John J. Stezowski

Conformational Space and Dynamic Stereochemistry of Overcrowded Homomerous Bistricyclic Aromatic Enes − A Theoretical Study

The conformational spaces and dynamic stereochemistry of representative overcrowded homomerous bistricyclic aromatic enes (1, X = Y) are investigated, applying the semiempirical PM3 method. The experimental energy barriers for E,Z isomerizations, enantiomerizations, and conformational inversions of 1 and related compounds, derived from DNMR and other kinetic studies, are reviewed. This study focuses on the analysis of the minima, transition states, and dynamic mechanisms of the conformational isomerizations of bifluorenylidene (2), dixanthylene (3), dithioxanthylene (9), and bi-5H-dibenzo[a,d]cyclohepten-5-ylidene (11). The four representative bistricyclic enes differ in the sizes of their central rings and in their bridging groups. The mechanisms of the interconversions of the twisted, anti-folded, and syn-folded conformations and of thermal E,Z isomerizations (topomerizations), enantiomerizations, and conformational inversions (including combinations) are elucidated. The calculated energy barriers for E,Z topomerizations of 2, 3, 9, and 11 are 25.3, 16.4, 24.3, and 39.3 kcal/mol, respectively. The corresponding barriers for enantiomerizations or conformational inversions are 4.9, 15.9, 24.3, and 37.6 kcal/mol, respectively. In most cases, the agreement with experimentally determined values is within 1−3 kcal/mol. New mechanisms are proposed for the E,Z isomerizations and conformational inversions of anti-folded 3, 9, and 11, involving low-symmetry folded/twisted transition states and the respective syn-folded intermediates.

Phase transition effects: A crystallographic characterization of the temperature dependency of the crystal structure of the 1:1 charge transfer complex between anthracene and tetracyanobenzene in the temperature range 297 to 119 K

Crystal structures of the charge transfer complex between anthracene and tetracyanobenzene, A:TCNB, C14H10: C10H2N4, at three temperatures (297, 234 and 226 K) above the order–disorder phase transition at 206 K and at four temperatures (202, 170, 138, and 119 K) below it have been determined from x‐ray diffraction data. The space group of the room temperature phase was assigned as Cm with a=9.528(2), b=12.779(3), c=7.441(2) A and β=92.39(2) degrees at 297 K and for the low temperature phase is P21/a with a=9.457(1), b=12.689(2), c=7.325(1) A and β=92.98(1)° at 119 K; Z=2 in both phases. The electron densities, plotted for both the donor and acceptor molecules at each temperature, indicate that there is dynamic librational disorder in the A molecules that gives rise to a single average orientation in the room temperature phase. Below the phase transition, two temperature dependent, symmetry related, orientations are observed; the libration diminishes slowly as a function of temperature in this phase. There are also modest reorientations, relative to the room temperature phase, in the TCNB molecules as the crystal is cooled. Crystal packing indicates that a network of intermolecular dipole–dipole interactions between the heteroatomic acceptor molecules accounts for their lack of libration comparable to that of the donors.

Chiral discrimination in cyclodextrin complexes of amino acid derivatives: β-cyclodextrin/ N-acetyl-l-phenylalanine and N-acetyl- d-phenylalanine complexes

In a systematic study of molecular recognition of amino acid derivatives in solid-state β-cyclodextrin (β-CD) complexes, we have determined crystal structures for complexes of β-cyclodextrin/N-acetyl-l-phenylalanine at 298 and 20 K and for N-acetyl-d-phenylalanine at 298 K. The crystal structures for the N-acetyl-l-phenylalanine complex present disordered inclusion complexes for which the distribution of guest molecules at room temperature is not resolvable; however, they can be located with considerable confidence at low temperature. In contrast, the complex with N-acetyl-d-phenylalanine is well ordered at room temperature. The latter complex presents an example of a complex in this series in which a water molecule is included deeply in the hydrophobic torus of the extended dimer host. In an effort to understand the mechanisms of molecular recognition giving rise to the dramatic differences in crystallographic order in these crystal structures, we have examined the intermolecular interactions in detail and have examined insertion of the enantiomer of the d-complex into the chiral β-CD complex crystal lattice.

Crystal structure of chloromuconate cycloisomerase from Alcaligenes eutrophus JMP134 (pJP4) at 3 Å resolution

Chloromuconate cycloisomerase (E.C. 5.5.1.7) is an enzyme involved in the 2,4-dichlorophenoxyacetate degradation pathway of Alcaligenes eutrophus JMP134 (pJP4). The crystal structure of this protein was determined at 3 A resolution by molecular-replacement techniques using atomic coordinates from the reported crystal structure of the homologous muconate cycloisomerase (E.C. 5.5.1.1) from Pseudomonas putida as the search model (42% identical positions in the sequences). Structure refinement by simulated-annealing and restrained least-squares techniques converged at R = 0.195. In the crystals studied, space group I4, the protein is present as two octamers per unit cell with two subunits per asymmetric unit. Each subunit consists of two globular domains, one of which forms an alpha/beta-barrel. Comparison of this structure with that of muconate cycloisomerase reveals the reasons for the altered substrate specificity of chloromuconate cycloisomerase. Marked differences are observed in polarity, accessibility and hydrogen-bonding potential in the channel leading into the active site as well as in the active center itself.

Metastable crystals of beta-cyclodextrin complexes and the membrane diffusion model.

