A Method for Rigorously Selective Capture and Simultaneous Fluorescent Labeling of N-Terminal Glycine Peptides.

Although chemical methods for the selective derivatization of amino acid (AA) side chains in peptides and proteins are available, selective N-terminal labeling is challenging, especially for glycine, which has no side chain at the α-carbon position. We report here a double activation at glycine's α-methylene group that allows this AA to be differentiated from the other 19 AAs. A condensation reaction of dibenzoylmethane with glycine results in the formation of an imine, and subsequent tautomerization is followed by intramolecular cyclization, leading to the formation of a fluorescent pyrrole ring. Additionally, the approach exhibits compatibility with AAs possessing reactive side chains. Further, the method allows for selective pull-down assays of N-terminal glycine peptides from mixtures without prior knowledge of the N-terminal peptide distribution.

A Janus carbaporphyrin pseudo-dimer.

Carbaporphyrin dimers, investigated for their distinctive electronic structures and exceptional properties, have predominantly consisted of systems containing identical subunits. This study addresses the associated knowledge gap by focusing on asymmetric carbaporphyrin dimers with Janus-like characteristics. The synthesis of a Janus-type carbaporphyrin pseudo-dimer 5 is presented. It displays antiaromatic characteristics on the fused side and nonaromatic behavior on the unfused side. A newly synthesized tetraphenylene (TPE) linked bis-dibenzihomoporphyrin 8 and a previously reported dibenzo[g,p]chrysene (DBC) linked bis-dicarbacorrole 9 were prepared as controls. Comprehensive analyses, including 1H NMR spectral studies, single crystal X-ray diffraction analyses, and DFT calculations, validate the mixed character of 5. A further feature of the Janus pseudo-dimer 5 is that it may be transformed into a heterometallic complex, with one side coordinating a Cu(III) center and the other stabilizing a BODIPY complex. This disparate regiochemical reactivity underscores the potential of carbaporphyrin dimers as versatile frameworks, with electronic features and site-specific coordination chemistry controlled through asymmetry. These findings position carbaporphyrin dimers as promising candidates for advances in electronic structure studies, coordination chemistry, materials science, and beyond.

Pervasive loss of regulated necrotic cell death genes in elephants, hyraxes, and sea cows (Paenungualta).

Gene loss can promote phenotypic differences between species, for example, if a gene constrains phenotypic variation in a trait, its loss allows for the evolution of a greater range of variation or even new phenotypes. Here, we explore the contribution of gene loss to the evolution of large bodies and augmented cancer resistance in elephants. We used genomes from 17 Afrotherian and Xenarthran species to identify lost genes, i.e., genes that have pseudogenized or been completely lost, and Dollo parsimony to reconstruct the evolutionary history of gene loss across species. We unexpectedly discovered a burst of gene losses in the Afrotherian stem lineage and found that the loss of genes with functions in regulated necrotic cell death modes was pervasive in elephants, hyraxes, and sea cows (Paenungulata). Among the lost genes are MLKL and RIPK3, which mediate necroptosis, and sensors that activate inflammasomes to induce pyroptosis, including AIM2, MEFV, NLRC4, NLRP1, and NLRP6. These data suggest that the mechanisms that regulate necrosis and pyroptosis are either extremely derived or potentially lost in these lineages, which may contribute to the repeated evolution of large bodies and cancer resistance in Paenungulates as well as susceptibility to pathogen infection.

Rapid evolution of genes with anti-cancer functions during the origins of large bodies and cancer resistance in elephants.

