No-alignment-strategies for exploring a set of two-way data tables obtained from capillary electrophoresis-mass spectrometry

Hyphenated techniques such as capillary electrophoresis-mass spectrometry (CE-MS) or high-performance liquid chromatography with diode array detection (HPLC-DAD), etc., are known to produce a huge amount of data since each sample is characterized by a two-way data table. In this paper different ways of obtaining sample-related information from a set of such tables are discussed. Working with original data requires alignment techniques due to time shifts caused by unavoidable variations in separation conditions. Other pre-processing techniques have been suggested to facilitate comparison among samples without prior peak alignment, for example, 'binning' and/or 'blurring' the data along the time dimension. All these techniques, however, require optimization of some parameters, and in this paper an alternative parameter-free method is proposed. The individual data tables (X) are represented as Gram matrices (XXT), where the summation is taken over the time dimension. Hence the possible variations in time scale are eliminated, while the time information is at least partly preserved by the correlation structure between the detection channels. For comparison among samples, a similarity matrix is constructed and explored by principal component analysis and hierarchical clustering. The Gram matrix approach was tested and compared to some other methods using 'binned' and 'blurred' data for a data set with CE-MS runs on urine samples. In addition to data exploration by principal component analysis and hierarchical clustering, a discriminant partial least squares model was constructed to discriminate between the samples that were taken with and without the prior intake of a drug. The result showed that the proposed method is at least as good as the others with respect to cluster identification and class prediction. A distinct advantage is that there is no need for parameter optimization, while a potential drawback is the large size of the Gram matrices for data with high mass resolution.     

A multiswitchable poly(terthiophene) bearing a spiropyran functionality: understanding photo- and electrochemical control

An electroactive nitrospiropyran-substituted polyterthiophene, poly(2-(3,3'-dimethylindoline-6'-nitrobenzospiropyranyl)ethyl 4,4'-didecyloxy-2,2':5',2'-terthiophene-3'-acetate), has been synthesized for the first time. The spiropyran, incorporated into the polymer backbone by covalent attachment to the alkoxyterthiophene monomer units, leads to multiple colored states as a result of both photochemical and electrochemical isomerization of the spiropyran moiety to merocyanine forms as well as electrochemical oxidation of the polyterthiophene backbone and the merocyanine substituents. While electrochemical polymerization of the terthiophene monomer can take place without oxidation of the spiropyran, increasing the oxidation potential leads to complex electrochemistry that clearly involves this substituent. To understand this complex behavior, the first detailed electrochemical study of the oxidation of the precursor spiropyran, 1-(2-hydroxyethyl)-3,3-dimethylindoline-6'-nitrobenzospiropyran, was undertaken, showing that, in solution, an irreversible electrochemical oxidation of the spiropyran occurs leading to reversible redox behavior of at least two merocyanine isomers. With these insights, an extensive electrochemical and spectroelectrochemical study of the nitrospiropyran-substituted polyterthiophene films reveals an initial irreversible electrochemical oxidative ring-opening of the spiropyran to oxidized merocyanine. Subsequent reduction and cyclic voltammetry of the resulting nitromerocyanine-substituted polyterthiophene film gives rise to the formation of both merocyanine π-dimers or oligomers and π-radical cation dimers, between polymer chains. Although merocyanine formation is not electrochemically reversible, the spiropyran can be photochemically regenerated, through irradiation with visible light. Subsequent electrochemical oxidation of the nitrospiropyran-substituted polymer reduces the efficiency of the spiropyran to merocyanine isomerization, providing electrochemical control over the polymer properties. SEM and AFM images support the conclusion that the bulky spiropyran substituent is electrochemically isomerized to the planar merocyanine moiety, affording a smoother polymer film. The conductivity of the freestanding polymer film was found to be 0.4 S cm(-1).     

A tetranuclear copper(II) cluster: bis(μ‐4‐chlorobenzoato‐κ2O:O′)(4‐chlorobenzoato‐κ2O,O′)(4‐chlorobenzoato‐κO)tetrakis(μ3‐2‐pyridylmethanolato‐κ4N,O:O:O)tetracopper(II)

The title compound, [Cu₄(C₇H₄ClO₂)₄(C₆H₆NO)₄], consists of isolated tetranuclear clusters, where the Cu²⁺ cations are five‐ and sixfold coordinated by O atoms from the 4‐chlorobenzoate anions and by pyridine N and methanolate O atoms from bidentate 2‐pyridylmethanolate ligands. While three Cu atoms are six‐coordinated by an NO₅ donor set forming distorted octahedra, the fourth Cu atom is five‐coordinated by an NO₄ donor set forming a distorted tetragonal–pyramidal coordination around the Cu atom. The nucleus is a deformed cubane‐like Cu₄O₄ structure, with Cu...Cu distances in the range 3.0266 (11)–3.5144 (13) Å.     

A convenient synthesis of 5-(1,2,4-oxadiazol-5-yl)pyrimidine-2,4(1H,3H)-diones

The synthesis of 5-heteroaryl-substituted uracil derivatives is presented. The 1,3-dipolar cycloaddition reaction was applied for the construction of a heterocyclic ring. The nitrile oxides were obtained from the appropriate 4-substituted benzaldoximes using N-chlorosuccinimide (NCS) under basic conditions. [2+3] Cycloaddition of nitrile oxides with 5-cyanouracil as a dipolarophile gave the corresponding 5-(3-substituited-1,2,4-oxadiazol-5-yl)uracils in satisfactory yields under mild conditions. 5-Substituted uracils having an additional heterocyclic ring were obtained as a result of the [2+3] cycloaddition of 5-cyanouracil to nitrile oxides generated from thiophene-2-carbaldehyde and 5-formyluracil derivatives.     

