Search

As(III) S-adenosylmethionine methyltransferases, pivotal enzymes in arsenic metabolism, facilitate the methylation of arsenic up to three times. This process predominantly yields trivalent mono- and dimethylarsenite, with trimethylarsine forming in smaller amounts. While this enzyme acts as a detoxifier in microbial systems by altering As(III), in humans, it paradoxically generates more toxic and potentially carcinogenic methylated arsenic species. The strong affinity of As(III) for cysteine residues, forming As(III)-thiolate bonds, is exploited in medical treatments, notably in arsenic trioxide (Trisenox®), an FDA-approved drug for leukemia. The effectiveness of this drug is partly due to its interaction with cysteine residues, leading to the breakdown of key oncogenic fusion proteins. In this study, we extend the understanding of As(III)'s binding mechanisms, showing that, in addition to As(III)-S covalent bonds, noncovalent O⋅⋅⋅As pnictogen bonding plays a vital role. This interaction significantly contributes to the structural stability of the As(III) complexes. Our crystallographic analysis using the PDB database of As(III) S-adenosylmethionine methyltransferases, augmented by comprehensive theoretical studies including molecular electrostatic potential (MEP), quantum theory of atoms in molecules (QTAIM), and natural bond orbital (NBO) analysis, emphasizes the critical role of pnictogen bonding in these systems. We also undertake a detailed evaluation of the energy characteristics of these pnictogen bonds using various theoretical models. To our knowledge, this is the first time pnictogen bonds in As(III) derivatives have been reported in biological systems, marking a significant advancement in our understanding of arsenic's molecular interactions., (© 2024 The Authors. Chemistry - An Asian Journal published by Wiley-VCH GmbH.)

Cocrystallization of the dimeric [Cu 2 (μ-I) 2 (CNXyl) 4 ] (Xyl = 2,6-Me 2 C 6 H 3 , 1 ) and polymeric catena -[Cu(μ-I)(CNC 6 H 3 -2-Cl-6-Me) 2 ] ( 2 ) complexes with I 2 at different molar ratios between the reactants resulted in a series of (RNC) 2 CuI-based crystal polyiodides formed along with gradual accumulation of iodine, namely the cocrystals [ 1 ·I 2 ]·[Cu(μ 1,1 -I 3 )(CNXyl) 2 ] 2 followed by the generation of [Cu(μ 1,3 -I 3 )(CNXyl) 2 ] 2 ·2I 2 ( 5 ·2I 2 ) or [Cu(μ 1,1 -I 3 )(CNC 6 H 3 -2-Cl-6-Me) 2 ] 2 and then [Cu(μ 1,3 -I 3 )(CNC 6 H 3 -2-Cl-6-Me) 2 ] n · n / 2 I 2 . The polyiodide 5 ·2I 2 exhibits a novel supramolecular motif─a purely inorganic halogen-bonded Cu 2 (μ 1,3 -I 3 ) 2 core in the chair conformation. The X-ray structure of 5 ·2I 2 featuring I···I contacts was analyzed by a set of theoretical methods and attributed to moderately strong halogen bonding (from -3.2 to -3.9 kcal/mol); these interactions determine the supramolecular architecture of 5 ·2I 2 .

Analyses of the Cambridge Structural Database and theoretical calculations (PBE0-D3/def2-TZVP level, atoms-in-molecules, natural bond orbital studies) prove the formation of net attractive noncovalent interactions between group 5 elements and electron-rich atoms (neutral or anionic). These kinds of bonding are markedly different from coordination bonds formed by the same elements and possess the distinctive features of σ-hole interactions. The term erythronium bond is proposed to denote these bonds. X-ray structures of vanadate-dependent bromoperoxidases show that these interactions are present also in biological systems., (© 2023 The Authors. Chemistry - A European Journal published by Wiley-VCH GmbH.)

