Isomerization Pathways Research Articles

Theoretical Investigation of the E/Z Photoisomerization Pathway in 1-(2-Pyrrolyl)-2-(2-thienyl)ethylene.

Molecular-level understanding of photochemistry in simple vinylene-linked systems such as ethylene and stilbene has been a major area of research. However, the effect of replacing the two benzene rings by five-membered heterocyclic rings, thiophene and pyrrole, is yet to be reported. In the present theoretical study, our aim is to illustrate photoinduced processes in a vinylene-linked thiophene-pyrrole system. Computational studies are carried out at the RI-MP2/RI-ADC(2)/cc-pVTZ level to explore different isomerization pathways. Minimum-energy conical intersection (MECI) structures are categorized into two types: closed-ring and twisted-pyramidalized structures. Relaxation through the former MECIs is accessible only from the cis isomers. However, the latter MECIs are inaccessible due to high energy barriers along the linear interpolation in internal coordinate paths.

Gut microbial fatty acid isomerization modulates intraepithelial T cells.

The human gut microbiome constantly converts natural products derived from the host and diet into numerous bioactive metabolites1-3. Dietary fats are essential micronutrients that undergo lipolysis to release free fatty acids (FAs) for absorption in the small intestine4. Gut commensal bacteria modify some unsaturated FAs-for example, linoleic acid (LA)-into various intestinal FA isomers that regulate host metabolism and have anticarcinogenic properties5. However, little is known about how this diet-microorganism FA isomerization network affects the mucosal immune system of the host. Here we report that both dietary factorsand microbial factors influence the level of gut LA isomers (conjugated LAs (CLAs)) and that CLAs in turn modulate a distinct population of CD4+ intraepithelial lymphocytes (IELs) that express CD8αα in the small intestine. Genetic abolition of FA isomerization pathways in individual gut symbionts significantly decreases the number of CD4+CD8αα+ IELs in gnotobiotic mice. Restoration of CLAs increases CD4+CD8αα+ IEL levels in the presence of the transcription factor hepatocyte nuclear factor 4γ (HNF4γ). Mechanistically, HNF4γ facilitates CD4+CD8αα+ IEL development by modulating interleukin-18 signalling. In mice, specific deletion of HNF4γ in T cells leads to early mortality from infection by intestinal pathogens. Our data reveal a new role for bacterial FA metabolic pathways in the control of host intraepithelial immunological homeostasis by modulating the relative number of CD4+ T cells that were CD4+CD8αα+.

Rotation of the η3‐Propargyl Ligand in [(C6Me5H)M(CO)2(η3‐C3H3)]+ (M=Cr, Mo, W) Complexes

AbstractThe dynamic behaviour of η3‐propargyl ligand in [(C6Me5H)M(CO)2(η3‐C3H3)]+ (comp : M, M=Cr, Mo, W) complexes was systematically studied using computational chemistry approaches. Two isomerization pathways were assessed: a simple rotation of the propargyl fragment around the metal‐ligand axis and the η3‐η1 hapticity slippage of the propargyl ligand. The former mechanism possesses the activation energies of +25.9 (comp : Cr), +20.7 (comp : Mo), and +20.3 kcal mol−1 (comp : W) and is feasible at near‐room temperatures. The η3‐η1 partial decoordination requires essentially the same energy for comp : Cr (+25.8 kcal mol−1) but is hindered for comp : Mo and comp : W (>+30 kcal mol−1). To analyse the factors that influenced these trends, the binding of analogous comp : M and η3‐allyl complexes was studied using the local energy decomposition method.

A bisphotochromic system featuring two modes of photoisomerization controlled by solvent polarity

Combining two or more photoswitchable units in one molecule results in multiphotochromic hybrids with attractive sophisticated performance. On-demand switching of light-induced isomerization pathways for such systems by change of solvent polarity is a virtually unexplored phenomenon. Using NMR spectroscopy, we have demonstrated that the competition between 6π-electrocyclization and E-/Z-isomerization of 2,3-bis(2,5-dimethylthiophen-3-yl)-5-(4-dialkylaminobenzylidene)cyclopent-2-en-1-ones depends on the solvent's nature. Cyclization of diarylethene predominates in less polar solvents, whereas isomerization of the arylidene moiety prevails in polar media. This result could be the starting point for the development of multiphotochromic hybrids with efficient solvent-controllable selectivity of photoreactions.

