The SAVED domain of the type III CRISPR protease CalpL is a ring nuclease.

Prokaryotic CRISPR-Cas immune systems detect and cleave foreign nucleic acids. In type III CRISPR-Cas systems, the Cas10 subunit of the activated recognition complex synthesizes cyclic oligoadenylates (cOAs), second messengers that activate downstream ancillary effector proteins. Once the viral attack has been weathered, elimination of extant cOA is essential to limit the antiviral response and to allow cellular recovery. Various families of ring nucleases have been identified, specializing in the degradation of cOAs either as standalone enzymes or as domains of effector proteins. Here we describe the ring nuclease activity inherent in the SAVED domain of the cA4-activated CRISPR Lon protease CalpL. We characterize the kinetics of cA4 cleavage and identify key catalytic residues. We demonstrate that cA4-induced oligomerization of CalpL is essential not only for activation of the protease, but is also required for nuclease activity. Further, the nuclease activity of CalpL poses a limitation to the protease reaction, indicating a mechanism for regulation of the CalpL/T/S signaling cascade. This work is the first demonstration of a catalytic SAVED domain and gives new insights into the dynamics of transcriptional adaption in CRISPR defense systems.

A General Iron-Catalyzed Decarboxylative Oxygenation of Aliphatic Carboxylic Acids.

We report an iron-catalyzed decarboxylative C(sp3)-O bond-forming reaction under mild, base-free conditions with visible light irradiation. The transformation uses readily available and structurally diverse carboxylic acids, iron photocatalyst, and 2,2,6,6-tetramethylpiperidine 1-oxyl (TEMPO) derivatives as oxygenation reagents. The process exhibits a broad scope in acids possessing a wide range of stereoelectronic properties and functional groups. The developed reaction was applied to late-stage oxygenation of a series of bio-active molecules. The reaction leverages the ability of iron complexes to generate carbon-centered radicals directly from carboxylic acids by photoinduced carboxylate-to-iron charge transfer. Kinetic, electrochemical, EPR, UV/Vis, HRMS, and DFT studies revealed that TEMPO has a triple role in the reaction: as an oxygenation reagent, an oxidant to turn over the Fe-catalyst, and an internal base for the carboxylic acid deprotonation. The obtained TEMPO adducts represent versatile synthetic intermediates that were further engaged in C-C and C-heteroatom bond-forming reactions using commercial organo-photocatalysts and nucleophilic reagents.

Elucidation of the Bridging Pattern of the Lantibiotic Pseudomycoicidin.

Lantibiotics are post-translationally modified antibiotic peptides with lanthionine thioether bridges that represent potential alternatives to conventional antibiotics. The lantibiotic pseudomycoicidin is produced by Bacillus pseudomycoides DSM 12442 and is effective against many Gram-positive bacteria, including methicillin-resistant Staphylococcus aureus. While prior work demonstrated that pseudomycoicidin possesses one disulfide bridge and four thioether bridges, the ring topology has so far remained unclear. Here, we analyzed several pseudomycoicidin analogues that are affected in ring formation via MALDI-TOF-MS and tandem mass spectrometry with regard to their dehydration and fragmentation patterns, respectively. As a result, we propose a bridging pattern involving Thr8 and Cys13, Thr10 and Cys16, Ser18 and Cys21, and Ser20 and Cys26, thus, forming two double ring systems. Additionally, we localized the disulfide bridge to connect Cys3 and Cys7 and, therefore, fully elucidated the bridging pattern of pseudomycoicidin.

Molecular Taphonomy of Heme: Chemical Degradation of Hemin under Presumed Fossilization Conditions.

The metalloporphyrin heme acts as the oxygen-complexing prosthetic group of hemoglobin in blood. Heme has been noted to survive for many millions of years in fossils. Here, we investigate its stability and degradation under various conditions expected to occur during fossilization. Oxidative, reductive, aerobic, and anaerobic conditions were studied at neutral and alkaline pH values. Elevated temperatures were applied to accelerate degradation. High-performance liquid chromatography coupled to tandem mass spectrometry (HPLC-MS/MS) identified four main degradation products. The vinyl residues are oxidized to formyl and further to carboxylate groups. In the presence of air or H2O2, cleavage of the tetrapyrrole ring occurs, and hematinic acid is formed. The highest stability of heme was observed under anaerobic reductive conditions (half-life 9.5 days), while the lowest stability was found in the presence of H2O2 (half-life 1 min). We confirmed that the iron cation plays a crucial role in degradation, since protoporphyrin IX, lacking iron, remained significantly more stable. Under anaerobic, reductive conditions, the above-mentioned degradation products were not observed, suggesting a different degradation pathway. To our knowledge, this is the first molecular taphonomy study on heme, which will be useful for understanding its fate during fossilization.

