N,N′‐Bis(2‐pyridyl)benzene‐1,2‐diamine

Hindered rotation about the partial double C—N bonds between the amine and pyridine moieties in the title mol­ecule, C₁₆H₁₄N₄, results in two different conformations of the N‐aryl‐2‐amino­pyridine units. One, assuming an E conformation, is involved in a pair of N—H⋯N hydrogen bonds that generate a centrosymmetric (8) motif. The second, adopting a Z conformation, is not engaged in any hydrogen bonding and is flattened, the dihedral angle between the benzene and pyridine rings being 12.07 (7)°. This conformation is stabilized by an intramolecular C—H⋯N interaction [C⋯N = 2.9126 (19) Å, H⋯N = 2.31 Å and C—H⋯N = 120°].     

The kinetics and mechanisms of the gas-phase unimolecular eliminations of halogeno esters. Participation of the carbomethoxy group

The kinetics of the gas-phase elimination of several chloroesters were determined in a static system over the temperature range of 410–490°C and the pressure range of 47–236 torr. The reactions in seasoned vessels, and in the presence of a free-radical inhibitor, are homogeneous, unimolecular, and follow a first-order law. The temperature dependence of the rate coefficients is given by the following Arrhenius equations: for methyl 3-chloropropionate, log k₁(s^?1) = (13.22 ± 0.07) - (231.5 ± 1.0) kJ/mol/2.303RT; for methyl 4-chlorobutyrate, log k₁(s^?1) = (13.31 ± 0.25) - (221.5 ± 3.4) kJ/mol/2.303RT; and for methyl 5-chlorovalerate, log k₁(s^?1) = (13.12 ± 0.25) - (221.7 ± 3.2) kJ/mol/2.303RT. Rate enhancements and lactone formation reveal the participation of carbonyl oxygen of the carbomethoxy group. The order COOCH₃-5 > COOCH₃-6 > COOCH₃-4 in assistance is similar to the sequence of group participation in solvolysis reactions. The partial rates for the parallel eliminations to normal dehydrohalogenation products and lactones have been estimated and reported. The present results lead us to consider that an intimate ion-pair mechanism through participation of the carbomethoxy group may well be operating in some of these reactions.     

Protein side chain modeling with orientation-dependent atomic force fields derived by series expansions

We describe the development of new force fields for protein side chain modeling called optimized side chain atomic energy (OSCAR). The distance‐dependent energy functions (OSCAR‐d) and side‐chain dihedral angle potential energy functions were represented as power and Fourier series, respectively. The resulting 802 adjustable parameters were optimized by discriminating the native side chain conformations from non‐native conformations, using a training set of 12,000 side chains for each residue type. In the course of optimization, for every residue, its side chain was replaced by varying rotamers, whereas conformations for all other residues were kept as they appeared in the crystal structure. Then, the OSCAR‐d were multiplied by an orientation‐dependent function to yield OSCAR‐o. A total of 1087 parameters of the orientation‐dependent energy functions (OSCAR‐o) were optimized by maximizing the energy gap between the native conformation and subrotamers calculated as low energy by OSCAR‐d. When OSCAR‐o with optimized parameters were used to model side chain conformations simultaneously for 218 recently released protein structures, the prediction accuracies were 88.8% for χ₁, 79.7% for χ_{1 + 2}, 1.24 Å overall root mean square deviation (RMSD), and 0.62 Å RMSD for core residues, respectively, compared with the next‐best performing side‐chain modeling program which achieved 86.6% for χ₁, 75.7% for χ_{1 + 2}, 1.40 Å overall RMSD, and 0.86 Å RMSD for core residues, respectively. The continuous energy functions obtained in this study are suitable for gradient‐based optimization techniques for protein structure refinement. A program with built‐in OSCAR for protein side chain prediction is available for download at http://sysimm.ifrec.osaka‐u.ac.jp/OSCAR/ . © 2011 Wiley Periodicals, Inc. J Comput Chem 2011     

N6‐Furfuryladenine (kinetin) hydrochloride

In the title compound, N⁶‐furfuryl­adenin‐3‐ium chloride, C₁₀H₁₀N₅O⁺·Cl⁻, the adenine moiety exists as the N3‐protonated N7–H tautomer. The orientation of the N6 substituent (furfuryl moiety) is distal to the imidazole ring of the adenine base. The dihedral angle between the adenine plane and the furfuryl ring plane is 76.1 (2)°. Three N—H⋯Cl hydrogen bonds are responsible for the formation of a supramolecular chain‐like pattern. These supramolecular chains are interconnected by C—H⋯Cl hydrogen bonds to form a hydrogen‐bonded sheet and a three‐dimensional hydrogen‐bonded network.     

