Observation of early ZIF-8 crystallization stages with X-ray absorption spectroscopy.

The present study investigates early stages of ZIF-8 crystallization up to 5 minutes post mixing of precursor solutions. Dispersive X-ray Absorption Spectroscopy (DXAS) provides a refined understanding of the evolution of the coordination environment during ZIF-8 crystallization. Linear Combination Analysis (LCA) suggests tetrakis(1-methylimidazole)zinc2+ to be a suitable and stable mononuclear structure analogue for some early stage ZIF-8 intermediates. Our results pave the way for more detailed studies on physico-chemical aspects of ZIF-8 crystallization to better control tailoring ZIF-8 materials for specific applications.

Controlling the Interparticular Distances of Extended Non-Close-Packed Colloidal Monolayers.

A versatile method for the preparation extended, well-ordered, non-close-packed monolayers of silica nanoparticles (137 ± 4 nm diameter) with adjustable interparticle distances is presented, which is based on a simple self-assembly procedure using aqueous dispersion with different ionic strengths. It is shown that these structures can be successfully transferred to air without suffering from aggregation. Scanning electron microscopy (SEM) is used to characterize the structures after transfer into the atmosphere. These investigations were combined with a quartz crystal microbalance with dissipation (QCM-D) experiments to follow the self-assembly process in solution. The nearest-neighbor distance distribution reveals a monotonous decrease of the average nearest-neighbor distance from 290 to 200 nm with increasing ionic strength from 0.05 to 1 mM, which indicates an increased shielding of the electrostatic interaction with increasing ionic strength. The observed saturation coverages for all studied ionic strengths are well explained with an effective hard-sphere model in which the saturation coverage is limited by Coulomb repulsion. However, at ionic strengths above 1 mM, significant amounts of aggregates are found in the dried samples, suggesting that the observed aggregates at high ionic strengths are formed during the drying process caused by capillary forces between the particles. Tuning the barrier for lateral diffusion, e.g., by changing the surface morphology or functionalization of the particles will offer a route to further extend the range of particle distances. The present approach can be easily expanded to a broad range of colloidal materials on surfaces, while it only requires low-cost laboratory equipment.

"End-to-end" stacking of small dsRNA.

PELDOR (pulsed electron-electron double resonance) is an established method to study intramolecular distances and can give evidence for conformational changes and flexibilities. However, it can also be used to study intermolecular interactions as for example oligerimization. Here, we used PELDOR to study the "end-to-end" stacking of small double-stranded (ds) RNAs. For this study, the dsRNA molecules were only singly labeled with the spin label TPA to avoid multispin effects and to measure only the intermolecular stacking interactions. It can be shown that small dsRNAs tend to assemble to rod-like structures due to π-π interactions between the base pairs at the end of the strands. On the one hand, these interactions can influence or complicate measurements aimed at the determining of the structure and dynamics of the dsRNA molecule itself. On the other hand, it can be interesting to study such intermolecular stacking interactions in more detail, as for example their dependence on ion concentration. We quantitatively determined the stacking probability as a function of the monovalent NaCl salt and the dsRNA concentration. From these data, the dissociation constant Kd was deduced and found to depend on the ratio between the NaCl salt and dsRNA concentrations. Additionally, the distances and distance distributions obtained predict a model for the stacking geometry of dsRNAs. Introducing a nucleotide overhangs at one end of the dsRNA molecule restricts the stacking to the other end, leading only to dimer formations. Introducing such an overhang at both ends of the dsRNA molecule fully suppresses stacking, as we demonstrate by PELDOR experiments quantitatively.

Structure guided fluorescence labeling reveals a two-step binding mechanism of neomycin to its RNA aptamer.

The ability of the cytidine analog Çmf to act as a position specific reporter of RNA-dynamics was spectroscopically evaluated. Çmf-labeled single- and double-stranded RNAs differ in their fluorescence lifetimes, quantum yields and anisotropies. These observables were also influenced by the nucleobases flanking Çmf. This conformation and position specificity allowed to investigate the binding dynamics and mechanism of neomycin to its aptamer N1 by independently incorporating Çmf at four different positions within the aptamer. Remarkably fast binding kinetics of neomycin binding was observed with stopped-flow measurements, which could be satisfactorily explained with a two-step binding. Conformational selection was identified as the dominant mechanism.

The role of charge and proton transfer in fragmentation of hydrogen-bonded nanosystems: the breakup of ammonia clusters upon single photon multi-ionization.

