Abstract: In this manuscript, we compare different analytical methodologies to validate or disprove the binding capabilities of aptamer sequences. This was prompted by the lack of a universally accepted and robust quality control protocol for the characterization of aptamer performances coupled with the observation of independent yet inconsistent data sets in the literature. As an example, we chose three aptamers with a reported affinity in the nanomolar range for ampicillin, a β-lactam antibiotic, used as biorecognition elements in several detection strategies described in the literature. Application of a well-known colorimetric assay based on aggregation of gold nanoparticles (AuNPs) yielded conflicting results with respect to the original report. Therefore, ampicillin binding was evaluated in solution using isothermal titration calorimetry (ITC), native nano-electrospray ionization mass spectrometry (native nESI-MS), and 1H-nuclear magnetic resonance spectroscopy (1H NMR). By coupling the thermodynamic data obtained with ITC with the structural information on the binding event given by native nESI-MS and 1H NMR we could verify that none of the ampicillin aptamers show any specific binding with their intended target. The effect of AuNPs on the binding event was studied by both ITC and 1H NMR, again without providing positive evidence of ampicillin binding. To validate the performance of our analytical approach, we investigated two well-characterized aptamers for cocaine/quinine (MN4), chosen for its nanomolar range affinity, and l-argininamide (1OLD) to show the versatility of our approach. The results clearly indicate the need for a multifaceted analytical approach, to unequivocally establish the actual detection potential and performance of aptamers aimed at small organic molecules.

Abstract: Understanding the electric dipole switching in multiferroic materials requires deep insight of the atomic-scale local structure evolution to reveal the ferroelectric mechanism, which remains unclear and lacks a solid experimental indicator in high-pressure prepared LiNbO3-type polar magnets. Here, we report the discovery of Zn-ion splitting in LiNbO3-type Zn2FeNbO6 established by multiple diffraction techniques. The coexistence of a high-temperature paraelectric-like phase in the polar Zn2FeNbO6 lattice motivated us to revisit other high-pressure prepared LiNbO3-type A(2)BB'O-6 compounds. The A-site atomic splitting (similar to 1.0-1.2 angstrom between the split-atom pair) in B/B'-mixed Zn2FeTaO6 and O/N-mixed ZnTaO2N is verified by both powder X-ray diffraction structural refinements and high angle annular dark field scanning transmission electron microscopy images, but is absent in single-B-site ZnSnO3. Theoretical calculations are in good agreement with experimental results and suggest that this kind of A-site splitting also exists in the B-site mixed Mn-analogues, Mn2FeMO6 (M = Nb, Ta) and anion-mixed MnTaO2N, where the smaller A-site splitting (similar to 0.2 angstrom atomic displacement) is attributed to magnetic interactions and bonding between A and B cations. These findings reveal universal A-site splitting in LiNbO3-type structures with mixed multivalent B/B', or anionic sites, and the splitting-atomic displacement can be strongly suppressed by magnetic interactions and/or hybridization of valence bands between d electrons of the A- and B-site cations.

Abstract: We report the synthesis of colloidal CsPbX3-Pb4S3Br2 (X = Cl, Br, I) nanocrystal heterostructures, providing an example of a sharp and atomically resolved epitaxial interface between a metal halide perovskite and a non-perovskite lattice. The CsPbBr3-Pb4S3Br2 nanocrystals are prepared by a two-step direct synthesis using preformed subnanometer CsPbBr3 clusters. Density functional theory calculations indicate the creation of a quasi-type II alignment at the heterointerface as well as the formation of localized trap states, promoting ultrafast separation of photogenerated excitons and carrier trapping, as confirmed by spectroscopic experiments. Postsynthesis reaction with either Cl- or I- ions delivers the corresponding CsPbCI3-Pb4S3Br2 and CsPbI3-Pb4S3Br2 heterostructures, thus enabling anion exchange only in the perovskite domain. An increased structural rigidity is conferred to the perovskite lattice when it is interfaced with the chalcohalide lattice. This is attested by the improved stability of the metastable gamma phase (or “black” phase) of CsPbI3 in the CsPbI3-Pb4S3Br2 heterostructure.

Abstract: The organic components in metal-organic frameworks (MOFs) are unique: they are embedded in a crystalline lattice, yet, as they are separated from each other by tunable free space, a large variety of dynamic behavior can emerge. These rotational dynamics of the organic linkers are especially important due to their influence over properties such as gas adsorption and kinetics of guest release. To fully exploit linker rotation, such as in the form of molecular machines, it is necessary to engineer correlated linker dynamics to achieve their cooperative functional motion. Here, we show that for MIL-53, a topology with closely spaced rotors, the phenylene functionalization allows researchers to tune the rotors' steric environment, shifting linker rotation from completely static to rapid motions at frequencies above 100 MHz. For steric interactions that start to inhibit independent rotor motion, we identify for the first time the emergence of coupled rotation modes in linker dynamics. These findings pave the way for function-specific engineering of gear-like cooperative motion in MOFs.