A Family of Heterobimetallic Cubes Shows Spin-Crossover Behaviour Near Room Temperature.

Using 4-(4'-pyridyl)aniline as a simple organic building block in combination with three different aldehyde components together with metal(II) salts gave three different Fe8 Pt6 -cubes and their corresponding Zn8 Pt6 analogues by employing the subcomponent self-assembly approach. Whereas the use of zinc(II) salts gave rise to diamagnetic cages, iron(II) salts yielded metallosupramolecular cages that show spin-crossover behaviour in solution. The spin-transition temperature T1/2 depends on the incorporated aldehyde component, giving a construction kit for the deliberate synthesis of spin-crossover compounds with tailored transition properties. Incorporation of 4-thiazolecarbaldehyde or N-methyl-2-imidazole-carbaldehyde yielded cages that undergo spin-crossover around room temperature whereas the cage obtained using 1H-4-imidazolecarbaldehyde shows a spin-transition at low temperatures. Three new structures were characterized by synchrotron X-ray diffraction and all structures were characterized by mass spectrometry, NMR and UV/Vis spectroscopy.

Self-Assembled, Highly Positively Charged, Allyl-Pd Crowns: Cavity-Pocket-Driven Interactions of Fluoroanions.

A series of dodecanuclear highly positively charged homo- and heterometallamacrocycles [{Pd(η3 -2-Me-C3 H4 )}6 (4-PPh2 py)12 {M2 (tpbz)}3 ]18+ (M=Pd, Pt; tpbz=1,2,4,5-tetrakis(diphenylphosphanyl)benzene were synthesized by the quantitative self-assembly of {Pd(η3 -2-Me-C3 H4 )}+ , {M2 (tpbz)}4+ and 4-PPh2 py moieties in 2:1:4 molar ratio. The cationic assemblies were obtained as salts of different fluorinated anions with diverse sizes and electronic properties, namely BF4 - , PF6 - , SbF6 - and CF3 SO3 - . The new crown-like metallamacrocycles showed remarkable differences in their NMR spectra due to the presence of the different counteranions. On the basis of the observed variations, the metallacycles have been tested as catalytic precursors in allylic alkylation reactions. The anion-dependent activity and selectivity has been analysed and compared with that of the corresponding monometallic allylic corners [Pd(η3 -2-Me-C3 H4 )(4-PPh2 py)2 ]X (X=BF4 - , PF6 - , SbF6 - , CF3 SO3 - ). DFT calculations have been employed in order to help to the interpretation of the experimental data and to model the anion-crown interactions.

Dynamic Complex-to-Complex Transformations of Heterobimetallic Systems Influence the Cage Structure or Spin State of Iron(II) Ions.

Two new heterobimetallic cages, a trigonal-bipyramidal and a cubic one, were assembled from the same mononuclear metalloligand by adopting the molecular library approach, using iron(II) and palladium(II) building blocks. The ligand system was designed to readily assemble through subcomponent self-assembly. It allowed the introduction of steric strain at the iron(II) centres, which stabilizes its paramagnetic high-spin state. This steric strain was utilized to drive dynamic complex-to-complex transformations with both the metalloligand and heterobimetallic cages. Addition of sterically less crowded subcomponents as a chemical stimulus transformed all complexes to their previously reported low-spin analogues. The metalloligand and bipyramid incorporated the new building block more readily than the cubic cage, probably because the geometric structure of the sterically crowded metalloligand favours the cube formation. Furthermore it was possible to provoke structural transformations upon addition of more favourable chelating ligands, converting the cubic structures into bipyramidal ones.

A heterobimetallic tetrahedron from a linear platinum(II)-bis(acetylide) metalloligand.