Conformational analysis of vitamin K<Subscript>1</Subscript> model molecule: a theoretical study

Isomerism, conformations, and molecular structure of a model molecule of vitamin K₁ with a truncated side chain have been studied by the density functional theory calculations using B3LYP method and double- and triple-ζ correlation consistent basis sets. The conformations of two possible (E and Z) isomers, formed by the rotations around three single C–C bonds closest to the naphthoquinone ring, have been studied. The lowest energy conformers are stabilized by additional hydrogen bonds between hydrogen atoms of the side chain and an oxygen atom in the naphthoquinone subunit. It is interesting to note that the structure of the energetically preferred conformer of the E-isomer (3c) has been found to be similar to the solid state structures of phylloquinones in the photosystem I of cyanobacterium Synechococcus elongatus. The excited electronic states of two lowest energy conformers have also been investigated.     

Rotational isomeric-state approximation for the unperturbed dimensions of a POLA polyester

Rotational isomeric-state theory has been applied to investigate chain configurations of a polyester prepared from 4′,5-(1,1,3-trimethyl-3-phenylindan) dicarboxylic acid and 2,2-bis(4′-hydroxyphenyl) propane (POLA polyester). Independent conformations for each repeat monomer unit of the chain have been assumed in the calculations of the unperturbed dimensions. Rotations about the oxygen-phenylene-carbon (O? ?? C) bonds are considered to be free with twofold symmetric potentials. The trans and cis conformations of the carbonyl-phenylene-carbon (O?C? ?? C) and the indan-carbonyl residues are assumed to have equal probability. Two rotational states, trans and cis, are assigned to the ester C? O bonds. Calculation of the reduced unperturbed dimensions (〈r₀²〉/M)_∞ with conformations thus assigned for the bonds in the repeat unit, and comparison with experiment (0.72 ± 0.02 Ų/g) indicate that the conformation in the ester C? O bonds is predominantly trans. An equation for the conformational potential as a function of rotational angle about the ester C? O bond has been formulated using data on potential barriers for low molecular weight compounds. This equation, yielding a potential difference between the cis the trans isomers of 2.5–3.0 kcal/mole, is in good agreement with the prediction made from the calculation of the unperturbed dimensions where a cis/trans ratio of 0.01 for the ester C? O bonds was obtained.     

Gas-phase elimination kinetics of 1-substituted ethyl acetates. Effect of polar substituents at the α carbon of secondary acetates

The gas-phase elimination of several polar substituents at the α carbon of ethyl acetates has been studied in a static system over the temperature range of 310–410°C and the pressure range of 39–313 torr. These reactions are homogeneous in both clean and seasoned vessels, follow a first-order rate law, and are unimolecular. The temperature dependence of the rate coefficients is given by the following Arrhenius equations: 2-acetoxypropionitrile, log k₁ (s^?1) = (12.88 ± 0.29) – (203.3 ± 2.6) kJ/mol (2.303RT)^?1; for 3-acetoxy-2-butanone, log ±₁(s^?1) = (13.40 ± 0.20) – (202.8 ± 2.4) kJ/mol (2.303RT)^?1; for 1,1,1-trichloro-2-acetoxypropane, log ?₁ (s^?1) = (12.12 ± 0.50) – (193.7 ± 6.0) kJ/mol (2.303RT)^?; for methyl 2-acetoxypropionate, log ?₁ (s^?1) = (13.45 ± 0.05) – (209.5 ± 0.5) kJ/mol (2.303RT)^?1; for 1-chloro-2-acetoxypropane, log ?₁ (s^?1) = (12.95 ± 0.15) – (197.5 ± 1.8) kJ/mol (2.303RT)^?1; for 1-fluoro-2-acetoxypropane, log ?₁ (s^?1) = (12.83 ± 0.15)– (197.8 ± 1.8) kJ/mol (2.303RT)^?1; for 1-dimethylamino-2-acetoxypropane, log ?₁ (s^?1) = (12.66 ± 0.22) –(185.9 ± 2.5) kJ/mol (2.303RT)^?1; for 1-phenyl-2-acetoxypropane, log ?₁ (s^?1) = (12.53 ± 0.20) – (180.1 ± 2.3) kJ/mol (2.303RT)^?1; and for 1-phenyl?3?acetoxybutane, log ?₁ (s^?1) = (12.33 ± 0.25) – (179.8 ± 2.9) kJ/mol (2.303RT)^?1. The C_α? O bond polarization appears to be the rate-determining process in the transmition state of these pyrolysis reactions. Linear correlations of electron-releasing and electron-withdrawing groups along strong σ bonds have been projected and discussed. The present work may provide a general view on the effect of alkyl and polar substituents at the C_α? O bond in the gas-phase elimination of secondary acetates.     

