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Abstract.—Hundreds or thousands of loci are now routinely used in modern phylogenomic studies. Concatenation approaches to tree inference assume that there is a single topology for the entire dataset, but different loci may have different evolutionary histories due to incomplete lineage sorting (ILS), introgression, and/or horizontal gene transfer; even single loci may not be treelike due to recombination. To overcome this shortcoming, we introduce an implementation of a multi-tree mixture model that we call mixtures across sites and trees (MAST). This model extends a prior implementation by Boussau et al. (2009) by allowing users to estimate the weight of each of a set of pre-specified bifurcating trees in a single alignment. The MAST model allows each tree to have its own weight, topology, branch lengths, substitution model, nucleotide or amino acid frequencies, and model of rate heterogeneity across sites. We implemented the MAST model in a maximum-likelihood framework in the popular phylogenetic software, IQ-TREE. Simulations show that we can accurately recover the true model parameters, including branch lengths and tree weights for a given set of tree topologies, under a wide range of biologically realistic scenarios. We also show that we can use standard statistical inference approaches to reject a single-tree model when data are simulated under multiple trees (and vice versa). We applied the MAST model to multiple primate datasets and found that it can recover the signal of ILS in the Great Apes, as well as the asymmetry in minor trees caused by introgression among several macaque species. When applied to a dataset of 4 Platyrrhine species for which standard concatenated maximum likelihood (ML) and gene tree approaches disagree, we observe that MAST gives the highest weight (i.e., the largest proportion of sites) to the tree also supported by gene tree approaches. These results suggest that the MAST model is able to analyze a concatenated alignment using ML while avoiding some of the biases that come with assuming there is only a single tree. We discuss how the MAST model can be extended in the future.

 

The redox non-innocent 2-isocyano-6,6′-biazulenic ligand platform exhibits reduction potential inversion and offers construction of molecular organometallic electron reservoirs with 2e⁻-per-ligand reversible redox capacity.

 

Twenty novel Mn, Fe, and Cu complexes of ethylene cross-bridged tetraazamacrocycles with potentially copolymerizable allyl and benzyl pendant arms were synthesized and characterized. Multiple X-ray crystal structures demonstrate the cis-folded pseudo-octahedral geometry forced by the rigidifying ethylene cross-bridge and show that two cis coordination cites are available for interaction with substrate and oxidant. The Cu complexes were used to determine kinetic stability under harsh acidic and high-temperature conditions, which revealed that the cyclam-based ligands provide superior stabilization with half-lives of many minutes or even hours in 5 M HCl at 50–90 °C. Cyclic voltammetry studies of the Fe and Mn complexes reveal reversible redox processes indicating stabilization of Fe2+/Fe3+ and Mn2+/Mn3+/Mn4+ oxidation states, indicating the likelihood of catalytic oxidation for these complexes. Finally, dye-bleaching experiments with methylene blue, methyl orange, and rhodamine B demonstrate efficient catalytic decolorization and allow selection of the most successful monomeric catalysts for copolymerization to produce future heterogeneous water purification materials.

 

Ethylene cross-bridged tetraazamacrocycles are known to produce kinetically stable transition metal complexes that can act as robust oxidation catalysts under harsh aqueous conditions. We have synthesized ligand analogs with single acetate pendant arms that act as pentadentate ligands to Mn, Fe, Co, Ni, Cu, and Zn. These complexes have been synthesized and characterized, including the structural characterization of four Co and Cu complexes. Cyclic voltammetry demonstrates that multiple oxidation states are stabilized by these rigid, bicyclic ligands. Yet, redox potentials of the metal complexes are modified compared to the “parent” ligands due to the pendant acetate arm. Similarly, gains in kinetic stability under harsh acidic conditions, compared to parent complexes without the pendant acetate arm, were demonstrated by a half-life seven times longer for the cyclam copper complex. Due to the reversible, high oxidation states available for the Mn and Fe complexes, the Mn and Fe complexes were examined as catalysts for the bleaching of three commonly used pollutant model dyes (methylene blue, methyl orange, and Rhodamine B) in water with hydrogen peroxide as oxidant. The efficient bleaching of these dyes was observed. 

Atomically precise thiolate-protected gold nanomolecules have attracted interest due to their distinct electronic and chemical properties. The structure of these nanomolecules is important for understanding their peculiar properties. Here, we report the X-ray crystal structure of a 24-atom gold nanomolecule protected by 16 tert -butylthiolate ligands. The composition of Au 24 (S-C 4 H 9 ) 16 {poly[hexadecakis(μ- tert -butylthiolato)tetracosagold]} was confirmed by X-ray crystallography and electrospray ionization mass spectrometry (ESI–MS). The nanomolecule was synthesized in a one-phase synthesis and crystallized from a hexane–ethanol layered solution. The X-ray structure confirms the 16-atom core protected by two monomeric and two trimeric staples with four bridging ligands. The Au 24 (S-C 4 H 9 ) 16 cluster follows the shell-closing magic number of 8. 

