Polymorphs and pseudo‐polymorphs of μ‐oxo‐bis{[N,N′‐bis(salicylidene)­propane‐1,3‐diamine]oxorhenium(V)}

Two new polymorphs of the title compound, μ‐oxo‐bis{oxo{2,2′‐[propane‐1,3‐diyl­bis­(nitrilo­methyl­idyne)]­diphen­olato}rhenium(V)}, [Re₂O(C₁₇H₁₆N₂O₃)₂], are reported, containing either a conformation other than the one already known in the literature or a disorder involving both the new and the previously reported conformations. Four pseudo‐polymorphs of the title compound are also reported, containing four chloro­form, two chloro­form, two disordered di­chloro­methane or two water solvate mol­ecules accompany­ing each Re complex molecule. Only in the hydrate does the Re complex adopt the old conformation. In all six structures, the complex molecule is located on a crystallographic inversion centre. Independent of the conformation, all ReV ions display the same, somewhat distorted, octahedral coordination. In all the solvates, hydrogen bonds are donated from the solvent to the O atoms bonded to Re, either of the C—H?O or O—H?O type, although the actual position of the solvent mol­ecule can vary. Only in the hydrate is a two‐dimensional hydrogen‐bonded network found; isolated clusters are formed in all the other solvates.     

Graphs, spectral triples and Dirac zeta functions

To a finite, connected, unoriented graph of Betti-number g ≥ 2 and valencies ≥ 3 we associate a finitely summable, commutative spectral triple (in the sense of Connes), whose induced zeta functions encode the graph. This gives another example where non-commutative geometry provides a rigid framework for classification.     

A note on iterated splitting schemes

Iterated splittings seem attractive in view of consistency and local accuracy. In this note it will be shown, however, that for stiff systems the stability properties are quite poor. Specific Runge–Kutta implementations can improve stability, but this leads to classes of methods that are better studied in their own right.     

An efficient synthesis of 4-bromo-N-substituted oxindoles by an intramolecular copper-catalyzed amidation reaction

A highly efficient synthetic approach to novel 4-bromo-N-substituted oxindoles is described. The method involves a mild intramolecular copper-catalyzed amidation reaction of N-substituted 2,6-dibromophenylacetamides. In contrast to our recently published palladium-catalyzed amidation reaction, no concomitant dimerization on the 3-position of the formed oxindole occurs.     

Learning to rank: a ROC-based graph-theoretic approach

This note summarizes the main results presented in the author’s Ph.D. thesis, supervised by Luc Boullart and Bernard De Baets. The thesis was defended on 14th October 2008 at Universiteit Gent. It is written in English and available for download at . The work deals with preference learning, with emphasis on the ranking and ordinal regression machine learning settings and their connections to decision theory. Based on receiver operator characteristics analysis and graph theory, new performance measures are proposed to evaluate this type of models, and new algorithms are presented to compute and optimize these performance measures efficiently. Furthermore, the relationship with other settings like pairwise preference learning and multi-class classification is discussed.     

Functional neural network analysis in frontotemporal dementia and Alzheimer's disease using EEG and graph theory

Background  

Although a large body of knowledge about both brain structure and function has been gathered over the last decades, we still have a poor understanding of their exact relationship. Graph theory provides a method to study the relation between network structure and function, and its application to neuroscientific data is an emerging research field. We investigated topological changes in large-scale functional brain networks in patients with Alzheimer's disease (AD) and frontotemporal lobar degeneration (FTLD) by means of graph theoretical analysis of resting-state EEG recordings. EEGs of 20 patients with mild to moderate AD, 15 FTLD patients, and 23 non-demented individuals were recorded in an eyes-closed resting-state. The synchronization likelihood (SL), a measure of functional connectivity, was calculated for each sensor pair in 0.5–4 Hz, 4–8 Hz, 8–10 Hz, 10–13 Hz, 13–30 Hz and 30–45 Hz frequency bands. The resulting connectivity matrices were converted to unweighted graphs, whose structure was characterized with several measures: mean clustering coefficient (local connectivity), characteristic path length (global connectivity) and degree correlation (network 'assortativity'). All results were normalized for network size and compared with random control networks.     

