An estimation on the mechanical stabilities of SAMs by low energy Ar+ cluster ion collision.

The stability of the molecular self-assembled monolayers (SAMs) is of vital importance to the performance of the molecular electronics and their integration to the future electronics devices. Here we study the effect of electron irradiation-induced cross-linking on the stability of self-assembled monolayer of aromatic 5,5'-bis(mercaptomethyl)-2,2'-bipyridine [BPD; HS-CH2-(C5H3N)2-CH2-SH] on Au (111) single crystal surface. As a refence, we also study the properties of SAMs of electron saturated 1-dodecanethiol [C12; CH3-(CH2)11-SH] molecules. The stability of the considered SAMs before and after electron-irradiation is studied using low energy Ar+ cluster depth profiling monitored by recording the X-ray photoelectron spectroscopy (XPS) core level spectra and the UV-photoelectron spectroscopy (UPS) in the valance band range. The results indicate a stronger mechanical stability of BPD SAMs than the C12 SAMs. The stability of BPD SAMs enhances further after electron irradiation due to intermolecular cross-linking, whereas the electron irradiation results in deterioration of C12 molecules due to the saturated nature of the molecules. The depth profiling time of the cross-linked BPD SAM is more than 4 and 8 times longer than the profiling time obtained for pristine and BPD and C12 SAMs, respectively. The UPS results are supported by density functional theory calculations, which show qualitative agreement with the experiment and enable us to interpret the features in the XPS spectra during the etching process for structural characterization. The obtained results offer helpful options to estimate the structural stability of SAMs which is a key factor for the fabrication of molecular devices.

Thermally activated superradiance and intersystem crossing in the water-soluble chlorophyll binding protein.

The crystal structure of the class IIb water-soluble chlorophyll binding protein (WSCP) from Lepidium virginicum is used to model linear absorption and circular dichroism spectra as well as excited state decay times of class IIa WSCP from cauliflower reconstituted with chlorophyll (Chl) a and Chl b. The close agreement between theory and experiment suggests that both types of WSCP share a common Chl binding motif, where the opening angle between pigment planes in class IIa WSCP should not differ by more than 10 degrees from that in class IIb. The experimentally observed (Schmitt et al. J. Phys. Chem. B 2008, 112, 13951) decrease in excited state lifetime of Chl a homodimers with increasing temperature is fully explained by thermally activated superradiance via the upper exciton state of the dimer. Whereas a temperature-independent intersystem crossing (ISC) rate is inferred for WSCP containing Chl a homodimers, that of WSCP with Chl b homodimers is found to increase above 100 K. Our quantum chemical/electrostatic calculations suggest that a thermally activated ISC via an excited triplet state T4 is responsible for the latter temperature dependence.

Refinement of a structural model of a pigment-protein complex by accurate optical line shape theory and experiments.

Time-local and time-nonlocal theories are used in combination with optical spectroscopy to characterize the water-soluble chlorophyll binding protein complex (WSCP) from cauliflower. The recombinant cauliflower WSCP complexes reconstituted with either chlorophyll b (Chl b) or Chl a/Chl b mixtures are characterized by absorption spectroscopy at 77 and 298 K and circular dichroism at 298 K. On the basis of the analysis of these spectra and spectra reported for recombinant WSCP reconstituted with Chl a only (Hughes, J. L.; Razeghifard, R.; Logue, M.; Oakley, A.; Wydrzynski, T.; Krausz, E. J. Am. Chem. Soc. U.S.A. 2006, 128, 3649), the "open-sandwich" model proposed for the structure of the pigment dimer is refined. Our calculations show that, for a reasonable description of the data, a reduction of the angle between pigment planes from 60 degrees of the original model to about 30 degrees is required when exciton relaxation-induced lifetime broadening is included in the analysis of optical spectra. The temperature dependence of the absorption spectrum is found to provide a unique test for the two non-Markovian theories of optical spectra. Based on our data and the 1.7 K spectra of Hughes et al. (2006), the time-local partial ordering prescription theory is shown to describe the experimental results over the whole temperature range between 1.7 K and room temperature, whereas the alternative time-nonlocal chronological ordering prescription theory fails at high temperatures. Modified-Redfield theory predicts sub-100 fs exciton relaxation times for the homodimers and a 450 fs time constant in the heterodimers. Whereas the simpler Redfield theory gives a similar time constant for the homodimers, the one for the heterodimers deviates strongly in the two theories. The difference is explained by multivibrational quanta transitions in the protein which are neglected in Redfield theory.

Effect of disorder on transport properties in a tight-binding model for lead halide perovskites.

The hybrid organic-inorganic lead halide perovskite materials have emerged as remarkable materials for photovoltaic applications. Their strengths include good electric transport properties in spite of the disorder inherent in them. Motivated by this observation, we analyze the effects of disorder on the energy eigenstates of a tight-binding model of these materials. In particular, we analyze the spatial extension of the energy eigenstates, which is quantified by the inverse participation ratio. This parameter exhibits a tendency, and possibly a phase transition, to localization as the on-site energy disorder strength is increased. However, we argue that the disorder in the lead halide perovskites corresponds to a point in the regime of highly delocalized states. Our results also suggest that the electronic states of mixed-halide materials tend to be more localized than those of pure materials, which suggests a weaker tendency to form extended bonding states in the mixed-halide materials and is therefore not favourable for halide mixing.

