Electron-rich pyridines with para-N-heterocyclic imine substituents: ligand properties and coordination to CO2, SO2, BCl3 and PdII complexes.

Electron-rich pyridines with π donor groups at the para position play an important role as nucleophiles in organocatalysis, but their ligand properties and utilization in coordination chemistry have received little attention. Herein, we report the synthesis of two electron-rich pyridines 1 and 2 bearing N-heterocyclic imine groups at the para position and explore their coordination chemistry. Experimental and computational methods were used to assess the donor ability of the new pyridines showing that they are stronger donors than aminopyridines and guanidinyl pyridines, and that the nature of the N-heterocyclic backbone has a strong influence on the pyridine donor strength. Coordination compounds with Lewis acids including the CO2, SO2, BCl3 and PdII ions were synthesized and characterized. Despite the ambident character of the new pyridines, coordination preferentially occurs at the pyridine-N atom. Methyl transfer experiments reveal that 1 and 2 can act as demethylation reagents.

Møller-Plesset Adiabatic Connection at Large Coupling Strengths for Open-Shell Systems.

We study the adiabatic connection that has as weak-coupling expansion the Møller-Plesset perturbation series, generalizing to the open-shell case previous closed-shell results for the large-coupling limit. We first focus on the hydrogen atom with fractional spins, providing results along the adiabatic connection from small to large coupling strengths. We reveal an intriguing phase diagram and an equation for the large-coupling leading order that has closed-form solutions for specific choices of its relevant quantum numbers. We then show that the hydrogen atom results provide variational estimates for the large-coupling leading terms for the general many-electron open-shell case in terms of functionals of the Hartree-Fock α-spin and ß-spin densities.

Receptor-like cytoplasmic kinases of different subfamilies differentially regulate SOBIR1/BAK1-mediated immune responses in Nicotiana benthamiana.

Cell-surface receptors form the front line of plant immunity. The leucine-rich repeat (LRR)-receptor-like kinases SOBIR1 and BAK1 are required for the functionality of the tomato LRR-receptor-like protein Cf-4, which detects the secreted effector Avr4 of the pathogenic fungus Fulvia fulva. Here, we show that the kinase domains of SOBIR1 and BAK1 directly phosphorylate each other and that residues Thr522 and Tyr469 of the kinase domain of Nicotiana benthamiana SOBIR1 are required for its kinase activity and for interacting with signalling partners, respectively. By knocking out multiple genes belonging to different receptor-like cytoplasmic kinase (RLCK)-VII subfamilies in N. benthamiana:Cf-4, we show that members of RLCK-VII-6, -7, and -8 differentially regulate the Avr4/Cf-4-triggered biphasic burst of reactive oxygen species. In addition, members of RLCK-VII-7 play an essential role in resistance against the oomycete pathogen Phytophthora palmivora. Our study provides molecular evidence for the specific roles of RLCKs downstream of SOBIR1/BAK1-containing immune complexes.

Genetic diversity of the banana Fusarium wilt pathogen in Cuba and across Latin America and the Caribbean.

Fusarium wilt of bananas (FWB) is a severe plant disease that leads to substantial losses in banana production worldwide. It remains a major concern for Cuban banana cultivation. The disease is caused by members of the soil-borne Fusarium oxysporum species complex. However, the genetic diversity among Fusarium species infecting bananas in Cuba has remained largely unexplored. In our comprehensive survey, we examined symptomatic banana plants across all production zones in the country, collecting 170 Fusarium isolates. Leveraging genotyping-by-sequencing and whole-genome comparisons, we investigated the genetic diversity within these isolates and compared it with a global Fusarium panel. Notably, typical FWB symptoms were observed in Bluggoe cooking bananas and Pisang Awak subgroups across 14 provinces. Our phylogenetic analysis revealed that F. purpurascens, F. phialophorum, and F. tardichlamydosporum are responsible for FWB in Cuba, with F. tardichlamydosporum dominating the population. Furthermore, we identified between five and seven distinct genetic clusters, with F. tardichlamydosporum isolates forming at least two subgroups. This finding underscores the high genetic diversity of Fusarium spp. contributing to FWB in the Americas. Our study sheds light on the population genetic structure and diversity of the FWB pathogen in Cuba and the broader Latin American and Caribbean regions.

Oomycete metabolism is highly dynamic and reflects lifestyle adaptations.

