Heavy-Atom Tunneling in the Covalent/Dative Bond Complexation of Cyclo[18]carbon–piperidine

Recent quantum chemical computations demonstrated the electron-acceptance behavior of this highly reactive cyclo[18]carbon (C18) ring with piperidine (pip). The C18–pip complexation exhibited a double-well potential along the N–C reaction coordinate, forming a van der Waals (vdW) adduct and a more stable, strong covalent/dative bond (DB) complex by overcoming a low activation barrier. By means of direct dynamical computations using canonical variational transition state theory (CVT), including the small-curvature tunneling (SCT), we show the conspicuous role of heavy atom quantum mechanical tunneling (QMT) in the transformation of vdW to DB complex in the solvent phase near absolute zero. Below 50 K, the reaction is entirely driven by QMT, while at 30 K, the QMT rate is too rapid (kT ~ 0.02 s-1), corresponding to a half-life time of 38 s, indicating that the vdW adduct will have a fleeting existence. We also explored the QMT rates of other cyclo[n]carbon–pip systems. This study sheds light on the decisive role of QMT in the covalent/DB formation of the C18–pip complex at cryogenic temperatures.

Mechanistic Study on Gold(I)-Catalyzed Unsaturated Spiroketalization Reaction

The mechanism of metal-catalyzed spiroketalization of propargyl acetonide is explored by employing DFT with the B3LYP/6-31+G(d) method. Acetonide is used as a regioselective regulator in the formation of monounsaturated spiroketal. The energies of transition states, intermediates, reactants and products are calculated to provide new insight into the mechanism of the reaction. The energetic features, validation of the observed trends in regioselectivity are conferred in terms of electronic indices via FMO analysis. The presence of acetonide facilitates a stepwise spiroketalization as it masks the competing nucleophile, and thus hydroxyl group present, exclusively acts as a nucleophile. The vinyl gold intermediate 3 is formed from 2 via activation barrier TS1. This is the first ring formation, which is 6-exo-dig cyclization. The intermediate 3 is converted into allenyl ether 4, which isomerizes to the intermediate oxocarbenium ion 5 via activation barrier TS2. The intermediate 5 cyclizes to 6 via TS3. This is the second ring formation. The intermediate 6 on protodeauration turns into 6,6-monounsaturated spiroketal 7. It is concluded that acetonide as a protecting group serves the purpose, and thus a wide range of spiroketals can be prepared, regioselectivity.

Quantum Mechanical Modeling Unveil the Effect of Substitutions on the Activation Barriers of the Diels-Alder Reactions of an Antiviral Compound 7H-Benzo[a]phenalene

Density functional theory has been utilized for exploring the mechanism of Diels-Alder reaction between 7H-benzo[a]phenalene and maleic anhydride. 7H-Benzo[a]phenalene is an antiviral compound and information available about its cycloaddition reactions with possible reaction path and mechanism is scarce. In order to work on the synthesis of its further potential derivatives, the mechanism of its reaction with all aspects should be well understood. Two novel intermediates involved in this reaction have been reported. Diels-Alder reaction of maleic anhydride has found many applications in the synthesis of wide range of useful products. The major concern of this work is to evaluate the consequences of introducing electron donating and electron withdrawing substituents on the reactivity of maleic anhydride towards 7H-benzo[a]phenalene. Thermodynamic parameters, activation parameters, energies of frontier orbitals, global reactivity indices and global electron density transfer (GEDT) have been determined for all the reactions. Fukui functions are computed for each reactant in order to identify the most reactive sites. All the reactions have been found to proceed via normal electron demand having polar nature. The substituents with opposite electronic properties were expected to affect the reactivity of dienophile in an inverse manner, however, the results are not according to this assumption. Rather, both kinds of substituents increased the activation barrier of the reaction. This behavior has been explained in the light of various parameters such as the stability of reacting species, gap of frontier molecular orbitals etc. Experimental studies reported previously are in agreement with these results.

