Thermal cis–trans isomerization and decomposition of polyacetylene

Thermal cis-trans isomerization and decomposition of polyacetylene film prepared with a Ti(OC₄H₉)₄–Al(C₂H₅)₃ (Al/Ti = 4) system were investigated under inert gas or in vacuum by means of thermal analysis and infrared spectroscopy. Thermograms of differential thermal analysis of cis-polyacetylene revealed the existence of two exothermic peaks at 145 and 325°C and one endothermic peak at 420°C which were assigned to cis-trans isomerization, hydrogen migration accompanied with crosslinking reaction, and thermal decomposition, respectively. The isomerization was followed by infrared spectroscopy over the temperature range 75–115°C. The reaction did not obey simple kinetics. The apparent activation energy for the cis-trans isomerization was 17.0 kcal/mole for the polymer containing 88% cis configuration and increased with increasing trans content up to 38.8 kcal/mole for 80% trans content.     

A DFT study of a novel oxime anticancer trans platinum complex: Monofunctional and bifunctional binding to purine bases

The first and second substitution reactions binding of the anticancer drug trans‐[Pt((CH₃)₂C?NOH)((CH₃)₂CHNH₂)Cl₂] to purine bases were studied computationally using a combination of density functional theory and isoelectric focusing polarized continuum model approach. Our calculations demonstrate that the trans monoaqua and diaqua reactant complexes (RCs) can generate either trans‐ or cis‐monoadducts via identical or very similar trans trigonal‐bipyramidal transition‐state structures. Furthermore, these monoadducts can subsequently close by coordination to the adjacent purine bases to form 1,2‐intrastrand Pt‐DNA adducts and eventually distort DNA in the same way as cisplatin. Thus, it is likely that the transplatin analogues have the same mechanism of anticancer activity as cisplatin. For the first substitutions, the activation free energies of monoaqua complexes are always lower than that of diaqua complexes. The lowest activation energy for monoaqua substitutions is 16.2 kcal/mol for guanine and 16.5 kcal/mol for adenine, whereas the lowest activation energy for diaqua substitutions is 17.1 kcal/mol for guanine and 25.9 kcal/mol for adenine. For the second substitutions, the lowest activation energy from trans‐monoadduct to trans‐diadduct is 19.1 kcal/mol for GG adduct and 20.7 kcal/mol for GA adduct, whereas the lowest activation energy from cis‐monoadduct to cis‐diadduct is 18.9 kcal/mol for GG adduct and 18.5 kcal/mol for GA adduct. In addition, the first and second substitutions prefer guanine over adenine, which is explained by the remarkable larger complexation energy for the initial RC in combination with lower activation energy for the guanine substitution. Overall, the hydrogen‐bonds play an important role in stabilizing these species of the first and second substitutions. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

An ab initio study of the electronic structure of diimide

Ab initio calculations on the structure and geometry of the three isomers of N₂H₂ (trans-diimide, cis-diimide, and 1,1-dihydrodiazine) were performed both on HF and CI level using gaussian basis sets with polarization functions. The trans and cis isomers have singlet ground states; the trans isomer is found to be lower in energy than the cis isomer by 6.9 kcal/mol (HF) and 5.8 kcal/mol (CI), respectively. The barrier for the trans-cis isomerization is predicted to be 56 (HF) and 55 (CI) kcal/mol. H₂ N=N has a triplet ground state with a non-planar equilibrium geometry and a rather long NN bond of 1.34 Å. Its lowest singlet state, however, is planar with an NN double bond of 1.22 Å; it is found to lie about 3 kcal/mol above the triplet and 26 kcal/mol above the singlet ground state of trans-diimide.     