Employing 4-ethynylaniline as a simple organic ligand we were able to prepare the stable trans-bis(acetylide)platinum(II) complex [Pt(L1)2(PBu3)2] as a linear metalloligand. The reaction of this metalloligand with iron(II) cations and pyridine-2-carbaldehyde according to the subcomponent self-assembly approach yielded decanuclear heterobimetallic tetrahedron [Fe4Pt6(L2)12](OTf)8. Thus, combination of these two design concepts - the subcomponent self-assembly strategy and the complex-as-a-ligand approach - ensured a fast and easy synthesis of large heterobimetallic coordination cages of tetrahedral shape with a diameter of more than 3 nm as a mixture of all three possible T-, S 4- and C 3-symmetric diastereomers. The new complexes were characterized by NMR and UV-vis spectroscopy and ESI mass spectrometry. Using GFN2-xTB we generated energy-minimized models of the diastereomers of this cage that further corroborated the results from analytical findings.

Subcomponent Self-Assembly of a Cyclic Tetranuclear FeII Helicate in a Highly Diastereoselective Self-Sorting Manner.

An enantiomerically pure diamine based on the 4,15-difunctionalized [2.2]paracyclophane scaffold and 2-formylpyridine self-assemble into an optically pure cyclic metallosupramolecular Fe4 L6 helicate upon mixing with iron(II) ions in a diastereoselective subcomponent self-assembly process. The cyclic assembly results from steric strain that prevents the formation of a smaller linear dinuclear triple-stranded helicate, and hence, leads to the larger strain-free assembly that fulfils the maximum occupancy rule. Interestingly, use of the racemic diamine also leads to a racemic mixture of the homochiral cyclic helicates as the major product in a highly diastereoselective narcissistic chiral self-sorting manner given the fact that the assembly contains ten stereogenic elements, which can in principle give rise to 149 different diastereomers. The metallosupramolecular aggregates could be characterized by NMR, UV/Vis and CD spectroscopy, mass spectrometry, and X-ray crystallography.

Probing the gas-phase structure of charge-tagged intermediates of a proline catalyzed aldol reaction - vibrational spectroscopy distinguishes oxazolidinone from enamine species.

An l-proline based catalyst with a charged phenyl-pyridium substituent (1) was used to analyze intermediates of an organocatalyzed aldol reaction by infrared multi-photon dissociation (IRMPD) mass spectrometry after transfer into the gas phase via electrospray ionization (ESI). IRMPD spectra were interpreted with the aid of density functional theory (DFT) computations. A structurally restricted enamine species was used as a reference molecule for the calculated vibrational frequencies. A close correlation between theory and experiment was found for the energetically most favoured oxazolidinone structures.

Mechanistic studies of an L-proline-catalyzed pyridazine formation involving a Diels-Alder reaction with inverse electron demand.

The mechanism of an L-proline-catalyzed pyridazine formation from acetone and aryl-substituted tetrazines via a Diels-Alder reaction with inverse electron demand has been studied with NMR and with electrospray ionization mass spectrometry. A catalytic cycle with three intermediates has been proposed. An enamine derived from L-proline and acetone acts as an electron-rich dienophile in a [4 + 2] cycloaddition with the electron-poor tetrazine forming a tetraazabicyclo[2.2.2]octadiene derivative which then eliminates N2 in a retro-Diels-Alder reaction to yield a 4,5-dihydropyridazine species. The reaction was studied in three variants: unmodified, with a charge-tagged substrate, and with a charge-tagged proline catalyst. The charge-tagging technique strongly increases the ESI response of the respective species and therefore enables to capture otherwise undetected reaction components. With the first two reaction variants, only small intensities of intermediates were found, but the temporal progress of reactants and products could be monitored very well. In experiments with the charge-tagged L-proline-derived catalyst, all three intermediates of the proposed catalytic cycle were detected and characterized by collision-induced dissociation (CID) experiments. Some of the CID pathways of intermediates mimic single steps of the proposed catalytic cycle in the gas phase. Thus, the charge-tagged catalyst proved one more time its superior effectiveness for the detection and study of reactive intermediates at low concentrations.

Investigations of the Copper-Catalyzed Oxidative Cross-Coupling of Tetrahydroisoquinolines with Diethylzinc by a Combination of Mass Spectrometric and Electrochemical Methods.