Progress with fluorescent flippers, small-molecule probes to image membrane tension in living systems, has been limited by the effort needed to synthesize the twisted push-pull mechanophore. Here, we move to a higher oxidation level to introduce a new design paradigm that allows the screening of flipper probes rapidly, at best in situ . Late-stage clicking of thioacetals and acetals allows simultaneous attachment of targeting units and interfacers and exploration of the critical chalcogen-bonding donor at the same time. Initial studies focus on plasma membrane targeting and develop the chemical space of acetals and thioacetals, from acyclic amino acids to cyclic 1,3-heterocycles covering dioxanes as well as dithiolanes, dithianes, and dithiepanes, derived also from classics in biology like cysteine, lipoic acid, asparagusic acid, DTT, and epidithiodiketopiperazines. From the functional point of view, the sensitivity of membrane tension imaging in living cells could be doubled, with lifetime differences in FLIM images increasing from 0.55 to 1.11 ns. From a theoretical point of view, the complexity of mechanically coupled chalcogen bonding is explored, revealing, among others, intriguing bifurcated chalcogen bonds., Competing Interests: The authors declare the following competing financial interest(s): The University of Geneva has licensed Flipper-TR probes to Spirochrome for commercialization., (© 2023 The Authors. Published by American Chemical Society.)

Four manganese(iii) complexes, [MnL 1 (H 2 O) 2 ]ClO 4 ·H 2 O (1), [MnL 2 (H 2 O) 2 ]ClO 4 (2), [MnL 3 (DMSO)(H 2 O)]ClO 4 (3) and [MnL 4 (DMSO)(H 2 O)]ClO 4 (4), where H 2 L 1 = N , N '-bis(5-bromosalicylidene)-1,3-diaminopropane, H 2 L 2 = 2,2-dimethyl- N , N -bis(3-methyloxysalicylidene)-1,3-diaminopropane, H 2 L 3 = N , N '-bis(5-chlorosalicylidene)-2,2-dimethyl-1,3-diaminopropane and H 2 L 4 = 2-hydroxy- N , N '-bis(3-ethyloxysalicylidene)-1,3-diaminopropane are tetradentate N 2 O 2 -donor ligands and DMSO = dimethyl sulfoxide, have been synthesized and characterised by elemental analysis, IR and UV-vis spectroscopy and single-crystal X-ray diffraction studies. All are monomeric complexes. Complex 1 crystallises in orthorhombic space group P 2 1 2 1 2 1 , complex 3 crystallises in triclinic space group P -1, whereas complexes 2 and 4 crystallize in monoclinic space groups, C 2/ c and C 2/ m respectively. In all the complexes, manganese(iii) has a six-coordinated pseudo-octahedral geometry in which imine nitrogen atoms and phenolate oxygen atoms of the deprotonated di-Schiff base constitute the equatorial plane. In complexes 1 and 2, water molecules are present in the fifth and sixth coordination sites in the axial positions while in complexes 3 and 4 they are occupied by one water and one DMSO. The coordinated water molecules initiate hydrogen-bonded networks in all complexes. DFT calculations have been carried out to analyze two aspects of these complexes viz. the formation of halogen (HaB) and chalcogen bonding (ChB) interactions in complexes 1 and 3 where the electron donor is the perchlorate anion and the acceptor either bromine or chlorine atoms for the HaBs and the sulfur atom of the coordinated DMSO for the ChB. In addition, other intermolecular effects are discussed in the solid state for complexes 1, 2 and 4, where the hydrogen atoms of the coordinated water molecules interact with the electron rich cavities formed by the phenolate and alkyloxy oxygen atoms of the Schiff-base ligand., Competing Interests: The authors declare no conflict of interest., (This journal is © The Royal Society of Chemistry.)

