Paracyclophanes as model compounds for strongly interacting π-systems. Part 2: mono-hydroxy[2.2]paracyclophane

The structure of the electronic ground- and first excited state of mono-hydroxy [2.2]paracyclophane (MHPC) and the S(1)← S(0) electronic transition have been investigated by resonance-enhanced multiphoton ionisation (REMPI) and by quantum chemical spin-component-scaled-approximate coupled cluster second order (SCS-CC2) computations. The origin of the S(1)← S(0) transition was located at 30,772 cm(-1) (3.815 eV) in the REMPI spectrum. The value has to be compared with a computed excitation energy of 3.79 eV. The vibrational structure of the spectrum confirms a significant geometry change upon excitation along the coordinates corresponding to twist- and shift-motions in the molecule. It gives rise to an experimentally observed progression with a fundamental of +30 cm(-1) and an inverse anharmonicity. From the experimental data a shallow potential along the twist coordinate was derived for the S(1) state. For the shift vibration a wavenumber of +91 cm(-1) was observed, while +85 cm(-1) was computed. The ionisation energy of MHPC was determined to be 7.63 ± 0.05 eV using synchrotron radiation. When compared to earlier results on the parent compound [2.2]paracyclophane and pseudo-ortho-dihydroxy[2.2]paracyclophane it can be seen that already small variations in the substitution pattern have a significant impact on the shapes of the involved potential energy surfaces leading to strong variations in ground and excited state geometries and opto-electronic properties governing the exciton transfer processes.     

Markov models of molecular kinetics: generation and validation

Markov state models of molecular kinetics (MSMs), in which the long-time statistical dynamics of a molecule is approximated by a Markov chain on a discrete partition of configuration space, have seen widespread use in recent years. This approach has many appealing characteristics compared to straightforward molecular dynamics simulation and analysis, including the potential to mitigate the sampling problem by extracting long-time kinetic information from short trajectories and the ability to straightforwardly calculate expectation values and statistical uncertainties of various stationary and dynamical molecular observables. In this paper, we summarize the current state of the art in generation and validation of MSMs and give some important new results. We describe an upper bound for the approximation error made by modeling molecular dynamics with a MSM and we show that this error can be made arbitrarily small with surprisingly little effort. In contrast to previous practice, it becomes clear that the best MSM is not obtained by the most metastable discretization, but the MSM can be much improved if non-metastable states are introduced near the transition states. Moreover, we show that it is not necessary to resolve all slow processes by the state space partitioning, but individual dynamical processes of interest can be resolved separately. We also present an efficient estimator for reversible transition matrices and a robust test to validate that a MSM reproduces the kinetics of the molecular dynamics data.     

Metallization of a thiol-terminated organic surface using chemical vapor deposition

The deposition and the subsequent decomposition of an organometallic precursor, (eta (3)-allyl)(eta (5)-cyclopentadienyl)palladium [Cp(allyl)Pd], on an organic surface exposed by self-assembled monolayers (SAM) was studied using X-ray photoelectron spectroscopy (XPS) and infrared reflection absorption spectroscopy (IRRAS). The interfacial chemical reactions of the vapor-deposited metal precursor with the pendant thiol group of the SAMs made from oligophenyldithiols, which are either prepared directly (terphenyldimethyldithiol, TPDMT) or by a deprotection route from SAMs formed by a monoacylated derivative of biphenyldimethyldithiol (dep. BPDMAc-1) have been studied in detail. When the TPDMT-SAMs were exposed to Cp(allyl)Pd vapor, a Pd (2+)/allyl-terminated SAM surface was obtained (to a lower extent this was also the case for dep. BPDMAc-1 SAMs), which was stable against exposure to H 2 gas. Reduction to Pd (0) by H 2 was only observed when small amounts of Pd (0) were already present, for example, after prolonged exposure to the precursor. The catalytic activity of the small Pd (0) particles also caused a decomposition of the SAMs upon exposure to air.     

Benchmarking the performance of spin-component scaled CC2 in ground and electronically excited states

A generalization of the spin-component scaling and scaled opposite-spin modifications of second-order M?ller-Plesset perturbation theory to the approximate coupled-cluster singles-and-doubles model CC2 (termed SCS-CC2 and SOS-CC2) is discussed and a preliminary implementation of ground and excited state energies and analytic gradients is reported. The computational results for bond distances, harmonic frequencies, adiabatic and 0-0 excitation energies are compared with experimental results to benchmark their performance. It is found that both variants of the spin-scaling increase the robustness of CC2 against strong correlation effects and lead for this method even to somewhat larger improvements than those observed for second-order M?ller-Plesset perturbation theory. The spin-component scaling also enhances systematically the accuracy of CC2 for 0-0 excitation energies for pi --> pi* and n --> pi* transitions, if geometries are determined at the same level.     

