceptor is a promising strategy for improving the performances of OSCs.

Machine Learning Approach to Calculate Electronic Couplings between Quasi-diabatic Molecular Orbitals: The Case of DNA

Diabatization of one-electron states in flexible molecular aggregates is a great challenge due to the presence of surface crossings between molecular orbital (MO) levels and the complex interaction between MOs of neighboring molecules. In this work, we present an efficient machine learning approach to calculate electronic couplings between quasi-diabatic MOs without the need of nonadiabatic coupling calculations. Using MOs of rigid molecules as references, the MOs that can be directly regarded to be quasi-diabatic in molecular dynamics are selected out, state tracked, and phase corrected. On the basis of this information, artificial neural networks are trained to characterize the structure-dependent onsite energies of quasi-diabatic MOs and the intermolecular electronic couplings. A representative sequence of DNA is systematically studied as an illustration. Smooth time evolution of electronic couplings in all base pairs is obtained with quasi-diabatic MOs. In particular, our method can calculate electronic couplings between different quasi-diabatic MOs independently, and thus, this possesses unique advantages in many applications.

The dynamics of light-induced interfacial charge transfer of different dyes in dye-sensitized solar cells studied by ab initio molecular dynamics

The charge-transport dynamics at the dye-TiO₂ interface plays a vital role for the resulting power conversion efficiency (PCE) of dye sensitized solar cells (DSSCs). In this work, we have investigated the charge-exchange dynamics for a series of organic dyes, of different complexity, and a small model of the semiconductor substrate TiO₂. The dyes studied involve L1, D35 and LEG4, all well-known organic dyes commonly used in DSSCs. The computational studies have been based on ab initio molecular dynamics (aiMD) simulations, from which structural snapshots have been collected. Estimates of the charge-transfer rate constants of the central exchange processes in the systems have been computed. All dyes show similar properties, and differences are mainly of quantitative character. The processes studied were the electron injection from the photoexcited dye, the hole transfer from TiO₂ to the dye and the recombination loss from TiO₂ to the dye. It is notable that the electronic coupling/transfer rates differ significantly between the snapshot configurations harvested from the aiMD simulations. The differences are significant and indicate that a single geometrically optimized conformation normally obtained from static quantum-chemistry calculations may provide arbitrary results. Both protonated and deprotonated dye systems were studied. The differences mainly appear in the rate constant of recombination loss between the protonated and the deprotonated dyes, where recombination losses take place at significantly higher rates. The inclusion of lithium ions close to the deprotonated dye carboxylate anchoring group mitigates recombination in a similar way as when protons are retained at the carboxylate group. This may give insight into the performance-enchancing effects of added salts of polarizing cations to the DSSC electrolyte. In addition, solvent effects can retard charge recombination by about two orders of magnitude, which demonstrates that the presence of a solvent will increase the lifetime of injected electrons and thus contribute to a higher PCE of DSSCs. It is also notable that no simple correlation can be identified between high/low transfer rate constants and specific structural arrangements in terms of atom-atom distances, angles or dihedral arrangements of dye sub-units.

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.

Electron ratcheting in self-assembled soft matter

Ratcheted multi-step hopping electron transfer systems can plausibly produce directional charge transport over very large distances without requiring a source-drain voltage bias. We examine molecular strategies to realize ratcheted charge transport based on multi-step charge hopping, and we illustrate two ratcheting mechanisms with examples based on DNA structures. The charge transport times and currents that may be generated in these assemblies are also estimated using kinetic simulations. The first ratcheting mechanism described for nanoscale systems requires local electric fields on the 10⁹ V/m scale to realize nearly 100% population transport. The second ratcheting mechanism for even larger systems, based on electrochemical gating, is estimated to generate currents as large as 0.1 pA for DNA structures that are a few μm in length with a gate voltage of about 5 V, a magnitude comparable to currents measured in DNA wires at the nanoscale when a source-drain voltage bias of similar magnitude is applied, suggesting an approach to considerably extend the distance range over which DNA charge transport devices may operate.