A dipole moment study of the conformational properties of diaryl diselenides and related compounds

The electric dipole moments of the diaryl diselenides (RC₆H₄)₂Se₂ (R  H, 4-F, 4-Br, 4-CH₃, 3-F) were measured in benzene solution at 25 and 45°C. The conformations of these compounds were deduced by matching experimental moments with values calculated for a variety of possible conformations. In the dissolved state the diselenides exist at 25°C in fixed “skew” conformations characterized by dihedral angles of 75–106° between the CSeSe planes, corresponding to the conformational energy minima. At 45°C oscillations about the SeSe bonds are excited in the diphenyl and bis(4-methylphenyl) diselenides, whereas the 4-bromophenyl derivative exhibits free rotation. The fluoro compounds have temperature-independent dipole moments, suggesting “rigid conformations” with dihedral angles of 106° (4-F) and 74.4° (3-F). An analysis of the dipole moments at 25 and 45°C obtained for the compounds (RC₆H₄)₂X₂ (R  H, 3-F, 4-F, 4-Br, 4-CH₃; X  S, Se, Te) showed that the conformational properties of these derivatives change on passing from X  S to X  Te. The observed variations are explicable in terms of a decreasing repulsion between the lone electron pairs of the chalcogen atoms on going from the disulfides to the ditellurides and a concomitant reduction of the energy barrier to rotations about the XX bonds.     

Dihedral‐Angle‐Controlled Crossover from Static Hole Delocalization to Dynamic Hopping in Biaryl Cation Radicals

In cases of coherent charge‐transfer mechanism in biaryl compounds the rates follow a squared cosine trend with varying dihedral angle. Herein we demonstrate using a series of biaryl cation radicals with varying dihedral angles that the hole stabilization shows two different regimes where the mechanism of the hole stabilization switches over from (static) delocalization over both aryl rings to (dynamic) hopping. The experimental data and DFT calculations of biaryls with different dihedral angles unequivocally support that a crossover from delocalization to hopping occurs at a unique dihedral angle where the electronic coupling (H _ab) is one half of reorganization (λ ), that is, H _ab=λ /2. The implication of this finding in non‐coherent charge‐transfer rates is being investigated.     

N,N′‐Bis(2‐hydroxybenzylidene)pentane‐1,5‐diamine

In the title potential O,N,N′,O′‐tetradentate Schiff base ligand {systematic name: 2,2′‐[pentane‐1,5‐diylbis(nitrilomethylidyne)]diphenol}, C₁₉H₂₂N₂O₂, the mutual orientation of the three planar fragments determines the conformation of the molecule. The dihedral angles between the planes of the two salicylidene groups and the plane of the central extended pentane chain are 78.4 (2) and 62.0 (3)°, and the angle between the terminal ring planes is 55.4 (1)°. Strong intramolecular O—H...N hydrogen bonds close almost‐planar six‐membered rings, and the O—H bonds are elongated as a result of hydrogen‐bond formation.     