Elephants have emerged as a model system to study the evolution of body size and cancer resistance because, despite their immense size, they have a very low prevalence of cancer. Previous studies have found that duplication of tumor suppressors at least partly contributes to the evolution of anti-cancer cellular phenotypes in elephants. Still, many other mechanisms must have contributed to their augmented cancer resistance. Here, we use a suite of codon-based maximum-likelihood methods and a dataset of 13,310 protein-coding gene alignments from 261 Eutherian mammals to identify positively selected and rapidly evolving elephant genes. We found 496 genes (3.73% of alignments tested) with statistically significant evidence for positive selection and 660 genes (4.96% of alignments tested) that likely evolved rapidly in elephants. Positively selected and rapidly evolving genes are statistically enriched in gene ontology terms and biological pathways related to regulated cell death mechanisms, DNA damage repair, cell cycle regulation, epidermal growth factor receptor (EGFR) signaling, and immune functions, particularly neutrophil granules and degranulation. All of these biological factors are plausibly related to the evolution of cancer resistance. Thus, these positively selected and rapidly evolving genes are promising candidates for genes contributing to elephant-specific traits, including the evolution of molecular and cellular characteristics that enhance cancer resistance.

Cyclopentadienyl capped thorium(IV) porphyrinoid complex.

The reaction between Th(IV) dipyriamethyrin dichloride and sodium cyclopentadienyl (Cp) results in the formation of a cyclopentadienyl capped thorium dipyriamethyrin complex, which to our knowledge represents the first expanded porphyrin f-element Cp complex.

Nanographene-Fused Expanded Carbaporphyrin Tweezers.

A nanographene-fused expanded carbaporphyrin (5) and its BF2 complex (6) were synthesized. Single-crystal X-ray structures revealed that 5 and 6 are connected by two hexa-peri-hexabenzocoronene (HBC) units and two dipyrromethene or BODIPY units, respectively. As prepared, 5 and 6 both show nonaromatic character with figure-of-eight carbaoctaphyrin (1.1.1.0.1.1.1.0) cores and adopt tweezers-like conformations characterized by a partially confined space between the two constituent HBC units. The distance between the HBC centers is >10 Å, while the dihedral angles between the two HBC planes are 30.5 and 35.2° for 5 and 6, respectively. The interactions between 5 and 6 and fullerene C60 were studied both in organic media and in the solid state. Proton NMR spectral titrations of 5 and 6 with C60 revealed a 1:1 binding mode for both macrocycles. In toluene-d8, the corresponding binding constants were determined to be 1141 ± 17 and 994 ± 10 M-1 for 5 and 6, respectively. Single-crystal X-ray diffraction structural analyses confirmed the formation of 1:1 fullerene inclusion complexes in the solid state. The C60 guests in both complexes are found within triangular pockets composed of two HBC units from the tweezers-like receptor most closely associated with the bound fullerene, as well as an HBC unit from an adjacent host. Femtosecond transient absorption measurements revealed subpicosecond ultrafast charge separation between 5 (and 6) and C60 in the complexes. To the best of our knowledge, the present report provides the first example wherein a nanographene building block is incorporated into the core of a porphyrinic framework.

Phylogenomics reveals an almost perfect polytomy among the almost ungulates (Paenungulata).

Phylogenetic studies have resolved most relationships among Eutherian Orders. However, the branching order of elephants (Proboscidea), hyraxes (Hyracoidea), and sea cows (Sirenia) (i.e., the Paenungulata) has remained uncertain since at least 1758, when Linnaeus grouped elephants and manatees into a single Order (Bruta) to the exclusion of hyraxes. Subsequent morphological, molecular, and large-scale phylogenomic datasets have reached conflicting conclusions on the branching order within Paenungulates. We use a phylogenomic dataset of alignments from 13,388 protein-coding genes across 261 Eutherian mammals to infer phylogenetic relationships within Paenungulates. We find that gene trees almost equally support the three alternative resolutions of Paenungulate relationships and that despite strong support for a Proboscidea+Hyracoidea split in the multispecies coalescent (MSC) tree, there is significant evidence for gene tree uncertainty, incomplete lineage sorting, and introgression among Proboscidea, Hyracoidea, and Sirenia. Indeed, only 8-10% of genes have statistically significant phylogenetic signal to reject the hypothesis of a Paenungulate polytomy. These data indicate little support for any resolution for the branching order Proboscidea, Hyracoidea, and Sirenia within Paenungulata and suggest that Paenungulata may be as close to a real, or at least unresolvable, polytomy as possible.

