Do 12-Membered Cycloalkane Rings Only Exist As One Conformation in the Solid-State? A Detailed Solid-State Analysis Involving Polymorphs of <i>N,N</i>′‑Biscyclododecyl Pyromellitic Diimide

Conformational flexibility in molecules plays a key role in many chemical and biological processes. It is a common belief that the larger the cycloalkane the more flexible it will be, and the more conformations it will adopt. While theoretical studies have shown that cyclododecane has many possible conformations, they have also consistently shown that one conformation is slightly more stable. In this work, we examine the effect of substitution and crystal packing on the conformation of singly substituted cyclododecane rings. This has been done by exploiting polymorphism in an attempt to induce new conformations in a specific molecule, as well as by examining structures reported in the Cambridge Structural Database (CSD). To this end, three polymorphs of <i>N,N</i>′-biscyclododecyl pyromellitic diimide (PMDI-12) have been identified and their structures elucidated. To rationalize the differences between the various polymorphs, molecule···molecule interaction energies have been calculated using atom–atom potential methods. Though the conformation of the PMDI-12 molecules as a whole may differ, examination of the conformation of the 12-membered ring indicates that it is conformationally identical in all three polymorphs. Examination of 20 other organic and organometallic structures containing this group in the CSD, indicates that they have the same conformation (only one possible exception in the 34 rings examined in this work), which suggests that the 12-membered ring adopts a single conformation ([3333] with <i>D</i>₂ symmetry) in the solid-state that is relatively unaffected by crystal packing

Do 12-Membered Cycloalkane Rings Only Exist As One Conformation in the Solid-State? A Detailed Solid-State Analysis Involving Polymorphs of <i>N,N</i>′‑Biscyclododecyl Pyromellitic Diimide

Conformational flexibility in molecules plays a key role in many chemical and biological processes. It is a common belief that the larger the cycloalkane the more flexible it will be, and the more conformations it will adopt. While theoretical studies have shown that cyclododecane has many possible conformations, they have also consistently shown that one conformation is slightly more stable. In this work, we examine the effect of substitution and crystal packing on the conformation of singly substituted cyclododecane rings. This has been done by exploiting polymorphism in an attempt to induce new conformations in a specific molecule, as well as by examining structures reported in the Cambridge Structural Database (CSD). To this end, three polymorphs of <i>N,N</i>′-biscyclododecyl pyromellitic diimide (PMDI-12) have been identified and their structures elucidated. To rationalize the differences between the various polymorphs, molecule···molecule interaction energies have been calculated using atom–atom potential methods. Though the conformation of the PMDI-12 molecules as a whole may differ, examination of the conformation of the 12-membered ring indicates that it is conformationally identical in all three polymorphs. Examination of 20 other organic and organometallic structures containing this group in the CSD, indicates that they have the same conformation (only one possible exception in the 34 rings examined in this work), which suggests that the 12-membered ring adopts a single conformation ([3333] with <i>D</i>₂ symmetry) in the solid-state that is relatively unaffected by crystal packing

Do 12-Membered Cycloalkane Rings Only Exist As One Conformation in the Solid-State? A Detailed Solid-State Analysis Involving Polymorphs of <i>N,N</i>′‑Biscyclododecyl Pyromellitic Diimide

Conformational flexibility in molecules plays a key role in many chemical and biological processes. It is a common belief that the larger the cycloalkane the more flexible it will be, and the more conformations it will adopt. While theoretical studies have shown that cyclododecane has many possible conformations, they have also consistently shown that one conformation is slightly more stable. In this work, we examine the effect of substitution and crystal packing on the conformation of singly substituted cyclododecane rings. This has been done by exploiting polymorphism in an attempt to induce new conformations in a specific molecule, as well as by examining structures reported in the Cambridge Structural Database (CSD). To this end, three polymorphs of <i>N,N</i>′-biscyclododecyl pyromellitic diimide (PMDI-12) have been identified and their structures elucidated. To rationalize the differences between the various polymorphs, molecule···molecule interaction energies have been calculated using atom–atom potential methods. Though the conformation of the PMDI-12 molecules as a whole may differ, examination of the conformation of the 12-membered ring indicates that it is conformationally identical in all three polymorphs. Examination of 20 other organic and organometallic structures containing this group in the CSD, indicates that they have the same conformation (only one possible exception in the 34 rings examined in this work), which suggests that the 12-membered ring adopts a single conformation ([3333] with <i>D</i>₂ symmetry) in the solid-state that is relatively unaffected by crystal packing

