Intramolecular MLOH/π and MLNH/π interactions in crystal structures of metal complexes

Intramolecular metal-ligand OH/π (MLOH/π) and metal-ligand NH/π (MLNH/π) interactions in transition metal complexes between aqua or ammine ligand and ligand containing a C6-aromatic ring were investigated in crystal structures deposited in the Cambridge Structural Database (CSD). These intramolecular interactions appear in 38 structures with aqua ligand as the hydrogen atom donor and in 10 structures with ammine ligand as the hydrogen atom donor. Among all these complexes only one is negatively charged, 14 are positively charged and 33 are neutral indicating that the overall charge of the molecule has an influence on the XH/π (X = O or N) interactions. Energy estimated by DFT calculations is approximately 19 kJ mol⁻¹ for the MLOH/π interactions and approximately 15 kJ mol⁻¹ for the MLNH/π interactions. Dedicated to Professor Milan Melník on the occasion of his 70th birthday     

On the directionality of anion-π interactions

The directionality of two important noncovalent interactions involving aromatic rings (namely anion-π and cation-π) is investigated. It has been recently published that the anion-π interactions observed in X-ray structures where the anion is located exactly over the center of the ring are scarce compared to cation-π interactions. To explain this behavior, we have analyzed how the interaction energy (RI-MP2/aug-cc-pVDZ level of theory) is affected by moving the anion from the center of the ring to several directions in anion-π complexes of chloride with either hexafluorobenzene or trifluoro-s-triazine. We have compared the results with the directionality of the cation-π interaction in the sodium-benzene complex. The results are useful to explain the experimental differences between both ion-π interactions. We have also computed the van der Waals radii of several halide anions and we have compared them to the neutral halogen atoms.     

On the Relative Importance of O–H/π Interactions in 7-Norbornenols

The geometries of the two H–O–C rotamers of synand two of anti-7-norbornenol have been optimized at the ab initio HF/6-31G** and B3LYP hybrid HF-DFT levels of theory by using a 6-31G** basis set. Contrary to an earlier report, we find that the (nongeometry constrained) anti-trans isomer (1d) is predicted to be more stable than the corresponding syn-cis form (1a). The increased stability of 1d vis-à-vis 1a can be accounted for in terms of relative H(1)–C(2)–O(3)–H(4) torsion energy effects. The computational results indicate that the hydroxyl proton in 1a enters into intramolecular hydrogen bonding with the proximate C=C bond. Supporting evidence for this conclusion resides in the fact that the 1a is predicted to possess the lowest O–H stretching frequency, a result that can be attributed to -hydrogen bonding.     

Bridged aromatic alkenes for the study of carbocation-π interaction

Toward the goal of gaining further insight into carbocation-π interactions, bridged-ring aromatic alkene model systems are being investigated in which one isomer will permit π complexation of an intramolecular tertiary carbocation with a benzene ring, but the other isomer will not. The syntheses of three sets of such isomers, having, respectively, benzobicyclo[3.2.1]octene, benzobicyclo[2.2.1]heptene, and benzobicyclo[4.2.1]nonene structures, are described.     

Carbocation-π interaction: the 1,1-dimethylallyl cation and benzene

Computational studies of the interaction of 1,1-dimethylallyl cation with benzene reveal that its potential energy surface has a rich complexity. The lowest energy π-complex, which involves binding of both ends of the cation to the benzene ring, is calculated to be 4.5 kcal mol⁻¹ lower in energy than its related σ-complex. The results provide further support for the idea that π complexation of carbocations is stronger over the periphery of aromatic systems, and offer insight into why biological reactions involving this type of carbocation do not lead via σ-complex formation to electrophilic substitution of the aromatic rings in proteins.     

Effects of the biological backbone on stacking interactions at DNA-protein interfaces: the interplay between the backbone···π and π···π components

