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Supramolecular polymers derived from the PtII and PdII schiff base complexes via C(sp2)–H … Hal hydrogen bonding: Combined experimental and theoretical study

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Abstract

A synthesis of the Pd II and Pt II N,N-diaryldiazabutadiene complexes and their self-assembly into infinite 1-dimensional chains in the solid state via rare C (sp ² )–H … Hal hydrogen bonding is reported. All the new compounds were characterized using elemental analyses (C, H, N), ESI-MS, IR, ¹ H and ¹³ C NMR techniques and X-ray diffraction analysis. The nature and energies of intermolecular non-covalent interactions, which are responsible for the supramolecular polymerization, were studied theoretically using DFT calculations and topological analysis of the electron density distribution within the formalism of Bader's theory (QTAIM method). While chloro-complexes, which feature a relatively stronger C (sp ² )–H … Hal hydrogen bonding, form supramolecular polymers, the iodo-derivative does not self-assemble into 1-D chains due to the dominance of other crystal packing forces over the potential H⋯I contacts. Thus, the C (sp ² )–H … Hal HB can dictate a packing preference in the solid state and serve as a useful tool for supramolecular engineers.

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In presence of different cations, reactions of [SbBr6]3- and I2 result in a new family of diverse supramolecular 1D polyiodide-bromoantimonate networks. Coordination number of Sb, as well as geometry of assembling {Ix}n- polyhalide units, can vary, resulting in unprecedented structural types. The nature of I···Br interactions was studied by DFT calculations; estimated energy values are 1.6-6.9 kcal/mol. Some of the compounds showed strong photoconductivity in thin films, suggesting multiple feasible applications in optoelectronics and solar energy conversion.
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Three novel polybromotellurates(IV) were obtained by reactions of TeO2 in conc. HBr with Br2 and tri‐ or tetraalkylammonium salts. They contain [TeBr6]2– octahedra connected by {Br2} linkers into one‐ or pseudo‐two‐dimensional networks. The thermal stability of the products was investigated by TGA; additionally, all compounds were characterized by Raman spectroscopy. Energies of Br···Br interactions were estimated by DFT calculations (QTAIM method). In the presence of tri‐ or tetraalkylammonium cations, [TeBr6]2– and Br2 form one‐ or two‐dimensional supramolecular polybromide/bromotellurate hybrids demonstrating remarkable stability.
Article
Reactions between BiCl3, Br2 and chlorides of pyridinium (1), 4,4`-propylenedipyridinium (2) or trimethylphenylammonium (3) in aqueous HCl lead to the formation of chlorobismuthate complexes trapping {Br2} in solid state into two-dimensional polyhalide supramolecular networks. The nature of non-covalent Br···Cl interactions was studied by theoretical methods; estimated energies of these interactions are 1.9-6.0 kcal/mol.
Article
Reactions of TeO2 and Br2 in concentrated HBr in presence of various organic cations resulted in formation of one- dimensional supramolecular polymers cation2{[TeBr6](Br2)]. In crystal structures, Br2 units are connected to [TeBr6]2- octahedra via halogen-halogen contacts, building linear chains of two different geometries. The nature of Br···Br, Br···Cl, and Cl···Cl contacts in present and previously reported complexes of this family was investigated by theoretical methods, allowing the estimation of their energies (0.9-3.8 kcal/mol).