The selective pressure of pathogen-host symbiosis drives adaptations. How these interactions shape the metabolism of pathogens is largely unknown. Here, we use comparative genomics to systematically analyse the metabolic networks of oomycetes, a diverse group of eukaryotes that includes saprotrophs as well as pathogens of animal- and plant pathogens, the latter causing devastating diseases with significant economic and/or ecological impact. In our analyses of 44 oomycete species, we uncover considerable variation in metabolism that can be linked to lifestyle differences. Comparisons of metabolic gene content reveal that plant pathogenic oomycetes have a bipartite metabolism consisting of a conserved core and an accessory set. The accessory set can be associated with the degradation of defence compounds produced by plants when challenged by pathogens. Obligate biotrophic oomycetes have smaller metabolic networks, and taxonomically distantly related biotrophic lineages display convergent evolution by repeated gene losses in both the conserved as well as the accessory set of metabolism. When investigating to what extent the metabolic networks in obligate biotrophs differ from those in hemibiotrophic plant pathogens, we observe that the losses of metabolic enzymes in obligate biotrophs are not random and that gene losses predominantly influence the terminal branches of the metabolic networks. Our analyses represent the first metabolism-focused comparison of oomycetes at this scale and will contribute to a better understanding of the evolution of oomycete metabolism in relation to lifestyle adaptation.

Supramolecular compounds assembled from the heteroleptic tetrahedral complex [{CpMo(CO)2}2(µ,η2-AsSb)] and metal salts.

The reaction of the tetrahedral complex [{CpMo(CO)2}2(µ,η2-AsSb)] with CuI and AgI salts is presented which gives unprecedented neutral and cationic supramolecular aggregates featuring mixed As/Sb-donor molecules as ligands/linkers between metal ions.

Implications of the three-dimensional chromatin organization for genome evolution in a fungal plant pathogen.

The spatial organization of eukaryotic genomes is linked to their biological functions, although it is not clear how this impacts the overall evolution of a genome. Here, we uncover the three-dimensional (3D) genome organization of the phytopathogen Verticillium dahliae, known to possess distinct genomic regions, designated adaptive genomic regions (AGRs), enriched in transposable elements and genes that mediate host infection. Short-range DNA interactions form clear topologically associating domains (TADs) with gene-rich boundaries that show reduced levels of gene expression and reduced genomic variation. Intriguingly, TADs are less clearly insulated in AGRs than in the core genome. At a global scale, the genome contains bipartite long-range interactions, particularly enriched for AGRs and more generally containing segmental duplications. Notably, the patterns observed for V. dahliae are also present in other Verticillium species. Thus, our analysis links 3D genome organization to evolutionary features conserved throughout the Verticillium genus.

Segmental duplications drive the evolution of accessory regions in a major crop pathogen.

Many pathogens evolved compartmentalized genomes with conserved core and variable accessory regions (ARs) that carry effector genes mediating virulence. The fungal plant pathogen Fusarium oxysporum has such ARs, often spanning entire chromosomes. The presence of specific ARs influences the host range, and horizontal transfer of ARs can modify the pathogenicity of the receiving strain. However, how these ARs evolve in strains that infect the same host remains largely unknown. We defined the pan-genome of 69 diverse F. oxysporum strains that cause Fusarium wilt of banana, a significant constraint to global banana production, and analyzed the diversity and evolution of the ARs. Accessory regions in F. oxysporum strains infecting the same banana cultivar are highly diverse, and we could not identify any shared genomic regions and in planta-induced effectors. We demonstrate that segmental duplications drive the evolution of ARs. Furthermore, we show that recent segmental duplications specifically in accessory chromosomes cause the expansion of ARs in F. oxysporum. Taken together, we conclude that extensive recent duplications drive the evolution of ARs in F. oxysporum, which contribute to the evolution of virulence.

A mesoionic carbene stabilized nickel(II) hydroxide complex: a facile precursor for C-H activation chemistry.