Ring buckling and C=N isomerization pathways for efficient photoprotection in two nature-inspired UVA sunscreens revealed through ultrafast dynamics and high-level calculations.

Sunscreens provide a frontline defense for our DNA against the damage caused by ultraviolet (UV) radiation. The active ingredients in topically applied sunscreens that provide this defense are UV filters, which preferentially absorb or reflect UV radiation before it penetrates the skin and interacts with photosensitive nucleic acids. However, there are concerns related to human and environmental toxicity of current UV filters, and consequently a shift toward nature-inspired, particularly microbial, UV filters. In this paper, new physical insight is provided into the fundamental mechanisms of photoprotection in two synthetic analogs of mycosporine-like amino acid-type UV filters, demonstrating new methods of protection that are distinct from those of current commercial sunscreens, extending previous work in this area. Transient absorption measurements (both transient electronic absorption spectroscopy and transient vibrational absorption spectroscopy) are combined with steady-state studies and high-level computational results to aid our mapping of the experimentally derived lifetimes to real-time photodynamic processes. The conclusions reached here pave the way toward developing new and more efficient biomimetic DNA photoprotectant materials.

Study on the initial pyrolysis kinetics of strained polycyclic hydrocarbons

Strained polycyclic hydrocarbons are one of the most important classes of high-energy density fuels. In this work, the thermodynamics and initial pyrolysis kinetics of five strained polycyclic hydrocarbons, which are isomers of JP-10 and are linearly aggregates of two cyclopropyl rings and one cyclobutyl ring, were investigated using quantum chemical computations. The initial pyrolysis reactions include ring bond breaking and bridge bond breaking. The ring bond breaking reactions include a diradical pathway which is the direct C-C bond breaking to produce a diradical and an isomerization pathway involving concert bond breaking and H-atom transfer, and the bridge bond breaking reactions lead to two radicals. Our potential energy calculation shows that the ring bond breaking reactions are much more energetically favorable than the bridge bond breaking reactions, which can be neglected in the initial pyrolysis process of strained polycyclic hydrocarbons. The rate constants of the ring bond breaking reactions were computed using variational transition state theory (VTST) or transition state theory (TST). Our calculated results demonstrated that ring bond breaking reactions of the three-membered ring are competitive with that of the four-membered ring. The studied reactions are divided into classes depending on the size of the rings (three- or four-membered ring) and the types of the carbon atoms of the breaking C-C bond (Cs-Cs, Cs-Ct, Ct-Ct and Cq-Cs). Reaction rate rules are established for each class, which are useful for the mechanism generation for analogous strained polycyclic hydrocarbons. Thermodynamic properties including net calorific values per mole, gravimetric net heat of combustion and impulse time of our studied strained polycyclic hydrocarbons are higher than those of JP-10. A comparison of the initial pyrolysis kinetics of our studied strained polycyclic hydrocarbons with the isomer JP-10 indicates that these compounds may be easier to pyrolyze.

Selective control of donor-acceptor Stenhouse adduct populations with non-selective stimuli

Selective control of donor-acceptor Stenhouse adduct populations with non-selective stimuli

Isotope Effects in the Zundel-Eigen Isomerization of H+(H2O)6.

The isomerization pathway between the energetically low-lying Zundel and Eigen isomers of the protonated water hexamer was investigated using high-level ab initio calculations including a treatment of zero-point corrections. On the basis of these calculations, the Zundel-Eigen isomerization was found to proceed through a stable intermediate isomer, which consists of a four-membered ring with two single acceptor water molecules. The inclusion of vibrational zero-point energy is shown to be important for accurately establishing the relative energies of the three relevant isomers involved in the Zundel-Eigen isomerization. Diffusion Monte Carlo calculations including anharmonic vibrational effects show that all three isomers of H+(H2O)6 and D+(D2O)6 have well-defined structures. The energetic ordering of the three isomers changes upon deuteration. The implications of these results for the vibrational spectra of H+(H2O)6 and D+(D2O)6 are also discussed.

