Open-chain Isomers Research Articles

Photochemical Ring-Opening Reaction of 1,3-Cyclohexadiene: Identifying the True Reactive State.

The photochemically induced ring-opening isomerization reaction of 1,3-cyclohexadiene to 1,3,5-hexatriene is a textbook example of a pericyclic reaction and has been amply investigated with advanced spectroscopic techniques. The main open question has been the identification of the single reactive state which drives the process. The generally accepted description of the isomerization pathway starts with a valence excitation to the lowest lying bright state, followed by a passage through a conical intersection to the lowest lying doubly excited state, and finally a branching between either the return to the ground state of the cyclic molecule or the actual ring-opening reaction leading to the open-chain isomer. Here, in a joint experimental and computational effort, we demonstrate that the evolution of the excitation-deexcitation process is much more complex than that usually described. In particular, we show that an initially high-lying electronic state smoothly decreasing in energy along the reaction path plays a key role in the ring-opening reaction.

Rotational spectrum of anti- and gauche-4-cyano-1-butyne (C5H5N) – An open-chain isomer of pyridine

The analysis of the rotational spectrum of 4-cyano-1-butyne, an open-chain isomer of pyridine, is presented herein for the first time. Transitions for the ground vibrational states of both conformational isomers, anti and gauche, were observed in the 8–38 GHz and 130–360 GHz frequency ranges and fit to effective sextic distorted-rotor Hamiltonians with low uncertainty (σfit < 50 kHz), allowing for their potential detection by radioastronomy or in harsh reaction environments. The microwave region includes hyperfine-split transitions for both conformers, allowing for the experimental determination of the χaa, χbb, and χcc quadrupole coupling constants. In the millimeter-wave region, not every observable ground-state transition could be satisfactorily addressed by a single-state Hamiltonian due to Coriolis coupling with the low-energy vibrationally excited states. Thus, effective single-state fits of the ground states were obtained by including only Ka-series transitions without obviously perturbed energy levels. Importantly, the effective fit does include the most intense transitions throughout the observed frequency ranges. The predicted values (MP2/cc-pVTZ) are in close agreement with the experimental spectroscopic constants. These data provide a sufficient foundation for the identification of anti- and gauche-4-cyano-1-butyne in the interstellar medium by radioastronomy. The gauche conformer is estimated to lie 1.00 (5) kcal/mol higher in energy than the anti conformer, as determined using experimental transition intensities.

Ring-chain isomerism in conjugated guanylhydrazones: Experimental and theoretical study

Treatment of 1,3-diaryl-propene-2-one with aminoguanidine under acidic conditions for a short reaction period (1 h) delivers - in accordance with a literature report - the corresponding guanylhydrazones. However, when the reaction time was increased to 12 h, formation of the ring annulated product 4,5-dihydro-1H-pyrazole-1-carboximidamide was observed. This is the first case of ring-chain isomerism in conjugated guanylhydrazones. The acyclic conjugated guanylhydrazone and the corresponding annulated product (4,5-dihydro-1H-pyrazole-1-carboximidamide) could be clearly distinguished by means of UV and NMR spectroscopy. The formation of the ring isomer was further confirmed by single crystal XRD analysis. The time-dependent 1H NMR study indicated the gradual transformation of the open-chain compound into the cyclic one. The mechanistic insights into the formation of these two products were explored using quantum chemical methods which revealed that the ring isomer is thermodynamically more stable than the open-chain isomer by 6–11 kcal/mol and the barrier for cyclization was found to be 31.37 kcal/mol.

Mystery of 1-Vinylpropargyl Formation from Acetylene Addition to the Propargyl Radical: An Open-and-Shut Case.

