Stacking interactions of organometallic sandwich and half-sandwich compounds: crystallographic evidence and quantum chemical support

Stacking interactions between two benzene molecules that coordinate transition metal ions within organometallic sandwich and half-sandwich compounds were investigated by performing Cambridge Structural Database (CSD) search and DFT-D calculations. Calculations of interaction energies revealed that stacking interactions between coordinating benzenes of sandwich (−3.69 kcal/mol) and half-sandwich compounds (−3.29 kcal/mol) are significantly stronger than the stacking interaction between noncoordinating benzenes (−2.73 kcal/mol). At large horizontal displacements (offset r = 5.0 A), these sandwich∥sandwich interactions are remarkably strong (−3.03 kcal/mol), while half-sandwich∥half-sandwich interactions are significantly weaker (−1.27 kcal/mol). The results of calculations are in good agreement with the data in the crystal structures from the CSD, where 76% of sandwich∥sandwich contacts have large horizontal displacements, which is significantly more than 46% of half-sandwich∥half-sandwich contacts arranged...

Stacking interactions of aromatic ligands in transition metal complexes

The study of crystal structures from the Cambridge Structural Database (CSD) shows that most of p-phenol/p-phenol and toluene/toluene stacking interactions are at large horizontal displacements (offsets) as well as benzene/benzene interactions. The interactions at large horizontal displacements are stabilized by the addition of simultaneous interactions in supramolecular structures in crystals. The stacking p-phenol/p-phenol tends to be orientated in a parallel and antiparallel fashion, while stacking toluene/toluene is almost all in an antiparallel orientation. It is in accordance with calculated interaction energies. Namely, the strongest interaction energies for parallel and antiparallel phenol/phenol dimers are −5.12 and −4.40 kcal/mol, at offsets of 1.5 and 3.0 Å, respectively, while for parallel and antiparallel toluene/toluene dimers, energies are −3.98 and −5.39 kcal/mol, at offsets of 3.0 Å. These interactions are stronger than benzene/benzene stacking (−2.85 kcal/mol), as a consequence of the presence of the substituents. Similar to benzene/benzene stacking, interactions for phenol/phenol and toluene/toluene stacking at large offsets (4.0 Å) can be strong, stronger than −2.0 kcal/mol.

Stacking interactions between pyridine molecules and the influence of simultaneous hydrogen bonds were studied by analyzing data in the Cambridge Structural Database (CSD) and by ab initio calculations. The results show remarkably stronger stacking interactions of pyridines with hydrogen bonds, because of local parallel alignment interactions of OH bonds with the aromatic ring. Data in the crystal structures from the CSD and ab initio calculations show that normal distances (R) in stacking interactions of pyridines with simultaneous hydrogen bonds are shorter than those in stacking interactions without simultaneous hydrogen bonds. Furthermore, the calculated binding energies for stacking are substantially stronger when the pyridines have hydrogen bonds; the binding energy of the stacking interaction between pyridine–water dimers is −6.86 kcal/mol, while that between pyridines is −4.08 kcal/mol. Surprisingly, in the minimum energy structure of the stacked pyridine–water dimers, the contribution of the local parallel-alignment interactions between water and the other pyridine (−2.98 kcal/mol) is slightly larger than the contribution of the stacking interaction between two pyridine molecules (−2.67 kcal/mol). The local influence of hydrogen bonds on stacking, via parallel alignment interactions, can be very important for all systems with heteroaromatic molecules and groups, especially DNA and RNA.

The synthesis of lanthanide‐based organometallic sandwich compounds is very appealing regarding their potential for single‐molecule magnetism. Here, it is exploited by on‐surface synthesis to design unprecedented lanthanide‐directed organometallic sandwich complexes on Au(111). The reported compounds consist of Dy or Er atoms sandwiched between partially deprotonated hexahydroxybenzene molecules, thus introducing a distinct family of homoleptic organometallic sandwiches based on six‐membered ring ligands. Their structural, electronic, and magnetic properties are investigated by scanning tunneling microscopy and spectroscopy, X‐ray absorption spectroscopy, X‐ray linear and circular magnetic dichroism, and X‐ray photoelectron spectroscopy, complemented by density functional theory‐based calculations. Both lanthanide complexes self‐assemble in close‐packed islands featuring a hexagonal lattice. It is unveiled that, despite exhibiting analogous self‐assembly, the erbium‐based species is magnetically isotropic, whereas the dysprosium‐based compound features an in‐plane magnetization.