A force field study of the chemical reaction between ethylene and cis-N2H2

The fully optimized geometry of the activated complex which occurs as an intermediate in the concerted H-transfer reaction between C₂H₄ and cis-N₂H₂ has been determined using the ab initio FORCE method of Pulay. The activation energy for the synchronous transfer of two hydrogen atoms from cis-N₂H₂ to ethylene is found to be 18.8kcal/mol, i.e. substantially lower than the previously estimated energy barrier of around 60 kcal/mol. The same method applied to trans-N₂H₂ and semilinear N₂H₂ gave an isomerization energy of 49.7 kcal/mol indicating that the isomerization of trans-N₂H₂ to the cis form might be the overall rate-controlling step.     

On the use of electrostatic potential derived charges in molecular mechanics force fields. The relative solvation free energy of cis- and trans-N-methyl-acetamide

We have carried out free energy perturbation calculations on the relative solvation free energy of cis- and trans-N-methyl-acetamide (NMA). Experimentally, the solvation free energy difference has been found to be near zero. Using 6-31G* ab initio electrostatic potential derived charges for both the cis and trans conformations, we calculate a solvation free energy difference of 0.1 ± 0.1 kcal/mol. Using the 6-31G* charges derived for the trans conformation for both the cis and trans models leads to a solvation free energy difference of 0.9 ± 0.1 kcal/mol, compared to the value of 2.2 kcal/mol determined for the OPLS model for trans-NMA.     

Ab initio MO and TST calculations for the rate constant of the HNO+NO2→HONO+NO reaction

Potential-energy surfaces for various channels of the HNO+NO₂ reaction have been studied at the G2M(RCC,MP2) level. The calculations show that direct hydrogen abstraction leading to the NO+cis-HONO products should be the most significant reaction mechanism. Based on TST calculations of the rate constant, this channel is predicted to have an activation energy of 6–7 kcal/mol and an A factor of ca. 10⁻¹¹ cm³ molecule⁻¹ s⁻¹ at ambient temperature. Direct H-abstraction giving NO+trans-HONO has a high barrier on PES and the formation of trans-HONO would rather occur by the addition/1,3-H shift mechanism via the HN(O)NO₂ intermediate or by the secondary isomerization of cis-HONO. The formation of NO+HNO₂ can take place by direct hydrogen transfer with the barrier of ca. 3 kcal/mol higher than that for the NO+cis-HONO channel. The formation of HNO₂ by oxygen abstraction is predicted to be the least significant reaction channel. The rate constant calculated in the temperature range 300–5000 K for the lowest energy path producing NO+cis-HONO gave rise to © 1998 John Wiley & Sons, Inc. Int J Chem Kinet 30: 729–736, 1998     

All-electron SCF LCAO MO calculations on various conformations of cis- and trans-stilbene

Ab initio SCF calculations of cis- and trans-stilbene at different conformations were performed using two program systems. Minimal energy is obtained for cis-stilbene when the phenyl rings are rotated by 52 ° out of the molecular plane. The deviation from planarity due to steric hindrance is smaller for the trans isomer yielding a rotational angle of 19 °. The trans isomer is calculated to be more stable by 5.7 kcal/mole than the cis isomer, confirming the experimental estimate according to which the energy of isomerization is about 3 kcal/mole. This is an improvement over semiempirical calculations which predict a lower energy for the trans configuration.     

Nucleophilic Reactions at Tertiary Carbon. Part 1. The 1,2-dimethyl-1-cyclohexyl cation

Stereoisomeric ion pairs are implicated as intermediates in the solvolysis of cis and trans-1-chloro-1,2-dimethylcyclohexane, cis- 4 and trans- 4 , respectively. This follows from the rates and products of these stereoisomeric tertiary chlorides in 80% ethanol and 50% acetone. The composition of elimination and substitution products from cis- 4 and trans- 4 differs markedly and the differences are accentuated by silver ion. Furthermore, substitution products are formed with predominant inversion of configuration. The equilibrium constant for isomerization of cis- 4 and trans- 4 shows the latter to be more stable by 0.7 kcal/mol. Since the solvolysis rates of the chlorides are equal, the transition state for trans- 4 is also more stable by 0.7 kcal. By inference the intermediates differ by a similar amount of energy which is ascribed to more efficient solvation of the trans ion pair 13 .     