The synthesis of fluorescein propargyl diether ( L ) and two different dinuclear gold(I) derivatives containing a water-soluble phosphane [1,3,5-triaza-7-phosphatricyclo[3.3.1.13.7]decane (PTA) for complex 1 and 3,7-diacetyl-1,3,7-triaza-5-phosphabicyclo[3.3.1]nonane (DAPTA) for complex 2 ] has been successfully performed. All compounds display intrinsic emission from fluorescein, being less intense for gold(I) complexes due to the heavy-atom effect. All compounds aggregate in acetonitrile/water mixtures with the formation of larger aggregates for those samples containing more water content, as evidenced by dynamic light scattering and small-angle X-ray scattering experiments, in agreement with the absorption and emission data. The emission of the samples increases when they are used to obtain luminescent materials with four different organic matrices [poly(methyl methacrylate, polystyrene (PS), cellulose, and Zeonex]. The compounds display very high values of singlet oxygen ( 1 O 2 ) production in dichloromethane. Singlet oxygen production was also evaluated in the doped matrices, being the highest in PS and with an exciting increase on PS microspheres. Density functional theory (BP86-D3) and GFN2-xTB calculations were used to model the assembly of L and complexes 1 and 2 with the different organic matrices and rationalize the experimental findings based on the geometries, molecular electrostatic potential surfaces, and complementarity and HOMO-LUMO gaps.

Cationic imidazoliumyl(phosphonio)-phosphanides [L C -P-PR 3 ] + ( 1a-e + , L C = 4,5-dimethyl-1,3-diisopropylimidazolium-2-yl; R = alkyl, aryl) are obtained via the nucleophilic fragmentation of tetracationic tetraphosphetane [(L C -P) 4 ][OTf] 4 ( 2 [OTf] 4 ) with tertiary phosphanes. They act as [L C -P] + transfer reagents in phospha-Wittig-type reactions, when converted with various thiocarbonyls, giving unprecedented cationic phosphaalkenes [L C -P═CR 2 ] + ( 5a-f [OTf]) or phosphanides [L C -P-CR(NR 2 ' )] + ( 6a-d [OTf]). Theoretical calculations suggest that three-membered cyclic thiophosphiranes are crucial intermediates of this reaction. To test this hypothesis, treatment of [L C -P-PPh 3 ] + with phosphaalkenes, that are isolobal to thioketones, permits the isolation of diphosphirane salts 11a,b [OTf]. Furthermore, preliminary studies suggest that the cationic phosphaalkene [L C -P═CPh 2 ] + may be employed to access rare examples of η 2 -P═C π-complexes with Pd 0 and Pt 0 when treated with [Pd(PPh 3 ) 4 ] and [Pt(PPh 3 ) 3 ] for which analogous complexes of neutral phosphaalkenes are scarce. The versatility of [L C -P] + as a valuable P 1 building block was showcased in substitution reactions of the transferred L C -substituent using nucleophiles. This is demonstrated through the reactions of 5a [OTf] and 6c [OTf] with Grignard reagents and KNPh 2 , providing a convenient, high-yielding access to MesP═CPh 2 ( 16 ) and otherwise difficult-to-synthesize 1,3-diphosphetane 17 and P-aminophosphaalkenes.

The relevance of hydrogen-bonding, π-π stacking and aurophilic interactions in the solid-state of two new heterobimetallic (Au I -Mn II ) complexes is analyzed in this manuscript. They are discrete complexes of formulae [Mn(bipy) 2 (H 2 O){Au(CN) 2 }][Au(CN) 2 ] and [Mn(dmbipy) 2 {Au(CN) 2 }] ⋅ H 2 O, (bipy=2,2'-bipyridine and dmbipy=5,5'-dimethyl-2,2'-bipyridine), which are based on dicyanidoaurate(I) groups and 2,2'-bipyridyl-like co-ligands. They have been synthesized in good yields and X-ray characterized. In both compounds, aurophilic, OH⋅⋅⋅N hydrogen bonding and π-π interactions governed the supramolecular assemblies in the solid state. These contacts with special emphasis on the aurophilic interactions have been studied using density functional theory calculations and characterized using the quantum theory of atoms-in-molecules and the noncovalent interaction plot. The aurophilic contacts have been also rationalized from an orbital point of view using the natural bond orbital methodology, evidencing stabilization energies up to 5.7 kcal/mol. Moreover, the interaction energies have been decomposed using the Kitaura-Morokuma energy decomposition analysis, confirming the importance of electrostatic and orbital effects., (© 2023 The Authors. ChemPlusChem published by Wiley-VCH GmbH.)