The charge and proton dynamics in hydrogen-bonded networks are investigated using ammonia as a model system. The fragmentation dynamics of medium-sized clusters (1-2 nm) upon single photon multi-ionization is studied, by analyzing the momenta of small ionic fragments. The observed fragmentation pattern of the doubly- and triply-charged clusters reveals a spatial anisotropy of emission between fragments (back-to-back). Protonated fragments exhibit a distinct kinematic correlation, indicating a delay between ionization and fragmentation (fission). The different kinematics observed for channels containing protonated and unprotonated species provides possible insights into the prime mechanisms of charge and proton transfer, as well as proton hopping, in such a nanoscale system.

Structural Characterization of Ordered, Non-Close-Packed Functionalized Silica Nanoparticles on Gold Surfaces.

Nanostructured surfaces play an important role in modern science and technology. In particular, ordered arrangements of nonclose-packed nanoparticles created by self-assembly offer a versatile route to prepare systems, which can be used in various applications such as sensing, plasmonic devices or antireflection coatings. Self-assembly based systems are particularly appealing as preparation is rather simple. The ability of nanoparticle systems to form nonclosed packed monolayers by self-assembly depends on the balance of various energetic contributions in particular the adsorption energy, the lateral barrier for diffusion and the repulsion between particles. Even for simple model systems such as the monodispersed silica particles adsorbed on a bare gold surface investigated here, none of these quantities is easy to determine experimentally. To this end, we will report on a detailed characterization of the adsorption in particular with respect to the structural properties of the above-mentioned model system. Based on experimental results obtained by using quartz crystal microbalance with dissipation monitoring (QCM-D) as well as scanning electron microscopy (SEM) it is possible to determine the electrostatic pair potential from the lateral arrangement of the nano particles in the limit of low coverage.

Three-State Fluorescence of a 2-Functionalized Pyrene-Based RNA Label.

The pyrene-based RNA-fluorescence label 2-(2-pyrenylethynyl) adenosine (2PyA) shows triexponential fluorescence, which depends strongly on the excitation wavelength. Most strikingly, a structured, long-lived fluorescence is observed in solution at room temperature after excitation into the S2 state, which is shifted hypsochromically by 30 nm compared to excitation into the S1 state. This very unusual behavior is investigated in detail with steady-state and time-resolved emission spectroscopy, ultrafast transient absorption spectroscopy, and quantum chemical calculations with both wave functions (CC2-level) and density-functional theory (DFT). 2PyA is found to emit simultaneously from two different intramolecular charge transfer states (mesomeric and twisted, MICT and TICT) which are populated most efficiently via the S1 state and a pyrene-like locally excited (LE) state. Rotational momentum derived from excess excitation energy is required to populate twisted LE configurations. Therefore, the LE state is most efficiently accessible via excitation to the S2. The stabilization of the different substates is related to two distinct reaction coordinates: the adenine-pyrene distance and the adenine-pyrene tilt angle, respectively.

Controlling the Interaction and Non-Close-Packed Arrangement of Nanoparticles on Large Areas.

In light of the importance of nanostructured surfaces for a variety of technological applications, the quest for simple and reliable preparation methods of ordered, nanometer ranged structures is ongoing. Herein, a versatile method to prepare ordered, non-close-packed arrangements of nanoparticles on centimeter sized surfaces by self-assembly is described using monodisperse (118-162 nm Ø), amino-functionalized silica nanoparticles as an exploratory example. It is shown that the arrangement of the particles is governed by the interplay between the electrostatic repulsion between the particles and the interaction between particles and surfaces. The latter is tuned by the properties of the particles such as their surface roughness as well as the chemistry of the linkage. Weak dispersive interactions between amino groups and gold surfaces are compared to a covalent amide linkage of the amino groups with carboxylic acid functionalized self-assembled monolayers. It was shown that the order of the former systems may suffer from capillary forces between particles during the drying process, while the covalently bonded systems do not. In turn, covalently bonded systems can be dried quickly, while the van der Waals bonded systems require a slow drying process to minimize aggregation. These highly ordered structures can be used as templates for the formation of a second, ordered, non-close-packed layer of nanoparticles exemplified for larger polystyrene particles (Ø 368 ± 14 nm), which highlights the prospect of this approach as a simple preparation method for ordered arrays of nanoparticles with tunable properties.

The Three Possible 2-(Pyrenylethynyl) Adenosines: Rotameric Energy Barriers Govern the Photodynamics of These Structural Isomers.

