Cyclic Isomers Research Articles

ROVIBRATIONAL SPECTROSCOPIC CONSTANTS AND FUNDAMENTAL VIBRATIONAL FREQUENCIES FOR ISOTOPOLOGUES OF CYCLIC AND BENT SINGLET HC2N ISOMERS

Through established, highly-accurate ab initio quartic force fields (QFFs), a complete set of fundamental vibrational frequencies, rotational constants, and rovibrational coupling and centrifugal distortion constants have been determined for both the cyclic 1(sup 1) 1A' and bent 2(sup 1)A' DCCN, H(C13)CCN, HC(C-13)N, and HCC(N-15) isotopologues of HCCN. Spectroscopic constants are computed for all isotopologues using second-order vibrational perturbation theory (VPT2), and the fundamental vibrational frequencies are computed with VPT2 and vibrational configuration interaction (VCI) theory. Agreement between VPT2 and VCI results is quite good with the fundamental vibrational frequencies of the bent isomer isotopologues in accord to within a 0.1 to 3.2 / cm range. Similar accuracies are present for the cyclic isomer isotopologues. The data generated here serve as a reference for astronomical observations of these closed-shell, highly-dipolar molecules using new, high-resolution telescopes and as reference for laboratory studies where isotopic labeling may lead to elucidation of the formation mechanism for the known interstellar molecule: X 3A0 HCCN.

Conformational studies of gas-phase ribose and 2-deoxyribose by density functional, second order PT and multi-level method calculations: the pyranoses, furanoses, and open-chain structures

We present an extensive computational study of a complex conformational isomerism of two gas phase pentoses of biological and potential astrobiological importance, d-ribose and 2-deoxy-d-ribose. Both cyclic (α- and β-pyranoses, α- and β-furanoses) and open-chain isomers have been probed using second order Møller–Plesset perturbation theory (MP2), M06-2X density functional, and multi-level G4 methods. This study revealed a multitude of existing minima structures. Numerous furanose conformers found are described with the Altona and Sundaralingam pseudorotation parameters. In agreement with the recent gas-phase microwave (MW) investigation of Cocinero et al., the calculated free ribose isomers of lowest energy are the two β-pyranoses with the 1C4 and 4C1 ring chair conformations. Both β-pyranoses lie within 0.9kJ/mol in terms of ΔG(298K) (G4), thus challenge the computational methods used to predict the ribose global minimum. The calculated most favoured ribofuranose is the α-anomer having the twist 2T1 ring conformation, put 10.4kJ/mol higher in ΔG than the global minimum. By contrast with d-ribose, the lowest energy 2-deoxy-d-ribose is the α-pyranose, with the most stable 2-deoxy-d-furanose (the α-anomer) being only 6.2kJ/mol higher in free energy. For both pentoses, the most favoured open-chain isomers are significantly higher in energy than the low-lying cyclic forms. A good overall agreement is observed between the M06-2X and MP2 results in terms of both the existing low-energy minima structures and intramolecular H-bonding geometrical parameters. The natural orbital analysis confirms the occuring of the endo- and exo-anomeric effects and maximization of intramolecular H-bonding in the lowest-lying pyranoses and furanoses of both sugars.

Structures and Bonding Situation of the Allyl Systems and Cyclic Isomers [H2E–E(H)–EH2]–,·,+ (E = C, Si, Ge, Sn)

AbstractQuantum chemical calculations using DFT and ab initio methods were carried out on the structures of the title compounds. The nature of the bonding was investigated with an energy decomposition analysis. The calculations predict that the planar C2v allyl structures of the neutral and charged heavier group‐14 homologues [H2E–E(H)–EH2]–,·,+ (E = Si – Sn) are no minima on the potential energy surface. Energy minima for allyl‐type structures of the latter systems possess Cs symmetry and pyramidal EH2 groups. The energetically lowest lying form of [H2E–E(H)–EH2]–,·,+ (E = Si – Sn) has a cyclic structure for the neutral molecules and the anion and a quasi‐cyclic equilibrium arrangement for the cations. In contrast, the cyclic isomers of the carbon molecules [H2C–C(H)–CH2]–,·,+ are significantly higher in energy than the allyl structures. Energy decomposition analyses show that the lower stability of the planar C2v allyl structures of [H2E–E(H)–EH2]–,·,+ (E = Si – Sn) does not come from weak π conjugation. The relative contribution of π conjugation in the latter species is even higher than in the allyl system of carbon. The cyclic form of [H2E–E(H)–EH2]–,·,+ (E = Si – Sn) is lower in energy than the allyl form, because the σ bonding in the former structures is much stronger than in the latter. This overcompensates the higher Pauli repulsion in the cyclic form. In the carbon systems, the Pauli repulsion of the cyclic structures is very strong, because the bonds are much shorter than in the heavier homologues. Consequently, the stronger Pauli repulsion in the cyclic isomers is not compensated by the stronger attraction compared with the allyl system.

