Optical excitations of chlorophyll a and b monomers and dimers.

A necessary first step in the development of technologies such as artificial photosynthesis is understanding the photoexcitation process within the basic building blocks of naturally occurring light harvesting complexes (LHCs). The most important of these building blocks in biological LHCs such as LHC II from green plants are the chlorophyll a (Chl a) and chlorophyll b (Chl b) chromophores dispersed throughout the protein matrix. However, efforts to describe such systems are still hampered by the lack of computationally efficient and accurate methods that are able to describe optical absorption in large biomolecules.

Real-Time Propagation TDDFT and Density Analysis for Exciton Coupling Calculations in Large Systems.

Photoactive systems are characterized by their capacity to absorb the energy of light and transform it. Usually, more than one chromophore is involved in the light absorption and excitation transport processes in complex systems. Linear-Response Time-Dependent Density Functional (LR-TDDFT) is commonly used to identify excitation energies and transition properties by solving the well-known Casida's equation for single molecules.

A Definition of the Magnetic Transition Temperature Using Valence Bond Theory.

Macroscopic magnetic properties are analyzed using Valence Bond theory. Commonly the critical temperature T for magnetic systems is associated with a maximum in the energy-based heat capacity C(T). Here a more broadly applicable definition of the magnetic transition temperature T is described using the spin moment expectation value (i.

The atomic simulation environment-a Python library for working with atoms.

The atomic simulation environment (ASE) is a software package written in the Python programming language with the aim of setting up, steering, and analyzing atomistic simulations. In ASE, tasks are fully scripted in Python. The powerful syntax of Python combined with the NumPy array library make it possible to perform very complex simulation tasks.

Optimized Effective Potential for Quantum Electrodynamical Time-Dependent Density Functional Theory.

We propose an orbital exchange-correlation functional for applying time-dependent density functional theory to many-electron systems coupled to cavity photons. The time nonlocal equation for the electron-photon optimized effective potential (OEP) is derived. In the static limit our OEP energy functional reduces to the Lamb shift of the ground state energy.

Resonant-convergent PCM response theory for the calculation of second harmonic generation in makaluvamines A-V: pyrroloiminoquinone marine natural products from poriferans of genus Zyzzya.

The first-order hyperpolarizability, β, has been calculated for a group of marine natural products, the makaluvamines. These compounds possess a common cationic pyrroloiminoquinone structure that is substituted to varying degrees. Calculations at the MP2 level indicate that makaluvamines possessing phenolic side chains conjugated with the pyrroloiminoquinone moiety display large β values, while breaking this conjugation leads to a dramatic decrease in the calculated hyperpolarizability.

Unraveling the intrinsic color of chlorophyll.

The exact color of light absorbed by chlorophyll (Chl) pigments, the light-harvesters in photosynthesis, is tuned by the protein microenvironment, but without knowledge of the intrinsic color of Chl it remains unclear how large this effect is. Experimental first absorption energies of Chl a and b isolated in vacuo and tagged with quaternary ammonium cations are reported. The energies are largely insensitive to details of the tag structure, a finding supported by first-principles calculations using time-dependent density functional theory.

The atomistic mechanism of carbon nanotube cutting catalyzed by nickel under an electron beam.

The cutting of single-walled carbon nanotubes by an 80 keV electron beam catalyzed by nickel clusters is imaged in situ using aberration-corrected high-resolution transmission electron microscopy. Extensive molecular dynamics simulations within the CompuTEM approach provide insight into the mechanism of this process and demonstrate that the combination of irradiation and the nickel catalyst is crucial for the cutting process to take place. The atomistic mechanism of cutting is revealed by a detailed analysis of irradiation-induced reactions of bond reorganization and atom ejection in the vicinity of the nickel cluster, showing a highly complex interplay of different chemical transformations catalysed by the metal cluster.

Quasi-particle energy spectra in local reduced density matrix functional theory.

Recently, we introduced [N. N. Lathiotakis, N.

Correlated electron-nuclear dynamics with conditional wave functions.

The molecular Schrödinger equation is rewritten in terms of nonunitary equations of motion for the nuclei (or electrons) that depend parametrically on the configuration of an ensemble of generally defined electronic (or nuclear) trajectories. This scheme is exact and does not rely on the tracing out of degrees of freedom. Hence, the use of trajectory-based statistical techniques can be exploited to circumvent the calculation of the computationally demanding Born-Oppenheimer potential-energy surfaces and nonadiabatic coupling elements.