Charge transport properties of open-shell graphene fragments: a computational study of the phenalenyl tilings

Thinking outside the box of the phenalenyl radical: a systematic structure design strategy, phenalenyl tiling, is found to benefit the electron transport properties of open-shell graphene fragments with one free radical. Compared with the closed-shell species, phenalenyl-based π-radicals exhibit smaller intramolecular reorganization energies and larger intermolecular electronic couplings. However, the on-site Coulomb repulsion can be too strong and impedes the charge transport efficiency of such materials. The repulsion can be weakened in radical species by spin delocalization. In this paper, the extended π-radicals we studied are categorized into three types of open-shell structures: the zigzag, the armchair and the discotic odd alternant hydrocarbons. The latter two belong to phenalenyl tilings. We found that the phenalenyl tilings fully inherit the desirable features of the singly occupied molecular orbital of the phenalenyl radical in a predictable and delocalized fashion, and their on-site Coulomb repulsion is effectively reduced. The zigzag π-radicals are less satisfactory. Therefore, the phenalenyl tilings are favorable candidates for charge transporting materials.

Predicting the DNA Conductance Using a Deep Feedforward Neural Network Model

Double-stranded DNA (dsDNA) has been established as an efficient medium for charge migration, bringing it to the forefront of the field of molecular electronics and biological research. The charge migration rate is controlled by the electronic couplings between the two nucleobases of DNA/RNA. These electronic couplings strongly depend on the intermolecular geometry and orientation. Estimating these electronic couplings for all the possible relative geometries of molecules using the computationally demanding first-principles calculations requires a lot of time and computational resources. In this article, we present a machine learning (ML)-based model to calculate the electronic coupling between any two bases of dsDNA/dsRNA and bypass the computationally expensive first-principles calculations. Using the Coulomb matrix representation which encodes the atomic identities and coordinates of the DNA base pairs to prepare the input dataset, we train a feedforward neural network model. Our neural network (NN) model can predict the electronic couplings between dsDNA base pairs with any structural orientation with a mean absolute error (MAE) of less than 0.014 eV. We further use the NN-predicted electronic coupling values to compute the dsDNA/dsRNA conductance.

Modeling nonlocal electron-phonon coupling in organic crystals using interpolative maps: The spectroscopy of crystalline pentacene and 7,8,15,16-tetraazaterrylene

Electron-phonon coupling plays a central role in the transport properties and photophysics of organic crystals. Successful models describing charge- and energy-transport in these systems routinely include these effects. Most models for describing photophysics, on the other hand, only incorporate local electron-phonon coupling to intramolecular vibrational modes, while nonlocal electron-phonon coupling is neglected. One might expect nonlocal coupling to have an important effect on the photophysics of organic crystals because it gives rise to large fluctuation in the charge-transfer couplings, and charge-transfer couplings play an important role in the spectroscopy of many organic crystals. Here, we study the effects of nonlocal coupling on the absorption spectrum of crystalline pentacene and 7,8,15,16-tetraazaterrylene. To this end, we develop a new mixed quantum-classical approach for including nonlocal coupling into spectroscopic and transport models for organic crystals. Importantly, our approach does not assume that the nonlocal coupling is linear, in contrast to most modern charge-transport models. We find that the nonlocal coupling broadens the absorption spectrum non-uniformly across the absorption line shape. In pentacene, for example, our model predicts that the lower Davydov component broadens considerably more than the upper Davydov component, explaining the origin of this experimental observation for the first time. By studying a simple dimer model, we are able to attribute this selective broadening to correlations between the fluctuations of the charge-transfer couplings. Overall, our method incorporates nonlocal electron-phonon coupling into spectroscopic and transport models with computational efficiency, generalizability to a wide range of organic crystals, and without any assumption of linearity.