Unraveling the Origin of the Relative Stabilities of Group 14 M2N22+ (M, N = C, Si, Ge, Sn, and Pb) Isomer Clusters

We analyze the molecular structure, relative stability, and aromaticity of the lowest-lying isomers of group 14 M2N2(2+) (M and N = C, Si, and Ge) clusters. We use the gradient embedded genetic algorithm to make an exhaustive search for all possible isomers. Group 14 M2N2(2+) clusters are isoelectronic with the previously studied group 13 M2N2(2-) (M and N = B, Al, and Ga) clusters that includes Al4(2-), the archetypal all-metal aromatic molecule. In the two groups of clusters, the cyclic isomers present both σ- and π-aromaticity. However, at variance with group 13 M2N2(2-) clusters, the linear isomer of group 14 M2N2(2+) is the most stable for two of the clusters (C2Si2(2+) and C2Ge2(2+)) , and it is isoenergetic with the cyclic D(4h) isomer in the case of C4(2+). Energy decomposition analyses of the lowest-lying isomers and the calculated magnetic- and electronic-based aromaticity criteria of the cyclic isomers help to understand the nature of the bonding and the origin of the stability of the global minima. Finally, for completeness, we have also analyzed the structure and stability of the heavier Sn and Pb group 14 M2N2(2+) analogues.

Adsorption and separation of n-hexane and cyclohexane on the UiO-66 metal–organic framework

Adsorption and separation of n-hexane and cyclohexane on the UiO-66 metal organic framework was studied by pulse gas chromatography and vapour phase breakthrough experiments. Vapour phase breakthrough experiments were performed with mixtures of both components, diluted in helium. Experiments were carried out at temperatures between 50 and 200°C, at partial pressures between 0.0024 and 0.05bar and varying mixture composition. In all conditions, separation between both components is observed, with cyclohexane being the most strongly retained component. This unusual preference for adsorbing the more bulky cyclic alkane isomer was further studied by pulse GC measurements at low coverage, at temperatures between 200 and 300°C. These experiments confirm the inverse shape selective behaviour of UiO-66 in the adsorption of linear and cyclic alkanes. Cyclohexane fits better in the cages of UiO-66, leading to a more negative adsorption enthalpy, together with a lower loss of entropy during adsorption as compared to n-hexane.

PHOTO- AND THERMOCHROMIC SPIRANS. 37. NEW SYMMETRICAL BISSPIROPYRANS OF THE INDOLINE SERIES

New symmetrical bisspiropyrans of the indoline series, which have photochromic properties and are characterized by substantially higher absorption capacity of cyclic isomers in comparison to the monospiropyrans, were obtained on the basis of 4,6-dihydroxy-5-methylisophthalaldehyde. Authors: N. A. Voloshin, E. V. Solov'eva, S. O. Bezugliy, A. V. Metelitsa, and V. I. Minkin English Translation in Chemistry of Heterocyclic Compounds, 2012, 48 (9), pp 1361-1370 http://link.springer.com/article/10.1007/s10593-012-1145-5

Correlation effects on aromaticity of [formula omitted] cluster: A quantum Monte Carlo study

Using diffusion Monte Carlo (DMC) simulation we investigate the electron correlation effects on stability and aromaticity of anionic beryllium Be32- cluster. The cyclic isomer is energetically more stable than its open linear counterpart by about 0.9, 0.7, and 0.2eV for Be3m- with m=1, 2, and 3, respectively. However, electron correlation has larger impact on linear isomers. Based on principles of minimum energy and electrophilicity, and maximum hardness, DMC indicates that Be32- cluster is aromatic.

Chromatographic separation through confinement in nanocages

Porous materials such as metal-organic frameworks offer great potential for separation technologies. Over the past decade the synthesis of a large number of new structures has been reported but relatively little attention has been given to the application of these novel adsorbents as stationary phases in gas or liquid chromatography. In this work, we report on the potential of the metal-organic framework UiO-66 for the separation of cyclic isomers. The extremely high preferential retention of cyclic hydrocarbons of the aromatic’s and functionalized cycloalkane’s type is exploited to achieve difficult separations. Confinement effects play a crucial role in fine-tuning the adsorbent’s properties.

Cyclic versus Polymeric Supramolecular Architectures in Metal Complexes of Dinucleating Ligands: Silver(I) Trifluoromethanesulfonate Complexes of the Isomers of Bis(di(1H-pyrazolyl)methyl)-1,1′-biphenyl.

