Reaction Channels Research Articles

Deciphering the Origin of Regioselectivity in Ru(II)-Catalyzed C-H Annulation of N-Chlorobenzamides with 1,3-Diynes.

Understanding the reaction mechanism and origin of regioselectivity in transition metal-catalyzed C-H activation/annulation reactions with 1,3-diynes has remained an intriguing challenge. In this article, to establish the mechanism and decipher the origin of regioselectivity, we report a detailed computational density functional theory-based mechanistic investigation on the recently developed Ru(II)-catalyzed [4 + 2] annulation of N-chlorobenzamides with 1,3-diynes for the synthesis of 3-alkynylated isoquinolone derivatives. Our calculations reveal a redox-neutral pathway for the annulation reaction. The stepwise analysis of the reaction channels indicates the migratory insertion step and the concerted reductive elimination/oxidative addition of the Ru(p-cymene) moiety to form the N-C bond leading to the 3-alkynylated product to be the selectivity- and rate-determining steps, respectively. Finally, the distortion/interaction analysis using the activation-strain model suggests the steric effect as the determining factor for the observed regioselectivity for the formation of the 3-alkynylated product. Overall, the computationally obtained key insights into the catalytic mechanism and the origin of regioselectivity in the C-H activation/annulation reaction can be used as a guide to rationally design and develop novel transformation strategies for heterocycle synthesis.

Radical Stereochemistry: Accounting for Diastereomers in Kinetic Mechanism Development.

Recent work in combustion and atmospheric chemistry has revealed cases in which diastereomers must be distinguished to accurately model a reacting flow. This paper presents an open-source framework for introducing such stereoisomer resolution into a kinetic mechanism. We detail our definitions and algorithms for labeling and enumerating the stereoisomers of a molecule and then generalize our system to describe the transition state (TS) of a reaction. This allows for the stereospecific enumeration of reactants and products while accounting for "fleeting" stereochemistry that is unique to the TS. We also present the AutoMech Chemical Identifier (AMChI), an InChI-like string identifier that accounts for stereocenters omitted by InChI. This identifier is extended to describe the TSs of reactions, providing a universal lookup key for specific reaction channels. The final piece of our methodology is an analytic formula to remove redundancy from a stereoresolved mechanism when its enantiomers exist as a racemic mixture, making it as compact as possible while fully accounting for the differences between diastereomers. In applying our methodology to two subsets of the NUIGMech1.1 mechanism, we find that our approach reduces the extra species added for large-fuel oxidation from 2231 (133%, full expansion) to 694 (41%, nonredundant expansion). We also find that for pyrolysis more than a quarter of the species in the expanded mechanism cannot be properly described by an InChI string, requiring an AMChI string to communicate their identity. Finally, we find that roughly one-quarter of the large-fuel oxidation reactions and one-third of the pyrolysis reactions include fleeting TS stereochemistry, which may have relevant effects on their kinetics.

Investigating the catalytic activity of Mgn (n = 4–8) clusters for the hydrogen evolution reaction using density functional theory

AbstractTo efficiently desorb H2, pure Mgn (n = 4–8) clusters were chosen for the hydrogen evolution reaction with H2O. At the PBE0/def2‐TZVP level and the PBE0‐D3/def2‐TZVP level, the lowest energy structures of Mgn (n = 4–8) clusters and the most stable structures of Mgn@H2O (n = 4–8) complexes were searched in the local region. The transition state was predicted, and then the hydrogen evolution reaction channel was obtained by using the intrinsic reaction coordinate (IRC) to confirm the transition state. To better analyze the hydrogen reaction mechanism, the character of Mgn@H2O (n = 4–8) complexes and MgnO (n = 4–8) clusters, as well as the atomic charge change trend, were investigated using interaction region indicator function analysis (IRI) and natural population analysis (NPA). The reaction effect of Mg4 cluster and H2O is the worst. The energy barrier does, however, progressively lower as the cluster atom count rises, improving the reaction effect.

