Competition between Halogen, Hydrogen and Dihydrogen Bonding in Brominated Carboranes

Chalcogen-Bond-Assisted Formation of the N→C Dative Bonds in the Complexes between Chalcogenadiazoles/Chalcogenatriazoles and Fullerene C60

The existence of the N→C dative bonds in the complexes between N-containing molecules and fullerenes have been verified both theoretically and experimentally. However, finding stable N→C dative bonds is still a highly challenging task. In this work, we investigated computationally the N→C dative bonds in the complexes formed by fullerene C60 with 1,2,5-chalcogenadiazoles, 2,1,3-benzochalcogenadiazoles, and 1,2,4,5-chalcogenatriazoles, respectively. It was found that the N→C dative bonds are formed along with the formation of the N-Ch···C (Ch = S, Se, Te) chalcogen bonds. In the gas phase, from S-containing complexes through Se-containing complexes to Te-containing complexes, the intrinsic interaction energies become more and more negative, which indicates that the N-Ch···C chalcogen bonds can facilitate the formation of the N→C dative bonds. The intrinsic interaction energies are compensated by the large deformation energy of fullerene C60. The total interaction energies of Te-containing complexes are negative, while both total interaction energies of the S-containing complexes and Se-containing complexes are positive. This means that the N→C dative bonds in the Te-containing complexes are more easily observed in experiments in comparison with those in the S-containing complexes and Se-containing complexes. This study provides a new theoretical perspective on the experimental observation of the N→C dative bonds in complexes involving fullerenes. Further, the formation of stable N→C dative bonds in the complexes involving fullerenes can significantly change the properties of fullerenes, which will greatly simulate and expand the application range of fullerenes.

A Method for Highly Selective Halogenation of o-Carboranes and m-Carboranes

A facile halogenation method for highly selective synthesis of 9-X-o-carboranes, 9,12-X₂-o-carboranes, 9-X-12-X'-o-carboranes, 9-X-m-carboranes, 9,10-X₂-m-carboranes, and 9-X-10-X'-m-carboranes (X, X' = Cl, Br, I) has been developed on the basis of our previous work. The success of this transformation relies on the usage of trifluoromethanesulfonic acid (HOTf), the easily available strong Brønsted acid. The addition of HOTf greatly increases the electrophilicity of N-haloamides through hydrogen bonding interaction, resulting in the low loading of N-haloamides, short reaction time, and mild reaction conditions. Additionally, the solvent 1,1,1,3,3,3-hexafluoro-2-propanol (HFIP) is also essential to further increase the acidity of HOTf.

How the Position of Substitution Affects Intermolecular Bonding in Halogen Derivatives of Carboranes: Crystal Structures of 1,2,3- and 8,9,12-Triiodo- and 8,9,12-Tribromo ortho-Carboranes

The crystal structures of two isomeric triiodo derivatives of ortho-carborane containing substituents in the three most electron-withdrawing positions of the carborane cage, 1,2,3-I₃-1,2-C₂B₁₀H₉, and the three most electron-donating positions, 8,9,12-I₃-1,2-C₂B₁₀H₉, as well as the crystal structure of 8,9,12-Br₃-1,2-C₂B₁₀H₉, were determined by single-crystal X-ray diffraction. In the structure of 1,2,3-I₃-1,2-C₂B₁₀H₉, an iodine atom attached to the boron atom (position 3) donates its lone pairs simultaneously to the σ-holes of both iodine atoms attached to the carbon atoms (positions 1 and 2) with the I⋯I distance of 3.554(2) Å and the C-I⋯I and B-I⋯I angles of 169.2(2)° and 92.2(2)°, respectively. The structure is additionally stabilized by a few B-H⋯I-shortened contacts. In the structure of 8,9,12-I₃-1,2-C₂B₁₀H₉, the I⋯I contacts of type II are very weak (the I⋯I distance is 4.268(4) Å, the B8-I8⋯I12 and B12-I12⋯I8 angles are 130.2(3)° and 92.2(3)°) and can only be regarded as dihalogen bonds formally. In comparison with the latter, the structure of 8,9,12-Br₃-1,2-C₂B₁₀H₉ demonstrates both similarities and differences. No Br⋯Br contacts of type II are observed, while there are two Br⋯Br halogen bonds of type I.

