Effects of Structural Dynamics on Charge Carrier Transfer in B-DNA: A Combined MD and RT-TDDFT Study

Four-channel model: An assessment of charge transfer via the backbone in B-DNA

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.

Modulating Charge Transfer Kinetics along Poly Adenine: Chemical Modifications, Temperature, and Conformational Effects

The charge transfer (CT) reactions in nucleic acids are crucial for genome damage and repair and nanoelectronics using DNA as a molecular conductor. Previous experimental and theoretical works underlined the significance of nucleic acid structural dynamics on CT kinetics, requiring models that incorporate the dynamics of the nucleic acid, solvents, and counterions. Here, we investigated hole transfer kinetics in poly adenine single and double strands at various temperatures and the rate enhancement due to adenine-to-7-deazaadenine mutation by means of a QM/MM approach. We found that the hole transfer rate in poly adenine double strands increases with temperature while the helix conformation is retained, whereas single strands exhibit the opposite thermal response. Additionally, the positive charge migrates more efficiently in poly-7-deazaadenine double strands. Our results, consistent with experimental data, suggest that a thermally induced hopping model can accurately describe CT kinetics in these sequences. The approach is transferable for studying CT reactions in other nucleic acid strands.

Machine-Learning Electron Dynamics with Moment Propagation Theory: Application to Optical Absorption Spectrum Computation Using Real-Time TDDFT

We present an application of our new theoretical formulation of quantum dynamics, moment propagation theory (MPT) (Boyer et al., J. Chem. Phys. 160, 064113 (2024)), for employing machine-learning techniques to simulate the quantum dynamics of electrons. In particular, we use real-time time-dependent density functional theory (RT-TDDFT) simulation in the gauge of the maximally localized Wannier functions (MLWFs) for training the MPT equation of motion. Spatially localized time-dependent MLWFs provide a concise representation that is particularly convenient for the MPT expressed in terms of increasing orders of moments. The equation of motion for these moments can be integrated in time, while the analytical expressions are quite involved. In this work, machine-learning techniques were used to train the second-order time derivatives of the moments using first-principles data from the RT-TDDFT simulation, and this MPT enabled us to perform electron dynamics efficiently. The application to computing optical absorption spectrum for various systems was demonstrated as a proof-of-principles example of this approach. In addition to isolated molecules (water, benzene, and ethene), condensed matter systems (liquid water and crystalline silicon) were studied, and we also explored how the principle of the nearsightedness of electrons can be employed in this context.

Ligand effect on surface reconstruction in CdSe quantum dots driven by electron injection in electroluminescence processes

The short lifetime of blue quantum dots (QDs) in the electroluminescence process is indeed one of the main obstacles that hinder their applications in new display technologies. One of the speculations about the short lifespan is believed to be the reduction reactions at the interface between the QD and the ligand caused by electron injection, but little is known about how the reactions proceed. The evolution of geometrical and electronic structures of ligated (CdSe)6 is simulated with the real-time time-dependent density functional theory (rt-TDDFT) method. Two distinct reactions are characterized in the QDs with different ligand types. One involves the localization of an electron at one specified surface atom, making the ligand separated from the QD, as well as large changes in the QD structures. The other involves the delocalization of an electron across the QD and the ligand, leading to only small changes. In the first case, the destroyed structure becomes irreversible once the ligand fails to re-bond with the QD after the electron-hole recombination. Our simulations provide direct evidence that the reduction reactions caused by electron injection are responsible for the performance loss of blue QDs in the electroluminescence process, and suggest that the delocalization of injected electrons is an interesting strategy for future studies.

Electronic structure, absorption spectra and oxidation dynamics in polyynes and dicyanopolyynes

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 Löwdin 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.

Reduction reactions at the interface between CdS quantum dot and Z-type ligands driven by electron injection in the electroluminescent processes

The efficient and stable electroluminescence of quantum dots (QDs) is of great importance in their applications in new display technologies. The short service life of blue QDs, however, hinders their development and commercialization. Different mechanisms have been proposed for the destabilization of QDs in electroluminescent processes. Based on real-time time-dependent density functional theory studies on the QD models covered by Z-type ligands (XAc2, X = Cd, Zn, Mg), the structural evolution is simulated to reveal the mechanism of the reduction reactions induced by electron injection. Our simulations reproduce the experimental observations that the reduction reactions occur at the QD-ligand interface, and the reduced Cd atom is almost in a zero valence state. However, different sites are predicted for the reactions in which the surface metal atom of the QD instead of the metal atom in the ligands is reduced. As a result, one of the arms of the chelate ligand leaves the QD, which tends to cause damage to its electroluminescent performance. Our findings contribute to a mechanistic understanding of the reduction reactions that occurred at the QD-ligand interface.