In the search for new examples of systems that self-assemble into cyclic metal–organic architectures, the six isomers of X,Y′-bis(di(1H-pyrazolyl)methane)-1,1′-biphenyl, LXY, and their silver(I) trifluoromethanesulfonate complexes were prepared. Five of the six silver complexes gave crystals suitable for single crystal X-ray diffraction, with only the microcrystalline derivative of 2,3′-bis(di(1H-pyrazolyl)methane)-1,1′-biphenyl, L23, proving to be unsuitable for this analysis. Of the structurally characterized silver(I) complexes, that with L22 showed an unusual trans-spanning chelating coordination mode to silver. At the same time the ligand was also bound to a second silver center giving rise to a cyclic supramolecular isomer with a 22-membered metallacycle. The complex of L34 also gave a cyclic dication but with a remarkable 28-membered metallacycle ring. The remaining three derivatives were polymeric. The results of this study underscore that a 120° angle between dipyrazolylmethyl moieties across aro...

New Pathways for Formation of Acids and Carbonyl Products in Low-Temperature Oxidation: The Korcek Decomposition of γ-Ketohydroperoxides

We present new reaction pathways relevant to low-temperature oxidation in gaseous and condensed phases. The new pathways originate from γ-ketohydroperoxides (KHP), which are well-known products in low-temperature oxidation and are assumed to react only via homolytic O-O dissociation in existing kinetic models. Our ab initio calculations identify new exothermic reactions of KHP forming a cyclic peroxide isomer, which decomposes via novel concerted reactions into carbonyl and carboxylic acid products. Geometries and frequencies of all stationary points are obtained using the M06-2X/MG3S DFT model chemistry, and energies are refined using RCCSD(T)-F12a/cc-pVTZ-F12 single-point calculations. Thermal rate coefficients are computed using variational transition-state theory (VTST) calculations with multidimensional tunneling contributions based on small-curvature tunneling (SCT). These are combined with multistructural partition functions (Q(MS-T)) to obtain direct dynamics multipath (MP-VTST/SCT) gas-phase rate coefficients. For comparison with liquid-phase measurements, solvent effects are included using continuum dielectric solvation models. The predicted rate coefficients are found to be in excellent agreement with experiment when due consideration is made for acid-catalyzed isomerization. This work provides theoretical confirmation of the 30-year-old hypothesis of Korcek and co-workers that KHPs are precursors to carboxylic acid formation, resolving an open problem in the kinetics of liquid-phase autoxidation. The significance of the new pathways in atmospheric chemistry, low-temperature combustion, and oxidation of biological lipids are discussed.

A New Interpretation of the Photoelectron Spectra of CrC2–

In this work, the computational quantum chemical DFT, CASPT2, and RCCSD(T) methods have been utilized to investigate the geometric and electronic structures of cyclic and linear CrC2(-/0) clusters. The neutral ground state is firmly identified as the cyclic (5)A1 state. For the anionic cluster, two nearly degenerate isomers were recognized, namely a cyclic (6)A1 state and a linear (6)Σ(+) state. Therefore, assignments of the observed bands in the photoelectron spectra of CrC2(-) have been made based on both of these isomers. With the exception of the B band all other experimental observed bands could be ascribed to the cyclic isomer. The computed detachment energies show that the former band must be exclusively assigned to the ionization of (6)Σ(+) of the linear structure, which can possibly also contribute to some higher energy bands. Additional support for the proposed assignments is provided by multidimensional Franck-Condon factor simulations for the (6)A1→(5)A1 and (6)A1→(5)B1 transitions that show a nearly perfect match with the observed vibrational progressions of the X and A bands in the 532 nm spectra.

Hydrophobic meddling in small water clusters

What would be the effects on the nature of hydrogen bonds, on the energies, and on the overall structural possibilities of replacing some hydrogen atoms by small hydrophobic groups in small water networks? Aiming at investigating this question, we performed an exhaustive search of the conformational space of the (Methanol)2(Water)3 representative model system, characterized the results, and made key comparative analysis with pentameric pure water clusters. The potential energy surface yielded a global minimum structural motif consisting of several puckered ring-like cyclic isomers very close in energy to each other. They are followed by other structural motifs, which, contrary to conventional belief, would also contribute to the properties of a macroscopic sample of this composition. We found that the C–H···O interactions play a subordinate structural role and preferably accommodate to the established O–H···O based structures. In comparison with the pure (H2O)5 case, we showed that (1) the same basic structural motifs and in a similar hierarchy energy order are obtained, but with a richer structural isomerism; (2) in general, the bonding is reinforced by the increase in the electrostatic and in the “degree of covalency” of the hydrogen-bonding components. Therefore, at least for this small cluster size, methyl groups slightly affect the structural isomerism and reinforce the hydrogen bonding. Additionally, we identified general factors of instability of the more unstable structures.

