Adsorption behavior of 4-methoxypyridine on gold nanoparticles

We demonstrate a phase transfer method to create stable colloidal solutions of Au nanoparticles with 4-methoxypyridine ligands. We then investigate the adsorption behavior of 4-methoxypyridine onto gold surfaces by Raman spectroscopy, DFT calculations, and (1)H NMR. In contrast to unsubstituted pyridine and the frequently used (N,N-dimethylamino)pyridine (DMAP), a flat adsorption of 4-methoxypyridine on gold was found.     

Synthesis,NMR‐Spectroscopy,and Molecular Structure of a Phosphonyl Ene Diamine

First examples of ene diamines with a phosphonate function at the C=C double bond were obtained by the reaction of dialkyl H‐phosphonates with bis(N‐tert‐butyl)‐diimine derived from glyoxal, [1,4‐bis(tert‐butyl)‐1,4‐diaza‐1,3‐butadiene], and isolated as hydrochlorides. Preferentially the cis‐diamine is formed. The new phosphonates are characterized by multinuclear NMR spectroscopy(¹H, ¹³C, ³¹P). In addition the methyl ester 8a was characterized by ^14,15N NMR spectroscopy as well as by several 2D NMR techniques and single‐crystal X‐ray diffraction, unequivocally establishing the ene diamine structure. In the crystal dimers of the cations are formed by P–O ··· H–N hydrogen bonding.     

Quantitative gel electrophoresis: new records in precision by elaborated staining and detection protocols

Gel electrophoresis (GE) is a very common analytical technique for proteome research and protein analysis. Despite being developed decades ago, there is still a considerable need to improve its precision. Using the fluorescence of Colloidal Coomassie Blue -stained proteins in near-infrared (NIR), the major error source caused by the unpredictable background staining is strongly reduced. This result was generalized for various types of detectors. Since GE is a multi-step procedure, standardization of every single step is required. After detailed analysis of all steps, the staining and destaining were identified as the major source of the remaining variation. By employing standardized protocols, pooled percent relative standard deviations of 1.2-3.1% for band intensities were achieved for one-dimensional separations in repetitive experiments. The analysis of variance suggests that the same batch of staining solution should be used for gels of one experimental series to minimize day-to-day variation and to obtain high precision.     

Accurate distance determination of nucleic acids via Förster resonance energy transfer: implications of dye linker length and rigidity

In Fo?rster resonance energy transfer (FRET) experiments, the donor (D) and acceptor (A) fluorophores are usually attached to the macromolecule of interest via long flexible linkers of up to 15 ? in length. This causes significant uncertainties in quantitative distance measurements and prevents experiments with short distances between the attachment points of the dyes due to possible dye-dye interactions. We present two approaches to overcome the above problems as demonstrated by FRET measurements for a series of dsDNA and dsRNA internally labeled with Alexa488 and Cy5 as D and A dye, respectively. First, we characterize the influence of linker length and flexibility on FRET for different dye linker types (long, intermediate, short) by analyzing fluorescence lifetime and anisotropy decays. For long linkers, we describe a straightforward procedure that allows for very high accuracy of FRET-based structure determination through proper consideration of the position distribution of the dye and of linker dynamics. The position distribution can be quickly calculated with geometric accessible volume (AV) simulations, provided that the local structure of RNA or DNA in the proximity of the dye is known and that the dye diffuses freely in the sterically allowed space. The AV approach provides results similar to molecular dynamics simulations (MD) and is fully consistent with experimental FRET data. In a benchmark study for ds A-RNA, an rmsd value of 1.3 ? is achieved. Considering the case of undefined dye environments or very short DA distances, we introduce short linkers with a propargyl or alkenyl unit for internal labeling of nucleic acids to minimize position uncertainties. Studies by ensemble time correlated single photon counting and single-molecule detection show that the nature of the linker strongly affects the radius of the dye's accessible volume (6-16 ?). For short propargyl linkers, heterogeneous dye environments are observed on the millisecond time scale. A detailed analysis of possible orientation effects (κ(2) problem) indicates that, for short linkers and unknown local environments, additional κ(2)-related uncertainties are clearly outweighed by better defined dye positions.     

