Calculated Reaction Pathways Research Articles

Exploring Bacillus species xylanases for industrial applications: screening via thermostability and reaction modelling.

Xylanases derived from Bacillus species hold significant importance in various large-scale production sectors, with increasing demand driven by biofuel production. However, despite their potential, the extreme environmental conditions often encountered in production settings have led to their underutilisation. To address this issue and enhance their efficacy under adverse conditions, we conducted a theoretical investigation on a group of five Bacillus species xylanases belonging to the glycoside hydrolase GH11 family. Bacillus sp. NCL 87-6-10 (sp_NCL 87-6-10) emerged as a potent candidate among the selected biocatalysts; this Bacillus strain exhibited high thermal stability and achieved a transition state with minimal energy requirements, thereby accelerating the biocatalytic reaction process. Our approach aims to provide support for experimentalists in the industrial sector, encouraging them to employ structural-based reaction modelling scrutinisation to predict the ability of targeted xylanases. Utilising crystal structure data available in the Carbohydrate-Active enzymes database, we aimed to analyse their structural capabilities in terms of thermal-stability and activity. Our investigation into identifying the most prominent Bacillus species xylanases unfolds with the help of the semi-empirical quantum mechanics MOPAC method integrated with the DRIVER program is used in calculations of reaction pathways to understand the activation energy. Additionally, we scrutinised the selected xylanases using various analyses, including constrained network analyses, intermolecular interactions of the enzyme-substrate complex and molecular orbital assessments calculated using the AM1 method with the MO-G model (MO-G AM1) to validate their reactivity.

N-Bu4NI/K2S2O8 Mediated Csp2-Csp2 Bond Cleavage - Transformylation from p-Anisaldehyde to Primary Amides.

n-Bu4NI/K2S2O8 mediated transformylation from p-anisaldehyde to primary amides is reported. The mechanistic studies suggest the reaction occurs via a single electron transfer pathway. Based on the DFT electronic structure calculations of various reaction pathways, the most plausible mechanism involves the formation of a phenyl radical cation and an arenium ion as the key intermediates. It represents the first example where p-anisaldehyde is employed as a formyl source via a non-metal mediated Csp2-Csp2 bond cleavage.

Catalytic Mechanism of Fatty Acid Photodecarboxylase: On the Detection and Stability of the Initial Carbonyloxy Radical Intermediate.

In fatty acid photodecarboxylase (FAP), light-induced formation of the primary radical product RCOO⋅ from fatty acid RCOO- occurs in 300 ps, upon which CO2 is released quasi-immediately. Based on the hypothesis that aliphatic RCOO⋅ (spectroscopically uncharacterized because unstable) absorbs in the red similarly to aromatic carbonyloxy radicals such as 2,6-dichlorobenzoyloxy radical (DCB⋅), much longer-lived linear RCOO⋅ has been suggested recently. We performed quantum chemical reaction pathway and spectral calculations. These calculations are in line with the experimental DCB⋅ decarboxylation dynamics and spectral properties and show that in contrast to DCB⋅, aliphatic RCOO⋅ radicals a) decarboxylate with a very low energetic barrier and on the timescale of a few ps and b) exhibit little red absorption. A time-resolved infrared spectroscopy experiment confirms very rapid, ≪300 ps RCOO⋅ decarboxylation in FAP. We argue that this property is required for the observed high quantum yield of hydrocarbons formation by FAP.

