Investigating Recurrent Matere Bonds in Pertechnetate Compounds.

In this manuscript we evaluate the X-ray structure of five new pertechnetate derivatives of general formula [M(H2O)4(TcO4)2], M=Mg, Co, Ni, Cu, Zn (compounds 1-5) and one perrhenate compound Zn(H2O)4(ReO4)2 (6). In these complexes the metal center exhibits an octahedral coordination with the pertechnetate units as axial ligands. All compounds exhibit the formation of directional Tc⋅⋅⋅O Matere bonds (MaBs) that propagate the [M(H2O)4(TcO4)2], into 1D supramolecular polymers in the solid state. Such 1D polymers are linked, generating 2D layers, by combining additional MaBs and hydrogen bonds (HBs). Such concurrent motifs have been analyzed theoretically, suggesting the noncovalent σ-hole nature of the MaBs. The interaction energies range from weak (~ -2 kcal/mol) for the MaBs to strong (~ -30 kcal/mol) for the MaB+HB assemblies, where HB dominates. In case of M=Zn, the corresponding perrhenate Zn(H2O)4(ReO4)2 complex, has been also synthesized for comparison purposes, resulting in the formation of an isostructural X-ray structure, corroborating the structure-directing role of Matere bonds.

Investigating the Impact of Packing and Environmental Factors on the Luminescence of Pt(N

Four Pt(II)(N^N^N) compounds featuring DMSO coordination at the fourth position were synthesized. Ligands varied in terms of pyridyl central ring (hydrogen/chlorine substituent) and lateral rings (triazoles with CF3 substitution or tetrazoles). Coordination to pyridine yielded tetra-nitrogen coordinated Pt(II) complexes or Pt-functionalized polymers using commercial 4-pyridyl polyvinyl (PV) or dimethylaminopyridine. Luminescence behaviors exhibited remarkable environmental dependence. While some of the molecular compounds (tetrazole derivatives) in solid state displayed quenched luminescence, all the polymers exhibited 3MMLCT emission around 600 nm. Conversely, monomer emission was evident on poly(methyl methacrylate) or polystyrene matrices. DFT calculations were used to analyze the aggregation of the complexes both at the molecular level and coordinated to the PV polymer and their influence on the HOMO-LUMO gaps.

Silver(I) Octanuclear Complexes Containing N'-(4-Oxotiazolidin-2-Iliden)picolinohydrazonamide and Nitrate as Bridge Ligands. An Example of Solvatomorphism?

The versatile coordination chemistry of (2Z,N'E)-N'-(4-oxothiazolidin-2-ylidene)picolinohydrazonamide (HAmDHotaz) facilitated the synthesis of new complexes with different silver(I) salts. This paper describes the synthesis and characterization, through elemental analysis and spectroscopic techniques (when solubility permits), of a series of compounds that illustrate the coordinative and structural diversity achievable with the HAmDHotaz ligand. Five silver clusters containing the [Ag8(AmDHotaz)4]4+ nucleus were structurally analyzed by single-crystal X-ray diffraction and were found to exhibit solvomorphism. The compositions of these are [Ag8(AmDHotaz)4(NO3)3(MeOH)(H2O)](NO3)·MeOH·7.5H2O (1), {[Ag8(AmDHotaz)4(NO3)3(H2O)2](NO3)·9.5(H2O)}n (2), {[Ag8(AmDHotaz)4(NO3)3(H2O)2](NO3)·11.5(H2O)}n (2a), {[Ag8(AmDHotaz)4(NO3)2(H2O)2](NO3)(OH)·6H2O}n (3), and {[Ag8(AmDHotaz)4(NO3)2(H2O)](NO3)(OH)·4.5H2O}n (3a). Argentophilic interactions are present in each of the octanuclear structures, where Ag···Ag distances range from 2.828(2) to 2.986(1) Å. These distances are influenced by crystal packing, determined by the counterion and solvent molecules in the structure. In the solvatomorphs, solvent molecules were observed to be disordered. Various hydrogen-bonding interactions, such as N-H···O-N, O-H···O, N-H···O═C, C-H···O-N, and π-π stacking interactions, contribute to the crystal packing. The influence of these weak interactions on the crystal packing was further analyzed using DFT calculations and Bader's theory of atoms-in-molecules, with a focus on argentophilic interactions and Ag···S interactions.

A novel approach for estimating the strength of argentophilic and aurophilic interactions using QTAIM parameters.