Probing the Nature of the Co(III) Ion in Corrins: Comparison of Reactions of Aquacyanocobyrinic Acid Heptamethyl Ester and Aquacyano-Stable Yellow Cobyrinic Acid Hexamethyl Ester with Neutral N‑Donor Ligands

Equilibrium constants (log <i>K</i>) for substitution of coordinated H₂O in aquacyanocobyrinic acid heptamethyl ester (aquacyanocobester, ACCbs) and aquacyano-stable yellow cobyrinic acid hexamethyl ester (aquacyano-stable yellow cobester, ACSYCbs), in which oxidation of the C5 carbon of the corrin interrupts the normal delocalized system of corrins, by neutral N-donor ligands (ammonia, ethanolamine, 2-methoxyethylamine, <i>N</i>-methylimidazole, and 4-methylpyridine) have been determined spectrophotometrically as a function of temperature. Log <i>K</i> values increase with the basicity of the ligand, but a strong compensation effect between Δ<i>H</i> and Δ<i>S</i> values causes a leveling effect. The aliphatic amines with a harder donor atom produce Δ<i>H</i> values that are more negative in their reactions with ACSYCbs than with ACCbs, while the softer, aromatic N donors produce more negative Δ<i>H</i> values with ACCbs than with ACSYCbs. Molecular modeling (DFT, M06L/SVP, and a quantum theory of atoms in molecules analysis of the electron density) shows that complexes of the aliphatic amines with SYCbs produce shorter and stronger Co–N bonds with less ionic character than the Co–N bonds of these ligands with the cobester. Conversely, the Co–N bond to the aromatic N donors is shorter, stronger, and somewhat less ionic in the complexes of the cobester than in those of the SYCbs. Therefore, the distinction between the harder Co­(III) in ACSYCbs and softer Co­(III) in ACCbs, reported previously for anionic ligands, is maintained for neutral N-donor ligands

The Synthesis of a Corrole Analogue of Aquacobalamin (Vitamin B_12a) and Its Ligand Substitution Reactions

The synthesis of a Co­(III) corrole, [10-(2-[[4-(1<i>H</i>-imidazol-1-ylmethyl)­benzoyl]­amino]­phenyl)-5,15-diphenylcorrolato]­cobalt­(III), DPTC-Co, bearing a tail motif terminating in an imidazole ligand that coordinates Co­(III), is described. The corrole therefore places Co­(III) in a similar environment to that in aquacobalamin (vitamin B_12a, H₂OCbl⁺) but with a different equatorial ligand. In coordinating solvents, DPTC-Co is a mixture of five- and six-coordinate species, with a solvent molecule occupying the axial coordination site trans to the proximal imidazole ligand. In an 80:20 MeOH/H₂O solution, allowed to age for about 1 h, the predominant species is the six-coordinate aqua species [H₂O–DPTC-Co]. It is monomeric at least up to concentrations of 60 μM. The coordinated H₂O has a p<i>K</i>_a = 9.76(6). Under the same conditions H₂OCbl⁺ has a p<i>K</i>_a = 7.40(2). Equilibrium constants for the substitution of coordinated H₂O by exogenous ligands are reported as log <i>K</i> values for neutral N-, P-, and S-donor ligands, and CN^–, NO₂^–, N₃^–, SCN^–, I^–, and Cys in 80:20 MeOH/H₂O solution at low ionic strength. The log <i>K</i> values for [H₂O–DPTC-Co] correlate reasonably well with those for H₂OCbl⁺; therefore, Co­(III) displays a similar behavior toward these ligands irrespective of whether the equatorial ligand is a corrole or a corrin. Pyridine is an exception; it is poorly coordinated by H₂OCbl⁺ because of the sterically hindered coordination site of the corrin. With few exceptions, [H₂O–DPTC-Co] has a higher affinity for neutral ligands than H₂OCbl⁺, but the converse is true for anionic ligands. Density functional theory (DFT) models (BP86/TZVP) show that the Co–ligand bonds tend to be longer in corrin than in corrole complexes, explaining the higher affinity of the latter for neutral ligands. It is argued that the residual charge at the metal center (+2 in corrin, 0 in corrole) increases the affinity of H₂OCbl⁺ for anionic ligands through an electrostatic attraction. The topological properties of the electron density in the DFT-modeled compounds are used to explore the nature of the bonding between the metal and the ligands