On basis set superposition error corrected stabilization energies for large n-body clusters

In this contribution, we propose an approximate basis set superposition error (BSSE) correction scheme for the site-site function counterpoise and for the Valiron-Mayer function counterpoise correction of second order to account for the basis set superposition error in clusters with a large number of subunits. The accuracy of the proposed scheme has been investigated for a water cluster series at the CCSD(T), CCSD, MP2, and self-consistent field levels of theory using Dunning's correlation consistent basis sets. The BSSE corrected stabilization energies for a series of water clusters are presented. A study regarding the possible savings with respect to computational resources has been carried out as well as a monitoring of the basis set dependence of the approximate BSSE corrections.     

Preparation of Titanium Oxide-Based Nanoparticles Modified with D-(+)-Mannose and Investigation of their Properties As A Potential Drug Carrier

Titanium oxide nanoparticles modified with D-(+)-mannose were obtained. In the process of their formation, they were conjugated with an active substance (tadalafil). The physicochemical properties of the obtained products were assessed, and the size and electrokinetic potential were determined using a dynamic light scattering technique. X-ray diffractometry was applied in order to define the crystalline properties, and Fourier-transform infrared spectroscopy was used to confirm the formation of the desired products. It was possible to obtain TiO₂ coated with D-(+)-mannose. The average size of nanoparticles was between 230 and 268 nm. The release of the active substance from the product over a time period of three hours was assessed against the reference material, which was not modified by D-(+)-mannose. The results indicate that covering titanium oxide nanoparticles with the modifying substance favours a slower rate of release for the active substance, which is the desired effect from a pharmacological point of view. The releasing of active substance from modified products was even 68% slower than that from the reference product. These modified titanium oxides are promising materials that may have found an application as drug carriers.

Graphic Abstract

     

Influence of d-Electron Divalent Metal Ions in Complex Formation with L-Tartaric and L-Malic Acids

Binary complexes of α-hydroxy acids (L-Tartaric acid and L-Malic acid) with d-electron metal ions (copper, cobalt, nickel) were investigated. Potentiometric measurements have been performed in aqueous solution with computer analysis of the data for determination of the stability constants of complexes formed in the studied systems. The coordination mode of the complexes was defined using spectroscopic methods: electron paramagnetic resonance (EPR), ultraviolet-visible (UV-Vis), circular dichroism (CD), and infrared (IR). Results of the equilibrium studies have provided evidence for the formation of dimers with copper(II) ions and monomers with cobalt(II) and nickel(II) ions.     

Distribution and behavior of some radionuclides associated with the Trinity nuclear test

The activities of ¹³³Ba, ¹³⁷Cs, ¹⁵²Eu, ¹⁵⁴Eu, ¹⁵⁵Eu, ²³⁹Pu, and ²⁴¹Am were determined by gamma spectroscopy on the largest sample set (n = 49) of bulk trinitite to date. The range in activity for all isotopes is large. For example, the activity of ²⁴¹Am (normalized to the time of detonation) ranges between 1 and 42 Bq/g. Comparison of activities for isotopes derived from the device, ²⁴¹Am versus ¹³⁷Cs, ¹⁵⁵Eu, and ²³⁹Pu, indicate positive trends. Correlations were not observed between the activities of the soil-derived activation products ¹⁵²Eu and ¹⁵⁴Eu and the radioisotopes from the device. The calculated ratio of fission products (¹⁵⁵Eu/¹³⁷Cs) is 0.012 ± .006 (1σ, n = 3), which is lower than predicted for the thermal neutron-induced fission of ²³⁹Pu (~0.03). This discrepancy may be attributed to the spontaneous fission of the natural U tamper resulting in mixing between fission products from ²³⁹Pu and ²³⁵U. The spatial distribution of the trinitite samples relative to ground zero has been modeled based on the activity of ¹⁵²Eu. The calculated distances do not correlate with any of the activities for the radioisotopes investigated here, and suggest a relatively homogeneous distribution. However, trinitite samples with the highest activities for ¹³⁷Cs, ²³⁹Pu, and ²⁴¹Am yield the shortest calculated distances of 50–60 m away from ground zero.     

Very high frequency EPR — 94 GHz instrument and applications to primary reaction centers from photosynthetic red bacteria and to other disordered systems

There are many advantages to carrying out electron paramagnetic resonance experiments at very high frequencies, either as part of a multifrequency strategy for solving problems or for special characteristics of high frequencies. These special characteristics include the potential for high point sensitivity, enhanced resolution, separation of similar species, altered sensitivity to motion, suppression of motional effects, and many others. This paper describes a three-millimeter-wavelength (W-band, 94 GHz) EPR spectrometer built for a multi-user facility and illustrates with some examples, most of them being disordered systems. One significant example is the oxidized primary reaction center, P ₈₆₅ ⁺ , isolated from the red photosynthetic bacteriaRhodobacter Sphaeroides R-26. The W-band technique applied to both centers isolated from bacteria grown from either deuterated or ordinary growth media allows extraction of the fullg anisotropy in these centers and sets the stage for multifrequency EPR spectroscopy to yield a full analysis of the various contributions to linewidths in these systems.