Isomerization Barrier Research Articles

Unraveling the Mechanism and Influence of Auxiliary Ligands on the Isomerization of Neutral [P,O]-Chelated Nickel Complexes for Olefin Polymerization.

The copolymerization of ethylene with polar monomers presents a significant challenge. While palladium catalysts have shown promise, nickel catalysts are more economical but suffer from poor activity. Previous studies suggest that the isomerization step involved in the nickel-catalyzed polymerization may influence the catalyst activities. Herein, we explore the isomerization mechanisms of two phosphine-phenoxide-ligated catalysts using density functional theory (DFT) studies. We found that out of dissociative, tetrahedral, and associative mechanisms, the associative mechanism is the likeliest, with a pendant methoxy oxygen atom from the ligand to fulfill the fifth coordination site on nickel before Berry pseudorotation. The effect of varying auxiliary ligands on the activation barrier heights was also investigated and found that electron-releasing alkyl groups on substituted pyridine ligands have diminished electronic influence on pseudorotational barriers, but if present at the ortho-positions, will elevate the barriers due to larger steric influences. The electron-withdrawing groups on the ligand result in weaker ligand binding and lower pseudorotational barriers. These insights into the mechanisms of cis-trans isomerization and auxiliary ligand effects may offer valuable guidance for optimizing catalyst performance in copolymerization processes by lowering the barrier of isomerization by fine-tuning the steric and electronic influences of auxiliary ligands and enhancing overall copolymerization efficiency.

Influence of pyridinic nitrogen on tautomeric shifts and charge transport in single molecule keto enol equilibria

Keto-enol tautomerism in organic molecules presents a potential for modulating the charge transport at the nanoscale. The reduction of the isomerization barrier and favoring the highly conductive enol form are the main challenges towards practical implementation of this phenomenon. Using density functional theory calculations, we have demonstrated that pyridinic nitrogen in biphenyl molecules with keto-enol tautomerism can successfully make the conductive enol form energetically more favorable. This enhanced stability originates from the hydrogen bonding between the pyridinic nitrogen and the hydroxyl group in the enol state. The presence of the pyridinic unit further enhances the conductance of the enol form while reducing that of the keto form compared to the pristine molecule. The novelty of our findings lies in the use of pyridinic nitrogen to control isomerization through hydrogen bonding, offering a new approach to tuning electronic properties for molecular devices. These findings can be valuable in the development of functional molecular devices based on the keto-enol isomerization phenomenon.

The Elusive Ternary Intermediates of Chiral Phosphoric Acids in Ion Pair Catalysis─Structures, Conformations, and Aggregation.

In ion-pair catalysis, the last intermediate structures prior to the stereoselective transition states are of special importance for predictive models due to the high isomerization barrier between E- and Z-substrate double bonds connecting ground and transition state energies. However, in prior experimental investigations of chiral phosphoric acids (CPA) solely the early intermediates could be investigated while the key intermediate remained elusive. In this study, the first experimental structural and conformational insights into ternary complexes with CPAs are presented using a special combination of low temperature and relaxation optimized 15N HSQC-NOESY NMR spectroscopy to enhance sensitivity. Combined NMR investigations and theoretical calculations revealed three conformers of the ternary complex, of which one also closely resembles the previously calculated transition states. In addition, a 2:1:1 ternary complex as well as an unprecedent [3:3] dimeric species consisting of two ternary complexes was revealed. Given the importance of the ground state energies for the transition state interpretation in ion pair catalysis we believe that the presented experimental insight into the structural and conformational variety of the ternary complexes is a key to the future development of predictive models in ion pair catalysis.

Characterization of an Unexpected μ3 Adsorption of Molecular Oxygen on Ag(100) with Low-Temperature STM.

Precise description of the interaction between molecular oxygen and metal surfaces is one of the most challenging topics in quantum chemistry. In this work, we use low-temperature scanning tunneling microscopy (STM) to identify and characterize an adsorption state of molecular oxygen that coordinates to three Ag atoms (μ3) on Ag(100). Surprisingly, μ3-O2 cannot be identified as a stable configuration with generalized gradient approximation (GGA)-level density functional theory (DFT) calculations. Through inelastic electron tunneling spectroscopy (IETS), we identify three vibrational modes of individual μ3-O2 and assign them to out-of-plane hindered rotation (HR) at 38.0 meV, in-plane HR at 32.4 meV, and in-plane hindered translation (HT) at 22.0 meV. We determine the barrier for rotational isomerization of μ3-O2 to be 69.3 meV from tunneling electrons-induced rotations. The inability of theory to predict the experiment stems most likely from self-interaction errors inherent to GGA-DFT, which leads to an inaccurate description of localized charges. We speculate that the μ3-O2 configuration represents a formal molecular oxygen anion and assign the ±11 meV excitation in the IETS to a transition between spin-orbit states of the surface-bound anion.

