A study of crystal structures from the Cambridge Structural Database (CSD) and DFT calculations reveals that parallel pyridine–pyridine and benzene–pyridine interactions at large horizontal ...displacements (offsets) can be important, similar to parallel benzene–benzene interactions. In the crystal structures from the CSD preferred parallel pyridine–pyridine interactions were observed at a large horizontal displacement (4.0–6.0 Å) and not at an offset of 1.5 Å with the lowest calculated energy. The calculated interaction energies for pyridine–pyridine and benzene–pyridine dimers at a large offset (4.5 Å) are about 2.2 and 2.1 kcal mol−1, respectively. Substantial attraction at large offset values is a consequence of the balance between repulsion and dispersion. That is, dispersion at large offsets is reduced, however, repulsion is also reduced at large offsets, resulting in attractive interactions.
This way or that: In crystal structures from the Cambridge Structural Database preferred parallel pyridine–pyridine interactions are observed at large horizontal displacements (4.0–6.0 Å, see picture) and not at an offset of 1.5 Å, which had the lowest calculated energy.
•Stacking interactions are stronger if aromatics are coordinated to transition metals.•Benzene and Cp in sandwich compounds form strong stacking at large offsets.•Branched ligands in half-sandwich ...compounds favor stacking at large offsets.•Stacking of substituted coordinated arenes is combined with C–H/π interactions.
In this review article we present all the recent research on stacking interactions of aromatic ligands that coordinate to transition metals through their π-electrons (η-coordination). These studies were mostly based on searching the crystal structures from the Cambridge Structural Database (CSD) and on quantum chemical calculations. Stacking interactions between coordinated and uncoordinated benzene reach the energy of −4.40 kcal/mol, while the strongest calculated staking between two coordinated benzenes has the energy of −4.01 kcal/mol; this is significantly stronger than stacking between two uncoordinated benzenes (−2.73 kcal/mol). It was determined that in crystal structures both coordinated benzene and coordinated cyclopentadienyl anion form stacking interactions that dominantly have large horizontal displacements (more than 4.5 Å). This dominance is caused by the relatively strong stacking interactions at large displacements between benzene or Cp ligands in sandwich compounds, while for half-sandwich compounds they are supported by additional interactions of the other (usually branched) ligands. Larger aromatic ligands, tropylium and cyclooctatetraenide, almost exclusively form stacking interactions with large horizontal displacements. Methyl substituted benzene and Cp ligands dominantly form stacking interactions in combination with C–H/π interactions. Moreover, there is an interplay of stacking and aromatic C–H/π interactions in the CSD crystal structures, both interactions being important energy contributors to the stability of supramolecular systems. Stacking interactions of η-coordinated aromatic ligands are important in materials science, crystal engineering and medicinal chemistry, primarily in the application of ruthenium-arene complexes, where they determine the strength of bonding of these complexes to the DNA.
Amyloids are proteins of a cross-β structure found as deposits in several diseases and also in normal tissues (nails, spider net, silk). Aromatic amino acids are frequently found in amyloid deposits. ...Although they are not indispensable, aromatic amino acids, phenylalanine, tyrosine and tryptophan, enhance significantly the kinetics of formation and thermodynamic stability, while tape or ribbon-like morphology is represented in systems with experimentally detected π-π interactions between aromatic rings. Analysis of geometries and energies of the amyloid PDB structures indicate the prevalence of aromatic-nonaromatic interactions and confirm that aromatic-aromatic interactions are not crucial for the amyloid formation.
The computation of metal-silyl interaction energies indicates the existence of situations in which the silyl group behaves as a Z-type ligand according to the Green method of covalent-bond ...classification. There is a scale of relative intrinsic silylicity Π, defined as the ratio of the intrinsic silyl-to-triflate interaction energy of a silyltriflate as a reference compound relative to the silyl-to-metal interaction of given complex, that can reveal in a straightforward manner the propensity of SiR3 groups to behave chemically as metal-bound "silylium" ions, namely, SiR3+. Emblematic cases, either taken from the Cambridge Structural Database (CSD) or constructed for the purpose of this study, were also investigated from the viewpoints of extended transition-state natural orbitals for chemical valence (ETS-NOCV) and quantum theory of atoms in molecules (QTAIM) analyses. It is shown in the case of POBMUP--which is the iridium 1,3-bis(di-tert-butylphosphino)oxybenzene (POCOP) complex isolated by Brookhart etal.--how slight variations of molecular charge and structure can drastically affect the relative intrinsic silylicity of the SiEt3 group that is weakly bonded to the hydrido-iridium motif.