Study of the 7Be(d,3He)6Li* reaction at 5 MeV/u

The measurement of the 7Be(d,3He)6Li* transfer cross section at 5 MeV/u is carried out. The population of the 2.186 MeV excited state of 6Li in this reaction channel is observed for the first time. The experimental angular distributions have been analyzed in the finite range DWBA and coupled-channel frameworks. The effect of the 7Be(d,3He)6Li reaction on both the 6Li and 7Li abundances are investigated at the relevant big-bang nucleosynthesis energies. The excitation function is calculated by TALYS and normalized to the experimental data. The S factor of the (d,3He) channel from the present work is about 50% lower than existing data at nearby energies. At big-bang energies, the S factor is about three orders of magnitude smaller than that of the (d,p) channel. The (d,3He) reaction rate is found to have a less than 0.1% effect on the 6,7Li abundances.

Global Potential Energy Surfaces by Compressed-State Multistate Pair-Density Functional Theory for Hyperthermal Collisions in the O2+O2 System.

Interactions between oxygen molecules play an important role in atmospheric chemistry and hypersonic flow chemistry in atmospheric entries. Recently, high-quality ab initio potential energy surface (PES) of the quintet O4 was reported by Paukku et al. [J. Chem. Phys. 147, 034301 (2017)]. 10543 configurations were sampled and calculated at the level of MS-CASPT2/maug-cc-pVTZ with scaled external correlation. The PES was fitted to a many-body (MB) form with the many-body part described by the permutationally invariant polynomial approach (MB-PIP). In this work, the PIP-Neural Network (PIP-NN) and MB-PIP-NN methods were used to refit the PES based on the same data by Paukku et al. Three PESs were compared. It was found that the performances differ significantly in the O+O3 region as well as in the long-range region. Therefore, additional 1300 points were sampled, and the efficient compressed-state multistate pair-density functional theory (CMS-PDFT) was used to calculate the electronic structure of these 1300 points and 10543 points by Paukku et al. Then, a completely new quintet PES was fitted using the MB-PIP-NN method. Based on this PES, the quasi-classical trajectory (QCT) approach was used to reveal all possible reaction channels for hyperthermal O2-O2 collisions.

Significant Isotope Effects from the Nonadiabatic Couplings in the Cl(2P) + HD(v = 0, j = 0) Reaction.

The impact of non-Born-Oppenheimer couplings on the isotopic effects in the reaction of the Cl(2P) atom with the HD (v = 0, j = 0) molecule is investigated with our recently developed nonadiabatic time-independent quantum scattering methods, where the full open-shell characteristics are included in the six-state model, and also with the recently developed two-state model solving by time-independent methods, where part of the open-shell characteristic is included. The same reaction is also calculated with the simple adiabatic model using the lowest adiabatic potential energy surface. Compared with the results from different models, it is found that the reactivity of the Cl + HD → HCl + D channel is significantly overestimated in the adiabatic model. In contrast, the reactivity of the other channel agrees well with the nonadiabatic models. This is due to the van der Waals well in the reactant channel being changed a lot by including the nonadiabatic couplings. These quantum dynamics calculations suggest that sometimes the adiabatic model should be used with caution; otherwise, it may result in significant deviations for some reactions.

Vibration to Vibration: Product Energy Distribution of F + HD Crossed Molecular Beam Experiments.

We investigated the F + HD(v = 1, j = 0) → HF + D reaction using the crossed molecular beam technique combined with the D atom Rydberg tagging time-of-flight spectroscopy. By detecting the products at various scattering angles for different collision energies in the range of 0.8-1.2 kcal/mol, we observed the forward-scattering products of HF(v' = 4) and determined the threshold energy for the opening of this reaction channel. Similar experiments were conducted for the F + HD(v = 0, j = 0) → HF + D reaction within the range of 1.1-1.6 kcal/mol, where forward-scattering products of HF(v' = 3) were observed, and the threshold energy for this reaction channel was determined as well. Furthermore, we measured the differential cross-sections for the F + HD → HF + D reaction in both the vibrational ground state and the excited state of HD and analyzed the vibrational quantum-state distribution of the HF products. It was found that the population of vibrational quantum states of the HF products increases synchronously with the excitation of the reactant HD vibrationally.