Electron-Transfer-Catalyzed cis → trans Isomerization of 1,1′-Azonorborane. Prototype of a reversible two-stage storage system

ESR and cyclic voltammetry investigations show that isomerization of the radical cation of cis-1,1′-azonorbornane (cis- 1 ) to the trans-radical ion proceeds too fast in solution for direct investigation of the cis-radical ion even at ?78°. The facile isomerization of the radical cation is in agreement with PM 3 calculations proposing an activation barrier of only 17 kJ/mol. As a consequence, quantitative cis → trans isomerization of 1,1′-azonorbornane can effectively be accomplished by addition of catalytic amounts of one-electron oxidants. This is the first evidence for a radical-cation-catalyzed cis → trans isomerization of azo compounds.     

Hydrogen-transfer polymerization of cis- and trans-crotonamides

cis- and trans-Crotonamides were polymerized in the presence of sodium tert-butoxide in pyridine. It was found that both monomers undergo concurrent geometrical isomerization as well as polymerization. Polymers resulting from these isomeric monomers had identical microstructures. The rates of both polymerization and isomerization were evaluated from kinetic measurements. Kinetic investigations have also shown that the specific first-order rate coefficient was independent of the isomer compositions and was identical for cis and trans monomers. The activation enthalpy was evaluated to be 15.0 kcal/mole.     

Theoretical investigations of molecules composed only of fluorine,oxygen and nitrogen: determination of the equilibrium structures of FOOF, (NO)2 and FNNF and the transition state structure for FNNF cis-trans isomerization

The deficiencies of common ab initio methods for the reliable prediction of the equilibrium structures of compounds composed of only the fluorine, oxygen and nitrogen atoms are investigated. Specifically, the importance of using large one-particle basis sets with multiple sets of polarization functions has been studied. Additionally, the need for a set of f basis functions was investigated. Several different single reference electron correlation methods have been tested in order to determine whether it is possible for a single reference based method to be routinely used on such chemical systems. These electron correlation methods include second order Møller-Plesset perturbation theory (MP2), singles and doubles configuration interaction (CISD), the coupled pair functional (CPF) approach and singles and doubles coupled cluster (CCSD) theory. The molecular systems studied include difluoroperoxide (FOOF), the cis form of the NO dimer, cis and trans difluorodiazene (FNNF) and the transition state to interconversion of the cis and trans isomers of FNNF. To the best of our knowledge, this is the first time that the cis-trans isomerization transition state has been reported. At the highest level of theory employed, the equilibrium structures of cis and trans FNNF agree very well with the experimental structures. However, the barrier to interconversion is predicted to be 65 kcal/mole, which is substantially higher than the experimental activation energy of 32 kcal/mole. Potential sources of error are discussed. A new diagnostic method for determining a priori the reliability of single reference based electron correlation methods is suggested and discussed.Contribution CCQC No. 36     

Theoretical study of thermal decomposition of azomethane

Summary.  Thermal one- and two-bond dissociation processes of cis- and trans-azomethane were studied by ab initio computation with DZP and TZ2P basis sets, using the d(N–C) bond lengths as the reaction coordinates. The geometries were optimized at the MP2 level, and the dissociation energies obtained exploiting a single-point, fourth-order M?ller–Plesset calculations [MP4SDTQ/TZ2P]. At this level of theory including zero-point energies, the trans-isomer is by 9.3 kcal/mol more stable than the cis-isomer. The results show that the energetically more favourable one-bond cleavage proceeds without transition state with the predicted bond dissociation energy D ₀ of 47.8 kcal/mol for trans-azomethane and 38.5 kcal/mol for cis-azomethane. With calculated barrier heights the unimolecular dissociation rate constants have been determined by means of the RRKM theory. The second-order saddle points localized for synchronous decomposition pathways lie 13 (trans)-23(cis) kcal/mol above the one-bond dissociation energies [MP2/DZP]. Received May 28, 1996/Final version received November 1, 1996 / Accepted November 1, 1996     