The (gas-phase) MP2/6-31G*(0.25) π···π stacking interactions between the five natural bases and the aromatic amino acids calculated using (truncated) monomers composed of conjugated rings and/or (extended) monomers containing the biological backbone (either the protein backbone or deoxyribose sugar) were previously compared. Although preliminary energetic results indicated that the protein backbone strengthens, while the deoxyribose sugar either strengthens or weakens, the interaction calculated using truncated models, the reasons for these effects were unknown. The present work explains these observations by dissecting the interaction energy of the extended complexes into individual backbone···π and π···π components. Our calculations reveal that the total interaction energy of the extended complex can be predicted as a sum of the backbone···π and π···π components, which indicates that the biological backbone does not significantly affect the ring system through π-polarization. Instead, we find that the backbone can indirectly affect the magnitude of the π···π contribution by changing the relative ring orientations in extended dimers compared with truncated dimers. Furthermore, the strengths of the individual backbone···π contributions are determined to be significant (up to 18 kJ mol(-1)). Therefore, the origin of the energetic change upon model extension is found to result from a balance between an additional (attractive) backbone···π component and differences in the strength of the π···π interaction. In addition, to understand the effects of the biological backbone on the stacking interactions at DNA-protein interfaces in nature, we analyzed the stacking interactions found in select DNA-protein crystal structures, and verified that an additive approach can be used to examine the strength of these interactions in biological complexes. Interestingly, although the presence of attractive backbone···π contacts is qualitatively confirmed using the quantum theory of atoms in molecules (QTAIM), QTAIM electron density analysis is unable to quantitatively predict the additive relationship of these interactions. Most importantly, this work reveals that both the backbone···π and π···π components must be carefully considered to accurately determine the overall stability of DNA-protein assemblies.     

Insight into the cation-π interaction at the metal binding site of the copper metallochaperone CusF

The periplasmic Cu(+)/Ag(+) chaperone CusF features a novel cation-π interaction between a Cu(+)/Ag(+) ion and Trp44 at the metal binding site. The nature and strength of the Cu(+)/Ag(+)-Trp44 interactions were investigated using computational methodologies. Quantum-mechanical (QM) calculations showed that the Cu(+) and Ag(+) interactions with Trp44 are of similar strength (~14 kcal/mol) and bond order. Quantum-mechanical/molecular-mechanical (QM/MM) calculations showed that Cu(+) binds in a distorted tetrahedral coordination environment in the Trp44Met mutant, which lacks the cation-π interaction. Molecular dynamics (MD) simulations of CusF in the apo and Cu(+)-bound states emphasized the importance of the Cu(+)-Trp44 interaction in protecting Cu(+) from water oxidation. The protein structure does not change over the time scale of hundreds of nanoseconds in the metal-bound state. The metal recognition site exhibits small motions in the apo state but remains largely preorganized toward metal binding. Trp44 remains oriented to form the cation-π interaction in the apo state and faces an energetic penalty to move away from the metal ion. Cu(+) binding quenches the protein's internal motions in regions linked to binding CusB, suggesting that protein motions play an essential role in Cu(+) transfer to CusB.     

Spin-spin interaction between phenyl nitroxides through the σ-π system

The spin states of a series of silicon- and carbon-bridged phenyl nitroxides were examined with respect to the temperature dependent ESR and SQUID measurements. Of those, a linear relationship between the ESR signal intensity and 1/T (T = absolute temperature) and an increase of χ_molT along lowering T were observed for a compound having disilanylene-bridged m- and p-phenyl nitroxide units (Si2mp), indicating ferromagnetic spin-spin interaction in this molecule. In contrast to this, no clear intramolecular spin-spin interaction took place in the monosilanylene analogue (Si1mp). Mono- and disilanylene-bridged phenylnitroxides with p-, p- or m-, m-substitution (Si1pp,Si1mm, Si1pp, and Si2mm) exhibited the singlet ground state. The trisilanylene and siloxanylene bridges did not play an obvious role in the spin interaction, in either a ferro- or antiferromagnetic fashion, regardless of the substitution modes of the phenylenes. MO calculations on the model compounds provided a mechanistic interpretation for the high-spin interaction through the σ-π system.     

Combined cation-π and anion-π interactions for zwitterion recognition

Brothers and enemies: Anion-π and cation-π interactions act in a synergistic way when gathered in the molecular cavity of a hemicryptophane host, affording an efficient contribution (-170?kJ?mol(-1)) in zwitterion recognition. NMR titration experiments and calculations reveal the positioning of the guest in the cavity of the heteroditopic receptor. This study emphasizes the importance of anion-π bonds in host-guest chemistry.     

