What Are the Preferred Horizontal Displacements in Parallel Aromatic-Aromatic Interactions? Significant Interactions at Large Displacements

Crystal structure of (1,4,7,10,13,16-hexa-oxa-cycloocta-decane-κ6 O)potassium-μ-oxalato-tri-phenylstannate(IV), the first reported 18-crown-6-stabilized potassium salt of tri-phenyl-oxalatostannate

The title complex, (1,4,7,10,13,16-hexa-oxa-cyclo-octa-decane-1κ6 O)(μ-oxalato-1κ2 O 1,O 2:2κ2 O 1',O 2')triphenyl-2κ3 C-potassium(I)tin(IV), [KSn(C6H5)3(C2O4)(C12H24O6)] or K[18-Crown-6][(C6H5)3SnO4C2], was synthesized. The complex consists of a potassium cation coordinated to the six oxygen atoms of a crown ether mol-ecule and the two oxygen atoms of the oxalatotri-phenyl-stannate anion. It crystallizes in the monoclinic crystal system within the space group P21. The tin atom is coordinated by one chelating oxalate ligand and three phenyl groups, forming a cis-trigonal-bipyramidal geometry around the tin atom. The cations and anions form ion pairs, linked through carbonyl coordination to the potassium atoms. The crystal structure features C-H⋯O hydrogen bonds between the oxygen atoms of the oxalate group and the hydrogen atoms of the phenyl groups, resulting in an infinite chain structure extending along a-axis direction. The primary inter-chain inter-actions are van der Waals forces.

Chiral amino acid-templated tin fluorides tailoring nonlinear optical properties, birefringence, and photoluminescence

In this study, we successfully synthesized two types of new chiral amino acid-templated tin fluoride crystals: (R)-[(C8H10NO3)2]Sn(IV)F6, (S)-[(C8H10NO3)2]Sn(IV)F6, (R)-[C8H10NO3]Sn(II)F3, and (S)-[C8H10NO3]Sn(II)F3, employing a slow evaporation method. The crystal structures of Sn(IV)-compounds were determined to belong to the noncentrosymmetric (NCS) nonpolar space group, P21212. Conversely, the structures of Sn(II)-compounds were found to crystallize in the NCS polar space group, P21, as revealed by single-crystal X-ray diffraction analysis. Remarkably, Sn(IV)-compounds exhibited a larger birefringence (0.328@546.1 nm), attributed to the well-stacked arrangement of planar π-conjugated benzene rings along the b-axis. The ability of tin(IV) fluorides to form more hydrogen bonds with ligands increased the probability of π-π interactions between benzene rings, enabling the growth of centimeter-sized crystals in Sn(IV)-compounds. In contrast, Sn(II)-compounds displayed a stronger second-harmonic generation (SHG) response (0.85 × KDP) than Sn(IV)-compounds (0.46 × KDP). This enhanced SHG response in Sn(II)-compounds was attributed to the increased dipole moments resulting from the presence of lone pairs. Additionally, Sn(II)-compounds exhibited photoluminescent properties due to the transition from the metal-to-ligand charge transfer state, facilitated by the presence of the lone pairs.

Anthryl-functionalized cyanide-bridged Fe/Co cubes

Two anthryl-functionalized cyanide-bridged [Fe4Co4] cube complexes, [(pzTp)Fe(CN)3Co(TpEtOAn)]4[OTf]4·8MeCN·7Et2O (1) and [NEt4]3[(pzTp)Fe(CN)3Co(TpEtOAn)]4[OTf]7·5MeCN·2Et2O (2) (pzTp- = tetrapyrazolylborate, TpEtOAn = 2,2,2-tris-(pyrazol-1-yl)ethoxy(9-methyl-anthracene)), were synthesized and characterized. The crystallographic study revealed that the [Fe4Co4] cubes are arranged into a linear supramolecular chain through significant anthryl-anthryl π-π stacking interactions in complex 1, whereas a zigzag supramolecular 1D assembly is observed in 2. The magnetic measurements showed that both compounds exhibited incomplete transitions from the paramagnetic {FeIIILS(μ-CN)CoIIHS} state to the diamagnetic {FeIILS(μ-CN)CoIIILS} state at about 200 K. The luminescence measurement of 1 in solution revealed an enhancement of the emission upon dilution or addition of perfluoronaphthalene (PFN) molecules, which could be attributed to the suppression of the aggregation-caused quenching (ACQ) effect, suggesting possible aggregation of the cube units in the solution.