Adsorption and Reaction Mechanisms of Direct Palladium Synthesis by ALD Using Pd(hfac)2 and Ozone on Si (100) Surface

Palladium nanoparticles made by atomic layer deposition (ALD) normally involve formaldehyde or H2 as a reducing agent. Since formaldehyde is toxic and H2 is explosive, it is advantageous to remove this reducing step during the fabrication of palladium metal by ALD. In this work we have successfully used Pd(hfac)2 and ozone directly to prepare palladium nanoparticles, without the use of reducing or annealing agents. Density functional theory (DFT) was employed to explore the reaction mechanisms of palladium metal formation in this process. DFT results show that Pd(hfac)2 dissociatively chemisorbed to form Pd(hfac)* and hfac* on the Si (100) surface. Subsequently, an O atom of the ozone could cleave the C–C bond of Pd(hfac)* to form Pd* with a low activation barrier of 0.46 eV. An O atom of the ozone could also be inserted into the hfac* to form Pd(hfac-O)* with a lower activation barrier of 0.29 eV. With more ozone, the C–C bond of Pd(hfac-O)* could be broken to produce Pd* with an activation barrier of 0.42 eV. The ozone could also chemisorb on the Pd atom of Pd(hfac-O)* to form O3-Pd(hfac-O)*, which could separate into O-Pd(hfac-O)* with a high activation barrier of 0.83 eV. Besides, the activation barrier was 0.64 eV for Pd* that was directly oxidized to PdOx by ozone. Based on activation barriers from DFT calculations, it was possible to prepare palladium without reducing steps when ALD conditions were carefully controlled, especially the ozone parameters, as shown by our experimental results. The mechanisms of this approach could be used to prepare other noble metals by ALD without reducing/annealing agents.

Nonenzymatic Deamidation Mechanism on a Glutamine Residue with a C-Terminal Adjacent Glycine Residue: A Computational Mechanistic Study

The deamidation of glutamine (Gln) residues, which occurs non-enzymatically under physiological conditions, triggers protein denaturation and aggregation. Gln residues are deamidated via the cyclic glutarimide intermediates to l-α-, d-α-, l-β-, and d-β-glutamate residues. The production of these biologically uncommon amino acid residues is implicated in the pathogenesis of autoimmune diseases. The reaction rate of Gln deamidation is influenced by the C-terminal adjacent (N +1) residue and is highest in the Gln-glycine (Gly) sequence. Here, we investigated the effect of the (N + 1) Gly on the mechanism of Gln deamidation and the activation barrier using quantum chemical calculations. Energy-minima and transition-state geometries were optimized by the B3LYP density functional theory, and MP2 calculations were used to obtain the single-point energy. The calculated activation barrier (85.4 kJ mol−1) was sufficiently low for the reactions occurring under physiological conditions. Furthermore, the hydrogen bond formation between the catalytic ion and the main chain of Gly on the C-terminal side was suggested to accelerate Gln deamidation by stabilizing the transition state.

Hydrodeoxygenation of Guaiacol Over Orthorhombic Molybdenum Carbide: A DFT and Microkinetic Study

The hydrodeoxygenation of guaiacol is modelled over a (100) β-Mo2C surface using density functional theory and microkinetic simulations. The thermochemistry of the process shows that the demethoxylation of the guaiacol, to form phenol, will be the initial steps, with a reaction energy of 29 kJ/mol (i.e. endothermic) and a highest activation barrier of 112 kJ/mol. Subsequently, the dehydroxylation of the phenol, which has a rate-determining activation barrier of 145 kJ/mol, will lead to the formation of benzene, with an overall reaction energy for conversion from guaiacol of -91 kJ/mol (i.e. exothermic).

Homogeneous Gold Catalysis: Mechanistic Investigation of Hydroalkoxylation of Various Alkynes

