Spodium bonding in five coordinated Zn(ii): a new player in crystal engineering?

This highlight evidences the existence and importance of spodium bonds (SpB) in solid state structures involving five-coordinated square-pyramidal Zn(ii) spodium atom.

Short X···N Halogen Bonds With Hexamethylenetetraamine as the Acceptor

Hexamethylenetetramine (HMTA) and N-haloimides form two types of short (imide)X···N and X-X···N (X = Br, I) halogen bonds. Nucleophilic substitution or ligand-exchange reaction on the peripheral X of X-X···N with the chloride of N-chlorosuccinimide lead to Cl-X···N halogen-bonded complexes. The 1:1 complexation of HMTA and ICl manifests the shortest I···N halogen bond [2.272(5) Å] yet reported for an HMTA acceptor. Two halogen-bonded organic frameworks are prepared using 1:4 molar ratio of HMTA and N-bromosuccinimide, each with a distinct channel shape, one possessing oval and the other square grid. The variations in channel shapes are due to tridentate and tetradentate (imide)Br···N coordination modes of HMTA. Density Functional Theory (DFT) studies are performed to gain insights into (imide)X···N interaction strengths (ΔE_int). The calculated ΔE_int values for (imide)Br···N (-11.2 to -12.5 kcal/mol) are smaller than the values for (imide)I···N (-8.4 to -29.0 kcal/mol). The DFT additivity analysis of (imide)Br···N motifs demonstrates Br···N interaction strength gradually decreasing from 1:1 to 1:3 HMTA:N-bromosuccinimide complexes. Exceptionally similar charge density values ρ(r) for N-I covalent bond and I···N non-covalent bond of a (saccharin)N-I···N motif signify the covalent character for I···N halogen bonding.

Toward N,P-Doped π-Extended PAHs: A One-Pot Synthesis to Diannulated 1,4,2-Diazaphospholium Triflate Salts

A novel method for the one-pot synthesis of diannulated 1,4,2-diazaphospholium triflate salts by a Me₃SiOTf-mediated self-condensation of dichlorophosphaneyl aza-(poly)cyclic aromatic hydrocarbons (aza-(P)AHs; namely, pyridine, quinoline, phenanthridine, and benzo[d]thiazole) is reported. The diannulated 1,4,2-diazaphospholium triflate salts are characterized by multinuclear NMR spectroscopy, X-ray analysis, as well as their calculated NICS values, underlining their aromatic character. Quantum mechanical calculations shed light on the intermolecular reaction mechanism. Follow up chemistry, such as the halogenation reaction with XeF₂ or SO₂Cl₂ with the dipyridinium derivative selectively yields the respective dihalo-σ⁴,λ⁵- and tetrahalo-σ⁵,λ⁶-diazaphospholium triflate salts. The dihalo-σ⁴,λ⁵-diazaphospholium triflate salt serves well as a surrogate for the introduction of the cationic 2-(1,2'-bipyridin)-1-iumyl ligand (1,2'-bipyl), the monocationic structural isomer of the prototypical 2,2'-bipyridine ligand (2,2'-bipy).

Regium-π Bonds Are Involved in Protein-Gold Binding

The regium-π interaction is an attractive noncovalent force between group 11 elements (Cu, Ag, and Au) acting as Lewis acids and aromatic surfaces. Herein, we report for the first time experimental (Protein Data Bank analysis) and theoretical (RI-MP2/def2-TZVP level of theory) evidence of regium-π bonds involving Au(I) and aromatic amino acids (Phe, Tyr, Trp, and His). These findings might be important in the field of drug design and for retrospectively understanding the role of gold in proteins.