We report the synthesis of a new nickel(II) hydroxide complex 2 supported by a rigid, tridentate triazolylidene-carbazolid ligand. The complex can be accessed in high yields following a simple and stepwise extraction protocol using dichloromethane and aqueous ammonium chloride followed by aqeous sodium hydroxide solution. We found that complex 2 is highly basic, undergoing various deprotonation/desilylation reactions with E-H and C-H acidic and silylated compounds. In this context we synthesized a variety of novel, functionalized nickel(II) complexes with trimethylsilylolate (3), trityl sulfide (4), tosyl amide (5), azido (6), pyridine (7), acetylide (8, 9), fluoroarene (10 & 11) and enolate (12) ligands. We furthermore found that 2 reacts with malonic acid dimethyl ester in a knoevennagel-type condensation reaction, giving access to a new enolate ligand in complex 13, consisting of two malonic acid units. Furthermore, complex 2 reacts with acetonitrile to form the cyanido complex 14. The formation of complexes 13 and 14 is particularly interesting, as they underline the potential of complex 2 in both C-C bond formation and cleavage reactions.

The soil-borne white root rot pathogen Rosellinia necatrix expresses antimicrobial proteins during host colonization.

Rosellinia necatrix is a prevalent soil-borne plant-pathogenic fungus that is the causal agent of white root rot disease in a broad range of host plants. The limited availability of genomic resources for R. necatrix has complicated a thorough understanding of its infection biology. Here, we sequenced nine R. necatrix strains with Oxford Nanopore sequencing technology, and with DNA proximity ligation we generated a gapless assembly of one of the genomes into ten chromosomes. Whereas many filamentous pathogens display a so-called two-speed genome with more dynamic and more conserved compartments, the R. necatrix genome does not display such genome compartmentalization. It has recently been proposed that fungal plant pathogens may employ effectors with antimicrobial activity to manipulate the host microbiota to promote infection. In the predicted secretome of R. necatrix, 26 putative antimicrobial effector proteins were identified, nine of which are expressed during plant colonization. Two of the candidates were tested, both of which were found to possess selective antimicrobial activity. Intriguingly, some of the inhibited bacteria are antagonists of R. necatrix growth in vitro and can alleviate R. necatrix infection on cotton plants. Collectively, our data show that R. necatrix encodes antimicrobials that are expressed during host colonization and that may contribute to modulation of host-associated microbiota to stimulate disease development.

A chromosome-level genome assembly of Zasmidium syzygii isolated from banana leaves.

Accurate taxonomic classification of samples from infected host material is essential for disease diagnostics and genome analyses. Despite the importance, diagnosis of fungal pathogens causing banana leaf diseases remains challenging. Foliar diseases of bananas are mainly caused by 3 Pseudocercospora species, of which the most predominant causal agent is Pseudocercospora fijiensis. Here, we sequenced and assembled four fungal isolates obtained from necrotic banana leaves in Bohol (Philippines) and obtained a high-quality genome assembly for one of these isolates. The samples were initially identified as P. fijiensis using PCR diagnostics; however, the assembly size was consistently 30 Mb smaller than expected. Based on the internal transcribed spacer (ITS) sequences, we identified the samples as Zasmidium syzygii (98.7% identity). The high-quality Zasmidium syzygii assembly is 42.5 Mb in size, comprising 16 contigs, of which 11 are most likely complete chromosomes. The genome contains 98.6% of the expected single-copy BUSCO genes and contains 14,789 genes and 10.3% repeats. The 3 short-read assemblies are less continuous but have similar genome sizes (40.4-42.4 Mb) and contain between 96.5 and 98.4% BUSCO genes. All 4 isolates have identical ITS sequences and are distinct from Zasmidium isolates that were previously sampled from banana leaves. We thus report the first continuous genome assembly of a member of the Zasmidium genus, forming an essential resource for further analysis to enhance our understanding of the diversity of pathogenic fungal isolates as well as fungal diversity.

NHC-Stabilized Mixed Group 13/14/15 Element Hydrides.

The syntheses of novel N-heterocyclic carbene (NHC) adducts of group 13, 14 and 15 element hydrides are reported. Salt metathesis reactions between NaPH2 and IDipp ⋅ GeH2 BH2 OTf (1) (IDipp=1,3-bis(2,6-diisopropylphenyl)imidazol-2-ylidene) led to mixtures of the two isomers IDipp ⋅ GeH2 BH2 PH2 (2 a) and IDipp ⋅ BH2 GeH2 PH2 (2 b); by altering the reaction conditions an almost exclusive formation of 2 b was achieved. Attempts to purify mixtures of 2 a and 2 b by re-crystallization from THF afforded a salt [IDipp ⋅ GeH2 BH2 ⋅ IDipp][PHGeH2 BH2 PH2 BH2 GeH2 ] (4) that contains the novel anionic cyclohexyl-like inorganic heterocycle [PHGeH2 BH2 PH2 BH2 GeH2 ]- . In addition, the borane adducts IDipp ⋅ GeH2 BH2 PH2 BH3 (3 a) and IDipp ⋅ BH2 GeH2 PH2 BH3 (3 b) as even longer chain compounds were obtained from reactions of 2 a/2 b with H3 B ⋅ SMe2 and were studied by NMR spectroscopy. Accompanying DFT computations give insight into the mechanism and energetics associated with 2 a/2 b isomerization as well as their decomposition pathways.

