Stereoelectronic Properties of Tetrahedral Species Derived from Carbonyl Groups. Ab initio study of aminodihydroxymethane,CH(OH)2NH2, a model tetrahedral intermediate in amide hydrolysis

An ab initio theoretical study of all fifteen fully staggered conformations of aminodihydroxymethane, CH(OH)₂NH₂ has been performed. Optimization of the C? O and C? N bond lengths, population analyses and orbital localisation reveal the presence of marked conformation dependent stereoelectronic effects which influence bond lengths and overlap populations. These effects may be parametrized as a function of number and nature of antiperiplanar (app) oriented electronic lone pairs (1p) and polar bonds. In a Y? C? X fragment an app orientation between a lone pair on Y and the C? X bond increases the length and weakens the C? X bond, shortens and strengthens the C? Y bond. Thus a C? X (X ? O, N) bond of CH(OH)₂NH₂ is longest and weakest when: (i) it is app to two vicinal lp's; (ii) the X 1p's are not app to a vicinal polar bond; (iii) the conformation of the molecule has as many axially oriented lp's as possible. Results (i) and (ii) agree with a simple hyperconjugation picture involving interaction between an electronic 1p and an app oriented antibonding bond orbital σ* (C? X). Bond properties, relative energies and effects on reactivity of the tetrahedral species are discussed, as well as their relations to experimental results on the cleavage of tetrahedral intermediates and to enzyme catalysis.     

Ab initio studies of structural features not easily amenable to experiment. 22. Structural aspects of a long-chain hydrocarbon (n-nonane) and a study of the transferability of electronic effects through C?C single bonds

The molecular structure of the stretched form of n-nonane, as a typical long-chain hydrocarbon, was refined by geometrically unconstrained ab initio force relaxation on the 4-21G level. The C? C bonds and C? H bond distances in the interior of the hydrocarbon chain are found to be longer (by about 0.001 Å and 0.002 Å, respectively) than those near the end of the chain. Similarly, interior C? C? C bond angles are 0.4° larger than the terminal angles. The variation of structural parameters with distance from the molecular ends levels off after the second carbon atom, and the geometry of methylene is practically constant from C₃ on. However, if one end of the system is perturbed by moving the inplane methyl hydrogen away from equilibrium, the resulting destabilizing electronic effects are transmitted through the C? C bond distance chain in such a way that significant perturbations are still experienced at C₅. Molecular mechanics (MM 2) gives a structure in which the small changes in bond lengths and angles with chain location are well reproduced.     

Die Strukturen der mittleren Ringverbindungen. XII. Kristallstruktur der 1,1,5,5-Tetramethylcyclodecan-8-carbonsäure

Crystals of 1,1,5,5-tetramethylcyclodecane-8-carboxylic acid are monoclinic, a = 9.22 Å, b = 14.81 Å, c = 11.58 Å, β = 111° 0′, space group P2₁/c with 4 molecules in the unit cell. The structure has been solved by direct methods and refined by full-matrix least-squares analysis of three-dimensional intensitiy data. The conformation of the ring differs from the previously observed cyclodecane conformation, but the detailed results are abnormal in a number of ways (extremely short C? C bond lengths, wide C? C? C bond angles, large temperature factors). The possibility is discussed that the crystal structure is disordered.     

Comparative study by single crystal X-ray structure determinations of tetramethylaminoborane and tetramethylethene at 110 K

The single crystal structures of the two isoelectronic and isosteric compounds tetramethylaminoborane and tetramethylethene have been determined by an X-ray study at 110 K. The distances of the central bonds are refined to 140.3(1) pm (B=N) and 134.8(1) pm (C=C), the CXXC-torsion angles (XX=CC, BN) are smaller than 1° in both compounds. A bond-length-bond-order correlation for the aminoboranes [(CH₃)₂N] _n B(CH₃)_3–n withn=1, 2, and 3 give a regression coefficient of 0.9977, the same is found for the CNC-angle as a function of the CBNC-torsion angle. Also, the comparison among these aminoboranes show that the variation of CBNC-torsion angles has more influence on bond lengths at small angles.     

