Rate-determining Reaction Research Articles

Guidelines for β-Lactam Synthesis: Glycal Protecting Groups Dictate Stereoelectronics and [2+2] Cycloaddition Kinetics.

The alkene-isocyanate cycloaddition method affords β-lactams from glycals with high regio- and stereoselectivity, but the factors that determine substrate reactivity are poorly understood. Thus, we synthesized a library of 17 electron-rich alkenes (glycals) with varied protecting groups to systematically elucidate the factors that influence their reactivity toward the electron-poor trichloroacetyl isocyanate. The experimentally determined reaction rates exponentially correlate with the computationally determined highest occupied molecular orbital-lowest unoccupied molecular orbital (HOMO-LUMO) gap and natural bond orbital (NBO) valence energies. The electron-withdrawing ability of the protecting groups, but not bulk, impacts the electron density of the glycal allyloxocarbenium system when oriented pseudo-axially (i.e., stereoelectronics). In this conformation, ring σC-O* orbitals oriented antiperiplanar to the allyloxocarbenium system decrease glycal reactivity via negative hyperconjugation as protecting group electron withdrawal increases. Transition-state calculations reveal that protecting group stereoelectronics direct the reaction to proceed via an asynchronous one-step mechanism through a zwitterionic species. The combined experimental and computational findings, along with experimental validation on an unknown glycal, provide insight on the reaction mechanism and the role of distant protecting groups in glycal reactivity. Together, these studies will aid in the synthesis of new β-lactam antibiotics, β-lactamase inhibitors, and bicyclic carbohydrate-β-lactam monomers prepared by the alkene-isocyanate method.

A Tale of Two Lab Courses: An Account and Reflection on the Teaching Challenges Experienced by Organic and Analytical Chemistry Laboratories During the COVID-19 Period

A comparison of the experiences of both organic and analytical lab faculty during the COVID-19 pandemic distance learning initiative is described here. Faculty of both lab courses experienced four shared challenges in the transition to the online format: (1) experimental implementation, (2) assessments and postlab activities, (3) technological inequalities, and (4) synchronization of student attendance. Edited video content of the experiments was created for the organic laboratories but not for the analytical laboratories due to a lack of time and resources. A guided-inquiry activity used to engage organic chemistry students in the determination of the relative reaction rates of substitution reactions appeared to be less successful in the online environment for the students. Analytical lab faculty described using online guided data analysis problems to encourage students to keep up with the content and learn from their mistakes to further prepare themselves for related content in the activities that followed. Extended due dates were given on postlab assignments to mitigate technical issues encountered by the students. Interactive lab experiences for organic chemistry laboratories and hybrid laboratories for analytical chemistry laboratories are proposed for future semesters. Both courses implemented flexible scheduling of lectures, office hours, and workshops to offset student concerns.

Mechanistic Insights into the Hydrogen Oxidation Reaction on PtNi Alloys in Alkaline Media: A First-Principles Investigation.

The promising alkaline anion exchange membrane fuel cell suffers from sluggish kinetics of the hydrogen oxidation reaction (HOR). However, the puzzling HOR mechanism hinders the further development of highly active catalysts in alkaline media. In this work, we conducted detailed first-principles calculations to acquire a deep understanding of the alkaline HOR mechanism on PtNi bulk alloys [Pt3Ni(111), Pt2Ni2(111), and PtNi3(111)] and its surface alloy [PtNisurf(111)]. The full free energy profiles suggest that the HOR on PtNi alloys proceeds via the Tafel-Volmer mechanism, that is, the direct decomposition of H2 into two adsorbed H, followed by its reaction with OH- in the electrolyte, as the rate-determining step, to form H2O. Therefore, the HOR activity of PtNi alloys is solely impacted by the adsorption of hydrogen, rather than hydroxyl species, though the oxophilicity is also enhanced by alloying Pt with Ni. Thermodynamically, a moderate H adsorption free energy, ΔGH* ≈ 0.414 eV, is calculated to be an optimal candidate for the HOR at pH = 13. Alloying Pt with Ni can elevate the d-band center (εd), push the value of ΔGH* closer to 0.414 eV, and thus lower the free energy barrier (Ea) of the rate-determining Volmer reaction, leading to the highest HOR activity of PtNi3(111) among all considered PtNi alloys. This situation is further confirmed by both the microkinetic model and the Tafel plot, where PtNi3(111) exhibits the highest reaction rate (r = 9.42 × 103 s-1 site-1) and the largest exchange current density (i0 = 1.42 mA cm-2) for HOR in alkaline media. This work provides a fundamental understanding of the HOR mechanism and theoretical guidance for rational design of electrocatalysts for HOR in alkaline media.