The addition of acetylene (C2H2) to the propargyl radical (C3H3) initiates a cascade of molecular weight growth reactions that result in the production of polycyclic aromatic hydrocarbons (PAHs) in flames. Although it is well-established that the first reaction step produces the cyclic C5H5 radical cyclopentadienyl (c-C5H5), recent studies have also detected significant quantities of the open-chain form, 1-vinylpropargyl (l-C5H5). This work presents a mechanism for the C3H3 + C2H2 reaction from ab initio calculations, which includes pathways for the formation of both the open and shut isomers as well as for their interconversion. Formation of both isomers proceeds from the initial HCCCH2CHCH• reaction adduct with similar barriers, both well below the entrance channel energy. Subsequent isomerization of l-C5H5 with c-C5H5 also transpires at below the energy of the reactants, although this process connects two deep wells (being resonance stabilized radicals), and must compete with collisional energy transfer. An RRKM theory/master equation model is developed for the reported C5H5 reaction mechanism. Master equation simulations suggest that both cyclic and open-chain isomers are expected to form from the C3H3 + C2H2 reaction across a range of temperatures, although the lifetime of l-C5H5 is relatively short for rearrangement to c-C5H5.

Alternative Route Toward Nitrones: Experimental and Theoretical Findings.

Nitrones are important building blocks for natural and biologically active compounds, used as spin-trap reagents and therapeutic agents. All this makes nitrones intriguing and valuable compounds for fundamental studies and as useful chemicals in various synthetic strategies. Therefore, nitrones are still of great interest and in the limelight of researches. With our initial goal to solve synthetic problems toward 5-phenyl-2,2'-bipyridine (Phbpy), we found that this reaction can proceed through the formation of 6-phenyl-3-(pyridin-2-yl)-1,2,4-triazin-4(3H)-ol (4-OH), which rapidly isomerizes to a 3,4-dihydro-1,2,4-triazine-based nitrone, namely 6-phenyl-3-pyridin-2-yl-2,3-dihydro-1,2,4-triazin-4-oxide (4'), This encouraged us to study condensation of hydrazonophenylacetaldehyde oxime (2), obtained from 2-isonitrosoacetophenone (1), with other aldehydes. The reaction with both salicylaldehyde and p-tolualdehyde leads to the open-chain isomers, namely (2-hydroxybenzylidene)hydrazono-2-phenylacetaldehyde oxime (5) and (4-methylbenzylidene)hydrazono-2-phenylacetaldehyde oxime (6), respectively. The latter product exists in solution in equilibrium with its cyclic isomer 6-phenyl-3-(4-methylphenyl)-2,3-dihydro-1,2,4-triazin-4-oxide (6'), while the former one exists in solution exclusively in the open-chain form. It was also found that 2 reacts with acetone with the formation of 3,3-dimethyl-6-phenyl-2,3-dihydro-1,2,4-triazin-4-oxide (7'), which also exists in solution in equilibrium with its open-chain isomer 2-phenyl-2-(propan-2-ylidenehydrazono)acetaldehyde oxime (7). The static DFT as well as ab initio molecular dynamics simulations have corroborated the experimental findings.

Tautomers of Gas-Phase Erythrose and Their Interconversion Reactions: Insights from High-Level ab Initio Study.

D-Erythrose is a C4 monosaccharide with a biological and potential astrobiological relevance. We have investigated low-energy structures of d-erythrose and their interconversion in the gas phase with the highest-level calculations up-to-date. We have identified a number of structurally distinct furanose and open-chain isomers and predicted α ↔ α and β ↔ β furanose interconversion pathways involving the O-H rotamers. We have estimated relative Gibbs free energies of the erythrose species based on the CCSD(T)/aug-cc-pVTZ electronic energies and MP2/aug-cc-pVTZ vibrational frequencies. By using natural bond orbital theory we have also quantified a stabilization of erythrose conformers and interconversion transition states by intramolecular H-bonds.

Isoxazolium N-ylides and 1-oxa-5-azahexa-1,3,5-trienes on the way from isoxazoles to 2H-1,3-oxazines.