Intermolecular coulomb couplings from ab initio electrostatic potentials: application to optical transitions of strongly coupled pigments in photosynthetic antennae and reaction centers.

An accurate and numerically efficient method for the calculation of intermolecular Coulomb couplings between charge densities of electronic states and between transition densities of electronic excitations is presented. The coupling of transition densities yields the Förster type excitation energy transfer coupling, and from the charge density coupling, a shift in molecular excitation energies results. Starting from an ab initio calculation of the charge and transition densities, atomic partial charges are determined such as to fit the resulting electrostatic potentials of the different states and the transition. The different intermolecular couplings are then obtained from the Coulomb couplings between the respective atomic partial charges. The excitation energy transfer couplings obtained in the present TrEsp (transition charge from electrostatic potential) method are compared with couplings obtained from the simple point-dipole and extended dipole approximations and with those from the ab initio transition density cube method of Krüger, Scholes, and Fleming. The present method is of the same accuracy as the latter but computationally more efficient. The method is applied to study strongly coupled pigments in the light-harvesting complexes of green sulfur bacteria (FMO), purple bacteria (LH2), and higher plants (LHC-II) and the "special pairs" of bacterial reaction centers and reaction centers of photosystems I and II. For the pigment dimers in the antennae, it is found that the mutual orientation of the pigments is optimized for maximum excitonic coupling. A driving force for this orientation is the Coulomb coupling between ground-state charge densities. In the case of excitonic couplings in the "special pairs", a breakdown of the point-dipole approximation is found for all three reaction centers, but the extended dipole approximation works surprisingly well, if the extent of the transition dipole is chosen larger than assumed previously. For the "special pairs", a large shift in local transition energies is found due to charge density coupling.

Band gap engineering in penta-graphene by substitutional doping: first-principles calculations.

Using density functional theory, we study the structure, electronic properties and partial charges of a new carbon allotrope-penta-graphene (PG)-substitutionally doped by Si, B and N. We found that the electronic bandgap of PG can be tuned down to 0.2 eV due to carbon substitutions. However, the value of the band gap depends on the type and location of the dopants. For example, the strongest reduction of the band gap is obtained for Si substitutions on the top (bottom) plane of PG, whereas the substitution in the middle plane of PG has a smaller effect on the band gap of the material. Surface termination with fluorine and hydroxyl groups results in an increase of the band gap together with considerable changes in electronic and atomic partial charge distribution in the system. Our findings, which are robust against the use of different exchange-correlation functionals, indicate the possibility of tuning the bandgap of the material to make it suitable for optoelectronic and photovoltaic applications.

How the molecular structure determines the flow of excitation energy in plant light-harvesting complex II.

Excitation energy transfer in the light-harvesting complex II of higher plants is modeled using excitonic couplings and local transition energies determined from structure-based calculations recently (Müh et al., 2010). A theory is introduced that implicitly takes into account protein induced dynamic localization effects of the exciton wavefunction between weakly coupled optical and vibronic transitions of different pigments. Linear and non-linear optical spectra are calculated and compared with experimental data reaching qualitative agreement. High-frequency intramolecular vibrational degrees of freedom are found important for ultrafast subpicosecond excitation energy transfer between chlorophyll (Chl) b and Chla, since they allow for fast dissipation of the excess energy. The slower ps component of this transfer is due to the monomeric excited state of Chlb 605. The majority of exciton relaxation in the Chla spectral region is characterized by slow ps exciton equilibration between the Chla domains within one layer and between the lumenal and stromal layers in the 10-20ps time range. Subpicosecond exciton relaxation in the Chla region is only found within the terminal emitter domain (Chls a 610/611/612) and within the Chla 613/614 dimer. Deviations between measured and calculated exciton state life times are obtained for the intermediate spectral region between the main absorbance bands of Chla and Chlb that indicate that besides Chlb 608 another pigment should absorb there. Possible candidates, so far not identified by structure-based calculations, but by fitting of optical spectra and mutagenesis studies, are discussed. Additional mutagenesis studies are suggested to resolve this issue.

Photoexcitation of a volume plasmon in C60 ions.

Neutral C60 is well known to exhibit a giant resonance in its photon absorption spectrum near 20 eV. This is associated with a surface plasmon, where delocalized electrons oscillate as a whole relative to the ionic cage. Absolute photoionization cross-section measurements for C+60, C2+60, and C3+60 ions in the 17-75 eV energy range show an additional resonance near 40 eV. Time-dependent density functional calculations confirm the collective nature of this feature, which is characterized as a dipole-excited volume plasmon made possible by the special fullerene geometry.