Catalytic Mechanism of Fatty Acid Photodecarboxylase: On the Detection and Stability of the Initial Carbonyloxy Radical Intermediate

AbstractIn fatty acid photodecarboxylase (FAP), light‐induced formation of the primary radical product RCOO⋅ from fatty acid RCOO− occurs in 300 ps, upon which CO2 is released quasi‐immediately. Based on the hypothesis that aliphatic RCOO⋅ (spectroscopically uncharacterized because unstable) absorbs in the red similarly to aromatic carbonyloxy radicals such as 2,6‐dichlorobenzoyloxy radical (DCB⋅), much longer‐lived linear RCOO⋅ has been suggested recently. We performed quantum chemical reaction pathway and spectral calculations. These calculations are in line with the experimental DCB⋅ decarboxylation dynamics and spectral properties and show that in contrast to DCB⋅, aliphatic RCOO⋅ radicals a) decarboxylate with a very low energetic barrier and on the timescale of a few ps and b) exhibit little red absorption. A time‐resolved infrared spectroscopy experiment confirms very rapid, ≪300 ps RCOO⋅ decarboxylation in FAP. We argue that this property is required for the observed high quantum yield of hydrocarbons formation by FAP.

Quantum-Chemistry Study of the Hydrolysis Reaction Profile in Borate Networks: A Benchmark.

This investigation involved an ab initio and Density Functional Theory (DFT) analysis of the hydrolysis mechanism and energetics in a borate network. The focus was on understanding how water molecules interact with and disrupt the borate network, an area where the experimental data are scarce and unreliable. The modeled system consisted of two boron atoms, bridging oxygen atoms, and varying numbers of water molecules. This setup allows for an exploration of hydrolysis under different environmental conditions, including the presence of OH- or H+ ions to simulate basic or acidic environments, respectively. Our investigation utilized both ab initio calculations at the MP2 and CCSD(T) levels and DFT with a range of exchange-correlation functionals. The findings indicate that the borate network is significantly more susceptible to hydrolysis in a basic environment, with respect to an acidic or to a neutral pH setting. The inclusion of explicit water molecules in the calculations can significantly affect the results, depending on the nature of the transition state. In fact, some transition states exhibited closed-ring configurations involving water and the boron-oxygen-boron network; in these cases, there were indeed more water molecules corresponding to lower energy barriers for the reaction, suggesting a crucial role of water in stabilizing the transition states. This study provides valuable insights into the hydrolysis process of borate networks, offering a detailed comparison between different computational approaches. The results demonstrate that the functionals B3LYP, PBE0, and wB97Xd closely approximated the reference MP2 and CCSD(T) calculated reaction pathways, both qualitatively in terms of the mechanism, and quantitatively in terms of the differences in the reaction barriers within the 0.1-0.2 eV interval for the most plausible reaction pathways. In addition, CAM-B3LYP also yielded acceptable results in all cases except for the most complicated pathway. These findings are useful for guiding further computational studies, including those employing machine learning approaches, and experimental investigations requiring accurate reference data for hydrolysis reactions in borate networks.

Revelation of HCl poisoning and enhancement mechanism on N-modified Al2O3 catalysts for COS and CS2 hydrolysis

The presence of HCl in blast furnace gas significantly inhibits hydrolytic activity and catalyst stability. The anti-chlorine capacity and poisoning mechanism of Al2O3 catalysts before and after nitrogen modification was investigated by activity evaluation, characterization analysis and theoretical calculations. In the presence of 0.01 vol% HCl, the COS and CS2 conversions of K0.1Al2O3 catalysts decreased rapidly after 4 h of reaction, which was amended by N doping. The N0.1K0.1Al2O3 catalyst maintained 48.23 % COS conversion and 45.41 % CS2 conversion, respectively, after 16 h reaction. The deteriorated reactivity was mainly associated with the decreased specific surface area, reduced chemisorbed oxygen, disrupted basicity and COS and CS2 adsorption ability. Sulfate and HCl on the surface of the unmodified catalyst mainly destroyed the Al sites and led to catalyst deactivation. N doping reinforced the tendency of toxic molecules to adsorb at the K site (K2SO4 and KCl) and thus protected the Al active site. DFT calculation results demonstrated the inhibition of HCl adsorption at the Al site by N modification, while the trapping of HCl by both K and N sites efficiently protected the Al site from acidification. The reaction pathway calculations certified that N doping increased the energy barrier of the HCl dissociation reaction, which inhibited the acidification and deactivation of Al2O3 to some extent.