Photochemical charge accumulation in a heteroleptic copper(i)-anthraquinone molecular dyad via proton-coupled electron transfer.

Developing efficient photocatalysts that perform multi electron redox reactions is critical to achieving solar energy conversion. One can reach this goal by developing systems which mimic natural photosynthesis and exploit strategies such as proton-coupled electron transfer (PCET) to achieve photochemical charge accumulation. We report herein a heteroleptic Cu(i)bis(phenanthroline) complex, Cu-AnQ, featuring a fused phenazine-anthraquinone moiety that photochemically accumulates two electrons in the anthraquinone unit via PCET. Full spectroscopic and electrochemical analyses allowed us to identify the reduced species and revealed that up to three electrons can be accumulated in the phenazine-anthraquinone ring system under electrochemical conditions. Continuous photolysis of Cu-AnQ in the presence of sacrificial electron donor produced doubly reduced monoprotonated photoproduct confirmed unambiguously by X-ray crystallography. Formation of this photoproduct indicates that a PCET process occurred during illumination and two electrons were accumulated in the system. The role of the heteroleptic Cu(i)bis(phenanthroline) moiety participating in the photochemical charge accumulation as a light absorber was evidenced by comparing the photolysis of Cu-AnQ and the free AnQ ligand with less reductive triethylamine as a sacrificial electron donor, in which photogenerated doubly reduced species was observed with Cu-AnQ, but not with the free ligand. The thermodynamic properties of Cu-AnQ were examined by DFT which mapped the probable reaction pathway for photochemical charge accumulation and the capacity for solar energy stored in the process. This study presents a unique system built on earth-abundant transition metal complex to store electrons, and tune the storage of solar energy by the degree of protonation of the electron acceptor.

Deferasirox Derivatives: Ligands for the Lanthanide Series.

Deferasirox is an FDA-approved iron chelator used in the treatment of iron toxicity. In this work, we report the use of several deferasirox derivatives as lanthanide chelators. Solid-state structural studies of three representative trivalent lanthanide cations, La(III), Eu(III), and Lu(III), revealed the formation of 2:2 complexes in the solid state. A 1:1 stoichiometry dominates in DMSO solution, with Ka values of 472 ± 14, 477 ± 11, and 496 ± 15 M-1 being obtained in the case of these three cations, respectively. Under the conditions of competitive precipitation in the presence of triethylamine, high selectivity (up to 80%) for lutetium(III) was observed in competition with La(III), Ce(III), and Eu(III). Theoretical calculations provided support for the observed selective crystallization.

Changing Directions: Influence of Ligand Electronics on the Directionality and Kinetics of Photoinduced Charge Transfer in Cu(I)Diimine Complexes.

A key challenge to the effective utilization of solar energy is to promote efficient photoinduced charge transfer, specifically avoiding unproductive, circuitous electron-transfer pathways and optimizing the kinetics of charge separation and recombination. We hypothesize that one way to address this challenge is to develop a fundamental understanding of how to initiate and control directional photoinduced charge transfer, particularly for earth-abundant first-row transition-metal coordination complexes, which typically suffer from relatively short excited-state lifetimes. Here, we report a series of functionalized heteroleptic copper(I)bis(phenanthroline) complexes, which have allowed us to investigate the directionality of intramolecular photoinduced metal-to-ligand charge transfer (MLCT) as a function of the substituent Hammett parameter. Ultrafast transient absorption suggests a complicated interplay of MLCT localization and solvent interaction with the Cu(II) center of the MLCT state. This work provides a set of design principles for directional charge transfer in earth-abundant complexes and can be used to efficiently design pathways for connecting the molecular modules to catalysts or electrodes and integration into systems for light-driven catalysis.