Theoretical and experimental studies of the reaction of isoxazoles with diazo compounds show that the formation of 2H-1,3-oxazines proceeds via the formation of (3Z)-1-oxa-5-azahexa-1,3,5-trienes which undergo a 6π-cyclization. The stationary points corresponding to the probable reaction intermediates, isoxazolium N-ylides, were located by DFT calculations at the B3LYP/6-31G(d) level only for derivatives without a substituent in position 3 of the isoxazole ring. These isoxazolium N-ylides are thermodynamically and kinetically very unstable. According to the calculations and experimental results 2H-1,3-oxazines are usually more thermodynamically stable than the corresponding open-chain isomers, (3Z)-1-oxa-5-azahexa-1,3,5-trienes. The exception are oxaazahexatrienes derived from 5-alkoxyisoxazoles, which are thermodynamically more stable than the corresponding 2H-1,3-oxazines. Therefore, the reaction of diazo esters with 5-alkoxyisoxazoles is a good approach to 1,4-di(alkoxycarbonyl)-2-azabuta-1,3-dienes. The reaction conditions for the preparation of aryl- and halogen-substituted 2H-1,3-oxazines and 1,4-di(alkoxycarbonyl)-2-azabuta-1,3-dienes from isoxazoles were investigated.

Structure elucidation of a new open chain isomer of the cannabimimetic cyclopropoylindole A-796,260

A new hitherto unknown ring opened isomer of the tetramethylcyclopropoylindole 1-(2-morpholin-4-ylethyl)-1H-indol-3-yl]-(2,2,3,3-tetramethylcyclopropyl)methanone (A-796,260) has been identified in a seizure of the German Customs. It bears an E-alkene moiety in the side chain with a tert.-butyl group, having a 3-penten-5-one skeleton. The isomer is not identical to the known products of thermal ring opening of tetramethylcyclopropoylindoles, which have a 1-pentene-5-one alkyl chain, instead. We postulate its formation via a Wagner–Meerwein-rearrangement under acidic conditions during the attempted synthesis of the desired tetramethylcyclopropoylindole. Whether the compound, found in high purity, has been the result of a synthesis fault or has been synthesized intentionally and if the new isomer has cannabimimetic potential, is still unknown. During structure elucidation with NMR spectroscopy and mass spectrometry, interesting phenomena have been detected concerning the product ion spectrometry of tetramethylcyclopropoylindoles.

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.

Electronic Transitions of C6H4+ Isomers: Neon Matrix and Theoretical Studies

Three open-chain isomers of C6H4(+) and two cyclic ones were detected following mass-selective trapping in 6 K neon matrixes. The open-chain cations 5-hexene-1,3-diyne (CH2═CH-CC-CC-H)(+) and cis- (cis-HCC-CH═CH-CCH)(+) and trans-3-hexene-1,5-diyne (trans-HCC-CH═CH-CCH)(+), possess two absorption systems commencing at 609 and 373, 622 and 385, and 585 and 373 nm, respectively. They are assigned to the 1 (2)A" and 2 (2)A" ← X (2)A", 1(2)A2 and 2 (2)A2 ← X (2)B1, and 1 (2)Bg and 2 (2)B(g) ← X (2)A(u) electronic transitions of these cations. Two overlapping systems are detected at around 420 nm and tentatively assigned to the 1 (2)A" ← X (2)A" electronic transitions of propargyl cyclopropene and 2 (2)B1 ← X (2)A2 of o-benzyne cation structures. The assignment of the electronic transitions is based on theoretical vertical excitation energies calculated with CASPT2 and EOMEE-CCSDT methods for 12 isomers of C6H4(+). These have been carried out at the geometries optimized using several ab initio methods. Adiabatic excitation energies were calculated for the five identified isomers of C6H4(+).