Metallophilic interactions, specifically argentophilic (Ag⋯Ag) and aurophilic (Au⋯Au) interactions, play a crucial role in stabilizing various molecular and solid-state structures. In this manuscript, we present a convenient method to estimate the strength of argentophilic and aurophilic interactions based on quantum theory of atoms in molecules (QTAIM) parameters evaluated at the bond critical points connecting the metal centres. We employ density functional theory (DFT) calculations and the QTAIM parameters to develop this energy predictor. To validate the reliability and applicability of our method, we test it using a selection of X-ray crystal structures extracted from the cambridge structural database (CSD), where argentophilic and aurophilic interactions are known to be significant in their solid-state arrangements. This method offers a distinct advantage in systems where multiple interactions, beyond metallophilic interactions, contribute to the overall stability of the structure. By employing our approach, researchers can distinctly quantify the strength of argentophilic and aurophilic interactions, facilitating a deeper understanding of their impact on molecular and solid-state properties. This method fills a critical gap in the existing literature, offering a valuable tool to researchers seeking to unravel the intricate interactions in metal-containing compounds.

On the influence of metal nanoparticle and π-system sizes in the stability of noncovalent adducts: a theoretical study.

Herein we have computationally evaluated the relationship between Ag and Au nanoparticle (Ag/AuNP) size and π-surface extension in the formation of noncovalent complexes at the PBE0-D3/def2-TZVP level of theory. The NP-π interaction is known in supramolecular chemistry as a Regium-π bond (Rg-π), and differentiates from classical coordination bonds in strength and type of metal orbitals involved. In this study, the Rg-π complexes involved small Ag/AuNPs composed by 1 to 5 atoms and benzene, naphthalene and anthracene as π-systems, being characterized using several molecular modeling tools, including molecular electrostatic potential (MEP) calculations, energy decomposition analysis (EDA), quantum theory of atoms in molecules (QTAIM), non covalent interaction plot (NCIplot) and natural bonding orbital (NBO) methodologies. We believe the results reported herein will be useful for those scientists working in catalysis, molecular recognition and materials science fields, where structural-energetic relationships of weak interactions are crucial to achieve product selectivity, a particular molecular recognition mode or a specific molecular assembly.

Manganese matere bonds in biological systems: PDB inspection and DFT calculations.

A Protein Data Bank (PDB) survey has revealed noncovalent contacts involving Mn centres and protein residues. Their geometrical features are in line with the interaction between low electron density sites located along the Mn-O/N coordination bonds (σ-holes) and the lone pairs belonging to TYR, SER or HIS residues, known as a matere bond (MaB). Calculations at the PBE0-D3/def2-TZVP level of theory were used to investigate the strength and shed light on the physical nature of the interaction. We expect the results presented herein will be useful for those scientists working in the fields of bioinorganic chemistry, particulary in protein-metal docking, by providing new insights into transition metal⋯Lewis base interactions as well as a retrospective point of view to further understand the structural and functional implications of this key transition metal ion.

From Coordination to π-Hole Chemistry of Transition Metals: Metalloporphyrins as a Case of Study.

Herein we have evidenced the formation of favorable π-hole Br···metal noncovalent interactions (NCIs) involving elements from groups 9, 11 and 12. More in detail, M (M = Co2+, Ni2+, Cu2+ and Zn2+) containing porphyrins have been synthesized and their supramolecular assemblies structurally characterized by means of single crystal X-ray diffraction and Hirshfeld surface analyses, revealing the formation of directional Br···M contacts in addition to ancillary hydrogen bond and lone pair-π bonds. Computations at the PBE0-D3/def2-TZVP level of theory revealed the π-hole nature of the Br···M interaction. In addition, the physical nature of these NCIs was studied using Quantum Chemistry methodologies, providing evidence of π-hole Spodium and Regium bonds in Zn2+ and Cu2+ porphyrins, in addition to unveiling the presence of  a π-hole for group 9 (Co2+). On the other hand, group 10 (Ni2+) acted as both electron donor and acceptor moiety without showing an electropositive π-hole. Owing to the underexplored potential of π-hole interactions in transition metal chemistry, we believe the results reported herein will be useful in supramolecular chemistry, organometallics, and solid-state chemistry by i) putting under the spotlight the π-hole chemistry involving first row transition metals and ii) unlocking a new tool to direct the self-assembly of metalloporphyrins.

Hg(II)⋠d8 [M] Interactions: Are they Metallophilic Interactions or Spodium Bonds?

Some literature reports have shown the existence of short Hg(II)⋅⋅⋅d8 [M] (M=Pd, Pt) contacts between linear Hg(II) and square planar d8 [M] complexes that have been defined as heterometallophilic interactions. Linear L-Hg(II)-L complexes exhibit a π-hole or positive belt of electrostatic potential at the Hg atom, whereas late transition metals can serve as effective electron donors through their filled dz 2 orbitals. This study provides compelling evidence that Hg(II)⋅⋅⋅d8 [M] interactions should be more appropriately termed spodium bonds.

Regium-π Bonds Involving Nucleobases: Theoretical Study and Biological Implications.