Measurement of very high threshold reactions using 252Cf source

Only neutron spectrum standard is 252Cf spontaneous fission neutron spectrum. However, the high energy tail of this spectrum is loaded with high uncertainty. To reduce this uncertainty, it is crucial to use validated cross sections with low uncertainty. The explored set of reactions covers 58Ni(n,X)57Co, 169Tm(n,3n)167Tm, 197Au(n,3n)195Au, 209Bi(n,3n)207Bi and 209Bi(n,4n)206Bi threshold reactions. Measurement of dosimetric 169Tm(n,3n)167Tm, 209Bi(n,3n)207Bi and 209Bi(n,4n)206Bi reactions spectral averaged cross sections (SACS) is included in NEA's High Priority Nuclear Data Request List. All these reactions SACS were measured for the first time. All SACS were derived from experimentally determined reaction rates by gamma spectrometry using the same high-purity germanium detector. In the case of 169Tm(n,3n)167Tm reaction, the difference between experimental and calculated value using the IRDFF-II library is only 1.45%. Concerning 197Au(n,3n)195Au reaction, the reasonable agreement is achieved only using the TENDL-2017 library. In the case of 209Bi(n,3n)207Bi reaction, agreement within uncertainty is not achieved with any library unlike 209Bi(n,4n)206Bi reaction where the agreement within uncertainty is achieved with IRDFF-II library. The best agreement for 58Ni(n,X)57Co reaction is achieved using ENDF/B-VIII library.

Experiment Optimization on the Reaction Rate Determination and Its Implementation in Chemistry Learning to Develop Science Process Skills

Keterampilan proses dalam sains sangat diperlukan untuk membangun konsep dan pemahaman peserta didik. Salah satu upaya yang dapat dilakukan untuk mengembangkan keterampilan proses ialah dengan aktivitas belajar di laboratorium. Penelitian ini dilakukan bertujuan untuk mengembangkan keterampilan proses sains mahasiswa melalui penggunaan perangkat praktikum yang dapat mengukur laju reaksi secara kuantitatif. Eksperimen untuk mengetahui kondisi optimum dari praktikum penentuan laju reaksi pembentukan gas dilakukan untuk selanjutnya diturunkan menjadi lembar kerja. Lembar kerja yang telah divalidasi diimplementasikan kepada mahasiswa dengan menggunakan pre-experimental design dengan bentuk one shot case study. Subjek penelitian ialah 38 orang mahasiswa semester IV program studi Pendidikan Kimia UIN Sunan Gunung Djati Bandung yang mengambil mata kuliah kinetika dan kesetimbangan. Pengumpulan data dilakukan dengan menggunakan instrumen lembar kerja, lembar observasi aktivitas mahasiswa dan daftar ceklis kinerja praktikum. Hasil penelitian menunjukkan bahwa kondisi optimum praktikum penentuan laju reaksi pada variasi konsentrasi H2O2 sebesar 1,5 - 6% ialah penggunaan tabung reaksi sebagai reaktor, pipet ukur sebagai penampung gas, katalis KI dan MnO2 sebanyak 0,002 mol, serta volume gas O2 yang diamati sebanyak 10 mL. Hasil observasi terhadap aktivitas mahasiswa pada saat berlangsungnya kegiatan praktikum menunjukkan nilai rata-rata sebesar 98±4,737%, nilai ini menunjukkan bahwa mahasiswa terlibat aktif dalam kegiatan praktikum. Hasil analisis keterampilan proses sains mahasiswa pada praktikum penentuan laju reaksi pembentukan gas secara keseluruhan diinterpretasikan sangat baik dengan nilai rata-rata sebesar 88±1,785. Aspek mengumpulkan data memiliki nilai rata-rata tertinggi yang diinterpretasikan sangat baik dengan nilai sebesar 100. Aspek KPS menyimpulkan memiliki nilai rata-rata terendah yang diinterpretasikan baik dengan nilai sebesar 76.