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.

Reconciling TD-DFT and CASPT2 electronic structure methods for describing the photophysics of DNA

Time-dependent density functional theory (TD-DFT) and multiconfigurational second-order perturbation theory (CASPT2) are two of the most widely used methods to investigate photoinduced dynamics in DNA-based systems. These methods sometimes give diverse dynamics in physiological environments usually modeled by quantum mechanics/molecular mechanics (QM/MM) protocol. In this work, we demonstrate for the uridine test case that the underlying topology of the potential energy surfaces of electronic states involved in photoinduced relaxation is similar in both electronic structure methods. This is verified by analyzing surface-hopping dynamics performed at the QM/MM level on aqueous solvated uridine at TD-DFT and CASPT2 levels. By constraining the dynamics to remain onπ π * state we observe similar fluctuations in energy and relaxation lifetimes in surface-hopping dynamics in both TD-DFT and experimentally validated CASPT2 methods. This finding calls for a systematic comparison of the ES potential energy surfaces of DNA and RNA nucleosides at the single- and multi-reference levels of theory. The anomalous long excited state lifetime at the TD-DFT level is explained byn π * trapping due to the tendency of TD-DFT in QM/MM schemes with electrostatic embedding to underestimate the energy of theπ π * state leading to a wrongπ π * / n π * energetic order. A study of the FC energetics suggests that improving the description of the surrounding environment through polarizable embedding or by the expansion of QM layer with hydrogen-bonded waters helps restore the correct state order at TD-DFT level. Thus by combining TDDFT with an accurate modeling of the environment, TD-DFT is positioned as the standout protocol to model photoinduced dynamics in DNA-based aggregates and multimers.

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.

Stretching effects on non-adiabatic electron dynamic behavior in poly(dG)-poly(dC) DNA upon the proton irradiation

The electronic excitations caused by DNA when exposed to ion radiation is essential to DNA damage. In this paper, we investigated the energy deposition and electron excitation process of DNA with reasonable stretching range upon proton irradiation based on time-dependent density functional theory. Stretching changes the strength of hydrogen bonding between the DNA base pairs, which in turn affects the Coulomb interaction between the projectile and DNA. As a semi-flexible molecule, the way of energy deposition is weakly sensitive to the stretching rate of DNA. However, the increase of stretching rate causes the increase of charge density along the trajectory channel, sequentially resulting in an increase in proton resistance along the intruding channel. The Mulliken charge analysis indicates that the guanine base and guanine ribose are ionized, meanwhile the cytosine base and cytosine ribose are reduced at all stretching rates. In a few femtoseconds, there exists an electron flow passing through the guanine ribose, guanine, cytosine base and the cytosine ribose in turn. This electron flow increases electron transfer and DNA ionization, promoting the side chain damage of the DNA upon ion irradiation. Our results provide a theoretical insight for deciphering the physical mechanism of the early stage of the irradiation process, and are also of great significance for the study of particle beam cancer therapy in different biological tissues.

Electronic Structure and Hole Transfer of All B-DNA Dimers and Homopolymers, via the Fishbone-Wire Model

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.

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.

Comparison of Length, Velocity, and Symmetric Gauges for the Calculation of Absorption and Electric Circular Dichroism Spectra with Real-Time Time-Dependent Density Functional Theory

A velocity and symmetric gauge implementation for real-time time-dependent density functional theory (RT-TDDFT) in the CP2K package using a Gaussian and plane wave approach is presented, including the explicit gauge-transformed contributions due to the nonlocal part of pseudopotentials. Absorption spectra of gas-phase α-pinene are calculated in length and velocity gauges in the long-wavelength approximation for the application of a δ pulse in linear and full order. The velocity gauge implementation is also applied to a solvated uracil molecule to showcase its use within periodic boundary conditions (PBC). For the calculation of the expectation value of the electric dipole moment in PBC, both the velocity representation and the modern theory of polarization give equivalent absorption spectra if a distributed reference point is used for the nonlocal term of the velocity operator. The discussion of linear response theory takes place in a unified framework in terms of linear response functions in propagator notation, distinguishing the parts of the linear response functions associated with perturbation and response. To further investigate gauge dependence, electric circular dichroism (ECD) spectra of α-pinene were calculated either as magnetic response to an electric field perturbation, in length or velocity gauge, or as electric response to a magnetic field perturbation in the symmetric gauge. Both approaches, electric and magnetic perturbations, have been found to yield equivalent ECD spectra.

LCAO Electronic Structure of Nucleic Acid Bases and Other Heterocycles and Transfer Integrals in B-DNA, Including Structural Variability

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.