Characterization of the Ligand Properties of Donor-stabilized Pnictogenyltrielanes.

A general synthesis and the characterization of novel alkyl-substituted NHC-stabilized pnictogenylboranes NHC ⋅ BH2 ER2 (NHC=N-heterocyclic carbene, E=P, As; R2 =Me2 , Ph2 , t BuH, Cy2 , (SiMe3 )2 ) are reported. These compounds were reacted with Ni(CO)4 to the corresponding complexes of the type [(NHC ⋅ BH2 ER2 )Ni(CO)3 ] to determine their donor strength by Tolman Electronic Parameters (TEPs) and their steric demand as ligands compared to classical phosphines, superbasic phosphines and other commonly applied donor systems. The results show that the NHC-stabilized pnictogenyltrielanes can be considered as being highly basic, while their steric influence depends strongly on the organic residues as well as the donor attached to the {BH2 } moiety. Although weaker than commonly used superbasic phosphines, the donor strength of pnictogenyltrielanes in general can be classified as of similar strength as NHCs. The steric and electronic properties can easily be modified by alkyl substitution as evident from the TEP trends.

Large-Z atoms in the strong-interaction limit of DFT: Implications for gradient expansions and for the Lieb-Oxford bound.

We numerically study the strong-interaction limit of the exchange-correlation functional for neutral atoms and Bohr atoms as the number of electrons increases. Using a compact representation, we analyze the second-order gradient expansion, comparing it with the one for exchange (weak interaction limit). The two gradient expansions, at strong and weak interaction, turn out to be very similar in magnitude but with opposite signs. We find that the point-charge plus continuum model is surprisingly accurate for the gradient expansion coefficient at strong coupling, while generalized gradient approximations, such as Perdew-Burke-Ernzerhof (PBE) and PBEsol, severely underestimate it. We then use our results to analyze the Lieb-Oxford bound from the point of view of slowly varying densities, clarifying some aspects on the bound at a fixed number of electrons.

Uncoupled evolution of the Polycomb system and deep origin of non-canonical PRC1.

Polycomb group proteins, as part of the Polycomb repressive complexes, are essential in gene repression through chromatin compaction by canonical PRC1, mono-ubiquitylation of histone H2A by non-canonical PRC1 and tri-methylation of histone H3K27 by PRC2. Despite prevalent models emphasizing tight functional coupling between PRC1 and PRC2, it remains unclear whether this paradigm indeed reflects the evolution and functioning of these complexes. Here, we conduct a comprehensive analysis of the presence or absence of cPRC1, nPRC1 and PRC2 across the entire eukaryotic tree of life, and find that both complexes were present in the Last Eukaryotic Common Ancestor (LECA). Strikingly, ~42% of organisms contain only PRC1 or PRC2, showing that their evolution since LECA is largely uncoupled. The identification of ncPRC1-defining subunits in unicellular relatives of animals and fungi suggests ncPRC1 originated before cPRC1, and we propose a scenario for the evolution of cPRC1 from ncPRC1. Together, our results suggest that crosstalk between these complexes is a secondary development in evolution.

Novel synthetic route towards heteroleptic pnictogen-rich organometallic-inorganic coordination compounds.

The reaction of the Ag(I) dimer [Ag2(η2-A)2(µ,η1:η1-A)2][TEF]2 (A = [{CpMo(CO)2}2(µ,η2-P2)]) possessing labile η2-coordinated P2 ligands with the organometallic dipnictogen compounds [{CpMo(CO)2}2(µ,η2-EE')] (E = E' = As, Sb; E = P, E' = As, Sb) represents a facile synthetic route towards unprecedented heteroleptic pnictogen-rich supramolecular complexes. This method can also be extended to the analogous Cu(I) dimer and is studied by DFT computations.

