Oxygen‐Initiated Stereoselective Thermal Isomerisation of a Cyclobutane Derivative in the Solid State

Solid‐state [2+2] photochemical cycloaddition reactions have been extensively studied after the classical work of Schmidt in the 1960s. Of these, trans‐1,2‐bis(4′‐pyridyl)ethylene (bpe) is one of the well‐studied alkenes to synthesize tetrakis(4‐pyridyl)cyclobutane (tpcb). However, almost all the solid‐state [2+2] cycloaddition reactions of bpe yielded, almost exclusively, one of the four possible isomers, namely, the rctt‐tpcb (r=regio c=cis and t=trans). Here we describe a stereoselective synthesis of the tetrahedrally disposed rtct‐tpcb by the solid‐state thermal isomerization of the rctt‐isomer in atmospheric air. We propose that this isomerization occurs through a topochemical unimolecular mechanism by a radical chain pathway, initiated by molecular oxygen. This is supported by the nature of products formed in air and nitrogen, detection of a radical in ESR spectral studies, ESI‐MS crossover experiments, VT PXRD studies along with QM, MD and docking calculations. The formation of a unique isomer by thermal isomerization may be a general phenomenon to quantitatively synthesize other useful stereoisomers from the existing isomers of cyclobutane derivatives.     

Barrierless Single‐Electron‐Induced cis–trans Isomerization

Lowering the activation energy of a chemical reaction is an essential part in controlling chemical reactions. By attaching a single electron, a barrierless path for the cis–trans isomerization of maleonitrile on the anionic surface is formed. The anionic activation can be applied in both reaction directions, yielding the desired isomer. We identify the microscopic mechanism that leads to the formation of the barrierless route for the electron‐induced isomerization. The generalization to other chemical reactions is discussed.     

Isomer‐dependent reaction mechanisms of cyclic ether intermediates: cis‐2,3‐dimethyloxirane and trans‐2,3‐dimethyloxirane

Oxiranes are a class of cyclic ethers formed in abundance during low‐temperature combustion of hydrocarbons and biofuels, either via chain‐propagating steps that occur from unimolecular decomposition of β‐hydroperoxyalkyl radicals (β‐?QOOH) or from reactions of H?O with alkenes. The cis‐ and trans‐isomers of 2,3‐dimethyloxirane are intermediates of n‐butane oxidation, and while rate coefficients for β‐?QOOH → 2,3‐dimethyloxirane + ?OH are reported extensively, subsequent reaction mechanisms of the cyclic ethers are not. As a result, chemical kinetics mechanisms commonly adopt simplified chemistry to describe the consumption of 2,3‐dimethyloxirane by convoluting several elementary reactions into a single step, which may introduce mechanism truncation error—uncertainty derived from missing or incomplete chemistry. The present research examines the isomer dependence of 2,3‐dimethyloxirane reaction mechanisms in support of ongoing efforts to minimize mechanism truncation error. Reaction mechanisms are inferred via the detection of products from Cl‐initiated oxidation of both cis‐2,3‐dimethyloxirane and trans‐2,3‐dimethyloxirane using multiplexed photoionization mass spectrometry (MPIMS). The experiments were conducted at 10 Torr and temperatures of 650 K and 800 K. To complement the experiments, the enthalpies of stationary points on the ?R + O₂ surfaces were computed at the ccCA‐PS3 level of theory. In total, 28 barrier heights were computed on the 2,3‐dimethyloxiranylperoxy surfaces. Two notable aspects are low‐lying pathways that form resonance‐stabilized ketohydroperoxide‐type radicals caused by ?QOOH ring‐opening when the unpaired electron is localized adjacent to the ether group, and cis‐trans isomerization of ?R and ?QOOH radicals, via inversion, which enable reaction pathways otherwise restricted by stereochemistry. Several species were identified in the MPIMS experiments from ring opening of 2,3‐dimethyloxiranyl radicals. Neither of the two conjugate alkene isomers prototypical of ?R + O₂ reactions were detected. Products were also identified from decomposition of ketohydroperoxide‐type radicals. The present work provides the first analysis of 2,3‐dimethyloxirane oxidation chemistry and reveals that consumption pathways are complex and require the expansion of submechanisms in chemical kinetics mechanisms.     