ChemInform Abstract: Synthesis of γ‐Azido‐β‐ureido Ketones and Their Transformation into Functionalized Pyrrolines and Pyrroles via Staudinger/Aza‐Wittig Reaction.

AbstractHydrolysis of acetals of type (I) and (XII) followed by treatment with the sulfinic acid (III), α‐functionalized ketones, and urea or urea derivatives allows a simple and efficient access to γ‐azido‐β‐ureido ketones and/or their cyclic isomers.

Quantum chemical study of the electronic structures of MnC2-/0 clusters and interpretation of the anion photoelectron spectra

Cyclic and linear MnC2-/0 clusters have been theoretically studied. The 7A1and6A1 states of the cyclic isomer are calculated to be the ground states of the anionic and neutral cluster, respectively. All observed bands in the experimental photoelectron spectra of MnC2- could be assigned to the cyclic isomer. The X band is ascribed to an ionization during which an electron is detached from a nonbonding 4s4p hybrid orbital. The higher bands in the spectra are the result of ionization processes in which an electron from the nonbonding HOMO of the C22- ligand is removed.

Tetragermacyclobutadiene: Energetically Disfavored with Respect to Its Structural Isomers

Germanium has been a central feature in the renaissance of main-group inorganic chemistry. Herein, we present the stationary-point geometries of tetragermacyclobutadiene and its related isomers on the singlet potential energy surface at the CCSD(T)/cc-pVTZ level of theory. Three of these 12 structures are reported for the first time and one of them is predicted to lie only 0.4 kcal mol(-1) above the previously reported global minimum. Focal-point analyses has provided electronic energies at the CCSD(T) level of theory, which are extrapolated to the complete basis-set limit and demonstrate the convergence behavior of the electronic energies with improving levels of theory and increasing basis-set size. The lowest-energy structure is the bicyclic structure, which lies 35 kcal mol(-1) below the "all-Ge" cyclobutadiene structure. The reaction energies for the association of known Ge hydrides (e.g., digermene) to form Ge4H4 indicate that Ge4H4 could be observed experimentally. We investigate the bonding patterns by examining the frontier molecular orbitals. Our results demonstrate that: 1) the cyclic isomers of (GeH)4 distort to maximize the mixing of the p orbitals that are involved in the π system of tetragermacyclobutadiene and 2) the lowest-energy isomers exhibit unusual bonding arrangements (e.g., bridging H bonds) that maximize the nonbonding electron density at the Ge centers.

Unexpected Formation of N-(1-(2-Aryl-hydrazono)isoindolin-2-yl)benzamides and Their Conversion into 1,2-(Bis-1,3,4-oxadiazol-2-yl)benzenes

Reaction between ortho-phthalaldehyde and various aroylhydrazines unexpectedly yields N-(1-(2-aryl-hydrazono)isoindolin-2-yl)benzamides as major products along with the predictable 1,2-bis-aroylhydrazones. NMR investigation of the major reaction products indicate the presence of a mixture of geometrical isomers, in various ratios. Single crystal X-ray diffraction confirms the proposed structure and indicates a Z configuration of the C═N double bond substitutents. Optimization of the condensation reaction conditions enabled quantitative isolation of the cyclic isomer. Oxidation of the isomers with bis(trifluoroacetoxy)iodobenzene (PIFA) leads to rapid formation of new highly fluorescent 1,2-bis(5-aryl-1,3,4-oxadiazol-2-yl)benzenes.

Synthesis of γ-Azido-β-ureido Ketones and Their Transformation into Functionalized Pyrrolines and Pyrroles via Staudinger/aza-Wittig Reaction

A simple two-step procedure yielding γ-azido-β-ureido ketones or/and their cyclic isomers, 6-(1-azidoalkyl)-4-hydroxyhexahydropyrimidin-2-ones, has been developed. The synthesis includes three-component condensation of acetals of 2-azidoaldehydes with urea or methylurea and p-toluenesulfinic acid in aqueous formic acid followed by reaction of the obtained N-[(2-azido-1-tosyl)alkyl]ureas with sodium enolates of α-functionalized ketones. The azido ketones or their cyclic isomers are transformed into ureido-substituted Δ(1)- or/and Δ(2)-pyrrolines via Staudinger/aza-Wittig reaction promoted by PPh(3). The obtained pyrrolines are converted into 3-functionalized 1H-pyrroles via elimination of urea under acidic conditions. Convenient one-pot syntheses of 1H-pyrroles starting from N-[(2-azido-1-tosyl)alkyl]ureas or γ-azido-β-ureido ketones have been also developed.