<p>The reaction mechanism of the gold(III)-catalysed hydroalkoxylation of alkynes is studied to provide a deeper understanding of homogeneous gold catalysis. The study is conducted computationally using Density Functional Theory (DFT), with the PBE0 and BP86 functionals and basis sets of triple-ζ quality (aug-cc-pVTZ and aug-cc-pVTZ-PP for the gold atom). It emphasises the mechanisms undergone by various alkynes when they are activated by gold(III) catalysts towards nucleophilic attack to first form an enol ether and followed by a second nucleophilic attack to form a ketal as the final product. Hydrogen bonding networks formed by the solvent methanols are found to play a crucial role in the mechanism especially in the hydrogen migration steps that follow after the nucleophilic attacks. The first nucleophilic attacks are predicted to have rather low activation energies and hence they are expected to proceed fast while the second additions vary in activation barriers, depending on the steric effects in the substrates. The activation barrier for the last hydrogen migration is highest for all of the three reactions investigated and is expected to be the rate determining step. Investigations of internal alkyne reactions reveal that each elementary step requires a higher activation energy compared to terminal alkynes, which explains the low experimental rate of such reactions. Due to the regioselectivity problem in internal alkyne reactions, this results in a mixture of products which is difficult to isolate due to the similarities in their reaction energies. The study also highlights the calculated thermodynamics and kinetics of the reactions, which can be useful in predicting experimental outcomes. Arrhenius plots of concentration of each intermediate species against time were produced to further help the understanding of these mechanisms, whether or not the reactions go to full completion or stop at the formation of enol ether.</p>

Homogeneous Gold Catalysis: Mechanistic Investigation of Hydroalkoxylation of Various Alkynes

<p>The reaction mechanism of the gold(III)-catalysed hydroalkoxylation of alkynes is studied to provide a deeper understanding of homogeneous gold catalysis. The study is conducted computationally using Density Functional Theory (DFT), with the PBE0 and BP86 functionals and basis sets of triple-ζ quality (aug-cc-pVTZ and aug-cc-pVTZ-PP for the gold atom). It emphasises the mechanisms undergone by various alkynes when they are activated by gold(III) catalysts towards nucleophilic attack to first form an enol ether and followed by a second nucleophilic attack to form a ketal as the final product. Hydrogen bonding networks formed by the solvent methanols are found to play a crucial role in the mechanism especially in the hydrogen migration steps that follow after the nucleophilic attacks. The first nucleophilic attacks are predicted to have rather low activation energies and hence they are expected to proceed fast while the second additions vary in activation barriers, depending on the steric effects in the substrates. The activation barrier for the last hydrogen migration is highest for all of the three reactions investigated and is expected to be the rate determining step. Investigations of internal alkyne reactions reveal that each elementary step requires a higher activation energy compared to terminal alkynes, which explains the low experimental rate of such reactions. Due to the regioselectivity problem in internal alkyne reactions, this results in a mixture of products which is difficult to isolate due to the similarities in their reaction energies. The study also highlights the calculated thermodynamics and kinetics of the reactions, which can be useful in predicting experimental outcomes. Arrhenius plots of concentration of each intermediate species against time were produced to further help the understanding of these mechanisms, whether or not the reactions go to full completion or stop at the formation of enol ether.</p>

Low potential electron generating enzymes serve different functions during aerobic nitrogen fixation in Azotobacter vinelandii

Biological nitrogen fixation requires large amounts of energy in the form of ATP and low potential electrons to overcome the high activation barrier for cleavage of the dinitrogen triple bond. The model aerobic nitrogen-fixing bacteria, Azotobacter vinelandii, generates low potential electrons in the form of reduced ferredoxin (Fd) and flavodoxin (Fld) using two distinct mechanisms via the enzyme complexes Rnf and Fix. Both Rnf and Fix are expressed during nitrogen fixation, and deleting either rnf1 or fix genes has little effect on diazotrophic growth. However, deleting both rnf1 and fix eliminates the ability to grow diazotrophically. Rnf and Fix both use NADH as a source of electrons, but overcoming the energetics of NADH's endergonic reduction of Fd/Fld is accomplished through different mechanisms. Rnf harnesses free energy from the proton motive force, whereas Fix uses electron bifurcation to effectively couple the endergonic reduction of Fd/Fld to the exergonic reduction of quinone. Different stoichiometries and gene expression analyses indicate specific roles for the two reactions under different conditions. In this work, complementary physiological studies and thermodynamic modeling reveal how Rnf and Fix simultaneously balance redox homeostasis in various conditions. Specifically, the Fix complex is required for efficient growth under low oxygen concentrations, while Rnf sustains homeostasis and delivers sufficient reduced Fd to nitrogenase under standard conditions. This work provides a framework for understanding how the production of low potential electrons sustains robust nitrogen fixation in various conditions.