Fractal nature of benzene stacking interactions

CONTEXT

Benzene and other aromatic groups, as planar groups with [Formula: see text] electrons cloud, tend to form stacking interactions which have an important role in various chemical and biological processes. In order to have a better insight in the nature of these interactions, we have performed a fractal analysis on patterns of electron density and electrostatic potential for two benzenes in stacking interaction. The calculated fractal dimension follows the trend of the calculated interaction energy for the interplanar distances of 4.0 to 6.0 Å, which partially coincides with the strongest attractive stacking interactions. The fractal dimension vs. energy dependences were fitted with the logistic curve, and the fitting coefficient was 0.96 up to 1.00.

METHODS

For the benzene stacking interaction energy, with a range of conformations and distances between two benzenes, DFT calculations at the B3LYP+D3/aug-cc-pVDZ level were performed with the TURBOMOLE software. The fractal analysis for electron density and electrostatic potential has been done by python scripting.

Alizarin as a potential protector of proteins against damage caused by hydroperoxyl radical

Alizarin is a natural anthraquinone molecule with moderate antioxidative capacity. Some earlier investigations indicated that it can inhibit osteosarcoma and breast carcinoma cell proliferation by inhibiting of phosphorylation process of ERK protein (extracellular signal-regulated kinases). Several mechanisms of deactivation of one of the most reactive oxygen species, hydroperoxyl radical, by alizarin are estimated: hydrogen atom abstraction (HAA), radical adduct formation (RAF), and single electron transfer (SET). The plausibility of those mechanisms is estimated using density functional theory. The obtained results indicated HAA as the only thermodynamically plausible mechanism. For that purpose, two possible mechanistic pathways for hydrogen atom abstraction are studied in detail: hydrogen atom transfer (HAT) and proton-coupled electron transfer (PCET). Water and benzene are used as models of solvents with opposite polarity. To examine the difference between HAT and PCET is used kinetical approach based on the Transition state theory (TST) and determined rate constants (k). Important data used for a distinction between HAT and PCET mechanisms are obtained by applying the Quantum Theory of Atoms in Molecules (QTAIM), and by the analysis of single occupied molecular orbitals (SOMOs) in transition states for two examined mechanisms. The molecular docking analysis and molecular dynamic are used to predict the most probable positions of binding of alizarin to the sequence of ApoB-100 protein, a protein component of plasma low-density lipoproteins (LDL). It is found that alizarin links the nitrated polypeptide forming the π-π interactions with the amino acids Phenylalanine and Nitrotyrosine. The ability of alizarin to scavenge hydroperoxyl radical when it is in a sandwich structure between the polypeptide and radical species, as the operative reaction mechanism, is not significantly changed concerning its antioxidant capacity in the absence of polypeptide. Therefore, alizarin can protect the polypeptide from harmful hydroperoxyl radical attack, positioning itself between the polypeptide chain and the reactive oxygen species.

Structural characterization of sodium and potassium 3-nitrohydrogenphthalate coordination polymers

The synthesis, crystal structures and properties of two alkali metal 3-nitrohydrogenphthalates obtained by a 1:2 reaction of M2CO3 (M = K or Na) with 3-nitrophthalic acid (LH2) are reported. In the anhydrous potassium coordination polymer [K(LH)] (LH = 2-carboxy-3-nitrobenzoate) 1, the K+ cation is bonded to nine oxygen atoms from six symmetry related (LH)– ligands resulting in a distorted {KO9} coordination polyhedron. Five of the six oxygen atoms including a nitro oxygen atom of the crystallographically unique 2-carboxy-3-nitrobenzoate are involved in metal binding. The μ6-bridging mode of (LH)– places the K+ cations into the layers of the two-dimensional (2D) coordination polymer. Each {KO9} polyhedron in 1 shares edges with two other polyhedra along the b and c axes. A low temperature structure redetermination of [Na(L#H)(H2O)3]·H2O (L#H = 2-carboxy-6-nitrobenzoate) 2 has revealed that the (L#H)− anion is bonded to the Na+ cation in a monodentate fashion via the carbonyl oxygen atom of the –COOH group and two of the three unique aqua ligands exhibit a bridging bidentate mode stabilizing a chain polymer. The structure of compound 2 thus consists of chains of edge-sharing {NaO6} octahedra. Thermal decomposition of 1 or 2 results in the formation of metal carbonate residues.