Reactivity of Perhalogenated Octahedral Phospha- and Arsaboranes toward THF: A Joint Experimental/Computational Study

Reactions of the perhalogenated polyhedral pnictogenaboranes closo-1,2-Pn₂B₄Hal₄ (Pn = P, As; Hal = Cl, Br) with Lewis bases are presently being studied with a focus on rationalizing the sites of nucleophilic attacks on clusters bearing σ-holes. These σ-holes are localized both on pnictogens and, for Hal = Br, on bromine atoms, as revealed by electrostatic potential (ESP) and intrinsic bond orbital (IBO) analyses. Surprisingly, the attack of the cyclic ether THF on closo-1,2-Pn₂B₄Br₄ does not occur on the site with the largest positive partial charge, centered in the middle of the pnictogen-pnictogen vector. Instead, presumably promoted by the positivated bromine substituents, THF inserts into the boron-bromine bonds of the negatively charged boron atoms opposite to the pnictogen atoms to form 4-(4-bromobut-1-oxy)-closo-1,2-Pn₂B₄Br₃ (1-PB and 1-AsB) and 4,6-(4-bromobut-1-oxy)₂-closo-1,2-Pn₂B₄Br₂ (2-PB and 2-AsB). ¹¹B and ³¹P chemical shift computations at various levels support the assignments of the signals, which reflect the correctness of the molecular geometries in solutions. The Lewis-acidic perchlorinated analogues closo-1,2-P₂B₄Cl₄, closo-1,2-As₂B₄Cl₄, and the mixed closo-1,2-AsPB₄Cl₄ bear negative charges. These negative charges are revealed by the V_s,max values when computing the electrostatic potentials both on the boron and the chlorine atoms. Due to this negative charge, the analogues do not react with THF unless they are heated above 66 °C, where they slowly decompose to borate esters B(OR)₃ without the formation of concrete intermediates. The evaluation of ³¹P NMR data of 1-PB has allowed the experimental determination of the coupling constant ¹J(³¹P(1), ³¹P(2)) = |143| Hz in a closo-diphosphaborane for the first time, which agrees well with the computed value of -178 Hz. The pioneering joint experimental vs computational interpretation of ³¹P NMR spectra in the area of boron cluster chemistry was decisive for the structural characterization of 1-PB and 2-PB.

Practical Synthesis of B(9)-Halogenated Carboranes with N-Haloamides in Hexafluoroisopropanol

The B(9)-H halogenation of o-carborane and m-carborane was achieved with excellent selectivities in hexafluoroisopropanol (HFIP) under simple reaction conditions: single reagent [trichloroisocyanuric acid (TCCA), tribromoisocyanuric acid (TBCA) or N-iodosuccinimide (NIS)], catalyst-free, air-/moisture-tolerant, and convenient work-up. With this method, a variety of 9-halogenated o-carboranes and m-carboranes were obtained in good to excellent yields with broad tolerance of functional groups.

Synthesis and Crystal Structure of 9,12-Dibromo-ortho-Carborane

Synthesis, NMR spectral data and crystal structure of 9,12-dibromo derivative of ortho-carborane are reported.

Dimerization-Induced Solid-State Excimer Emission Showing Consecutive Thermochromic Luminescence Based on Acridine-Modified o-Carboranes

Although excimer emission is a useful luminescent phenomenon for fabricating optical sensors and probes, it is difficult to apply excimer emission for film sensors due to critical concentration quenching in the solid state. Therefore, robust molecular designs for solid-state excimer emission are still being explored. One of the key examples is the previously reported acridine-ethynyl-o-carborane AcE1, which showed a bright solid-state excimer emission assisted by characteristic C_cageH···N interactions. In this paper, we report the newly synthesized acridine-diehynyl-o-carborane AcE2 and comprehensively compare it to AcE1. Both compounds had the same crystalline packing mode based on dimer formation, resulting in an efficient π-overlapping area and solid-state excimer emission. Variable-temperature photoluminescence (VT-PL) measurements revealed the consecutive thermochromic luminescence of these compounds. Finally, on the basis of the easily accessible spray-coating method, we constructed the thermochromic luminescent sensors on quartz substrates. According to the mechanistic studies, it is demonstrated that the design strategy based on a dimer-induced solid-state excimer should have great potential for applications as a molecular thermometer.

