Hydrocarbon Rings Research Articles

Do Ligand Binding and Solvent Exclusion Alter the Electrostatic Character within the Oxyanion Hole of an Enzymatic Active Site?

We report the site-specific incorporation of a thiocyanate vibrational probe into the active-site oxyanion hole of ketosteroid isomerase (KSI) to test the effect of hydrophobic steroid binding and solvent exclusion on the local electrostatic environment at this position. While binding of an uncharged ground state steroid analogue shifts the observed −CN vibrational frequency by +0.4 cm-1 relative to unliganded KSI, binding of an intermediate steroid analogue containing localized negative charge results in a +2.8 cm-1 shift. On the basis of a Stark tuning rate of 0.7 cm-1/(MV/cm), this shift indicates a fivefold larger change in the projection of the local electric field along the −CN bond in the presence of the charged ligand. Binding of a single ring phenolate with oxyanion charge localization equivalent to the intermediate steroid analogue but lacking distal hydrocarbon rings results in an identical −CN peak shift. We conclude that solvent exclusion and replacement by hydrophobic steroid rings negligibl...

Are Antiaromatic Rings Stacked Face-to-Face Aromatic?

The stacking of 4n pi electron hydrocarbon rings into superphane structures can eliminate their antiaromaticity and result in through-space three-dimensional aromatic character. This is demonstrated by the bond length equalized geometries and diatropic NICS values of the methano-bridged superphane series with interacting three- to nine-membered 4n pi electron rings. Along with triplet and Möbius strategies, stacking is the third way to achieve aromatic ring systems with 4n pi electrons.

π-Bond cooperativity and anticooperativity effects in resonance-assisted hydrogen bonds (RAHBs)

Bond cooperativity effects, which are typical of ;resonant' chains or rings of pi-conjugated hydrocarbons, can also occur in hydrogen-bonded systems in the form of sigma-bond and pi-bond cooperativity or anticooperativity. sigma-Bond cooperativity is associated with the long chains of O-H...O bonds in water and alcohols while sigma-bond anticooperativity occurs when the cooperative chain is interrupted by a local defect reversing the bond polarity. pi-Bond cooperativity is the driving force controlling resonance-assisted hydrogen bonds (RAHBs), while pi-bond anticooperativity has never been considered so far and is investigated here by studying couples of hydrogen-bonded beta-enolone and/or beta-enaminone six-membered rings fused through a common C=O or C-C bond. The effect is studied by X-ray crystal structure determination of five compounds [(2Z)-1-(2-hydroxyphenyl)-3-phenyl-1,3-propanedione enol (1), (2Z)-1-(2-hydroxy-5-chlorophenyl)-3-phenyl-1,3-propanedione enol (2), (2Z)-1-(2-hydroxy-5-methylphenyl)-3-phenyl-1,3-propanedione enol (3), (2Z)-1-(2-hydroxy-4-methyl-5-chlorophenyl)-3-phenyl-1,3-propanedione enol (4) and dimethyl(2E)-3-hydroxy-2-{[(4-chlorophenyl)amino]carbonyl}pent-2-enedioate (5)] and by extensive analysis of related fragments found in the CSD (Cambridge Structural Database). It is shown that fusion through the C=O bond is always anticooperative and such to weaken the symmetric O-H...O...H-O and N-H...O...H-N bonds formed, but not the asymmetric O-H...O...H-N bond. Fusion through the C-C bond may produce either cooperative or anticooperative hydrogen bonds, the former being more stable than the latter and giving rise to a unique resonance-assisted ten-membered ring running all around the two fused six-membered rings, which can be considered a type of tautomerism never described before.