In this study, we provide crystallographic (Protein Data Bank (PDB) inspection) and theoretical (RI-MP2/def2-TZVP//PBE0-D3/def2-SVP level of theory) evidence of the involvement of nucleobases in Regium-π bonds (RgBs). This noncovalent interaction involves an electrophilic site located on an element of group 11 (Cu, Ag, and Au) and an electron-rich species (lone pair, LP donor, or π-system). Concretely, an initial PDB search revealed several examples where RgBs were undertaken involving DNA bases and Cu(II), Ag(I), and Au(I/III) ions. While coordination positions (mainly at the N atoms of the base) are well known, the noncovalent binding force between these counterparts has been scarcely studied in the literature. In this regard, computational models shed light on the strength and directionality properties of the interaction, which was also further characterized from a charge-density perspective using Bader's "atoms in molecules" (AIM) theory, noncovalent interaction plot (NCIplot) visual index, and natural bonding orbital (NBO) analyses. As far as our knowledge extends, this is the first time that RgBs in metal-DNA complexes are systematically analyzed, and we believe the results might be useful for scientists working in the field of nucleic acid engineering and chemical biology as well as to increase the visibility of the interaction among the biological community.

Spodium Bonds Involving Methylmercury and Ethylmercury in Proteins: Insights from X-ray Analysis and Computations.

In this study, the stability, directionality, and physical nature of Spodium bonds (SpBs, an attractive noncovalent force involving elements from group 12 and Lewis bases) between methylmercury (MeHg) and ethylmercury (EtHg) and amino acids (AAs) have been analyzed from both a structural (X-ray analysis) and theoretical (RI-MP2/def2-TZVP level of theory) point of view. More in detail, an inspection of the Protein Data Bank (PDB) reported evidence of noncovalent contacts between MeHg and EtHg molecules and electron-rich atoms (e.g., O atoms belonging to the protein backbone and S atoms from MET residues or the π-systems of aromatic AAs such as TYR or TRP). These results were rationalized through a computational study using MeHg coordinated to a thiolate group as a theoretical model and several neutral and charged electron-rich molecules (e.g., benzene, formamide, or chloride). The physical nature of the interaction was analyzed from electrostatics and orbital perspectives by performing molecular electrostatic potential (MEP) and natural bonding orbital (NBO) analyses. Lastly, the noncovalent interactions plot (NCIplot) technique was used to provide a qualitative view of the strength of the Hg SpBs and compare them to other ancillary interactions present in these systems as well as to shed light on the extension of the interaction in real space. We believe that the results derived from our study will be useful to those scientists devoted to protein engineering and bioinorganic chemistry as well as to expanding the current knowledge of SpBs among the chemical biology community.

Biological noncovalent N/O⋯V interactions: insights from theory and protein data bank analyses.

Computations at the PBE0-D3/def2-TZVP level of theory in conjunction with a Protein Data Bank (PDB) survey have provided first time evidence of favorable noncovalent interactions between ADP metavanadate (VO4) and ADP orthovanadate (VO5) and electron rich atoms. These involve a σ-hole present in the V atom and the lone pairs belonging to (i) protein residues (e.g., serine (SER), glutamate (GLU) or histidine (HIS)), (ii) backbone carbonyl groups and (iii) water molecules. A computational study has been carried out to rationalize the physical nature and directionality of the interaction in addition to its plausible biological role. The results reported herein are expected to have an impact in the fields of medicinal chemistry, bioinorganic chemistry and chemical biology.

Tuning the Nucleophilicity and Electrophilicity of Group 10 Elements through Substituent Effects: A DFT Study.

In this study, a series of electron donor (-NH2, -NMe2 and -tBu) and electron-withdrawing substituents (-F, -CN and -NO2) were used to tune the nucleophilicity or electrophilicity of a series of square planar Ni2+, Pd2+ and Pt2+ malonate coordination complexes towards a pentafluoroiodobenzene and a pyridine molecule. In addition, Bader's theory of atoms in molecules (AIM), noncovalent interaction plot (NCIplot), molecular electrostatic potential (MEP) surface and natural bond orbital (NBO) analyses at the PBE0-D3/def2-TZVP level of theory were carried out to characterize and discriminate the role of the metal atom in the noncovalent complexes studied herein. We hope that the results reported herein may serve to expand the current knowledge regarding these metals in the fields of crystal engineering and supramolecular chemistry.

Substituent Effects in Tetrel Bonds Involving Aromatic Silane Derivatives: An ab initio Study.