OH-Formation following vibrationally induced reaction dynamics of H2COO.

The reaction dynamics of H2COO to form HCOOH and dioxirane as first steps for OH-elimination is quantitatively investigated. Using a machine learned potential energy surface (PES) at the CASPT2/aug-cc-pVTZ level of theory vibrational excitation along the CH-normal mode νCH with energies up to 40.0 kcal mol-1 (∼5νCH) leads almost exclusively to HCOOH which further decomposes into OH + HCO. Although the barrier to form dioxirane is only 21.4 kcal mol-1 the reaction probability to form dioxirane is two orders of magnitude lower if the CH-stretch mode is excited. Following the dioxirane-formation pathway is facile, however, if the COO-bend vibration is excited together with energies equivalent to ∼2νCH or ∼3νCOO. For OH-formation in the atmosphere the pathway through HCOOH is probably most relevant because the alternative pathways (through dioxirane or formic acid) involve several intermediates that can de-excite through collisions, relax via internal vibrational relaxation (IVR), or pass through loose and vulnerable transition states (formic acid). This work demonstrates how, by selectively exciting particular vibrational modes, it is possible to dial into desired reaction channels with a high degree of specificity.

Temperature-Dependent Selectivity and Detection of Hidden Carbon Deposition in Methane Oxidation.

Reaction products in heterogeneous catalysis can be detected either on the catalyst surface or in the gas phase after desorption. However, if atoms are dissolved in the catalyst bulk, then reaction channels can become hidden. This is the case if the dissolution rate of the deposits is faster than their formation rate. This might lead to the underestimation or even overlooking of reaction channels such as, e.g., carbon deposition during hydrocarbon oxidation reactions, which is problematic as carbon can have a significant influence on the catalytic activity. Here, we demonstrate how such hidden deposition channels can be uncovered by carefully measuring the product formation rates in the local gas phase just above the catalyst surface with time-resolved ambient pressure X-ray photoelectron spectroscopy. As a case study, we investigate methane oxidation on a polycrystalline Pd catalyst in an oxygen-lean environment at a few millibar pressure. By ramping the temperature between 350 and 525 °C, we follow the time evolution of the different reaction pathways. Only in the oxygen mass-transfer limit do we observe CO production, while our data suggests that carbon deposition also happens outside this limit.

Surprising Radiolytic Stability of 8-Thiomethyladenine in an Aqueous Solution.

8-Thiomethyladenine (ASCH3), a potentially radiosensitizing modified nucleobase, has been synthesized in a reaction between 8-thioadenine and methyl iodide. Despite favorable dissociative electron attachment (DEA) characteristics, the radiolysis of an aqueous solution of ASCH3 with a dose of X-ray amounting to as much as 300 Gy leads to no effects. Nevertheless, crossed electron-molecule beam experiments in the gas phase on ASCH3 confirm the theoretical findings regarding the stability of its radical anion, namely, the most abundant reaction channel is related to the dissociation of the S-CH3 bond in the respective anion. Furthermore, electron-induced degradation of ASCH3 has been observed in aprotic acetonitrile, which is strong evidence for the involvement of proton transfer (PT) in stabilizing the radical anion in an aqueous solution. These findings demonstrate that PT in water can be the main player in deciding the radiosensitizing properties of modified nucleobases/nucleosides.

