A TDDFT study of the excited states of DNA bases and their assemblies

We present a detailed study of the optical absorption spectra of DNA bases and base pairs, carried out by means of time dependent density functional theory. The spectra for the isolated bases are compared to available theoretical and experimental data and used to assess the accuracy of the method and the quality of the exchange-correlation functional: Our approach turns out to be a reliable tool to describe the response of the nucleobases. Furthermore, we analyze in detail the impact of hydrogen bonding and $\pi$-stacking in the calculated spectra for both Watson-Crick base pairs and Watson-Crick stacked assemblies. We show that the reduction of the UV absorption intensity (hypochromicity) for light polarized along the base-pair plane depends strongly on the type of interaction. For light polarized perpendicular to the basal plane, the hypochromicity effect is reduced, but another characteristic is found, namely a blue shift of the optical spectrum of the base-assembly compared to that of the isolated bases. The use of optical tools as fingerprints for the characterization of the structure (and type of interaction) is extensively discussed.Comment: 31 pages, 8 figure

Theoretical description of protein field effects on electronic excitations of biological chromophores

Photoinitiated phenomena play a crucial role in many living organisms. Plants, algae, and bacteria absorb sunlight to perform photosynthesis, and convert water and carbon dioxide into molecular oxygen and carbohydrates, thus forming the basis for life on Earth. The vision of vertebrates is accomplished in the eye by a protein called rhodopsin, which upon photon absorption performs an ultrafast isomerisation of the retinal chromophore, triggering the signal cascade. Many other biological functions start with the photoexcitation of a protein-embedded pigment, followed by complex processes comprising, for example, electron or excitation energy transfer in photosynthetic complexes. The optical properties of chromophores in living systems are strongly dependent on the interaction with the surrounding environment (nearby protein residues, membrane, water), and the complexity of such interplay is, in most cases, at the origin of the functional diversity of the photoactive proteins. The specific interactions with the environment often lead to a significant shift of the chromophore excitation energies, compared with their absorption in solution or gas phase. The investigation of the optical response of chromophores is generally not straightforward, from both experimental and theoretical standpoints; this is due to the difficulty in understanding diverse behaviours and effects, occurring at different scales, with a single technique. In particular, the role played by ab initio calculations in assisting and guiding experiments, as well as in understanding the physics of photoactive proteins, is fundamental. At the same time, owing to the large size of the systems, more approximate strategies which take into account the environmental effects on the absorption spectra are also of paramount importance. Here we review the recent advances in the first-principle description of electronic and optical properties of biological chromophores embedded in a protein environment. We show their applications on paradigmatic systems, such as the light-harvesting complexes, rhodopsin and green fluorescent protein, emphasising the theoretical frameworks which are of common use in solid state physics, and emerging as promising tools for biomolecular systems

Quantum dot states and optical excitations of edge-modulated graphene nanoribbons

We investigate from first principles the electronic and optical properties of edge-modulated armchair graphene nanoribbons, including both quasiparticle corrections and excitonic effects. Exploiting the oscillating behavior of the ribbon energy gap, we show that minimal width-modulations are sufficient to obtain confinement of both electrons and holes, thus forming optically active quantum dots with unique properties, such as the coexistence of dotlike and extended excitations and the fine tunability of optical spectra, with great potential for optoelectronic applications

Theoretical S1 \u2192S0 Absorption Energies of the Anionic Forms of Oxyluciferin by Variational Monte Carlo and Many-Body Green's Function Theory

The structures of three negatively charged forms (anionic keto-1 and enol-1 and dianionic enol-2) of oxyluciferin (OxyLuc), which are the most probable emitters responsible for the firefly bioluminescence, have been fully relaxed at the variational Monte Carlo (VMC) level. Absorption energies of the S1 \u2190 S0 vertical transition have been computed using different levels of theory, such as TDDFT, CC2, and many-body Green\u2019s function theory (MBGFT). The use of MBGFT, by means of the Bethe\u2013Salpeter (BS) formalism, on VMC structures provides results in excellent agreement with the value (2.26(8) eV) obtained by action spectroscopy experiments for the keto-1 form (2.32 eV). To unravel the role of the quality of the optimized ground-state geometry, BS excitation energies have also been computed on CASSCF geometries, inducing a non-negligible blue shift (0.08 and 0.07 eV for keto-1 and enol-1 forms, respectively) with respect to the VMC ones. Structural effects have been analyzed in terms of over- or undercorrelation along the conjugated bonds of OxyLuc by using different methods for the ground-state optimization. The relative stability of the S1 state for the keto-1 and enol-1 forms depends on the method chosen for the excited-state calculation, thus representing a fundamental caveat for any theoretical study on these systems. Finally, Kohn\u2013Sham HOMO and LUMO orbitals of enol-2 are (nearly) bound only when the dianion is embedded into a solvent (water and toluene in the present work); excited-state calculations are therefore meaningful only in the presence of a dielectric medium which localizes the electronic density. The combination of VMC for the ground-state geometry and BS formalism for the absorption spectra clearly outperforms standard TDDFT and quantum chemistry approaches

