vdW-TSSCDS—An automated and global procedure for the computation of stationary points on intermolecular potential energy surfaces

We present a generalization of the transition state search using chemical dynamics simulations (TSSCDS) methodology (discussed in a previous study) which allows the topographical characterization of intermolecular potential energy surfaces (IPES) for non-covalently bound complexes (vdW-TSSCDS). Starting from a single random input geometry, we show that vdW-TSSCDS is able to globally and automatically locate stationary points of an IPES, even in limiting cases such as extremely flat regions or nontrivial topologies (eg, bifurcation points). The basic idea is the expression of the connectivity matrix in block structure, where diagonal blocks correspond to the isolated fragments and off-diagonal blocks provide the intermolecular connectivity. To this end, we introduce a new definition of bound or not, in a non-covalent sense, utilizing an extra set of van der Waals distances, which encompasses all kinds of non-covalent distances. To discuss the use of the vdW-TSSCDS method, we present a series of 2-body van der Waals systems, namely, Ar-Benzene (3D), N₂-Benzene (6D) and H₂O-Benzene (9D). Finally, we further illustrate its capabilities by presenting some applications for n-body problems (n > 2), (H₂O)₂-Benzene (12D) and (H₂O)₃-Benzene (21D), as well as to a reactive, fully-flexible, system (Benzene-NO₂)⁺ (39D) in which the simultaneous breaking/formation of both covalent and non-covalent interactions takes place.     

The Reactivity of Cr‐Te Superlattice Reactants and of Co‐deposited Cr‐Te Films: Studies with in‐situ X‐ray Diffractometry

The reactivity of a Cr‐Te multilayer film consisting of 326 Cr/Te double‐layers with about 88(3) at% Te was investigated with in‐situ X‐ray diffraction. The occurrence of a superstructure reflection caused by the multilayer system is observed. During the annealing procedure between 80 and 90 °C the layer‐by‐layer arrangement is destroyed and elemental Te crystallizes. After 6 h isothermal annealing at 140 °C CrTe₃ starts to crystallize. The amount and the crystal size of CrTe₃ increase with raising temperature and Te is consumed during the growth process. At 220 °C the formation of crystalline Cr₂Te₃ is observed and between 220 and 260 °C CrTe₃ is completely decomposed into Cr₂Te₃. The two Cr tellurides grow as highly textured materials. The size of CrTe₃ crystals is significantly larger than that of Cr₂Te₃. For a co‐deposited Cr‐Te film with composition 77(3) at% Te the tri‐telluride and elemental Te crystallize simultaneously. The texture of CrTe₃ is less pronounced and different reflections of the tri‐telluride occur besides the (h00)‐reflections. Up to 160 °C a pronounced increase of the crystallite size is observed and the crystals are significantly larger than those obtained with the multifilm sample. At 130 °C the crystallization kinetics seem to be controlled by nucleation.     

Structural Investigation of New Lithium Amidinates and Guanidinates

A series of potentially useful lithium amidinates and guanidinates were prepared and fully characterized. Treatment of N,N′‐diisopropylcarbodiimide with phenyllithium in diethyl ether afforded the lithium amidinate [PhC(NiPr)₂Li(OEt₂)]₂ ( 1 ). Similar treatment of N,N′‐diorganocarbodiimides R′–N=C=N–R′ [R′ = iPr, cyclohexyl (Cy)] with secondary lithium amides LiNR₂ [R₂ = Et₂, iPr₂, (CH₂)₄] followed by crystallization from THF or 1,4‐dioxane gave the lithium guanidinates [R₂NC(NR′)₂Li(S)]₂ [ 2 : R = Et, R′ = iPr, S = THF; 3 : R₂ = (CH₂)₄, R′ = iPr, S = THF; 4 : R = R′ = iPr, S = ½ 1,4‐dioxane; 5 : R₂ = (CH₂)₄, R′ = Cy, S = 1,4‐dioxane] as crystalline solids. Reaction of N‐lithioaziridine with the corresponding carbodiimides afforded solvent‐deficient [{C₂H₄NC(NiPr₂)₂}₂Li₂(THF)]₂ ( 6 ), and [C₂H₄NC(NEt)(NtBu)Li(THF)]₂ ( 7 ). Crystal structure determination revealed the presence of common ladder‐type dimeric structures for 1 – 5 . Compound 6 exists as a dimer of two ladder‐type dimers in the crystal, and 7 exhibits an unusual dimeric structure comprising an eight‐membered C₂N₄Li₂ ring.     

Guest‐Assisted Proton Conduction in the Sulfonic Mesoporous MIL‐101 MOF

Post‐synthesis modification of MIL‐101(Cr)‐NO₂ was explored in order to decorate the organic backbone by propyl‐sulfonic groups, with the aim to incorporate mobile and acidic protons for solid‐state proton electrolyte applications. The resulting solid switched from insulating towards proton superconductive behavior under humidity, while the conductivity recorded at 363 K and 95 % relative humidity reached 4.8×10^?3 S cm^?1. Propitiously, the impregnation of the material by strong acidic molecules (H₂SO₄) further boosted the proton conductivity performances up to the remarkable σ value of 1.3×10^?1 S cm^?1 at 363 K/95 % RH, which reaches the performances of the best proton conductive MOF reported so far.     

