Liquid-phase epitaxy of multicomponent layer-based porous coordination polymer thin films of [M(L)(P)0.5] type: importance of deposition sequence on the oriented growth

The progressive liquid-phase layer-by-layer (LbL) growth of anisotropic multicomponent layer-based porous coordination polymers (PCPs) of the general formula [M(L)(P)(0.5)] (M: Cu(2+), Zn(2+); L: dicarboxylate linker; P: dinitrogen pillar ligand) was investigated by using either pyridyl- or carboxyl-terminated self-assembled monolayers (SAMs) on gold substrates as templates. It was found that the deposition of smooth, highly crystalline, and oriented multilayer films of these PCPs depends on the conditions at the early growth cycles. In the case of a two-step process with an equimolar mixture of L and P, growth along the [001] direction is strongly preferred. However, employing a three-step scheme with full separation of all components allows deposition along the [100] direction on carboxyl-terminated SAMs. Interestingly, the growth of additional layers on top of previously grown oriented seeding layers proved to be insensitive to the particular growth scheme and full retention of the initial orientation, either along the [001] or [100] direction, was observed. This homo- and heteroepitaxial LbL growth allows full control over the orientation and the layer sequence, including introduction of functionalized linkers and pillars.     

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.     

An LC-MS screening method with library identification for the detection of steroids in dietary supplements

For many years anabolic-androgenic steroids (AAS) are by far the most frequently detected pharmacological substances in doping control. In order to improve their performances, professional sportsmen are often tempted to take dietary supplements. However, due to the frequent and widespread occurrence of contaminated supplements, the use of such products is not without risk for the athletes involved. In order to minimize the chances of an unattended positive doping test or serious health problems, fast and reliable screening methods for the detection of anabolic steroids in dietary supplements are needed. A general screening procedure requires the fast and unambiguous detection of a large range of steroids. Gas chromatography-mass spectrometry (GC-MS) has been used intensively in the detection of doping substances for the past 40 years. Over time, many laboratories have delivered spectra to be included in standard reference databases, one of which is maintained by the National Institute of Standards and Technology (NIST) (Gaithersburg, MD, USA). In recent years, however, liquid chromatography coupled to mass spectrometry (LC-MS) has gained popularity. Unfortunately, existing GC-MS libraries are not applicable to LC-MS analysis. In the present study, a new mass spectral library of 88 steroids was developed, along with a fast UPLC-MS method. For the construction of this mass spectral library, three different mass spectra were measured for each steroid, with a sample cone voltage of 30, 60 and 100 V, respectively. This method was then successfully tested on contaminated dietary supplements which had previously been tested by means of a targeted LC-MS/MS method. Overall, the library search was shown to identify the same compounds as the MRM method.     

The use of library identification and common fragments for the identification of corticosteroids in forensic samples

The detection of corticosteroids and sex steroids in samples with no content indication, which are confiscated for forensic investigation, is a challenge in doping analysis. A screening method based on the identification of androgens, estrogens, gestagens, and their esters by means of a mass spectral library, along with a fast ultra-performance liquid chromatography–mass spectrometry (UPLC-MS) method, was recently developed in our lab for the analysis of dietary supplements. However, for forensic investigations, it is important to extend the scope of the method to corticosteroids in various matrices. Therefore, 36 corticosteroids were added to the mass spectral library, and the sample preparation step was modified so that androgens, gestagens, corticosteroids, and their esters could be analyzed with only one injection with the UPLC-MS method. A complementary tool to the existing library identification was found in the extraction of common fragment ions out of the full scan data obtained for the library search. The fragment ion with m/z 147 was found to be a good marker for the detection of steroids. Extra confirmation was obtained from the fragment ions with m/z 135 (for all steroids) and 237 (specific for corticosteroids) or from the fragment ions with m/z 77, 91, and 105. The effectiveness of this approach was evaluated on some samples previously screened for forensic investigation with thin-layer chromatography and confirmed with a targeted gas chromatography–mass spectrometry method. This study shows that the combination of the library identification and the common fragment ions approach can be a valuable tool in the detection of steroids without defining any target at the start of the analysis.     

Post-synthetic modification of epitaxially grown, highly oriented functionalized MOF thin films

Thin films of MOFs grown on solid substrates offer a huge potential with regard to tailoring the properties of a surface, in particular if used in connection with post-synthesis modification (PSM). Here, we report on the PSM of surface-supported crystalline MOFs, with target molecules using an amine-based coupling strategy.     

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.     

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.