Article
The reaction of cis-[PdCl2(CNXyl)2] (Xyl = 2,6-Me2C6H3) with various 1,3-thiazol- and 1,3,4-thiadiazol-2-amines in chloroform gives a mixture of two regioisomeric binuclear diaminocarbene complexes. For 1,3-thiazol-2-amines the isomeric ratio depends on the reaction conditions and kinetically (KRs) or thermodynamically (TRs) controlled regioisomers were obtained at room temperature and on heating, respectively. In CHCl3 solutions, the isomers are subject to reversible isomerization accompanied by the cleavage of Pd-N and C-N bonds in the carbene fragment XylNCN(R)Xyl. Results of DFT calculations followed by the topological analysis of the electron density distribution within the formalism of Bader's theory (AIM method) reveal that in CHCl3 solution the relative stability of the regioisomers (ΔGexp = 1.2 kcal/mol; ΔGcalcd = 3.2 kcal/mol) is determined by the energy difference between two types of the intramolecular chalcogen bonds, viz. S⋯Cl in KRs (2.8-3.0 kcal/mol) and S⋯N in TRs (4.6-5.3 kcal/mol). In the case of the 1,3,4-thiadiazol-2-amines, the regioisomers are formed in approximately equal amounts and, accordingly, the energy difference between these species is only 0.1 kcal/mol in terms of ΔGexp (ΔGcalcd = 2.1 kcal/mol). The regioisomers were characterized by elemental analyses (C, H, N), HRESI⁺-MS and FTIR, 1D (¹H, ¹³C{¹H}) and 2D (¹H,¹H-COSY, ¹H,¹H-NOESY, ¹H,¹³C-HSQC, ¹H,¹³C-HMBC) NMR spectroscopies, and structures of six complexes (three KRs and three TRs) were elucidated by single-crystal X-ray diffraction.
Article
The halogen bond occurs when there is evidence of a net attractive interaction between an electrophilic region associated with a halogen atom in a molecular entity and a nucleophilic region in another, or the same, molecular entity. In this fairly extensive review, after a brief history of the interaction, we will provide the reader with a snapshot of where the research on the halogen bond is now, and, perhaps, where it is going. The specific advantages brought up by a design based on the use of the halogen bond will be demonstrated in quite different fields spanning from material sciences to biomolecular recognition and drug design.
Article
In this report, multiple-stimulus-responsive materials were synthesized via supramolecular self-assembly. One-dimensional nanorods were constructed by the self-aggregation of 4-(phenyl-azo)benzoic acid (PBA) molecules in aqueous solution at pH 3.2. As the pH of the solution was increased to 6.5, these nanorods transformed into two-dimensional polygons. Upon UV irradiation, the as-prepared nanorods disappeared completely, and nanospheres were subsequently obtained. On the basis of the weak interactions between PBA and additive molecules, for example, N-alkyl-N′-carboxymethyl imidazolium bromide, β-cyclodextrin, and cetyltrimethylammonium bromide, materials with various morphologies were also fabricated by a surfactant-assistant self-assembly strategy. Noteworthy is that Salvia officinalis-shaped material is among them. To the best of our knowledge, this type of microstructured material has been rarely reported. In addition, slender fibers, sphere-like particles, and aggregates of spheres were also observed. These results suggest that the rational fabrication of materials with desired shapes and sizes can be achieved by changing external environments during the self-aggregation of PBA molecules. Both cyclic voltammogram experiments and density functional theory calculations exhibit the optoelectronic behavior of these materials, which is expected to have potential applications in the fabrication of photoelectronic nanodevices.
Article
A study is conducted to investigate halogen bonding in supramolecular chemistry. The study gives an overview of how computational methods have been applied to understand the nature of halogen bonding (XB) interactions, starting with quantum mechanics (QM) and moving on to methods based on classical force fields. QM is used to study weak intermolecular interactions as the characteristics of the noncovalently bonded system can be difficult to separate from other effects in condensed phases. Extensive investigations also reveal that halogen atoms are among the more electronegative elements, and covalently bonded halogens are usually considered to be electron rich.
Article
The double-inversion and front-side attack transition states as well as the proton abstraction channels of the X- + CH3Y [X,Y = F, Cl, Br, I] reactions are characterized by the explicitly-correlated CCSD(T)-F12b/aug-cc-pVTZ(-PP) level of theory using small-core relativistic effective core potentials and the corresponding aug-cc-pVTZ-PP bases for Br and I. In the X = F case the double-inversion classical(adiabatic) barrier heights are 28.7(25.6), 15.8(13.4), 13.2(11.0), and 8.6(6.6) kcal mol-1 for Y = F, Cl, Br, and I, respectively, whereas the barrier heights are in the 40-90 kcal mol-1 range for the other 12 reactions. The abstraction channels are always above the double-inversion saddle points. For X = F the front-side attack classical(adiabatic) barrier heights, 45.8(44.8), 31.0(30.3), 24.7(24.2), and 19.5(19.3) kcal mol-1 for Y = F, Cl, Br, and I, respectively, are higher than the corresponding double-inversion ones, whereas for the other systems the front-side attack saddle points are in the 35-70 kcal mol-1 range. The double-inversion transition states have XH•••CH2Y- structures with Cs point-group symmetry and the front-side attack saddle points have either Cs (X = F or X = Y) or C1 symmetry with XCY angles in the 78-88 range. On the basis of the previous reaction dynamics simulations and the minimum energy path computations along the inversion coordinate of selected XH•••CH2Y- systems, we suggest that the double inversion may be a general mechanism for SN2 reactions.
