Charge transfer in B-DNA oligomers following oxidation (hole creation) is investigated using the Tight Binding Fishbone Wire model: each site represents either a base pair or a backbone position, with backbone positions not directly connected. Homopolymeric sequences (e.g., 5 '-GGGGG-3 ') are employed as reference systems for their uniform on-site energies and interaction integrals between sites. The impact of transition mutations (e.g., G -> A) and structural disorder on charge transfer is examined. Disorder is introduced along the pi-stacking pathway and at the sugar-phosphate backbone, affecting base pair and backbone on-site energies and interaction parameters between sites. Electronic properties and charge transfer are analyzed through the calculation of the highest occupied molecular orbital (HOMO) regime (the energy regime made by the interaction of all sites' HOMOs) eigenstates, participation ratios, site occupation probabilities, and charge transfer rates. The lowest unoccupied molecular orbital (LUMO) regime can be treated similarly. Charge motion is also quantified using weighted mean frequencies of sites and the total weighted mean frequency of the system, with higher values corresponding to faster charge transfer. The presence of mutations and disorder is found to enhance localization and reduce transfer efficiency. These results elucidate how sequence alterations and structural disorder modulate charge transfer in DNA.

The study of DNA charge dynamics is a highly interdisciplinary field that bridges physics, chemistry, biology, and medicine, and plays a critical role in processes such as DNA damage detection, protein-DNA interactions, and DNA-based nanotechnology. However, despite significant progress in each of these areas, knowledge often remains inaccessible to researchers in other scientific communities, limiting the broader impact of advances across disciplines. To bridge this gap, we present QuantumDNA, an open-source Python package for simulating DNA charge transfer and excited state dynamics using quantum physical methods. QuantumDNA combines an efficient Linear Combination of Atomic Orbitals (LCAO) approach combined with tight-binding models and incorporates open quantum systems techniques to account for environmental effects. This approach allows for a rapid yet sufficiently accurate analysis of large DNA ensembles, enabling statistical studies of genetic and epigenetic phenomena. To ensure accessibility, the package features a graphical user interface, making it suitable for researchers across disciplines. Program summary Program Title: QuantumDNA CPC Library link to program files: https://doi.org/10.17632/5mw48c7gbb.1 Developer's repository link: https://github.com/dehe1011/QuantumDNA Licensing provisions: BSD 3-clause Programming language: Python Nature of the Problem: Over the past 60 years, a variety of advanced simulation methods have been employed to explore charge dynamics of DNA. However, most of these approaches are computationally too expensive for the large-scale statistical screening required in genetics and epigenetics. Therefore, theoretical and computational results are often restricted to specialized fields, limiting their accessibility and reproducibility to researchers across disciplines. Solution Method: QuantumDNA combines computational methods from quantum physics and theoretical chemistry to facilitate high-throughput analysis of DNA charge dynamics with sufficient accuracy. Unlike computationally expensive ab initio methods, it utilizes the efficiency of LCAO and TB models to simulate charge dynamics while considering environmental effects, making simulations more accessible and encouraging interdisciplinary research. Additional comments: QuantumDNA is an open-source package featuring a graphical user interface, tutorial Jupyter notebooks, and a dedicated documentation website. The package also supports CPU parallel computing.

We illuminate the influence of transition mutations and disorder on charge localization and transfer along B-DNA sequences. Homopolymers are the best for charge transfer. Hence, we consider an ideal homopolymer sequence and then disturb it, introducing transition mutations and disorder. We exclude the possibility of charge transfer via the backbone that has been addressed in another -just published- work. We employ the Tight Binding (TB) Wire model to study the influence of transition mutations and the TB Fishbone Wire model to evaluate the influence of disorder emanating either from the pi path or from the backbone. For the TB Wire parameters, we employ a parametrization in which another TB at atomic level was used, considering all valence orbitals of all atoms. We calculate the HOMO and LUMO regime eigenenergies and eigenvectors, the participation ratio (a measure of the localization of each eigenstate), the time-dependent probability to find the carrier at each site, the mean over time probability at each site, and the mean transfer rate from site to site. Transition mutations increase localization in terms of participation ratio and impede charge transfer in terms of mean probability and transfer rates, provided the TB parameters involving mutated sites are significantly modified relative to the original. Disorder leads to severe modifications of participation ratios, i.e., increase of localization. Relevant changes occur on eigenenergies, mean probabilities at each site, and transfer rates.