Advances in exploration of photoinduced electron transfer reactions involving small molecules probed by magnetic field effect

The review focuses on photoinduced electron transfer (PET) reactions between small molecules and various kinds of chemical and biological systems using a weak external magnetic field (MF). Laser flash photolysis is a competent tool to characterize the intermediates which are formed due to PET. A weak MF, very close to the hyperfine interaction of the system, has the potential to inhibit or enhance reaction channels for singlet and triplet states, which eventually effects the product distribution. At first, well-documented examples of PET involving small molecules like derivatives of phenazines, carbazoles and acridines with classical electron donors in varying homogeneous and heterogeneous media have been discussed and the influence of a weak MF on the dynamics of PET is highlighted. Secondly, utilization of magnetic field effect (MFE) to probe PET in protein pockets has been described. Thirdly, an extensive discussion on PET involving nucleobases, nucleosides, nucleotides and nucleic acids and subsequent MFE on such reactions has been reported. Next, MFE has been exploited to study PET involving nanomaterials. Finally, some very recent studies of MFE have been discussed. Thus, this review is an attempt to unravel various aspects of PET in a large number of systems of varying dimensions by means of several facets of MFE like B1/2 parameter, its capability to authenticate the initial spin state and distance dependence property.

Practical and efficient oxygenation of benzylic C-H bonds with dioxygen catalyzed by two-dimensional porous organic frameworks possessing porphyrin cobalt(II) units

Metalloporphyrin T(4-Br)PPCo was used in the construction of two-dimensional porous organic framework materials (2D POFs) in order to achieve the direct benzyl C-H bonds oxygenation. In order to prevent the disordered diffusion of free radicals in 2D POFs, a restricted reaction channel was constructed, and heterogeneous catalysis was applied to decrease the deep oxygenation of partial oxygenation products due to central metal sites. All 2D POFs were characterized as amorphous microporous materials containing highly and uniformly dispersed Co2+. It was used to partially oxygenate C-H bonds at benzyl position employing dioxygen in solvent-free condition, and the conversion and selectivity were improved at the same time, especially when residual -B(OH)2 and -Br were capped. Compared with T(4-Br)PPCo, the substrate conversion increased from 39 % to 66 %, and the selectivity for 4-nitroacetophenone increased from 66 % to 91 %. The reaction mechanism, apparent kinetics and substrate compatibility were also studied. In this work, it provided a guiding reference for the effective C-H bonds oxygenation and other free radical based chemical reactions. The use of POFs in catalytic chemistry was further broadened, and a successful method for improving the catalytic characteristics of POFs by capping the remaining active groups was suggested.

Ozonolysis of 2-Methyl-2-pentenal: New Insights from Master Equation Modeling.

Experimental and theoretical studies were carried out to investigate the ozonolysis of trans-2-methyl-2-pentenal. The experiments were conducted in atmospheric simulation chambers coupled to a Fourier transform infrared (FTIR) spectrometer and a gas chromatograph-mass spectrometer at room temperature and atmospheric pressure in the presence of an excess of cyclohexane in dry conditions (RH < 1%). The ozonolysis reaction was investigated theoretically from the results of accurate density functional (M06-2X) and ab initio [CCSD(T)] computations, employing the AVTZ basis set. The sequence of reaction steps was established, and the system of kinetics equations was modeled using MESMER. In the first step, a primary ozonide is formed, which then decomposes along two pathways. The principal ozonolysis products are propanal, methylglyoxal, ethylformate, and a secondary ozonide. An interesting competition between sequential reaction steps and well-skipping is found, which leads to an inversion of the expected methylglyoxal/propanal product ratio at temperatures below 210 K. The mechanism of the "hot ester" reaction channel of the Criegee intermediate was revisited. The computed ozonolysis rate constant and product branching ratio are in excellent agreement with the experimental data that are also reported in the present work.