Glycosidic linkage,N‐acetyl side‐chain,and other structural properties of methyl 2‐acetamido‐2‐deoxy‐β‐d‐glucopyranosyl‐(1→4)‐β‐d‐mannopyranoside monohydrate and related compounds

The crystal structure of methyl 2‐acetamido‐2‐deoxy‐β‐d ‐glycopyranosyl‐(1→4)‐β‐d ‐mannopyranoside monohydrate, C₁₅H₂₇NO₁₁·H₂O, was determined and its structural properties compared to those in a set of mono‐ and disaccharides bearing N‐acetyl side‐chains in βGlcNAc aldohexopyranosyl rings. Valence bond angles and torsion angles in these side chains are relatively uniform, but C—N (amide) and C—O (carbonyl) bond lengths depend on the state of hydrogen bonding to the carbonyl O atom and N—H hydrogen. Relative to N‐acetyl side chains devoid of hydrogen bonding, those in which the carbonyl O atom serves as a hydrogen‐bond acceptor display elongated C—O and shortened C—N bonds. This behavior is reproduced by density functional theory (DFT) calculations, indicating that the relative contributions of amide resonance forms to experimental C—N and C—O bond lengths depend on the solvation state, leading to expectations that activation barriers to amide cis–trans isomerization will depend on the polarity of the environment. DFT calculations also revealed useful predictive information on the dependencies of inter‐residue hydrogen bonding and some bond angles in or proximal to β‐(1→4) O‐glycosidic linkages on linkage torsion angles ? and ψ. Hypersurfaces correlating ? and ψ with the linkage C—O—C bond angle and total energy are sufficiently similar to render the former a proxy of the latter.     

Ruthenium(II)‐Catalyzed C−H Activation of Imidamides and Divergent Couplings with Diazo Compounds: Substrate‐Controlled Synthesis of Indoles and 3H‐Indoles

Indoles are an important structural motif that is commonly found in biologically active molecules. In this work, conditions for divergent couplings between imidamides and acceptor–acceptor diazo compounds were developed that afforded NH indoles and 3H‐indoles under ruthenium catalysis. The coupling of α‐diazoketoesters afforded NH indoles by cleavage of the C(N₂)?C(acyl) bond whereas α‐diazomalonates gave 3H‐indoles by C?N bond cleavage. This reaction constitutes the first intermolecular coupling of diazo substrates with arenes by ruthenium‐catalyzed C?H activation.     

Alkoxyamines of Stable Aromatic Nitroxides: N?O vs. C?O Bond Homolysis

A series of stable 2,2‐disubstituted 3‐(phenylimino)indol‐1‐oxyls, the alkoxyamines 3 , were prepared, characterized, and tested as possible candidates in controlled radical polymerization (CRP). The sturctures of 3d and 10 were additionally solved by X‐ray diffraction. The lability of the N? O(C) and (N)O? C bonds of compounds 3 were compared, and the possibility of N? O vs. O? C bond cleavage was evaluated by thermal degradation, ESR spin trapping, MS experiments, and DFT calculations. Alkoxyamines with a primary‐ or secondary‐alkyl group bound to the O‐atom of the nitroxide function (hexyl and i‐Pr) mainly underwent (undesired) N? O bond homolysis. When the O‐alkyl radical was a tertiary or a benzyl group (crotonyl or styryl), O? C bond cleavage occurred as the main process, thus suggesting a possible use of these compounds in CRP processes.     

Crystal Structure and Conformation of a Bilirubin Ester

Summary. Crystal structures determined for three bilirubin analogs with gem-dimethyl groups at C(10) are reported, including the first X-ray structure of a bilirubin dimethyl ester. Conformation-determining torsion angles and key hydrogen bond distances and angles were compared to those from molecular dynamics calculations. Like other rubins, the component dipyrrinones of the three compounds were found to adopt the syn conformation, with Z-configuration double bonds at C(4) and C(15) and bis-lactam tautomeric structures of the end rings. No large differences in bond lengths and bond angles at C(10) were found, and the crystal structures of the two 10,10-dimethyl rubin acids showed considerable similarity to that of bilirubin: both pigments adopt a folded, intramolecularly hydrogen bonded ridge-tile conformation stabilized by six hydrogen bonds, with an interplanar angle in ridge-tile of 98° and 86°. In contrast, the dimethyl ester is intermolecularly hydrogen bonded in the crystal. Each molecule of the ester has its two syn-Z-dipyrrinones rotated into a conformation syn to the gem-dimethyl group, whereas in the acids they are anti.     