Biogenesis of the unique 4',5'-dehydronucleoside of the uridyl peptide antibiotic pacidamycin

The pacidamycins belong to a class of antimicrobial nucleoside antibiotics that act by inhibiting the clinically unexploited target translocase I, a key enzyme in peptidoglycan assembly. As with other nucleoside antibiotics, the pacidamycin 4',5'-dehydronucleoside portion is an essential pharmacophore. Here we show that the biosynthesis of the pacidamycin nucleoside in Streptomyces coeruleorubidus proceeds through three steps from uridine. The transformations involve oxidation of the 5'-alcohol by Pac11, transamination of the resulting aldehyde by Pac5, and dehydration by the Cupin-domain protein Pac13.     

Water behavior in mesoporous materials as studied by NMR relaxometry

Water in mesoporous materials possessing a two-dimensional hexagonal structure has been studied by the variation of its NMR longitudinal relaxation time T(1) as a function of the static magnetic field value, or equivalently of the NMR measurement frequency. This technique, dubbed relaxometry, has been applied from 5 kHz (measurement frequency) up to 400 MHz with various instruments including a variable-field spectrometer operating between 8 and 90 MHz. Moreover, the range 0-5 kHz could be investigated by transverse relaxation, T(2) denoting the corresponding relaxation time, and relaxation in the rotating frame, T(1ρ) denoting the corresponding relaxation time. Measurements of proton relaxation rates (inverse of relaxation times) have been performed with H(2)O and HOD (residual protons of heavy water) at water volumes of 80%, 60%, and 40% relative to the porous volume. Comparison between H(2)O and HOD shows clearly that, above 1 MHz where both sets of data are superposed, relaxation is purely intermolecular and due to paramagnetic relaxation (dipolar interactions of water protons with unpaired electrons of paramagnetic entities). Below 1 MHz, it is possible to subtract the intermolecular contribution (given by HOD data) from H(2)O data so that one is left with intramolecular relaxation which is solely due to water reorientational motions. The analysis of these low-frequency data (in terms of Lorentzian functions) reveals two types of water within the pores: one interacting strongly with the surface and the other corresponding to a second layer. High-frequency data, which arise from paramagnetic relaxation, exhibit again two types of water. Due to their correlation times, one type is assigned to relatively free water within the pores while the other type corresponds to bulk (interparticular) water. Their proportions, given as a function of the volume fraction, are consistent with the above assignments.     

Photoswitchable rotaxanes on gold nanoparticles

We studied rotaxanes that consisted of a molecular axle, with a photoactive 9-Aryl-9-methoxy-acridane moiety at one end, and a tetracationic ring of cyclobis(paraquat-p-phenylene) (CBQT(4+)). The aim of the study was to deposit the axle ends onto gold nanoparticles (AuNPs). First, we introduced thioctic acid into the axle molecules. Then, rotaxanes were deposited on AuNPs by two methods: 1) Pseudorotaxanes were deposited on the gold surface by forming rotaxanes with the AuNP as a terminator to prevent unthreading of the ring structure; and 2) a chain containing the thioctic ester was introduced into a complete rotaxane, and then it was deposited on the AuNP with the aid of an exchange process. The photoheterolysis of the acridane unit resulted in formation of the corresponding acridinium methoxide; this, in turn, could thermally react to return to the acridane moiety. Due to the creation of a positive charge, the ring moved from the acridane station to a second, evasive station within the axle. This switching cycle could also take place when deposited on the gold surface. However, on the gold surface, the ring movement associated with the switching process was unidirectional.     

Metal-free direct arylations of indoles and pyrroles with diaryliodonium salts

Direct arylations of indoles and pyrroles with differently substituted diaryliodonium salts were shown to efficiently proceed in the absence of metal catalysts.     

Hydrophobin can prevent secondary protein adsorption on hydrophobic substrates without exchange

By combining several surface analytical tools, we show that an adsorbed layer of the protein H*Protein B prevents the adsorption of secondary proteins bovine serum albumin, casein, or collagen at low-salinity conditions and at pH 8. H*Protein B is an industrially producible fusion protein of the hydrophobin family, known for its high interfacial activity. While applications of hydrophobin have been reported to facilitate adhesion of proteins under different pH conditions, careful analysis by quartz-crystal microbalance and ellipsometry prove that no additional adsorption can be found on top of the H*Protein B layer in this study. Surface analysis by X-ray photoelectron spectroscopy and secondary ion mass spectrometry proves that the hydrophobin layer stays intact even after hours of exposure to solutions of the secondary proteins and that no exchange of proteins can be detected.