Search Results (17)

This study examines a series of organic–inorganic crystal structures containing the periodate anion (IO₄⁻) to clarify the nature of the anion–anion interactions that are frequently referred to as halogen bonds. Our analysis demonstrates that, in many cases, IO₄⁻ does not develop an electrophilic σ-hole on the iodine center, even in the presence of organic cations, and therefore cannot reliably function as a halogen-bond donor. In its discrete (0D) form, the anion retains its character as a Lewis base. In crystal structures where extended architectures are observed—such as one-dimensional chains, two-dimensional layers, or three-dimensional cage-like assemblies—these structures arise predominantly from strong coulombic interactions with surrounding cations, as the interaction between the anions is intrinsically repulsive in the gas phase. Hydrogen bonding, together with other noncovalent interactions including chalcogen, tetrel, and/or pnictogen bonding, plays a dominant role in stabilizing the anionic arrangements and governing their structural organization. Full article

A series of Group 10 metal dithiocarbonate complexes [M(S₂COⁱPr)₂] (M = Ni 1, Pd 2, Pt 3) was prepared following procedures from the literature and cocrystallized with the ditopic σ/π-hole donor 1,4-diiodotetrafluorobenzene. Single-crystal X-ray diffraction revealed a consistent I···S halogen bonding motif alongside a remarkable diversity in metal-involving interactions across the Ni–Pd–Pt triad. While nickel(II) exhibits strong electrophilic M···S semicoordination, the palladium(II) center displays ambiphilic behavior, and platinum(II) acts exclusively as a nucleophile via π-hole···M bonding. Comprehensive density functional theory studies, including molecular electrostatic potential (MEP) mapping, quantum theory of atoms in molecules/noncovalent interaction plot analyses, and energy decomposition analysis, were used to quantify this competitive balance. The results demonstrate that the increasing nucleophilicity from Ni to Pt, supported by shifting MEP minima and stronger π-hole stabilization energies, dictates the preference for nucleophilic over electrophilic metal-centered contact. Full article

The cocrystallization of trans-[PtI₂(NCR)₂] (R = NMe₂1, NEt₂2, Ph 3, o-ClC₆H₄4) with iodine and iodoform gave the crystalline adducts 1∙4I₂, 2∙2CHI₃, 3∙2CHI₃, and 4∙4I₂, whose structures were studied by single-crystal X-ray diffractometry (XRD). In the structures, apart from the rather predictable C–H⋯I hydrogen bonds (HBs) and I–I⋯I or C–I⋯I halogen bonds (XBs) with the iodide ligands, we identified bifurcated I–I⋯(I–Pt) and C–I⋯(I–Pt) metal-involving XBs, where the platinum center and iodide ligands function as simultaneous XB acceptors toward σ-holes of I atoms in I₂ or CHI₃. Appropriate density functional theory (DFT) calculations (PBE-D3/jorge-DZP-DKH with plane waves in the GAPW method) performed with periodic boundary conditions confirmed the existence of the bifurcated metal-involving I–I⋯(I–Pt) and C–I⋯(I–Pt) interactions and their noncovalent nature. Full article

The synthesis and structural characterization of α-haloalkyl-substituted pyridinium-fused 1,2,4-selenadiazoles with various counterions is reported herein, demonstrating a strategy for directed supramolecular dimerization in the solid state. The compounds were obtained through a recently discovered 1,3-dipolar cycloaddition reaction between nitriles and bifunctional 2-pyridylselenyl reagents, and their structures were confirmed by the X-ray crystallography. α-Haloalkyl-substituted pyridinium-fused 1,2,4-selenadiazoles exclusively formed supramolecular dimers via four-center Se···N chalcogen bonding, supported by additional halogen bonding involving α-haloalkyl substituents. The introduction of halogens at the α-position of the substituent R in the selenadiazole core proved effective in promoting supramolecular dimerization, which was unaffected by variation of counterions. Additionally, the impact of cocrystallization with a classical halogen bond donor C₆F₃I₃ on the supramolecular assembly was investigated. Non-covalent interactions were studied using density functional theory calculations and topological analysis of the electron density distribution, which indicated that all ChB, XB and HB interactions are purely non-covalent and attractive in nature. This study underscores the potential of halogen and chalcogen bonding in directing the self-assembly of functional supramolecular materials employing 1,2,4-selenadiazoles derived from recently discovered cycloaddition between nitriles and bifunctional 2-pyridylselenyl reagents. Full article