Herringbone and Helical Self-Assembly of π-Conjugated Molecules in the Solid State through CH/π Hydrogen Bonds

Self-organization of organic molecules through weak noncovalent forces such as CH/π interactions and creation of large hierarchical supramolecular structures in the solid state are at the very early stage of research. The present study reports direct evidence for CH/π interaction driven hierarchical self-assembly in π-conjugated molecules based on custom-designed oligophenylenevinylenes (OPVs) whose structures differ only in the number of carbon atoms in the tails. Single-crystal X-ray structures were resolved for these OPV synthons and the existence of long-range multiple-arm CH/π interactions was revealed in the crystal lattices. Alignment of these π-conjugated OPVs in the solid state was found to be crucial in producing either right-handed herringbone packing in the crystal or left-handed helices in the liquid-crystalline mesophase. Pitch- and roll-angle displacements of OPV chromophores were determined to trace the effect of the molecular inclination on the ordering of hierarchical structures. Furthermore, circular dichroism studies on the OPVs were carried out in the aligned helical structures to prove the existence of molecular self-assembly. Thus, the present strategy opens up new approaches in supramolecular chemistry based on weak CH/π hydrogen bonding, more specifically in π-conjugated materials.     

Infrared laser spectroscopy of the fundamental band of a 3π CO

Many rotational components of the fundamental band of metastable a ³Π CO have been measured in absorption using diode laser spectroscopy with concentration modulation detection. Line positions are in good agreement with predictions from optically derived parameters. Resolved or partially resolved splittings arising from lambda-doubling appear for the three Ω components. Splittings in the Ω = 1 and 2 spectra agree satisfactorily with molecular beam (rf) and microwave results while those in the Ω = 0 fundamental deviate by several linewidths (up to 0.015 cm-⁻¹) from calculated values.     

Relative substituent position on the strength of π-π stacking interactions

It was observed that the relative position of the arene substituents has a profound influence on the strength of π-π stacking in the 9-benzyl-substituted triptycene system. A new series of model compounds (3a-i) capable of revealing quantitatively π-π stacking interactions was studied. This series of compounds (3a-i) has an ortho-substituted methyl group in one of the two interacting arenes and the syn/anti ratios were determined and compared to a series previously studied compounds (4a-i) that have a para methyl group on the corresponding arene. A greater than 50% increase in the strength of π-π stacking interactions was observed with the methyl group in the ortho position comparing to that in the para position. No difference in π-π stacking interactions was observed when the other aromatic ring was a pentafluorobenzoate group.     

Preference of intra- and intermolecular cation-π interaction: cis-trans geometrical effects of amide bond on the interaction mode

An intermolecular cation-π interaction is observed in trans-amide 3, whereas an intramolecular interaction is observed in cis-amide 4, suggesting that cis-trans conformational difference plays a critical role in the preference of the interaction modes.     

Study on the Cation-π Interactions between Ammonium Ion and Aromatic π Systems

The nature and strength of the cation-π interactions between NH4^＋ and toluene, p-cresol, or Me-indole were studied in terms of the topological properties of molecular charge density and binding energy decomposition. The results display that the diversity in the distribution pattern of bond and cage critical points reflects the profound influence of the number and nature of substituent on the electron density of the aromatic rings. On the other hand, the energy decomposition shows that dispersion and repulsive exchange forces play an important role in the organic cation （NH4^＋）-π interaction, although the electrostatic and induction forces dominate the interaction. In addition, it is intriguing that there is an excellent correlation between the electrostatic energy and ellipticity at the bond critical point of the aromatic π systems, which would be helpful to further understand the electrostatic interaction in the cation-π complexes.     

π-π interactions in the self-assembly of melamine and barbituric acid derivatives

Self-assembly of a pair of complementary molecular components, 5-(4-dodecyloxyben-zylidene)-(1H,3H)-2,4,6-pyrimidinetrione (PB12) and 4-amino-2,6-didodecylamino-1, 3, 5-triazine (M12) was studied by cyclic voltammogram, surface photovoltage spectroscopy, fluorescence spectroscopy, FTIR and X-ray diffraction. It is found that after mixing equimolar amount of PB12 and M12 at room temperature, not only triply complementary hydrogen bonds are formed between PB12 and M12 but also further self-assembly of the supermolecules based on network of hydrogen bonds occurs via π-π interactions. During the self-assembly of the supermolecules, π-π interactions are induced by delocalized interactions between the HOMO of M12 and the LUMO of PB12, resulting in the formation of a supramolecular nanotube with a layered structure bearing a d value of 0.41 nm and PB12 and M12are arranged alternatively between adjacent supermolecules.     