Abstract: In order to increase the accuracy of the linearized augmented plane wave (LAPW) method, we present a new approach where the plane wave basis function is augmented by two different atomic radial components constructed at two different linearization energies corresponding to two different electron bands (or energy windows). We demonstrate that this case can be reduced to the standard treatment within the LAPW paradigm where the usual basis set is enriched by the basis functions of the tight binding type, which go to zero with zero derivative at the sphere boundary. We show that the task is closely related with the problem of extended core states which is currently solved by applying the LAPW method with local orbitals (LAPW+LO). In comparison with LAPW+LO, the number of supplemented basis functions in our approach is doubled, which opens up a new channel for the extension of the LAPW and LAPW+LO basis sets. The appearance of new supplemented basis functions absent in the LAPW+LO treatment is closely related with the existence of the ul-component in the canonical LAPW method. We discuss properties of additional tight binding basis functions and apply the extended basis set for computation of electron energy bands of lanthanum (face and body centered structures) and hexagonal close packed lattice of cadmium. We demonstrate that the new treatment gives lower total energies in comparison with both canonical LAPW and LAPW+LO, with the energy difference more pronounced for intermediate and poor LAPW basis sets.

Abstract: In this work, we have fabricatedan aryl amino-substitutedgraphiticcarbon nitride (g-C3N4) catalyst with atomicallydispersed Mn capable of generating hydrogen peroxide (H2O2) directly from seawater. This new catalyst exhibitedexcellent reactivity, obtaining up to 2230 & mu;M H2O2 in 7 h from alkaline water and up to 1800 & mu;Mfrom seawater under identical conditions. More importantly, the catalystwas quickly recovered for subsequent reuse without appreciable lossin performance. Interestingly, unlike the usual two-electron oxygenreduction reaction pathway, the generation of H2O2 was through a less common two-electron water oxidation reaction(WOR) process in which both the direct and indirect WOR processesoccurred; namely, photoinduced h(+) directly oxidized H2O to H2O2 via a one-step 2e(-) WOR, and photoinduced h(+) first oxidized a hydroxide (OH-) ion to generate a hydroxy radical ((OH)-O-& BULL;), and H2O2 was formed indirectly by thecombination of two (OH)-O-& BULL;. We have characterized thematerial, at the catalytic sites, at the atomic level using electronparamagnetic resonance, X-ray absorption near edge structure, extendedX-ray absorption fine structure, high-resolution transmission electronmicroscopy, X-ray photoelectron spectroscopy, magic-angle spinningsolid-state NMR spectroscopy, and multiscale molecular modeling, combiningclassical reactive molecular dynamics simulations and quantum chemistrycalculations.

Abstract: Epitaxial heterostructures of two-dimensional (2D) halide perovskites offer a new platform for studying intriguing structural, optical, and electronic properties. However, difficulties with the stability of Pb- and Sn-based heterostructures have repeatedly slowed the progress. Recently, Pb-free halide double perovskites are gaining a lot of attention due to their superior stability and greater chemical diversity, but they have not been successfully incorporated into epitaxial heterostructures for further investigation. Here, we report epitaxial core-shell heterostructures via growing Pb-free double perovskites (involving combinations of Ag(I)-Bi(III), Ag-Sb, Ag-In, Na-Bi, Na-Sb, and Na-In) around Pb perovskite 2D crystals. Distinct from Pb-Pb and Pb-Sn perovskite heterostructures, growths of the Pb-free shell at 45 degrees on the (100) surface of the lead perovskite core are observed in all Pb-free cases. The in-depth structural analysis carried out with electron diffraction unequivocally demonstrates the growth of the Pb-free shell along the [110] direction of the Pb perovskite, which is likely due to the relatively lower surface energy of the (110) surface. Furthermore, an investigation of anionic interdiffusion across heterostructure interfaces under the influence of heat was carried out. Interestingly, halide anion diffusion in the Pb-free 2D perovskites is found to be significantly suppressed as compared to Pb-based 2D perovskites. The great structural tunability and excellent stability of Pb-free perovskite heterostructures may find uses in electronic and optoelectronic devices in the near future.

Abstract: Convergent beam electron diffraction (CBED) is used in this study to investigate the stress distribution around shallow trench isolation (STI) structures. Attention is given to the influence of the different processing parameters and the width and spacing of the structures. The use of a wet or a dry pregate oxidation is found to have a strong influence on the stress behavior. Isolated lines show more stress, leading to the formation of defects in the silicon substrate if a wet pregate oxidation is used. The CBED analyses are compared with micro-Raman and bright-field transmission electron microscopy measurements. (C) 2001 The Electrochemical Society.