Ring opening of pyridines: the pseudo‐cis and pseudo‐trans isomers of tetra‐n‐butylammonium 4‐nitro‐5‐oxo‐2‐pentenenitrilate

The reaction of 2‐chloro‐5‐nitropyridine with two equivalents of base produces the title carbanion as an intermediate in a ring‐opening/ring‐closing reaction. The crystal structures of the tetra‐n‐butylammonium salts of the intermediates, C₁₆H₃₆N⁺·C₅H₃N₂O₃⁻, revealed that pseudo‐cis and pseudo‐trans isomers are possible. One crystal structure displayed a mixture of the two isomers with approximately 90% pseudo‐cis geometry and confirms the structure predicted by the S_N(ANRORC) mechanism. The pseudo‐cis intermediate undergoes a slow isomerization over a period of months to the pseudo‐trans isomer, which does not have the appropriate geometry for the subsequent ring‐closing reaction. The structure of the pure pseudo‐trans isomer is also reported. In both isomers, the negative charge is highly delocalized, but relatively small differences in C—C bond distances indicate a system of conjugated double bonds with the nitro group bearing the negative charge. The packing of the two unit cells is very similar and largely determined by the interactions between the planar carbanion and the bulky tetrahedral cation.     

Thermoanalytical Study of Linkage Isomerism in Coordination Compounds. Part 7. A DSC and DFT Investigation of Solid‐state Linkage Isomerization in Bis(thiocyanato)‐bipyridineplatinum(II) Complex

The linkage isomerization of [Pt(SCN)₂(bipy)] complex in solid‐state was investigated by differential scanning calorimetry (DSC) at diverse heating rates. The conversion of the bis‐thiocyanato isomer (–SCN)₂ to the bis‐isothiocyanato isomer (–NCS)₂ was accompanied by the appearance of an exothermic peak. However, no DSC peak was obtained for isomerization of the (–NCS)₂. The results imply that the (–SCN)₂ isomer is metastable which can convert to the stable isomer (–NCS)₂ at elevated temperatures. Assuming a two‐stage irreversible isomerization, the enthalpy changes of the first stage ΔH _SCN¹ and also second stage ΔH _SCN² isomerization were obtained (–2.99 ± 0.44 and –2.81 ± 0.45 kJ · mol^–1, respectively) using the mathematical resolution of the observed DSC peaks. The thermokinetic parameters of this conversion were determined using Kissinger method. The activation energy values for the first and second stages of isomerization are evaluated, 101.78 ± 7.58 and 106.26 ± 5.87 kJ · mol^–1, respectively. The low values of the activation enthalpy, ΔH ^? and the high negative activation entropy ΔS ^?, obtained by Eyring equation, supported an associative mechanism. A DFT study was employed to detect the electronic structures and the thermodynamic stabilities of the three linkage isomers and the transition states.     

Chlorophyll‐Derived Yellow Phyllobilins of Higher Plants as Medium‐Responsive Chiral Photoswitches

The fall colors are signs of chlorophyll breakdown, the biological process in plants that generates phyllobilins. Most of the abundant natural phyllobilins are colorless, but yellow phyllobilins (phylloxanthobilins) also occur in fall leaves. As shown here, phylloxanthobilins are unique four‐stage photoswitches. Which switching mode is turned on is controlled by the molecular environment. In polar media, phylloxanthobilins are monomeric and undergo photoreversible Z/E isomerization, similar to that observed for bilirubin. Unlike bilirubin, however, the phylloxanthobilin Z isomers photodimerize in apolar solvents by regio‐ and stereospecific thermoreversible [2+2] cycloadditions from self‐assembled hydrogen‐bonded dimers. X‐ray analysis revealed the first stereostructure of a phylloxanthobilin and its hydrogen‐bonded self‐templating architecture, helping to rationalize its exceptional photoswitch features. The chemical behavior of phylloxanthobilins will play a seminal role in identifying biological roles of phyllobilins.     