1,12-Diiodo-Ortho-Carborane: A Classic Textbook Example of the Dihalogen Bond

The crystal structure of 1,12-diiodo-ortho-carborane 1,12-I2-1,2-C2B10H10 was determined by single crystal X-ray diffraction. In contrary to earlier studied 1,12-dibromo analogue 1,12-Br2-1,2- C2B10H10, its crystal packing is governed by the presence of the intermolecular I⋯I dihalogen bonds between the iodine atom attached to the carbon atom (acceptor) and the iodine atom attached to the antipodal boron atom (donor) of the carborane cage. The observed dihalogen bonds belong to the II type and are characterized by classical parameters: shortened I⋯I distance of 3.5687(9) Å, C–I⋯I angle of 172.61(11)° and B–I⋯I angle of 92.98(12)°.

Strong σ-Hole Activation on Icosahedral Carborane Derivatives for a Directional Halide Recognition

Crystal engineering based on σ-hole interactions is an emerging approach for realization of new materials with higher complexity. Neutral inorganic clusters derived from 1,2-dicarba-closo-dodecaborane, substituted with -SeMe, -TeMe, and -I moieties on both skeletal carbon vertices are experimentally demonstrated herein as outstanding chalcogen- and halogen-bond donors. In particular, these new molecules strongly interact with halide anions in the solid-state. The halide ions are coordinated by one or two donor groups (μ₁ - and μ₂ -coordinations), to stabilize a discrete monomer or dimer motifs to 1D supramolecular zig-zag chains. Crucially, the observed chalcogen bond and halogen bond interactions feature remarkably short distances and high directionality. Electrostatic potential calculations further demonstrate the efficiency of the carborane derivatives, with V_s,max being similar or even superior to that of reference organic halogen-bond donors, such as iodopentafluorobenzene.

Understanding noncovalent bonds and their controlling forces

The fundamental underpinnings of noncovalent bonds are presented, focusing on the σ-hole interactions that are closely related to the H-bond. Different means of assessing their strength and the factors that control it are discussed. The establishment of a noncovalent bond is monitored as the two subunits are brought together, allowing the electrostatic, charge redistribution, and other effects to slowly take hold. Methods are discussed that permit prediction as to which site an approaching nucleophile will be drawn, and the maximum number of bonds around a central atom in its normal or hypervalent states is assessed. The manner in which a pair of anions can be held together despite an overall Coulombic repulsion is explained. The possibility that first-row atoms can participate in such bonds is discussed, along with the introduction of a tetrel analog of the dihydrogen bond.

Bromination Mechanism of closo-1,2-C2 B10 H12 and the Structure of the Resulting 9-Br-closo-1,2-C2 B10 H11 Determined by Gas Electron Diffraction

9-Br-closo-1,2-C₂ B₁₀ H₁₁ has been prepared and its gas-phase structure has been examined by means of gas electron diffraction. The structure of the carbaborane core is similar to the structure of the parent compound, which is of C_2v symmetry. A DFT-based search for the corresponding reaction pathway of the bromination of closo-1,2-C₂ B₁₀ H₁₂ revealed that the catalytic amount of aluminum reduces the barrier of the initial attack of the bromination agent toward the negatively charged part of the icosahedral carbaborane, i. e., the first transition state, from about 40 to about 27 kcalmol^-1 . The Br-Br bond is weakened by an intermediate binding to the large π-hole on the aluminum atom of AlBr₃ , which is the driving force for the AlBr₃ -catalyzed bromination.

Complexation and stability of the fungicide penconazole in the presence of zinc and copper ions

RATIONALE

For the risk assessment of penconazole in the environment and the evaluation of the possible consequences of its use, it is important to determine how its reactivity and degradation are influenced by metals commonly found in nature, such as copper and zinc.