Effect of substituents in hydroxyl radical-mediated degradation of azo pyridone dyes: Theoretical approaches on the reaction mechanism

Understanding the degradation behavior of azo dyes in photocatalytic wastewater treatment is of fundamental and practical importance for their application in textile-processing and other coloration industries. In this study, quantum chemistry, as density functional theory, was used to elucidate different degradation pathways of azo pyridone dyes in a hydroxyl radical (HO•)-initiated photocatalytic system. A series of substituted azo pyridone dyes were synthesized by changing the substituent group in the para position of the benzene moiety, ranging from strong electron-donating to strong electron-withdrawing groups. The effect of dye molecular structure on the photocatalytic degradation reaction mechanism was analyzed and quantification of substituent effects on the thermodynamic and kinetics parameters was performed. Potential energy surface analysis revealed the most susceptible reaction site for the HO• attack. The calculated reaction barriers are found to be strongly affected by the nature of substituent group with a good correlation using Hammett σp constants and experimentally determined reaction rates. The stability of pre-reaction complexes and transition state complexes were analyzed applying the distortion-interaction model. The increased stability of the transition state complexes with the distancing from the substituent group has been established.

Time-Resolved Fluorescence Anisotropy of a Molecular Rotor Resolves Microscopic Viscosity Parameters in Complex Environments.

Understanding viscosity in complex environments remains a largely unanswered question despite its importance in determining reaction rates in vivo. Here, time-resolved fluorescence anisotropy imaging (TR-FAIM) is combined with fluorescent molecular rotors (FMRs) to simultaneously determine two non-equivalent viscosity-related parameters in complex heterogeneous environments. The parameters, FMR rotational correlation time and lifetime, are extracted from fluorescence anisotropy decays, which in heterogeneous environments show dip-and-rise behavior due to multiple dye populations. Decays of this kind are found both in artificially constructed adiposomes and in live cell lipid droplet organelles. Molecular dynamics simulations are used to assign each population to nano-environments within the lipid systems. The less viscous population corresponds to the state showing an average 25° tilt to the lipid membrane normal, and the more viscous population to the state showing an average 55° tilt. This combined experimental and simulation approach enables a comprehensive description of the FMR probe behavior within viscous nano-environments in complex, biological systems.

Material erosion measurements and expected operational lifetime of a deployable photon sieve payload

Spacecraft operating in low-Earth orbit are subjected to a number of hazardous environmental constituents that can lead to decreased system performance and reduced operational lifetimes. Due to their thermal, optical, and mechanical properties, polymers are used extensively in space systems; however they are particularly susceptible to material erosion and degradation as a result of exposure to the LEO environment. The focus of this research is to examine the material erosion and mass loss experienced by a custom Kapton-like polyimide due to exposure in a simulated low-earth orbit environment. The deployable membrane telescope design discussed in this research is named Peregrine and is the scientific payload for FalconSat-7, a 3U cubesat designed and developed at the United States Air Force Academy (USAFA) for the purpose of demonstrating the capability of deployable membrane telescope technology on a nano-satellite platform. In addition to the polymer samples, chrome, silver and gold specimens will be examined to measure the oxidation rate and act as a control specimen, respectively. A magnetically filtered atomic oxygen plasma source has previously been developed and characterized for the purpose of simulating the low-Earth orbit environment. The plasma source can be operated at a variety of discharge currents and gas flow rates, of which the plasma parameters downstream of the source are dependent. The characteristics of the generated plasma were examined as a function of these operating parameters to optimize the production of O+ ions with energy relevant to LEO applications. The erosion yield of the Kapton-like polyimide was experimentally determined to be 2.84 × 10−24 cm3 per atom which is in close agreement when compared to the on-orbit measurement for reaction efficiency of Kapton HN. The experimentally determined reaction rate for the Kapton-like polyimide was used to estimate the operational lifetime of the photon sieve during the solar conditions expected beginning in May 2019. The effective lifetime is estimated between 126 and 153 days.

