Analysis of rapidly synthesized guest-filled porous complexes with synchrotron radiation: practical guidelines for the crystalline sponge method

A detailed set of synthetic and crystallographic guidelines for the crystalline sponge method based upon the analysis of expediently synthesized crystal sponges using third-generation synchrotron radiation are reported. The procedure for the synthesis of the zinc-based metal–organic framework used in initial crystal sponge reports has been modified to yield competent crystals in 3 days instead of 2 weeks. These crystal sponges were tested on some small molecules, with two being unexpectedly difficult cases for analysis with in-house diffractometers in regard to data quality and proper space-group determination. These issues were easily resolved by the use of synchrotron radiation using data-collection times of less than an hour. One of these guests induced a single-crystal-to-single-crystal transformation to create a larger unit cell with over 500 non-H atoms in the asymmetric unit. This led to a non-trivial refinement scenario that afforded the best Flack x absolute stereochemical determination parameter to date for these systems. The structures did not require the use of PLATON/SQUEEZE or other solvent-masking programs, and are the highest-quality crystalline sponge systems reported to date where the results are strongly supported by the data. A set of guidelines for the entire crystallographic process were developed through these studies. In particular, the refinement guidelines include strategies to refine the host framework, locate guests and determine occupancies, discussion of the proper use of geometric and anisotropic displacement parameter restraints and constraints, and whether to perform solvent squeezing/masking. The single-crystal-to-single-crystal transformation process for the crystal sponges is also discussed. The presented general guidelines will be invaluable for researchers interested in using the crystalline sponge method at in-house diffraction or synchrotron facilities, will facilitate the collection and analysis of reliable high-quality data, and will allow construction of chemically and physically sensible models for guest structural determination

Structure–conductivity correlation in ferric chloride-doped poly(3-hexylthiophene)

Poly(3-hexylthiophene) (P3HT) matrix has been chemically doped (redox doping) by ferric chloride (FeCl3) with different molar concentrations to get P3HT–FeCl3 charge-transfer complexes. The effect of redox doping on photo-physical, structural, and morphological properties and dc electrical conductivity of P3HT matrices has been examined. The dc conductivity has been measured on films of pristine P3HT and P3HT–FeCl3 charge-transfer complexes in the temperature range 6–300 K. Analysis of dc conductivity data reveals that in the temperature range 40–300 K, the dc conductivity is predominantly governed by Mott's 3-dimensional variable range hopping (3D-VRH); however, below 40 K tunnelling seems to dominate. A slight deviation from 3D-VRH to 1D-VRH is observed with an increase in doping level or precisely with an increase in the extent of P3HT–FeCl3 charge-transfer complexes. We attribute this deviation to the induced expansion in crystallographic lattices as revealed by x-ray diffraction data and formation of discrete conducting domains as observed by atomic force microscope imaging

GABA-modulating bacteria of the human gut microbiota.

The gut microbiota affects many important host functions, including the immune response and the nervous system1. However, while substantial progress has been made in growing diverse microorganisms of the microbiota2, 23-65% of species residing in the human gut remain uncultured3,4, which is an obstacle for understanding their biological roles. A likely reason for this unculturability is the absence in artificial media of key growth factors that are provided by neighbouring bacteria in situ5,6. In the present study, we used co-culture to isolate KLE1738, which required the presence of Bacteroides fragilis to grow. Bioassay-driven purification of B. fragilis supernatant led to the isolation of the growth factor, which, surprisingly, is the major inhibitory neurotransmitter GABA (γ-aminobutyric acid). GABA was the only tested nutrient that supported the growth of KLE1738, and a genome analysis supported a GABA-dependent metabolism mechanism. Using growth of KLE1738 as an indicator, we isolated a variety of GABA-producing bacteria, and found that Bacteroides ssp. produced large quantities of GABA. Genome-based metabolic modelling of the human gut microbiota revealed multiple genera with the predicted capability to produce or consume GABA. A transcriptome analysis of human stool samples from healthy individuals showed that GABA-producing pathways are actively expressed by Bacteroides, Parabacteroides and Escherichia species. By coupling 16S ribosmal RNA sequencing with functional magentic resonance imaging in patients with major depressive disorder, a disease associated with an altered GABA-mediated response, we found that the relative abundance levels of faecal Bacteroides are negatively correlated with brain signatures associated with depression

Tundrenone: An Atypical Secondary Metabolite from Bacteria with Highly Restricted Primary Metabolism

Methane-oxidizing bacteria, aerobes that utilize methane as their sole carbon and energy source, are being increasingly studied for their environmentally significant ability to remove methane from the atmosphere. Their genomes indicate that they also have a robust and unusual secondary metabolism. Bioinformatic analysis of the Methylobacter tundripaludum genome identified biosynthetic gene clusters for several intriguing metabolites, and this report discloses the structural and genetic characterization of tundrenone, one of these metabolites. Tundrenone is a highly oxidized metabolite that incorporates both a modified bicyclic chorismate-derived fragment and a modified lipid tail bearing a β,γ-unsaturated α-hydroxy ketone. Tundrenone has been genetically linked to its biosynthetic gene cluster, and quorum sensing activates its production. M. tundripaludum’s genome and tundrenone’s discovery support the idea that additional studies of methane-oxidizing bacteria will reveal new naturally occurring molecular scaffolds and the biosynthetic pathways that produce them

Solid-state host–guest influences on a BODIPY dye hosted within a crystalline sponge

Manipulating the emission characteristics of phosphors is a viable strategy to produce unique, and thus difficult to replicate, security optical features that are useful in anticounterfeiting applications. Here, a fluorophore, BODIPY 493/503, displayed altered solid-state emission characteristics upon being hosted within a crystalline molecular flask. Specifically, a bathochromic shift of 939 cm−1 was observed (λ(max): 633 → 673 nm), with a concomitant reduction in emission intensity, and emission dependency on excitation wavelength. Multiple factors likely contribute to this behaviour, such as emission filtering by the host framework, exciplex formation between BODIPY and the electron-deficient framework, and collisional quenching between the host and guest. Here we prioritize solid-state analyses to explore these factors, including electron density mapping of the framework pores, and multinuclear solid-state NMR spectroscopy