Synthesis and structural characterization of three new mixed ligand alkaline-earth metal picrates

The dissolution of alkaline-earth metal carbonate in aqueous picric acid followed by reaction with nicotinamide results in the formation of [M(H2O) n (nic)2(pic)2] (nic = nicotinamide; pic = picrate; n = 1 and M = Ba 1; n = 2 and M = Ca (or Sr) 2 (or 3)). In [Ba(H2O)(nic)2(pic)2] 1, the barium and the oxygen atoms of a terminal aqua ligand are located on a two-fold axis. Compound 1 exhibits a {BaO7N2} coordination sphere, where the barium atom is bonded to a unique bidentate picrate and the crystallographically independent nicotinamide bridges to two symmetry related barium atoms with a Ba···Ba separation of 9.799 Å via the pyridine nitrogen and the amide oxygen atoms leading to the formation of a two-dimensional coordination polymer. The compounds 2 and 3 are isostructural with discrete molecules. The central Ca atom in 2 (or Sr in 3) located on a two-fold axis is bonded to a crystallographically unique terminal aqua ligand, an independent monodentate nicotinamide and a unique bidentate picrate anion resulting in a distorted {MO8} polyhedron. The mixed ligand alkaline-earth metal picrates 1–3 exhibit three varieties of hydrogen bonding and π–π stacking interactions. Several alkaline-earth metal picrates are compared in this study.

Correlation of solid-state order to optoelectronic behavior in heterocyclic oligomers

Here we address a longstanding challenge in the field of optoelectronic materials by evaluating the molecular and solid-state arrangements of heterocyclic oligomers and correlating their crystal structures to their optical properties.

Experimental and computational evidence for stabilising parallel, offset π[C(O)N(H)NC]⋯π(phenyl) interactions in acetohydrazide derivatives

Stabilising π[C(O)N(H)NC]⋯π(phenyl) interactions are described.

Supramolecular architectures sustained by delocalised C–I⋯π(arene) interactions in molecular crystals and the propensity of their formation

A survey of delocalised C–I⋯π(chelate ring) interactions is presented.

On the supramolecular outcomes of fluorination of cyclohexane-5-spirohydantoin derivatives

The crystal packing of two spirohydantoins was analyzed through the contribution of dimeric motifs and different interactions. The cooperative effect was rationalized in terms of the formation of a new region, as a result of the F⋯F interaction.

Stacking interactions of resonance-assisted hydrogen-bridged rings and C6-aromatic rings

Stacking interactions between six-membered resonance-assisted hydrogen-bridged (RAHB) rings and C6-aromatic rings were systematically studied by analyzing crystal structures in the Cambridge Structural Database (CSD). The interaction energies were calculated by quantum-chemical methods. Although the interactions are stronger than benzene/benzene stacking interactions (-2.7 kcal mol-1), the strongest calculated RAHB/benzene stacking interaction (-3.7 kcal mol-1) is significantly weaker than the strongest calculated RAHB/RAHB stacking interaction (-4.7 kcal mol-1), but for a particular composition of RAHB rings, RAHB/benzene stacking interactions can be weaker or stronger than the corresponding RAHB/RAHB stacking interactions. They are also weaker than the strongest calculated stacking interaction between five-membered saturated hydrogen-bridged rings and benzene (-4.4 kcal mol-1) and between two five-membered saturated hydrogen-bridged rings (-4.9 kcal mol-1). SAPT energy decomposition analyses show that the strongest attractive term in RAHB/benzene stacking interactions is dispersion, however, it is mostly canceled by a repulsive exchange term; hence the geometries of the most stable structures are determined by an electrostatic term.

