Hole Transfer in Open Carbynes

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.

Cyclo[18]carbon including zero-point motion: ground state, first singlet and triplet excitations, and hole transfer

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.

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

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.