METHODS

Changes in the reactivity of penconazole in the presence of zinc/copper ions were studied using electrospray ionisation mass spectrometry and density functional theory calculations.

RESULTS

Many penconazole complexes with copper and zinc ions were created; a comparison of the elements showed that a few complexes were formed analogously (doubly charged complexes with four penconazole molecules, singly charged complexes with chlorine as a counterion and singly charged complexes with deprotonated penconazole as a counterion). The metal complexes with different structures indicated different reactivity of penconazole with copper and zinc.

CONCLUSIONS

The experimental and computational approaches have revealed different changes in the structure of penconazole. In the Zn(II) complex, penconazole deprotonated to stabilise the bond to Zn(II). In the Cu(II) complex, it loses one chlorine atom, creates an additional ring between the triazole ring and the phenyl ring, and/or creates a double bond in the short aliphatic chain.

Hydrogen vs. Halogen Bonds in 1-Halo-Closo-Carboranes

A theoretical study of the hydrogen bond (HB) and halogen bond (XB) complexes between 1-halo-closo-carboranes and hydrogen cyanide (NCH) as HB and XB probe has been carried out at the MP2 computational level. The energy results show that the HB complexes are more stable than the XBs for the same system, with the exception of the isoenergetic iodine derivatives. The analysis of the electron density with the quantum theory of atoms in molecules (QTAIM) shows the presence of a unique intermolecular bond critical point with the typical features of weak noncovalent interactions (small values of the electron density and positive Laplacian and total energy density). The natural energy decomposition analysis (NEDA) of the complexes shows that the HB and XB complexes are dominated by the charge-transfer and polarization terms, respectively. The work has been complemented with a search in the CSD database of analogous complexes and the comparison of the results, with those of the 1-halobenzene:NCH complexes showing smaller binding energies and larger intermolecular distances as compared to the 1-halo-closo-carboranes:NCH complexes.

The Influence of Halogenated Hypercarbon on Crystal Packing in the Series of 1-Ph-2-X-1,2-dicarba-closo-dodecaboranes (X = F, Cl, Br, I)

Although 1-Ph-2-X-closo-1,2-C₂B₁₀H₁₀ (X = F, Cl, Br, I) derivatives had been computed to have positive values of the heat of formation, it was possible to prepare them. The corresponding solid-state structures were computationally analyzed. Electrostatic potential computations indicated the presence of highly positive σ-holes in the case of heavy halogens. Surprisingly, the halogen•••π interaction formed by the Br atom was found to be more favorable than that of I.

The ditetrel bond: noncovalent bond between neutral tetrel atoms

The ability of a tetrel atom to serve in the capacity of electron donor in a σ-hole noncovalent bond is tested by quantum calculations.

Chalcogen Bonding due to the Exo-Substitution of Icosahedral Dicarbaborane

Chalcogen atoms are a class of substituents capable of generating inner and outer derivatives of boron clusters. It is well known that chalcogenated boron clusters can form strong σ-hole interactions when a chalcogen atom is a part of an icosahedron. This paper studies σ-hole interactions of dicarbaboranes with two exopolyhedral chalcogen atoms bonded to carbon vertices. Specifically, a computational investigation has been carried out on the co-crystal of (1,2-C₂B₁₀H₁₀)₂Se₄•toluene and a single crystal of (1,2-C₂B₁₀H₁₀)₂Te₄.

Halogen bonding in mono- and dihydrated halobenzene

Density functional theory calculations were performed on halogen-bonded and hydrogen-bonded systems consisting of a halobenzene (XPh; X = F, Cl, Br, I, and At) and one or two water molecules, using the M06-2X density functional with the 6-31+G(d) (for C, H, F, Cl, and Br) and aug-cc-pVDZ-PP (for I, At) basis sets. The counterpoise procedure was performed to counteract the effect of basis set superposition error. The results show halogen bonds form in the XPh-H₂ O system when X > Cl. There is a trend toward stronger halogen bonding as the halogen group is descended, as assessed by interaction energy and X•••O_w internuclear separation (where O_w is the water oxygen). For all XPh-H₂ O systems hydrogen-bonded systems exist, containing a combination of CH•••O_w and O_w H_w •••X hydrogen bonds. For all systems except X = At the X•••H_w hydrogen-bonding interaction is stronger than the X•••O_w halogen bond. In the XPh-(H₂ O)₂ system halogen bonds form only for X > Br. The two water molecules prefer to form a water dimer, either located around the CH bond (for X = Br, At, and I) or located above the benzene ring (for all halogens). Thus, even in the absence of competing strong interactions, halogen bonds may not form for the lighter halogens due to (1) competition from cooperative weak interactions such as CH•••O and OH•••X hydrogen bonds, or (2) if the formation of the halogen bond would preclude the formation of a water dimer. © 2018 Wiley Periodicals, Inc.