Structure, Vibrational Spectrum, and Ring Puckering Barrier of Cyclobutane

We present the results of high level ab initio calculations for the structure, harmonic and anharmonic spectroscopic constants, and ring puckering barrier of cyclobutane (C4H8) in an effort to establish the minimum theoretical requirements needed for their accurate description. We have found that accurate estimates for the barrier between the minimum (D(2d)) and transition state (D(4h)) configurations require both higher levels of electron correlation [MP4, CCSD(T)] and orbital basis sets of quadruple-zeta quality or larger. By performing CCSD(T) calculations with basis sets as large as cc-pV5Z, we were able to obtain, for the first time, a value for the puckering barrier that lies within 10 cm(-1) (or 2%) from experiment, whereas the best previously calculated values were in errors exceeding 40% of experiment. Our best estimate of 498 cm(-1) for the puckering barrier is within 10 cm(-1) of the experimental value proposed originally, but it lies approximately 50 cm(-1) higher than the revisited value, which was obtained more recently using different assumptions regarding the coupling between the various modes. It is therefore suggested that revisiting the analysis of the experimental data might be warranted. Our best computed values (at the CCSD(T)/aug-cc-pVTZ level of theory) for the equilibrium structural parameters of C4H8 are r(C-C) = 1.554 A, r(C-H(alpha)) = 1.093 A, r(C-H(beta)) = 1.091 A, phi(C-C-C) = 88.1 degrees , alpha(H(alpha)-C-H(beta)) = 109.15 degrees , and theta = 29.68 degrees for the puckering angle. We have found that the puckering angle theta is more sensitive to the level of electron correlation than to the size of the basis set for a given method. We furthermore present anharmonic calculations that are based on a second-order perturbative evaluation of rovibrational parameters and their effects on the vibrational spectra and average structure. We have found that the anharmonic calculations predict the experimentally measured fundamental band origins within 1% (< or =30 cm(-1)) for most vibrations. The results of the current study can serve as a guide for future calculations on the substituted four-member ring hydrocarbon compounds. To this end we present a method for estimating the puckering barrier height at higher levels of electron correlation [MP4, CCSD(T)] from the MP2 results that can be used in chemically similar compounds.

Monocyclic and dicyclic hydrocarbons: structural requirements for proximal giant axonopathy

The chromogenic and neurotoxic gamma-diketone 1,2-diacetylbenzene (1,2-DAB), but not its isomer 1,3-DAB, induces blue discoloration of tissues and urine, clustering of axonal microtubules and proximal neurofilament-filled axonal swellings in rodents. The remarkable chromogenic property of 1,2-DAB, a monocyclic aromatic hydrocarbon, arises from reaction with lysine residues of proteins and formation of dimeric and polymeric derivatives. Tetralin, a dicyclic solvent structurally related to acetyl ethyl tetramethyl tetralin, a chromogenic and neurotoxic agent, reportedly induces excretion of green urine, and causes neurological disturbances in humans. Monocyclic aromatic 1,2,4-triethylbenzene (1,2,4-TEB), but not its isomer 1,3,5-TEB, is also reportedly chromogenic and induces neurophysiological deficits in rodents consistent with axonal neuropathy, but without neuropathological confirmation. We treated 12-week-old C57Bl/6 mice by gavage with 300, 600, or 900 mg/kg/day 1,2,4-TEB, or equivalent doses of 1,3,5-TEB, 3 days/week, for up to 12 weeks, or intraperitoneally with 400 mg/kg/day tetralin, or 50 or 100 mg/kg/day of its alpha-tetralol analogue, 5 days/week, for up to 5 weeks. Animals treated with 1,2,4-TEB, but not 1,3,5-TEB, tetralin or alpha-tetralol, developed hind limb weakness, excreted greenish urine, and showed 1,2-DAB-like neuropathology. These findings support the hypothesis that 1,2-spaced ethyl (or acetyl) moieties on a benzene ring of hydrocarbons are required for hydrocarbons to induce chromogenic changes and proximal giant neurofilamentous axonopathy. Key molecular targets of these compounds likely reside in the axon where they serve to maintain normal cytoskeletal organization.