A molecular balance to measure the strength of N-H?π hydrogen bonds based on the tautomeric equilibria of C-benzylphenyl substituted NH-pyrazoles

A theoretical (B3LYP/6-31G^∗∗) study of 30 pyrazoles, most of them existing in two tautomeric forms, has been carried out. 3(5)-(2-Benzylphenyl)-5(3)-methyl-1H-pyrazole (11) and 3(5)-(2-benzylbenzylphenyl)-5(3)-phenyl-1H-pyrazole (20) were synthesized from 2-benzoylacetophenone, and their annular tautomeric equilibrium determined. The substituent effects were statistically analyzed and discussed with the help of Hammett substituent constants. In the case of the 5-(2-benzylphenyl) groups, the strength of the N-H?π hydrogen bond depends on the electronic effect of the substituent at position 3.     

Functionally Important Aromatic-Aromatic and Sulfur-π Interactions in the D2 Dopamine Receptor

The recently published crystal structure of the D3 dopamine receptor shows a tightly packed region of aromatic residues on helices 5 and 6 in the space bridging the binding site and what is thought to be the origin of intracellular helical motion. This highly conserved region also makes contacts with residues on helix 3, and here we use double mutant cycle analysis and unnatural amino acid mutagenesis to probe the functional role of several residues in this region of the closely related D2 dopamine receptor. Of the eight mutant pairs examined, all show significant functional coupling (Ω > 2), with the largest coupling coefficients observed between residues on different helices, C3.36/W6.48, T3.37/S5.46, and F5.47/F6.52. Additionally, three aromatic residues examined, F5.47, Y5.48, and F5.51, show consistent trends upon progressive fluorination of the aromatic side chain. These trends are indicative of a functionally important electrostatic interaction with the face of the aromatic residue examined, which is likely attributed to aromatic-aromatic interactions between residues in this microdomain. We also propose that the previously determined fluorination trend at W6.48 is likely due to a sulfur-π interaction with the side chain of C3.36. We conclude that these residues form a tightly packed structural microdomain that connects helices 3, 5, and 6, thus forming a barrier that prevents dopamine from binding further toward the intracellular surface. Upon activation, these residues likely do not change their relative conformation, but rather act to translate agonist binding at the extracellular surface into the large intracellular movements that characterize receptor activation.     

π-π interactions in the self-assembly of melamine and barbituric acid derivatives

Self-assembly of a pair of complementary molecular components, 5-(4-dodecyloxyben-zylidene)-(1H,3H)-2, 4,6-pyrimidinetrione (PB₁₂)and 4-amino-2,6-didodecylamino-1, 3, 5-triazine (M₁₂) was studied by cyclic voltammogram, surface photovoltage spectroscopy, fluorescence spectroscopy, FTIR and X-ray diffraction. It is found that after mixing equimolar amount of PB₁₂ and M₁₂ at room temperature, not only triply complementary hydrogen bonds are formed between PB₁₂and M₁₂ but also further self-assembly of the supermolecules based on network of hydrogen bonds occurs via π-π interactions. During the self-assembly of the supermolecules, π -π interactions are induced by delocalized interactions between the HOMO of M₁₂ and the LUMO of PB₁₂, resulting in the formation of a supramolecular nanotube with a layered structure bearing a d value of 0.41 nm and PB₁₂ and M₁₂are arranged alternatively between adjacent supermolecules.     

Al4(2-); the anion-π interactions and aromaticity in the presence of counter ions

The influence of presence of counter ions and π-complexation with benzene on the bonding and magnetic properties of Al(4)(2-), the most studied all-metal cluster, is studied here. It is shown that complexation by either counter ions or benzene decreases the delocalization index between Al atoms and the magnitude of bond magnetizability, that is a Quantum Theory of Atoms in Molecules, QTAIM, -based magnetic index of aromaticity. Benzene forms two types of π-complexes with the Al(4) framework; CH-π (T-shaped) complexes and parallel π-π stacking (PPS) complexes. It is shown that variation in the π-charge of the Al(4) framework affects the relative stability of the T-shaped/PPS complexes. Free Al(4)(2-) forms a stable T-shaped anion-π complex with benzene but in the presence of cations, formation of PPS complexes is more favourable, energetically. It is suggested that this property could be used for designing molecular switches and tuneable anion sensors.