Deciphering the Olefin Isomerization-Polymerization Paradox of Palladium(II) Diimine Catalysts: Discovery of Simultaneous and Independent Pathways of Olefin Isomerization and Living Polymerization

This work elucidates a long-standing unexplained paradox commonly observed within the polymerization of α-olefin using palladium (Pd)(II)-diimine catalysts, in which isomerization and living polymerization of α-olefins are both observed. With a classical mechanistic understanding of these complexes, this behavior is often dismissed and interpreted as experimental error. Herein, we present a comprehensive mechanistic investigation into this phenomenon that supports the existence of a novel mechanistic pathway for Pd(II)-diimine complexes. Part one of the mechanistic study lays the foundation of the proposed mechanism, in which neutral Pd(II)-diimine complexes were found to exhibit a moderate to good catalytic activity for olefin isomerization of α-olefins despite the established notion that catalyst activation is required. Extensive experimental and computational studies reveal the possibility of a partial dissociation of the diimine ligand, which frees up one coordination site and enables coordination-insertion. This finding is significant as the coexistence of two reactive coordination sites at the palladium center becomes a valid proposal for the activated cationic Pd(II)-diimine complexes. In part two, we examined and validated the simultaneously observed α-olefin isomerization and living polymerization using the cationic Pd(II)-diimine catalyst, which supports the presence of two independent reaction pathways of isomerization and polymerization, respectively. Moreover, the addition of a strong Lewis acid, such as AlCl3, accelerates the ligand dissociation and the consequential isomerization as it weakens the palladium-nitrogen bond through competitive binding. In part three, Lewis acid-triggered olefin isomerization-polymerization is employed to prepare living olefinic block copolymers and further synthesize novel polyolefin-polar block copolymers with unique architectures, distinct levels of branching, crystallinity, and polar functionality in a one-pot manner.

Collision excitation of nitrous acid (HONO) by helium: isomerization effect

ABSTRACTWe generated new 3D-potential energy surfaces (3D-PESs) for the cis-HONO–He and trans-HONO–He weakly bound complexes along the intermonomer coordinates. We used the explicitly correlated Coupled Clusters with single, double, and perturbative triple excitations (CCSD(T)-F12) approach for the electronic structure computations, where the atoms were described using the aug-cc-pVTZ basis set. Then, we derived analytical forms for each PES. These PESs exhibit different shapes and present strong anisotropies. After quantum close-coupling scattering calculations for the lower rotational levels (up to ${9}_{2,7}$), and the coupled-states approximation for higher levels (up to ${22}_{1,22}$) using these PESs, we derived the collisional excitation cross sections of cis-HONO and trans-HONO by He for total energies 0.1 ≤ E ≤ 900 cm−1 and the rate coefficients for kinetic temperatures T ≤ 100 K. Our work shows that the collision data of cis-HONO and trans-HONO are different mainly because of the different 3D-PESs since the rotational energy structures of both isomers are very similar. Also, computations show that the data of the non-detected cis-HONO are as large as those of the detected trans-HONO isomer. They confirm the large values for the detected transition 52,4 → 41,3 of trans-HONO. Therefore, our work strongly suggests revisiting radiative transfer calculations to determine accurately the population of the rotational levels of these isomers. Our work should help astrophysicists for the detectability of such nitrogen oxide molecules and for the possible formation mechanisms and isomerization pathways specificities.

Direct and Indirect Pathways of CdTeSe Magic-Size Cluster Isomerization Induced by Surface Ligands at Room Temperature.

The field of isomerization reactions for colloidal semiconductor magic-size clusters (MSCs) remains largely unexplored. Here, we show that MSCs isomerize via two fundamental pathways that are regulated by the acidity and amount of an incoming ligand, with CdTeSe as the model system. When MSC-399 isomerizes to MSC-422 at room temperature, the peak red-shift from 399 to 422 nm is continuous (pathway 1) and/or stepwise (pathway 2) as monitored in situ and in real time by optical absorption spectroscopy. We propose that pathway 1 is direct, with intracluster configuration changes and a relatively large energy barrier. Pathway 2 is indirect, assisted by the MSC precursor compounds (PCs), from MSC-399 to PC-399 to PC-422 to MSC-422. Pathway 1 is activated when PC-422 to MSC-422 is suppressed. Our findings unambiguously suggest that when a change occurs directly on a nanospecies, its absorption peak continuously shifts. The present study provides an in-depth understanding of the transformative behavior of MSCs via ligand-induced isomerization upon external chemical stimuli.