Disulfide bond cleavage in TEMPO-free radical initiated peptide sequencing mass spectrometry

The gas‐phase free radical initiated peptide sequencing (FRIPS) fragmentation behavior of o‐TEMPO‐Bz‐conjugated peptides with an intra‐ and intermolecular disulfide bond was investigated using MSⁿ tandem mass spectrometry experiments. Investigated peptides included four peptides with an intramolecular cyclic disulfide bond, Bactenecin (RLC RIVVIRVC R), TGF‐α (C HSGYVGVRC ), MCH (DFDMLRC MLGRVFRPC WQY) and Adrenomedullin (16–31) (C RFGTC TVQKLAHQIY), and two peptides with an intermolecular disulfide bond. Collisional activation of the benzyl radical conjugated peptide cation, which was generated through the release of a TEMPO radical from o‐TEMPO‐Bz‐conjugated peptides upon initial collisional activation, produced a large number of peptide backbone fragments in which the S? S or C? S bond was readily cleaved. The observed peptide backbone fragments included a‐, c‐, x‐ or z‐types, which indicates that the radical‐driven peptide fragmentation mechanism plays an important role in TEMPO‐FRIPS mass spectrometry. FRIPS application of the linearly linked disulfide peptides further showed that the S? S or C? S bond was selectively and preferentially cleaved, followed by peptide backbone dissociations. In the FRIPS mass spectra, the loss of ?SH or ?SSH was also abundantly found. On the basis of these findings, FRIPS fragmentation pathways for peptides with a disulfide bond are proposed. For the cleavage of the S? S bond, the abstraction of a hydrogen atom at C_β by the benzyl radical is proposed to be the initial radical abstraction/transfer reaction. On the other hand, H‐abstraction at C_α is suggested to lead to C? S bond cleavage, which yields [ion ± S] fragments or the loss of ?SH or ?SSH. Copyright © 2011 John Wiley & Sons, Ltd.     

Iridium‐Catalyzed Reductive Carbon–Carbon Bond Cleavage Reaction on a Curved Pyridylcorannulene Skeleton

The cleavage of C? C bonds in π‐conjugated systems is an important method for controlling their shape and coplanarity. An efficient way for the cleavage of an aromatic C? C bond in a typical buckybowl corannulene skeleton is reported. The reaction of 2‐pyridylcorannulene with a catalytic amount of IrCl₃?n H₂O in ethylene glycol at 250 °C resulted in a structural transformation from the curved corannulene skeleton to a strain‐free flat benzo[ghi]fluoranthene skeleton through a site‐selective C? C cleavage reaction. This cleavage reaction was found to be driven by both the coordination of the 2‐pyridyl substituent to iridium and the relief of strain in the curved corannulene skeleton. This finding should facilitate the design of carbon nanomaterials based on C? C bond cleavage reactions.     

A DFT Study on the Conversion of Aryl Iodides to Alkyl Iodides: Reductive Elimination of R−I from Alkylpalladium Iodide Complexes with Accessible β‐Hydrogens

DFT calculations have been performed on the palladium‐catalyzed carboiodination reaction. The reaction involves oxidative addition, alkyne insertion, C?N bond cleavage, and reductive elimination. For the alkylpalladium iodide intermediate, LiOtBu stabilizes the intermediate in non‐polar solvents, thus promoting reductive elimination and preventing β‐hydride elimination. The C?N bond cleavage process was explored and the computations show that PPh₃ is not bound to the Pd center during this step. Experimentally, it was demonstrated that LiOtBu is not necessary for the oxidative addition, alkyne insertion, or C?N bond cleavage steps, lending support to the conclusions from the DFT calculations. The turnover‐limiting steps were found to be C?N bond cleavage and reductive elimination, whereas oxidative addition, alkyne insertion, and formation of the indole ring provide the driving force for the reaction.     