Quantifying Intramolecular Halogen Bonds in Nucleic Acids: A Combined Protein Data Bank and Theoretical Study

In this study, we report experimental (Protein Data Bank (PDB) search) and theoretical (RI-MP2/def2-TZVP level of theory) evidence of the nature, stability, and directionality properties of intramolecular halogen bonding interactions (HaBs) between 5-bromo/5-iodoracil bases and backbone phosphate groups in nucleic acids (NAs). A PDB survey revealed relevant examples where intramolecular HaBs are undertaken and serve as a structural source of stability in RNA and DNA molecules. In order to develop suitable energy predictors, we started this investigation by calculating the interaction energy values and both the potential V(r) and kinetic G(r) energy densities (using Bader's "atoms in molecules" theory) of several halogen bond complexes involving 5-bromo/5-iodoracil molecules and biologically relevant electron donors. Once the energy predictors based on V(r)/G(r) energy densities were developed, we analyzed the HaBs observed in the biological examples retrieved from the PDB search in order to estimate the strength of the interaction. As far as our knowledge extends, intramolecular halogen bonds in NAs have not been previously quantified in the literature using this methodology and may be of great importance in understanding their structural properties as well as in the construction of molecular materials with DNA and other biological macromolecules.

Spodium Bonds: Noncovalent Interactions Involving Group 12 Elements

The term spodium (Sp) bond is proposed to refer to a net attractive interaction between any element of Group 12 and electron-rich atoms (Lewis bases or anions). These noncovalent interactions are markedly different from coordination bonds (antibonding Sp-ligand orbital involved). Evidence is provided for the existence of this interaction by calculations at the RI-MP2/aug-cc-pVTZ level of theory, atoms-in-molecules, and natural bond orbital analyses and by examining solid-state structures in the Cambridge Structure Database.

Halogen Bonds in Protein Nucleic Acid Recognition

Identifying new binding forces between electron donor and acceptor entities is key to properly understanding molecular recognition and aggregation phenomena, which are of inmense importance to biology. For decades, the halogenation of DNA/RNA bases has been routinely carried out to solve solid state structures of nucleic acids (NA). However, the effects of this modification might be deeper than just a simple atom substitution since halogens are also known to undergo noncovalent binding (halogen bonding). Herein we show that halogenated NAs with either Br or I atoms are able to establish halogen bonds with properly disposed protein residues. An inspection of the Protein Data Bank (PDB) reveals several examples involving 5-iodo/5-bromouracil, 8-bromoadenine, and 5-iodocytosine bases that are consistent with the halogen bond geometry features. Computations reveal the favorable and moderately strong nature of this interaction, thus confirming the ability of halogenated bases to actively participate in protein-NA binding.

Binuclear and tetranuclear Zn(ii) complexes with thiosemicarbazones: synthesis, X-ray crystal structures, ATP-sensing, DNA-binding, phosphatase activity and theoretical calculations

Two Zinc(ii) complexes [Zn₄(L¹)₄]·2H₂O (1) and [Zn₂(L²)₂]·2H₂O (2) of pyruvaldehydethiosemicarbazone ligands are reported. The complexes were characterized by elemental analysis, IR, NMR, UV-vis spectroscopy and by single-crystal X-ray crystallography. X-ray crystal structure determinations of the complexes show that though Zn : ligand stoichiometry is 1 : 1 in both the complexes, the molecular unit is tetranuclear for 1 and binuclear for 2. Both the complexes show selective sensing of ATP at pH 7.4 (0.01 M HEPES) in CH₃CN–H₂O (9 : 1) medium in the presence of other anions like AcO⁻, NO₃⁻, F⁻, Cl⁻, H₂PO₄⁻, HPO₄²⁻ and P₂O₇²⁻. The UV-titration experiments of complexes 1 and 2 with ATP results in binding constants of 2.0(±0.07) × 10⁴ M⁻¹ and 7.1(±0.05) × 10³ M⁻¹ respectively. The calculated detection limits of 6.7 μM and 1.7 μM for 1 and 2 respectively suggest that the complexes are sensitive detectors of ATP. High selectivity of the complexes is confirmed by the addition of ATP in presence of an excess of other anions. DFT studies confirm that the ATP complexes are more favorable than those with the other inorganic phosphate anions, in agreement with the experimental results. Phosphatase like activity of both complexes is investigated spectrophotometrically using 4-nitrophenylphosphate (NPP) as a substrate, indicating the complexes possess significant phosphate ester hydrolytic efficiency. The kinetics for the hydrolysis of the substrate NPP was studied by the initial rate method at 25 °C. Michaelis–Menten derived kinetic parameters indicate that rate of hydrolysis of the P–O bond by complex 1 is much greater than that of complex 2, the k_cat values being 212(±5) and 38(±2) h⁻¹ respectively. The DNA binding studies of the complexes were investigated using electronic absorption spectroscopy and fluorescence quenching. The absorption spectral titrations of the complexes with DNA indicate that the CT-DNA binding affinity (K_b) of complex 1 (2.10(±0.07) × 10⁶ M⁻¹) is slightly greater than that of 2 (1.11(±0.04) × 10⁶ M⁻¹). From fluorescence spectra the apparent binding constant (K_app) values were calculated and they are found to be 5.41(±0.01) × 10⁵ M⁻¹ for 1 and 3.93(±0.02) × 10⁵ M⁻¹ for 2. The molecular dynamics simulation demonstrates that the Zn(ii) complex 1 is a good intercalator of DNA.