Localization to delocalization transition in a double stranded helical geometry: effects of conformation, transverse electric field and dynamics

Conformational effect on electronic localization is critically investigated for the first time considering a double-stranded helical geometry (DSHG) subjected to an electric field. In the presence of electric field the DSHG behaves like a correlated disordered system whose site potentials are modulated in a cosine form like the well known Aubry-André-Harper model. The potential distribution can be modulated further by changing the orientation of the incident field. A similar kind of cosine modulation is also introduced in the inter-strand hopping integrals of the DSHG. Suitably adjusting the orientation of the electric field, we can achieve fully extended energy eigenstates or completely localized ones or a mixture of both. The effects of short-range and long-range hopping integrals along with the chirality on localization are thoroughly studied. Finally, we inspect the role of helical dynamics to make the model more realistic. The interplay between the helical geometry and electric field may open up several notable features of electronic localization and can be verified by using different chiral molecules.

One Way Traffic: Base-to-Backbone Hole Transfer in Nucleoside Phosphorodithioate

The directionality of the hole-transfer processes between DNA backbone and base was investigated by using phosphorodithioate [P(S- )=S] components. ESR spectroscopy in homogeneous frozen aqueous solutions and pulse radiolysis in aqueous solution at ambient temperature confirmed initial formation of G.+ -P(S- )=S. The ionization potential of G-P(S- )=S was calculated to be slightly lower than that of guanine in 5'-dGMP. Subsequent thermally activated hole transfer from G.+ to P(S- )=S led to dithiyl radical (P-2S. ) formation on the μs timescale. In parallel, ESR spectroscopy, pulse radiolysis, and density functional theory (DFT) calculations confirmed P-2S. formation in an abasic phosphorodithioate model compound. ESR investigations at low temperatures and higher G-P(S- )=S concentrations showed a bimolecular conversion of P-2S. to the σ2 -σ*1 -bonded dimer anion radical [-P-2S- . 2S-P-]- [ΔG (150 K, DFT)=-7.2 kcal mol-1 ]. However, [-P-2S- . 2S-P-]- formation was not observed by pulse radiolysis [ΔG° (298 K, DFT)=-1.4 kcal mol-1 ]. Neither P-2S. nor [-P-2S- . 2S-P-]- oxidized guanine base; only base-to-backbone hole transfer occurs in phosphorodithioate.

Ballistic transport and quantum unfurling in molecular junctions via minimal representations of quantum master equations

Quantum furling and unfurling are inelastic transitions between localized and delocalized electronic states. We predict scenarios where these processes govern charge transport through donor-bridge-acceptor molecular junctions. Like in the case of ballistic transport, the resulting currents are nearly independent of the molecular bridge length. However, currents involving quantum furling and unfurling processes can be controlled by the coupling to vibrations in the intra-molecular and the extra-molecular environment, which can be experimentally tuned. Our study is based on rate equations for exchange of energy (bosons) and particles (fermions) between the molecular bridge and its environment. An efficient algorithm is introduced for a compact representation of the relevant rate equations, which utilizes the redundancies in the rate matrix and the sparsity of the creation and annihilation operators in the molecular Fock space.

Density-functional tight-binding: basic concepts and applications to molecules and clusters

The scope of this article is to present an overview of the Density Functional based Tight Binding (DFTB) method and its applications. The paper introduces the basics of DFTB and its standard formulation up to second order. It also addresses methodological developments such as third order expansion, inclusion of non-covalent interactions, schemes to solve the self-interaction error, implementation of long-range short-range separation, treatment of excited states via the time-dependent DFTB scheme, inclusion of DFTB in hybrid high-level/low level schemes (DFT/DFTB or DFTB/MM), fragment decomposition of large systems, large scale potential energy landscape exploration with molecular dynamics in ground or excited states, non-adiabatic dynamics. A number of applications are reviewed, focusing on -(i)- the variety of systems that have been studied such as small molecules, large molecules and biomolecules, bare orfunctionalized clusters, supported or embedded systems, and -(ii)- properties and processes, such as vibrational spectroscopy, collisions, fragmentation, thermodynamics or non-adiabatic dynamics. Finally outlines and perspectives are given.