Article
Structure-based ligand design in medicinal chemistry and crop protection relies on the identification and quantification of weak noncovalent interactions and understanding the role of water. Small-molecule and protein structural database searches are important tools to retrieve existing knowledge. Thermodynamic profiling, combined with X-ray structural and computational studies, is the key to elucidate the energetics of the replacement of water by ligands. Biological receptor sites vary greatly in shape, conformational dynamics, and polarity, and require different ligand-design strategies, as shown for various case studies. Interactions between dipoles have become a central theme of molecular recognition. Orthogonal interactions, halogen bonding, and amide⋅⋅⋅π stacking provide new tools for innovative lead optimization. The combination of synthetic models and biological complexation studies is required to gather reliable information on weak noncovalent interactions and the role of water.
Article
CF3H as a proton donor was paired with a variety of anions, and its properties were assessed by MP2/aug-cc-pVDZ calculations. The binding energy of monoanions halide, NO3−, formate, acetate, HSO4−, and H2PO4− lie in the 12–17 kcal mol−1 range, although F− is more strongly bound, by 26 kcal mol−1. Dianions SO42− and HPO42− are bound by 27 kcal mol−1, and trianion PO43− by 45 kcal mol−1. When two O atoms are available on the anion, the CHO− H-bond (HB) is usually bifurcated, although asymmetrically. The CH bond is elongated and its stretching frequency redshifted in these ionic HBs, but the shift is reduced in the bifurcated structures. Slightly more than half of the binding energy is attributed to Coulombic attraction, with smaller contributions from induction and dispersion. The amount of charge transfer from the anions to the σ*(CH) orbital correlates with many of the other indicators of bond strength, such as binding energy, CH bond stretch, CH redshift, downfield NMR spectroscopic chemical shift of the bridging proton, and density at bond critical points.
Article
For the traditional model of gas-phase X– + CH3Y SN2 reactions, C3v ion-dipole pre- and postreaction complexes X–---CH3Y and XCH3---Y–, separated by a central barrier, are formed. Statistical intramolecular dynamics are assumed for these complexes, so that their unimolecular rate constants are given by RRKM theory. Both previous simulations and experiments have shown that the dynamics of these complexes are not statistical and of interest is how these nonstatistical dynamics affect the SN2 rate constant. This work also found there was a transition from an indirect, nonstatistical, complex forming mechanism, to a direct mechanism, as either the vibrational and/or relative translational energy of the reactants was increased. The current Account reviews recent collaborative studies involving molecular beam ion-imaging experiments and direct (on-the-fly) dynamics simulations of the SN2 reactions for which Cl–, F–, and OH– react with CH3I. Also considered are reactions of the microsolvated anions OH–(H2O) and OH–(H2O)2 with CH3I. These studies have provided a detailed understanding of the atomistic mechanisms for these SN2 reactions.
Article
The title compound, C20H24N2, (I), has crystallographic Ci symmetry, with the central C—C bond located on a centre of inversion. The dihedral angle between the central 1,4-di­aza­buta-1,3-diene moiety and the attached substituted phenyl ring is 64.0 (2) Å.