We model charge transfer in B-DNA, the most common form of deoxyribonucleic acid, with the aim of assessing the role of the backbone. We achieve this by employing a four-channel tight binding model, where B-DNA is analyzed at the base and backbone sites level. The significant difference of our model, with other similar models that have appeared in the literature so far, is that we have calculated all tight binding on-site energies and interaction integrals using DFT; these are not roughly estimated or guessed. We study two kinds of sequences: homopolymers and randomly generated sequences. This enables us to effectively compare the relative ease of charge transfer through the backbone channels with that of the π pathway formed by the nucleobases' frontier molecular orbitals, since the latter is highly sensitive to sequence periodicity, as it determines the degree of energy uniformity across the base-pair sequence. Results are presented for the electronic structure, the localization of the energy eigenstates, and the ease of carrier transfer. Emphasis is given to results for holes, due to the inherent unreliability of DFT calculations for excited states. We demonstrate that the backbone could be essential for B-DNA charge transfer, provided limited backbone energy disorder.

Correction for 'Electronic structure, absorption spectra and oxidation dynamics in polyynes and dicyanopolyynes' by Lazaros Chalkopiadis et al., Phys. Chem. Chem. Phys., 2024, 26, 22149-22163, https://doi.org/10.1039/D4CP02719A.

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-Buttiker 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.

The advent of femtosecond to attosecond experimental tools has made now possible to study such ultrafast carrier dynamics, e.g., the spatial and temporal charge density evolution, after an initial oxidation or reduction in molecules, candidates for atomic wires like polyynes and dicyanopolyynes. Here, we study the electronic structure and hole transfer in symmetric molecules containing carbon, nitrogen and hydrogen, the first members in the series of polyynic carbynes and dicyanopolyynes, using methods based on density functional theory (DFT): constrained DFT (CDFT), time-dependent DFT (TDDFT) and real-time TDDFT (RT-TDDFT), with L & ouml;wdin population analysis, comparing many levels of theory and obtaining convergence of the results. For the same purposes, we develop a tight binding (TB) variant using all valence orbitals of all atoms. This TB variant is applied here in linear molecules, but it is also adequate for electronic structure, charge transfer and charge transport of non-linear molecules and clusters of molecules. We calculate the electronic structure, the time-dependent dipole moment and the probabilities of finding the hole at each site, their mean over time values, the mean transfer rates from the oxidation site to other sites and the frequency content (using charge as well as dipole moment oscillations). We take into account zero-point motion. The initial conditions for RT-TDDFT are obtained by CDFT. For TB, we explore different initial conditions: we place the hole at a particular orbital or distribute it among a number of orbitals; it is also possible to include phase differences between orbitals. Finally, we compare with available experimental data. Electronic structure, absorption spectra, oxidation dynamics: polyynes & dicyanopolyynes.

We employ the Tight Binding Fishbone-Wire Model to study the electronic structure and coherent transfer of a hole (the absence of an electron created by oxidation) in all possible ideal B-DNA dimers as well as in homopolymers (one base pair repeated along the whole sequence with purine on purine). The sites considered are the base pairs and the deoxyriboses, with no backbone disorder. For the time-independent problem, we calculate the eigenspectra and the density of states. For the time-dependent problem after oxidation (i.e., the creation of a hole either at a base pair or at a deoxyribose), we calculate the mean-over-time probabilities to find the hole at each site and establish the frequency content of coherent carrier transfer by computing the Weighted Mean Frequency at each site and the Total Weighted Mean Frequency of a dimer or polymer. We also evaluate the main oscillation frequencies of the dipole moment along the macromolecule axis and the relevant amplitudes. Finally, we focus on the mean transfer rates from an initial site to all others. We study the dependence of these quantities on the number of monomers that are used to construct the polymer. Since the value of the interaction integral between base pairs and deoxyriboses is not well-established, we treat it as a variable and examine its influence on the calculated quantities.

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.

Energy transport within biological systems is critical for biological functions in living cells and for technological applications in molecular motors. Biological systems have very complex dynamics supporting a large number of biochemical and biophysical processes. In the current work, we study the energy transport along protein chains. We examine the influence of different factors such as temperature, salt concentration, and external mechanical drive on the energy flux through protein chains. We obtain that energy fluctuations around the average value for short chains are greater than for longer chains. In addition, the external mechanical load is the most effective agent on bioenergy transport along the studied protein systems. Our results can help design a functional nano-scaled molecular motor based on energy transport along protein chains.

