Assessment of TD-DFT- and TD-HF-based approaches for the prediction of exciton coupling parameters, potential energy curves, and electronic characters of electronically excited aggregates

The reliability of linear response approaches such as time-dependent Hartree-Fock (TD-HF) and time-dependent density functional theory (TD-DFT) for the prediction of the excited state properties of 3,4;9,10-tetracarboxylic-perylene-bisimide (PBI) aggregates is investigated. A dimer model of PBI is investigated as a function of a torsional motion of the monomers, which was shown before to be an important intermolecular coordinate in these aggregates. The potential energy curves of the ground state and the two energetically lowest neutral excited and charge-transfer (CT) states were obtained with the spin-component scaling modification of the approximate coupled-cluster singles-and-doubles (SCS-CC2) method as a benchmark for dispersion corrected TD-HF and a range of TD-DFT approaches. The highly accurate SCS-CC2 results are used to assess the other, computationally less demanding methods. TD-HF predicts similar potential energy curves and transition dipole moments as SCS-CC2, as well as the correct order of neutral and CT states. This supports an exciton trapping mechanism, which was found on the basis of TD-HF data. However, the investigated TD-DFT methods provide generally the opposite character for the excited states. As a consequence, these TD-DFT results have unacceptably large errors for optical properties of these dye aggregates.     

Pharmacophore alignment search tool: influence of the third dimension on text-based similarity searching

Previously (Hähnke et al., J Comput Chem 2010, 31, 2810) we introduced the concept of nonlinear dimensionality reduction for canonization of two‐dimensional layouts of molecular graphs as foundation for text‐based similarity searching using our Pharmacophore Alignment Search Tool (PhAST), a ligand‐based virtual screening method. Here we apply these methods to three‐dimensional molecular conformations and investigate the impact of these additional degrees of freedom on virtual screening performance and assess differences in ranking behavior. Best‐performing variants of PhAST are compared with 16 state‐of‐the‐art screening methods with respect to significance estimates for differences in screening performance. We show that PhAST sorts new chemotypes on early ranks without sacrificing overall screening performance. We succeeded in combining PhAST with other virtual screening techniques by rank‐based data fusion, significantly improving screening capabilities. We also present a parameterization of double dynamic programming for the problem of small molecule comparison, which allows for the calculation of structural similarity between compounds based on one‐dimensional representations, opening the door to a holistic approach to molecule comparison based on textual representations. © 2011 Wiley Periodicals, Inc. J Comput Chem , 2011.     

Interpretation of nuclear resonant vibrational spectra of rubredoxin using a combined quantum mechanics and molecular mechanics approach

Nuclear resonant vibrational spectra of the reduced and oxidized form of a mutant of rubredoxin from Pyrococcus abyssii were measured and are compared with simulated spectra that were calculated by a combined quantum mechanics (QM) and molecular mechanics (MM) method. Density functional theory was used for the QM level. Calculations were performed for different models of rubredoxin. Realistic spectra were simulated with reduced models that include at least the iron center, the four cysteins coordinating it, and the residues connected to the cysteins together with a QM layer that comprises the first two coordination shells of the iron center. Larger QM layers did not lead to significant changes of the simulated spectra.     

Asymmetric pyrene derivatives for organic field-effect transistors

For the synthesis of an ortho-dithienylpyrene, a K-region bromination of pyrene was developed which enabled the first reported, non-statistical asymmetric functionalization of pyrene at the 4, 5, 9 and 10 positions. Crystal structures, optical and electronic properties and FET characteristics have been investigated.     

A porphyrin-related macrocycle from carbazole and pyridine building blocks: synthesis and metal coordination

In this communication, we report the synthesis of a novel porphyrin-related macrocycle. The core modifications result in aromatic building blocks connected exclusively via aryl-aryl bonds. The concept of synthesis permits the formation of a cavity similar to that of a porphyrin combined with the ability to bind metal ions to provide neutral metal complexes.     