Multiple‐Well,multiple‐path unimolecular reaction systems. I. MultiWell computer program suite

Unimolecular reaction systems in which multiple isomers undergo simultaneous reactions via multiple decomposition reactions and multiple isomerization reactions are of fundamental interest in chemical kinetics. The computer program suite described here can be used to treat such coupled systems, including the effects of collisional energy transfer (weak collisions). The program suite consists of MultiWell, which solves the internal energy master equation for complex unimolecular reactions systems; DenSum, which calculates sums and densities of states by an exact‐count method; MomInert, which calculates external principal moments of inertia and internal rotation reduced moments of inertia; and Thermo, which calculates equilibrium constants and other thermodynamics quantities. MultiWell utilizes a hybrid master equation approach, which performs like an energy‐grained master equation at low energies and a continuum master equation in the vibrational quasicontinuum. An adaptation of Gillespie's exact stochastic method is used for the solution. The codes are designed for ease of use. Details are presented of various methods for treating weak collisions with virtually any desired collision step‐size distribution and for utilizing RRKM theory for specific unimolecular rate constants. © 2001 John Wiley & Sons, Inc. Int J Chem Kinet 33: 232–245, 2001     

Tetramethyl‐m‐benziporphodimethene and Isomeric α,β‐Unsaturated γ‐Lactam Embedded N‐Confused Tetramethyl‐m‐benziporphodimethenes

The condensation reaction of α,α′‐dihydroxy‐1,3‐diisopropylbenzene, pyrrole, and an aldehyde leads to the formation of tetramethyl‐m‐benziporphodimethene and outer α‐pyrrolic carbon oxygenated N‐confused tetramethyl‐m‐benziporphodimethenes containing a γ‐lactam ring in the macrocycle. Two isomers with the carbonyl group of the lactam ring either close to (O‐Up) or away from (O‐Down) the neighboring sp³ meso carbon were synthesized and characterized. The single crystal X‐ray diffraction analysis on the regular and γ‐lactam containing tetramethyl‐m‐benziporphodimethenes showed highly distorted macrocycles for all compounds. For O‐Up and O‐Down isomers, dimeric structures, assembling by intermolecular hydrogen‐bonding interactions through lactam rings, were observed in the solid state. Fitting the concentration dependent chemical shifts of the outer NH proton using the non‐linear regression method give a maximum association constant of 108.9 M ^?1 for the meso 4‐methylcarboxyphenyl substituted O‐Down isomer. The DFT calculations concluded that the O‐Up isomer is energetically more stable, and the keto form is more stable than the enol form.     

Travelling‐wave ion mobility and negative ion fragmentation of high‐mannose N‐glycans

The isomeric structure of high‐mannose N‐glycans can significantly impact biological recognition events. Here, the utility of travelling‐wave ion mobility mass spectrometry for isomer separation of high‐mannose N‐glycans is investigated. Negative ion fragmentation using collision‐induced dissociation gave more informative spectra than positive ion spectra with mass‐different fragment ions characterizing many of the isomers. Isomer separation by ion mobility in both ionization modes was generally limited, with the arrival time distributions (ATD) often showing little sign of isomers. However, isomers could be partially resolved by plotting extracted fragment ATDs of the diagnostic fragment ions from the negative ion spectra, and the fragmentation spectra of the isomers could be extracted by using ions from limited areas of the ATD peak. In some cases, asymmetric ATDs were observed, but no isomers could be detected by fragmentation. In these cases, it was assumed that conformers or anomers were being separated. Collision cross sections of the isomers in positive and negative fragmentation mode were estimated from travelling‐wave ion mobility mass spectrometry data using dextran glycans as calibrant. More complete collision cross section data were achieved in negative ion mode by utilizing the diagnostic fragment ions. Examples of isomer separations are shown for N‐glycans released from the well‐characterized glycoproteins chicken ovalbumin, porcine thyroglobulin and gp120 from the human immunodeficiency virus. In addition to the cross‐sectional data, details of the negative ion collision‐induced dissociation spectra of all resolved isomers are discussed. Copyright © 2016 John Wiley & Sons, Ltd.     