Article
Organic materials naturally lend themselves to the crafting of structure and function using the strategies of self-assembly and supramolecular chemistry employed so effectively by biological systems. This perspective illustrates progress over the past two decades on self-assembly in materials chemistry through research on systems where function is directly linked to noncovalent interactions among molecules. The genesis of this approach in chemistry of materials involves the design of relatively simple structures using hydrogen bonding, π–π stacking, metal–ligand interactions, electrostatic forces, strong dipole–dipole association, hydrophobic forces, and steric repulsion. Gradually many new and exciting opportunities have emerged, such as supramolecular nanostructures that assemble into functional bulk materials and supramolecular polymers in which the motif of covalent connections among monomers is imitated by creating one-dimensional assemblies of an arbitrarily large set of molecules in both composition and size. Supramolecular polymers offer the opportunity to create structures that integrate unprecedented order in 1D assemblies with interesting dynamics through bond reversibility. Other fascinating systems are those in which intermolecular interactions and other forces can be used to create the hierarchical and highly functional structures ubiquitous in biology, such as bone and muscle, in which different types of order exist within the same structure at different length scales. Directions that have a bright future include nonequilibrium dynamic materials with the capacity to be adaptive, self-repairing, chemically alterable, and even replicative—all characteristics we see in living organic matter. Additional promising areas include 2D and 3D systems that are not necessarily classical crystals and the rational synthesis of functional organic–inorganic hybrid materials. The most exciting aspect of self-assembly and supramolecular chemistry is their open ended nature, and these are two areas of chemistry for which many new principles will be established in this century.
Article
Interatomic interactions such as hydrogen bonds (HB) can be adequately described and classified by the topological properties of the electron density ρ(r) at the (3,−1) critical points rCP where the gradients of ρ(r) vanish. We have analysed the topological properties of ρ(r) at the intermolecular critical points of 83 experimentally observed HBs [X–H⋯O (X=C,N,O)], using accurate X-ray diffraction experiments. In spite of different models, methods and experimental conditions employed to obtain the topological properties of ρ(r), we show that, for closed-shell interactions, the kinetic energy density G(rCP) and the potential energy density V(rCP) at the critical point depend exponentially on the H⋯O distance. Moreover, theoretical calculations for several HB dissociation energies follow the same law as does V(rCP), with a simple change of scale.
Article
The design and synthesis of anion selective receptors and chemosensors continues to attract considerable interest within the supramolecular community. In recent years, increasing attention has focused on the use of neutral and cationic CH hydrogen bond donors as anion recognition elements. Over the last five years, motifs that support CHX (X = anion) hydrogen bonds have been actively used in various shape persistent macrocycles, foldamers and "molecular machines". This tutorial review highlights recent developments in host-guest chemistry based on the use of neutral and cationic CH hydrogen bond donors. Also discussed are various structural classifications, including alkyl CH, phenyl CH, triazole-based CH, imidazolium (CH)(+) and triazolium (CH)(+) hydrogen bond donor systems.
Article
Natural bond orbital (NBO) methods encompass a suite of algorithms that enable fundamental bonding concepts to be extracted from Hartree-Fock (HF), Density Functional Theory (DFT), and post-HF computations. NBO terminology and general mathematical formulations for atoms and polyatomic species are presented. NBO analyses of selected molecules that span the periodic table illustrate the deciphering of the molecular wavefunction in terms commonly understood by chemists: Lewis structures, charge, bond order, bond type, hybridization, resonance, donor–acceptor interactions, etc. Upcoming features in the NBO program address ongoing advances in ab initio computing technology and burgeoning demands of its user community by introducing major new methods, keywords, and electronic structure system/NBO communication enhancements. © 2011 John Wiley & Sons, Ltd.
Article
Summary Nonrelativistic and quasirelativisticab initio pseudopotentials substituting the M(Z-28)+-core orbitals of the second row transition elements and the M(Z-60)+-core orbitals of the third row transition elements, respectively, and optimized (8s7p6d)/[6s5p3d]-GTO valence basis sets for use in molecular calculations have been generated. Additionally, corresponding spin-orbit operators have also been derived. Atomic excitation and ionization energies from numerical HF as well as from SCF pseudopotential calculations using the derived basis sets differ in most cases by less than 0.1 eV from corresponding numerical all-electron results. Spin-orbit splittings for lowlying states are in reasonable agreement with corresponding all-electron Dirac-Fock (DF) results.
