The Resolved Mutual Information Function as a Structural Fingerprint of Biomolecular Sequences for Interpretable Machine Learning Classifiers

In the present article we propose the application of variants of the mutual information function as characteristic fingerprints of biomolecular sequences for classification analysis. In particular, we consider the resolved mutual information functions based on Shannon-, Rényi-, and Tsallis-entropy. In combination with interpretable machine learning classifier models based on generalized learning vector quantization, a powerful methodology for sequence classification is achieved which allows substantial knowledge extraction in addition to the high classification ability due to the model-inherent robustness. Any potential (slightly) inferior performance of the used classifier is compensated by the additional knowledge provided by interpretable models. This knowledge may assist the user in the analysis and understanding of the used data and considered task. After theoretical justification of the concepts, we demonstrate the approach for various example data sets covering different areas in biomolecular sequence analysis.     

Potential‐induced optimization of ultra‐thin rear surface passivated CIGS solar cells

Ultra‐thin Cu(In,Ga)Se₂ (CIGS) solar cells with an Al₂O₃ rear surface passivation layer between the rear contact and absorber layer frequently show a “roll‐over” effect in the J–V curve, lowering the open circuit voltage (V_OC), short circuit current (J_SC) and fill factor (FF), similar to what is observed for Na‐deficient devices. Since Al₂O₃ is a well‐known barrier for Na, this behaviour can indeed be interpreted as due to lack of Na in the CIGS absorber layer. In this work, applying an electric field between the backside of the soda lime glass (SLG) substrate and the SLG/rear‐contact interface is investi‐gated as potential treatment for such Na‐deficient rear surface passivated CIGS solar cells. First, an electrical field of +50 V is applied at 85 °C, which increases the Na concentration in the CIGS absorber layer and the CdS buffer layer as measured by glow discharge optical emission spectroscopy (GDOES). Subsequently, the field polarity is reversed and part of the previously added Na is removed. This way, the J –V curve roll‐over related to Na deficiency disappears and the V_OC (+25 mV), J_SC(+2.3 mA/cm²) and FF (+13.5% absolute) of the rear surface passivated CIGS solar cells are optimized. (© 2014 WILEY‐VCH Verlag GmbH &Co. KGaA, Weinheim)     

Fluorescence lifetimes and quantum yields of rhodamine derivatives: new insights from theory and experiment

Although lifetimes and quantum yields of widely used fluorophores are often largely characterized, a systematic approach providing a rationale of their photophysical behavior on a quantitative basis is still a challenging goal. Here we combine methods rooted in the time-dependent density functional theory and fluorescence lifetime imaging microscopy to accurately determine and analyze fluorescence signatures (lifetime, quantum yield, and band peaks) of several commonly used rhodamine and pyronin dyes. We show that the radiative lifetime of rhodamines can be correlated to the charge transfer from the phenyl toward the xanthene moiety occurring upon the S(0) ← S(1) de-excitation, and to the xanthene/phenyl relative orientation assumed in the S(1) minimum structure, which in turn is variable upon the amino and the phenyl substituents. These findings encourage the synergy of experiment and theory as unique tool to design finely tuned fluorescent probes, such those conceived for modern optical sensors.     

Snapshot of the palladium(II)-catalyzed oxidative biaryl bond formation by X-ray analysis of the intermediate diaryl palladium(II) complex

Pd(II) caught in the act: The diaryl Pd(II) intermediate of a Pd(II)-catalyzed oxidative biaryl bond formation proceeding via a double C-H bond activation has been isolated and fully characterized, including an X-ray crystal structure analysis. Stabilization due to chelation by adjacent pivaloyloxy and acetyl groups has allowed the isolation of this long-sought crucial intermediate. On gentle warming, the complex is transformed into a carbazole product, and the catalytically active Pd(II) species is regenerated by oxidation with Cu(II).     