Considering the properties of water and benzene molecules, one can expect very different benzene/benzene and water/water interactions. Benzene does not have a dipole moment, while water does. Analysis of the data in the crystal structures in the Cambridge Structural Database (CSD) revealed the most frequent benzene/benzene and water/water geometries. The majority of the benzene/benzene interactions in the crystal structures in the CSD are stacking interactions with large horizontal displacements, and not geometries that are minima on benzene/benzene potential surface. A large number of the water/water contacts in the CSD are hydrogen bonds, 70% of all attractive water/water interactions. In addition, water/water contacts with two water forming antiparallel interactions are 20% of all attractive water/water contacts. In these contacts, the O-H bonds of water molecules are in antiparallel orientation. In benzene/benzene interactions at large horizontal displacements, two C-H bonds also are in the antiparallel orientation. This shows that although the two molecules are different, both of them form antiparallel interactions with a local O-H and C-H dipole moments.

Analysis of crystal structures from the Cambridge Structural Database (CSD) and high level ab initio calculations reveals that the water/aromatic parallel alignment interactions, where the water molecule or one of its O–H bonds is parallel to the aromatic ring plane, can be significantly strong at large horizontal displacements. We found out that the strongest energies of the interactions are calculated for the water position with the large horizontal displacements, out of the aromatic ring and out of the C–H bond region. For calculated systems, normal distances were decreasing with increasing the horizontal displacement, in accord with the data found in crystal structures. The calculated energies of the interactions are significant, up to ΔECCSD(T)(limit) = −10.25 kJ/mol (at a horizontal displacement of 2.6 A), and comparable with the energy of the slipped-parallel benzene/benzene dimer. Both dispersion and electrostatic components of the interaction energy are important. The calculated interaction energ...

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.

Cambridge Structural Database (CSD) is the largest repository of crystal data, containing over 1.2 million crystal structures of organic, metal–organic and organometallic compounds. It is a powerful research tool in many areas, including the extensive studying of noncovalent interactions. In this review, we show how a thorough analysis of CSD crystal data resulted in recognition of novel types of stacking interactions. Even though stacking interactions were traditionally related to aromatic systems, a number of crystallographic studies have shown that nonaromatic metal–chelate rings, as well as hydrogen-bridged rings, can also form stacking interactions. Joined efforts of a CSD analysis and quantum chemical calculations showed that these new stacking interactions are stronger than stacking interactions of aromatic species and recognized them as very important attractive forces in numerous supramolecular systems.

Parallel stacking interactions between pyridines in crystal structures and the influence of hydrogen bonding and supramolecular structures in crystals on the geometries of interactions were studied by analyzing data from the Cambridge Structural Database (CSD). In the CSD 66 contacts of pyridines have a parallel orientation of molecules and most of these pyridines simultaneously form hydrogen bonds (44 contacts). The geometries of stacked pyridines observed in crystal structures were compared with the geometries obtained by calculations and explained by supramolecular structures in crystals. The results show that the mean perpendicular distance (R) between pyridine rings with (3.48 Å) and without hydrogen bonds (3.62 Å) is larger than that calculated, because of the influence of supramolecular structures in crystals. The pyridines with hydrogen bonds show a pronounced preference for offsets of 1.25-1.75 Å, close to the position of the calculated minimum (1.80 Å). However, stacking interactions of pyridines without hydrogen bonds do not adopt values at or close to that of the calculated offset. This is because stacking interactions of pyridines without hydrogen bonds are less strong, and they are more susceptible to the influence of supramolecular structures in crystals. These results show that hydrogen bonding and supramolecular structures have an important influence on the geometries of stacked pyridines in crystals.