In-core dosimetry for the validation of neutron spectra in the CROCUS reactor

The present article describes the preliminary validation study of simulated in-core and reflector n eutron spectra in preparation of oncoming experimental programs in the zeropower reactor CROCUS at EPFL. For this purpose, a set of activation foils were irradiated at three characteristic positions in the CROCUS reactor, and the subsequent activities were analyzed via γ spectrometry. The experimental setup was then modeled with the Monte Carlo neutron transport code Serpent2 and associated with an analysis tool to include the effect of the reactor power history during experiments. The comparison of calculated and measured reaction rates (C/E) indicates a general consistency (at 2σ) between calculated and measured spectra. However, offsets of C/E values were observed in (n, γ) reactions, up to 18% for 115In and 8% for 63Cu dosimeters. This could be caused by an unexpected isotopic composition, uncertainties in nuclear data, or the spectrometry analysis. In addition, a 100-groups spectrum unfolding was performed using the experimentally determined reaction rates and the Serpent2 spectra as the prior knowledge. The unfolded spectra were mainly adjusted in the thermal and fast ranges, while few modifications w ere m ade i n t he e pithermal r egion d ue t o the low contribution of epithermal neutrons in activation processes. Moreover, within energy groups where the capture reactions show resonant behavior, flux depletion (up to 38% as compared to the prior spectra) is observed due to the absence of self-shielding effect in the unfolding process. For this purpose, an unfolding method based on energy groups weighting is developed and tested.

Beyond thermodynamic-based material-screening concepts: Kinetic scaling relations exemplified by the chlorine evolution reaction over transition-metal oxides

State-of-the-art material screening in the field of electrocatalysis mainly uses the concept of linear scaling relationships in order to express the (free) adsorption energies of different reaction intermediates, adsorbed on the surface of a solid-state electrocatalyst, as function of a descriptor. This thermodynamic analysis, based on the application of the computational hydrogen electrode approach (CHE), ultimately results in the construction of a Volcano plot, which facilitates identifying promising catalysts within a class of materials. The conventional ab initio Volcano concept, however, lacks of two critical aspects: on the one hand the applied overpotential, which constitutes the driving force of an electrocatalytic reaction, is not included in the underlying approach, since the thermodynamic analysis refers to the standard equilibrium potential of the electrocatalytic process; on the other hand, the kinetics is not accounted for. Herein, an alternate material-screening concept is presented, which promotes a discussion of the catalytic performance within a class of materials by explicitly including both the kinetic description and applied overpotential: kinetic scaling relations enable resolving the rate-determining reaction step in a homologous series of single-crystalline electrocatalysts in the overpotential regime of interest for practical applications. The proposed methodology is exemplified by the chlorine evolution reaction over transition-metal oxides, which corresponds to the anode reaction in the industrially relevant chlor-alkali process for the production of gaseous chlorine as basic chemical.

Cross section of α -induced reactions on Au197 at sub-Coulomb energies

Statistical model calculations have to be used for the determination of reaction rates in large-scale reaction networks for heavy-element nucleosynthesis. A basic ingredient of such a calculation is the a-nucleus optical model potential. Several different parameter sets are available in literature, but their predictions of a-induced reaction rates vary widely, sometimes even exceeding one order of magnitude. This paper presents the result of a-induced reaction cross-section measurements on gold which could be carried out for the first time very close to the astrophysically relevant energy region. The new experimental data are used to test statistical model predictions and to constrain the a-nucleus optical model potential. For the measurements the activation technique was used. The cross section of the (a,n) and (a,2n) reactions was determined from g-ray counting, while that of the radiative capture was determined via X-ray counting. The cross section of the reactions was measured below E$_a=20.0$~MeV. In the case of the $^{197}$Au(a,2n)$^{199}$Tl reaction down to 17.5~MeV with 0.5-MeV steps, reaching closer to the reaction threshold than ever before. The cross section of $^{197}$Au(a,n)$^{200}$Tl and $^{197}$Au(a,g)$^{201}$Tl was measured down to E$_a=13.6$ and 14.0~MeV, respectively, with 0.5-MeV steps above the (a,2n) reaction threshold and with 1.0-MeV steps below that. The new dataset is in agreement with the available values from the literature, but is more precise and extends towards lower energies. Two orders of magnitude lower cross sections were successfully measured than in previous experiments which used g-ray counting only, thus providing experimental data at lower energies than ever before. The new precision dataset allows us to find the best-fit a-nucleus optical model potential and to predict cross sections in the Gamow window with smaller uncertainties.

