Molecular structure of nitrobenzene in the planar and orthogonal conformations

The molecular structure and ring distortions of nitrobenzene have been determined by gas-phase electron diffraction and ab initio molecular orbital (MO) calculations as well as from the structures of six derivatives studied by X-ray crystallography. The experimental value of the ring angle at the ipso position is = 123.4 ± 0.3° in the free molecule; this is about 1.5° less than the hitherto reported values. Regression analysis of the ring angles in the six derivatives studied by X-ray crystallography yields = 122.7(1)° for nitrobenzene in a crystalline environment. The small difference in the two values of a is interpreted as an effect of intermolecular interactions in the crystal. The value produced by the MO calculations, = 122.3° at the 6–31G^* (5D) level, is smaller than either of the experimental results. As regards the ring angles at the meta and para positions, the three techniques of structure determination consistently indicate that these are larger than 120° by a few tenths of a degree. Other important geometrical parameters from the electron diffraction study are r _g (C-C) = 1.399 ± 0.003 Å,r _g (C-N) = 1.486 ± 0.004 Å,r _g (N-O) = 1.223 ± 0.003 Å, and A sO-N-O = 125.3 ± 0.2°. X-ray diffraction experiments on 3,5-dimethyl-4-nitrobenzoic acid and 3,5-dimethylbenzoic acid and ab initio MO calculations provide solid evidence that the geometry of nitrobenzene is little affected when the nitrogroup is twisted by 90° out of the planar equilibrium conformation. This indicates that the extent of -electron transfer from the benzene ring to the nitro group is small. The barrier to rotation is estimated to be 17 ± 4 kJ mol^–1 from the electron diffraction data.     

Computational analysis of side-chain conformations in polyaspartates exhibiting reversible helical sense inversion in the solid state

Poly(β-phenylpropyl -aspartate), poly(β-phenylbutyl -aspartate), and poly(β-phenylpentyl -aspartate) exhibit a reversible transformation from a right-handed -helix (_R) to a left-handed ω-helix (ω_L) in the solid state. During this transition, the infrared (IR) dichroism of the side-chain ester group and the birefringence change drastically, showing that the side-chain conformations are different for these two helices. In the present study, for the purpose of elucidating the preferred side-chain conformation in each helix, we performed the computational analyses. The energy contours, the directions of the IR transition moments and the anisotropies in polarizability as functions of the first two dihedral angles of the side chain, χ₁ and χ₂ were calculated. Then, comparing them with the experimental IR dichroism and birefringence data, we elucidated the specific side-chain conformation preferred for each _R or ω_L skeleton. The preferred values of (χ₁, χ₂) were found to be (−75, −60°) for _R and (180, 45°) for ω_L.     

Synthesis of naphthalenes and 2-naphthols by the electrophilic cyclization of alkynes

[reactions: see text] A wide variety of substituted naphthalenes are readily prepared regioselectively under mild reaction conditions by the 6-endo-dig electrophilic cyclization of appropriate arene-containing propargylic alcohols by ICl, I2, Br2, NBS, and PhSeBr. 3-Iodo-2-naphthols have also been prepared in excellent yields by the cyclization of analogous 1-aryl-3-alkyn-2-ones. This methodology readily accommodates various functional groups and has been successfully extended to the synthesis of substituted carbazoles and dibenzothiophenes.     

Tandem cyclization of alkynes via rhodium alkynyl and alkenylidene catalysis

A rhodium(I)-catalyzed tandem cyclization of alkynes has been developed. The reaction allows for multiple bond formations to occur at both the alpha- and beta-positions of alkynes under mild conditions to yield a variety of fused ring systems as the products. In the presence of triethylamine and the complex derived from [Rh(COD)Cl]2 and P(4-F-C6H4)3, a terminal alkyne is converted to a rhodium alkynyl species which reacts with a tethered alkyl halide at the beta-position to provide a beta,beta-disubstituted alkenylidene complex. The rhodium alkenylidene species then undergoes additional ring closures with a range of pendent functional groups such as alkene, hydroxyl, and phenyl groups through [2 + 2] cycloaddition, nucleophilic addition, and 6pi-electrocyclization processes, respectively.     