Crystalline modulation of zirconia for efficient nitrate reduction to ammonia under ambient conditions.

Zirconia as a polycrystalline catalyst can be effectively tuned by doping low-valence elements and meanwhile form abundant oxygen vacancies. Herein, the crystalline structures of zirconia are modulated by scandium doping and proposed as a robust catalyst for nitrate reduction to ammonia. The tetragonal zirconia achieves a maximum ammonia yield of 16.03 mg h-1 mgcat.-1, superior to the other crystal forms. DEMS tests unveil the reaction pathway and theoretical calculations reveal the low free energy of -0.22 eV for nitrate adsorption at the tetragonal zirconia.

Revisiting dispersion and reactivity of active sites via a restricted random distribution model over supported vanadia catalysts for NO reduction

The structure and dispersion of active sites substantially impact the performance of supported metal oxide catalysts, as exemplified by the V2O5/TiO2 catalysts used for NH3-SCR reaction. Due to the complexity of the active site dispersion on the catalyst surface, the intrinsic law of this structure–activity relationship remains controversial. Herein, we proposed a restricted random distribution model to describe the stochastic anchoring behavior of active sites on the TiO2 surface during the loading process of vanadia. The structures of monomeric, dimeric, and polymeric VOx sites were determined by DFT calculations and verified with spectroscopy and adsorption information experimentally. The calculated reaction pathways and energy profiles for these structures indicated that the dual sites configuration and terminal V(=O)2 bond are responsible for the high reactivity of aggregated VOx sites. Combining the reactivity of these various sites and the random distribution method, we built a general profile of the correlation between the V2O5/TiO2 catalyst surface and its reaction performance. The reactivity results obtained from experimental in situ DRIFTS and kinetic tests validate our theoretical model. The random distribution method links DFT calculations and experiments, coupling the structure and dispersion of the VOx active sites to the catalyst reactivity.

Development of a Reactive Force Field for Simulating Photoinitiated Acrylate Polymerization.

Light-driven and photocurable polymer-based additive manufacturing (AM) has enormous potential due to its excellent resolution and precision. Acrylated resins that undergo radical chain-growth polymerization are widely used in photopolymer AM due to their fast kinetics and often serve as a departure point for developing other resin materials for photopolymer-based AM technologies. For successful control of the photopolymer resins, the molecular basis of the acrylate free-radical polymerization has to be understood in detail. We present an optimized reactive force field (ReaxFF) for molecular dynamics (MD) simulations of acrylate polymer resins that captures radical polymerization thermodynamics and kinetics. The force field is trained against an extensive training set including density functional theory (DFT) calculations of reaction pathways along the radical polymerization from methyl acrylate to methyl butyrate, bond dissociation energies, and structures and partial charges of several molecules and radicals. We also found that it was critical to train the force field against an incorrect, nonphysical reaction pathway observed in simulations that used parameters not optimized for acrylate polymerization. The parameterization process utilizes a parallelized search algorithm, and the resulting model can describe polymer resin formation, crosslinking density, conversion rate, and residual monomers of the complex acrylate mixtures.

Probing the pyrolysis of ethyl formate in the dilute gas phase by synchrotron radiation and theory.