Persulfurated Coronene and Its Chalcogenide Analogues: Insight into Effects of Peripheral Substitution

The density functional theory (DFT) and time-dependent DFT methods have been used to investigate the persulfurated coronene (PSC) and its chalcogenide analogues (POC and PSeC), derived from the substitution of sulfur, oxygen, and selenium for all hydrogen atoms in coronene, respectively. The presence of peripheral S-S in PSC results in a σ-type lowest unoccupied molecular orbital and the dark low-lying states (S₁ ∼ S₁₅). The peripheral S-S bond is responsible for its electron capture, which maintains a planar configuration of the singly and doubly negative-charged PSC. POC is predicted to have the most stable saddle-shaped structure with the C═O group, and its bowl-shaped isomer with the O-O moiety is less stable by 279.2 kcal/mol energetically. PSeC has similar electronic and structural features with PSC, but its dimer is predicted to have much better hole mobility, compared to PSC. The present results indicate that the chalcogenide substitution at the periphery of the polycyclic aromatic hydrocarbons may remarkably change their electronic and spectroscopic properties as well as the carrier transport behavior of their molecular materials.

Unexpectedly Large Couplings Between Orthogonal Units in Anthraquinone Polymers

The unusual electronic properties of directly linked 1,4-polyanthraquinones (14PAQs) are investigated. The dihedral angle between the molecular planes of anthraquinones (AQs) is found to be close to 90°. Contrary to the prevailing notion that the interaction between orthogonal units is negligible due to broken π-electron conjugation, the coupling between neighboring AQ units does not have a minimum at 90° and is much larger than that expected. The unexpectedly large electronic coupling between orthogonal AQ units is explained by the interaction between the lone pairs of the carbonyl oxygen and the π system of the neighboring unit, which allows favorable overlap between frontier molecular orbitals at the orthogonal geometry. It is shown that this effect, which is described computationally for the first time, can be strengthened by adding more quinone units. The effect of thermal fluctuations on the couplings is assessed through ab initio molecular dynamics simulations. The distributions of the couplings reveal that electron transport is resilient to dynamic disorder in all systems considered, whereas the hole couplings are much more sensitive to disorder. Lone pair-π interactions are described, as a previously largely overlooked conjugation mechanism, for incorporation into a new class of disorder-resilient semiconducting redox polymers.

The Dynamics of Hole Transfer in DNA

High-energy radiation and oxidizing agents can ionize DNA. One electron oxidation gives rise to a radical cation whose charge (hole) can migrate through DNA covering several hundreds of Å, eventually leading to irreversible oxidative damage and consequent disease. Understanding the thermodynamic, kinetic and chemical aspects of the hole transport in DNA is important not only for its biological consequences, but also for assessing the properties of DNA in redox sensing or labeling. Furthermore, due to hole migration, DNA could potentially play an important role in nanoelectronics, by acting as both a template and active component. Herein, we review our work on the dynamics of hole transfer in DNA carried out in the last decade. After retrieving the thermodynamic parameters needed to address the dynamics of hole transfer by voltammetric and spectroscopic experiments and quantum chemical computations, we develop a theoretical methodology which allows for a faithful interpretation of the kinetics of the hole transport in DNA and is also capable of taking into account sequence-specific effects.

How To Extract Quantitative Information on Electronic Transitions from the Density Functional Theory "Black Box"

Electronic couplings and vertical excitation energies are crucial determinants of charge and excitation energy transfer rates in a broad variety of processes ranging from biological charge transfer to charge transport through inorganic materials, from molecular sensing to intracellular signaling. Density Functional Theory (DFT) is generally used to calculate these critical parameters, but the quality of the results is unpredictable because of the semiempirical nature of the available DFT approaches. This study identifies a small set of fundamental rules that enables accurate DFT computation of electronic couplings and vertical excitation energies in molecular complexes and materials. These rules are applied to predict efficient DFT approaches to coupling calculations. The result is an easy-to-use guide for reliable DFT descriptions of electronic transitions.

