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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. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

In this study, Fe3O4 nanoparticles (FeNPs) decorated with halogenated perylene diimides (PDIs) have been used for capturing VOCs (volatile organic compounds) through noncovalent binding. Concretely, we have used tetrachlorinated/brominated PDIs as well as a nonhalogenated PDI as a reference system. On the other hand, methanol, ethanol, propanol, and butanol were used as VOCs. Experimental studies along with theoretical calculations (the BP86-D3/def2-TZVPP level of theory) pointed to two possible and likely competitive binding modes (lone pair–π through the π-acidic surface of the PDI and a halogen bond via the σ-holes at the Cl/Br atoms). More in detail, thermal desorption (TD) experiments showed an increase in the VOC retention capacity upon increasing the length of the alkyl chain, suggesting a preference for the interaction with the PDI aromatic surface. In addition, the tetrachlorinated derivative showed larger VOC retention times compared to the tetrabrominated analog. These results were complemented by several state-of-the-art computational tools, such as the electrostatic surface potential analysis, the Quantum Theory of Atoms in Molecules (QTAIM), as well as the noncovalent interaction plot (NCIplot) visual index, which were helpful to rationalize the role of each interaction in the VOC···PDI recognition phenomena. [ABSTRACT FROM AUTHOR]

Volatile Organic Compounds (VOCs) are chemicals that vaporize at room temperature and exert short- or long-term adverse effects on human health and the environment. In this study, Ag and Au nanoparticles (NPs) were used to capture aromatic VOCs (e.g. benzene derivatives) through the establishment of CH⋯Ag/Au interactions and regium–π bonds (Rg–π), namely, an attractive noncovalent force involving low electron density sites located on noble metal NPs acting as electron acceptors and π-systems as electron donors. Using a set of computational tools (PBE0-D3/def2-TZVP level of theory), we modeled the interaction between the VOCs and the Ag/Au NPs, being useful to understand its strength and physical nature. On the other hand, thermal desorption (TD) experiments evidenced the presence of a noncovalent interaction between the surface of the NPs and VOCs that drives the molecular recognition process, in line with the results gathered from calculations. We believe the results gathered herein will be useful (i) to bring the attention of the materials science community to this novel type of noncovalent force, (ii) to expand the current knowledge and usage of Ag and Au NPs and (iii) to develop new nanoscale materials for capturing volatile compounds. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]