The thermal decomposition of the atmospheric constituent ethyl formate was studied by coupling flash pyrolysis with imaging photoelectron photoion coincidence (iPEPICO) spectroscopy using synchrotron vacuum ultraviolet (VUV) radiation at the Swiss Light Source (SLS). iPEPICO allows photoion mass-selected threshold photoelectron spectra (ms-TPES) to be obtained for pyrolysis products. By threshold photoionization and ion imaging, parent ions of neutral pyrolysis products and dissociative photoionization products could be distinguished, and multiple spectral carriers could be identified in several ms-TPES. The TPES and mass-selected TPES for ethyl formate are reported for the first time and appear to correspond to ionization of the lowest energy conformer having a cis (eclipsed) configuration of the O=C(H)-O-C(H2 )-CH3 and trans (staggered) configuration of the O=C(H)-O-C(H2 )-CH3 dihedral angles. We observed the following ethyl formate pyrolysis products: CH3 CH2 OH, CH3 CHO, C2 H6 , C2 H4 , HC(O)OH, CH2 O, CO2 , and CO, with HC(O)OH and C2 H4 pyrolyzing further, forming CO + H2 O and C2 H2 + H2 . The reaction paths and energetics leading to these products, together with the products of two homolytic bond cleavage reactions, CH3 CH2 O + CHO and CH3 CH2 + HC(O)O, were studied computationally at the M06-2X-GD3/aug-cc-pVTZ and SVECV-f12 levels of theory, complemented by further theoretical methods for comparison. The calculated reaction pathways were used to derive Arrhenius parameters for each reaction. The reaction rate constants and branching ratios are discussed in terms of the residence time and newly suggest carbon monoxide as a competitive primary fragmentation product at high temperatures.

Water activation and splitting by single anionic iridium atoms.

Mass spectrometric analysis of anionic products that result from interacting Ir- with H2O shows the efficient generation of [Ir(H2O)]- complexes and IrO- molecular anions. Anion photoelectron spectra of [Ir(H2O)]-, formed under various source conditions, exhibit spectral features that are due to three different forms of the complex: the solvated anion-molecule complex, Ir-(H2O), as well as the intermediates, [H-Ir-OH]- and [H2-Ir-O]-, where one and two O-H bonds have been broken, respectively. The measured and calculated vertical detachment energy values are in good agreement and, thus, support identification of all three types of isomers. The calculated reaction pathway shows that the overall reaction Ir- + H2O → IrO- + H2 is exothermic. Two minimum energy crossing points were found, which shuttle intermediates and products between singlet and triplet potential surfaces. This study presents the first example of water activation and splitting by single Ir- anions.

Density functional theory calculation of reaction pathways for AP decomposition over g-C3N4 surface

The profound understanding of decomposition mechanism of ammonium perchlorate (AP) is significant to the design of AP-based solid propellants. Herein, the possible decomposition reactions of AP over graphitic carbon nitride (g-C3N4) catalyst were investigated by employing density functional theory calculation to explore the reaction network of HClO4 and degradation pathway of NH3 on g-C3N4 surface. The energy barriers of elementary reactions in the network were obtained, the main reaction channels of the decomposition of HClO4 over g-C3N4 catalyst was found out to be HClO4 → ClO3- → ClO2- → ClO− → Cl−. The rate-limiting step along the pathway was the formation of ClO− from ClO2-, with the energy barrier as high as 1.903 eV. The oxidation of g-C3N4 surface would weaken the catalytic capacity of g-C3N4 for the decomposition of HClO4. However, the oxidation of g-C3N4 surface would enhance the catalytic capacity for the adsorption and dehydrogenation of NH3. The pre-adsorbed OH* on g-C3N4 surface would inhibit the adsorption of NH3 but it could promote the dehydrogenation of NH2* and NH*. This work provides new insights about the molecular-level decomposition mechanism of AP over g-C3N4.

Quantum Chemical Study on Interstellar Synthesis of Cytosine by the Automated Reaction Path Search

Novel reaction pathways with the neutral radical–molecule reaction to form cytosine, a nucleobase of DNA and RNA, which can proceed in the interstellar environment, were discovered by automated reaction pathway calculations based on the transition state theory. We suggested the barrierless and exothermic formation of cytosine in two steps. First, the reaction between the O radical and ethynamine forms a key precursor species, NH2CCHO. Then, this radical reacts with CN and HNCH to form cytosine. This study would contribute to elucidating possible reactions on nucleobases under lower temperatures, and further tests are effective by astronomical modeling/observations and laboratory experiments.

Photocatalytic Generations of Secondary and Tertiary Silyl Radicals from Silylboranes Using an Alkoxide Cocatalyst.