The Pt^II isocyanide complex [Pt(ppy)Cl(CNC₆H₄-C≡C-Ph)] (1, Hppy=2-phenylpyridine) was co-crystallized with 1,4-diiodotetrafluorobenzene (1,4-DITFB), yielding 1·½(1,4-DITFB) adduct. The I···Cl halogen-bonding and π-π-stacking interactions combined with the rare π-hole(isocyano group)⋅⋅⋅d_z²[Pt^II] interactions were identified via analysis of X-ray diffraction data of the co-crystals. These two types of structure-determining interactions supplemented each other, and the system of I⋯Cl and π-hole(isocyano group)⋅⋅⋅d_z²[Pt^II] contacts achieved a 1D extended ladder-type architecture. The density functional theory calculations, employing a set of computational tools, verified the role of I⋯Cl and π-hole(isocyano group)⋅⋅⋅d_z²[Pt^II] noncovalent bonds in the spectrum of noncovalent forces. The solid-state photophysical study revealed an amplification of luminescence intensity in the co-crystals, which is attributed to the suppression of the nonradiative relaxation pathways due to an increase in the rigidity of the chromophore center. Full article

Treatment of the [AuCl(tetrahydrothiophene)] complex with 4-chloro-2-iodo-1-isocyanobenzene furnished the gold(I) compound [AuCl(CNC₆H₃-4-Cl-2-I)] (1). In the crystal structure of 1, the linear C–Au–Cl group is subject to the solid-state head-to-tail pairing, which is determined by the aurophilic Au⋯Au and the rare π-hole_CN⋯Cl interactions. These two types of structure-determining interactions are complementary to each other, and the system of Au⋯Au and C_CN⋯Cl contacts accomplishes a 2D extended ladder-type architecture. In addition, the terminal I-atoms are involved in the three-center halogen bonding. Density functional theory calculations, employing a set of computational tools, verified the role of Au⋯Au and π-hole_CN⋯Cl noncovalent bonds in the spectrum of noncovalent forces. Full article

The cocrystallization of trans-[PtI₂(NCN(CH₂)₅)₂] and iodoform (CHI₃) yields crystalline adduct trans-[PtI₂(NCN(CH₂)₅)₂]∙2CHI₃, the structure of which was studied via single-crystal X-ray diffractometry (XRD). In the XRD structure of trans-[PtI₂(NCN(CH₂)₅)₂]∙2CHI₃, apart from rather predictable C–H∙∙∙I hydrogen bonds (HBs) and C−I∙∙∙I halogen bonds (XBs) with the iodide ligands, we identified C–I∙∙∙Pt metal-involving XBs, where the platinum center functions as an XB acceptor (that includes a metal d_z²-orbital) toward the σ-holes of I atoms of CHI₃. DFT calculations (PBE-D3/jorge-TZP-DKH with plane waves in the GAPW method) were carried out in the CP2K program for isolated molecules, complex–iodoform clusters, and crystal models with periodic boundary conditions, where the noncovalent nature and the existence of the interactions were confirmed using charge analysis, Wiberg bond indexes, and QTAIM topology analysis of electron density, whereas the philicities of the noncovalent partners were proved using charge analysis, electron localization function, electron density deformation, and one-electron potential projections, as well as electron density/electrostatic potential profiles for cluster models and electrostatic potential surfaces (ρ = 0.001 a.u.) for isolated molecules. Full article

In this paper, density functional theory and wave function theory calculations are carried out to investigate the strength and nature of the intermolecular C-X∙∙∙N bond interaction as a function of the number of cyano groups, CN, in the X-bond donor while maintaining the X-bond acceptor as fixed. Specifically, complexes of X-cyanomethanes with trimethyl amine CH_3−n(CN)_nX∙∙∙NMe₃ (n = 0–3; X = H, Cl, Br, I) are used as model systems. Geometrical parameters and vibrational C-X-stretching frequencies as well as interaction energies are used as relevant indicators to gauge hydrogen or halogen bond strength in the complexes. Additional characteristics of interactions that link these complexes, i.e., hydrogen or halogen bonds, are calculated with the use of the following theoretical tools: the atoms in molecules (AIM) approach, the natural bond orbital (NBO) method, and energy decomposition analysis (EDA). The results show that, for the specified X-center, the strength of C-X∙∙∙N interaction increases significantly and in a non-additive fashion with the number of CN groups. Moreover, the nature (noncovalent or partly covalent) of the interactions is revealed via the AIM approach. Full article