Dihalogen and Pnictogen Bonding in Crystalline Icosahedral Phosphaboranes

Noncovalent interactions in the single crystal of 3,6-Cl2-closo-1,2-P2B10H8 and in the crystal of closo-1,7-P2B10Cl10•toluene were analyzed by means of quantum chemical computations. The crystal packing in the second crystal was dominated by numerous B-Cl···Cl-B dihalogen and strong B-P···π pnictogen bonds, the latter of which were characterized by a small length of 3.08 Å and a large interaction energy value, exceeding −10 kcal mol−1.

Outerly functionalized and non-functionalized boron clusters intercalated into layered hydroxides with different modes of binding: materials for superacid storage

Two binary boron hydrides (NH4)2B10H10 and Na2B12H12 and mono- and dicarboxy p- and m-carboranes (namely, 1-(COOH)-closo-1,7-C2B10H11, 1,12-(COOH)2-closo-1,12-C2B10H10 and 1,7-(COOH)2-closo-1,7-C2B10H10) were intercalated into ZnAl-layered double hydroxides (ZnAl-LDH) and into Zn5(OH)8(NO3)2·2H2O. The formed compounds were characterized using elemental analysis, thermogravimetry analysis, X-ray powder diffraction, infrared spectroscopy and solid state NMR. All the intercalated boron compounds are present in the interlayer space of the layered hosts as anions. It is presumed that in the case of B10H102-, B12H122- and 1,12-(COO)2-closo-1,12-C2B10H102-, the guest molecules form a monolayer, whereas in the case of 1-(COO)-closo-1,7-C2B10H111- and 1,7-(COO)2-closo-1,7-C2B10H102- a bilayer arrangement is more probable. In the case of 1,7-(COO)2-closo-1,7-C2B10H102-, the guest molecules are strongly interdigitated resulting in lowering of the interlayer distance. Two different modes of binding were found. Whereas the carboxylate derivatives of p- and m-carboranes are bonded through classical hydrogen bonds, the corresponding parent borane anions interact with the host structures by mainly dihydrogen bonding. In effect, both kinds of hydrogen bonding are mainly of an electrostatic nature. The dihydrogen bond is detected, e.g. in crystal engineering, and represents a driving force for interactions of boranes with biomolecules. Since the latter dicarboxylic acids were found to be superacids, their interactions with the host structures should be stronger than in the case of the benzoic and terephthalic acid intercalates.

Chalcogen Bonding in Protein-Ligand Complexes: PDB Survey and Quantum Mechanical Calculations

A chalcogen bond is a nonclassical noncovalent interaction which can stabilise small-molecule crystals as well as protein structures. Here, we systematically explore the stabilising potential of chalcogen bonding in protein-ligand complexes in the Protein Data Bank (PDB). We have found that a large fraction (23 %) of complexes with a S/Se-containing ligand feature close S/Se⋅⋅⋅O/N/S contacts. Eleven non-redundant representative potential S/Se⋅⋅⋅O chalcogen-bond motifs were selected and truncated to model systems and seven more model systems were prepared by S-to-Se substitution. These systems were then subjected to analysis by quantum chemical (QM) methods-electrostatic potential, geometry optimisation or interaction energy calculations, including solvent effects. The QM calculations indicate that chalcogen bonding does indeed play a dominant role in stabilising some of the interaction motifs studied. We thus advocate further exploration of chalcogen bonding with the aim of potential future use in structure-based drug design.