Transient and Enduring Electronic Resonances Drive Coherent Long Distance Charge Transport in Molecular Wires

It is shown that the yields of oxidative damage observed in double-stranded DNA oligomers consisting of two guanines separated by adenine-thymine (A:T) _n bridges of various lengths are reliably accounted for by a multistep mechanism, in which transient and nontransient electronic resonances induce charge transport and solvent relaxation stabilizes the hole transfer products. The proposed multistep mechanism leads to results in excellent agreement with the observed yield ratios for both the short and the long distance regime; the almost distance independence of yield ratios for longer bridges ( n ≥ 3) is the consequence of the significant energy decrease of the electronic levels of the bridge, which, as the bridge length increases, become quasi-degenerate with those of the acceptor and donor groups (enduring resonance). These results provide significant guidelines for the design of novel DNA sequences to be employed in organic electronics.

Machine Learning Prediction of DNA Charge Transport

First-principles calculations of charge transfer in DNA molecules are computationally expensive given that conducting charge carriers interact with intra- and intermolecular atomic motion. Screening sequences, for example, to identify excellent electrical conductors, is challenging even when adopting coarse-grained models and effective computational schemes that do not explicitly describe atomic dynamics. We present a machine learning (ML) model that allows the inexpensive prediction of the electrical conductance of millions of long double-stranded DNA (dsDNA) sequences, reducing computational costs by orders of magnitude. The algorithm is trained on short DNA nanojunctions with n = 3-7 base pairs. The electrical conductance of the training set is computed with a quantum scattering method, which captures charge-nuclei scattering processes. We demonstrate that the ML method accurately predicts the electrical conductance of varied dsDNA junctions tracing different transport mechanisms: coherent (short-range) quantum tunneling, on-resonance (ballistic) transport, and incoherent site-to-site hopping. Furthermore, the ML approach supports physical observations that clusters of nucleotides regulate DNA transport behavior. The input features tested in this work could be used in other ML studies of charge transport in complex polymers in the search for promising electronic and thermoelectric materials.

Periodic, quasiperiodic, fractal, Kolakoski, and random binary polymers: Energy structure and carrier transport

We study periodic, quasiperiodic (Thue-Morse, Fibonacci, period doubling, Rudin-Shapiro), fractal (Cantor, generalized Cantor), Kolakoski, and random binary sequences using a tight-binding wire model, where a site is a monomer (e.g., in DNA, a base pair). We use B-DNA as our prototype system. All sequences have purines, guanine (G) or adenine (A), on the same strand, i.e., our prototype binary alphabet is {G,A}. Our aim is to examine the influence of sequence intricacy and magnitude of parameters on energy structure, localization, and charge transport. We study quantities such as autocorrelation function, eigenspectra, density of states, Lyapunov exponents, transmission coefficients, and current-voltage curves. We show that the degree of sequence intricacy and the presence of correlations decisively affect the aforementioned physical properties. Periodic segments have enhanced transport properties. Specifically, in homogeneous sequences transport efficiency is maximum. There are several deterministic aperiodic sequences that can support significant currents, depending on the Fermi level of the leads. Random sequences is the less efficient category.

Charge Separation and Recombination Pathways in Diblock DNA Hairpins

Achieving high-yielding photoinduced charge separation through the π-stacked bases of DNA is a critical requirement for realizing numerous DNA-based technologies. In the current work, we combine two strategies for achieving high-yield charge separation. First, a chromophore with a high driving force for charge injection, naphthalenediimide (NDI), is used because it generates hot carriers that enhance charge-transfer rates. Second, a diblock DNA sequence is used with two or three adenines followed by a series of guanines to implement an energy landscape that accelerates charge separation while retarding charge recombination. The photoinduced dynamics of these NDI diblock oligomers with and without a terminal hole acceptor are probed by femtosecond transient absorption spectroscopy. The measured rate constants for various charge separation and recombination processes are interpreted within the context of a full kinetic model of these systems. We find that the A₂ and A₃ oligomers achieve similar charge separation yields (as high as 20-25%) for a given length, yet the critical recombination process that determines these yields occurs at different distances from the NDI chromophore and on different time scales. This type of analysis could be used to predict charge separation efficiencies in candidate DNA structures.