Structures and stabilities of non-linear VC n+/− ( n = 1–8) clusters

A theoretical study of the different fan and cyclic isomers of VC n +/− ( n = 2–8) clusters has been carried out. Predictions for different molecular properties, such as electronic energies, harmonic vibrational frequencies or rotational constants, have been made using the B3LYP method with different basis set including effective core potentials, ECPs. In general, fan and cyclic structures have been predicted to prefer triplet ground states. The stability of fan and cyclic clusters as a function of the size has been discussed in terms of the incremental binding energies. For cationic systems a clear even–odd alternation in stability is found, n-even clusters being more stable than n-odd ones. This parity effect is also found for the first members of the fan isomers of VC n −, whereas for cyclic VC n − structures the stability decreases along the series. It is also found that VC n + systems with n < 5 prefer fan structures over linear ones, whereas for n = 5–7 the open-chain isomers are the most stable and for n = 8 cluster the cyclic structure is the most stable. Anionic vanadium-doped carbon clusters with n ≤ 5 prefer fan structures, whereas for n > 5 n-even clusters prefer open-chain structures and for VC 7 − the cyclic structure is the most stable.

Ge3Hn- Anions (n = 0−5) and Their Neutral Analogues: A Theoretical Investigation on the Structure, Stability, and Thermochemistry

The structure, stability, and thermochemistry of various Ge3H(n)- isomers (n = 0-5) and of their neutral analogues have been investigated at the B3LYP/6-311+G(d), MP2(full)/6-31G(d), and Gaussian-2 (G2) level of theory. For Ge3H(-), both the B3LYP and the G2/MP2 methods predict the cyclic, H-bridged structure 1a- as the global minimum, more stable than another cyclic isomer and an open-chain isomer by ca. 10 and 25 kcal mol(-1), respectively. For Ge3H2(-), the B3LYP and the G2/MP2 methods provide a somewhat different description of the potential energy surface. At the G2/MP2 level of theory, the global minimum is the cyclic, H2Ge-bridged structure 2a-, separated by other three nearly degenerate isomers by ca. 10 kcal mol(-1). On the other hand, at the B3LYP level of theory, the cyclic, H-bridged structure 2e-, not located at the MP2 level of theory, is more stable than 2a- by ca. 1 kcal mol(-1). For Ge3H3(-), both the B3LYP and the G2/MP2 methods predict the cyclic, H3Ge-bridged isomer 3a- as the global minimum, but the energy differences with the other five located isomeric structures predicted by the two methods are quantitatively different. Similar to Ge3H2(-), the B3LYP and the G2/MP2 theoretical levels provide a somewhat different description of the Ge3H4(-) potential energy surface. At the G2/MP2 level of theory, the global minimum is the cyclic structure 4b- of C(2v) symmetry, featuring a Ge2H4 moiety and a Ge-bridged atom, which is more stable than other three located isomers by 3, 9, and 17 kcal mol(-1). On the other hand, at the B3LYP level of theory, the open-chain isomer 4a- of H3Ge-Ge-GeH(-) connectivity is more stable than 4b- by ca. 1 kcal mol(-1) and nearly degenerate with the alternative open-chain isomer H3Ge-GeH-Ge(-). For Ge3H5(-), both the B3LYP and the G2/MP2 methods predict the 2-propenyl-like isomer H3Ge-Ge-GeH2(-) as the global minimum, with energy differences with other four isomeric structures which range from ca. 1-2 to 13-17 kcal mol(-1). At the G2 level of theory and 298.15 K, the electron affinities of Ge3H(n) are computed as 2.17 (n = 0), 2.57 (n = 1), 1.70 (n = 2), 2.41 (n = 3), 2.07/1.80 (n = 4), and 2.71/2.46 eV (n = 5). The two alternative values reported for Ge3H4 and Ge3H5 reflect the alternative conceivable choice for the structure of the involved neutrals and ions. The G2 enthalpies of formation of Ge3H(n) and Ge3H(n)- (n = 0-5) have also been calculated using the atomization procedure. Finally, we have briefly discussed the implications of our calculations for previously performed mass spectrometric experiments on the negative ion chemistry of GeH4.

Isomers of cyclo‐Heptasulfur and Their Coordination to Li+: An ab initio Molecular Orbital Study

AbstractFor Abstract see ChemInform Abstract in Full Text.