Comparative Strengths of Tetrel, Pnicogen, Chalcogen, and Halogen Bonds and Contributing Factors

Ab initio calculations are employed to assess the relative strengths of various noncovalent bonds. Tetrel, pnicogen, chalcogen, and halogen atoms are represented by third-row atoms Ge, As, Se, and Br, respectively. Each atom was placed in a series of molecular bonding situations, beginning with all H atoms, then progressing to methyl substitutions, and F substituents placed in various locations around the central atom. Each Lewis acid was allowed to engage in a complex with NH₃ as a common nucleophile, and the strength and other aspects of the dimer were assessed. In the context of fully hydrogenated acids, the strengths of the various bonds varied in the pattern of chalcogen > halogen > pnicogen ≈ tetrel. Methyl substitution weakened all bonds, but not in a uniform manner, resulting in a greatly weakened halogen bond. Fluorosubstitution strengthened the interactions, increasing its effect as the number of F atoms rises. The effect was strongest when the F atom lay directly opposite the base, resulting in a halogen > chalcogen > pnicogen > tetrel order of bond strength. Replacing third-row atoms by their second-row counterparts weakened the bonds, but not uniformly. Tetrel bonds were weakest for the fully hydrogenated acids and surpassed pnicogen bonds when F had been added to the acid.

Effect of Magnesium Bond on the Competition Between Hydrogen and Halogen Bonds and the Induction of Proton and Halogen Transfer

HOX (X=Cl, Br, I, and At) can engage in either a H-bond (HB) or halogen bond (XB) with a base-like HCN, NH₃ , and imidazole. Although the former is energetically preferred for X=Cl and Br, it is the XB that is more stable for At, with I showing little preference. MgY₂ forms a Mg-bond with the O atom of HOX, which grows stronger in the order X=Cl<Br<I<At and Y=F<Cl<Br. When all three molecules are combined, both the Mg and the H/X bonds are cooperatively strengthened to a large degree. Rather than causing a reversal in the HB/XB competition, the Mg-bond acts primarily to amplify the natural preference within the dimer. The Mg-bond induces a certain degree of transfer from O to N of the bridging atom in the H/X bond. Comparison is also made with the effects of a Be-bond.

Amphiphiles without Head-and-Tail Design: Nanostructures Based on the Self-Assembly of Anionic Boron Cluster Compounds

Anionic boron cluster compounds (ABCCs) are intrinsically amphiphilic building blocks suitable for nanochemistry. ABCCs are involved in atypical weak interactions, notably dihydrogen bonding, due to their peculiar polyhedral structure, consisting of negatively charged B-H units. The most striking feature of ABCCs that differentiates them from typical surfactants is the lack of head-and-tail structure. Furthermore, their structure can be described as intrinsically amphiphilic or aquaneutral. Therefore, classical terms established to describe self-assembly of classical amphiphiles are insufficient and need to be reconsidered. The opinions and theories focused on the solution behavior of ABCCs are briefly discussed. Moreover, a comparison between ABCCs with other amphiphilic systems is made focusing on the explanation of enthalpy-driven micellization or relations between hydrophobic and chaotropic effects. Despite the unusual structure, ABCCs still show self- and coassembly properties comparable to classical amphiphiles such as ionic surfactants. They self-assemble into micelles in water according to the closed association model. The most typical features of ABCCs solution behavior is demonstrated on calorimetry, NMR spectroscopy, and tensiometry experiments. Altogether, the unique features of ABCCs makes them a valuable inclusion into the nanochemisty toolbox to develop novel nanostructures both alone and with other molecules.

