RESUMEN
The -N+(CH3)3 residue is present in acetylcholine (ACh) and in many of its analogues which are used as selective ACh agonist or antagonists for human therapy. The X-ray structures of four ACh derivatives show the presence of short and linear contacts between the C atoms of -N+(CH3)3 groups and lone pair possessing atoms. These contacts can be rationalized as tetrel bonds (TtBs) thanks to their geometric features. Interrogation of the Protein Data Bank suggests that similar -N+âC···nucleophile contacts affect the details of the binding of ACh and its derivatives to proteins. Quantum theory of atoms in molecules, noncovalent interaction plot, and natural bond orbital analyses consistently confirm that the -N+âC···nucleophile contacts observed in small molecule crystals and in substrate/protein complexes are attractive in nature and can be rationalized as TtBs. TtBs involving methyl groups of the -N+(CH3)3 moiety can be proposed as a new item in the palette of interactions allowing the compounds containing this pharmacophoric unit to bind to their target protein and/or to express their biological/pharmacological properties.
RESUMEN
The electrostatic attraction between charges of opposite signs and the repulsion between charges of the same sign are ubiquitous and influential phenomena in recognition and self-assembly processes. However, it has been recently revealed that specific attractive forces between ions with the same sign are relatively common. These forces can be strong enough to overcome the Coulomb repulsion between ions with the same sign, leading to the formation of stable anionâ¯anion and cationâ¯cation adducts. Hydroden bonds (HBs) are probably the best-known interaction that can effectively direct these counterintuitive assembly processes. In this review we discuss how σ-hole and π-hole bonds can break the paradigm of electrostatic repulsion between like-charges and effectively drive the self-assembly of anions into discrete as well as one-, two-, or three-dimensional adducts. σ-Hole and π-hole bonds are the attractive forces between regions of excess electron density in molecular entities (e.g., lone pairs or π bond orbitals) and regions of depleted electron density that are localized at the outer surface of bonded atoms opposite to the σ covalent bonds formed by atoms (σ-holes) and above and below the planar portions of molecular entities (π-holes). σ- and π-holes can be present on many different elements of the p and d block of the periodic table and the self-assembly processes driven by their presence can thus involve a wide diversity of mono- and di-anions. The formed homomeric and heteromeric adducts are typically stable in the solid phase and in polar solvents but metastable or unstable in the gas phase. The pivotal role of σ- and π-hole bonds in controlling anionâ¯anion self-assembly is described in key biopharmacological systems and in molecular materials endowed with useful functional properties.
RESUMEN
Adducts between OsO4 and Lewis bases exert a role in important oxidation processes such as epoxidation and dihydroxylation. It has been shown that the attractive interaction driving the formation of these adducts is a σ-hole bond involving the metal as the electrophilic species; the term Osme Bond (OmB) was proposed for designating it. Here some new adducts between OsO4 and various bases have been characterized through single crystal x-ray diffraction (XRD) and computational studies (density functional theory, DFT), confirming the existence of a robust correlation between σ-hole interaction energy and deformation of the tetrahedral geometry of OsO4. Also, some adducts formed by RuO4 with nucleophiles were investigated computationally.
RESUMEN
H-selenite anions (HSeO3 - ) form in the solid unprecedented anionic supramolecular chains wherein single units are assembled via alternating short Seâ â â O and Hâ â â O contacts. Crystallographic analyses and computational studies (the quantum theory of "atoms-in-molecules", QTAIM, and the noncovalent interaction plot, NCIPlot) consistently prove the attractive nature of these chalcogen bonds (ChBs) and hydrogen honds (HBs), the Janus-type character of HSeO3 - anions which act as both donors and acceptors of ChB and HB, and the possible stability of anion dimers in solution. The effectiveness of the ChBs herein described may lead to consider the HSeO3 - moiety as a new entry in the toolbox of crystal engineering based on ChB.
RESUMEN
Matere bonds (MaB) to rhenium in a set of organic perrhenates are probed via185/187Re solid-state NMR in applied magnetic fields of up to 35.2 T, and via185/187Re NQR. 185/187Re quadrupolar couplings distinguish between MaB samples and control samples, and their precise values are governed by shear strain of the ReO4- anions.
RESUMEN
C(sp3) atoms are known to act as electrophilic sites in self-assembly processes, and in all cases reported till now, they form only one interaction with nucleophiles; that is, they function as monodentate tetrel bond donors. This manuscript reports experimental (X-ray structural analysis) and theoretical evidence (DFT calculations), proving that the methylene carbon in bis-pyridinium methylene salts establishes two short and directional C(sp3)···anion interactions; that is, they function as bidentate tetrel bond donors.