Equivalence of Two Models for Partitioning of π-Electrons in Rings of Benzenoid Hydrocarbons

Two recently proposed methods for assessing the π-electron contents of rings of benzenoid hydrocarbons are shown to be equivalent

The Cyclopropene Pyrolysis Story

AbstractFor Abstract see ChemInform Abstract in Full Text.

Novel Ni 2Mo 3N/zeolite catalysts used for aromatics hydrogenation as well as polycyclic hydrocarbon ring opening

A series novel of bifunctional catalysts consisting of bulk and zeolite-supported Ni 2Mo 3N were prepared., characterized and investigated in the hydrogenation of aromatics as well as ring opening of polycyclic hydrocarbons. All supported catalysts had shown high activity of aromatics saturation (almost 100%) at 523 K while different activity of ring opening at 603 K. The essential factor of ring opening activity was acidity of catalysts, while the pore structure of the supports also affected it. The results show that the suitable catalyst Hbeta-supported and USY-supported Ni 2Mo 3N provide high ring opening conversion (>90%) under mild moderate condition ( T = 603 K, P = 3.0 MPa).

Supramolecular synthons in crystals of partially fluorinated fused aromatics: 1,2,3,4-Tetrafluoronaphthalene and its aza-analogue 1,3,4-trifluoroisoquinoline

From X-ray diffraction data, the crystal lattice of 1,2,3,4-tetrafluoronaphthalene 1 is composed of infinite π-stacks revealing π–π interactions of the arene-arene, arene-polyfluoroarene and polyfluoroarene-polyfluoroarene types. On replacement of the C2-F fragment of 1 by a N atom (i.e. in going from 1 to 1,3,4-trifluoroisoquinoline 2) the enlarged offset of neighboring molecules within the stacks excludes their π–π interactions, and only the F ⋯ π interaction of fluorine atom of the C1-F bond of one molecule with hydrocarbon ring of another is observed. Networks of shortened C F ⋯ H C ( 1 and 2) and N ⋯ H C ( 2) contacts also contribute to supramolecular tectonics of the crystals. Quantum chemical calculations at the PBE/cc-pVTZ level of theory on dimers of 1 and 2 result in geometries somewhat different from those observed in the solid state.

π-ELECTRON CONTENTS OF RINGS IN THE DOUBLE-HEXAGONAL-CHAIN HOMOLOGOUS SERIES (PYRENE, ANTHANTHRENE AND OTHER ACENOACENES)

Recently three methods for calculating the π-electron content of rings of benzenoid hydrocarbons were put forward: one based on the consideration of Kekuléstructural formulas, and the other two based on an analogous treatment of the Clar aromatic sextet formulas. These three methods are applied to the homologous series consisting of two condensed acene chains (whose first members are pyrene, anthanthrene, peri-naphthacenonaphthacene, …), leading to basically identical results. In contrast to acenes (in which the partition of π-electrons into rings is uniform), in the double-hexagonal-chain species the partition of π-electrons is highly non-uniform. The electron content monotonically decreases, in opposite directions, along the two acene chains, being maximal in the least annelated rings. Some other generally valid regularities in the π-electron properties of the double–hexagonal–chain benzenoids are also pointed out.

On the Distribution of π-Electrons into Rings of Conjugated Hydrocarbons Containing a Linear Polyacene Fragment

A method for assessing the π-electron contents (EC) of rings of benzenoid hydrocarbons, based on the examination of their Kekule structures, was recently put forward by Balaban and Randic. We now show that all hexagons belonging to a linear polyacene fragment of a conjugated hydrocarbon (not necessarily benzenoid) have mutually equal EC-values.