Determination of the geometric structure of three substituted polyacetylenes: Polymethylacetylene,polypentylacetylene, and poly(tbutylacetylene)

The geometric structure of polymethylacetylene (PMA), polypentylacetylene (PPA), and poly(t-butylacetylene) (PTA) was investigated by ¹H NMR, ¹³C NMR, and IR spectroscopies. It was shown that both NMR techniques can be used to determine the trans isomer content of PPA and PTA, whereas the ¹H NMR and IR methods can be used for PMA. A calibration curve was constructed by using the 965- and 720-cm^?1 bands of the IR spectrum of PPA, and could be used in future work for the same purpose if the samples had molecular weights similar to that of the one used in this study. The isomerization kinetics of PTA was investigated and cis^→ trans activation energies of 88 and 121 kJ/mol were calculated in solution and in the solid state, respectively. Heat treatment of the PMA and PPA samples always leads to a cis^→ trans isomerization with a 100% trans content under extreme conditions. Moreover, a cis^→ trans isomerization of PTA was induced in CCl₄, CDCl₃, toluene, and benzene, but a trans^→ cis isomerization was induced in decalin. The reversible isomerization of PTA covered a trans isomer concentration ranging form 25 to 60%.     

A theoretical study of the chemical reaction between ethylene and N2H2

The interaction between the molecules ethylene and cis-N₂H₂ has been studied using a gaussian basis in a series of ab initio SCF calculations. The results obtained indicate that the synchronous hydrogen transfer reaction is a one-step reaction having an activation energy of around 60 kcal/mol. Our results do not lend support to the hypothesis that the rate of the overall reaction between C₂H₄ and N₂H₂ is controlled by the rate of isomerization of trans-diimide to the cis form.     

The photoisomerization of retinal

Abstract— –Quantum efficiencies have been measured for the photoisomerization of four stereoisomers of retinal (all-trans, 13-cis, 11 cis, and 9-cis) in two solvents at different wavelengths of irradiation and at various temperatures. In heane at 25°C the quantum efficiencies for isomerization at 365 nm are: 9-cis to trans, 0.5; 13-cis to trans, 0.4; 11-cis to trans, 0.2; all-trans to monocis isomers, 0.2-0.06, depending upon assumptions made regarding the stereo-isomeric composition of the product. These values vary somewhat with the wavelength of the irradiating light. The quantum efficiency for the photoisomerization of all-trans retinal in hexane decreases by a factor of 30 when the temperature is lowered from 25° to – 65°C; the activation energy for this photoisomerization is about 5 kcal/mole. The quantum efficiencies for the isomerization of the monocis isomers to all-trans retinal in hexane are virtually independent of temperature. In ethanol the rates of photoisomerization from trans to cis or cis to trans depend only slightly on the temperature between 25° and – 65°C. The photosensitivities of the stereoisomers of retinal are of the same order of magnitude as those of the retinylidene chromophores of rhodopsin (11 -cis), metarhodopsin I (all-trans), and isorhodopsin (9-cis); but it is not yet possible to derive the photochemistry of rhodopsin uniquely and quantitatively from that of retinal.     

Quantum chemical modeling of the cis-trans isomerization of the allyl ligand in Ni(η3-C3H5)2 in the presence of norbornadiene

Quantum chemical (DFT/PBE) modeling of the cis-trans isomerization of the allyl ligand in bis(η³-allyl)nickel in the presence of norbornadiene revealed that the type of coordination of the norbornadiene ligand affects the energy parameters of its isomerization. The Gibbs energies of activation of the rate-limiting step for different isomerization pathways range from 23.7 to 27.8 kcal mol^?1.     