This article presents a comprehensive study of the photophysics of 2-(2-pyrenylethynyl) adenosine and 2-(4-pyrenylethynyl) adenosine, which are structural isomers of the well-established fluorescent RNA label 2-(1-pyrenylethynyl) adenosine. We performed steady-state and ultrafast transient absorption spectroscopy studies along with time-resolved fluorescence emission experiments in different solvents to work out the interplay of locally excited and charge-transfer states. We found the ultrafast photodynamics to be crucial for the fluorescence decay behavior, which extends up to tens of nanoseconds and is partially multi-exponential. These features in the ultrafast dynamics are indicative of the rotational energy barriers in the first excited state.

Ordered Structures of Functionalized Silica Nanoparticles on Gold Surfaces: Correlation of Quartz Crystal Microbalance with Structural Characterization.

Quartz crystal microbalance (QCM) is frequently used to investigate adsorption of nanometer-sized objects such as proteins, viruses, or organic as well as inorganic nanoparticles from solution. The interpretation of the data obtained for heterogeneous adsorbate layers is not straightforward in particular if the systems exhibit sizable amounts of dissipation. In this study we investigate the deposition of monodisperse, amine functionalized silica nanoparticles on gold surfaces using QCM with dissipation (QCM-D) to obtain frequency and dissipation changes during adsorption from the liquid phase. These investigations are combined with ex situ scanning electron microscopy (SEM) measurements to study both coverage as well as lateral arrangement of the particles. An ordered layer of particles is found at saturation coverage due to the charged particle surface resulting in a repulsive interaction between the particles. The repulsion ensures a minimal distance between the particles, which leads to a saturation coverage of 15% for particles of 137 nm diameter. The frequency shift is shown to be a linear function of coverage which is a behavior expected for an elastic medium according to the Sauerbrey equation. However, the system shows a strong dependence of the normalized frequency shift on the overtones as well as a large dissipation, which is a clear indication for a system with viscoelastic properties. The analysis of the data show that a reliable determination of the adsorbed mass solely on the basis of QCM-D results is not possible, but additional information as determined by SEM in the present case is required to determine the coverage. From a correlation of the QCM-D results with the structural characterization it is possible to infer that the dissipation is a long ranged phenomenon. A lower boundary of the interaction length could be derived being twice the particle diameter for the particles studied here. In contrast to that the frequency response behaves like local phenomenon.

Polyglycerol based coatings to reduce non-specific protein adsorption in sample vials and on SPR sensors.

Coatings based on dendritic polyglycerol (dPG) were investigated for their use to control nonspecific protein adsorption in an assay targeted to analyze concentrations of a specific protein. We demonstrate that coating of the sample vial with dPG can significantly increase the recovery of an antibody after incubation. First, we determine the concentration dependent loss of an antibody due to nonspecific adsorption to glass via quartz crystal microbalance (QCM). Complementary to the QCM measurements, we applied the same antibody as analyte in an surface plasmon resonance (SPR) assay to determine the loss of analyte due to nonspecific adsorption to the sample vial. For this purpose, we used two different coatings based on dPG. For the first coating, which served as a matrix for the SPR sensor, carboxyl groups were incorporated into dPG as well as a dithiolane moiety enabling covalent immobilization to the gold sensor surface. This SPR-matrix exhibited excellent protein resistant properties and allowed the immobilization of amyloid peptides via amide bond formation. The second coating which was intended to prevent nonspecific adsorption to glass vials comprised a silyl moiety that allowed covalent grafting to glass. For demonstrating the impact of the vial coating on the accuracy of an SPR assay, we immobilized amyloid beta (Aß) 1-40 and used an anti-Aß 1-40 antibody as analyte. Alternate injection of analyte into the flow cell of the SPR device from uncoated and coated vials, respectively gave us the relative signal loss (1-RUuncoated/RUcoated) caused by the nonspecific adsorption. We found that the relative signal loss increases with decreasing analyte concentration. The SPR data correlate well with concentration dependent non-specific adsorption experiments of the analyte to glass surfaces performed with QCM. Our measurements show that rendering both the sample vial and the sensor surface is crucial for accurate results in protein assays.

Efficient microwave-assisted synthesis, antibacterial activity and high fluorescence of 5 benzimidazolyl-2'-deoxyuridines.

A series of novel C-5 benzimidazolyl-2'-deoxyuridines was synthesized in good yields under solvent-free conditions and microwave irradiation from 5-formyl-2'-deoxyuridine and arylenediamine derivatives in the presence of NaHSO(3) as catalyst. Their absorption and fluorescence spectra were measured. They showed intense fluorescence around 400-500nm with quantum yields between 0.3 and 0.5. All compounds studied in this work were screened for their antibacterial activities against a series of Gram positive and negative bacteria. The trifluoromethyl substituted benzimidazole derivatives showed some antibacterial activity.