疎水性構造を有するα, α-二置換グリシン誘導体を組み込んだペプチドの自己組織化構造

疎水性構造を有するα, α-二置換グリシン誘導体を組み込んだペプチドの自己組織化構造

Comprehensive multi-dimensional chromatographic studies on the separation of saturated hydrocarbon ring structures in petrochemical samples

Characterization of complex petrochemical samples has been a classical subject of comprehensive two-dimensional (2D) gas chromatography (GC × GC). Macroscopic properties of these samples can be described accurately by separation of compounds in classes of identical molecular functionality. Ring structures in the carbon backbone of these compounds, which can be divided in saturated and unsaturated, are amongst the foremost functionalities affecting samples properties. Unfortunately, GC × GC tuned for separation of both saturated and unsaturated ring structures is likely to result in convoluted chromatograms when a distribution of both molecular properties is present in the sample. An independent liquid chromatographic (LC) separation preceding GC × GC could be used to resolve the mixture based on unsaturated rings, allowing saturated rings to be resolved separately in the GC × GC separation. This three-dimensional separation (abbreviated LC–GC × GC) was performed after rigorous evaluation of LC as part of a multidimensional separation using LC × GC. Group-type separation was achieved using this separation for components with either saturated or unsaturated rings. Results of this separation were used to compare information obtained by GC × GC with LC–GC × GC.

Synthesis, Structure, and Redox Chemistry of Ethenyl and Ethynyl Ferrocene Polyaromatic Dyads

A series of ferrocenyl−arene dyads, Fc−C⋮C−Ar, trans-Fc−CHCH−Ar, and Fc−CHCH−CHCH−Ar (Ar = phenyl, 1-naphthyl, 2-naphthyl, 9-phenanthryl, 9-anthryl, 1-pyrenyl, 3-perylenyl) have been synthesized. Their structures and spectroelectrochemical properties are discussed. The molecular structures of several have been determined by X-ray diffraction and the observed structures compared with global free-energy minimized calculated structures. In the solid state all ethynyl dyads have the aromatic ring orthogonal to the ferrocenyl cyclopentadienyl rings, whereas calculations predict a coplanar orientation. Calculated and observed structures agree for the ethenyl dyads with the rings orthogonal and coplanar for the anthryl and pyrenyl dyads, respectively. In most cases the solid-state structures are stabilized by offset π-stacking interactions between the polycyclic hydrocarbon rings. The two bands in the electronic spectra of the neutral dyads are due to the individual aryl and ferrocenyl end-groups. Upon oxidation...

Partitioning of π-Electrons in Rings of Fibonacenes

The partitioning of π-electrons into rings of benzenoid hydrocarbons is examined in the case of fibonacenes. It is demonstrated that the π-electron contents (ECs) of the hexagons of fibonacenes satisfy the following peculiar regularities: Let h be the number of hexagons, and EC(i) the electron content of the i-th hexagon. Then EC(i) is maximal for i = 1 and i = h, and minimal for i = 2 and i = h−1 . Going from the end towards the center of the fibonacene chain, EC(1) &gt;EC(3)&gt; EC(5)&gt; · · · and EC(2)&lt; EC(4) &lt;EC(6) &lt;· · · and EC(1)&gt; EC(2)&lt; EC(3) &gt;EC(4) &lt;EC(5) &gt;EC(6) &lt;· · · . For large values of h, the asymptotic values of EC(1) and EC(2) are 5.146 and 3.798, whereas of the central ring(s) 4 π-electrons.

Optimized Intermolecular Potential for Aromatic Hydrocarbons Based on Anisotropic United Atoms. III. Polyaromatic and Naphthenoaromatic Hydrocarbons

In this third article of the series, a new anisotropic united atoms (AUA) intermolecular potential parameter set has been proposed for the carbon force centers connecting the aromatic rings of polyaromatic hydrocarbons to predict thermodynamic properties using both the Gibbs ensemble and NPT Monte Carlo simulations. The model uses the same parameters as previous AUA models used for the aromatic CH force centers. The optimization procedure is based on the minimization of a dimensionless error criterion incorporating various thermodynamic data of naphthalene at 400 and 550 K. The new model has been evaluated on a series of polyaromatic and naphthenoaromatic hydrocarbons over a wide range of temperatures up to near-critical conditions. Vaporization enthalpy, liquid density, and normal boiling temperature are reproduced with good accuracy. The new potential parameters have also been tested successfully on toluene, 1,3,5-trimethylbenzene, styrene, m-xylene, n-hexylbenzene, and n-dodecylbenzene to demonstrate their transferability to alkylbenzenes.