A binuclear and a tetranuclear zinc(ii) of pyruvaldehyde thiosemicarbazone show selective sensing of ATP at pH 7.4 (0.01 M HEPES) in CH₃CN–H₂O (9 : 1) medium. The DNA binding and phosphatase activities of the complexes are also reported.

On the supramolecular properties of neutral, anionic and cationic cadmium complexes harvested from dithiolate–polyamine binary ligand systems

Three Cd(ii) complexes [Cd(i-mnt)(DMSO)₂]_n (1), {[Cd(i-mnt)pn]·2H₂O} (2), and [Cd(i-mnt)₃][Cd(tren)₂]₂ (3) harvested from 1,1-dicyanoethylene-2,2-dithiolate (i-mnt²⁻) and polyamine ligand systems have been designed, synthesized and structurally characterized.

Biological promiscuity of a binuclear Cu(ii) complex of aminoguanidine Schiff base: DNA binding, anticancer activity and histidine sensing ability of the complex

A binuclear Cu(ii) complex of aminoguanidine shows strong DNA binding activity and encouraging anti-cancer activity against HCT-16 cells. The complex can also be used for selective spectrophotomteric or fluorometric determination of histidine.

Supramolecular assemblies involving salt bridges: DFT and X-ray evidence of bipolarity

Three new aminopyridinium/4,4′-oxydibenzoate salts have been synthesized and structurally characterized. A common feature of these compounds is the formation of antiparallel π-stacked salt bridges.

Halogen⋯halogen interactions in decahalo-closo-carboranes: CSD analysis and theoretical study

We theoretically (PBE0-D3/def2TZVP) and experimentally (CSD analysis) demonstrate the importance of “like–like” halogen interactions for the stability of several decahalo-closo-carborane dimers.

Halogen and Chalcogen Bond Energies Evaluated Using Electron Density Properties

Halogen (X-bond) and chalcogen bond (Ch-bond) energies for 36 complexes have been obtained at the RI-MP2/def2-TZVP level of theory, involving the heavier halogen and chalcogen atoms (Br, I, Se, Te). We have explored the existence of linear relationships between the interaction energies and the local kinetic energy densities at the bond critical points that characterize the σ-hole interactions (both electronic G(r) and potential V(r) energy densities). Interestingly, we have found strong relationships for halogen and chalcogen bonding energies, especially for the V(r) energy density, thus allowing to estimate the interaction energy without computing the separate monomers. This is also useful to estimate the interaction in monomeric systems (intramolecular X/Ch-bonds), as illustrated using several examples. Remarkably, we have also found a good relationship when in the same representation both halogen and chalcogen atoms are included, thus allowing to use the same empirical correlation for both interactions.

π-Hole Interactions Involving Nitro Aromatic Ligands in Protein Structures

Studying noncanonical intermolecular interactions between a ligand and a protein constitutes an emerging research field. Identifying synthetically accessible molecular fragments that can engage in intermolecular interactions is a key objective in this area. Here, it is shown that so-called "π-hole interactions" are present between the nitro moiety in nitro aromatic ligands and lone pairs within protein structures (water and protein carbonyls and sulfurs). Ample structural evidence was found in a PDB analysis and computations reveal interaction energies of about -5 kcal mol-1 for ligand-protein π-hole interactions. Several examples are highlighted for which a π-hole interaction is implicated in the superior binding affinity or inhibition of a nitro aromatic ligand versus a similar non-nitro analogue. The discovery that π-hole interactions with nitro aromatics are significant within protein structures parallels the finding that halogen bonds are biologically relevant. This has implications for the interpretation of ligand-protein complexation phenomena, for example, involving the more than 50 approved drugs that contain a nitro aromatic moiety.