Conformational transformations of N-[arylsulfonylimino(methyl)methyl]-1,4-benzoquinonemonoimines

In solutions of N-[arylsulfonylimino(methyl)methyl]-1,4-benzoquinonemonoimines, several Z,E-isomerization processes occur simultaneously: a fast inversion isomerization process (topomerization) relative to the C=N1 quinoneimine bond; a slow inversion isomerization process relative to the C=N2 exocyclic bond; and a process of inhibited rotation around the =N1–С= bond that connects two imine fragments. In the 1H NMR spectra, isomerization with respect to the C=N2 exocyclic bond was only detected. The theoretical values of the isomerization barriers for the C=N1 and C=N2 bonds, as well as for the inhibited rotation around the =N1–C= bond were determined, along with the experimental Z,E-isomerization barriers for to the C=N2 bond. It was established that in the 1H NMR spectra for N-[arylsulfonylimino(methyl)methyl]-1,4-benzoquinonemonoimines, only Z, E-isomerization relative to the C=N2 bond can be observed.

Characterization of glycylglycyltyrosine radical cations: Insights into β-radical formation and N–Cα peptide bond dissociation at the tyrosine residue

We investigated the dissociation and characterization of radical cations of glycylglycyltyrosine [GGY]•+, focusing on β-radical-induced N–Cα peptide bond cleavage reactions at the tyrosyl residue. By combining density functional theory (DFT) calculations with experimental studies utilizing low-energy collision-induced dissociation (CID) mass spectrometry and deuterium labeling on the two β-hydrogen atoms of the tyrosyl residue in [GGY]•+, we elucidated the intricacies of the β-radical structure and its origin. Unlike tryptophan-containing [GGW]•+, which forms canonical π-radical precursors, infrared multiphoton dissociation (IRMPD) spectroscopy results reveal that the β-radical [GGYβ•]+ isomerizes from the phenoxy-radical [GGYo•]+, with the radical localized on the β-carbon of the tyrosyl residue and the phenolic oxygen atom, respectively. The isomerization barriers from [GGYo•]+ to [GGYβ•]+ are <109 kJ mol−1.

Impact of Protonation Sites on Collision-Induced Dissociation-MS/MS Using CIDMD Quantum Chemistry Modeling.

Protonation is the most frequent adduct found in positive electrospray ionization collision-induced mass spectra (CID-MS/MS). In a parallel report Lee, J. J. Chem. Inf. Model. 2024, 10.1021/acs.jcim.4c00760, we developed a quantum chemistry framework to predict mass spectra by collision-induced dissociation molecular dynamics (CIDMD). As different protonation sites affect fragmentation pathways of a given molecule, the accuracy of predicting tandem mass spectra by CIDMD ultimately depends on the choice of its protomers. To investigate the impact of molecular protonation sites on MS/MS spectra, we compared CIDMD-predicted spectra to all available experimental MS/MS spectra by similarity matching. We probed 10 molecules with a total of 43 protomers, the largest study to date, including organic acids (sorbic acid, citramalic acid, itaconic acid, mesaconic acid, citraconic acid, and taurine) as well as aromatic amines including uracil, aniline, bufotenine, and psilocin. We demonstrated how different protomers can converge different fragmentation pathways to the same fragment ions but also may explain the presence of different fragment ions in experimental MS/MS spectra. For the first time, we used in silico MS/MS predictions to test the impact of solvents on proton affinities, comparing the gas phase and a mixture of acetonitrile/water (1:1). We also extended applications of in silico MS/MS predictions to investigate the impact of protonation sites on the energy barriers of isomerization between protomers via proton transfer. Despite our initial hypothesis that the thermodynamically most stable protomer should give the best match to the experiment, we found only weak inverse relationships between the calculated proton affinities and corresponding entropy similarities of experimental and CIDMD-predicted MS/MS spectra. CIDMD-predicted mechanistic details of fragmentation reaction pathways revealed a clear preference for specific protomer forms for several molecules. Overall, however, proton affinity was not a good predictor corresponding to the predicted CIDMD spectra. For example, for uracil, only one protomer predicted all experimental MS/MS fragment ions, but this protomer had neither the highest proton affinity nor the best MS/MS match score. Instead of proton affinity, the transfer of protons during the electrospray process from the initial protonation site (i.e., mobile proton model) better explains the differences between the thermodynamic rationale and experimental data. Protomers that undergo fragmentation with lower energy barriers have greater contributions to experimental MS/MS spectra than their thermodynamic Boltzmann populations would suggest. Hence, in silico predictions still need to calculate MS/MS spectra for multiple protomers, as the extent of distributions cannot be readily predicted.