Isolation and Characterization of Naphthenic Acids from a Metal Naphthenate Deposit: Molecular Properties at Oil‐Water and Air‐Water Interfaces

Naphthenic acids from a West African metal naphthenate deposit have been isolated and characterized by infrared (IR), nuclear magnetic resonance (NMR), and Fourier transform ion cyclotron resonance mass spectrometry (FT‐ICR MS). The sample has been shown to comprise a narrow group of 4‐protic naphthenic acids of molecular weight ∼1230 Da. The determined mass of 1230.0627 Da suggests a compound with the elemental composition C80H142O8. The NMR data show no sign of carbon‐carbon multiple bonds. Hence, the elemental composition indicates the presence of six saturated hydrocarbon rings. The naphthenic acids have proved to be highly oil‐water (o/w) interfacially active. On elevation of the pH from 5.6 to 9.0, interfacial activity increases gradually due to a higher degree of dissociation of the carboxylic groups. At pH 9.0, the interfacial tension (IFT) between water and toluene‐hexadecane (1–9 vol.) is lowered by ∼40 mN/m at concentrations of only 0.0050–0.010 mM naphthenic acid. The time rate of decrease of the IFT (dγ/dt) is also concentration‐dependent, and a well‐defined IFT is attained at long observation periods. The C80 naphthenic acids form relatively unstable Langmuir monolayers. The stability decreases further with increasing pH as more monomers become dissociated and dissolve into the aqueous phase. The stability is altered upon addition of calcium ions into the subphase due to formation of calcium naphthenate at the surface. In the undissociated state, the acids have a molecular area of ∼160 Å2/molecule in the noninteracting region. The high area reflects an extended molecular structure comprising four carboxylic head groups, which are likely to be separated by hydrocarbon chains.

Fine tuning the hydrophilic–hydrophobic balance in inositols through annulation: An analysis of the hydrogen-bonded architectures of ‘annulated inositols’

The crystal structures of conformationally locked, bicyclic cycloalkane-annulated variants of myo- and chiro-inositols have been analysed, in order to understand their mode of expression of the axial rich conformations and amphiphilicity in the solid state. Thus, while cyclohexa-annulated myo- and chiro-inositols exhibit a head-to-head bilayer molecular assembly, consisting of dimeric or octameric columnar architectures, cyclopenta-annulated chiro-inositol shows no such aggregation of the hydrophilic and hydrophobic faces, rather preferring to pack in a manner akin to a hydrophilic inositol. The differences in the two packing modes can be attributed to the size of the hydrocarbon ring, fine-tuning the hydrophilic-hydrophobic balance in the annulated inositols. An analysis of the non-polar molecular surface area (a measure of the intermolecular hydrophobic van der Waals interactions) for all the annulated inositols under study further vindicates the conclusion.

The cyclopropene pyrolysis story

Cyclopropene is the last of the small strained ring hydrocarbons to have its thermal decomposition subjected to intensive investigation. This critical review describes the nearly 40 year history of this investigation largely by gas kinetic methods with chromatographic analysis. These studies have revealed that cyclopropenes can decompose by a variety of mechanisms involving diradicals, vinylcarbenes and vinylidenes. Much detailed information has been obtained about the reactivity of these intermediates which has wider implications for thermal hydrocarbon pyrolysis. Theory has also played a important role. Cyclopropene itself has been shown to be an intermediate in the allene --> propyne rearrangement. The story itself illustrates how the evolution of mechanistic understanding has been anything but straightforward.

Three‐Membered Benzylic Thia Rings of Polycyclic Aromatic Hydrocarbons: Synthesis, Molecular Calculations and Properties

AbstractFor Abstract see ChemInform Abstract in Full Text.