Self-Assembly and Biorecognition of a Spirohydantoin Derived from α-Tetralone: Interplay between Chirality and Intermolecular Interactions

A racemic spirohydantoin derivative with two aromatic substituents, a tetralin and a 4-methoxybenzyl unit, was synthesized and its crystal structure was determined. To define the relationship between molecular stereochemistry and spatial association modes, development of the crystal packing was analyzed through cooperativity of intermolecular interactions. Homo and heterochiral dimeric motifs were stabilized by intermolecular N-H⋅⋅⋅O, C-H⋅⋅⋅O, C-H⋅⋅⋅π interactions and parallel interactions at large offsets (PILO), thus forming alternating double layers. The greatest contribution to the total stabilization came from a motif of opposite enantiomers linked by N-H⋅⋅⋅O bonds (interaction energy=-13.72 kcal/mol), followed by a homochiral motif where the 4-methoxybenzyl units allowed C-H⋅⋅⋅π, C-H⋅⋅⋅O interactions and PILO (interaction energy=-11.56 kcal/mol). The number of the contact fragments in the environment of the tetralin unit was larger, but the 4-methoxybenzyl unit had greater contribution to the total stabilization. The statistical analysis of the data from the Cambridge Structural Database (CSD) showed that this is a general trend. The compound is a potential inhibitor of kinase enzymes and antigen protein-coupled receptors. A correlation between the docking study and the results of the CSD analysis can be drawn. Due to a greater flexibility, the 4-methoxybenzyl unit is more adaptable for interactions with the biological targets than the tetralin unit.

Stacking interactions of the methylated cyclopentadienyl ligands in the crystal structures of transition metal complexes

In the crystal structures of methylated cyclopentadienyl (Cp) complexes (MeCp, Me₄Cp and Me₅Cp) deposited in the Cambridge Structural Database, certain orientation types of stacked contacts can be noted as the most frequent. These orientation preferences can be well explained by the matching of oppositely charged regions of electrostatic potential. Parallel displaced stacking, large offset stacking and C-H...π interactions are the dominant interaction types that are responsible for the arrangement in the crystal structures of stacked methylated Cp complexes.

What Is Special about Aromatic-Aromatic Interactions? Significant Attraction at Large Horizontal Displacement

High-level ab initio calculations show that the most stable stacking for benzene-cyclohexane is 17% stronger than that for benzene-benzene. However, as these systems are displaced horizontally the benzene-benzene attraction retains its strength. At a displacement of 5.0 Å, the benzene-benzene attraction is still ∼70% of its maximum strength, while benzene-cyclohexane attraction has fallen to ∼40% of its maximum strength. Alternatively, the radius of attraction (>2.0 kcal/mol) for benzene-benzene is 250% larger than that for benzene-cyclohexane. Thus, at relatively large distances aromatic rings can recognize each other, a phenomenon that helps explain their importance in protein folding and supramolecular structures.

Strong stacking interactions at large horizontal displacements of tropylium and cyclooctatetraenide ligands of transition metal complexes: crystallographic and DFT study

Large offset stacking of tropylium and COT ligands, which is dominant in crystal structures, surpasses an energy of −3.0 kcal mol⁻¹.

Stacking interactions of borazine: important stacking at large horizontal displacements and dihydrogen bonding governed by electrostatic potentials of borazine

Potential energy surfaces of borazine-benzene and borazine-borazine stacking interactions were studied by performing DFT, CCSD(T)/CBS and SAPT calculations. The strongest borazine-benzene stacking was found in a parallel-displaced geometry, with a CCSD(T)/CBS interaction energy of -3.46 kcal mol-1. The strongest borazine-borazine stacking has a sandwich geometry, with a CCSD(T)/CBS interaction energy of -3.57 kcal mol-1. The study showed that borazine forms significant stacking interactions at large horizontal displacements (over 4.5 Å), with energies of -2.20 kcal mol-1 for the borazine-benzene and -1.96 kcal mol-1 for the borazine-borazine system. The strength of interactions and their geometrical preferences can be rationalized by observing the electrostatic potentials of borazine and benzene, which is in agreement with SAPT analysis showing that electrostatics is the most important energy component for borazine stacking. All the interactions found in crystal structures of borazine and related compounds were identified either as potential curve minima or the geometries obtained from their optimizations. We also report a new dihydrogen bonding dimer with a CCSD(T)/CBS interaction energy of -2.37 kcal mol-1, which is encountered in the borazine crystal structures and enables the formation of additional simultaneous interactions that contribute to the overall stability of the crystals.