Photo-excitation of a light-harvesting supra-molecular triad: a Time-Dependent DFT study

We present the first time-dependent density-functional theory (TDDFT) calculation on a light harvesting triad carotenoid-diaryl-porphyrin-C60. Besides the numerical challenge that the ab initio study of the electronic structure of such a large system presents, we show that TDDFT is able to provide an accurate description of the excited state properties of the system. In particular we calculate the photo-absorption spectrum of the supra-molecular assembly, and we provide an interpretation of the photo-excitation mechanism in terms of the properties of the component moieties. The spectrum is in good agreement with experimental data, and provides useful insight on the photo-induced charge transfer mechanism which characterizes the system.Comment: Accepted for publication on JPC, March 09th 200

A monolayer transition-metal dichalcogenide as a topological excitonic insulator

Monolayer transition-metal dichalcogenides in the T\u2032 phase could enable the realization of the quantum spin Hall effect1 at room temperature, because they exhibit a prominent spin\u2013orbit gap between inverted bands in the bulk2,3. Here we show that the binding energy of electron\u2013hole pairs excited through this gap is larger than the gap itself in the paradigmatic case of monolayer T\u2032 MoS2, which we investigate from first principles using many-body perturbation theory4. This paradoxical result hints at the instability of the T\u2032 phase in the presence of spontaneous generation of excitons, and we predict that it will give rise to a reconstructed \u2018excitonic insulator\u2019 ground state5\u20137. Importantly, we show that in this monolayer system, topological and excitonic order cooperatively enhance the bulk gap by breaking the crystal inversion symmetry, in contrast to the case of bilayers8\u201316 where the frustration between the two orders is relieved by breaking time reversal symmetry13,15,16. The excitonic topological insulator is distinct from the bare topological phase because it lifts the band spin degeneracy, which results in circular dichroism. A moderate biaxial strain applied to the system leads to two additional excitonic phases, different in their topological character but both ferroelectric17,18 as an effect of electron\u2013electron interaction

Spin-polarized stable phases of the 2-D electron fluid at finite temperatures

The Helmholtz free energy F of the interacting 2-D electron fluid is calculated nonperturbatively using a mapping of the quantum fluid to a classical Coulomb fluid [Phys. Rev. Letters, vol. 87, 206404 (2001)]. For density parameters rs such that rs<~25, the fluid is unpolarized at all temperatures t=T/EF where EF is the Fermi energy. For lower densities, the system becomes fully spin polarized for t<~0.35, and partially polarized for 0.35<t< 2, depending on the density. At rs ~25-30, and t ~0.35, an ''ambispin'' phase where F is almost independent of the spin polarization is found. These results support recent claims, based on quantum Monte Carlo results, for a stable, fully spin-polarized fluid phase at T = 0 for rs larger than about 25-26.Comment: Latex manuscript (4-5 pages) and two postscript figures; see also http://nrcphy1.phy.nrc.ca/ims/qp/chandre/chnc

Spin-Polarization transition in the two dimensional electron gas

We present a numerical study of magnetic phases of the 2D electron gas near freezing. The calculations are performed by diffusion Monte Carlo in the fixed node approximation. At variance with the 3D case we find no evidence for the stability of a partially polarized phase. With plane wave nodes in the trial function, the polarization transition takes place at Rs=20, whereas the best available estimates locate Wigner crystallization around Rs=35. Using an improved nodal structure, featuring optimized backflow correlations, we confirm the existence of a stability range for the polarized phase, although somewhat shrunk, at densities achievable nowadays in 2 dimensional hole gases in semiconductor heterostructures . The spin susceptibility of the unpolarized phase at the magnetic transition is approximately 30 times the Pauli susceptibility.Comment: 7 pages, 4 figure

Ab-initio angle and energy resolved photoelectron spectroscopy with time-dependent density-functional theory

We present a time-dependent density-functional method able to describe the photoelectron spectrum of atoms and molecules when excited by laser pulses. This computationally feasible scheme is based on a geometrical partitioning that efficiently gives access to photoelectron spectroscopy in time-dependent density-functional calculations. By using a geometrical approach, we provide a simple description of momentum-resolved photoe- mission including multi-photon effects. The approach is validated by comparison with results in the literature and exact calculations. Furthermore, we present numerical photoelectron angular distributions for randomly oriented nitrogen molecules in a short near infrared intense laser pulse and helium-(I) angular spectra for aligned carbon monoxide and benzene.Comment: Accepted for publication on Phys. Rev.

Spin Susceptibility of an Ultra-Low Density Two Dimensional Electron System

We determine the spin susceptibility in a two dimensional electron system in GaAs/AlGaAs over a wide range of low densities from 2$\times10^{9}$cm$^{-2}$ to 4$\times10^{10}$cm$^{-2}$. Our data can be fitted to an equation that describes the density dependence as well as the polarization dependence of the spin susceptibility. It can account for the anomalous g-factors reported recently in GaAs electron and hole systems. The paramagnetic spin susceptibility increases with decreasing density as expected from theoretical calculations.Comment: 5 pages, 2 eps figures, to appear in PR