Zn II and Fe II chloride complexes of a di(methylthiazolidinyl)pyridine ligand were deprotonated to form the corresponding thiolate complexes supported by redox-active iminopyridine moieties. The thiolate donor groups are nucleophilic and reactive toward oxidants, electrophiles, and protons, while the pendant thiazolidine rings are available for hydrogen bonding. Anion exchange with the weakly-coordinating triflate anion resulted in self-assembly of the iminopyridine complexes to form a trimeric [M 3 S 3 ] cluster. Hydrogen bonding closely associates anions with this trimetallic core. 

Co-crystal engineering is a promising method to create new classes of advanced materials. Co-crystal structure prediction is more challenging when one or more of the lattice constituents (tectons) are flexible molecules. This study reports four co-crystals that were prepared by mixing HAuCl 4 or HAuBr 4 with C 3 -symmetric tectons based on a 1,3,5-(methylacetamide)benzene scaffold. X-ray analysis of the co-crystals revealed the presence of three dominant supramolecular interactions; (a) hydrogen bonding between tecton amide NH residues and the AuX 4 − anion, (b) electrostatic stacking of the Au center against the tecton's π-electrons, (c) very short hydrogen bonds within a proton-bridged-carbonyls motif. Within all four co-crystals, the sterically-geared tecton was trapped in a high energy molecular conformation, which increased the number of favorable intermolecular interactions in the lattice. We infer from the results that the likelihood of high energy molecular conformations within a co-crystal increases if there are multiple dominant intermolecular interactions. Application of this generalizable rule should lead to improved crystal structure prediction. 

Abstract Microplastic particles (MPs) are ubiquitous across a wide range of aquatic habitats but determining an appropriate level of risk management is hindered by a poor understanding of environmental risk. Here, we introduce a risk management framework for aquatic ecosystems that identifies four critical management thresholds, ranging from low regulatory concern to the highest level of concern where pollution control measures could be introduced to mitigate environmental emissions. The four thresholds were derived using a species sensitivity distribution (SSD) approach and the best available data from the peer-reviewed literature. This included a total of 290 data points extracted from 21 peer-reviewed microplastic toxicity studies meeting a minimal set of pre-defined quality criteria. The meta-analysis resulted in the development of critical thresholds for two effects mechanisms: food dilution with thresholds ranging from ~ 0.5 to 35 particles/L, and tissue translocation with thresholds ranging from ~ 60 to 4100 particles/L. This project was completed within an expert working group, which assigned high confidence to the management framework and associated analytical approach for developing thresholds, and very low to high confidence in the numerical thresholds. Consequently, several research recommendations are presented, which would strengthen confidence in quantifying threshold values for use in risk assessment and management. These recommendations include a need for high quality toxicity tests, and for an improved understanding of the mechanisms of action to better establish links to ecologically relevant adverse effects. 

D-Mannosamine hydrochloride (2-amino-2-deoxy-D-mannose hydrochloride), C 6 H 14 NO 5 + ·Cl − , (I), crystallized from a methanol/ethyl acetate/ n -hexane solvent mixture at room temperature in a 4 C 1 chair conformation that is slightly distorted towards the C3,O5 B form. A comparison of the structural parameters of (I) with the corresponding parameters in α-D-glucosamine hydrochloride, (II), and β-D-galactosamine hydrochloride, (III)/(III′), was undertaken to evaluate the effects of ionic hydrogen bonding on structural properties. Three types of ionic hydrogen bonds are present in the crystals of (I)–(III)/(III′), i.e. N + —H...O, N + —H...Cl − , and O—H...Cl − . The exocyclic structural parameters in (I), (II), and (III)/(III′) appear to be most influenced by this bonding, especially the exocyclic hydroxy groups, which adopt eclipsed conformations enabled by ionic hydrogen bonding to the chloride anion. Anomeric disorder was observed in crystals of (I), with an α:β ratio of 37:63. However, anomeric configuration appears to exert minimal structural effects; that is, bond lengths, bond angles, and torsion angles are essentially identical in both anomers. The observed disorder at the anomeric C atom of (I) appears to be caused by the presence of the chloride anion and atom O3 or O4 in proximal voids, which provide opportunities for hydrogen bonding to atom O1 in both axial and equatorial orientations.