Isomers of cyclo-Heptasulfur and Their Coordination to Li+: an Ab Initio Molecular Orbital Study

The potential energy hypersurfaces (PESs) of heptasulfur (S7) and of [LiS7]+ have been investigated by ab initio molecular orbital calculations at the G3X(MP2) level of theory. Besides the chair-like seven-membered ring (1a) as the global minimum structure, eight local minimum structures and one transition state have been located on the PES of S7. The barrier for pseudorotation of 1a is only 5.6 kJ mol(-1). The boat-like S7 ring (1b) is 12.1 kJ mol(-1) less stable than 1a, followed by three isomers of connectivity S6=S and four open-chain isomers. On the basis of multireference calculations at the MRCI(4,4)+Q/6-311G(d) level, the most stable open-chain form of S7 is a triplet of relative energy 133.1 kJ mol(-1). Thus, the reaction energy (deltaE0) for the ring opening of 1a is 133.1 kJ mol(-1), halfway between those of the highly symmetrical rings S6 and S8. Because of their strong multireference characters, the stabilities of the biradicalic singlet chains are significantly overestimated by the single-reference-based G3X(MP2) method. The calculated vibrational spectrum of 1a is in good agreement with experimental data. The various isomers of S7 form stable complexes with Li+ with coordination numbers of 1-4 for the metal atom and binding energies in the range of -93.8 to -165.7 kJ mol(-1). A total of 15 isomeric complexes have been located, with 13 of them containing cyclic ligands. The global minimum structure (2a) is composed of 1a, with the Li+ cation linked to the four negatively charged sulfur atoms (symmetry C(s)). The corresponding complex 2c containing the ligand 1b is by 23.4 kJ mol(-1) less stable than 2a, and a bicyclic crown-shaped LiS7 cation (2e) is by 34.9 kJ mol(-1) less stable than 2a. Even less stable are four complexes with the branched S6=S ligand. SS bond activation by polarization of the valence electrons takes place on coordination of Li+ to cyclo-S7 (1a).

Ring Opening of 2,5-Didehydrothiophene: Structures and Rearrangements of C4H2S Isomers

Electronic structures and rearrangement pathways of several C4H2S isomers are computationally investigated by methods based on coupled cluster theory and density functional theory. Six singlet C4H2S isomers lie within ca. 30 kcal/mol above butatrienethione (6), the apparent global minimum. Ethynylthioketene (7) lies only 2 kcal/mol higher in energy than cumulene 6. Two open-chain isomers, butadiynylthiol (8) and diethynyl sulfide (9), reside ca. 9 and 24 kcal/mol above 6, respectively. Lying 30 kcal/mol above 6, two cyclic singlet isomers, ethynylthiirene (10) and cyclopropenylidenemethanthione (11), are nearly degenerate in energy. Thiophene-2,5-diyl (12) lies substantially higher in energy than 6 (ca. 45 kcal/mol) and is predicted to rearrange preferentially by C-S bond cleavage, leading to thioketene 7, rather than by C-C bond cleavage, leading to diethynyl sulfide (9; retro-Bergman cyclization). Accurate spectroscopic properties of these C4H2S isomers, as well as an understanding of their rearrangement pathways, should facilitate the detection and characterization of these isomers in the laboratory and the interstellar medium.

Spiropyrans: Synthesis, Properties, and Application. (Review)

Published data on the synthesis and structural modification of spiropyrans and bisspiropyrans and production of the heteroanalogs of spiropyrans are classified and analyzed. The chemical characteristics of spiropyrans, including complexation of the open-chain isomers and cyclic forms are examined. Special attention is paid to the photochromic characteristics of spiropyrans at interfaces between phases.

A theoretical study of the structures and stabilities of N4O2 isomers

Five N4O2 isomers and their possible decomposition pathways were investigated with Møller–Plesset perturbation theory (MP2) and density functional theory (DFT). The most stable isomer is the open-chain C2v structure, which has not been reported before. For all five N4O2 isomers, dissociation energies and eight transition states were studied in the present paper. The open-chain isomer 1 and the planar (C2h) isomer 3 could be potential candidates for high energy density materials (HEDM) due to their large dissociation energy and moderate dissociation barrier.