Dynamics of NO Release and Linkage Isomer Formation from S-Nitroso-Mercaptoethanol in Aqueous Solutions: Insights from Femtosecond Infrared Spectroscopy.

Understanding the photodynamics of S-nitroso-thiol (RSNO), an effective NO transporter in biological systems, is essential for its photochemical applications. S-nitroso-mercaptoethanol (MceSNO), a simple water-soluble RSNO, facilitates high-level quantum calculations. We investigated the photoexcitation dynamics of MceSNO in an aqueous solution, focusing on NO dissociation, recombination, and linkage isomerization using quantum calculations and femtosecond infrared spectroscopy. Upon excitation at 320 nm, MceSNO rapidly dissociates into NO and MceS radicals. Approximately 31 ± 3% of MceS reacts with unexcited MceSNO molecules, forming MceSSMce and releasing additional NO. The remaining MceS undergoes geminate recombination with NO, forming either MceSNO (41 ± 4%) or MceSON (28 ± 3%), the latter being a sulfur-ON linkage isomer observed for the first time in a room-temperature solution. MceSON isomerizes back to MceSNO in 470 ± 30 ps. The formation mechanism of MceSON was verified through a potential energy surface constructed at the CASPT2D(16,11)/cc-pVTZ level. The isomerization barrier was determined to be 3.3 ± 1.2 kcal/mol in water.

Ultrafast excited state intramolecular proton transfer and isomerization of long-chain linked Schiff bases.

The ultrafast proton transfer and the following dynamics for aromatic Schiff bases N,N'-bis(salicylidene)ethylenediamine (salen) and N,N'-bis(salicylidene)-1,4-butylenediamine (salbn) were investigated with experimental and theoretical methods. A dual emission property with a large Stokes shift in salen and salbn indicates that excited state intramolecular proton transfer occurs with photoexcitation. An efficient single proton transfer was confirmed within 200fs for both molecules. Subsequently, a fast twisted motion of the keto moiety carries cis-keto to a relaxed stable geometry in the S1 state. Following the twisted motion, the phenol ring at keto moiety further rotates to a conical intersection with the ground state and a cis-trans isomerization occurs. The isomerization rate is high, which dominates the competition with the radiative transition, resulting in weak emission intensity. It is confirmed that the length of alkyl chain affects the direction of phenol ring twisting and rotation during the whole subsequent relaxation of excited cis-keto tautomer. Compared with polar solvent acetonitrile, the barrier of isomerization is higher and the hydrogen bond on keto moiety is stronger in nonpolar solvent toluene. It makes fluorescence radiation channels competing with isomerism more likely to occur, contributing to the observed difference of enol/keto emission ratios of salen and salbn in toluene and acetonitrile.

Exploring the mechanisms of excited-state intramolecular proton transfer in hydroxyphenyl-benzimidazole derivatives: A theoretical perspective

We conducted a comprehensive theoretical exploration for the ESIPT mechanism in a set of HBI derivatives in THF solution (Cpd-A and Cpd-B, and three isomers: Cpd-1, Cpd-2 and Cpd-3), employing time-dependent density functional theory (TD-DFT) methods for the excited-state calculations. An energy scan for the excited-state proton transfer pathway indicates that both Cpd-A and Cpd-B exhibit a low transition barrier from Enol* to Keto*, with the energy of Keto* much lower than Enol* state, which implies a rapid ESIPT process. The high instability of Enol* state contradicts the experimental observed dual emission bands for Cpd-A, where the emission band predominantly contributed from Keto* state. We propose a new mechanism to account for this dual fluorescence phenomenon of Cpd-A, where the overall fluorescence band can be ascribed to the emissions from both Keto* and a stable rotamer of Cpd-A. Calculations suggest that Cpd-A can exist in both syn and anti rotamers, with a relatively low isomerization barrier of 14.0 kcal/mol. The coexistence of two stable isomers in solution gives rise to the phenomenon of dual emission for Cpd-A. Further investigation for the substituent effects on the ESIPT dynamics of three isomers (Cpd-1, Cpd-2 and Cpd-3) indicates that varying substituent positions can have a substantial impact on both ESIPT process and excited-state charge transfer. The methoxy group substitution proximate to the hydroxy functional group decreases the energy barrier for Enol*-Keto* transition, and also promotes a more substantial charge transfer. Our study demonstrates a new mechanism of the dual fluorescence observed for the target HBI derivatives, offering a novel understanding for the ESIPT mechanism in solvent.