The 1:1 inclusion compounds zolmitriptan–benzene and zolmitriptan–phenol

In the benzene and phenol solvates of (S)‐4‐{3‐[2‐(dimethylamino)ethyl]‐1H‐indol‐5‐ylmethyl}oxazolidin‐2‐one, viz. C₁₆H₂₁N₃O₂·C₆H₆, (I), and C₁₆H₂₁N₃O₂·C₆H₅OH, (II), the host molecule has three linked residues, namely a planar indole ring system, an ethylamine side chain and an oxazolidinone system. It has comparable features to that of sumatriptan, although the side‐chain orientations of (I) and (II) differ from those of sumatriptan. Both (I) and (II) have host–guest‐type structures. The host molecule in (I) and (II) has an L‐shaped form, with the oxazolidinone ring occupying the base and the remainder of the molecule forming the upright section. In (I), each benzene guest molecule is surrounded by four host molecules, and these molecules are linked by a combination of N—H...N, N—H...O and C—H...O hydrogen bonds into chains of edge‐fused R₄⁴(33) rings. In (II), two independent molecules are present in the asymmetric unit, with similar conformations. The heterocyclic components are connected through N—H...N, N—H...O and C—H...O interactions to form chains of edge‐fused R₆⁴(38) rings, from which the phenol guest molecules are pendent, linked by O—H...O hydrogen bonds. The structures are further stabilized by extensive C—H...π interactions.     

(2S,RS)‐6‐Phenyl‐1‐(p‐tolyl­sulfinyl)­hexa‐3(E),5(E)‐dien‐2‐ol

The mol­ecule of the title compound, C₁₉H₂₀O₂S, corresponds to a chiral sulfinyldienol with two stereogenic centres, viz. the C atom susbtituted by the hydr­oxy group and the sulfinyl S atom. The mol­ecule displays a V‐shape in the solid state. The dihedral angle defined by the least‐squares planes of the aromatic rings is 72.9 (1)°. The packing pattern exhibits the following inter­molecular hydrogen bonds: one O—H⋯O [H⋯O = 1.98 Å, O⋯O = 2.785 (4) Å and O—H⋯O = 166°] and two C—H⋯O [H⋯O = 2.58 and 2.60 Å, C⋯O = 3.527 (5) and 3.347 (5) Å, and C—H⋯O = 164 and 134°]. These define a chain along b.     

Two isomorphous azastilbene derivatives: 1‐(2‐chlorobenzyl)‐4‐[(E)‐2‐(4‐hydroxyphenyl)ethenyl]pyridinium chloride and 1‐(2‐bromobenzyl)‐4‐[(E)‐2‐(4‐hydroxyphenyl)ethenyl]pyridinium bromide

The crystal structures of the two title (E)‐stilbazolium halogenates, C₂₀H₁₇ClNO⁺·Cl⁻ and C₂₀H₁₇BrNO⁺·Br⁻, are isomorphous, with an isostructurality index of 0.985. The azastyryl fragments are almost planar, with dihedral angles between the benzene and pyridine rings of ca 4.5°. The rings of the benzyl groups are, in turn, almost perpendicular to the azastyryl planes, with dihedral angles larger than 80°. The cations and anions are connected by O—H...X⁻ (X = halogen) hydrogen bonds. The halide anions are `sandwiched' between the charged pyridinium rings of neighbouring molecules, and weak C—H...O hydrogen bonds and C—H...X and C—H...π interactions also contribute to the crystal structures.     

A 2′‐deoxycytidine long‐linker click adduct forming two conformers in the asymmetric unit

The title compound {systematic name: 4‐amino‐1‐(2‐deoxy‐β‐d ‐erythro‐pentofuranosyl)‐5‐[6‐(1‐benzyl‐1H‐1,2,3‐triazol‐4‐yl)hex‐1‐ynyl]pyrimidin‐2(1H)‐one}, C₂₄H₂₈N₆O₄, shows two conformations in the crystalline state, viz. (I‐1) and (I‐2). The pyrimidine groups and side chains of the two conformers are almost superimposable, while the greatest differences between them are observed for the sugar groups. The N‐glycosylic bonds of both conformers adopt similar anti conformations, with χ = −168.02 (12)° for conformer (I‐1) and χ = −159.08 (12)° for conformer (I‐2). The sugar residue of (I‐1) shows an N‐type (C3′‐endo) conformation, with P = 33.1 (2)° and τ_m = 29.5 (1)°, while the conformation of the 2′‐deoxyribofuranosyl group of (I‐2) is S‐type (C3′‐exo), with P = 204.5 (2)° and τ_m = 33.8 (1)°. Both conformers participate in hydrogen‐bond formation and exhibit identical patterns resulting in three‐dimensional networks. Intermolecular hydrogen bonds are formed with neighbouring molecules of different and identical conformations (N—H...N, N—H... O, O—H...N and O—H...O).     