Synthesis and characterization of trinuclear square-planar Ni3 and Cu3 complexes of an extended phloroglucinol ligand: Experimental evidence for the relative contributions of benzene-like and radialene-like resonance structures

The synthesis and characterization of the extended phloroglucinol ligand H₃felddien, its trinuclear Ni^II complex [(felddien)Ni₃](BF₄)₃ and its trinuclear Cu^II complex [(felddien)Cu₃](ClO₄)₃ is presented. Detailed NMR studies provide strong evidence that the ligand H₃felddien has to be described as the N-protonated tautomer and not as the O-protonated tautomer, with strong contribution of a radialene-like keto-enamine resonance structure resulting in a C_s and a C_3h isomer. The trinucleating tris(tetradentate) ligand provides three donor sets comprised of a phenolate, an imine, and two tertiary amine donors. This donor set enables the synthesis of the diamagnetic square-planar coordinated Ni^II complex [(felddien)Ni₃](BF₄)₃ which provides the opportunity to perform detailed NMR spectroscopic characterizations for the evaluation of the electronic structure of the central phloroglucinol unit. In conjunction with a single-crystal X-ray diffraction and a UV-vis absorption spectroscopic analysis, these data indicate that in the coordinated form, the benzene-like phenolate-imine and the radialene-like keto-enamine resonance structures have contributions to the overall resonance hybrid. The weakening of the central π system as a consequence of the contribution of the keto-enamine resonance structure explains the relative small ferromagnetic interactions in the trinuclear Cu^II complex [(felddien)Cu₃](ClO₄)₃. This detailed analysis identifies the strong resonance with unsaturated groups in 2,4,6 position of phloroglucinol as the main source for the low ferromagnetic couplings by the spin-polarization mechanism in all our extended phloroglucinol ligands. A replacement of the unsaturated imine functions by saturated amine functions may be a synthetic opportunity to enhance the ferromagnetic interactions by the spin-polarization mechanism in this ligand system.     

Temperature and ionic strength effects on the chlorosome light-harvesting antenna complex

Chlorosomes, the peripheral light-harvesting antenna complex from green photosynthetic bacteria, are the largest and one of the most efficient light-harvesting antenna complexes found in nature. In contrast to other light-harvesting antennas, chlorosomes are constructed from more than 150,000 self-assembled bacteriochlorophylls (BChls) and contain relatively few proteins that play secondary roles. These unique properties have led to chlorosomes as an attractive candidate for developing biohybrid solar cell devices. In this article, we investigate the temperature and ionic strength effects on the viability of chlorosomes from the photosynthetic green bacterium Chloroflexus aurantiacus using small-angle neutron scattering and dynamic light scattering. Our studies indicate that chlorosomes remain intact up to 75 °C and that salt induces the formation of large aggregates of chlorosomes. No internal structural changes are observed for the aggregates. The salt-induced aggregation, which is a reversible process, is more efficient with divalent metal ions than with monovalent metal ions. Moreover, with treatment at 98 °C for 2 min, the bulk of the chlorosome pigments are undamaged, while the baseplate is destroyed. Chlorosomes without the baseplate remain rodlike in shape and are 30-40% smaller than with the baseplate attached. Further, chlorosomes are stable from pH 5.5 to 11.0. Together, this is the first time such a range of characterization tools have been used for chlorosomes, and this has enabled elucidation of properties that are not only important to understanding their functionality but also may be useful in biohybrid devices for effective light harvesting.     

Scattering studies of hydrophobic monomers in liposomal bilayers: an expanding shell model of monomer distribution

Hydrophobic monomers partially phase separate from saturated lipids when loaded into lipid bilayers in amounts exceeding a 1:1 monomer/lipid molar ratio. This conclusion is based on the agreement between two independent methods of examining the structure of monomer-loaded bilayers. Complete phase separation of monomers from lipids would result in an increase in bilayer thickness and a slight increase in the diameter of liposomes. A homogeneous distribution of monomers within the bilayer would not change the bilayer thickness and would lead to an increase in the liposome diameter. The increase in bilayer thickness, measured by the combination of small-angle neutron scattering (SANS) and small-angle X-ray scattering (SAXS), was approximately half of what was predicted for complete phase separation. The increase in liposome diameter, measured by dynamic light scattering (DLS), was intermediate between values predicted for a homogeneous distribution and complete phase separation. Combined SANS, SAXS, and DLS data suggest that at a 1.2 monomer/lipid ratio approximately half of the monomers are located in an interstitial layer sandwiched between lipid sheets. These results expand our understanding of using self-assembled bilayers as scaffolds for the directed covalent assembly of organic nanomaterials. In particular, the partial phase separation of monomers from lipids corroborates the successful creation of nanothin polymer materials with uniform imprinted nanopores. Pore-forming templates do not need to span the lipid bilayer to create a pore in the bilayer-templated films.