Consecutive Chemical Activation Steps in the OH‐Initiated Atmospheric Degradation of Isoprene: An Analysis with Coupled Master Equations

The influence of a two‐step chemical activation on 1,5‐H and 1,6‐H shift reactions of hydroxyl‐peroxy radicals formed in the atmospheric photooxidation of isoprene was investigated by means of a master equation analysis. To account for multiple chemical activation processes, three master equations were coupled. The general approach of this coupling is described, and consequences for steady‐state regimes are examined. The specific calculations show that chemical activation has no substantial influence on the rate coefficients of the above‐mentioned reactions under tropospheric conditions. However, it is demonstrated that high‐pressure limits of the thermal rate coefficients instead of the falloff‐corrected values have to be used for kinetic modeling. This is a consequence of the continuous population of the high‐energy part of the isoprene‐OH‐O₂ adduct distribution by the forming reactions under steady‐state conditions. The rate coefficients of the isomerization reactions at T = 298 K were calculated to be k_3a^∞ = 1.5 × 10^?3 s^?1 (1,5‐H‐shift of the 1,2‐isomer) and k_4a^∞ = 6.5 s^?1 (1,6‐H‐shift of the (Z)‐1,4‐isomer). The calculated value of k_4a^∞ is three orders of magnitude larger than a recently reported experimentally observed rate coefficient for the hydrogen shift reactions of the hydroxyl‐peroxy intermediates. It is shown that this discrepancy is in part due to the fact that the experiment does not distinguish between different structural isomers. A comparison of the experimentally determined isotope effect with the calculated value shows a reasonable agreement.     

2‐(4′‐Pyridyl‐N‐oxide)‐Substituted Hemithioindigos as Photoresponsive Guests for a Super Aryl‐Extended Calix[4]pyrrole Receptor

We report the synthesis of two 2‐(4′‐pyridyl‐N‐oxide)‐substituted hemithioindigos (HTIs). We probed their photoisomerization by using UV/Vis and ¹H NMR spectroscopy techniques. Light irradiation at λ=450 nm provoked the isomerization of the HTI Z isomer to the E counterpart to a large extent (≈80 % at the photostationary state). ¹H NMR titration experiments revealed the formation of thermodynamically and kinetically stable 1:1 inclusion complexes of the (Z)‐HTI isomers with a super aryl‐extended host (association constant>10⁴ m ^?1). Photoirradiation at λ=450 nm of the inclusion complexes induced the isomerization of the bound HTI N‐oxide to afford the (E)‐HTI?calix[4]pyrrole complex. We determined accurate association constant values for the 1:1 inclusion complexes of the (Z)‐ and (E)‐HTI isomers by using isothermal titration calorimetry experiments. The results showed that the stability constants of the (E)‐HTI complexes were 2.2–2.8‐fold lower than those of the (Z)‐HTI counterparts, which explains the lack of light‐induced release of the former to the bulk solution.     