In this manuscript substituent effects in several silicon tetrel bonding (TtB) complexes were investigated at the RI-MP2/def2-TZVP level of theory. Particularly, we have analysed how the interaction energy is influenced by the electronic nature of the substituent in both donor and acceptor moieties. To achieve that, several tetrafluorophenyl silane derivatives have been substituted at the meta and para positions by several electron donating and electron withdrawing groups (EDG and EWG, respectively), such as -NH2, -OCH3, -CH3, -H, -CF3 and -CN substituents. As electron donor molecules, we have used a series of hydrogen cyanide derivatives using the same EDGs and EWGs. We have obtained the Hammett's plots for different combinations of donors and acceptors and in all cases we have obtained good regression plots (interaction energies vs. Hammet's σ parameter). In addition, we have used the electrostatic potential (ESP) surface analysis as well as the Bader's theory of atoms in molecules (AIM) and noncovalent interaction plot (NCI plot) techniques to further characterize the TtBs studied herein. Finally, a Cambridge Structural Database (CSD) inspection was carried out, retrieving several structures where halogenated aromatic silanes participate in tetrel bonding interactions, being an additional stabilization force of their supramolecular architectures.

Substituent Effects in π-Hole Regium Bonding Interactions Between Au(p-X-Py)2 Complexes and Lewis Bases: An ab initio Study.

Long range substituent effects in regium bonding interactions involving Au(I) linear complexes are investigated for the first time. The Au(I) atom is coordinated to two para-substituted pyridine ligands. The interaction energy (RI-MP2/def2-TZVP level of theory) of the π-hole regium bonding assemblies is affected by the pyridine substitution. The Hammett's plot representations for several sets of Lewis bases have been carried out and, in all cases, good regression plots have been obtained (interaction energies vs. Hammett's σ parameter). The Bader's theory of "atoms-in-molecules" has been used to evidence that the electron density computed at the bond critical point that connects the Au-atom to the electron donor can be used as a measure of bond order in regium bonding. Several X-ray structures retrieved from the Cambridge Structural Database (CSD) provide experimental support to the existence of π-hole regium bonding in [Au(Py)2 ]+ derivatives.

Selenoxides as Excellent Chalcogen Bond Donors: Effect of Metal Coordination.

The chalcogen bond has been recently defined by the IUPAC as the attractive noncovalent interaction between any element of group 16 acting as an electrophile and any atom (or group of atoms) acting as a nucleophile. Commonly used chalcogen bond donor molecules are divalent selenium and tellurium derivatives that exhibit two σ-holes. In fact, the presence of two σ-hole confers to the chalcogen bonding additional possibilities with respect to the halogen bond, the most abundant σ-hole interaction. In this manuscript, we demonstrate that selenoxides are good candidates to be used as σ-hole donor molecules. Such molecules have not been analyzed before as chalcogen bond donors, as far as our knowledge extends. The σ-hole opposite to the Se=O bond is adequate for establishing strong and directional ChBs, as demonstrated herein using the Cambridge structural database (CSD) and density functional theory (DFT) calculations. Moreover, the effect of the metal coordination of the selenoxide to transition metals on the strength of the ChB interaction has been analyzed theoretically. The existence of the ChBs has been further supported by the quantum theory of atoms in molecules (QTAIM) and the noncovalent interaction plot (NCIPlot).

Enzymatic reversion of Pt(II) nucleophilicity through charge dumping: the case of Pt(CN)42.

Combining computations and X-ray structure analysis we have demonstrated that [Pt(CN4)]2- can behave as a Lewis acid inside an enzyme's cavity. The nature of a counterintuitive contact found between a catalytically active GLN residue belonging to a mitochondrial synthase and the Pt(II) center was investigated by combining molecular dynamics and quantum mechanics calculations. Results confirm the electron acceptor role of [Pt(CN4)]2-, serving as an inspiration for the design of biomolecular cages able to tweak the nucleophilic/electrophilic character of an organometallic compound.

Group-10 π-hole⋯dz2[MII] interactions: a theoretical study of model systems inspired by CSD structures.

In recent years Pd(II) and Pt(II) cases have been reported wherein metals in square planar complexes were used as nucleophilic partners to construct supramolecular assemblies with electrophilic molecules like σ-hole and π-hole donors. The formation of such assemblies is based on the nucleophilicity and accessibility of the dz2 orbital (in group-10 elements) in the square-planar complexes. This opens new avenues in inorganic chemistry and crystal engineering as it enriches the current toolbox of noncovalent interactions and supramolecular synthons thus allowing the design of new types of architectures in the solid state. This manuscript reports a comprehensive theoretical study characterizing π-hole⋯dz2[MII] (M = group 10 element) interactions from an energetic point of view. Several computational tools based on the topology of the electron density are used. Examined systems had been identified by considering structures in the Cambridge Structural Database where this interaction was used to construct supramolecular assemblies. Several aromatic rings have been used, varying from π-basic to π-acid rings by adjusting the number of fluorine substituents. Moreover, the influence of metal⋯metal interactions on the nucleophilicity of the dz2 orbital has been studied using MEP surface analysis. The π-hole energies are moderately strong (from -5 to -10 kcal mol-1) and the crucial role of dispersion forces is revealed.