The aerobic oxidative cross-coupling of tetrahydroisoquinolines (THIQs) with diethylzinc catalyzed by CuCl2 has been examined by means of electrospray mass spectrometry (ESI-MS). Substrates, intermediates, and the product were readily detected. Particular emphasis has been placed on the role of CuCl2 . Formation of the intermediate iminium species has been investigated in more detail by ESI-MS, electrochemistry-coupled ESI mass spectrometry (EC-MS), and cyclic voltammetry (CV). Our experiments have consistently revealed strong influences of the N-substituent of the THIQ derivative and its oxidation stability with respect to CuCl2 . The results may help to expand the synthetic scope of the reaction, while also further establishing EC-MS as a valuable technique for linking mass spectrometry with cyclic voltammetry in mechanistic studies of organic redox reactions.

Styrene Polymerization under Ambient Conditions by using a Transient 1,3,2-Diazaphospholane-2-oxyl Complex.

A combined theoretical and experimental study on the formation and reactivity of a P-OTEMP (P-bound TEMPO (TEMPO=2,2,6,6-tetramethyl-piperidin-1-oxyl)) substituted 1,3,2-diazaphospholane W(CO)5 complex is presented, including DFT-based mechanistic details. The complex possesses a thermally labile O-N bond that cleaves homolytically yielding the transient 1,3,2-diazaphospholane-2-oxyl complex [(CO)5 W(R2 PO. )], which acts as a radical initiator for styrene polymerization under ambient conditions.

Bond Dissociation Energies of Metallo-supramolecular Building Blocks: Insight from Fragmentation of Selectively Self-Assembled Heterometallic Metallo-supramolecular Aggregates.

A series of selectively self-assembled metallo-supramolecular square-like macrocycles with unsymmetric ditopic linkers and two different types of metal corners, i.e., {Pd(η3-2-Me-C3H4)} and {M(dppp)} with dppp = 1,3-bis(diphenylphosphino)propane and M = Pd2+ or Pt2+, have been studied in the gas phase using collision-induced dissociation. The aggregates show distinct fragmentation patterns determined by ligand length, i.e, aggregate size, and type of metal corner. Information on relative binding strength can be deduced. This is of particular interest for (methylallyl)Pd as a relatively new building block in metallo-supramolecular chemistry. The phosphane end of the unsymmetric ligand connected to (η3-2-Me-C3H4)Pd is bound significantly stronger than its pyridine end to (dppp)Pt and (dppp)Pd. These results are corroborated by DFT calculations.

An Octanuclear Metallosupramolecular Cage Designed To Exhibit Spin-Crossover Behavior.

By employing the subcomponent self-assembly approach utilizing 5,10,15,20-tetrakis(4-aminophenyl)porphyrin or its zinc(II) complex, 1H-4-imidazolecarbaldehyde, and either zinc(II) or iron(II) salts, we were able to prepare O-symmetric cages having a confined volume of ca. 1300 Å3 . The use of iron(II) salts yielded coordination cages in the high-spin state at room temperature, manifesting spin-crossover in solution at low temperatures, whereas corresponding zinc(II) salts led to the corresponding diamagnetic analogues. The new cages were characterized by synchrotron X-ray crystallography, high-resolution mass spectrometry, and NMR, Mössbauer, IR, and UV/Vis spectroscopy. The cage structures and UV/Vis spectra were independently confirmed by state-of-the-art DFT calculations. A remarkably high-spin-stabilizing effect through encapsulation of C70 was observed. The spin-transition temperature T1/2 is lowered by 20 K in the host-guest complex.

Strong Evidence of a Phosphanoxyl Complex: Formation, Bonding, and Reactivity of Ligated Phosphorus Analogues of Nitroxides.

Facile access to [W(CO)5 (Ph2 P-OTEMP)] is used to initiate a study on the generation, properties, and reactions of transient phosphanoxyl complexes [MLn (R2 PO)], the first example of which could be trapped via heterocoupling with the trityl radical. It is also demonstrated that the phosphorus nitroxyl complex acts as radical initiator in the polymerization of styrene. The quest for P-O versus O-N bond homolysis, as well as the initial steps of the polymerization were studied by DFT methods.

Stretch Out or Fold Back? Conformations of Dinuclear Gold(I) N-Heterocyclic Carbene Macrocycles.