Mechanistic Study of Chemoselectivity for Carbon Radical Hydroxylation versus Chlorination with FeIII (OH)(Cl) Complexes.

The FeIII (OH)(Cl) complex resembles the key intermediate proposed for the non-heme iron halogenases. Goldberg and co-workers reported that the FeIII (OH)(Cl) RC reacts with triphenylmethyl radical 1 to give an exclusive hydroxylation product. To understand the chemoselectivity of the reaction of RC with 1, density functional theory (DFT) calculations have been conducted. From RC, the competing pathways were identified as the OH-transfer, Cl-transfer, and isomerization pathways. The direct Cl-transfer is more favorable than direct OH-transfer by 2.8 kcal/mol. The hydrogen bonding interactions between the hydroxyl group and the pendent amine ligand impede the direct OH-transfer from RC. Compared with the direct Cl-transfer pathway, the isomerization pathways require lower barriers. In isomer RCiso2 , the equatorial hydroxyl group, which has smaller diabatic bond dissociation energy, prefers to transfer to form the hydroxylation product. In FeIII (Cl)2 RC2 and RC2iso , the equatorial chloride group also prefers to transfer to give the chlorination product.

Isomerization pathway of N-ethylcarbazole hydrogenation products affected by metal-support interactions

N-ethylcarbazole (NEC) is a widely studied liquid organic hydrogen carrier, and a large number of catalysts with excellent reactivity has been designed and developed thus far. However, the phenomenon of isomeric transformation of 12H-NEC products during the reaction was not explained. Here, we studied the process based on three different Ru catalysts supported on zirconium-based supports, and based on the experimental results, we identified that supported metal-support strong interaction (SMSI), metal-support anion interaction (MSAI) and hydrogen spillover will have coupling effect on the hydrogenation reaction path and the occurrence of isomerization in 12H-NEC product. Higher 12 [H] B content in 12H-NEC under Ru/ZrN catalyst was caused by the large number of secondary active centers on the surface of the support reacting in the hydrogenation reaction. The active site for the isomerization of 12 [H] B to 12 [H] A may be the electronegativity interface formed by Ru and the support, while the electroneutral or electropositive interface rich in hydrogen is not conducive to the catalytic conversion. To sum up, an image model for the isomeric transformation of 12H-NEC products was proposed.

Efficient discovery of multiple minimum action pathways using Gaussian process

We present a new efficient transition pathway search method based on the least action principle and the Gaussian process regression method. Most pathway search methods developed so far rely on string representations, which approximate a transition pathway by a series of slowly varying system replicas. Such string methods are computationally expensive in general because they require many replicas to obtain smooth pathways. Here, we present an approach employing the Gaussian process regression method, which infers the shape of a potential energy surface with a few observed data and Gaussian-shaped kernel functions. We demonstrate a drastic elevation of computing efficiency of the method about five orders of magnitude than existing methods. Further, to demonstrate its real-world capabilities, we apply our method to find multiple conformational transition pathways of alanine dipeptide using a quantum mechanical potential. Owing to the improved efficiency of our method, Gaussian process action optimization (GPAO), we obtain the multiple transition pathways of alanine dipeptide and calculate their transition probabilities successfully with density-functional theory (DFT) accuracy. In addition, GPAO successfully finds the isomerization pathways of small molecules and the rearrangement of atoms on a metallic surface.

Protonation state control of electric field induced molecular switching mechanisms.

Scanning tunneling microscopy tip-induced deprotonation has been demonstrated experimentally and can be used as an additional control mechanism in electric-field induced molecular switching. The goal of the current work is to establish whether (de)protonation can be used to inhibit or enhance the electric field controlled thermal and photoisomerization processes. Dihydroxyazobenzene is used as a model system, where protonation/deprotonation of the free hydroxyl moiety changes the azo bond order, and so modifies the rate of electric field induced isomerization. Through the combined action of deprotonation and applied field, it was found that the cis-to-trans thermal isomerization barrier could be completely removed, changing the isomerization half-life from the order of several months. In addition, due to the presence of multiple isomerization mechanisms, electric fields could modify the isomerization kinetics by increasing the number of energetically viable isomerization pathways, rather than reducing the activation barrier of the lowest energy pathway. Excited state calculations indicated that the protonation state and electric field could be used together to control the presence of electronic degeneracies along the rotation pathway between S0/S1, and along all three pathways between S1/S2. This work provides insight into the mechanisms that enable the use of protonation state, light, and electric fields in concert to control molecular switches.