Structural Isomerism and Competitive Proton Solvation between Methanol and Water in H+(CH3OH)m(H2O)n, m + n = 4

Competitive solvation of the excess proton in protonated mixed methanol−water clusters [H+(CH3OH)m(H2O)n, m + n = 4] has been characterized by vibrational predissociation spectroscopy in combination with density functional theory calculations. The solvation topology of the clusters can be classified as (1) the closed shell, in which a hydronium ion H3O+ is fully solvated by three neutral molecules forming a complete solvation shell, and (2) the open chain, where the excess proton is tugged between two mixed subunits in a linear chain. The existence of these two types of isomer is verified from a close examination of the characteristic free-OH and hydrogen-bonded-OH stretching modes in the spectra. It is found that sequential replacement of the water molecule in H+(H2O)4 by methanol redistributes the population between the closed-shell and the open-chain isomers. While the excess proton is preferentially taken by methanol (instead of water) in the chain configuration, it can be either localized as CH3OH2+ or delocalized as CH3OH···H+···CH3OH at m ≥ 2, depending sensitively on the number of the methanol molecules and the symmetry of the cluster isomers. In contrast to that of NH4+(NH3)m(H2O)n, m + n = 4, previously studied, this work provides a clear picture of competitive solvation of a charge between the constituent solvent molecules within a cluster.

Theoretical Study of Small MgCn, MgCn+, and MgCn- Cyclic Clusters

A theoretical study of the MgC n , MgC n +, and MgC n - (n = 2-7) cyclic clusters has been carried out. Predictions for their electronic energies, rotational constants, dipole moments, and vibrational frequencies have been made at the B3LYP/6-311G(d) and B3LYP/6-311+G(d) levels. MgC n cyclic clusters generally have singlet ground states, whereas both cationic and anionic clusters have doublet ground states. An even-odd parity effect (n-even clusters being more stable than n-odd ones) is observed for both the neutral and anionic species, whereas in the case of the cations, there is no clear alternation in stability. Ionization potentials exhibit also a clear parity alternation trend, with n-even clusters having larger values than n-odd ones. In the case of electron affinities, initially the same behavior is observed, but for larger members the trend is reversed and n-odd compounds have higher electron affinity. It is also found that neutral clusters prefer cyclic structures over open-chain isomers, especially for high n. On the other hand open-chain ground states are predicted for both anionic and cationic clusters, except for the first members of the series.

Theoretical Study of the Reaction of HCl with C3H2+: A Possible Source of Carbon−Chlorine Compounds in Space

A theoretical study of the (ClC 3 H 3 ) + species has been carried out. Two different models, G2 and QCISD(T) at the B3LYP geometries, have been employed. Our calculations predict that the global minimum is an open-chain isomer ClHCCCH 2 +( 2 A), whereas five different open-chain structures are also quite stable, lying about 5.9-13.1 kcal/mol above the ground state. The lowest-lying cyclic isomer, with a three-membered carbon ring, lies about 18.3 kcal/mol higher in energy. These theoretical results allow the development of thermodynamic arguments about the reaction pathways of the process HCI + C 3 H 2 +. For the reaction of HCl with CCCH 2 +, formation of different chlorine-carbon compounds is exothermic and there are several mechanisms leading to these species that are barrier-free. However, production of carbocation compounds (cyclopropenyl cation, c-C 3 H 3 +, and propargyl cation, l-C 3 H 3 +) could be competitive with the formation of chlorine-carbon species. The predicted dominant channels for the reaction with both HCCCH + and c-C 3 H 2 + isomers are l-C 3 H 3 + and c-C 3 H 3 +, respectively. Therefore, only the reaction of HCl with the CCCH 2 + isomer seems to be a possible source of chlorine-carbon compounds in space.