Cartography of liquid-liquid flow in corrugated millichannels

If the interest of heat exchanger/reactors have been demonstrated for homogeneous liquid phase applications, many chemical syntheses take place in multiphase media (gas-liquid, liquid-liquid, gas-liquid-solid…). Thus, in order to evaluate the versatility of a plate-type heat exchanger/reactor with a 2D-meandering millichannel, this work is focused on the characterization of hydrodynamics of liquid-liquid flow in the reaction channel. Therefore, several prototypes are built with millichannels of increasing dimensions to address the scale-up issue. Flow visualizations are performed with a high-speed camera; four flow regimes with octanol/water fluid system are observed: annular/plug, annular, annular/dispersed, and dispersed. The study shows that interfacial tension and dispersed phase inertia are the main forces driving the interface. A dimensionless map based on the dispersed phase Weber number as a function of the continuous phase internal Dean number is built up. This map turns out to be valid in the range (2–4 mm) of the tested corrugated millichannel size.

Dissociation of Hydrofluorocarbon Molecules after Electron Impact in Plasma.

The process of dissociation for two hydrofluorocarbon molecules in low triplet states excited by electron impact in plasma is investigated by ab initio molecular dynamics (AIMD). The interest in the dissociation of hydrofluorocarbons in plasma is motivated by their role in plasma etching in microelectronic technologies. Dissociation of triplet states is very fast, and the reaction products can be predicted. In this work, it was found that higher triplet states relax into the lowest triplet state within a few femtoseconds due to nonadiabatic dynamics, such that the simplest ab initio MD on the lowest triplet state seems to give a reasonable estimate of the reaction channels branching ratios. We provide evidence of the existence of simple rules for the dissociation of hydrofluorocarbon molecules in triplet states. For molecules with a double bond, the bonds adjacent to the double bond dissociate faster than the other bonds.

Unexpected high yield of acrolein underlies the importance of the hydrogen-abstraction mechanism in photooxidation of allyl methyl sulfide (AMS).

This work explores theoretically the gas phase oxidation of allyl methyl sulfide (AMS, H2CCHCH2SCH3) initiated by •OH radicals, focusing on the H-abstraction pathway at the M06-2X-D3/aug-cc-pVTZ and MN15/aug-cc-pVTZ levels of theory (m06Tz and mn15Tz). The formation of a prereactive complex (PRC) is involved in H-abstraction processes with two potential directions of approach for the OH radical, denoted as “α” and “β”. The PRCs, demonstrate increased reactivity, primarily due to the interaction between the sulfur atoms and the hydroxyl hydrogen. A scheme for the H-abstraction mechanism that supports the experimentally identified products and predicts the formation of some S-containing low volatility products is proposed. The comparison of the potential energy surface (PES) between the double bond addition and H-abstraction paths in the AMS molecule shows that at the m06Tz level of theory, the H-abstraction on C3 and the addition to C1 have nearly the same profile of energy, while at the mn15Tz level, the minimum energy channel is the addition to C1. The theoretical rate coefficient for each reaction channel was calculated, considering the formation of a PRC prior to reaching the transition state of each channel and assuming thermal equilibrium between reactants and the PRC. The rate constants were calculated in a multi-TS/multi-conformer way at the SVECV-f12/m06Tz and SVECV-f12/mn15Tz levels of theory. The SVECV-f12 method is consistent in its predictions in both systems and exhibits only minor deviations from the experimental rate constants. Despite some specific differences due to the DFT method supporting the SVECV-f12 calculations, both methodologies predict a significant H-abstraction contribution in the AMS + OH gas phase reaction, which explains the high formation yield for acrolein determined experimentally.

Modulating and Accelerating Photolysis of Photoactivatable [2.2]Paracyclophane Aryl Azide in Supramolecular Host for Bioimaging

AbstractPhotolysis of aryl azides offers a versatile approach to achieve more sophisticated functionalization, for instance in the field of chemical biology. In this study, a photoactivatable aryl azide named Pcp‐Az is presented that forms three distinct emissive molecules after irradiation. Computational studies unveiled that the photolysis of Pcp‐Az in aqueous medium undergoes different reaction channels, leading to the three mentioned distinct products. When the photoreaction is performed using the supramolecular host cucurbit[8]uril(CB8) for Pcp‐Az, the reaction is found to be tuned and accelerated. Finally, the potential application of the photoproducts are showcased in bioimaging, and also the time‐dependent photoactivating imaging.