Rhodium-catalyzed arylative and alkenylative cyclization of 1,5-enynes induced by geminal carbometalation of alkynes

A rhodium(I)-catalyzed addition-cyclization of 1,5-enynes with aryl- and alkenylboronic acids has been developed. The reaction allows for efficient C-C coupling of multiple reactive components while accomplishing a net R,H-addition in a single step under mild conditions. In the presence of [Rh(OH)(COD)]2 catalyst and triethylamine base in methanol solvent, a range of 1,5-enynes undergo an intermolecular addition with a wide variety of aryl- and alkenylboronic acids and concomitant endo-selective cyclization to yield 1-aryl and alkenyl-substituted cyclopentene derivatives as the products. Deuterium labeling studies suggest that the reaction involves formation of a rhodium vinylidene complex with the terminal alkyne of the enyne substrate. The subsequent migration of the aryl or alkenyl group from the rhodium center to the alpha-carbon of the vinylidene ligand gives a vinyl rhodium complex, a formal 1,1-carbometalation process of the alkyne. This vinyl rhodium then adds to the pendent alkene, and the protodemetalation of the resulting rhodium enolate affords the product.     

Synthesis of indoles by intermolecular cyclization of unfunctionalized nitroarenes and alkynes, catalyzed by palladium-phenanthroline complexes

Palladium-phenanthroline complexes efficiently catalyze the reaction of nitroarenes with arylalkynes and CO to give 3-arylindoles by an ortho-C-H functionalization of the nitroarene ring. Both electron-withdrawing and electron-donating substituents are tolerated on the nitroarene, except for bromide and activated chloride. Nitroarenes bearing electron-withdrawing substituents react faster, but the selectivity of the reaction depends on both polar and radical stabilization effects. Among those tested, only arylalkynes afforded indoles under the investigated conditions. The reaction mechanism was partly investigated. The kinetics is first order in nitroarene concentration and the rate-determining step of the cycle is the initial nitroarene reduction. No primary isotope effect is observed on either rate or selectivity, implying that the cyclization step is fast.     

Detergent-associated solution conformations of helical and beta-barrel membrane proteins

Membrane proteins present major challenges for structural biology. In particular, the production of suitable crystals for high-resolution structural determination continues to be a significant roadblock for developing an atomic-level understanding of these vital cellular systems. The use of detergents for extracting membrane proteins from the native membrane for either crystallization or reconstitution into model lipid membranes for further study is assumed to leave the protein with the proper fold with a belt of detergent encompassing the membrane-spanning segments of the structure. Small-angle X-ray scattering was used to probe the detergent-associated solution conformations of three membrane proteins, namely bacteriorhodopsin (BR), the Ste2p G-protein coupled receptor from Saccharomyces cerevisiae, and the Escherichia coli porin OmpF. The results demonstrate that, contrary to the traditional model of a detergent-associated membrane protein, the helical proteins BR and Ste2p are not in the expected, compact conformation and associated with detergent micelles, while the beta-barrel OmpF is indeed embedded in a disk-like micelle in a properly folded state. The comparison provided by the BR and Ste2p, both members of the 7TM family of helical membrane proteins, further suggests that the interhelical interactions between the transmembrane helices of the two proteins differ, such that BR, like other rhodopsins, can properly refold to crystallize, while Ste2p continues to prove resistant to crystallization from an initially detergent-associated state.     

Synthesis of pyrroloazepinones: platinum- and gold-catalyzed cyclization reactions of alkynes

The synthesis of potentially bioactive pyrroloazepinones based on the catalytic intramolecular cyclization of alkyne-substituted 1H-pyrrole-2-carboxylic acid amides has been developed. In the presence of either H₂PtCl₆·6H₂O at 120 °C or AuCl₃ at room temperature pyrrolo[3,2-c]azepin-4-ones are formed.     

Regioselective synthesis of isocoumarins by ruthenium-catalyzed aerobic oxidative cyclization of aromatic acids with alkynes

The highly regioselective aerobic oxidative cyclization of aromatic, heteroaromatic and alkenyl acids with alkynes in the presence of catalytic amounts of [{RuCl(2)(p-cymene)}(2)], AgSbF(6) and Cu(OAc)(2)·H(2)O providing isocoumarin derivatives was investigated.     