Diphenylpyrrole-Strapped Calix[4]pyrrole Extractant for the Fluoride and Chloride Anions.

The anion binding features of diphenylpyrrole-strapped calix[4]pyrrole 1 have been investigated by means of 1 H NMR spectroscopy and ITC (isothermal titration calorimetry), as well as single crystal X-ray diffraction analyses. Receptor 1 bearing an auxiliary pyrrolic NH donor and solubilizing phenyl groups on the strap was found to bind F- , Cl- , and Br- as their tetrabutylammonium salts with high affinity in DMSO-d6 . In addition, receptor 1 was found to extract the fluoride anion (as both its tetraethylammonium (TEA+ ) and tetrabutylammonium (TBA+ ) salts), as well as the chloride anion into chloroform-d from an aqueous source phase. Cation metathesis using TBAI or the use of a dual host approach involving crown ethers enabled receptor 1 to extract simple alkali metal fluoride or chloride salts from water. Quantitative binding of NaF by receptor 1 was observed in 20 % D2 O-DMSO-d6 allowing for the direct determination of the NaF concentration in an unknown sample.

Optical detection of alcohols with a Cu(I)HETPHEN complex by reversible aldehyde to hemiacetal conversion.

A heteroleptic copper(I) bis(phenanthroline) complex with aldehyde groups at the 4,7 positions of the phenanthroline ligand was synthesized. The complex is responsive to alcohol, resulting in a distinct colour change caused by the facile reaction of the aldehyde group with alcohol, forming a hemiacetal product. The aldehyde species can be regenerated after heating the intermediate at 80 °C for 10 minutes, demonstrating the reusability of the complex for alcohol detection. This work presents a new strategy for applying transition metal complexes in small molecule sensing by installing functional groups in the secondary coordination sphere which reversibly react with analytes.

Direct Extraction of Sodium Hydroxide by Calix[4]pyrrole-Based Ion-Pair Receptors.

Described in this work are calix[4]pyrrole-based ion-pair receptors, cis/trans-1 and cis/trans-2, designed for the extraction of sodium hydroxide. An X-ray diffraction analysis of a single crystal of the cis-1·NaOH isomer isolated from a mixture of cis/trans-1 revealed a unique dimeric supramolecular structure. An average dimer in toluene-d8 solution was inferred on the basis of diffusion-ordered spectroscopy (DOSY). Support for the proposed stoichiometry came from density functional theory (DFT) calculations. The structural stability of the dimeric cis-1·NaOH complex in toluene solution was further confirmed by ab initio molecular dynamics (AIMD) simulation with explicit representation of solvent. Under conditions of liquid-liquid extraction (LLE), purified receptors cis- and trans-2 were both found to remove NaOH from a pH 11.01 aqueous source phase into toluene with extraction efficiencies (E%) of 50-60% when used equimolar to NaOH. However, in all cases, precipitation was observed. Complexities associated with precipitation could be avoided by immobilization of the receptors onto a chemically inert poly(styrene) resin by means of solvent impregnation. The use of solvent-impregnated resins (SIRs) eliminated precipitation in solution while retaining the extraction efficiency toward NaOH. This allowed both the pH and salinity of the alkaline source phase to be lowered.

Multifaceted Chiral Probe 2,3-Dihydro-4-hydroxy-chromene Schiff Base in Detecting Cu2+ Ions, l-Histidine, and Indazole: Spectroscopic Investigation and Confocal and Live Cell Imaging.