Photoswitchable electron-rich phosphines: using light to modulate the electron-donating ability of phosphines.

The synthesis and properties of photoswitchable electron-rich phosphines containing N-heterocyclic imines equipped with a photochromic dithienylethene unit are reported. Heteronuclear NMR spectroscopy and UV/vis studies reveal that the imine substituents undergo reversible electrocyclic ring-closing and ring-opening reactions upon exposure to UV and visible light, respectively. The photoisomerization alters the electron-donating ability of the phosphines by up to ΔTEP = 8 cm-1.

Epigenetic regulation of nuclear processes in fungal plant pathogens.

Through the association of protein complexes to DNA, the eukaryotic nuclear genome is broadly organized into open euchromatin that is accessible for enzymes acting on DNA and condensed heterochromatin that is inaccessible. Chemical and physical alterations to chromatin may impact its organization and functionality and are therefore important regulators of nuclear processes. Studies in various fungal plant pathogens have uncovered an association between chromatin organization and expression of in planta-induced genes that are important for pathogenicity. This review discusses chromatin-based regulation mechanisms as determined in the fungal plant pathogen Verticillium dahliae and relates the importance of epigenetic transcriptional regulation and other nuclear processes more broadly in fungal plant pathogens.

Controlled introduction of functional groups at one P atom in [Cp*Fe(η5-P5)] and release of functionalised phosphines.

By salt metathesis reactions of the anionic complexes of the type [Cp*Fe(η4-P5R)]- (R = tBu (1a), Me (1b), -C[triple bond, length as m-dash]CPh (1c); Cp* = 1,2,3,4,5-pentamethylcyclopentadienyl) with organic electrophiles (XRFG; X = halogen; RFG = (CH2)3Br, (CH2)4Br, Me) a variety of organo-substituted polyphosphorus ligand complexes of the type [Cp*Fe(η4-P5RRFG)] (2) are obtained. Thereby, organic substituents with different functional groups (FG), such as halogens or nitriles, are introduced. In [Cp*Fe(η4-P5RR')] (2a: R = tBu, R' = (CH2)3Br), the bromine substituent can be easily substituted, leading to functionalized complexes [{Cp*Fe(η4-P5tBu)}(CH2)3{Cp*Fe(η4-P5Me)}] (4) and [Cp*Fe(η4-P5RR')] (5) (R = tBu, R' = (CH2)3PPh2) or by abstraction of a phosphine to the asymmetric substituted phosphine tBu(Bn)P(CH2)3Bn (6). The reaction of the dianionic species [K(dme)2]2[Cp*Fe(η4-P5)] (I') with bromo-nitriles leads to [Cp*Fe{η4-P5((CH2)3CN)2}] (7), allowing the introduction of two functional groups attached to one phosphorus atom. 7 reacts with ZnBr2 in a self-assembly reaction to form the supramolecular compound [Cp*Fe{η4-P5((CH2)3CN)2}ZnBr2]n (8).

A General Pathway towards NHC ⋠GaH2 (OTf) Adducts - The Key for the Synthesis of NHC-Stabilized Cationic 13/15 Chain Compounds of Gallium.

A general pathway towards NHC (NHC=N-heterocyclic carbene)-stabilized galliummonotriflates NHC ⋅ GaH2 (OTf) (NHC=IDipp, 1 a; IPr2 Me2 , 1 b; IMes, 1 c; IDipp=1,3-bis(2,6-diisopropylphenyl)-imidazolin-2-ylidene, IPr2 Me2 =1,3-bis-(diisopropyl)-4,5-dimethyl-imidazolin-2-ylidene, IMes=1,3-bis(2,4,6-trimethylphenyl)-imidazolin-2-ylidene) is reported. Quantum chemical calculations give detailed insight into the underlying reaction pathway. The obtained NHC ⋅ GaH2 (OTf) compounds were employed in reactions with donor-stabilized pnictogenylboranes to synthesize the elusive cationic parent 13/15/13 chain compounds [IDipp ⋅ GaH2 ER2 E'H2 ⋅ D][OTf] (3 a: D=IDipp, E=P, E'=B, R=H; 3 b: D=NMe3 , E=P, E'=B, R=H, 3 c: D=NMe3 , E=P, E'=B, R=Ph, 3 d: D=IDipp, E=P, E'=Ga, R=H). Supporting computational studies highlight the electronic features of the products.