Synthesis of cyclophanes with planar and helical chirality

Novel helical macrocyclic imines derived from planar chiral [2.2]paracyclophane were synthesized. The chiroptical properties of the enantiopure compounds were investigated and their absolute configurations were assigned.     

The perfluoroallylation of alkynes and transformation of the products

The addition of perfluoroallyl iodide to alkynes 1 initiated by AIBN in the absence of solvent 65 °C gave the corresponding 1:1 adducts (1,1,2,3,3-pentafluoro-5-iodopenta-1,4-dienes) 2. The reaction of 2 with boronic acids 3 and terminal alkynes 1 in the presence of catalytic palladium afforded the cross-coupling products 4 and 5, respectively.     

Iron-mediated and -catalyzed metalative cyclization of electron-withdrawing-group-substituted alkynes and alkenes with Grignard reagents

Treatment of ethyl (E)‐5,5‐bis[(benzyloxy)methyl]‐8‐(N,N‐diethylcarbamoyl)‐2‐octen‐7‐ynoate with an iron reagent generated from FeCl₂ and tBuMgCl in a ratio of 1:4 (abbreviated as FeCl₂/4 tBuMgCl) afforded ethyl [4,4‐bis[(benzyloxy)methyl]‐2‐[(E)‐(N,N‐diethylcarbamoyl)methylene]cyclopent‐1‐yl]acetate in good yield. Deuteriolysis of an identical reaction mixture afforded the bis‐deuterated product ethyl [4,4‐bis[(benzyloxy)methyl]‐2‐[(E)‐(N,N‐diethylcarbamoyl)deuteriomethylene]cyclopent‐1‐yl]deuterioacetate, thus confirming the existence of the corresponding dimetalated intermediate. The latter intermediate can react with halogens or aldehydes to facilitate further synthetic transformations. The amount of FeCl₂ was reduced to catalytic levels (10 mol % relative to enyne), and catalytic cyclizations of this sort proceeded with yields comparable to those of the aforementioned stoichiometric reactions. The cyclization of diethyl (E,E)‐2,7‐nonadienedioate with a stoichiometric amount of FeCl₂/4 tBuMgCl, followed by the addition of sBuOH as a proton source, afforded a mixture of 2‐(ethoxycarbonyl)‐3‐bicyclo[3.3.0]octanone and its enol form in good yield. The use of aldehyde or ketone in place of sBuOH afforded 2‐(ethoxycarbonyl)‐3‐bicyclo[3.3.0]octanone, which has an additional hydroxyalkyl side chain. Additionally, the metalation of a carbon–carbon unsaturated bond in N,N‐diethyl‐5,5‐bis[(benzyloxy)methyl]‐7,8‐epoxy‐2‐octynamide or (E)‐3,3‐dimethyl‐6‐(N,N‐diethylcarbamoyl)‐5‐hexenyl p‐toluenesulfonate with FeCl₂/4 tBuMgCl or FeCl₂/4 PhMgBr was followed by an intramolecular alkylation with an epoxide or alkyl p‐toluenesulfonate to afford 5,5‐bis[(benzyloxy)methyl]‐3‐[(E)‐(N,N‐diethylcarbamoyl)methylene]‐1‐cyclohexanol or N,N‐diethyl(3,3‐dimethylcyclopentyl)acetamide after hydrolysis. In both cases, the remaining metalated portion α to the amide group was confirmed by deuteriolysis and could be utilized for an alkylation with methyl iodide.     

Synchronized stereocontrol of planar chirality by crystallization-induced asymmetric transformation

Synchronized stereocontrol of two planar-chiral units was accomplished by using crystallization-induced asymmetric transformation (CIAT) of cyclophane-type bridged bisnicotinate derivatives 5b and 7. After screening various linkers, (S)-2-amino-1-butanol and (S)-tert-leucinol were found to be the most effective for CIAT of the corresponding bridged bisnicotinate 5b and 7, respectively, whose diastereomeric ratio finally reached 97% and 88%, respectively.     