Förster-Induced Energy Transfer in Functionalized Graphene.

Carbon nanostructures are ideal substrates for functionalization with molecules since they consist of a single atomic layer giving rise to an extraordinary sensitivity to changes in their surrounding. The functionalization opens a new research field of hybrid nanostructures with tailored properties. Here, we present a microscopic view on the substrate-molecule interaction in the exemplary hybrid material consisting of graphene functionalized with perylene molecules.

Classical to quantum transition of heat transfer between two silica clusters.

Heat transfer between two silica clusters is investigated by using the nonequilibrium Green's function method. In the gap range between 4 Å and 3 times the cluster size, the thermal conductance decreases as predicted by the surface charge-charge interaction. Above 5 times the cluster size, the volume dipole-dipole interaction predominates.

Solvent-mediated folding of dicarboxylate dianions: aliphatic chain length dependence and origin of the IR intensity quenching.

We combine infrared photodissociation spectroscopy with quantum chemical calculations to characterize the hydration behavior of microsolvated dicarboxylate dianions, (CH2)m(COO(-))2·(H2O)n, as a function of the aliphatic chain length m. We find evidence for solvent-mediated folding transitions, signaled by the intensity quenching of the symmetric carboxylate stretching modes, for all three species studied (m = 2, 4, 8). The number of water molecules required to induce folding increases monotonically with the chain length and is n = 9-12, n = 13, and n = 18-19 for succinate (m = 2), adipate (m = 4), and sebacate (m = 8), respectively.

Time-dependent density functional theory for many-electron systems interacting with cavity photons.

Time-dependent (current) density functional theory for many-electron systems strongly coupled to quantized electromagnetic modes of a microcavity is proposed. It is shown that the electron-photon wave function is a unique functional of the electronic (current) density and the expectation values of photonic coordinates. The Kohn-Sham system is constructed, which allows us to calculate the above basic variables by solving self-consistent equations for noninteracting particles.

Bond breaking and bond formation: how electron correlation is captured in many-body perturbation theory and density-functional theory.

For the paradigmatic case of H(2) dissociation, we compare state-of-the-art many-body perturbation theory in the GW approximation and density-functional theory in the exact-exchange plus random-phase approximation (RPA) for the correlation energy. For an unbiased comparison and to prevent spurious starting point effects, both approaches are iterated to full self-consistency (i.e.

Substitution effects on the absorption spectra of nitrophenolate isomers.

Charge-transfer excitations highly depend on the electronic coupling between the donor and acceptor groups. Nitrophenolates are simple examples of charge-transfer systems where the degree of coupling differs between ortho, meta and para isomers. Here we report the absorption spectra of the isolated anions in vacuo to avoid the complications of solvent effects.

Fractional spin in reduced density-matrix functional theory.

We study the behavior of different functionals of the one-body reduced density matrix (1RDM) for systems with fractional z-component of the total spin. We define these systems as ensembles of integer spin states. It is shown that, similarly to density functional theory, the error in the dissociation of diatomic molecules is directly related to the deviation from constancy of the atomic total energies as functions of the fractional spin.

Communication: Systematic shifts of the lowest unoccupied molecular orbital peak in x-ray absorption for a series of 3d metal porphyrins.

Porphyrins are widely used as dye molecules in solar cells. Knowing the energies of their frontier orbitals is crucial for optimizing the energy level structure of solar cells. We use near edge x-ray absorption fine structure (NEXAFS) spectroscopy to obtain the energy of the lowest unoccupied molecular orbital (LUMO) with respect to the N(1s) core level of the molecule.

Many-body effects in the excitation spectrum of a defect in SiC.

We show that electron correlations control the photophysics of defects in SiC through both renormalization of the quasiparticle band structure and excitonic effects. We consider the carbon vacancy with two possible excitation channels that involve conduction and valence bands. Corrections to the Kohn-Sham ionization levels strongly depend on the defect charge state.

Exact Kohn-Sham potential of strongly correlated finite systems.

The dissociation of molecules, even the most simple hydrogen molecule, cannot be described accurately within density functional theory because none of the currently available functionals accounts for strong on-site correlation. This problem led to a discussion of properties that the local Kohn-Sham potential has to satisfy in order to correctly describe strongly correlated systems. We derive an analytic expression for the nontrivial form of the Kohn-Sham potential in between the two fragments for the dissociation of a single bond.