A multiphase nickel iron sulfide hybrid electrode for highly active oxygen evolution

Development of highly active electrocatalysts for oxygen evolution reaction (OER) is one of the critical issues for water splitting, and most reported catalysts operate at overpotentials above 190 mV. Here we present a multiphase nickel iron sulfide (MPS) hybrid electrode with a hierarchical structure of iron doped NiS and Ni3S2, possessing a benchmark OER activity in alkaline media with a potential as low as 1.33 V ( vs . reversible hydrogen electrode) to drive an OER current density of 10 mA cm−2. The Fe doped NiS, combined with highly conductive disulfide phase on porous Ni foam, is believed to be responsible for the ultrahigh activity. Furthermore, density functional theory simulation reveals that partially oxidized sulfur sites in Fe doped NiS could dramatically lower the energy barrier for the rate-determining elementary reaction, thus contributing to the active oxygen evolution.

Pleione: A tool for statistical and multi-objective calibration of Rule-based models

Mathematical models based on Ordinary Differential Equations (ODEs) are frequently used to describe and simulate biological systems. Nevertheless, such models are often difficult to understand. Unlike ODE models, Rule-Based Models (RBMs) utilise formal language to describe reactions as a cumulative number of statements that are easier to understand and correct. They are also gaining popularity because of their conciseness and simulation flexibility. However, RBMs generally lack tools to perform further analysis that requires simulation. This situation arises because exact and approximate simulations are computationally intensive. Translating RBMs into ODEs is commonly used to reduce simulation time, but this technique may be prohibitive due to combinatorial explosion. Here, we present the software called Pleione to calibrate RBMs. Parameter calibration is essential given the incomplete experimental determination of reaction rates and the goal of using models to reproduce experimental data. The software distributes stochastic simulations and calculations and incorporates equivalence tests to determine the fitness of RBMs compared with data. The primary features of Pleione were thoroughly tested on a model of gene regulation in Escherichia coli. Pleione yielded satisfactory results regarding calculation time and error reduction for multiple simulators, models, parameter search strategies, and computing infrastructures.

A Proposal for the Mechanism of the CH + CO2 Reaction

Few experimental studies on the CH + CO2 global reaction propose H, CO, and HCO as major products. However, the reaction mechanisms behind this process have not yet been elucidated. Moreover, some intriguing kinetic particularities were noticed in these previous investigations. The advanced theoretical study performed here shows that a CH insertion mechanism is capable of explaining all the experimental data available. Hence, the strong deviations from a traditional Arrhenius behavior ascribed to the rate-determining elementary reaction (the CH insertion step) account for the kinetic particularities observed experimentally. A change in the preferred product channel as temperatures increase (from HCO + CO to H + 2CO) is also predicted to occur due to the HCO decomposition, although the CH depletion rates in typical conditions are not affected by this additional step.