Association mechanisms of unsaturated C2 hydrocarbons with their cations: acetylene and ethylene

The ion-molecule association mechanism of acetylene and ethylene with their cations is investigated by ab initio quantum chemical methods to understand the structures, association energies, and the vibrational and electronic spectra of the products. Stable puckered cyclic isomers are found as the result of first forming less stable linear and bridge isomers. The puckered cyclic complexes are calculated to be strongly bound, by 87, 35 and 56 kcal mol(-1) for acetylene-acetylene cation, ethylene-ethylene cation and acetylene-ethylene cation, respectively. These stable complexes may be intermediates that participate in further association reactions. There are no association barriers, and no significant inter-conversion barriers, so the initial linear and bridge encounter complexes are unlikely to be observable. However, the energy gap between the bridged and cyclic puckered isomers greatly differs from complex to complex: it is 44 kcal mol(-1) in C(4)H(4)(+), but only 6 kcal mol(-1) in C(4)H(8)(+). The accurate CCSD(T) calculations summarized above are also compared against less computationally expensive MP2 and density functional theory (DFT) calculations for structures, relative energies, and vibrational spectra. Calculated vibrational spectra are compared against available experiments for cyclobutadiene cation. Electronic spectra are also calculated using time-dependent DFT.

Coordination of CO to low-valent phosphorus centres and other related P–C bonding situations. A theoretical case study

The multi-faceted bonding of CO in molecular phosphorus compounds is described using calculated P–C bond strengths as a criterion. Full compliance matrices at coupled cluster level of HPCO (1a), singlet oxaphosphirane-3-ylidene HP(η2-CO)), the dimer (HPCO)2 as well as PCH, HPCH2 and H2P–CH3 were calculated to obtain quantifiable data and enable comparison. The quest for CO coordination and activation was examined for phosphaketenes 1a–f: the P–C compliance constants (in A mdyn−1) reveal a clear trend that shows a weakening of the P–CO bond strength from 1a to mono-ligation as in [(OC)5W{P(CO)Me}] (1c) (0.301), in H3BP(CO)Me (1b) (0.322), to bis-ligation as in [{(OC)5W}2P(CO)R] (1f) (0.488) to (H3BP)2(CO)Me (1d) (0.649). Availability of p-type electron density at phosphorus drastically strengthens the P–CO bond and weakens the C–O bond via π–back-donation, bis complexes are better described as weak CO (C→P) adducts to phosphorus. In complexes [(OC)5W{P(CO)R}] the CO activation by phosphorus equals that of CO activation through tungsten in pentacarbonyltungsten complexes. A comparative study of various CO bonding motifs in molecular compounds indicates that acyclic (2) or cyclic diphospha-urea derivatives (2–5) or isomers (6) display P–CO bond strengths (compliance constants range 0.502–0.640) well below that of the P–C bond of H2P–CH3 (0.364), thus providing insight into the bonding and the ease of CO extrusion, experimentally known for some cases. A highly unusual adduct of CO was obtained in silico through two-fold P-ligation in diphosphiren-3-ones 2a–d, the parent compound of which was found to be properly described as a side-on (PP)→(CO) complex, in contrast to its aza-analogue 2aN. A drastic weakening of the P–CO bond strength is observed from P2CO (2a) (0.502) to the C2-symmetrical (H3BP)2CO (2b) (0.913); the latter represents an extreme case of a weakly bound CO. Furthermore, calculated 31P NMR shifts and scalar 1J(P,E) couplings were correlated with P–CO and PC–O compliance constants as a tool for experimentalists.

Source Determination for Subsurface Light Non-Aqueous Phase Liquid (LNAPL) Using Trimethylcyclopentane and Trimethylcyclohexane Isomer Ratios

Ratios of two pairs of cyclic hydrocarbon isomers are developed to link petroleum hydrocarbon pools and residuals in the subsurface to their probable source product. The ratios 1,2,4- trimethylcyclopentane/1,2,3- trimethylcyclopentane, and 1,1,3- trimethylcyclohexane/1,2,4- trimethylcyclohexane are proposed for LNAPL-source correlation because the pairs are present in a wide range of refinery feeds and refined products, they are resistant to aerobic biodegradation, and have similar solubility and volatility. The proposed ratios and other conventional methods are used to evaluate the source of hydrocarbon product encountered in wells at the Shiraz Oil Refinery, Iran.