The first water‐soluble copper(I) complexes bearing sulfonated imidazole‐ and benzimidazole‐derived N‐heterocyclic carbenes: Synthesis and anticancer studies

The first water‐soluble bis(NHC^SO3)CuCl complexes (NHC^SO3 = NaIm^Bn,PrSO3, Na₂(4‐Me)Im^PrSO3 and Na₂BzIm^PrSO3) derived from the sulfonated N‐heterocyclic carbene precursors HIm^Bn,PrSO3 (3‐(1‐benzyl‐1H‐imidazol‐3‐ium‐3‐yl)propane‐1‐sulfonate), Na(4‐Me)HIm^PrSO3 (sodium 3,3′‐(4‐methyl‐1H‐imidazole‐3‐ium‐1,3‐diyl)dipropane‐1‐sulfonate) and NaHBzIm^PrSO3 (sodium 3,3′‐(1H‐benzoimidazole‐3‐ium‐1,3‐diyl)dipropane‐1‐sulfonate) have been synthesized. These compounds have been characterized using infrared and NMR spectroscopy and electrospray ionization mass spectrometry. The in vitro anti‐tumour effects of the bis(NHC^SO3)CuCl complexes and the corresponding free ligands were evaluated for a panel of various human tumour cell lines, including examples of lung, colon, ovarian and cervical carcinoma as well as of melanoma. Their cytotoxic properties were also evaluated against non‐transformed human cells and on a cellular model of cisplatin resistance. NHC–copper complexes induced cell killing effects preferentially against tumour cells, with IC₅₀ values in the micromolar range. Additionally, they were found able to overcome acquired cisplatin resistance.     

The interaction of highly helical structural mutants with the NOP receptor discloses the role of the address domain of nociceptin/orphanin FQ

Nociceptin is a heptadecapeptide whose sequence is similar to that of Dynorphin A, sharing a message domain characterized by two glycines and two aromatic residues, and a highly basic C-terminal address domain but, in spite of these similarities, displays no opioid activity. Establishing the relative importance of the message and address domains of nociceptin has so far been hampered by its extreme conformational flexibility. Here we show that mutants of this peptide, designed to increase the helical content in the address domain, can be employed to explain the mode of interaction with the NOP receptor. Nociceptin analogues in which Ala residues are substituted with aminoisobutyric acid (Aib) show a substantial increment of activity in their interaction with the NOP receptor. The increment of biological activity was attributed to the well-documented ability of Aib to induce helicity. Here we have verified this working hypothesis by a conformational investigation extended to new analogues in which the role of Aib is taken up by Leu. The NMR conformational analysis confirms that all Ala/Aib peptides as well as [Leu(7,11)]-N/OFQ-amide and [Leu(11,15)]-N/OFQ-amide mutants (N/OFQ=nociceptin/orphanin FQ) have comparable helix content in helix-promoting media. We show that the helical address domain of nociceptin can place key basic residues at an optimal distance from complementary acidic groups of the EL(2) loop of the receptor. Our structural data are used to rationalize pharmacological data which show that although [Leu(11,15)]-N/OFQ-amide has an activity comparable to those of Ala/Aib peptides, [Leu(7,11)]-N/OFQ-amide is less active than N/OFQ-amide. We hypothesize that bulky residues cannot be hosted in or near the hinge region (Thr(5)-Gly(6)-Ala(7)) without severe steric clash with the receptor. This hypothesis is also consistent with previous data on this hinge region obtained by systematic substitution of Thr, Gly, and Ala with Pro.     

The fluorescence properties and NMR analysis of protopine and allocryptopine

The fluorescence properties of protopine and allocryptopine in aqueous and organic environments are described for the first time. The fluorescence of alkaloids and their pH-dependent interconversion to cationic forms (transannular interaction) were studied using steady-state and time-resolved fluorescence techniques. For the analysis of tricyclic base and cis/trans tetracyclic cations of the alkaloids, NMR and X-ray crystallography were used.