We revisit, in the key of structural chemistry, one of the most known and important drugs: the aspirin. Although apparently simple, the factors determining the molecular structure and supramolecular ...association in crystals are not trivial. We addressed the problem from experimental and theoretical sides, considering issues from X-ray measurements and results of first-principle reconstruction of molecule and lattices by ab initio calculations. Some puzzling problems can give headaches to specialists and intrigue the general public. Thus, the reported polymorphism of aspirin is disputed, a so-called form II being alleged as a result of misinterpretation. At the same time, were presented evidences that the structure of common form I can be disrupted by domains where the regular packing is changed to the pattern of form II. The problems appear even at the level of independent molecule: the most stable conformation computed by various techniques of electronic structure differs from those encountered in crystals. Because the energy difference between the related conformational isomers (computed as most stable vs. the experimental structure) is small, about 1 kcal/mol, comprised in the error bars of used methods, the unresting question is whether the modelling is imprecise, or the supramolecular factors are mutating the conformational preferences. By a detective following of the issue, the intermolecular effects were made responsible for the conformation of the molecule in crystal. The presented problems were gathered from literature results, debates, glued with modelling and analysis redone by ourselves, in order to secure the unitary view of the considered prototypic topic.
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•The electrostatic potentials for cubane and fluorinated derivatives were calculated.•Fluorination drastically increase positive potential in the core of the molecules.•The calculated ...electrostatic potentials correlate well with the experimental data.•The electrostatic potential correlates with accepting abilities of octafluorocubane.
The recent results on fluorinated cubanes showed good electron accepting abilities of octafluorocubane. Here we did the calculation of electrostatic potentials for cubane and its fluorinated derivatives. Maps of the electrostatic potential of fluorinated cubanes show regions, in the cores of the molecules, with significant positive potential (34.5 to 45.5 kcal/mol), which is in accordance with experimentally observed electron accepting abilities of the fluorinated cubanes. The increasing number of fluorine on the cubane increases positive potentials in the core of the molecule. Maps of electrostatic potentials can also explain structural motifs in crystals of fluorinated cubanes.
Accurate values for the energies of stacking interactions of nickel‐ and copper‐based six‐membered chelate rings with benzene are calculated at the CCSD(T)/CBS level. The results show that ...calculations made at the ωB97xD/def2‐TZVP level are in excellent agreement with CCSD(T)/CBS values. The energies of Cu(C3H3O2)(HCO2) and Ni(C3H3O2)(HCO2) chelates stacking with benzene are −6.39 and −4.77 kcal mol−1, respectively. Understanding these interactions might be important for materials with properties that are dependent on stacking interactions.
Stacks of energy: Energies of stacking interactions between benzene and metal chelates are calculated at the CCSD(T)/CBS level of theory. A copper chelate is found to stack more favorably with benzene than a nickel chelate. The energies of these interactions are significantly higher than that of benzene–benzene stacking. These results might be important for tuning the magnetic and electrical properties of organic–inorganic materials.
•Chelate rings in square-planar transition-metal complexes stack with aromatic rings.•Chelate rings stack with other isolated or fused chelate rings in the CSD structures.•Binding energies for these ...interactions exceed that for two benzene molecules.•These interactions are important for crystal packing and supramolecular structures.
Analysis of crystal structure data deposited in the Cambridge Structural Database (CSD) has shown that aromatic rings tend to stack with square planar transition metal complexes when they contain chelate rings. In these interactions, the orientation between chelate and aryl ring is a parallel-displaced orientation, like stacking interactions between aromatic molecules. In fused systems containing chelate and aryl rings, the aryl rings prefer to stack with the chelate rather than with other aryl rings. Quantum chemical calculations show that chelate-aryl stacking is stronger than aryl-aryl stacking. Interaction energies of six-membered chelates of the acetylacetonato type with benzene exceed −6kcal/mol (CCSD(T)/CBS), more that twice as strong as that for two benzene molecules. Further analysis of the CSD has shown that chelate rings, both isolated and fused stack with other chelate rings. These chelate-chelate stacking interactions can have both face-to-face and parallel-displaced geometries, unlike the stacking interactions between aromatic molecules, for which face-to-face geometry is not typical. Chelate-chelate stacking is stronger than aryl-aryl stacking and stronger even than chelate-aryl stacking. Stacking energies between six-membered chelates of acetylacetonato type exceed −9kcal/mol, while those between five-membered dithiolene chelates are even stronger. Calculated interaction energies and analysis of supramolecular structures have shown that chelate-chelate and chelate-aryl stacking must be considered in understanding the packing and organization of supramolecular systems and crystal engineering.
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