Intramolecular Cooperative CC Bond Cleavage Reaction of 1,3‐Dicarbonyl Compounds with 2‐Iodoanilines to Give o‐(N‐Acylamino)aryl Ketones and Multisubstituted Indoles

A copper‐catalyzed C?C bond cleavage reaction of 1,3‐dicarbonyl compounds with 2‐iodoanilines was developed. In this process, the ortho effect played an important role in the reactivity and a new reaction pathway that involved a (2‐aminophenyl)‐bis‐(1,3‐dicarbonyl) copper species was clearly observed by a time‐course HRMS analysis of the reaction mixture. Unlike the previous reports, both the nucleophilic and electrophilic parts of the 1,3‐dicarbonyl compound were coupled with 2‐iodoaniline by C?C bond cleavage to form o‐(N‐acylamino)aryl ketones, which could be efficiently converted into multisubstituted indoles.     

Synthesis and liquid crystalline properties of novel compounds containing a 3‐fluoro‐4‐cyanophenoxy group

A series of novel compounds containing a 3‐fluoro‐4‐cyanophenoxy group were synthesized and fully characterized by IR and ¹H NMR, and their mesomorphic properties were studied. Seven compounds exhibited enantiotropic nematic phases and three compounds exhibited monotropic nematic phases, as confirmed by differential scanning calorimetry and polarizing optical microscopy. Selected properties of the liquid crystalline compounds synthesized were calculated by ab initio methods at a HF/6‐31G level. The bond lengths, bond angles and dihedral angles of the fragments with the same structure change little between the compounds. All the compounds with a terminal alkoxy chain approached a planar structure.     

Rational Development of Remote C−H Functionalization of Biphenyl: Experimental and Computational Studies

A simple and efficient nitrile‐directed meta‐C?H olefination, acetoxylation, and iodination of biaryl compounds is reported. Compared to the previous approach of installing a complex U‐shaped template to achieve a molecular U‐turn and assemble the large‐sized cyclophane transition state for the remote C?H activation, a synthetically useful phenyl nitrile functional group could also direct remote meta‐C?H activation. This reaction provides a useful method for the modification of biaryl compounds because the nitrile group can be readily converted to amines, acids, amides, or other heterocycles. Notably, the remote meta‐selectivity of biphenylnitriles could not be expected from previous results with a macrocyclophane nitrile template. DFT computational studies show that a ligand‐containing Pd–Ag heterodimeric transition state (TS) favors the desired remote meta‐selectivity. Control experiments demonstrate the directing effect of the nitrile group and exclude the possibility of non‐directed meta‐C?H activation. Substituted 2‐pyridone ligands were found to be key in assisting the cleavage of the meta‐C?H bond in the concerted metalation–deprotonation (CMD) process.     

An ab initio study of the geometry and energy of six planar conformers of β-hydroxyacrolein

Ab initio calculations with full geometry optimization have been carried out on the planar cCc, cTc, tTc, tCt, tTt, and cCt conformers of β-hydroxyacrolein using the 4-21G basis set, and on the cCc and cCt conformers using the 4-31G basis set. The hydrogen-bonded cCc conformer is the most stable and the cCt conformer the least stable, with the other conformers following the above sequence. β-Hydroxy substitution has scarcely any influence on the geometry of the trans-acrolein structure, whereas the geometry of the cis-acrolein structure shows significant changes which depend on whether the O? H group is cis or trans with respect to the CHO group about the C?C bond. The ΔE_T values for cis → trans isomerization about the C? C bond in cCt and cTc support the hypothesis that these changes in geometry are the result of a destabilizing interaction in cCt and a stabilizing interaction in cTc. The geometry of the hydrogen-bonded structure cCc sets it apart from all the other conformers: it has by far the longest C?C, the longest C?O, the longest O? H, the shortest C? C, and the shortest C? O. Its formation from cCt involves a lengthening of C?C, C?O, and O? H and a shortening of C? C and C? O, indicating a delocalization of charge within the ring. 4-21G calculations have also been made for a distorted cCt structure that has the same bond lengths and angles as the equilibrium cCc structure, and the distortion energy, cCt (equm. geom.) → cCt (distorted geom.), is found to be +13.1 kJ mole^?1. Taking the energy of this distorted cCt structure as the baseline, the hydrogen-bonding energy in cCc is found to be —80.3 kJ mole^?1.     