Platinum(ii) complexes showing high cytotoxicity toward A2780 ovarian carcinoma cells

2,6-Bis(thiazol-2-yl)pyridines functionalized with 9-anthryl (L¹), 9-phenanthryl (L²), and 1-pyrenyl (L³) groups were used for the preparation of [Pt(Lⁿ)Cl]CF₃SO₃ (1-3). The constitution of the Pt(ii) complexes was determined by ¹H and ¹³C NMR spectroscopy, HR-MS spectrometry, elemental analysis and X-ray analysis (for (1)). The electrochemical and photophysical properties of [Pt(Lⁿ)Cl]CF₃SO₃ were compared with the behaviour of the Pt(ii) complexes with aryl-substituted 2,2':6',2''-terpyridine ligands. What is noteworthy is that the coordination ability of dtpy toward the Pt(ii) centre was investigated for the first time. All complexes were tested in vitro by MTS assay on four tumor cell lines, A2780 (ovarian carcinoma), HTC116 (colon rectal carcinoma), MCF7 (breast adenocarcinoma), and PC3 (prostate carcinoma) and on normal primary fibroblasts. Compounds (1-3) showed a dose dependent antiproliferative effect in the A2780 cell line with (3) > (2) > (1) and this loss of A2780 cell viability was due to a combination of an apoptotic cell death mechanism via mitochondria and autophagic cell death. Exposure to IC₅₀ concentration of (2) induced an increase in the number of apoptotic nuclei and a depolarization of the mitochondrial membrane which is consistent with the induction of apoptosis while exposure to IC₅₀ concentration of (3) showed an increase in the apoptotic nuclei with a slight hyperpolarization of the mitochondrial membrane that might indicate an initial step of apoptosis induction. The complexes (2) and (3) induce an increase in the production of intracellular ROS which is associated with the trigger of the apoptotic pathways. The ROS production was augmented by the presence of oxidants and correlated with an increase of oxygen radicals. The IC₅₀ of (2) and (3) (4.4 μM and 2.9 μM, respectively) was similar to the IC₅₀ of cisplatin (3.4 μM) in the A2780 cell line, which together with their low cytotoxicity in normal fibroblasts, demonstrates their potential for further studies.

Influence of chelate ring type on chelate-chelate and chelate-aryl stacking: the case of nickel bis(dithiolene)

Chelate-aryl and chelate-chelate stacking interactions of nickel bis(dithiolene) were studied at the CCSD(T)/CBS and DFT levels. The strongest chelate-aryl stacking interaction between nickel bis(dithiolene) and benzene has a CCSD(T)/CBS stacking energy of -5.60 kcal mol^-1. The strongest chelate-chelate stacking interactions between two nickel bis(dithiolenes) has a CCSD(T)/CBS stacking energy of -10.34 kcal mol^-1. The most stable chelate-aryl stacking has the benzene center above the nickel atom, while the most stable chelate-chelate dithiolene stacking has the chelate center above the nickel atom. Comparison of chelate-aryl stacking interactions of dithiolene and acac-type nickel chelate shows similar strength. However, chelate-chelate stacking is stronger for dithiolene nickel chelate than for acac-type nickel chelate, which has a CCSD(T)/CBS interaction energy of -9.50 kcal mol^-1.

Study of stacking interactions between two neutral tetrathiafulvalene molecules in Cambridge Structural Database crystal structures and by quantum chemical calculations

Tetrathiafulvalene (TTF) and its derivatives are very well known as electron donors with widespread use in the field of organic conductors and superconductors. Stacking interactions between two neutral TTF fragments were studied by analysing data from Cambridge Structural Database crystal structures and by quantum chemical calculations. Analysis of the contacts found in crystal structures shows high occurrence of parallel displaced orientations of TTF molecules. In the majority of the contacts, two TTF molecules are displaced along their longer C 2 axis. The most frequent geometry has the strongest TTF–TTF stacking interaction, with CCSD(T)/CBS energy of −9.96 kcal mol−1. All the other frequent geometries in crystal structures are similar to geometries of the minima on the calculated potential energy surface.

Stacking interactions between ruthenium p-cymene complexes: combined crystallographic and density functional study

Stacking interactions between ruthenium p-cymene complexes are significantly strengthened by additional simultaneous C–H/π interactions of aromatic rings and their substituents.