Synthesis and characterization of alkylated N‐vinylformamide monomers and their polymers

N‐alkyl‐N‐vinylformamide monomers (alkyl: n‐butyl, hexyl, decyl, and dodecyl) are synthesized in two steps: first, preparation of N‐vinylformamide potassium salt by the reaction of N‐vinylformamide (NVF) with potassium t‐butoxide, then reaction with alkyl bromide. All four monomers are liquid and are characterized by IR, ¹H NMR, ¹³C NMR, and mass spectra. They exist as rotomers in solution and a 2D NOE experiment on the N‐hexyl containing polymer shows the E isomer to be favored. The polymerizability of the four monomers is from good to fair, depending upon the length of alkyl chain on the N‐atom‐‐the longer the chain length, the lower lower the polymerizability of monomer. The hydrolysis of poly(N‐hexyl‐N‐vinylformamide) and poly(N‐dodecyl‐N‐vinylformamide) under acidic and basic conditions was examined. Studies show that hydrolytic cleavage of formyl groups of poly (N‐alkylated‐N‐vinylformamide) depends on the hydrophobicity of the alkyl substituent on the N‐atom under acidic conditions; both polymers were hydrolyzed to only a minor extent under alkaline conditions. The N‐alkylated monomers can copolymerize with NVF and demonstrate amphiphilic properties. The copolymers demonstrate a critical aggregation concentration above which they can solubilize a water insoluble dye; the N‐hexyl containing copolymer stabilizes a castor oil‐in‐water emulsion. © 2004 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 42: 4994–5004, 2004     

Facile Synthesis of 5‐Hexyl‐4‐methyl‐γ‐butyrolactone via Nef Reaction as a Key Step

A racemic cis/trans mixture of 5‐hexyl‐4‐methyl‐γ‐butyrolactone was easily synthesized from 1‐iodoheptane in four steps with inexpensive and readily available reagents. Our new synthesis method can be potentially employed for mass production of the 4‐methyl‐5‐hexyl‐γ‐butyrolactone as well as other poly‐alkyl substituted γ‐butyrolactones.     

Understanding the electronic reorganization in the thermal isomerization reaction of trans‐3,4‐dimethylcyclobutene. Origins of outward Pseudodiradical {2n + 2π} torquoselectivity

The thermal isomerization reaction of trans‐3,4‐dimethylcyclobutene (1,2,3,4‐DMC) to produce the isomer (2E, 4E)‐hexadiene have been studied using density functional theory at the B3LYP/6‐31+G level. For this reaction, two different channels of the conrotatory torquoselectivity allowing the formation of the two isomeric (E,E) and (Z,Z) have been characterized. The isomer (Z,Z) occurs through the inward conrotatory mechanism, whereas the isomer (E,E) occurs through the outward conrotatory mechanism. The outward conrotatory is favored by 11.3 kcal/mol with respect to inward conrotatory one. This behavior is consistent with the thermodynamic properties: enthalpy, free energy, and entropy calculated in both reaction pathways. The topological analysis of the electron localization function at the outward conrotatory transition state explicated the electronic reorganization through a pseudodiradical {2n + 2π} process and not a pericyclic reorganization. © 2012 Wiley Periodicals, Inc.     

Nanoscale Chemical Imaging of Reversible Photoisomerization of an Azobenzene‐Thiol Self‐Assembled Monolayer by Tip‐Enhanced Raman Spectroscopy

An understanding of the photoisomerization mechanism of molecules bound to a metal surface at the molecular scale is required for designing photoswitches at surfaces. It has remained a challenge to correlate the surface structure and isomerization of photoswitches at ambient conditions. Herein, the photoisomerization of a self‐assembled monolayer of azobenzene‐thiol molecules on a Au surface was investigated using scanning tunneling microscopy and tip‐enhanced Raman spectroscopy. The unique signature of the cis isomer at 1525 cm^?1 observed in tip‐enhanced Raman spectra was clearly distinct from the trans isomer. Furthermore, tip‐enhanced Raman images of azobenzene thiols after ultraviolet and blue light irradiation are shown with nanoscale spatial resolution, demonstrating a reversible conformational change. Interestingly, the cis isomers of azobenzene‐thiol molecules were preferentially observed at Au grain edges, which is confirmed by density functional theory.     