Unraveling the binding preferences involved in the formation of a supramolecular complex is key to properly understand molecular recognition and aggregation phenomena, which are of pivotal importance to biology. The halogenation of nucleic acids has been routinely carried out for decades to assist in their X-ray diffraction analysis. The incorporation of a halogen atom on a DNA/RNA base not only affected its electronic distribution, but also expanded the noncovalent interactions toolbox beyond the classical hydrogen bond (HB) by incorporating the halogen bond (HalB). In this regard, an inspection of the Protein Data Bank (PDB) revealed 187 structures involving halogenated nucleic acids (either unbound or bound to a protein) where at least 1 base pair (BP) exhibited halogenation. Herein, we were interested in disclosing the strength and binding preferences of halogenated A···U and G···C BPs, which are predominant in halogenated nucleic acids. To achieve that, computations at the RI-MP2/def2-TZVP level of theory together with state of the art theoretical modeling tools (including the computation of molecular electrostatic potential (MEP) surfaces, the quantum theory of "Atoms in Molecules" (QTAIM) and the non-covalent interactions plot (NCIplot) analyses) allowed for the characterization of the HB and HalB complexes studied herein.

A discrete π-hole···σ-hole dimer is synthesized and X-ray characterized. It presents a perfect thumbtack geometry where the σ-hole of the linear [AuI 2 ] - anion points to the π-hole located above the central Au-atom of the [AuI 4 ] - anion. Such discrete π-hole···σ-hole dimers are unprecedented in literature, since all mixed-valence gold(I/III) iodide compounds reported to date form infinite ···([AuI 4 ] - ···[AuI 2 ] - ) n ·· chains in the solid state. If an excess of iodine is used for the synthesis, triiodide [I 3 ] - ions are partially incorporated into the [AuI 2 ] - sites, forming infinite chains. The nature of the anion···anion interaction has been studied considering two possibilities: (i) a π-hole coinage bond or (ii) σ-hole halogen bond using high-level density functional theory calculations, the quantum theory of atoms in molecules, and the noncovalent interaction plot index., Competing Interests: The authors declare no competing financial interest., (© 2022 The Authors. Published by American Chemical Society.)

Cocrystallization of a bis[1-(4-pyridyl)butane-1,3-dionato]copper(II) (1) complex and 1,4-diiodoperfluorobenzene in the presence of pyridine yields a 1 : 1 cocrystal where both the σ and π-holes of 1,4-diiodoperfluorobenzene play a role. The crystal structure shows short arene CuO 4 ⋯π-hole stacking contacts, where the {d z 2 -Cu II O 4 } moiety functions as an integrated five-center π-hole acceptor. DFT calculations combined with quantum theory of atoms-in-molecules and noncovalent interaction plot analyses corroborated the structure-defining role of the {d z 2 -Cu II O 4 }⋯π-hole contacts.

A new Ni(ii) complex [NiL] (complex 1) of an asymmetrically di-condensed N 2 O 3 donor Schiff base ligand, N-salicylidene-N'-3-methoxysalicylidene-1,3-propanediamine (H 2 L), has been synthesized and utilized for the synthesis of three heterometallic complexes, [(NiL) 2 Mn(NCS) 2 (CH 3 OH) 2 ]·CH 3 OH (2) [(NiL) 2 Mn(N(CN) 2 ) 2 (CH 3 OH) 2 ]·CH 3 OH (3) and [(NiL) 2 Mn 2 (N 3 ) 2 (μ 1,1 -N 3 ) 2 (CH 3 OH) 2 ] (4). Single crystal X-ray diffraction analyses show that complexes 2 and 3 have linear trinuclear structures where two tridentate O 3 donor (NiL) units are coordinated to the central octahedral Mn(ii) centre, whereas complex 4 has a centrosymmetric tetranuclear structure where two binuclear (NiL)Mn units are linked via two phenoxido and two μ 1,1 -N 3 bridges. Among the heterometallic complexes (2-4), only 4 is active towards the catalytic oxidation of 3,5-di-tert-butylcatechol to the corresponding quinone. The turnover number for the aerobic oxidation of 3,5-DTBC is 935 h -1 . ESI-mass spectra have been recorded to scrutinize the mechanistic pathway of this catalytic reaction. Variable temperature magnetic susceptibility measurements suggest that complexes 2-4 are antiferromagnetically coupled with coupling constants (J) of -4.84 and -5.23 cm -1 for complexes 2 and 3, respectively and J 1 = -2.20 cm -1 , J 2 = 1.13 cm -1 and J 3 = -1.12 cm -1 for complex 4. DFT calculations have been used to rationalize the magnetic super-exchange in complexes 2-4, by computing the theoretical coupling constants and analyzing the spin density plots.