Tt‐Tt (Tt = Si,Ge) Dumb‐Bell Structures at Different Valence Electron Concentrations: Ln2MgSi2 (Ln = La,Ce), Yb2Li0.5Ge2, and Yb1.75Mg0.75Si2

The isostructural compounds Yb₂MgSi₂, La_2.05Mg_0.95Si₂, and Ce_2.05Mg_0.95Si₂, as well as Yb₂Li_0.5Ge₂ and Yb_1.75Mg_0.75Si₂, respectively, were synthesized from stoichiometric mixtures of the corresponding elements in sealed Nb‐ ampoules under argon atmosphere. The structures were determined by single crystal X‐ray diffraction: Yb₂MgSi₂ (P4/mbm (No. 127), a = 7.056(1), c = 4.130(1) ų, Z = 2), La_2.05Mg_0.95Si₂ (P4/mbm, a = 7.544(1), c = 4.464(1) ų, Z = 2), and Ce_2.05Mg_0.95Si₂ (P4/mbm, a = 7.425(1), c = 4.370(1) ų, Z = 2), Yb₂Li_0.5Ge₂ (Pnma (No. 62), a = 7.0601(6), b = 14.628(1), c = 7.6160(7) Å, V = 786.5ų, Z = 4), Yb_1.75Mg_0.75Si₂ (Pnma, a = 6.9796(1), b = 14.4009(1), c = 7.5357(1) Å, V = 757.43(2) ų, Z = 4). All compounds contain exclusively Tt‐Tt dumb‐bells (Tt = Si, Ge). The Si‐Si Zintl anions exhibit only very small variations of bond lengths which seem to be more due to cation matrix effects than to effective bond orders.     

Selective covalent conjugation of phosphorothioate DNA oligonucleotides with streptavidin

Protein-DNA conjugates have found numerous applications in the field of diagnostics and nanobiotechnology, however, their intrinsic susceptibility to DNA degradation by nucleases represents a major obstacle for many applications. We here report the selective covalent conjugation of the protein streptavidin (STV) with phosphorothioate oligonucleotides (psDNA) containing a terminal alkylthiolgroup as the chemically addressable linking unit, using a heterobifunctional NHS-/maleimide crosslinker. The psDNA-STV conjugates were synthesized in about 10% isolated yields. We demonstrate that the terminal alkylthiol group selectively reacts with the maleimide while the backbone sulfur atoms are not engaged in chemical conjugation. The novel psDNA-STV conjugates retain their binding capabilities for both biotinylated macromolecules and the complementary nucleic acid. Moreover, the psDNA-STV conjugate retained its binding capacity for complementary oligomers even after a nuclease digestion step, which effectively degrades deoxyribonucleotide oligomers and thus the binding capability of regular DNA-STV conjugates. The psDNA-STV therefore hold particular promise for applications e.g. in proteome research and novel biosensing devices, where interfering endogenous nucleic acids need to be removed from analytes by nuclease digestion.     

Quantitative analysis of energy transfer between fluorescent proteins in CFP-GBP-YFP and its response to Ca2+

This article reports the full characterisation of the optical properties of a biosynthesised protein consisting of fused cyan fluorescent protein, glucose binding protein and yellow fluorescent protein. The cyan and yellow fluorescent proteins act as donors and acceptors for intramolecular fluorescence resonance energy transfer. Absorption, fluorescence, excitation and fluorescence decays of the compound protein were measured and compared with those of free fluorescent proteins. Signatures of energy transfer were identified in the spectral intensities and fluorescence decays. A model describing the fluorescence properties including energy transfer in terms of rate equations is presented and all relevant parameters are extracted from the measurements. The compound protein changes conformation on binding with calcium ions. This is reflected in a change of energy transfer efficiency between the fluorescent proteins. We track the conformational change and the kinetics of the calcium binding reaction from fluorescence intensity and decay measurements and interpret the results in light of the rate equation model. This visualisation of change in protein conformation has the potential to serve as an analytical tool in the study of protein structure changes in real time, in the development of biosensor proteins and in characterizing protein-drug interactions.     

Organic molecular beam deposition of oligophenyls on Au111: A study by X-ray absorption spectroscopy.

Near-edge X-ray absorption fine structure (NEXAFS) spectroscopy has been applied to reveal the molecular arrangement of ultrathin oligophenyl films [p-quaterphenyl (4P) and p-hexaphenyl (6P)] on Au(111). In the half-monolayer films the molecules lie flat on the surface but still have a considerable inter-ring twist of 30 degrees -40 degrees , similar to the gas-phase conformation. In the saturated monolayer film the second half of the molecules is side-tilted by an angle of less than 66 degrees with respect to the surface. This arrangement is already similar to that in bulk net planes of thicker films parallel to the surface, that is, the 4P(211) and 6P(21-3) planes, respectively.