Silyl radicals are valuable species to prepare diverse organosilicon compounds. However, unlike stable tertiary silyl radicals, the use of secondary silyl radicals has been problematic in silylation reactions due to their instability. Here, we present photocatalytic in situ generations of both secondary and tertiary silyl radicals by one-electron oxidation of ate complexes, formed from silylboranes and an alkoxide cocatalyst, achieving highly efficient hydrosilylation and deuterosilylation of electron-rich alkenes and dienes as well as electron-deficient alkenes. The theoretical studies show that anionic borate complexes activated with an alkoxide have lower oxidation potentials than neutral borate complexes, allowing the formation of secondary silyl radicals. The calculated reaction pathways reveal that anionic conditions using the conjugate acid-base pair of NaOEt (cocatalyst) and EtOH (solvent) are the key to expanding the scope of silyl radicals and alkenes.

Theoretical calculations of formation and reactivity of o-quinomethide derivatives of resorcin[4]arene with reference to empirical data.

This paper describes theoretical reaction pathways of alkoxybenzyl derivatives of resorcin[4]arene leading to the formation of o-quinomethide derivatives of resorcin[4]arene (o-QMR[4]A). For each case, the activation energies for the formation of one o-QMR[4]A unit and the activation energies for the backward reaction were calculated. Based on the calculated reaction pathways, the reaction mechanism of o-QMR[4]A formation was proposed. Using the example of o-QMR[4]A generated from a methoxy derivative of resorcin[4]arene, the activation energies with selected nucleophiles were calculated and the reaction mechanisms discussed. Reaction path calculations were performed using the nudged elastic band method and semiempirical extended tight-binding method (GFN2-xTB). Using hydroxybenzyl derivatives of resorcin[4]arene as an example, a comparison of calculated activation energies by selected density-functional theory methods with GFN2-xTB and B97-3c geometries was performed. B97-3c and wB97XD methods were used to calculate the energies of the reactants (R), transition states (TS) and products (P) of the analysed reactions. Theoretical reaction mechanisms were discussed with respect to the orbital-weighted Fukui dual descriptor (Δfw) and experimental data.

Large Conformational Change in the Isomerization of Flexible Crown Ether Observed at Low Temperature.

The dynamic processes of conformational changes of supramolecules are important to understand the motion in synthetic supramolecules. Although a host-guest complex is the most basic supramolecule, a detailed mechanism of its conformational changes has rarely been studied. Here, we observed the large conformational change of a dibenzo-24-crown-8 complex with four guest ions (Ag+, Na+, K+, and NH4+) at low temperature in the gas phase. The isomerization between the two types of conformers, which have different distances between the two benzene rings, proceeds even at 86 K. Using variable-temperature ion mobility-mass spectrometry (IM-MS) at 100-210 K, the activation energy for the isomerization is determined to be rather small (4.8-9.0 kJ mol-1). Reaction pathway calculations revealed that the isomerization is caused by the sequential rotation of two single bonds in the crown ether ring. The present cryogenic IM-MS study of the host-guest complexes at the molecular level opens an approach to detailed understanding of the motion in supramolecules.

Diels-Alder Reaction of Photochemically Generated (E)-Cyclohept-2-enones: Diene Scope, Reaction Pathway, and Synthetic Application.

Upon irradiation at λ = 350 nm, cyclohept-2-enone undergoes an isomerization to the strained (E)-isomer. The process was studied by XMS-CASPT2 calculations and found to proceed by two competitive reaction channels on either the singlet or the triplet hypersurface. (E)-Cyclohept-2-enone is a reactive dienophile in thermal [4 + 2] cycloaddition reactions with various dienes. Ten different dienes were probed, most of which─except for 1,3-cyclohexadiene─underwent a clean Diels-Alder reaction and gave the respective trans-fused six-membered rings in good yields (68-98%). The reactions with furan were studied in detail, both experimentally and by DLPNO-CCSD(T) calculations. Two diastereoisomers were formed in a ratio of 63/35 with the exo-product prevailing, and the configuration of both diastereoisomers was corroborated by single crystal X-ray crystallography. The outcome of the photoinduced Diels-Alder reaction matched both qualitatively and quantitatively the calculated reaction pathway. Apart from cyclohept-2-enone, five additional cyclic hept-2-enones and cyclooct-2-enone were employed in their (E)-form as dienophiles in the Diels-Alder reaction with 1,3-cyclopentadiene (80-98% yield). The method was eventually applied to a concise total synthesis of racemic trans-α-himachalene (four steps, 14% overall yield).