Solvent dependent photo-isomerization of 4-dimethylaminoazobenzene carboxylic acid

We have observed reversible trans–cis photo-isomerization behaviors of 4-dimethylaminoazobenzene carboxylic acid (4DAzC) in ethyl acetate by alternating irradiations at 370 and 430 nm. The photo-isomerization from trans- to cis-isomer was found to be strongly solvent dependent and not to occur efficiently in water and ethanol. Also photo-isomerization from cis- to trans-isomer was occurred upon 370 nm illumination or via thermal relaxation. The activation energy for the thermal isomerization from cis to trans-isomer was estimated to be 49.2 kJ/mol in ethyl acetate from the temperature-dependent kinetic absorption measurements.     

Theoretical Study of the Catalytic Cycle for Ethylene Hydrogenation on a Dipalladium Cluster

A theoretical study of the potential energy surface is carried out for the catalytic cycle of ethylene hydrogenation on a Pd₂cluster using the reaction-path Hamiltonian. The catalytic cycle consists of five related reactions involving ten stationary points. The isomerization of the bridged Pd₂H₂complex into the transcomplex with a maximal barrier of 21.5 kcal/mol rather than the activation of the H–H bond is the most important reaction step. A conclusion is drawn that catalysts based on dipalladium complexes in which the dihydride product readily forms a transform can be active in ethylene hydrogenation.     

Kinetics of the thermal isomerization of 1,1,2‐trimethylcyclopropane

The Arrhenius parameters for the gas phase, unimolecular structural isomerizations of 1,1,2‐trimethylcyclopropane to three isomeric methylpentenes and two dimethylbutenes have been determined over a wide range of temperatures, 688–1124 K, using both static and shock tube reactors. For the overall loss of reactant, E_a = 63.7 (± 0.5) kcal/mol and log₁₀ A = 15.28 (± 0.12). These values are higher by 2.6 kcal/mol and 0.7–0.8 than previously reported from experimental work or predicted from thermochemical calculations. E_a for the formation of trans‐4‐methyl‐2‐pentene is 1.5 kcal/mol higher than E_a for the formation of the cis isomer, which is identical to the E_a difference previously reported for the formation of trans‐ and cis‐2‐butene from methylcyclopropane. Substitution of methyl groups for hydrogen atoms on the cyclopropane ring is expected to weaken the C? C ring bonds, and it has been reported previously that activation energies for structural isomerizations of methylcyclopropanes do decrease substantially over the series cyclopropane > methylcyclopropane > 1,1‐ or 1,2‐dimethylcyclopropane. However, the present study shows that the trend does not continue beyond dimethylcyclopropane isomerization. Besides reductions in C? C bond energy, steric interactions may be increasingly important in determining the energy surface and conformational restrictions near the transition state in isomerizations of the more highly substituted methylcyclopropanes. © 2006 Wiley Periodicals, Inc. Int J Chem Kinet 38: 475–482, 2006     

Quantum mechanical study of energetics and mechanisms of cis–trans isomerization of some four-membered heterocycles

Ab initio quantum mechanical calculations using density functional (B3LYP) method and 6-311G** basis set have been performed on two cis and trans conformers of 2,4-diphenyl thietane dioxide (DPTD), 2,4-diphenyl thietane (DPT), 2,4-diphenyl azetidine (DPA) and 2,4-diphenyl oxetane (DPO). The calculated stability energy for cis–trans isomerization in gas phase and in different solvents such as benzene, DMSO, water and methanol indicated that the cis conformer is more stable than trans in all above-mentioned compounds about 11–2 kcal mol^?1. In the next step, a transition states for cis–trans inter-conversion for all four-membered heterocycles (DPTD, DPT, DPA and DPO) were proposed in methanol as solvent. Thermodynamic functions such as standard enthalpies of isomerization (?Hº_iso), standard entropy of isomerization (?Sº_iso) and standard Gibbs free energy of isomerization (?Gº_iso) for all studied compounds were also evaluated. The calculation showed that the conversion of trans to cis isomer is exothermic and spontaneous. In all calculations, solvent effects were considered using a polarized continuum model.