Read between the Molecules: Computational Insights into Organic Semiconductors

The performance and key electronic properties of molecular organic semiconductors are dictated by the interplay between the chemistry of the molecular core and the intermolecular factors of which manipulation has inspired both experimentalists and theorists. This Perspective presents major computational challenges and modern methodological strategies to advance the field. The discussion ranges from insights and design principles at the quantum chemical level, in-depth atomistic modeling based on multiscale protocols, morphological prediction and characterization as well as energy-property maps involving data-driven analysis. A personal overview of the past achievements and future direction is also provided.

Polaron States in Fullerene Adducts Modeled by Coarse-Grained Molecular Dynamics and Tight Binding

Strong electron-phonon coupling leads to polaron localization in molecular semiconductor materials and influences charge transport, but it is expensive to calculate atomistically. Here, we propose a simple and efficient model to determine the energy and spatial extent of polaron states within a coarse-grained representation of a disordered molecular film. We calculate the electronic structure of the molecular assembly using a tight-binding Hamiltonian and determine the polaron state self-consistently by perturbing the site energies by the dielectric response of the surrounding medium to the charge. When applied to fullerene derivatives, the method shows that polarons extend over multiple molecules in C60 but localize on single molecules in higher adducts of phenyl-C61-butyric-acid-methyl-ester (PCBM) because of packing disorder and the polar side chains. In PCBM, polarons localize on single molecules only when energetic disorder is included or when the fullerene is dispersed in a blend. The method helps to establish the conditions under which a hopping transport model is justified.

Manipulation of the magnetoresistance effect in a double-helix DNA

Magnetoresistance (R _m) of a double-stranded (G:C) _N DNA sandwiched between ferromagnetic electrodes has been studied using the transfer matrix method of the tight-binding model. A R _m magnitude up to 72.5% for DNA in its natural structure is observed when the spin-orbit coupling with the helix spring geometry and a possible dephasing effect are taken into account. It can be greatly manipulated by stress or torque applied to the DNA with respect to its axis. In addition, the external voltage bias can also be used to efficiently control R _m. The dependence of R _m on the DNA length in a decaying oscillation form is observed.

Probing charge transfer dynamics in a single iron tetraphenylporphyrin dyad adsorbed on an insulating surface

Although the dynamics of charge transfer (CT) processes can be probed with ultimate lifetime resolution, the inability to control CT at the nanoscale is one of the most important roadblocks to revealing some of its deep fundamental aspects. In this work, we present an investigation of CT dynamics in a single iron tetraphenylporphyrin (Fe-TPP) donor/acceptor dyad adsorbed on a CaF2/Si(100) insulating surface. The tip of a scanning tunneling microscope (STM) is used to create local ionic states in one fragment of the dyad. The CT process is monitored by imaging subsequent changes in the neighbor acceptor molecule and its efficiency is mapped, revealing the influence of the initial excited state in the donor molecule. In the validation of the experiments, simulations based on density functional theory show that holes have a higher donor-acceptor CT rate compared to electrons and highlight a noticeable initial state dependence on the CT process. We leverage the unprecedented spatial resolution achieved in our experiments to show that the CT process in the dyad is governed via molecule-molecule coherent tunneling with negligible surface-mediated character.

Single-Stranded DNA Oligonucleotides Retain Rise Coordinates Characteristic of Double Helices

The structures of single-stranded DNA oligonucleotides from dimeric to hexameric sequences have been thoroughly investigated. Computations performed at the density functional level of theory including dispersion forces and solvation show that single-stranded helices adopt conformations very close to crystallographic B-DNA, with rise coordinates amounting up to 3.3 Å. Previous results, suggesting that single strands should be shorter than double helices, largely originated from the incompleteness of the adopted basis set. Although sensible deviations with respect to standard B-DNA are predicted, computations indicate that sequences rich in stacked adenines are the most ordered ones, favoring the B-DNA pattern and inducing regular arrangements also on flanking nucleobases. Several structural properties of double helices rich in adenine are indeed already reflected by the corresponding single strands.