Recent synthesis of cyclo[18]carbon has spurred increasing interest in carbon rings. We focus on a comparative inspection of ground and excited states, as well as of hole transfer properties of cumulenic and polyynic cyclo[18]carbon via Density Functional Theory (DFT), time-dependent DFT (TD-DFT) and real-time time-dependent DFT (RT-TDDFT). Zero-point vibrations are also accounted for, using a Monte Carlo sampling technique and a less exact, yet mode-resolved, quadratic approximation. The inclusion of zero-point vibrations leads to a red-shift on the HOMO-LUMO gap and the first singlet and triplet excitation energies of both conformations, correcting the values of the 'static' configurations by 9% to 24%. Next, we oxidize the molecule, creating a hole at one carbon atom. Hole transfer along polyynic cyclo[18]carbon is decreased in magnitude compared to its cumulenic counterpart and lacks the symmetric features the latter displays. Contributions by each mode to energy changes and hole transfer between diametrically opposed atoms vary, with specific bond-stretching modes being dominant.

To describe the molecular electronic structure of nucleic acid bases and other heterocycles, we employ the Linear Combination of Atomic Orbitals (LCAO) method, considering the molecular wave function as a linear combination of all valence orbitals, i.e., 2s, 2px, 2py, 2pz orbitals for C, N, and O atoms and 1s orbital for H atoms. Regarding the diagonal matrix elements (also known as on-site energies), we introduce a novel parameterization. For the non-diagonal matrix elements referring to neighboring atoms, we employ the Slater–Koster two-center interaction transfer integrals. We use Harrison-type expressions with factors slightly modified relative to the original. We compare our LCAO predictions for the ionization and excitation energies of heterocycles with those obtained from Ionization Potential Equation of Motion Coupled Cluster with Singles and Doubles (IP-EOMCCSD)/aug-cc-pVDZ level of theory and Completely Normalized Equation of Motion Coupled Cluster with Singles, Doubles, and non-iterative Triples (CR-EOMCCSD(T))/aug-cc-pVDZ level of theory, respectively, (vertical values), as well as with available experimental data. Similarly, we calculate the transfer integrals between subsequent base pairs, to be used for a Tight-Binding (TB) wire model description of charge transfer and transport along ideal or deformed B-DNA. Taking into account all valence orbitals, we are in the position to treat deflection from the planar geometry, e.g., DNA structural variability, a task impossible for the plane Hückel approach (i.e., using only 2pz orbitals). We show the effects of structural deformations utilizing a 20mer evolved by Molecular Dynamics.

We study Rabi oscillations in a two-level system within the semiclassical approximation as an archetype test field of the Averaging Method (AM). The population transfer between the two levels is approached within the first and the second order AM. We systematically compare AM predictions with the rotating wave approximation (RWA) and with the complete numerical solution utilizing standard algorithms (NRWA). We study both the resonance (∆ = 0) and out-of-resonance (∆ 6= 0) cases, where ∆ = ω − Ω, and ~Ω = E2 − E1 is the two-level energetic separation, while ω is the (cyclic) frequency of the electromagnetic field. We introduce three types of dimensionless factors ǫ, i.e., ΩR/∆, ΩR/Σ, and ΩR/ω, where ΩR is the Rabi (cyclic) frequency and Σ = ω + Ω and explore the range of ǫ where the AM results are equivalent to NRWA. Finally, by allowing for a phase difference in the initial electron wave functions, we explore the prospects coherence can offer. We illustrate that even with equal initial probabilities at the two levels, but with phase difference, strong oscillations can be generated and manipulated.

Hole transfer along the axis of duplex DNA has been the focus of physical chemistry research for decades, with implications in diverse fields, from nanotechnology to cell oxidative damage. Computational approaches are particularly amenable for this problem, to complement experimental data for interpretation of transfer mechanisms. To be predictive, computational results need to account for the inherent mobility of biological molecules during the time frame of experimental measurements. Here, we address the structural variability of B-DNA and its effects on hole transfer in a combined molecular dynamics (MD) and real-time time-dependent density functional theory (RT-TDDFT) study. Our results show that quantities that characterize the charge transfer process, such as the time-dependent dipole moment and hole population at a specific site, are sensitive to structural changes that occur on the nanosecond time scale. We extend the range of physical properties for which such a correlation has been observed, further establishing the fact that quantitative computational data on charge transfer properties should include statistical averages. Furthermore, we use the RT-TDDFT results to assess an efficient tight-binding method suitable for high-throughput predictions. We demonstrate that charge transfer, although affected by structural variability, on average, remains strong in AA and GG dimers.