Article
The hydrogen bond (HB) basicity of a series of ylides containing nitrogen, oxygen, or carbon as heavy atoms, as well as the influence of the formation of the HB complexes on their structure, has been studied. In addition, in this paper we propose the formation of some rather strong HBs (that could be considered low-barrier hydrogen bonds, LBHBs) between ylides and different neutral molecules. The ylides chosen for the study were H3N+−N-H, Me3N+−N-H, H2O+−N-H, Me2O+−N-H, H2O+−O-, Me2O+−O-, and Me3N+−C-H2. As HB donors, classical donors such as HF, HCN, and HCCH were used. The analysis of the protonation energies of the ylides and the optimized geometries, interaction energies, and characteristics of the electron density of the complexes shows that these ylides are very good HB acceptors, forming stable complexes even with weak HB donors. With strong donors, when the proton transfer did not take place, very strong HBs were formed with quite large interaction energies and very short HB distances which could be considered as LBHBs. Moreover, we have found that the sign of the Laplacian of the electron density at the bond critical point (2ρBCP) and that of the energy density (HBCP) could characterize the strength of HBs. Thus, weak HBs (EI < 12.0 kcal/mol) show both 2ρBCP and HBCP > 0, and medium HBs (12.0 < EI < 24.0 kcal/mol) show 2ρBCP > 0 and HBCP < 0, while strong HBs (and therefore LBHBs; EI > 24.0 kcal/mol) show both 2ρBCP and HBCP < 0.
Article
Comments on aspects of the new definition of the hydrogen bond specific to crystal engineering are given.
Article
Intermolecular van der Waals radii of the nonmetallic elements have been assembled into a list of "recommended" values for volume calculations. These values have been arrived at by selecting from the most reliable X-ray diffraction data those which could be reconciled with crystal density at 0°K. (to give reasonable packing density), gas kinetic collision cross section, critical density, and liquid state properties. A qualitative understanding of the nature of van der Waals radii is provided by correlation with the de Broglie wave length of the outermost valence electron. Tentative values for the van der Waals radii of metallic elements - in metal organic compounds - are proposed. The paper concludes with a list of increments for the volume of molecules impenetrable to thermal collision, the so-called van der Waals volume, and of the corresponding increments in area per molecule.
Article
Molecular structure does not easily identify the intricate noncovalent interactions that govern many areas of biology and chemistry, including design of new materials and drugs. We develop an approach to detect noncovalent interactions in real space, based on the electron density and its derivatives. Our approach reveals the underlying chemistry that compliments the covalent structure. It provides a rich representation of van der Waals interactions, hydrogen bonds, and steric repulsion in small molecules, molecular complexes, and solids. Most importantly, the method, requiring only knowledge of the atomic coordinates, is efficient and applicable to large systems, such as proteins or DNA. Across these applications, a view of nonbonded interactions emerges as continuous surfaces rather than close contacts between atom pairs, offering rich insight into the design of new and improved ligands.
Article
The hydrogen bond is the most important of all directional intermolecular interactions. It is operative in determining molecular conformation, molecular aggregation, and the function of a vast number of chemical systems ranging from inorganic to biological. Research into hydrogen bonds experienced a stagnant period in the 1980s, but re-opened around 1990, and has been in rapid development since then. In terms of modern concepts, the hydrogen bond is understood as a very broad phenomenon, and it is accepted that there are open borders to other effects. There are dozens of different types of X-H.A hydrogen bonds that occur commonly in the condensed phases, and in addition there are innumerable less common ones. Dissociation energies span more than two orders of magnitude (about 0.2-40 kcal mol(-1)). Within this range, the nature of the interaction is not constant, but its electrostatic, covalent, and dispersion contributions vary in their relative weights. The hydrogen bond has broad transition regions that merge continuously with the covalent bond, the van der Waals interaction, the ionic interaction, and also the cation-pi interaction. All hydrogen bonds can be considered as incipient proton transfer reactions, and for strong hydrogen bonds, this reaction can be in a very advanced state. In this review, a coherent survey is given on all these matters.