Exploiting 1,4-naphthoquinone and 3-iodo-1,4-naphthoquinone motifs as anion binding sites by hydrogen or halogen-bonding interactions

We describe here the utilization of 1,4-naphthoquinone and 3-iodo-1,4-naphthoquinone motifs as new anion binding sites by hydrogen- or halogen-bonding interactions, respectively. These binding sites have been integrated in bidentate ester based receptors. Emission experiments reveal that both receptors selectively recognize sulfate anions, which induced a remarkable increase of a new emission band attributed to the formation of π-stacking interactions between two 1,4-naphthoquinone units. Absorption spectroscopy and mass spectrometry indicate the disruption of the ester group of the 1,4-naphthoquinone based receptor in the presence of HP₂O₇^3-, H₂PO₄^-, F^-, AcO^- and C₆H₅CO₂^- and in the halogenated receptor with HP₂O₇^3-, F^- and AcO^- anions, while the presence of sulfate anions showed the clasical complexation behaviour. The ¹H-NMR experiment showed a slow exchange process of the receptors with their sulfate complexes. The binding mode of the receptors with sulfate has been studied by DFT calculations along with the Molecular Electrostatic Potential (MEP) surface computational tool that reveals those parts of the receptors which are more suitable for interacting with anions.

Formation of an imidazoliumyl-substituted [(LC)4P4]4+ tetracation and transition metal mediated fragmentation and insertion reaction (LC = NHC)

Tetracationic cyclo-tetraphosphane [(L_C)₄P₄]⁴⁺ as triflate salt (3[OTf]₄) (L_C = 4,5-dimethyl-1,3-diisopropyl-imidazol-2-yl) is obtained in high yield from the reduction of [L_CPCl₂]⁺ (4[OTf]) with 1,4-bis(trimethylsilyl)-1,4-dihydropyrazine (6) and represents the first salt of the cationic cyclo-phosphane series with the general formula [L _n P _n ] ⁿ⁺. Theoretical calculations reveal the electrophilic nature of the P atoms within the P₄-ring due to the influence of the imidazoliumyl-substituents. Further reduction of 3[OTf]₄ with 6 affords the unexpected formation of the notricyclane P₇-type cation [(L_C)₃P₇]³⁺ (9[OTf]₃). Selective transition metal mediated [2 + 2]-fragmentation of 3 ⁴⁺ is achieved when 3[OTf]₄ is reacted with Fe₂(CO)₉, Pd(PPh₃)₄ and Pt(PPh₃)₄ leading to the formation of the dicationic diphosphene complexes [(η²-L_CP[double bond, length as m-dash]PL_C)Fe(CO)₄]²⁺ (12[OTf]₂) and [(η²-L_CP[double bond, length as m-dash]PL_C)M(PPh₃)₂]²⁺ (13[OTf]₂ for M = Pd; 14[OTf]₂ for M = Pt). In contrast, the reaction of 3[OTf]₄ with an excess of AuCl(tht) gives rise to the formation of the five-membered ring complex [((L_C)₄P₄)AuCl₂]³⁺ (15[OTf]₃), where the Au(i) atom reductively inserts into a P-P bond of 3 ⁴⁺.

An inorganic–organic hybrid supramolecular framework based on the γ-[Mo8O26]4− cluster and cobalt complex of aspartic acid: X-ray structure and DFT study