Circular dichroism induced by the helical conformations of acylated chitosan derivatives bearing cinnamate chromophores

Through regioselective modifications, some acylated chitosan derivatives, O‐cinnamoyl chitosans with degree of substitution (DS) varying from 0.8 to 2.0 and N‐fatty acyl‐O‐dicinnamoyl chitosans with different fatty acyl chain lengths (C₂–C₁₂), were prepared, and their chiroptical properties in dilute solutions were investigated by circular dichroism (CD). Exciton coupling between two vicinal cinnamoyl chromophores appended to the helical mainchains gave rise to bisignate Cotton effects (CEs), which were used to deduce the absolute sense of the twisting structures in solution phase. It was found that the absolute helicities vary with DS, length of the fatty chain, and solvent property, but are nearly independent of thermal stimulus. The molecular interactions (hydrogen bonding and hydrophobic interaction) involved possibly in the self‐assembled ordered structures were discussed. © 2005 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 43: 1354–1364, 2005     

A theoretical study of the intramolecular interaction between proximal atoms in planar conformations of biphenyl and related systems

The nature of the interaction between proximal hydrogens in planar biphenyl has been recently a matter of debate as arguments in favor of and against the existence of “H–H” bonding have been recently put forward. This issue is addressed here through the study of both the electron density ρ(r) and the electron localization function (ELF) η(r) obtained in quantum calculations on molecular systems with F atoms replacing hydrogens in the moiety that presents this interaction. The analysis of geometries and properties of ρ(r) and η(r) at both planar and twisted equilibrium conformations of those systems along with biphenyl, permits to get information on this intramolecular interaction that is compared with the use of the traditional chemical concepts (steric hindrance and π-resonance effects) involved. It is shown that although the ELF gives information compatible with these classical terms, this does not preclude the existence of bonds between proximal atoms with features rather similar to those of well-established intramolecular hydrogen bonds.     

Alkali-cation affinities of polyoxyethylene dodecylethers and helical conformations of their cationized molecules studied by electrospray mass spectrometry

Relative alkali-cation affinity of polyoxyethylene (POE) dodecylethers in gas phase was studied by electrospray ionization (ESI) mass spectrometry using dodecylether-poly-ethoxylate (C(12)EO:n, "n" denotes ethyleneoxide unit number) nonionic surfactants, and possible helical conformations of the cationized molecules were demonstrated. The alkali-cation affinity highly depended on the cation diameters. The mass spectra of C(12)EO:8 cationized by alkali-metal ions were dominated by potassiated molecules. The results indicated that the POE moiety could have specific affinity to K(+) ions based on a host-guest interaction between POE helix and potassium ions. This is very similar to the relationships between 18-crown-6 and K(+). The ESI mass spectra exhibited the multiply cationized C(12)EO:n in addition to the singly cationized molecules. The critical EO unit numbers necessary for producing the multiply-charged cationized molecules also depended on the cation diameters. In addition, the POE surfactants highly preferred alkali cations to proton. The results were strongly supported by molecular mechanics/dynamics calculations. A helical conformation of the POE moiety of C(12)EO:15 including two K(+) ions gave a potential minimum, while a lowest energy structure of the protonated molecule took irregular conformations due to the formation of local hydrogen bonds.     

Mechanistic details of metal-free cyclization reaction of organophosphorus oxide with alkynes mediated by 2,6-lutidine and Tf2O

Theoretical investigations have elucidated the mechanism of metal-free electrophilic phosphinative cyclization of alkynes reaction reported by Miura and coworkers. Two competitive mechanisms I and II were explored without or with 2,6-lutidine. Both of I and II involve transformation of P(V) to P(III), electrophilic addition, ring opening and cyclization/cyclization, hydrogen-transfer, and oxidation. The rate-determining step of mechanism I and competitive less-step II is electrophilic [2 + 1] cycloaddition and electrophilic addition via single C P bond formation with activation barrier of 13.5 and 10.6 kcal/mol, respectively. Our calculation results suggested that the cumulative effect of the isomer of 2,6-lutidine and Tf₂O as well as TfO⁻ affects the title reaction to some extent, and simultaneously activates key reaction sites and reverses the polarities of them via the formation of abundant noncovalent interactions to decrease activation barriers of TSs. In addition, the effects of two series substituents on reactivity of phosphine oxide were investigated. Therefore, our study will serve as useful guidance for more efficient metal-free synthesis of organophosphorus compounds mediated by pyridine reagents.