Redshifted and Near‐infrared Active Analog Pigments Based upon Archaerhodopsin‐3

Archaerhodopsin‐3 (AR3) is a member of the microbial rhodopsin family of hepta‐helical transmembrane proteins, containing a covalently bound molecule of all‐trans retinal as a chromophore. It displays an absorbance band in the visible region of the solar spectrum (λmax 556 nm) and functions as a light‐driven proton pump in the archaeon Halorubrum sodomense. AR3 and its mutants are widely used in neuroscience as optogenetic neural silencers and in particular as fluorescent indicators of transmembrane potential. In this study, we investigated the effect of analogs of the native ligand all‐trans retinal A1 on the spectral properties and proton‐pumping activity of AR3 and its single mutant AR3 (F229S). While, surprisingly, the 3‐methoxyretinal A2 analog did not redshift the absorbance maximum of AR3, the analogs retinal A2 and 3‐methylamino‐16‐nor‐1,2,3,4‐didehydroretinal (MMAR) did generate active redshifted AR3 pigments. The MMAR analog pigments could even be activated by near‐infrared light. Furthermore, the MMAR pigments showed strongly enhanced fluorescence with an emission band in the near‐infrared peaking around 815 nm. We anticipate that the AR3 pigments generated in this study have widespread potential for near‐infrared exploitation as fluorescent voltage‐gated sensors in optogenetics and artificial leafs and as proton pumps in bioenergy‐based applications.     

Triple-ion interactions for the construction of supramolecular capsules

A novel type of [2+4] capsules based on triple-ion interactions was obtained. Four monovalent anions (bromide, nitrate, acetate, and tosylate) bring together two tetrakis(pyridiniummethyl)tetramethyl cavitands by pyridinium-anion-pyridinium interactions. ESI-MS experiments have confirmed the capsule structure due to different fragmentation pathways of triple ions, cations, and ion-pairs. Each capsule encapsulates one or two anions, depending on its size. The capsules exist in equilibrium with hemicapsules containing three walls. The latter form complexes with phenols and anilines to give new unsymmetrical capsules containing both pyridinium-anion-pyridinium and pyridinium-guest-pyridinium walls.     

Accurate measurements of 13C-13C J-couplings in the rhodopsin chromophore by double-quantum solid-state NMR spectroscopy

A new double-quantum solid-state NMR pulse sequence is presented and used to measure one-bond 13C-13C J-couplings in a set of 13C2-labeled rhodopsin isotopomers. The measured J-couplings reveal a perturbation of the electronic structure at the terminus of the conjugated chain but show no evidence for protein-induced electronic perturbation near the C11-C12 isomerization site. This work establishes NMR methodology for measuring accurate 1JCC values in noncrystalline macromolecules and shows that the measured J-couplings may reveal local electronic perturbations of mechanistic significance.     

Precursors of biological cofactors from ultraviolet irradiation of circumstellar/interstellar ice analogues

Biological cofactors include functionalized derivatives of cyclic tetrapyrrole structures that incorporate different metal ions. They build up structural partnerships with proteins, which play a crucial role in biochemical reactions. Porphyrin, chlorin, bacteriochlorin, and corrin are the basic structures of cofactors (heme, chlorophyll, bacteriochlorophyll, siroheme, F 430, and vitamin B12). Laboratory and theoretical work suggest that the molecular building blocks of proteins (alpha-amino acids) and nucleic acids (carbohydrates, purines, and pyrimidines) were generated under prebiotic conditions. On the other hand, experimental data on the prebiotic chemistry of cofactors are rare. We propose to search directly for the pathways of the formation of cofactors in the laboratory. Herein we report on the detection of N-heterocycles and amines in the room-temperature residue obtained after photo- and thermal processing of an interstellar ice analogue under high vacuum at 12 K. Among them, hexahydro-1,3,5-triazine and its derivatives, together with monopyrrolic molecules, are precursors of porphinoid cofactors. Hexahydropyrimidine was also detected. This is the first detection of these compounds in experiments simulating circumstellar/interstellar conditions. Except for 2-aminopyrrole and 2,4-diaminofuran, which were only found in 13C-labeled experiments, all the reported species were detected in both 12C- and 13C-labeled experiments, excluding contamination. The molecules reported here might be present in circumstellar/interstellar grains and cometary dust and could be detected by the Stardust and Rosetta missions.