Intra-/Intermolecular Bifurcated Chalcogen Bonding in Crystal Structure of Thiazole/Thiadiazole Derived Binuclear (Diaminocarbene)PdII Complexes

The coupling of cis-[PdCl2(CNXyl)2] (Xyl = 2,6-Me2C6H3) with 4-phenylthiazol-2-amine in molar ratio 2:3 at RT in CH2Cl2 leads to binuclear (diaminocarbene)PdII complex 3c. The complex was characterized by HRESI+-MS, 1H NMR spectroscopy, and its structure was elucidated by single-crystal XRD. Inspection of the XRD data for 3c and for three relevant earlier obtained thiazole/thiadiazole derived binuclear diaminocarbene complexes (3a EYOVIZ; 3b: EYOWAS; 3d: EYOVOF) suggests that the structures of all these species exhibit intra-/intermolecular bifurcated chalcogen bonding (BCB). The obtained data indicate the presence of intramolecular S•••Cl chalcogen bonds in all of the structures, whereas varying of substituent in the 4th and 5th positions of the thiazaheterocyclic fragment leads to changes of the intermolecular chalcogen bonding type, viz. S•••π in 3a,b, S•••S in 3c, and S•••O in 3d. At the same time, the change of heterocyclic system (from 1,3-thiazole to 1,3,4-thiadiazole) does not affect the pattern of non-covalent interactions. Presence of such intermolecular chalcogen bonding leads to the formation of one-dimensional (1D) polymeric chains (for 3a,b), dimeric associates (for 3c), or the fixation of an acetone molecule in the hollow between two diaminocarbene complexes (for 3d) in the solid state. The Hirshfeld surface analysis for the studied X-ray structures estimated the contributions of intermolecular chalcogen bonds in crystal packing of 3a–d: S•••π (3a: 2.4%; 3b: 2.4%), S•••S (3c: less 1%), S•••O (3d: less 1%). The additionally performed DFT calculations, followed by the topological analysis of the electron density distribution within the framework of Bader’s theory (AIM method), confirm the presence of intra-/intermolecular BCB S•••Cl/S•••S in dimer of 3c taken as a model system (solid state geometry). The AIM analysis demonstrates the presence of appropriate bond critical points for these interactions and defines their strength from 0.9 to 2.8 kcal/mol indicating their attractive nature.

Mimicking of cyproconazole behavior in the presence of Cu and Zn

RATIONALE

The frequently used pesticide cyproconazole (Cyp) interacts with the essential elements commonly present in soil which play important roles in various enzymatic processes. These interactions predetermine the Cyp degradation pathways. We suggest a simple experimental and theoretical approach for the prediction of pesticide behavior.

METHODS

Cu/Cyp complexes are explored because of the typical Cu(II) reduction in complexes. Its level and the stability of the Cu-ligand bond depend on the type and the number of the surrounding ligands. Zn/Cyp complexes were compared as it is not expected that Zn(II) will reduce. The complexations were studied by means of electrospray ionization ion trap mass spectrometry and MS/MS collision-induced dissociations with comparative and explicative density functional theory calculations.

RESULTS

The Cyp ligand allows both Cu(II) reduction as well as, in specific cases, it protects the higher Cu oxidation state. The reduction is observed in the complexes with solely neutral Cyp where the number of ligands is below 3; a higher number protects the Cu(II) state. The metal atom binds to Cyp via N2 of the triazole ring as well as via π-electrons of the benzene ring; additional stabilization brings an interaction with the deprotonated OH group.

CONCLUSIONS

The character of Cyp interactions with doubly charged metals (Cu(II), Zn(II)) clarified the creation of Cyp metabolites. The phenyl and triazole rings are bound to the metal cation and enable access for the isopropyl ring to be cleaved leaving the common metabolite (CAS Number: 58905-19-4).

General and Modular Strategy for Designing Potent, Selective, and Pharmacologically Compliant Inhibitors of Rhomboid Proteases

Rhomboid-family intramembrane proteases regulate important biological processes and have been associated with malaria, cancer, and Parkinson's disease. However, due to the lack of potent, selective, and pharmacologically compliant inhibitors, the wide therapeutic potential of rhomboids is currently untapped. Here, we bridge this gap by discovering that peptidyl α-ketoamides substituted at the ketoamide nitrogen by hydrophobic groups are potent rhomboid inhibitors active in the nanomolar range, surpassing the currently used rhomboid inhibitors by up to three orders of magnitude. Such peptidyl ketoamides show selectivity for rhomboids, leaving most human serine hydrolases unaffected. Crystal structures show that these compounds bind the active site of rhomboid covalently and in a substrate-like manner, and kinetic analysis reveals their reversible, slow-binding, non-competitive mechanism. Since ketoamides are clinically used pharmacophores, our findings uncover a straightforward modular way for the design of specific inhibitors of rhomboid proteases, which can be widely applicable in cell biology and drug discovery.