Planar pentacoordinate carbon in a 16-electron neutral CCu2Be3H4 cluster.

Planar hypercoordination in carbon is a fascinating area, which departs from the usual view of coordination geometry in carbon. Herein, we propose a planar pentacoordinate carbon species in the global minimum of the CCu2Be3H4 cluster. The cluster is a 16-electron species that is thermodynamically and kinetically very stable. Bonding analyses reveal 2π/6σ double aromaticity in the cluster. A low-energy isomerization pathway also reveals that the cluster has a sufficient lifetime for its experimental detection.

Theoretical insights into the synthesis mechanism of two amino‐substituted derivatives of FOX‐7

AbstractFOX‐7 is a typical high‐energy and low‐sensitivity material. Due to the unique “push‐pull” nitroenamine structure, abundant derivatives with good performance can be synthesized. DFT method is used to study the synthesis mechanism for two FOX‐7 amino‐substituted derivatives. The synthesis mechanism of amino‐substituted derivative MTNzA is cyclization followed by isomerization, which is different from the pathway of isomerization followed by cyclization proposed by previous authors. Carbohydrazide is tend reacted with two FOX‐7 to produce BADCh, rather than ring formation with one FOX‐7.

Shape-Selectivity of Cyclopentenyl Cation Isomerization: Investigating Kinetic Control in Medium-Pore Zeolites

We performed periodic density functional theory (DFT) calculations to study the dynamics of alkyl substituents on cyclopentenyl cations in medium-pore acid zeolites, H-ZSM-5 and H-ZSM-22. Our study seeks to shed light on how zeolite shape selectivity can influence key reaction intermediates in the methanol-to-hydrocarbon process, which can lead to both value-added products and coke species. We considered the isomerization of 4-ethyl-4,5,5-trimethylcyclopentenyl cation (A), which has been shown by Hernandez et al. [ACS Catal.2021, 11, 12893–12914] to lead to IR spectra and alkyl substitution patterns that vary with zeolite pore structure, in contrast to DFT-predicted thermodynamics. Here, we investigate the role of kinetic control on zeolite shape-selectivity by computing exhaustive DFT dynamics of substituent rearrangement in medium-pore zeolites starting with cation A. We used the Rule Input Network Generator (RING) code to enumerate isomerization pathways from A to five product isomers that differ mainly in the presence or absence of an alkyl substituent on the central allylic carbon of the cyclopentenyl ring, yielding a reaction network with a total of 24 distinct species. We combined metadynamics and climbing-image nudged elastic band (CI-NEB) methods to compute the free-energy landscapes, including barriers for all species in H-ZSM-5 and H-ZSM-22 zeolites. Integrating kinetic equations for the reaction network in the two zeolites predicts that equilibrium product distributions are obtained after 103 s in H-ZSM-5, while 108–109 s is required for equilibration in H-ZSM-22, suggesting the clear possibility of kinetic control depending on zeolite structure.

Automated Variable Electric-Field DFT Application for Evaluation of Optimally Oriented Electric Fields on Chemical Reactivity

Recent theoretical work and experiments at molecular junctions have provided a strong conceptualization for the effects of oriented electric fields (OEFs) on organic reactions. Depending on the axis of application, OEFs can increase (or decrease) the reaction rate or distinguish between isomeric pathways. Despite the conceptual elegance of OEFs, which may be applied externally or induced locally, as tools for catalyzing organic reactions, implementation in synthetically relevant systems has been hampered by inefficiencies in evaluating reaction sensitivity to field effects. Herein, we describe the development of the Automated Variable Electric-Field DFT Application (A.V.E.D.A.) for streamlined evaluation of a reaction's susceptibility to OEFs. This open-source software was designed to be accessible for nonexpert users of computational and programming tools. Following initiation by a single command (and with no subsequent intervention) the Linux workflow manages a series of density functional theory calculations and mathematical manipulations to optimize local-minimum and transition-state structures in oriented electric fields of increasing magnitude. The resulting molecular and reaction dipole moments, field-perturbed geometries, and net effective activation energies are compiled for user interpretation. Ten representative pericyclic reactions that showcase the development and evaluation of A.V.E.D.A. are described.

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.