Investigation of interactions in Lewis pairs between phosphines and boranes by analyzing crystal structures from the Cambridge Structural Database

The interactions between phosphines and boranes in crystal structures have been investigated by analyzing data from the Cambridge Structural Database (CSD). The interactions between phosphines and boranes were classified into three types; two types depend on groups on the boron atom, whereas the third one involves frustrated Lewis pairs (FLPs). The data enabled geometric parameters in structures to be compared with phosphine-borane FLPs with classical Lewis pairs. Most of the crystal structures (78.1%) contain BH₃ as the borane group. In these systems, the boron-phosphorus distance is shorter than systems where the boron atom is surrounded by groups other than hydrogen atoms. The analysis of the CSD data has shown that FLPs have a tendency for the longest boron-phosphorus distance among all phosphine-borane pairs, as well as different other geometrical parameters. The results show that most of the frustrated phosphine-borane pairs found in crystal structures are bridged ones. The minority of non-bridged FLP structures contain, beside phosphorus and boron atoms, other heteroatoms (O, N, S for instance).

Chelated metal ions modulate the strength and geometry of stacking interactions: energies and potential energy surfaces for chelate-chelate stacking

Quantum chemical calculations were performed on model systems of stacking interactions between the acac type chelate rings of nickel, palladium, and platinum. CCSD(T)/CBS calculations showed that chelate-chelate stacking interactions are significantly stronger than chelate-aryl and aryl-aryl stacking interactions. Interaction energy surfaces were calculated at the LC-ωPBE-D3BJ/aug-cc-pVDZ level, which gives energies in good agreement with CCSD(T)/CBS. The stacking of chelates in an antiparallel orientation is stronger than the stacking in a parallel orientation, which is in agreement with the larger number of antiparallel stacked chelates in crystal structures from the Cambridge Structural Database. The strongest antiparallel chelate-chelate stacking interaction is formed between two platinum chelates, with a CCSD(T)/CBS interaction energy of -9.70 kcal mol-1, while the strongest stacking between two palladium chelates and two nickel chelates has CCSD(T)/CBS energies of -9.21 kcal mol-1 and -9.50 kcal mol-1, respectively. The strongest parallel chelate-chelate stacking was found for palladium chelates, with a LC-ωPBE-D3BJ/aug-cc-pVDZ energy of -6.51 kcal mol-1. The geometries of the potential surface minima are not the same for the three metals. The geometries of the minima are governed by electrostatic interactions, which are the ones determining the positions of the energy minima. Electrostatic interactions are governed by different electrostatic potentials above the metals, which are very positive for nickel, slightly positive for palladium, and slightly negative for platinum.

Influence of hydrogen bonds on edge-to-face interactions between pyridine molecules

Edge-to-face interactions between two pyridine molecules and the influence of simultaneous hydrogen bonding of one or both of the pyridines to water on those interactions were studied by analyzing data from ab initio calculations. The results show that the edge-to-face interactions of pyridine dimers that are hydrogen bonded to water are generally stronger than those of non-H-bonded pyridine dimers, especially when the donor pyridine forms a hydrogen bond. The binding energy of the most stable edge-to-face interacting H-bonded pyridine dimer is -5.05 kcal/mol, while that for the most stable edge-to-face interacting non-H-bonded pyridine dimer is -3.64 kcal/mol. The interaction energy data obtained in this study cannot be explained solely by the differences in electrostatic potential between pyridine and the pyridine-water dimer. However, the calculated cooperative effect can be predicted using electrostatic potential maps.

Strong CH/O interactions between polycyclic aromatic hydrocarbons and water: Influence of aromatic system size

Energies of CH/O interactions between water molecule and polycyclic aromatic hydrocarbons with a different number of aromatic rings were calculated using ab initio calculations at MP2/cc-PVTZ level. Results show that an additional aromatic ring in structure of polycyclic aromatic hydrocarbons significantly strengthens CH/O interactions. Calculated interaction energies in optimized structures of the most stable tetracene/water complex is -2.27 kcal/mol, anthracene/water is -2.13 kcal/mol and naphthalene/water is -1.97 kcal/mol. These interactions are stronger than CH/O contacts in benzene/water complex (-1.44 kcal/mol) while CH/O contacts in tetracene/water complex are even stronger than CH/O contacts in pyridine/water complexes (-2.21 kcal/mol). Electrostatic potential maps for different polycyclic aromatic hydrocarbons were calculated and used to explain trends in the energies of interactions.

Stacking of cyclopentadienyl organometallic sandwich and half-sandwich compounds. Strong interactions of sandwiches at large offsets

73% of stacking of Cp sandwiches in the CSD is at large offsets, since these interactions are relatively strong. Much weaker stacking between Cp half-sandwiches is surprising 60% of all stacks, due to more simultaneous interactions.