We report the synthesis and characterization of 12 new dinuclear gold(I) N-heterocyclic carbene (NHC) complexes and the corresponding imidazolium precursors. The focus lies in a systematic study of conformational changes and intra- and intermolecular gold-gold and π-π interactions of dinuclear gold(I) carbene complexes. Common to all members of the series of gold macrocycles are NHC ligands on the basis of imidazole with ethyl side chains and bromide as well as hexafluorophosphate counterions, respectively. The compounds vary in the length of a flexible alkyl linker between the NHC units. For the methylene and ethylene bridged macrocycles, a ring inversion movement can be observed by VT-NMR. In total, 11 molecular structures have been characterized by X-ray diffraction. Open ring conformations with intermolecular π-π and Au-Au interactions prevail, but a backfolded conformation with a short intramolecular Au-Au distance has been found for the ethylene-bridged species. The presence of Au-Au interactions could be proven by quantum chemical calculations.

Enantiomerically pure trinuclear helicates via diastereoselective self-assembly and characterization of their redox chemistry.

A tris(bipyridine) ligand 1 with two BINOL (BINOL = 2,2'-dihydroxy-1,1'-binaphthyl) groups has been prepared in two enantiomerically pure forms. This ligand undergoes completely diastereoselective self-assembly into D2-symmeteric double-stranded trinuclear helicates upon coordination to copper(I) and silver(I) ions and to D3-symmetric triple-stranded trinuclear helicates upon coordination to copper(II), zinc(II), and iron(II) ions as demonstrated by mass spectrometry, NMR and CD spectroscopy in combination with quantum chemical calculations and X-ray diffraction analysis. According to the calculations, the single diastereomers that are formed during the self-assembly process are strongly preferred compared to the next stable diastereomers. Due to this strong preference, the self-assembly of the helicates from racemic 1 proceeds in a completely narcissistic self-sorting manner with an extraordinary high degree of self-sorting that proves the power and reliability of this approach to achieve high-fidelity diastereoselective self-assembly via chiral self-sorting to get access to stereochemically well-defined nanoscaled objects. Furthermore, mass spectrometric methods including electron capture dissociation MS(n) experiments could be used to elucidate the redox behavior of the copper helicates.

Identification and in vitro analysis of the GatD/MurT enzyme-complex catalyzing lipid II amidation in Staphylococcus aureus.

The peptidoglycan of Staphylococcus aureus is characterized by a high degree of crosslinking and almost completely lacks free carboxyl groups, due to amidation of the D-glutamic acid in the stem peptide. Amidation of peptidoglycan has been proposed to play a decisive role in polymerization of cell wall building blocks, correlating with the crosslinking of neighboring peptidoglycan stem peptides. Mutants with a reduced degree of amidation are less viable and show increased susceptibility to methicillin. We identified the enzymes catalyzing the formation of D-glutamine in position 2 of the stem peptide. We provide biochemical evidence that the reaction is catalyzed by a glutamine amidotransferase-like protein and a Mur ligase homologue, encoded by SA1707 and SA1708, respectively. Both proteins, for which we propose the designation GatD and MurT, are required for amidation and appear to form a physically stable bi-enzyme complex. To investigate the reaction in vitro we purified recombinant GatD and MurT His-tag fusion proteins and their potential substrates, i.e. UDP-MurNAc-pentapeptide, as well as the membrane-bound cell wall precursors lipid I, lipid II and lipid II-Gly5. In vitro amidation occurred with all bactoprenol-bound intermediates, suggesting that in vivo lipid II and/or lipid II-Gly5 may be substrates for GatD/MurT. Inactivation of the GatD active site abolished lipid II amidation. Both, murT and gatD are organized in an operon and are essential genes of S. aureus. BLAST analysis revealed the presence of homologous transcriptional units in a number of gram-positive pathogens, e.g. Mycobacterium tuberculosis, Streptococcus pneumonia and Clostridium perfringens, all known to have a D-iso-glutamine containing PG. A less negatively charged PG reduces susceptibility towards defensins and may play a general role in innate immune signaling.

Unexpected self-assembly of a homochiral metallosupramolecular M4L4 catenane.

Two enantiomerically pure 9,9'-spirobifluorene-based bis(pyridine) ligands 1 and 2 were prepared to study their self-assembly behavior upon coordination to cis-protected palladium(II) ions. Whereas the sterically more demanding ligand, 2, gave rise to the expected dinuclear metallosupramolecular M2L2 rhombi, the sterically less demanding ligand, 1, acts as a template to give rise to a homochiral metallosupramolecular M4L4 catenane.