Two phosphorescent Pt II -based cyclometalated complexes were co-crystallized with perfluorinated arenes to give 1:1 co-crystals. The X-ray study revealed that each of the complexes is embraced by arenes F to give infinite reverse sandwich structures. In four out of six structures, a d z 2 orbital of Pt II is directed to the arenes F ring via π-hole··· d z 2 [Pt II ] interactions, whereas in the other two structures, the filled d z 2 orbital is directed toward the arene C atoms. Computed molecular electrostatic potential surfaces of the arenes F and the complexes, noncovalent interaction indexes for the co-crystals, and natural bond orbital calculations indicate that π-hole··· d z 2 [Pt II ] contacts (and, generally, the stacking) are of electrostatic origin. The solid-state photophysical study revealed up to 3.5-fold luminescence quantum yield and 15-fold lifetime enhancements in the co-crystals. This increase is associated with the strength of the π-hole··· d z 2 [Pt II ] contact that is dependent on the π-acidity of the arene F and its spatial characteristics.

A noble gas bond (also known in the literature as aerogen bond) can be defined as the attractive interaction between any element of group-18 acting as a Lewis acid and any electron rich atom of group of atoms, thus following the IUPAC recommendation available for similar π,σ-hole interactions involving elements of groups 17 (halogens) and 16 (chalcogens). A significant difference between noble gas bonding (NgB) and halogen (HaB) or chalcogen (ChB) bonding is that whilst the former is scarcely found in the literature, HaB and ChB are very common and their applications in important fields like catalysis, biochemistry or crystal engineering have exponentially grown in the last decade. This article combines theory and experiment to highlight the importance of non-covalent NgBs in the solid state of several xenon fluorides [XeF n ] m+ were the central oxidation state of Xe varies from +2 to +6 and the number of fluorine atoms varies from n = 2 to 6. The compounds with an odd number of fluorine atoms ( n = 3 and 5) are cationic ( m = 1). The Inorganic Crystal Structural Database (ICSD) strongly evidences the relevance of NgBs in the solid state structures of xenon derivatives. The ability of Xe compounds to participate in π,σ-hole interactions has been studied using different types of electron donors (Lewis bases and anions) using DFT calculations (PBE1PBE-D3/def2-TZVP) and the molecular electrostatic potential (MEP) surfaces., (Copyright © 2020 Gomila and Frontera.)

Pseudomonas is the bacterial genus of Gram-negative bacteria with the highest number of recognized species. It is divided phylogenetically into three lineages and at least 11 groups of species. The Pseudomonas putida group of species is one of the most versatile and best studied. It comprises 15 species with validly published names. As a part of the Genomic Encyclopedia of Bacteria and Archaea (GEBA) project, we present the genome sequences of the type strains of five species included in this group: Pseudomonas monteilii (DSM 14164 T ), Pseudomonas mosselii (DSM 17497 T ), Pseudomonas plecoglossicida (DSM 15088 T ) , Pseudomonas taiwanensis (DSM 21245 T ) and Pseudomonas vranovensis (DSM 16006 T ). These strains represent species of environmental and also of clinical interest due to their pathogenic properties against humans and animals. Some strains of these species promote plant growth or act as plant pathogens. Their genome sizes are among the largest in the group, ranging from 5.3 to 6.3 Mbp. In addition, the genome sequences of the type strains in the Pseudomonas taxonomy were analysed via genome-wide taxonomic comparisons of ANIb, gANI and GGDC values among 130 Pseudomonas strains classified within the group. The results demonstrate that at least 36 genomic species can be delineated within the P. putida phylogenetic group of species., Competing Interests: The authors declare that there are no conflicts of interest., (© 2019 The Authors.)