Azobenzene-Imidazolium ionic liquid crystals: Phase properties and photoisomerization in solution state

This is the first report of phase properties and photoisomerization behaviour of a series of amphiphilic azobenzene-imidazolium derivatives. The cationic imidazolium moiety was functionalised with varying alkyl chain length (C10-C18) and connected to an azobenzene via a flexible ether spacer. Their phase transitional properties and photoisomerization in solution were modulated by the alkyl chains in the imidazolium moiety. C14 was the shortest chain length to induce the formation of a liquid crystal phase, wherein compounds having C14-C18 exhibited stable smectic A phase. All compounds photo switched from trans-to-cis isomers in solution when illuminated with UV radiation. DFT calculations revealed that the trans isomers could adopt two geometries, however, folded geometry (global minima) was thermodynamically more stable than the open chain structure. The long conjugate (C16) had a higher trans-cis isomerization barrier due to the multilayer folding geometry that reduced its structural flexibility as compared to the C10 homologue. The photo conversion efficiency (CE) was alkyl chain length dependent. The C10 salt had a larger CE than C16 homologue due to the transition gap between S1 excited state and ground surface is smaller in the former (0.211 eV) than that in the latter (0.278 eV), thus resulting in efficient photoisomerization in the former.

Voltage-driven control of single-molecule keto-enol equilibrium in a two-terminal junction system

Keto-enol tautomerism, describing an equilibrium involving two tautomers with distinctive structures, provides a promising platform for modulating nanoscale charge transport. However, such equilibria are generally dominated by the keto form, while a high isomerization barrier limits the transformation to the enol form, suggesting a considerable challenge to control the tautomerism. Here, we achieve single-molecule control of a keto-enol equilibrium at room temperature by using a strategy that combines redox control and electric field modulation. Based on the control of charge injection in the single-molecule junction, we could access charged potential energy surfaces with opposite thermodynamic driving forces, i.e., exhibiting a preference for the conducting enol form, while the isomerization barrier is also significantly reduced. Thus, we could selectively obtain desired and stable tautomers, which leads to significant modulation of the single-molecule conductance. This work highlights the concept of single-molecule control of chemical reactions on more than one potential energy surface.

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

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

BF3-Catalyzed Intramolecular Fluorocarbamoylation of Alkynes via Halide Recycling

A BF3-catalyzed atom-economical fluorocarbamoylation reaction of alkyne-tethered carbamoyl fluorides is reported. The catalyst acts as both a fluoride source and Lewis acid activator, thereby enabling the formal insertion of alkynes into strong C-F bonds through a halide recycling mechanism. The developed method provides access to 3-(fluoromethylene) oxindoles and γ-lactams with excellent stereoselectivity, including fluorinated derivatives of known protein kinase inhibitors. Experimental and computational studies support a stepwise mechanism for the fluorocarbamoylation reaction involving a turnover-limiting cyclization step, followed by internal fluoride transfer from a BF3-coordinated carbamoyl adduct. For methylene oxindoles, a thermodynamically driven Z-E isomerization is facilitated by a transition state with aromatic character. In contrast, this aromatic stabilization is not relevant for γ-lactams, which results in a higher barrier for isomerization and the exclusive formation of the Z-isomer.

Synthesis of Bioctacene-Incorporated Nanographene with Near-Infrared Chiroptical Properties.

We report the synthesis of a hexabenzoperihexacene (HBPH) with two incorporated octacene substructures, which was unambiguously characterized by single-crystal X-ray analysis. The theoretical isomerization barrier of the (P,P)-/(P,M)-forms was estimated to be 38.4 kcal mol-1 , and resolution was achieved by chiral HPLC. Notably, the enantiomers exhibited opposite circular dichroism responses up to the near-infrared (NIR) region (830 nm) with a high gabs value of 0.017 at 616 nm. Moreover, HBPH demonstrated NIR emission with a maximum at 798 nm and an absolute PLQY of 41 %. The excited-state photophysical properties of HBPH were investigated by ultrafast transient absorption spectroscopy, revealing an intriguing feature that was attributed to the rotational and/or conformational dynamics of HBPH after excitation. These results provide new insight into the design of chiral nanographene with NIR optical properties for potential chiroptical applications.