Reactions of NO<sub>3</sub> with aromatic aldehydes: gas-phase kinetics and insights into the mechanism of the reaction

Abstract. Rate coefficients for the reaction of NO3 radicals with a series of aromatic aldehydes were measured in a 7300 L simulation chamber at ambient temperature and pressure by relative and absolute methods. The rate coefficients for benzaldehyde (BA), ortho-tolualdehyde (O-TA), meta-tolualdehyde (M-TA), para-tolualdehyde (P-TA), 2,4-dimethyl benzaldehyde (2,4-DMBA), 2,5-dimethyl benzaldehyde (2,5-DMBA) and 3,5-dimethyl benzaldehyde (3,5-DMBA) were k1= 2.6 ± 0.3, k2= 8.7 ± 0.8, k3= 4.9 ± 0.5, k4= 4.9 ± 0.4, k5= 15.1 ± 1.3, k6= 12.8 ± 1.2 and k7= 6.2 ± 0.6, respectively, in the units of 10−15 cm3 molec.−1 s−1 at 298 ± 2 K. The rate coefficient k13 for the reaction of the NO3 radical with deuterated benzaldehyde (benzaldehyde-d1) was found to be half that of k1. The end product of the reaction in an excess of NO2 was measured to be C6H5C(O)O2NO2. Theoretical calculations of aldehydic bond energies and reaction pathways indicate that the NO3 radical reacts primarily with aromatic aldehydes through the abstraction of an aldehydic hydrogen atom. The atmospheric implications of the measured rate coefficients are briefly discussed.

Computations on Pericyclic Reactions Reveal the Richness of Ambimodal Transition States and Pericyclases

AbstractThe pericyclic reaction concept was developed by Woodward and Hoffmann 56 years ago, before accurate quantum mechanical calculations of organic reaction pathways were possible. Since then, computational methods such as density functional theory and coupled‐cluster methods have been formulated, and computer speeds have increased a hundred trillion (1011)‐fold. The subtleties and timings of bond formation in reactions have been established by high‐accuracy quantum mechanical calculations. The field of pericyclic reactions has been enriched by understanding of the borderline between concerted pericyclic reactions and stepwise reactions. Higher‐order pericyclic reactions, involving more than six electrons, have ambimodal transition states that can form two, three, or even four products. In addition, while only imagined in the last century, the fact that enzymes can catalyze many pericyclic reactions has been repeatedly established in the 21st century, aided enormously by computational studies.

Atomistic simulations of surface reactions in ultra-high-temperature ceramics: O[formula omitted], H[formula omitted]O and CO adsorption and dissociation on ZrB[formula omitted](0001) surfaces

Understanding surface reactivity is crucial in many fields, going from heterogeneous catalysis to materials oxidation and corrosion. In order to decipher the surface reactions of ZrB2 exposed to the harsh environment of aerospace components, the chemical activity of both Zr- and B-surfaces is predicted and compared by using density functional theory and nudged elastic band methods. In particular the adsorption, dissociation and diffusion of O2, CO and H2O are extensively examined through the calculation of surface adsorption energies and reaction pathways. We find the dissociative adsorption of O2 dominating the reactivity of ZrB2 surfaces, while the dissociation of H2O and CO is weakly active on Zr-surfaces, and even less activated on B-terminated ones. Importantly, we discover that the reaction of O2 and CO can trigger strong surface reconstruction at B-surfaces. Our work thus provides significant insights into the diverse adsorption and reaction mechanisms on ZrB2 surfaces.