Abstract: Using first principles calculations, we study the structural and phononic properties of the recently synthesized Janus type single layers of molybdenum dichalcogenides. The Janus MoSSe single layer possesses 2H crystal structure with two different chalcogenide sides that lead to out-of-plane anisotropy. By virtue of the asymmetric structure of the ultra-thin Janus type crystal, we induced the out-of-plane anisotropy to show the distinctive vertical pressure effect on the vibrational properties of the Janus material. It is proposed that for the corresponding Raman active optical mode of the Janus structure, the phase modulation and the magnitude ratio of the strained atom and its first neighbor atom adjust the distinctive change in the eigen-frequencies and Raman activity. Moreover, a strong variation in the Raman activity of the Janus structure is obtained under bivertical and univertical strains. Not only eigen-frequency shifts but also Raman activities of the optical modes of the Janus structure exhibit distinguishable features. This study reveals that the vertical anisotropic feature of the Janus structure under Raman measurement allows us to distinguish which side of the Janus crystal interacts with the externals (substrate, functional adlayers, or dopants). Published by AIP Publishing.

Abstract: Infrared absorption spectra of oxygen precipitates in boron-doped silicon with a boron concentration between 10(17) and 10(19) cm(-3) are analyzed, applying the spectral function representation of composite materials. The aspect ratio of the platelet precipitates is determined by transmission electron microscopy measurements. The analysis shows that in samples with moderate doping levels (<10(18) B cm(-3)) SiOγ precipitates are formed with the same composition as in the lightly doped case. In the heavily boron-doped (>10(18) cm(-3)) samples, however, the measured spectra of the precipitates are consistent with a mixture of SiO2 and B2O3, with a volume fraction of B2O3 as high as 0.41 in the most heavily doped case. (C) 2004 The Electrochemical Society.

Abstract: By means of density functional theory based first-principles calculations, the structural, vibrational, and electronic properties of 1H- and 1T-phases of single-layer CaX2 (X = F, Cl, Br, or I) structures are investigated. Our results reveal that both the 1H- and 1T-phases are dynamically stable in terms of their phonon band dispersions with the latter being the energetically favorable phase for all single-layers. In both phases of single-layer CaX2 structures, significant phonon softening occurs as the atomic radius increases. In addition, each structural phase exhibits distinctive Raman active modes that enable one to characterize either the phase or the structure via Raman spectroscopy. The electronic band dispersions of single-layer CaX2 structures reveal that all structures are indirect bandgap insulators with a decrease in bandgaps from fluorite to iodide crystals. Furthermore, the calculated linear elastic constants, in-plane stiffness, and Poisson ratio indicate the ultra-soft nature of CaX2 single-layers, which is quite important for their nanoelastic applications. Overall, our study reveals that with their dynamically stable 1T- and 1H-phases, single-layers of CaX2 crystals can be alternative ultra-thin insulators.

Abstract: Atomistic simulation methods for the quantification of free energies are in wide use. These methods operate by sampling the probability density of a system along a small set of suitable collective variables (CVs), which is, in turn, expressed in the form of a free energy surface (FES). This definition of the FES can capture the relative stability of metastable states but not that of the transition state because the barrier height is not invariant to the choice of CVs. Free energy barriers therefore cannot be consistently computed from the FES. Here, we present a simple approach to calculate the gauge correction necessary to eliminate this inconsistency. Using our procedure, the standard FES as well as its gauge-corrected counterpart can be obtained by reweighing the same simulated trajectory at little additional cost. We apply the method to a number of systems—a particle solvated in a Lennard-Jones fluid, a Diels–Alder reaction, and crystallization of liquid sodium—to demonstrate its ability to produce consistent free energy barriers that correctly capture the kinetics of chemical or physical transformations, and discuss the additional demands it puts on the chosen CVs. Because the FES can be converged at relatively short (sub-ns) time scales, a free energy-based description of reaction kinetics is a particularly attractive option to study chemical processes at more expensive quantum mechanical levels of theory.

Abstract: The evaluation of nucleation rates from molecular dynamics trajectories is hampered by the slow nucleation time scale and impact of finite size effects. Here, we show that accurate nucleation rates can be obtained in a very general fashion relying only on the free energy barrier, transition state theory, and a simple dynamical correction for diffusive recrossing. In this setup, the time scale problem is overcome by using enhanced sampling methods, in casu metadynamics, whereas the impact of finite size effects can be naturally circumvented by reconstructing the free energy surface from an appropriate ensemble. Approximations from classical nucleation theory are avoided. We demonstrate the accuracy of the approach by calculating macroscopic rates of droplet nucleation from argon vapor, spanning 16 orders of magnitude and in excellent agreement with literature results, all from simulations of very small (512 atom) systems.