We study Rabi oscillations in a two-level system within the semiclassical approximation as an archetype test field of the Averaging Method (AM). The population transfer between the two levels is approached within the first and the second order AM. We systematically compare AM predictions with the rotating wave approximation (RWA) and with the complete numerical solution utilizing standard algorithms (NRWA). We study both the resonance (Δ = 0) and out-of-resonance ( Δ ≠ 0 ) cases, where Δ = ω − Ω, and ℏΩ = E 2 − E 1 is the two-level energetic separation, while ω is the (cyclic) frequency of the electromagnetic field. We introduce three types of dimensionless factors ϵ , i.e., Ω R /Δ, Ω R /Σ, and Ω R / ω , where Ω R is the Rabi (cyclic) frequency and Σ = ω + Ω and explore the range of ϵ where the AM results are equivalent to NRWA. Finally, by allowing for a phase difference in the initial electron wave functions, we explore the prospects coherence can offer. We illustrate that even with equal initial probabilities at the two levels, but with phase difference, strong oscillations can be generated and manipulated.

We investigate hole transfer in open carbynes, i.e., carbon atomic nanowires, using Real-Time Time-Dependent Density Functional Theory (RT-TDDFT). The nanowire is made of N carbon atoms. We use the functional B3LYP and the basis sets 3-21G, 6-31G*, cc-pVDZ, cc-pVTZ, cc-pVQZ. We also utilize a few Tight-Binding (TB) wire models, a very simple model with all sites equivalent and transfer integrals given by the Harrison ppπ expression (TBI) as well as a model with modified initial and final sites (TBImod) to take into account the presence of one or two or three hydrogen atoms at the edge sites. To achieve similar site occupations in cumulenes with those obtained by converged RT-TDDFT, TBImod is sufficient. However, to achieve similar frequency content of charge and dipole moment oscillations and similar coherent transfer rates, the TBImod transfer integrals have to be multiplied by a factor of four (TBImodt4times). An explanation for this is given. Full geometry optimization at the B3LYP/6-31G* level of theory shows that in cumulenes bond length alternation (BLA) is not strictly zero and is not constant, although it is symmetrical relative to the molecule center. BLA in cumulenic cases is much smaller than in polyynic cases, so, although not strictly, the separation to cumulenes and polyynes, approximately, holds. Vibrational analysis confirms that for N even all cumulenes with coplanar methylene end groups are stable, for N odd all cumulenes with perpendicular methylene end groups are stable, and the number of hydrogen atoms at the end groups is clearly seen in all cumulenic and polyynic cases. We calculate and discuss the Density Functional Theory (DFT) ground state energy of neutral molecules, the CDFT (Constrained DFT) “ground state energy” of molecules with a hole at one end group, energy spectra, density of states, energy gap, charge and dipole moment oscillations, mean over time probabilities to find the hole at each site, coherent transfer rates, and frequency content, in general. We also compare RT-TDDFT with TB results.

This corrects the article DOI: 10.1103/PhysRevE.94.062403.

We study hole transfer in open cumulenic and polyynic nanowires made of N carbon atoms, using real-time time-dependent density functional theory (RT-TDDFT) and tight-binding (TB) wire models. For RT-TDDFT, we mainly use functional B3LYP and basis sets cc-pVDZ, cc-pVTZ, and cc-pVQZ, obtaining clear convergence; cc-pVTZ is the smallest basis set of sufficient quality; cc-pVQZ is better with a higher computational cost. For TB, we use a simplistic wire model where all sites are equivalent (TBI) and models with modified initial and final sites, mimicking the existence of one or two or three hydrogens at edge sites (TBImod, TBlmodt4times). We compare the ground state energy, E-Gs, obtained by density functional theory (DFT) for cumulenic molecules with coplanar (co) or perpendicular (pe) methylene end groups as well as polyynic molecules starting with short (sl) or with long (ls) C-C bonds. For odd N, cumulenic pe molecules have lower E-Gs than cumulenic co molecules, that are probably transition states. We examine energy spectra, density of states, energy gap, charge oscillations, mean over time probabilities to find the hole at each site, coherent transfer rates, electric dipole moment, and frequency content. DFT shows that due to the impact of end groups, there exists a cumulenic energy gap, smaller than the polyynic one. TBI and TBImod reproduce approximately the magnitude of the energy gap in the polyynic case at the limit of large N. TBImod is capable of predicting the same site occupations with the nicely converged RT-TDDFT ones for the cumulenic case. However, charge and dipole moment oscillations as well as transfer rates by RT-TDDFT are approximately four times faster than those by TBImod. The site occupations of polyynic sl and of polyynic ls molecules are modified relative to cumulenic molecules; the trends can be explained qualitatively.

This corrects the article DOI: 10.1103/PhysRevE.94.062403.