Stability of the gold/silica thin film interface: electrochemical and surface plasmon resonance studies

This article reports chemical stability studies of a gold film electrode coated with thin silicon oxide (SiOx) layers using electrochemical, surface plasmon resonance (SPR) and atomic force microscopy (AFM) techniques. Silica films with different thicknesses (d = 6.4, 9.7, 14.5, and 18.5 nm) were deposited using a plasma-enhanced chemical vapor deposition technique (PECVD). For SiOx films with d >/= 18.5 nm, the electrochemical behavior is characteristic of a highly efficient barrier for a redox probe. SiOx films with thicknesses between 9.5 and 14.5 nm were found to be less efficient barriers for electron transfer. The Au/SiOx interface with 6.4 nm of SiOx, however, showed an enhanced steady-state current compared to that of the other films. The stability of this interface in solutions of different pH was investigated. Whereas a strongly basic solution led to a continuous dissolution of the SiOx interface, acidic treatment produced a more reticulated SiOx film and improved electrochemical behavior. The electrochemical results were corroborated by SPR measurements in real time and AFM studies.     

Structural change of the heme pocket due to disulfide bridge formation is significantly larger for neuroglobin than for cytoglobin

Human neuroglobin (hNgb) and human cytoglobin (hCygb), two recently discovered members of the vertebrate globin family, are known to be able to form an intramolecular disulfide bridge. Using electron paramagnetic resonance (EPR), we show that formation of a disulfide bridge in ferric hNgb causes a considerable change in the heme pocket structure, whereas this is not so clear for ferric hCygb. The structural results can be related nicely to earlier histidine and dioxygen affinity studies of the ferrous proteins.     

Determination of the LOQ in real-time PCR by receiver operating characteristic curve analysis: application to qPCR assays for Fusarium verticillioides and F. proliferatum

Real-time PCR (qPCR) is the principal technique for the quantification of pathogen biomass in host tissue, yet no generic methods exist for the determination of the limit of quantification (LOQ) and the limit of detection (LOD) in qPCR. We suggest using the Youden index in the context of the receiver operating characteristic (ROC) curve analysis for this purpose. The LOQ was defined as the amount of target DNA that maximizes the sum of sensitivity and specificity. The LOD was defined as the lowest amount of target DNA that was amplified with a false-negative rate below a given threshold. We applied this concept to qPCR assays for Fusarium verticillioides and Fusarium proliferatum DNA in maize kernels. Spiked matrix and field samples characterized by melting curve analysis of PCR products were used as the source of true positives and true negatives. On the basis of the analysis of sensitivity and specificity of the assays, we estimated the LOQ values as 0.11 pg of DNA for spiked matrix and 0.62 pg of DNA for field samples for F. verticillioides. The LOQ values for F. proliferatum were 0.03 pg for spiked matrix and 0.24 pg for field samples. The mean LOQ values correspond to approximately eight genomes for F. verticillioides and three genomes for F. proliferatum. We demonstrated that the ROC analysis concept, developed for qualitative diagnostics, can be used for the determination of performance parameters of quantitative PCR.     

Nanomolar hydrogen peroxide detection using horseradish peroxidase covalently linked to undoped nanocrystalline diamond surfaces

In this article, we report on the low-level detection of hydrogen peroxide, a key player in the redox signaling pathway and a toxic product in the cellular system, using a colorimetric solution assay. Amine-terminated undoped nanocrystalline diamond thin films were grown on glass using a linear-antenna microwave plasma CVD process. The diamond surface consists mainly of -NH(2) termination. The aminated diamond surface was decorated with horseradish peroxidase (HRP) enzyme using carbodiimide coupling chemistry. The success of the HRP immobilization was confirmed by X-ray photoelectron spectroscopy (XPS). The enzymatic activity of immobilized HRP was determined with a colorimetric test based on the HRP-catalyzed oxidation of 2,2'-azino-bis(3-ethylbenzothiazoline-6-sufonic acid (ABTS) in the presence of hydrogen peroxide. The surface coverage of active HRP was estimated to be Γ = 7.3 × 10(13) molecules cm(-2). The use of the functionalized diamond surface as an optical sensor for the detection of hydrogen peroxide with a detection limit of 35 nM was demonstrated.     

Triphenylene silanes for direct surface anchoring in binary mixed self-assembled monolayers

New triphenylene-based silanes 2-(ω-(chlorodimethylsilyl)-n-alkyl)-3,6,7,10,11-penta-m-alkoxytriphenylene 4 (Tm-Cn) with n = 8 or 9 and m = 7, 8, 9, 10, or 11 were synthesized, and their self-assembly behavior in the liquid state and at glass and silicon oxide surfaces was investigated. The mesomorphic properties of triphenylene silanes 4 (Tm-Cn) and their precursors 3 (Tm-Cn) were determined by differential scanning calorimetry (DSC), polarizing optical microscopy (POM), and X-ray diffraction. From the small-angle X-ray scattering (SAXS) regime, a preferential discotic lamellar mesophase can be deduced, and wide-angle X-ray scattering (WAXS) highlights the liquid-like characteristics of the alkyl side chains. To transfer these bulk structural properties to thin films, self-assembled monolayers (SAMs) were obtained by adsorption from solution and characterized by water contact angle measurements, null ellipsometry, and atomic force microscopy (AFM). Employing the concentration as an additional degree of freedom, binary SAMs of 2-(ω-(chlorodimethylsilyl)-undecyl)-3,6,7,10,11-penta-decyloxytriphenylene 4 (T10-C11) were coassembled with chlorodecyldimethylsilane or chlorodimethyloctadecylsilane, and their capability as model systems for organic templating was evaluated. The structure of the resulting binary mixed SAMs was analyzed by water contact angle measurements, null ellipsometry, and X-ray reflectivity (XRR) in combination with theoretical modeling by a multidimensional Parratt algorithm and AFM. The composition dependence of film thickness and roughness can be explained by a microscopic model including the steric hindrance of the respective molecular constituents.