The pnictogen bond, a somewhat overlooked supramolecular chemical synthon known since the middle of the last century, is one of the promising types of non-covalent interactions yet to be fully understood by recognizing and exploiting its properties for the rational design of novel functional materials. Its bonding modes, energy profiles, vibrational structures and charge density topologies, among others, have yet to be comprehensively delineated, both theoretically and experimentally. In this overview, attention is largely centered on the nature of nitrogen-centered pnictogen bonds found in organic-inorganic hybrid metal halide perovskites and closely related structures deposited in the Cambridge Structural Database (CSD) and the Inorganic Chemistry Structural Database (ICSD). Focusing on well-characterized structures, it is shown that it is not merely charge-assisted hydrogen bonds that stabilize the inorganic frameworks, as widely assumed and well-documented, but simultaneously nitrogen-centered pnictogen bonding, and, depending on the atomic constituents of the organic cation, other non-covalent interactions such as halogen bonding and/or tetrel bonding, are also contributors to the stabilizing of a variety of materials in the solid state. We have shown that competition between pnictogen bonding and other interactions plays an important role in determining the tilting of the MX₆ (X = a halogen) octahedra of metal halide perovskites in one, two and three-dimensions. The pnictogen interactions are identified to be directional even in zero-dimensional crystals, a structural feature in many engineered ordered materials; hence an interplay between them and other non-covalent interactions drives the structure and the functional properties of perovskite materials and enabling their application in, for example, photovoltaics and optoelectronics. We have demonstrated that nitrogen in ammonium and its derivatives in many chemical systems acts as a pnictogen bond donor and contributes to conferring stability, and hence functionality, to crystalline perovskite systems. The significance of these non-covalent interactions should not be overlooked, especially when the focus is centered on the rationale design and discovery of such highly-valued materials. Full article

In chemical systems, the arsenic-centered pnictogen bond, or simply the arsenic bond, occurs when there is evidence of a net attractive interaction between the electrophilic region associated with a covalently or coordinately bound arsenic atom in a molecular entity and a nucleophile in another or the same molecular entity. It is the third member of the family of pnictogen bonds formed by the third atom of the pnictogen family, Group 15 of the periodic table, and is an inter- or intramolecular noncovalent interaction. In this overview, we present several illustrative crystal structures deposited into the Cambridge Structure Database (CSD) and the Inorganic Chemistry Structural Database (ICSD) during the last and current centuries to demonstrate that the arsenic atom in molecular entities has a significant ability to act as an electrophilic agent to make an attractive engagement with nucleophiles when in close vicinity, thereby forming σ-hole or π-hole interactions, and hence driving (in part, at least) the overall stability of the system’s crystalline phase. This overview does not include results from theoretical simulations reported by others as none of them address the signatory details of As-centered pnictogen bonds. Rather, we aimed at highlighting the interaction modes of arsenic-centered σ- and π-holes in the rationale design of crystal lattices to demonstrate that such interactions are abundant in crystalline materials, but care has to be taken to identify them as is usually done with the much more widely known noncovalent interactions in chemical systems, halogen bonding and hydrogen bonding. We also demonstrate that As-centered pnictogen bonds are usually accompanied by other primary and secondary interactions, which reinforce their occurrence and strength in most of the crystal structures illustrated. A statistical analysis of structures deposited into the CSD was performed for each interaction type As···D (D = N, O, S, Se, Te, F, Cl, Br, I, arene’s π system), thus providing insight into the typical nature of As···D interaction distances and ∠R–As···D bond angles of these interactions in crystals, where R is the remainder of the molecular entity. Full article

A stibium bond, i.e., a non-covalent interaction formed by covalently or coordinately bound antimony, occurs in chemical systems when there is evidence of a net attractive interaction between the electrophilic region associated with an antimony atom and a nucleophile in another, or the same molecular entity. This is a pnictogen bond and are likely formed by the elements of the pnictogen family, Group 15, of the periodic table, and is an inter- or intra-molecular non-covalent interaction. This overview describes a set of illustrative crystal systems that were stabilized (at least partially) by means of stibium bonds, together with other non-covalent interactions (such as hydrogen bonds and halogen bonds), retrieved from either the Cambridge Structure Database (CSD) or the Inorganic Crystal Structure Database (ICSD). We demonstrate that these databases contain hundreds of crystal structures of various dimensions in which covalently or coordinately bound antimony atoms in molecular entities feature positive sites that productively interact with various Lewis bases containing O, N, F, Cl, Br, and I atoms in the same or different molecular entities, leading to the formation of stibium bonds, and hence, being partially responsible for the stability of the crystals. The geometric features, pro-molecular charge density isosurface topologies, and extrema of the molecular electrostatic potential model were collectively examined in some instances to illustrate the presence of Sb-centered pnictogen bonding in the representative crystal systems considered. Full article