Crystal Structure and Conformation of a 10-Thiabilirubin

 A crystal structure determination of a bilirubin analog with a sulfur instead of a C(10)–CH₂ linking the two dipyrrinones is reported. Conformation-determining torsion angles and key hydrogen bond distances and angles are compared to those obtained from molecular dynamics calculations as well as to the corresponding data from X-ray determinations and molecular dynamics calculations of bilirubin. Like other bilirubins, the component dipyrrinones of the analog are present in the bis-lactam form with (Z)-configurated double bonds at C(4) and C(15). Despite the large differences in bond lengths and angles at –S–vs.–CH₂–, the crystal structure shows considerable similarity to bilirubin: both pigments adopt a folded, intramolecularly hydrogen-bonded ridge-tile conformation stabilized by six hydrogen bonds – although the interplanar angle of the ridge-tile conformation of the title compound is smaller (∼ 86°) than that of bilirubin (∼ 98°). The collective data indicate that even with long C–S bond lengths and a smaller C–S–C bond angle at the pivot point on the ridge-tile seam, intramolecular hydrogen bonding persists.     

Photochemical reactions. 144th Communication. Photochemistry of 5,6-epoxy-1,3-dienes in the ionone series: Influence of a methoxy group in position 7

On triplet excitation (λ > 280 nm, acetone), the epoxydiene (E)- 5 undergoes initial cleavage of the C(5)? O bond of the oxirane and subsequent cleavage of the C(6)? C(7) bond leading to the diradical intermediate e which reacts by recombination furnishing the cyclic compounds (E/Z)- 6 , (E/Z)- 7,8 , and 9 . Alternatively, a H -shift leads to the aliphatic methyl-enol ether 10 which undergoes a photochemical [2+2]-cycloaddition to compounds 12 and 13 , the main products on triplet excitation of (E)- 5 . On singlet excitation (λ = 254 nm, MeCN), (E)- 5 undergoes cleavage to the carbene intermediates f and g . The vinyl carbene f reacts with the adjacent double bond furnishing the cyclopropene 14 as the main product. From the carbene intermediate g , the methyl-enol ether 15 arises by carbene insertion into the neighboring C? H bond. Furthermore, the diastereomer of the starting material, the epoxydiene (E)- 16 , and compounds 17A+B are formed via the ylide intermediate h . Finally, the cyclobutene 18 is the product of an electrocyclic reaction of the diene side chain.     

Facile P−C/C−H Bond‐Cleavage Reactivity of Nickel Bis(diphosphine) Complexes

Unusual cleavage of P?C and C?H bonds of the P₂N₂ ligand, in heteroleptic [Ni(P₂N₂)(diphosphine)]²⁺ complexes under mild conditions, results in the formation of an iminium formyl nickelate featuring a C,P,P‐tridentate coordination mode. The structures of both the heteroleptic [Ni(P₂N₂)(diphosphine)]²⁺ complexes and the resulting iminium formyl nickelate have been characterized by NMR spectroscopy and single‐crystal X‐ray diffraction analysis. Density functional theory (DFT) calculations were employed to investigate the mechanism of the P?C/C?H bond cleavage, which involves C?H bond cleavage, hydride rotation, Ni?C/P?H bond formation, and P?C bond cleavage.     

The Scent of Maibowle – π Electron Localization in Coumarin from Its Microwave-Determined Structure

The microwave spectra of the natural substance coumarin, a planar aromatic molecule with the specific scent of maibowle, a popular fruit punch served in spring and early summer, were recorded using a molecular jet Fourier transform microwave spectrometer working in the frequency range from 4.0 to 26.5 GHz. The rotational constants and centrifugal distortion constants were determined with high precision, reproducing the spectra to experimental accuracy. The spectra of all singly-substituted ¹³C and ¹⁸O isotopologues were observed in their natural abundances to determine the experimental heavy atom substitution r_s and semi-experimental equilibrium r_e^SE structures. The experimental bond lengths and bond angles were compared to those obtained from quantum chemical calculations and those of related molecules reported in the literature with benzene as the prototype. The alternation of the C−C bond lengths to the value of 1.39 Å found for benzene reflects the localization of π electrons in coumarin, where the benzene ring and the lactone-like chain −CH=CH−(C=O)−O− are fused. The large, negative inertial defect of coumarin is consistent with out-of-plane vibrations of the fused rings.