Stacking interaction potential energy surfaces of square-planar metal complexes containing chelate rings

We have recently been investigating the phase behavior of salts of cationic sandwich complexes in pursuit of novel ionic plastic crystals (IPCs). In this study, we synthesized salts containing sandwich complexes [Ru(Cp)(C6H6)]X ([1]X; X = CPFSA− (1,1,2,2,3,3-hexafluoropropane-1,3-disulfonimide), SbCl6−) and half-sandwich complexes [Ru(Cp)(DMSO)3]X ([2]X; X = CPFSA−, FSA− ((FSO2)2N−), PF6−). In addition, we examined their thermal properties and crystal structures. Among them, [1]CPFSA exhibited an IPC phase between 365 and 630 K, whereas the others did not undergo phase transitions at 123–403 K. The cations and anions were alternately arranged in the crystals of [1]X, whereas [2]X did not exhibit the alternating arrangement except for [2]PF6. The results showed that alternating molecular arrangements are crucial for the IPC formation, although low symmetry of the ion environment and intermolecular steric hindrance may inhibit it.

A new class of platinum(ii) terpyridine complexes with a phosphole-derived bridging alkynyl ligand have been prepared. The X-ray crystal structure of complex 2 has been determined, and reveals a polymeric zig-zag chain structure with the existence of π-π stacking interactions. The photophysical properties have also been studied, with 3MLCT/3LLCT phosphorescence exhibited in degassed CH2Cl2; the energy of which is varied by the π-conjugation of the terpyridine ligands. The solvent-induced assembly of complex 1 has been studied. The incorporation of hydrophobic hydrocarbon chains has been shown to play an important role in assisting the formation of self-assembled nanostructures via Pt···Pt, π-π stacking and hydrophobic-hydrophobic interactions. It has been established that an isodesmic growth mechanism operates in polar media to give nanospheres, while fibrous networks originate from the self-assembly of the complexes in non-polar media, predominantly driven by π-π stacking interactions.

Stacking interactions between square-planar metal complexes containing bipyridine ligands (bipy) were studied by analyzing data in the Cambridge Structural Database (CSD) and by density functional theory (DFT) calculations. In most of the crystal structures, two bipy complexes were head-to-tail oriented. On the basis of the data from CSD, we classified the overlaps of bipy complexes into six types. The types were defined by values of geometrical parameters, and the interactions of the same type have very similar overlap geometries. The most frequent are the structures with quite large overlap area including chelate rings and pyridine fragments. The overlap is often influenced by ligands coordinated at the third and fourth coordinating positions or by molecules (ions) from the environment in the crystal structure. The interaction energies of all types of overlap were calculated on model systems using the DFT (TPSS-D3) method. The strongest calculated interaction has an energy of −31.66 kcal/mol and large area of overlap. By decreasing the overlap area, the strength of interactions decreases. The weakest calculated interaction has an energy of −7.26 kcal/mol and the small overlap area of pyridine fragments. These results presenting the geometries and energies of stacking interactions can be very important for various molecular systems.

According to our survey of the Cambridge Structural Database (CSD), a great number of crystal structures, in which halogen bonds and aromatic stacking interactions are present and play an important role in crystal packing, have been extracted. In this work, ab initio calculations at the MP2 level of theory were performed to investigate the mutual influence between halogen bonds and π-π stacking interactions. Different energetic effects are observed in the studied complexes where the two kinds of noncovalent interactions coexist, which can be rationalized by the direction of charge transfer for the two interactions. These effects have been analyzed in detail in terms of the structural, energetic, and charge transfer properties of the complexes. In addition, the quantum theory of atoms in molecules (QTAIM) was also employed to characterize the interactions and to examine the strengthening or weakening of the interactions, depending on the variations of electron density on the bond and cage critical points. Finally, certain crystal structures retrieved from the CSD have been selected to provide experimental evidence of the combination of the two interactions.