The thermal decomposition of peroxyacetic nitric anhydride (PAN) and peroxymethacrylic nitric anhydride (MPAN)

The rate coefficients of thermal decomposition of peroxyacetic nitric anhydride (PAN) and peroxymethacrylic nitric anhydride (MPAN) were measured over the temperature range 302–323 K. The resulting Arrhenius expressions were k = 10^17.4±0.4 exp(?28.5 ± 0.5/RT) for PAN, and k = 10^16.2±0.7 exp(?26.8 ± 1.0/RT) for MPAN, where the activation energy is in Kcal/mol. These results are in good agreement with previous studies of PAN and other PAN-type compounds, and imply that energies of RC(O)OO? NO₂ bonds are relatively independent of the nature of R.     

Conformational Analysis of 1,2:3,4-Diepoxides: Ab Initio and semiempirical molecular-orbital calculations

Using semiempirical and ab initio procedures, the most stable conformations of meso- and rac-bioxirane and of some substituted 1,2:3,4-diepoxides were calculated. For threo-diepoxides (having the same relative configurations as rac-bioxirane, 3 ), two stable conformations with CCCC dihedral angles of ca. 90 and ca. 270° were found. For erythro-diepoxides (derivatives of meso-bioxirane, 4 ) the calculations suggest three preferred conformations with corresponding dihedral CCCC angles of ca. 90°, ca. 180°, and ca. 270°. The calculations are in fair agreement with the experimental data available for the unsubstituted compounds 3 and 4 .     

The peculiar conformational characteristics of cis-poly(tert-butlacetylene)

Molecular mechanics was applied to investigate the conformational structure of cis-poly(tert-butylacetylene) (c-PTBA). The program CHAMP, adopting a MM2-based force field, was used for a thorough search of the minimum-energy conformers of oligomers, helices and long segments of the c-PTBA chain. The results show that short oligomers are not good models of the polymer, as their preferred conformations are not allowed inside the chain. Segments of 8₃ and 8₅ helices appear as the most probable feature. Junctions between right- and left-handed helices can occur at the cost of 1,7 kcal/mol: such defects may run through the chain, the barrier to their shift being 7,8 kcal/mol. Other conformational defects, having energies in the range of 1–3 kcal/mol above the minimum, form knuckle-joints in the helix, changing the axial direction by 70–80°. The present calculations suggest a disordered model of c-PTBA in solution, made of rather stiff helical segments. Such a picture corresponds to a chain less rigid than proposed by previous computations on substituted polyacetylenes, and seems consistent with the observed physical aging of c-PTBA films. Preliminary packing calculations of right- and left-handed helices lead to density values not much higher than observed, indicating rather low degrees of disorder and free volume in the solid state.     

Pyrolysis of vinylacetylene between 300 and 450°C

Vinylacetylene was pyrolyzed at 300–450°C in a packed and an unpacked static reactor with a pinhole bleed to a quadrupole mass spectrometer. The reactant and C₈H₈ products were monitored continuously during a reaction by mass spectrometry. In some runs, the products were also analyzed by gas chromatography after the run. In these runs CH₄, C₂H₆, C₃H₆, and C₂H₄ were also detected. The reaction for vinylacetylene removal and C₈H₈ formation is homogeneous, second order in reactant, and independent of the presence of a large excess of N₂ or He. However, C₈H₈ formation is about half-suppressed by the addition of the free-radical scavengers NO or O₂. The rate coefficient for total vinylacetylene removal is 1.7 × 10⁶ exp(?79 ± 13 kJ/mol RT) L/mol · s. The major reaction for C₄H₄ removal is polymerization. In addition four C₈H₈ isomers, carbon, and small hydrocarbons are formed. The three major C₈H₈ isomers are styrene, cyclooctatetraene (COT), and 1,5? dihydropentalene (DHP). The C₈H₈ compounds are formed by both molecular and free-radical processes in a second-order process with an overall k ? 3 × 10⁸ exp(?122 kJ/mol RT) L/mol · s (average of packed and unpacked cell results). The molecular process occurs with an overall k = 8.5 × 10⁷ exp (?118 kJ/mol RT) L/mol · s. The COT, DHP, and an unidentified isomer (d), are formed exclusively in molecular processes with respective rate coefficients of 4.4 × 10⁴ exp(?77 kJ/mol RT), 1.7 × 10⁵ exp(?89 kJ/mol RT), and 3.1 × 10⁹ exp(? 148 kJ/mol RT) L/mol · s. The styrene is formed both by a direct free-radical process and by isomerization of COT.