Validation of IRDFF-II library by means of 252Cf spectral averaged cross sections

Spectrum-averaged cross sections (SACS) is an important quantity usable in validation of nuclear cross sections. Especially in case of dosimetrical reactions there is a request on precise validation. This paper presents SACS measured in the reference 252Cf(sf) neutron field for neutron dosimetry reactions to validate recently updated IRDFF-II library intended mainly for neutron metrology applications. It covers 46Ti(n,p)46Sc, 47Ti(n,p)47Sc, 48Ti(n,p)48Sc, 58Ni(n,p)58Co, 60Ni(n,p)60Co, 58Ni(n,2n)57Ni, 24Mg(n,p)24Na, 27Al(n,α)24Na and 63Cu(n,α)60Co threshold reactions. Measurement of 60Ni(n,p)60Co SACS is included in NEA's High Priority Nuclear Data Request List since existing data are discrepant. Spectral averaged cross sections were derived from experimentally determined reaction rates by gamma spectrometry using a same high-purity germanium detector to measure all irradiated samples. Measured spectrum-averaged cross sections agree very well within quoted uncertainties with those calculated using the IRDFF-II library. No other library achieves such good performance. Thus, the presented data support use of the cross sections of the mentioned reactions from IRDFF-II library.

Importance of Nitrogen-Hydrogen Bond pKa in the Catalytic Coupling of Alkenes and Amines by Amidate Tantalum Complexes: A Computational Study.

Density functional theory (DFT) was carried out to study the impact of substituents with different electronic properties upon hydrogen transfer as the rate-determining step in the hydroaminoalkylation catalytic cycle in order to determine the character of the hydrogen atom in the transition state. In the transition state of the rate-determining step, an N-methylaniline substrate ligates to Ta and transfers its hydrogen to the α-carbon of a five-membered tantallacycle and a Ta-C bond is thus broken. Study of the activation energy barriers resulting from the different para- and meta-substituted N-methylanilines and their correlation with computed pKa and bond dissociation free energy (BDFE) values of the N-methylanilines show more obvious correlations between pKa and ΔG‡ values. Assessing the asynchronicity parameter (η) for the studied substituents reveals that pKa is a larger driving force in the rate-determining hydrogen transfer reaction than the BDFE, which suggest a reasonable amount of protic character in the transition state, and possible routes to the design of more active catalysts with greater substrate scope.

Kinetics of Reductive Degradation of 2,4-dinitroanisole (DNAN) Using Mg-Based Bimetals

Technology advancements and modern use of explosives have led to the development of insensitive munitions such as 2,4-dinitroanisole (DNAN). Treatment systems using zero-valent iron (ZVI) and Fe-based bimetals are well-known, however, Mg-based bimetals can be advantageous over iron because of the more negative reduction potential and relative insensitivity to pH conditions. This work reports on the use of ZVMg and Mg-bimetals (Mg/Cu, Mg/Ni, Mg/Zn) to treat pure compound aqueous solutions and wastewater containing DNAN. Kinetic experiments were carried out in bench-scale batch reactors at unadjusted initial pH, 0.5% solids-to-liquid ratio (S/L), and 10:1 Mg to catalytic metal ratio. The results, modelled with a pseudo-first order kinetic expression, are used to determine reaction rate constants via nonlinear regression. For pure DNAN aqueous solutions, the pseudo-first order kinetic rate constants are 0.119, 0.102, 0.020, and 0.009 min−1 for Mg/Cu, Mg/Zn, Mg/Ni, and ZVMg, respectively. Reaction rate constants for DNAN wastewater are 0.114, 0.046, and 0.021 min−1 for Mg/Cu, Mg/Zn and Mg/Ni, respectively. Parametric studies investigated the impact of catalytic metal, reagent dose, and initial pH on DNAN degradation. Reagent dose levels tested were 0.25, 0.50 and 0.75% S/L. Initial pH, lowered with acetic acid (pH range 3.3–4.0), significantly enhanced reaction rates of all bimetal pairs and ZVMg yielding half-lives between 0.7–1.4 min. The bimetal pair showing the fastest kinetics at unadjusted initial pH, Mg/Cu, was characterized in constant temperature experiments. Under identical conditions (unadjusted initial pH, 0.5% S/L, 10:1 Mg: Cu), the activation energy of DNAN degradation by Mg/Cu is 8.47 kJ/mol.