A new inorganic–organic hybrid based on an aspartate functionalized polyoxomolybdate, [pentaaquacobalt(II)]-μ-aspartate-[γ-octamolybdate]-μ-aspartate-[pentaaquacobalt(II)] tetrahydrate, [Co2(C4H6NO4)2(γ-Mo8O26)(H2O)10]·4H2O (1), has been synthesized under hydrothermal conditions from the reaction of an Evans–Showell-type polyoxometalate, (NH4)6[Co2Mo10H4O38], and L-aspartic acid. The complex exhibits a supramolecular three-dimensional framework structure in the crystal lattice. Compound 1 was structurally characterized by elemental analyses, IR and UV–Vis (diffuse reflectance) spectroscopy and single-crystal X-ray diffraction. In this compound, aspartic acid acts as a bridge between the two Co atoms and the Mo centres, with the –CH2COOH side chain directly linked to the Mo centre in γ-[Mo8O26]4− and the α-carboxylate side chain bound to the Co centre. Commonly, the binding of transition-metal complexes to POMs involves coordination of the metal to a terminal O atom of the POM so that 1, with a bridging ligand between Mo and Co atoms, belongs to a separate class of hybrid materials. While the starting materials are both chiral and one might expect them to form a chiral hybrid, the decomposition of the chiral Evans–Showell-type POM and its conversion to the centrosymmetric γ-octamolybdate POM, plus the presence of two aspartate ligands centrosymmetrically placed on either side of the POM, leads to the formation of an achiral hybrid. We have studied energetically by means of density functional theory (DFT) calculations and using the Bader's `atoms-in-molecules' analysis the electrostatically enhanced hydrogen bonds (EEHBs) observed in the solid state of 1, which are crucial for the formation of one-dimensional supramolecular assemblies.

The role of π-π stacking and hydrogen-bonding interactions in the assembly of a series of isostructural group IIB coordination compounds

This article describes the syntheses, crystal structures and theoretical calculations of six group IIB coordination compounds containing a 2-{[(2-meth­oxy­phen­yl)imino]­meth­yl}phenol ligand to provide further insight into the role of π-stacking and hydrogen bonding in metallo­supra­molecular assembly.

The supra­molecular chemistry of coordination compounds has become an im­portant research domain of modern inorganic chemistry. Herein, six iso­structural group IIB coordination compounds containing a 2-{[(2-meth­oxy­phen­yl)imino]­meth­yl}phenol ligand, namely di­chlorido­bis­(2-{(E)-[(2-meth­oxy­phen­yl)aza­niumyl­idene]meth­yl}pheno­lato-κO)zinc(II), [ZnCl₂(C₂₈H₂₆N₂O₄)], 1, di­iodido­bis­(2-{(E)-[(2-meth­oxy­phen­yl)aza­niumyl­idene]meth­yl}pheno­lato-κO)zinc(II), [ZnI₂(C₂₈H₂₆N₂O₄)], 2, di­bromido­bis­(2-{(E)-[(2-meth­oxy­phen­yl)aza­n­iumyl­idene]meth­yl}pheno­lato-κO)cadmium(II), [CdBr₂(C₂₈H₂₆N₂O₄)], 3, di­iodido­bis­(2-{(E)-[(2-meth­oxy­phen­yl)aza­niumyl­idene]meth­yl}pheno­lato-κO)cadmium(II), [CdI₂(C₂₈H₂₆N₂O₄)], 4, di­chlorido­bis­(2-{(E)-[(2-meth­oxy­phen­yl)aza­niumyl­idene]meth­yl}pheno­lato-κO)mercury(II), [HgCl₂(C₂₈H₂₆N₂O₄)], 5, and di­iodido­bis­(2-{(E)-[(2-meth­oxy­phen­yl)aza­niumyl­idene]meth­yl}pheno­lato-κO)mercury(II), [HgI₂(C₂₈H₂₆N₂O₄)], 6, were synthesized and characterized by X-ray crystallography and spectroscopic techniques. All six compounds exhibit an infinite one-dimensional ladder in the solid state governed by the formation of hydrogen-bonding and π–π stacking inter­actions. The crystal structures of these compounds were studied using geometrical and Hirshfeld surface analyses. They have also been studied using M06-2X/def2-TZVP calculations and Bader’s theory of ‘atoms in mol­ecules’. The energies associated with the inter­actions, including the contribution of the different forces, have been evaluated. In general, the π–π stacking inter­actions are stronger than those reported for conventional π–π complexes, which is attributed to the influence of the metal coordination, which is stronger for Zn than either Cd or Hg. The results reported herein might be useful for understanding the solid-state architecture of metal-containing materials that contain M^IIX₂ subunits and aromatic organic ligands.