Different Reaction Modes Operating in ansa-Half-Sandwich Magnesium Catalysts.

Magnesium-based catalysts are becoming popular for hydroelementation reactions specially using p-block reagents. Based on the seminal report from Schäfer's group (ChemCatChem 2022, 14, e202201007), our study demonstrates that the reaction mechanisms exhibit a far greater degree of complexity than originally presumed. Magnesium has a variety of coordination modes (and access to different hybridizations) which allows this electron-deficient centre to modulate its catalytic power depending on the σ-donor properties of the reagent. DFT calculations demonstrate several reaction channels closely operating in these versatile catalysts. In addition, variations in limiting energy barriers resulting from catalyst modifications were examined as a function of the Hammett constant, thereby predicting enhanced efficiency in reaction conversions.

Research on natAg(γ,xn)103-106Ag reaction cross sections with the bremsstrahlung end-point energy of 70 and 75 MeV

The flux-weighted average cross sections of natAg(γ,xn)103-106Ag reactions were measured with the bremsstrahlung end-point energy of 70 and 75 MeV using an activation and off-line γ-ray spectrometric technique. The GEANT4 code was used for the simulation of the bremsstrahlung spectra. The cross sections of natAg(γ,xn) 103-106Ag reactions as a function of mono-energetic photons were theoretically calculated by using the TALYS-1.96 code. The data of the present work and literature at different bremsstrahlung end-point energy are found to be in agreement with the theoretical values within the uncertainty limit. It can be seen that the flux-weighted average cross sections of the natAg(γ,xn)105.106Ag reactions increase with bremsstrahlung energy up to the Giant Dipole Resonance region. Thereafter, a small decrease trend with the bremsstrahlung energy was seen due to the opening of another reaction channel.

Photodegradation of 2-chlorodibenzo-p-dioxin (2-CDD) on the surface of municipal solid waste incineration fly ash: Kinetics and product analysis

Considering that waste incineration fly ash is the main carrier of dioxins and can migrate over long distances in the atmosphere, it is of great significance to study the photochemical transformation behavior of dioxins on the surface of fly ash. In this work, 2-chlorodibenzo-p-dioxin (2-CDD) was selected to conduct a systematic photochemical study. The influence of various factors on the photodegradation of 2-CDD were first explored, and the results showed that small particle size of fly ash, low concentration of 2-CDD and appropriate level of humidity were more conducive to photodegradation, with the highest degradation percentage reaching 76%–84%. The components of fly ash (Zn (Ⅱ), Al (Ⅲ), Cu (Ⅱ) and SiO2) also had a certain promoting effect on the degradation of 2-CDD, which increases the degradation efficiency by 10%–20%, because they could act as effective photocatalysts to produce free radicals for reaction. With a higher total light exposure intensity, natural light environments led to a more complete degradation of 2-CDD than laboratory Xe lamp irradiation (90% degradation Vs. 79% degradation). Based on chemical probe and radical quenching experiment, hydroxyl radical also contributed to 2-CDD photodegradation on fly ash. A total of 16 intermediate products were detected by mass spectrometry analysis, and four initial reaction pathways of 2-CDD were speculated in the process, including dechlorination, ether bond cleavage, hydroxyl substitution, and hydroxyl addition. According to the results of density functional theory calculation, the reaction channels of ether bond cleavage and •OH attack were determined. The toxicity assessment software tool (TEST) was used to assess the toxicity and bioconcentration coefficient of reaction products, and it was found that the overall toxicity of the photodegradation products was reduced. This study would provide new insights into the environmental fate of dioxins during long-range atmospheric migration process.