2,3-Dihydro-4-hydroxy-chromene-4(N)-ethyl thiosemicarbazone (probe F4) is used as a chemosensor, and it selectively detected Cu2+ ions among the metal ions by showing fluorescence "TURN ON" behavior. The stoichiometric binding of the probe with Cu2+ (CF4) was confirmed by Job's plot and mass spectroscopy. Further, CF4 was used as a sensor for the detection of l-amino acids and N-heterocyclic compounds. Among them, CF4 selectively detected l-histidine by showing fluorescence "TURN-OFF" behavior and selectively detected indazole by showing fluorescence "TURN-ON" behavior. These behaviors were further confirmed by in vivo live cell imaging studies by using Caenorhabditis elegans as a model. In vitro cytotoxicity was assayed for probe F4, complex CF4, and CF4 with l-histidine and indazole. The IC50 concentration was used for confocal imaging studies by using the MDA-MB-231 cell line (breast cancer cell line).

Human embryo implantation.

Embryo implantation in humans is interstitial, meaning the entire conceptus embeds in the endometrium before the placental trophoblast invades beyond the uterine mucosa into the underlying inner myometrium. Once implanted, embryo survival pivots on the transformation of the endometrium into an anti-inflammatory placental bed, termed decidua, under homeostatic control of uterine natural killer cells. Here, we examine the evolutionary context of embryo implantation and elaborate on uterine remodelling before and after conception in humans. We also discuss the interactions between the embryo and the decidualising endometrium that regulate interstitial implantation and determine embryo fitness. Together, this Review highlights the precarious but adaptable nature of the implantation process.

Fluorescent copolymer aggregate sensor for lithium chloride.

We report a copolymeric fluorescent sensor that is selective for lithium chloride. The two constituent polymers comprise pendent triphenylethylene (TPE) moieties for aggregate induced emission (AIE) along with either strapped-calix[4]pyrrole or secondary ammonium groups that drive aggregation via self-assembly upon polymer mixing. Addition of LiCl in acetonitrile disrupts the strapped-calix[4]pyrrole/secondary ammonium chloride salt host-guest crosslinks leading to disaggregation of the polymer chains and a decrease in TPE emission. The lack of AIE perturbation upon addition of NaCl, KCl, MgCl2 or CaCl2 provides for high selectivity for LiCl relative to potential interferants. This supramolecular dual polymer approach could serve as a complement to more traditional sensor systems.

Elephants as an animal model for self-domestication.

Humans are unique in their sophisticated culture and societal structures, their complex languages, and their extensive tool use. According to the human self-domestication hypothesis, this unique set of traits may be the result of an evolutionary process of self-induced domestication, in which humans evolved to be less aggressive and more cooperative. However, the only other species that has been argued to be self-domesticated besides humans so far is bonobos, resulting in a narrow scope for investigating this theory limited to the primate order. Here, we propose an animal model for studying self-domestication: the elephant. First, we support our hypothesis with an extensive cross-species comparison, which suggests that elephants indeed exhibit many of the features associated with self-domestication (e.g., reduced aggression, increased prosociality, extended juvenile period, increased playfulness, socially regulated cortisol levels, and complex vocal behavior). Next, we present genetic evidence to reinforce our proposal, showing that genes positively selected in elephants are enriched in pathways associated with domestication traits and include several candidate genes previously associated with domestication. We also discuss several explanations for what may have triggered a self-domestication process in the elephant lineage. Our findings support the idea that elephants, like humans and bonobos, may be self-domesticated. Since the most recent common ancestor of humans and elephants is likely the most recent common ancestor of all placental mammals, our findings have important implications for convergent evolution beyond the primate taxa, and constitute an important advance toward understanding how and why self-domestication shaped humans' unique cultural niche.

Interpreting the Evolutionary Echoes of a Protein Complex Essential for Inner-Ear Mechanosensation.