Synthesis of Bioctacene‐Incorporated Nanographene with Near‐Infrared Chiroptical Properties

AbstractWe report the synthesis of a hexabenzoperihexacene (HBPH) with two incorporated octacene substructures, which was unambiguously characterized by single‐crystal X‐ray analysis. The theoretical isomerization barrier of the (P,P)‐/(P,M)‐forms was estimated to be 38.4 kcal mol−1, and resolution was achieved by chiral HPLC. Notably, the enantiomers exhibited opposite circular dichroism responses up to the near‐infrared (NIR) region (830 nm) with a high gabs value of 0.017 at 616 nm. Moreover, HBPH demonstrated NIR emission with a maximum at 798 nm and an absolute PLQY of 41 %. The excited‐state photophysical properties of HBPH were investigated by ultrafast transient absorption spectroscopy, revealing an intriguing feature that was attributed to the rotational and/or conformational dynamics of HBPH after excitation. These results provide new insight into the design of chiral nanographene with NIR optical properties for potential chiroptical applications.

IrI(η4-diene) precatalyst activation by strong bases: formation of an anionic IrIII tetrahydride.

The reaction between [IrCl(COD)]2 and dppe in a 1 : 2 ratio was investigated in detail under three different conditions. [IrCl(COD)(dppe)], 1, is formed at room temperature in the absence of base. In the presence of a strong base at room temperature, hydride complexes that retain the carbocyclic ligand in the coordination sphere are generated. In isopropanol, 1 is converted into [IrH(1,2,5,6-η2:η2-COD)(dppe)] (2) on addition of KOtBu, with k12 = (1.11 ± 0.02) × 10-4 s-1, followed by reversible isomerisation to [IrH(1-κ-4,5,6-η3-C8H12)(dppe)] (3) with k23 = (3.4 ± 0.2) × 10-4 s-1 and k32 = (1.1 ± 0.3) × 10-5 s-1 to yield an equilibrium 5 : 95 mixture of 2 and 3. However, when no hydride source is present in the strong base (KOtBu in benzene or toluene), the COD ligand in 1 is deprotonated, followed by β-H elimination of an IrI-C8H11 intermediate, which leads to complex [IrH(1-κ-4,5,6-η3-C8H10)(dppe)] (4) selectively. This is followed by its reversible isomerisation to 5, which features a different relative orientation of the same ligands (k45 = (3.92 ± 0.11) × 10-4 s-1; k5-4 = (1.39 ± 0.12) × 10-4 s-1 in C6D6), to yield an equilibrated 32 : 68 mixture of 4 and 5. DFT calculations assisted in the full rationalization of the selectivity and mechanism of the reactions, yielding thermodynamic (equilibrium) and kinetic (isomerization barriers) parameters in excellent agreement with the experimental values. Finally, in the presence of KOtBu and isopropanol at 80 °C, 1 is transformed selectively to K[IrH4(dppe)] (6), a salt of an anionic tetrahydride complex of IrIII. This product is also selectively generated from 2, 3, 4 and 5 and H2 at room temperature, but only when a strong base is present. These results provide an insight into the catalytic action of [IrCl(COD)(LL)] complexes in the hydrogenation of polar substrates in the presence of a base.

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.

Synthesis, Crystal Analysis, and Physical Properties of Double [6]helicene-Containing Heteroarenes with Circularly Polarized Luminescence.

Two novel helical heteronanographenes bearing a [6]helicene unit (3a and 5a) have been synthesized, and their molecular structures are unambiguously determined via single-crystal X-ray diffraction analyses. Density functional theory calculations suggest that the as-prepared compounds have isomerization barriers of 29.02 kcal/mol for 3a and 34.07 kcal/mol for 5a, respectively. Optical enantiomers of 5a exhibit appealing chiroptical properties.

Photoswitching Properties of 5‐Methoxy‐2‐ (2‐phenyldiazenyl) Pyridine

AbstractHeteroaryl azobenzene molecular switches often have superior performance compared to their parent azobenzene derivatives. Herein, we report the efficient photoswitching of phenylazopyridine 5‐methoxy‐2‐(2‐phenyldiazenyl)pyridine using 1H NMR and UV/vis spectroscopy demonstrating &gt;92 % Z at the photostationary state and a thermal half‐life of 6.3 days at room temperature. Kinetic studies are in good agreement with the DFT predicted isomerization barrier.