WE have previously suggested1 that dimers of β-cyclodextrin (β-CD) may mimic membrane diffusion transport phenomena. This proposal was based on the orientation of guest molecules in the crystalline 3:2 p-iodophenol complex with β-CD, with the assumption that complex formation with guest molecules capable of hydrogen bond formation occurs through an initial interaction with one of the hydroxyl groups of β-CD. The 7:14 distribution of hydroxyl groups on the primary and secondary sides of the β-CD torus, respectively, was interpreted as favouring formation of a complex with the hydrogen bonding moiety on the secondary side of the torus. The fact that the guest molecules in the above complex were orientated in the opposite direction was taken as an indication that exchange of guest molecules between a dimeric complex and the solution had occurred. We report here that β-CD inclusion complexes with various guest molecules produce metastable crystals (designated CII) when growth is achieved by slow cooling, and we have determined the crystal structure of an n-propanol complex of this phase. We find that comparison of the structure of this metastable phase and that of the thermodynamically more stable phase1, CI, provides information relevant to the question of the presence of β-CD dimers in solution; this information is relevant to the suggestion that such dimers mimic bilayer membrane diffusion transport.

Purification, growth, structure, optical and electrical properties of single crystals of the π‐molecular complex of phenothiazine with pyromellitic dianhydride

Single crystals of the black phenothiazine : pyromellitic dianhydride (PTZ:PMDA) 1:1 donor–acceptor complex, have been grown by sublimation from the zone‐refined components. The PTZ:PMDA complex crystalizes with P1 symmetry (Z=2), a=7.197(1), b=19.072(5), c=6.886(1) A, α=84.79(1) °, β=72.98(1) °, γ=85.72(2) ° at T=23 °C. The crystal structure model was refined with 5214 data { (sin ϑ/λ)max=0.8071 A−1} to give R=0.049 and Rw=0.089. The crystal packing consists of two polar endless ...DADA... stacks related to one another by 1. The packing is compared with that in the analogous anthracene : PMDA complex. The PTZ molecule displays a modest fold about the N...S axis (dihedral angle 176.4°), however, the deviation from planarity is small in comparison with that in PTZ crystals. The stack axis is nearly perpendicular to the molecular planes, consequently the CT‐dichroism lies essentially in the principal axis system of the indicatrix. The absorption edge is not very sharp, even at 4.2 K; it is located at 900±...

Thermochromism of overcrowded bistricyclic aromatic enes (BAEs). A theoretical study

A criterion for thermochromism has been derived from ab initio DFT B3LYP/6-31G* calculations of the anti-folded, syn-folded and twisted conformations of thermochromic and non-thermochromic overcrowded bistricyclic aromatic enes (BAEs) 1–8: the thermochromic species is the twisted conformation, a necessary condition being a small energy difference, <30 kJ mol−1, between the global minimum anti-folded and the thermochromic conformations.

Chemical insight from crystallographic disorder-structural studies of supramolecular photochemical systems. Part 2. The β-cyclodextrin–4,7-dimethylcoumarin inclusion complex: a new β-cyclodextrin dimer packing type, unanticipated photoproduct formation, and an examination of guest influence on β-CD dimer packing

As part of an ongoing structural study of supramolecular photochemical β-cyclodextrin(β-CD)–coumarin derivatives systems the crystal structure of the β-CD–4,7-dimethylcoumarin complex has been determined at 13 K and complemented with ab initio molecular orbital calculations on selected guest coumarin molecules. The 4,7-dimethylcoumarin molecules form a crystalline 2∶2 host–guest (H–G) complex with β-CD that is appropriately described as a “reaction nano-vessel” in which the inter-molecular interactions of import to the outcome of the reaction are confined to a single β-CD dimer host. Structure determination of the isolated photoproduct showed the product formed is the anti-HT photodimer. Production of this dimer is only possible with much rearrangement of the guests. This appears to occur because of a preferential spatial fit of this product to the β-CD dimer cavity. The crystal structure reveals a new β-CD dimer packing pattern, designated tetrad type, with reduced reaction tube intermolecular interactions among guest molecules. Tetrad packing is characterized in comparison with the previously reported β-CD dimer packing types. Guest influence on packing of β-CD dimers is examined in β-CD inclusion complexes with different derivatized coumarins. To probe basic molecular properties giving rise to inter-molecular interactions influencing crystal packing, ab initio molecular orbital calculations for the guest coumarin molecules were carried out to examine electrostatic interactions.

Synthesis of oligodeoxynucleotides containing diastereomeric dihydrodiol epoxide-N6-deoxyadenosine adducts of polycyclic aromatic hydrocarbons

Abstract A generally applicable route is reported for the synthesis of oligodeoxynucleotides which contain structurally defined N 6 -deoxyadenosine adducts, derived from sterically highly hindered dihydrodiol epoxides of polycyclic aromatic hydrocarbons (PAH).

The structure of an aromatic 10π electron ‘dianion’: dilithium pentalenide

In agreement with the predictions of MNDO calculations, a crystal structure determination shows that the metal atoms in a dilithium pentalenide–dimethoxyethane complex bridge opposite faces of the 10π aromatic system; this arrangement (5) is favoured because each carbon atom in the delocalized dianion moiety has a lithium neighbour, the lithium cations ‘communicate’ elctrostatically, and dipolar repulsion does not occur.