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, , 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.

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.

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.

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 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.

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.

Hole Transfer in Open Carbynes.

We investigate hole transfer in open carbynes, i.e., carbon atomic nanowires, using Real-Time Time-Dependent Density Functional Theory (RT-TDDFT).

Quasi-Periodic and Fractal Polymers: Energy Structure and Carrier Transfer.

We study the energy structure and the coherent transfer of an extra electron or hole along aperiodic polymers made of monomers, with fixed boundaries, using B-DNA as our prototype system. We use a Tight-Binding wire model, where a site is a monomer (e.g.