The CH₃Cl molecule has been used in several studies as an example purportedly to demonstrate that while Cl is weakly negative, a positive potential can be induced on its axial surface by the electric field of a reasonably strong Lewis base (such as O=CH₂). The induced positive potential then has the ability to attract the negative site of the Lewis base, thus explaining the importance of polarization leading to the formation of the H₃C–Cl···O=CH₂ complex. By examining the nature of the chlorine’s surface in CH₃Cl using the molecular electrostatic surface potential (MESP) approach, with MP2/aug-cc-pVTZ, we show that this view is not correct. The results of our calculations demonstrate that the local potential associated with the axial surface of the Cl atom is inherently positive. Therefore, it should be able to inherently act as a halogen bond donor. This is shown to be the case by examining several halogen-bonded complexes of CH₃Cl with a series of negative sites. In addition, it is also shown that the lateral portions of Cl in CH₃Cl features a belt of negative electrostatic potential that can participate in forming halogen-, chalcogen-, and hydrogen-bonded interactions. The results of the theoretical models used, viz. the quantum theory of atoms in molecules; the reduced density gradient noncovalent index; the natural bond orbital analysis; and the symmetry adapted perturbation theory show that Cl-centered intermolecular bonding interactions revealed in a series of 18 binary complexes do not involve a polarization-induced potential on the Cl atom. Full article

We employ a variety of natural bond orbital (NBO) and natural resonance theory (NRT) tools to comprehensively investigate the nature of halogen and pnicogen bonding interactions in RPH₂···IF/FI binary complexes (R = CH₃, OH, CF₃, CN, and NO₂) and the tuning effects of R-substituents. Though such interactions are commonly attributed to “sigma-hole”-type electrostatic effects, we show that they exhibit profound similarities and analogies to the resonance-type 3-center, 4-electron (3c/4e) donor-acceptor interactions of hydrogen bonding, where classical-type “electrostatics” are known to play only a secondary modulating role. The general 3c/4e resonance perspective corresponds to a continuous range of interatomic A···B bond orders (b_AB), spanning both the stronger “covalent” interactions of the molecular domain (say, b_AB ≥ ½) and the weaker interactions (b_AB ˂ ½, often misleadingly termed “noncovalent”) that underlie supramolecular complexation phenomena. We show how a unified NBO/NRT-based description of hydrogen, halogen, pnicogen, and related bonding yields an improved predictive utility and intuitive understanding of empirical trends in binding energies, structural geometry, and other measurable properties that are expected to be manifested in all such supramolecular interaction phenomena. Full article

In addition to the underlying basic concepts and early recognition of halogen bonding, this paper reviews the conflicting views that consistently appear in the area of noncovalent interactions and the ability of covalently bonded halogen atoms in molecules to participate in noncovalent interactions that contribute to packing in the solid-state. It may be relatively straightforward to identify Type-II halogen bonding between atoms using the conceptual framework of σ-hole theory, especially when the interaction is linear and is formed between the axial positive region (σ-hole) on the halogen in one monomer and a negative site on a second interacting monomer. A σ-hole is an electron density deficient region on the halogen atom X opposite to the R–X covalent bond, where R is the remainder part of the molecule. However, it is not trivial to do so when secondary interactions are involved as the directionality of the interaction is significantly affected. We show, by providing some specific examples, that halogen bonds do not always follow the strict Type-II topology, and the occurrence of Type-I and -III halogen-centered contacts in crystals is very difficult to predict. In many instances, Type-I halogen-centered contacts appear simultaneously with Type-II halogen bonds. We employed the Independent Gradient Model, a recently proposed electron density approach for probing strong and weak interactions in molecular domains, to show that this is a very useful tool in unraveling the chemistry of halogen-assisted noncovalent interactions, especially in the weak bonding regime. Wherever possible, we have attempted to connect some of these results with those reported previously. Though useful for studying interactions of reasonable strength, IUPAC’s proposed “less than the sum of the van der Waals radii” criterion should not always be assumed as a necessary and sufficient feature to reveal weakly bound interactions, since in many crystals the attractive interaction happens to occur between the midpoint of a bond, or the junction region, and a positive or negative site. Full article

Can two sites of positive electrostatic potential localized on the outer surfaces of two halogen atoms (and especially fluorine) in different molecular domains attract each other to form a non-covalent engagement? The answer, perhaps counterintuitive, is yes as shown here using the electronic structures and binding energies of the interactions for a series of 22 binary complexes formed between identical or different atomic domains in similar or related halogen-substituted molecules containing fluorine. These were obtained using various computational approaches, including density functional and ab initio first-principles theories with M06-2X, RHF, MP2 and CCSD(T). The physical chemistry of non-covalent bonding interactions in these complexes was explored using both Quantum Theory of Atoms in Molecules and Symmetry Adapted Perturbation Theories. The surface reactivity of the 17 monomers was examined using the Molecular Electrostatic Surface Potential approach. We have demonstrated inter alia that the dispersion term, the significance of which is not always appreciated, which emerges either from an energy decomposition analysis, or from a correlated calculation, plays a structure-determining role, although other contributions arising from electrostatic, exchange-repulsion and polarization effects are also important. The 0.0010 a.u. isodensity envelope, often used for mapping the electrostatic potential is found to provide incorrect information about the complete nature of the surface reactive sites on some of the isolated monomers, and can lead to a misinterpretation of the results obtained. Full article