Complexation of 4‐dimethylaminoazobenzene with various kinds of cyclodextrins: Effects of cyclodextrins on the thermal cis‐to‐trans isomerization

On the basis of the change in electronic and induced circular dichroism spectra for complex formation, the complexation of 4‐dimethylaminoazobenzene (DAAB) with four kinds of cyclodextrins (α‐ and β‐cyclodextrin (CD), heptakis(2,6‐di‐O‐methyl)‐β‐cyclodextrin, and heptakis(2,3,6‐tri‐O‐methyl)‐β‐cyclodextrin) was studied in methanol–water and dimethyl sulfoxide–water mixtures. It was found that the trans and cis isomers of DAAB form two different types of complex (inclusion and lid type) with CDs, depending on the kinds of CDs and solvents. Further, we have examined the effect of CDs on the thermal cis‐to‐trans isomerization of DAAB. The accelerated or decelerated effect on the thermal isomerization was observed upon adding CDs. The effects of CDs on the thermal isomerization are discussed in connection with the complexation of the cis‐isomer of DAAB with CDs. © 2002 Wiley Periodicals, Inc. Int J Chem Kinet 34: 481–487, 2002     

Synthesis and isomerization studies of cyclotrisazobiphenyl

We report an efficient synthesis of cyclotris[(E)‐3′‐(biphenyl‐3‐yldiazenyl)] compounds (CTBs). An unsubstituted CTB molecule is accessible in four steps in 10 % yield overall, whereas a hexa(methoxymethyl ether) CTB analogue was prepared in nine steps (26 % yield). The final macrocyclization step was accomplished in up to 80 % yield by using a metal‐template effect. Furthermore, the photochromic properties were investigated, and all four isomers were detected and characterized by NMR spectroscopy. A strong influence from the solvent and the irradiation wavelength on the switching process was observed. Irradiation in pyridine yielded the highest amount of the all‐Z isomer in the photostationary state. For a full conversion to the all‐E isomer, the reaction has to be heated to 45 °C. The isomerization to the all‐E isomer is slow at room temperature, with a half‐life time of the all‐Z isomer of more than nine days in dimethyl sulfoxide (DMSO). Conditions were established to access each possible isomer as the major component in the photostationary state.     

A Thermo‐ and Photo‐Switchable Ruthenium Initiator For Olefin Metathesis

A ruthenium carbene complex bearing azobenzene functionality is reported. The complex exists in the form of two isomers differing by the size of the chelate ring. Both isomers were isolated by applying kinetic or thermodynamic control during the synthesis and characterized by X‐ray diffraction analysis. The isomerization of the complex was studied by UV/Vis spectroscopy. The stable isomer was tested as a catalyst in olefin metathesis. The complex was activated at about 100 °C to promote ring‐closing and ring‐opening polymerization metathesis reactions. The activation took place also at room temperature under middle ultraviolet radiation.     

An experimental and computational study on the dissociation behavior of hydroxypyridine N‐oxides in atmospheric pressure ionization mass spectrometry

A tandem mass spectrometric study of protonated isomeric hydroxypyridine N‐oxides was carried out with a hybrid quadrupole/time‐of‐flight mass spectrometer coupled with different atmospheric pressure ionization sources. The behavior observed in the collision‐induced dissociation (CID) mass spectra of the parent cations, was similar irrespective of the source employed. However, there were intrinsic differences in the intensities of the two fragments observed for each isomer. The major fragment because of elimination of a hydroxyl radical, dominated the CID spectra (in contrast with weaker water loss) at different energy thresholds. Therefore, it was possible to differentiate both isomers at collision energies above 13 eV by comparing the ratio of intensities of the major fragment relative to the precursor cation. In addition, quantum chemical calculations at the B3LYP/6‐31 + + G(d,p) level of theory were performed for the protonated isomers of hydroxypyridine N‐oxide and their radical cation products in order to gain insight into the major routes of dissociation. The results suggest that dissociation from the lowest triplet excited state of the protonated species would provide a reasonable rationalization for the difference in behavior of both isomers. Copyright © 2010 John Wiley & Sons, Ltd.     

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