RESUMEN
Due to their high electron density, fluoride anions can be considered the most effective halogen bond (HaB) acceptors among the halides. However, under common experimental conditions, F- uncommonly acts as HaB acceptor, expectedly as it is present in hydrated form. Herein we report that under specific crystallization conditions a hydrogen bond-free F- functioning as donor of electron density can be obtained, with the formed HaBs constituting the driving force of the observed crystal packings. Computations confirm the strength of these HaBs compared to analogous interactions involving other halides.
RESUMEN
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 groupâ 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.
RESUMEN
Single crystal X-ray diffraction of iodate and bromate salts shows that the I and Br atoms in IO3 - and BrO3 - anions form short and linear O-I/Brâ â â O contacts with the O atoms of nearby anions. Non-centrosymmetric systems are formed wherein anions are orderly aligned into supramolecular 1D and 2D networks. Theoretical evidences, namely the outcome of QTAIM and NCIplot studies, prove the attractive nature of these contacts and the ability of iodate and bromate anions to act as robust halogen bond (HaB) donors. The HaB is proposed as a general and effective assisting tool to control the architecture of acentric iodate salts.
RESUMEN
1,2-benzisothiazol-3(2H)-one derivatives are highly active against a broad spectrum of fungi as well as Gram positive and Gram negative bacteria. For this reason they are extensively used, for example, as additives in detergents, leather products, paper coatings, and antifouling paintings. In this paper experimental findings are reported proving that the sulfur atom of benzisothiazolinones have a remarkable tendency to form short and directional chalcogen bondings on the extension of the covalent N-S bond and, to a lesser extent, of the C-S bond. Analyses of the Cambridge Structural Database confirm the interaction as a primary recognition motif of these systems. The electrophilicity of sulfur is crucial in the chemical reactions initiating the cascade of events resulting in the biopharmacological activities of benzisothiazolinones. The reported results suggest that the electrophility of sulfur may play a role also at earlier stages than the reactive ones, namely it may pin the compounds at the active site of target enzymes via chalcogen bondings that preorganize the system in the conformation required for the bonds formation/cleavage determining the biopharmacological activity.
Asunto(s)
Antibacterianos , Bacterias Gramnegativas , Antibacterianos/farmacología , Bacterias Grampositivas , Azufre/químicaRESUMEN
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-holeâ¯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 metalâ¯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.
RESUMEN
Methyltrioxorhenium(VII) (MTO) is a widely employed catalyst for metathesis, olefination, and most importantly, oxidation reactions. It is often preferred to other oxometal complexes due to its stability in air and higher efficiency. The seminal papers of K. B. Sharpless showed that when pyridine derivatives are used as co-catalysts, MTO-catalyzed olefin epoxidation with H2O2 as oxidant, a particularly useful reaction, is accelerated, with pyridine speeding up catalytic turnover and increasing the lifetime of MTO under the reaction conditions. In this paper, combined experimental and theoretical results show that the occurrence of σ-hole interactions in catalytic systems extends to MTO. Four crystalline adducts between MTO and aliphatic and heteroaromatic bases are obtained, and their X-ray analyses display short Reâ¯N/O contacts opposite to both O-Re and C-Re covalent bonds with geometries consistent with σ-hole interactions. Computational analyses support the attractive nature of these close contacts and confirm that their features are typical of σ-hole interactions. The understanding of the nature of Reâ¯N/O interactions may help to optimize the ligand-acceleration effect of pyridine in the epoxidation of olefins under MTO catalysis.
Asunto(s)
Peróxido de Hidrógeno , Compuestos Organometálicos , Peróxido de Hidrógeno/química , Compuestos Organometálicos/química , Catálisis , Alquenos/química , PiridinasRESUMEN
The increasing demand of species for the efficient capture and sensing of anions benefits from a systematic study of anion binding capabilities in the solid state. This work reports a detailed crystallographic study of ten structurally related podands and shows that these charged receptors bind anions with a combination of charge-assisted halogen and hydrogen bonds. Computational tools helped in highlighting the role of the different involved interaction and afforded possible design principles for the design of improved podands.
RESUMEN
Five structures bearing the N,N,N-trimethylammonium unit have been investigated to address the ability of the N+-CH3 unit to function as a tetrel bond donor site. Charged and neutral electron density donors display close contacts with different carbon atoms of methyl groups on the ammonium moiety. The Hirshfeld atom refinement (HAR) technique was used on selected structures to accurately and precisely determine the hydrogen atom positions and, consequently, to get better insights into the N+-Câ¯Nu (Nu = nucleophile) interactions occurring in the crystals. In particular, the performed analyses highlighted specific geometrical features of the moieties involved in the interactions and allowed distinguishing between tetrel and hydrogen bonds.