•

N-substituted peptidyl α-ketoamides are nanomolar inhibitors of rhomboid proteases

•

Peptidyl ketoamides inhibit rhomboids covalently, reversibly, and non-competitively

•

The peptide and ketoamide substituent independently modulate potency and selectivity

•

Peptidyl ketoamides are selective for rhomboids, sparing most human serine proteases

A novel stibacarbaborane cluster with adjacent antimony atoms exhibiting unique pnictogen bond formation that dominates its crystal packing

We have prepared nido-7,8,9,11-Sb₂C₂B₇H₉, the first cluster with simultaneous Sb-B, Sb-C and Sb-Sb atom pairs with interatomic separations with magnitudes that approach the respective sums of covalent radii. However, the length of the Sb-Sb separation in this cluster is slightly less than the sum of the covalent radii. Quantum chemical analysis has revealed that the crystal packing of nido-7,8,9,11-Sb₂C₂B₇H₉ is predominantly dictated by pnictogen (Pn) bonding, an unconventional σ-hole interaction. Indeed, the interaction energy of a very strong Sb₂H-B Pn-bond in the nido-7,8,9,11-Sb₂C₂B₇H₉ dimer exceeds -6.0 kcal mol^-1. This is a very large value and is comparable to the strengths of known Pn-bonds in Cl₃Pnπ complexes (Pn = As, Sb).

Theoretical Study of Intramolecular Interactions in Peri-Substituted Naphthalenes: Chalcogen and Hydrogen Bonds

A theoretical study of the peri interactions, both intramolecular hydrogen (HB) and chalcogen bonds (YB), in 1-hydroxy-8YH-naphthalene, 1,4-dihydroxy-5,8-di-YH-naphthalene, and 1,5-dihydroxy-4,8-di-YH-naphthalene, with Y = O, S, and Se was carried out. The systems with a OH:Y hydrogen bond are the most stable ones followed by those with a chalcogen O:Y interaction, those with a YH:O hydrogen bond (Y = S and Se) being the least stable ones. The electron density values at the hydrogen bond critical points indicate that they have partial covalent character. Natural Bond Orbital (NBO) analysis shows stabilization due to the charge transfer between lone pair orbitals towards empty Y–H that correlate with the interatomic distances. The electron density shift maps and non-covalent indexes in the different systems are consistent with the relative strength of the interactions. The structures found on the CSD were used to compare the experimental and calculated results.

Unusual Cage Rearrangements in 10-Vertex nido-5,6-Dicarbaborane Derivatives: An Interplay between Theory and Experiment

The reaction between selected X-nido-5,6-C₂B₈H₁₁ compounds (where X = Cl, Br, I) and "Proton Sponge" [PS; 1,8-bis(dimethylamino)naphthalene], followed by acidification, results in extensive rearrangement of all cage vertices. Specifically, deprotonation of 7-X-5,6-C₂B₈H₁₁ compounds with one equivalent of PS in hexane or CH₂Cl₂ at ambient temperature led to a 7 → 10 halogen rearrangement, forming a series of PSH⁺[10-X-5,6-C₂B₈H₁₀]^- salts. Reprotonation using concentrated H₂SO₄ in CH₂Cl₂ generates a series of neutral carbaboranes 10-X-5,6-C₂B₈H₁₁, with the overall 7 → 10 conversion being 75%, 95%, and 100% for X = Cl, Br, and I, respectively. Under similar conditions, 4-Cl-5,6-C₂B₈H₁₁ gave ∼66% conversion to 3-Cl-5,6-C₂B₈H₁₁. Since these rearrangements could not be rationalized using the B-vertex swing mechanism, new cage rearrangement mechanisms, which are substantiated using DFT calculations, have been proposed. Experimental ¹¹B NMR chemical shifts are well reproduced by the computations; as expected δ(¹¹B) for B(10) atoms in derivatives with X = Br and I are heavily affected by spin-orbit coupling.