The sensory epithelium of the inner ear, found in all extant lineages of vertebrates, has been subjected to over 500 million years of evolution, resulting in the complex inner ear of modern vertebrates. Inner-ear adaptations are as diverse as the species in which they are found, and such unique anatomical variations have been well studied. However, the evolutionary details of the molecular machinery that is required for hearing are less well known. Two molecules that are essential for hearing in vertebrates are cadherin-23 and protocadherin-15, proteins whose interaction with one another acts as the focal point of force transmission when converting sound waves into electrical signals that the brain can interpret. This "tip-link" interaction exists in every lineage of vertebrates, but little is known about the structure or mechanical properties of these proteins in most non-mammalian lineages. Here, we use various techniques to characterize the evolution of this protein interaction. Results show how evolutionary sequence changes in this complex affect its biophysical properties both in simulations and experiments, with variations in interaction strength and dynamics among extant vertebrate lineages. Evolutionary simulations also characterize how the biophysical properties of the complex in turn constrain its evolution and provide a possible explanation for the increase in deafness-causing mutants observed in cadherin-23 relative to protocadherin-15. Together, these results suggest a general picture of tip-link evolution in which selection acted to modify the tip-link interface, although subsequent neutral evolution combined with varying degrees of purifying selection drove additional diversification in modern tetrapods.

Cyclo[2]carbazole[2]pyrrole: a preorganized calix[4]pyrrole analogue.

A cyclo[2]carbazole[2]pyrrole (2) consisting of two carbazoles and two pyrroles has been synthesized by directly linking the carbazole 1- and 8-carbon atoms to the pyrrole α-carbon atoms. Macrocycle 2 is an extensively conjugated 16-membered macrocyclic ring that is fixed in a pseudo-1,3-alternate conformation. This provides a preorganized anion binding site consisting of two pyrrole subunits. 1H NMR spectroscopic analysis revealed that only the two diagonally opposed pyrrole NH protons, as opposed to the carbazole protons, take part in anion binding. Nevertheless, cyclo[2]carbazole[2]pyrrole 2 binds representative anions with higher affinity in CD2Cl2 than calix[4]pyrrole (1), a well-studied non-conjugated tetrapyrrole macrocycle that binds anions via four pyrrolic NH hydrogen bond interactions. On the basis of computational studies, the higher chloride anion affinity of receptor 2 relative to 1 is rationalized in terms of a larger binding energy and a lower host strain energy associated with anion complexation. In the presence of excess fluoride or bicarbonate anions, compound 2 loses two pyrrolic NH protons to produce a stable dianionic macrocycle [2-2H]2- displaying a quenched fluorescence.

Cyclic Carbaporphyrin Arrays.

Two cyclic carbaporphyrin arrays (trimer 6 and tetramer 7) were synthesized from a dibrominated carbaporphyrin precursor (5) via a one-pot Yamamoto-type coupling. Single-crystal X-ray diffraction analyses revealed that 6 and 7 contain three and four covalently linked carbaporphyrin (formally dicarbacorrole) units, respectively. Trimer 6 adopts a roughly planar conformation and tetramer 7 adopts an up-and-down zig-zag conformation. Both 6 and 7 contain a [n]cyclo-meta-phenylene ([n]CMP) core, namely, [6]- and [8]CMP for 6 and 7, respectively. Transient absorption (TA) anisotropy and pump-power-dependent excited-state decay studies provided evidence for excitation energy transfer (EET) within both trimer 6 and tetramer 7. The exciton energy hopping (EEH) times were estimated to be 18 and 35 ps for 6 and 7, respectively, as inferred from pump-power-dependent TA measurements. Since the center-to-center distances between adjacent carbaporphyrin units are similar in 6 and 7, the different EEH times are attributed to differences in the orientation of the transition dipoles in these two congeneric arrays. The orientation factor κ2, the key parameter defining the Förster resonance energy transfer efficiency, was calculated to be 2.15 and 1.03 for 6 and 7, respectively, a finding that supports the shorter excitation energy hopping time seen in the case of trimer 6. To our knowledge, this is the first time that covalently linked cyclic carbaporphyrin arrays were synthesized using a single carbaporphyrin as the starting point and that EET between carbaporphyrin subunits constrained within a well-defined polycyclic framework has been correlated with structural differences.