RESUMEN
The co-crystallization of tetracyanobenzene (TCB) with haloarenes ArX provided six new co-crystals TCB â ArX (ArX=PhCl, PhBr, 4-MeC6 H4 Cl, 4-MeC6 H4 Br, 4-MeOC6 H4 Cl, 1,2-Br2 C6 H4 ) which were studied by X-ray diffraction. In these systems, the strong collective effect of πâ â â π stacking interactions and lone pair-(X)â â â π-hole-(C) bondings between TCB and ArX promote the strength of Xâ â â Ncyano halogen bonding (HaB). Theoretical studies showed that the stacking interactions affect the σ-hole depth of the haloarenes, thus significantly boosting their ability to function as HaB donors. According to the molecular electrostatic potential calculations, the σ- hole-(Cl) value (1.5â kcal/mol) in the haloarene 4-MeOC6 H4 Cl (featuring an electron-rich arene moiety and exhibiting very poor σ-hole-(Cl) ability) increases significantly in the stacked trimer (TCB)2 â 4-MeOC6 H4 Cl (12.5â kcal/mol). Theoretical DFT calculations demonstrate the dramatic increase of Xâ â â Ncyano HaB strength for stacked trimers in comparison with parent unstacked haloarenes.
RESUMEN
Single crystal X-ray analyses show that iodine in pyridinium periodates acts as a halogen bond (HaB) donor forming short and almost linear contacts with neutral and anionic electron donors. A combination of QTAIM and NCIplot computational tools proves the attractive nature of these contacts.
Asunto(s)
Halógenos , Yodo , Aniones/química , Halógenos/química , Yodo/química , Ácido Peryódico , PolímerosRESUMEN
Porous architectures characterized by parallel channels arranged in honeycomb or rectangular patterns are identified in two polymorphic crystals of a zwitterionic 4-(aryliodonio)-benzenesulfonate. The channels are filled with disordered water molecules which can be reversibly removed on heating. Consistent with the remarkable strength and directionality of the halogen bonds (XBs) driving the crystal packing formation, the porous structure is stable and fully preserved on almost quantitative removal and readsorption of water. The porous systems described here are the first reported cases of one-component 3D organic frameworks whose assembly is driven by XB only (XOFs). These systems are a proof of concept for the ability of zwitterionic aryliodonium tectons in affording robust one-component 3D XOFs. The high directionality and strength of the XBs formed by these zwitterions and the geometrical constraints resulting from the tendency of their hypervalent iodine atoms to act as bidentate XB donors might be key factors in determining this ability.
RESUMEN
In this communication experimental and theoretical results are reported affording strong evidence that interactions between electron rich atoms and the metal of tetroxide anions of groupâ 7 elements are a new case of attractive and σ-hole interactions. Single crystal X-ray analyses, molecular electrostatic potentials, quantum theory of atoms-in-molecules, and noncovalent interaction plot analyses show that in crystalline permanganate and perrhenate salts the metal in Mn/ReO4- anion can act as electron acceptors, the oxygen of another Mn/ReO4- anion can act as the donor and supramolecular anionic dimers or polymers are formed. The name matere bond (MaB) is proposed to categorize these noncovalent interactions and to differentiate them from the classical metal-ligand coordination bond.
RESUMEN
Chalcogen bonds are the specific interactions involving group 16 elements as electrophilic sites. The role of chalcogen atoms as sticky sites in biomolecules is underappreciated, and the few available studies have mostly focused on S. Here, we carried out a statistical analysis over 3562 protein structures in the Protein Data Bank (PDB) containing 18â¯266 selenomethionines and found that Se···O chalcogen bonds are commonplace. These findings may help the future design of functional peptides and contribute to understanding the role of Se in nature.
Asunto(s)
Calcógenos/química , Fructoquinasas/química , Selenio/química , Aminoácidos/química , Cristalografía por Rayos X , Bases de Datos de Proteínas , Modelos Moleculares , Conformación Proteica , Selenometionina/química , Relación Estructura-Actividad , Xylella/enzimologíaRESUMEN
The controlled oxidation reaction of L-selenocystine under neutral pH conditions affords selenocysteine seleninic acid (3-selenino-L-alanine) which is characterized also by means of single-crystal X-ray diffraction. This technique shows that selenium forms three chalcogen bonds (ChBs), one of them being outstandingly short. A survey of seleninic acid derivatives in the Cambridge Structural Database (CSD) confirms that the C-Se(=O)O- functionality tends to act as a ChB donor robust enough to systematically influence the interactional landscape in the solid. Quantum Theory of Atom in Molecules (QTAIM) analysis proves the attractive nature of the short contacts observed in crystals containing the seleninic functionality and calculation of surface molecular electrostatic potential (MEP) reveals that remarkably positive σ-holes can frequently be found opposite to the covalent bonds at selenium. Both CSD searches and QTAIM and MEP approaches show that also the sulfinic acid moiety can function as a ChB donor, albeit less frequently than the seleninic acid one. These findings may contribute to a better understanding, at the atomic level, of the mechanism of action of the enzymes that control oxidative stress and ROS deactivation and that contain selenocysteine seleninic acid and cysteine sulfinic acid in the active site.