Modeling DNA oxidation in water

A novel set of hole-site energies and electronic coupling parameters to be used, in the framework of the simplest tight-binding approximation, for predicting DNA hole trapping efficiencies and rates of hole transport in oxidized DNA is proposed. The novel parameters, significantly different from those previously reported in the literature, have been inferred from reliable density functional calculations, including both the sugar-phosphate ionic backbone and the effects of the aqueous environment. It is shown that most of the experimental oxidation free energies of DNA tracts and of oligonucleotides available from photoelectron spectroscopy and voltammetric measurements are reproduced with great accuracy, without the need for introducing sequence dependent parameters.

Modelling of the charge carrier mobility in disordered linear polymer materials

We introduced a molecular-scale description of disordered on-chain charge carrier states into a theoretical model of the charge carrier transport in polymer semiconductors. The presented model combines the quantum mechanical approach with a semi-classical solution of the inter-chain charge hopping. Our model takes into account the significant local anisotropy of the charge carrier mobility present in linear conjugated polymers. Contrary to the models based on the effective medium approximation, our approach allowed avoiding artefacts in the calculated concentration dependence of the mobility originated in its problematic configurational averaging. Monte Carlo numerical calculations show that, depending on the degree of the energetic and structural disorder, the charge carrier mobility increases significantly with increasing charge concentration due to trap filling. At high charge carrier concentrations, the effect of the energetic disorder disappears and the mobility decreases slightly due to the lower density of unoccupied states available for the hopping transport. It could explain the experimentally observed mobility degradation in organic field-effect transistors at high gate voltage.

Theoretical insights into the 1D-charge transport properties in a series of hexaazatrinaphthylene-based discotic molecules

Discotic liquid crystal (DLC) materials have attracted considerable attention mainly due to their high charge carrier mobilities in quasi-one-dimensional columns. In this article, five hexaazatrinaphthylene-based DLC molecules were investigated theoretically, and their frontier molecular orbital energy levels, crystal structures, and electron/hole drift mobilities were calculated by combination of density functional theory (DFT) and semiclassical Marcus charge transfer theory. The systems studied in this work include three experimentally reported molecules (1, 2, and 3) and two theoretically designed molecules (4 and 5). Compared with the 1-3 compounds, 4 and 5 have three more extended benzene rings in the π-conjugated core. The present results show that the orders of the frontier molecular orbital energy levels and electron drift mobilities agree very well with the experiment. For 4 and 5, the electron/hole reorganization energies are lower than those of compounds 1-3. Furthermore, the calculated electron/hole transfer integral of 5 is the largest among all the five systems, leading to the highest electron and hole mobilities. In addition, the hydrophobicity and solubility were also evaluated by DFT, indicating that compound 5 has good hydrophobicity and good solubility in trichloromethane. As a result, it is expected that compound 5 can be a potential charge transport material in electronic and optoelectronic devices. © 2017 Wiley Periodicals, Inc.

Role of photoresponse of π electrons in light-driven DNA dissociations

The role of photoresponse of π electrons in light-driven DNA dissociations is theoretically studied. A new model combining the Peyrard-Bishop-Dauxois model and the charge ladder model is first proposed. Then the evolutions of π-electronic states and H-bond stretching in the light-driven DNA dissociations are studied. The results show that light irradiation will induce ultrafast charge redistribution among bases, leading to the precursory insulator-to-metallic transition. This electronic transition will assist DNA to dissociate. Effects of screened Coulomb interactions on dissociation dynamics is emphatically discussed. Finally, it is also found that light-driven DNA dissociation preferentially occurs in the adenine-thymine-rich region rather than the guanine-cytosine-rich region.