Utilization of Carbon Nanotube Based Catalyst for the Performance Enhancement of Aqueous Organic Redox Flow Battery

Alloxazine and ferrocyanide were introduced as redox couple for aqueous organic redox flow battery (AORFB). Alloxazine was further modified by carboxylic acid (COOH) (COOH-alloxazine) to increase the aqueous solubility. For improving the performance of AORFB, the redox reactivity of the rate determining reaction (RDR) should be enhanced. Carboxylic acid group doped carbon nanotube (CA-CNT) catalyst was used for increasing the redox reactivity of RDR. The CA-CNT induced a better redox reactivity of COOH-alloxazine that was RDR because of the function of COOH as a proton donor. The strengthened hydrophilic property of COOH-alloxazine and the increased number of active sites were another reasons for causing the better redox reactivity. Regarding AORFB full cell testing, when the CA-CNT was adopted as the catalyst for the negative electrode, the performance of AORFB increased. According to the detailed results, charge/discharge overpotential and IR drop potential were enhanced, coulombic and energy efficiencies also increased, and discharging capacity reached to the similar level to that of vanadium redox flow battery. Reference [1] "Effect of carboxylic acid doped carbon nanotube catalyst on the performance of aqueous organic redox flow battery using the modified alloxazine and ferrocyanide redox couple", W. Lee, B.W. Kwon and Y. Kwon, ACS Applied Materials & Interfaces, 10, 36882-36891, 2018

Water-Mediated Reduction of Aqueous N-Nitrosodimethylamine with Pd.

Pd-catalyzed reduction has emerged as a promising treatment strategy to remove the recalcitrant disinfection byproduct N-nitrosodimethylamine (NDMA). However, the reaction pathways remain unexplored, and questions remain about how water solvent influences NDMA reduction mechanisms and selectivity. Here, we compute the energies and barriers of all relevant elementary steps in NDMA reduction by H2 on Pd(111) using density functional theory. We further calculate water-assisted H-shuttling for all hydrogenation reactions explicitly and include water solvation for all elementary reactions implicitly. We parametrize microkinetic models to predict product formation rates and selectivities over a wide range of NDMA concentrations. We show that H2O-mediated H-shuttling lowers the reaction barriers for all hydrogenation reactions involved in NDMA reduction while implicit solvation has negligible impact on the reaction and activation energies. We further conduct batch experiments with SiO2-supported Pd nanoparticles and compare them with the microkinetic models. The predicted rates, selectivity, and apparent activation energy from the model parametrized with both explicit H2O-mediated H-shuttling and implicit solvation correspond well with experimental observations. Models that ignore water as an H-shuttle or solvent fail to recover the experimental rates and apparent activation energy. We identified the rate-determining steps of the reaction and show the reaction flow pathways of the complicated reaction network. Finally, we demonstrate that water-mediated H-shuttling changes the rate-determining steps and reaction flows of elementary reactions.

Flavonol biosynthesis by nonheme iron dioxygenases: A computational study into the structure and mechanism

Plants produce flavonol compounds for vital functions regarding plant growth, fruit and flower colouring as well as fruit ripening processes. Several of these biosynthesis steps are stereo- and regioselective and are being carried out by nonheme iron enzymes. Using density functional theory calculations on a large active site model complex of flavanone-3β-hydroxylase (FHT), we established the mechanism for conversion of naringenin to its dihydroflavonol, which is a key step in the mechanism of flavonol biosynthesis. The reaction starts with dioxygen binding to the iron(II) centre and a reaction with α-ketoglutarate co-substrate gives succinate, an iron(IV)-oxo species and CO2 with large exothermicity and small reaction barriers. The rate-determining reaction step in the mechanism; however, is hydrogen atom abstraction of an aliphatic CH bond by the iron(IV)-oxo species. We identify a large kinetic isotope effect for the replacement of the transferring hydrogen atom by deuterium. In a final step the OH and substrate radicals combine to form the alcohol product with a barrier of several kcal mol−1. We show that the latter is the result of geometric constraints in the active site pocket. Furthermore, the calculations show that a weak tertiary CH bond is shielded from the iron(IV)-oxo species in the substrate binding position and therefore the enzyme is able to activate a stronger CH bond. As such, the flavanone-3β-hydroxylase enzyme reacts regioselectively with one specific CH bond of naringenin by avoiding activation of weaker bonds through tight substrate and oxidant positioning.