Ultrafast dynamics of 1-ethynylpyrene-modified RNA: a photophysical probe of intercalation.

The photophysics of pyrene attached to an adenine base within RNA single strands and duplexes is examined with respect to the position of the pyrene within the strand and the number of pyrenes attached to one duplex. Compounds with pyrenes intercalating sequence specifically are examined, as well as a doubly modified compound, where the two pyrenes are located close enough to each other for significant excimer interaction. Femtosecond transient absorption measurements and time correlated single photon counting measurements allow a thorough examination of the local influences on the pyrene photophysics. Our results suggest that optical excitation establishes an equilibration between two molecular states of different spectroscopic properties and lifetimes that are coupled only via the excited state as a gateway. One of them is a neutral pyrene-adenine excited state, S*, while the second one is connected to an excited charge transfer state, S*(CT). In all compounds, an ultrafast sub-ps decay from a higher excited state into the lowest excited state S* occurs, and an excited charge transfer species S*(CT) is formed within picoseconds. The fluorescence behavior of the pyrene-modified adenine, however, is strongly dependent on RNA conformation. Both S* and S*(CT) states are fluorescent, and decay within hundreds of picoseconds and approximately 2 ns, respectively. The ratio between S* and S*(CT) fluorescence depends strongly on pyrene intercalation, and it is found that the S* state is quenched selectively upon intercalation of the pyrene into RNA. The doubly modified duplex exhibits an additional fluorescent state with a lifetime of 18.7 ns, which is associated with the pyrene excimer state. This state coexists with a significant population of the pyrene monomer, since the characteristic features of the latter can still be observed. Formation of the excimer occurs on femtosecond time scales. The pyrene label thus provides a sensitive tool to monitor the local structural dynamics of RNA with the chromophore acting as a molecular beacon.

2-(1-Ethynylpyrene)-adenosine as a folding probe for RNA - pyrene in or out.

A series of short RNA duplexes containing one or two 1-ethynylpyrene-modified adenine bases was synthesised. The melting behaviour of these duplexes was examined by monitoring temperature-dependent pyrene fluorescence. In the singly modified RNA duplexes, the bases flanking the ethynylpyrene-rA were varied to examine the sequence specificity of the fluorescence change of pyrene upon RNA hybridisation. Because an increase in pyrene fluorescence upon melting of the duplex can be correlated with intercalation of pyrene, and a decrease is usually associated with the position of pyrene outside the strand, a relationship between the flanking bases and the tendency of the dye to intercalate has been established. It was found that pyrene intercalation is less likely to take place if the modified base is flanked only by A-U base pairs. Flanking G-C base pairs, even only in the 5'-direction of the modified base, will favour intercalation. In addition, we examined a doubly modified compound that had a pyrene located on each strand. The spectra indicated that the two pyrenes were close enough for interaction. Upon melting of the strand, a fluorescence blue shift corresponding to the dissociation of the pyrene-pyrene complex could be observed in addition to the intensity effect already known from the singly modified compounds. Two melting curves based on the different properties of the fluorophore could be extracted, leading to different melting points corresponding to the global duplex melting and to the change of local pyrene environment, respectively.

RNA as scaffold for pyrene excited complexes.

Synthesis and spectral properties of 1-ethynylpyrene base modified RNA are reported. The fluorophore attached to the 2-position of adenosine is directed into the easily accessible minor groove in RNA. Through an intermolecular interaction of the pyrene residues in twofold labelled RNA, single and double strands can be distinguished by their fluorescence maxima around 450 and 480 nm, respectively. This behaviour allows the kinetic investigation of RNA hybridisation and folding by fluorescence spectroscopy.

Synthesis of pyrene labeled RNA for fluorescence measurements.

The fluorophores 1-ethynylpyrene and 1-(p-ethynyl-phenylethynyl)-pyrene were attached to RNA through a Sonogashira cross-coupling with 5-iodocytidine either in solution through phosphoamidite synthesis or via on-column conjugation during solid-phase oligonucleotide synthesis. Six probes with the sequence 5'-CUU UUC UUU CUU-3' were derivatized with both fluorophores, whereby the position of the modified cytidine was varied. Fluorescence measurements showed sensitivity of the pyrene group to its environment in the single strands and corresponding duplexes.