Precise elucidations of stacking manners of hydrogen-bonded two-dimensional organic frameworks composed of X-shaped π-conjugated systems

Stacking manners of 2D-nCOFs with a porous rhombic network framework was precisely characterized based on single crystal X-ray diffraction analysis.

The stacking interactions of bipyridine complexes: the influence of the metal ion type on the strength of interactions

The strength of the stacking interactions in the bipy complexes of nickel, palladium, and platinum, [M(CN)2 bipy]2 (M = Ni, Pd, Pt), was calculated using the ωB97xD/def2-TZVP method. The results show that for all considered geometries, interactions are the strongest for platinum, and weakest for nickel complexes, as a result of higher dispersion contributions of platinum over the palladium and nickel complexes. It was also shown that strength of interactions considerably rises with an increase of the stacking overlap area. As a consequence of the favorable electrostatic term, the strength of interactions also rises when metal atom and cyano ligands are involved in the overlap with bipy ligand. The strongest interaction was calculated in the platinum complex, for the geometry that has overlap of metal and cyano ligands with bipy ligand with an energy of -39.80 kcal mol(-1). The energies for similar geometries of palladium and nickel complexes are -34.60 and -32.45 kcal mol(-1). These energies, remarkably, exceed the strength of the stacking interactions between organic aromatic molecules. These results can be of importance in all systems with stacking interactions, from materials to biomolecules.

Aliphatic–aromatic stacking interactions in cyclohexane–benzene are stronger than aromatic–aromatic interaction in the benzene dimer

Stacking interactions between cyclohexane and benzene were studied in crystal structures from the Cambridge Structural Database and by ab initio calculations.

Stacking of metal chelates with benzene: can dispersion-corrected DFT be used to calculate organic-inorganic stacking?

CCSD(T)/CBS energies for stacking of nickel and copper chelates are calculated and used as benchmark data for evaluating the performance of dispersion-corrected density functionals for calculating the interaction energies. The best functionals for modeling the stacking of benzene with the nickel chelate are M06HF-D3 with the def2-TZVP basis set, and B3LYP-D3 with either def2-TZVP or aug-cc-pVDZ basis set, whereas for copper chelate the PBE0-D3 with def2-TZVP basis set yielded the best results. M06L-D3 with aug-cc-pVDZ gives satisfying results for both chelates. Most of the tested dispersion-corrected density functionals do not reproduce the benchmark data for stacking of benzene with both nickel (no unpaired electrons) and copper chelate (one unpaired electron), whereas a number of these functionals perform well for interactions of organic molecules.

Stacking interactions of hydrogen-bridged rings – stronger than the stacking of benzene molecules

Planar hydrogen-bridged rings form parallel interactions in crystal structures. The interactions can be as strong as −4.89 kcal mol⁻¹.

The propargylbenzene dimer: C–H⋯π assisted π–π stacking

The infrared spectrum of a size-selected propargylbenzene dimer suggests the formation of a π-stacked dimer.

Parallel water/aromatic interactions of non-coordinated and coordinated water

The parallel interactions of non-coordinated and coordinated water molecules with an aromatic ring were studied by analyzing data in the Cambridge structural database (CSD) and by using quantum chemical calculations. The CSD data show that water/aromatic contacts prefer parallel to OH/π interactions, which indicates the importance of parallel interactions. The results reveal the influence of water coordination to a metal ion; the interactions of aqua complexes are stronger. Coordinated water molecules prefer a parallel-down orientation in which one OH bond is parallel to the aromatic ring, whereas the other OH bond points to the plane of the ring. The interactions of aqua complexes with parallel-down water/benzene orientation are as strong as the much better known OH/π orientations. The strongest calculated interaction energy is -14.89 kcal mol(-1) . The large number of parallel contacts in crystal structures and the quite strong interactions indicate the importance of parallel orientation in water/benzene interactions.

What are the preferred horizontal displacements of aromatic–aromatic interactions in proteins? Comparison with the calculated benzene–benzene potential energy surface

Stacking interactions of phenylalanine residues show preference for large offsets (3.5–5.0 Å), while the calculations show substantially strong interactions, of about −2.0 kcal mol⁻¹.