Free Energy Barrier Research Articles

DFT mechanistic study on the synthesis of 2-fluorinated allylic scaffolds via PdII-catalyzed defluorinative arylation of gem-difluorocyclopropanes with phenylboronic acids

DFT calculations were conducted to understand the mechanism details and the Z/E-, regio-, and chemoselectivities observed in the synthesis of 2-fluorinated allylic scaffolds through PdII-catalyzed defluorinative arylation of gem-difluorocyclopropanes with arylboronic acids. The reaction is determined to proceed sequentially through oxidative addition, β-F elimination, two consecutive transmetalations, and reductive elimination. The β-F elimination dictates the Z/E-selectivity, primarily influenced by steric effects, while the reductive elimination step controls the regioselectivities, driven by electronic effects. The second transmetalation process serves as the bottleneck process with a free energy barrier of 26.5 kcal/mol. The chemoselective preference for gem-difluorocyclopropane over its corresponding chloride and its unsubstituted parent is attributed to the stronger electron-withdrawing capability of the F substituent compared to Cl and H, which polarizes the C1-C3 bond more than chlorine or hydrogen, making it easier to break.

Experimental and theoretical investigation of an ionic liquid-based biphasic solvent for post-combustion CO2 Capture: Breaking through the “Trade-off” effect of viscosity and loading

To break through the “trade-off” effect of biphasic solvents between rich-phase viscosity and CO2 loading, we synthesized a novel ionic liquid (diethylenetriamine-3-hydroxypyridine, [DETA][3HPyr]) with multiple active sites and combined it with the organic solvent diethylene glycol monobutyl ether (DGME) and water to prepare a biphasic solvent for CO2 absorption, the best absorption condition was optimized. The results demonstrated that after absorption, the solvent transformed from homogeneous to biphasic with highly self-concentrated absorption products in the rich phase. The volume of the rich phase accounted for only 36.3 % of the total solvent, while its viscosity decreased significantly to 28.1 mPa·s, with a high blend absorption capacity of 2.67 mol·kg−1. The species of absorption product and absorption mechanism was investigated using 13C NMR. The stable presence of carbamic acid in the system was confirmed, contributing to enhanced absorption capacity. Density functional theory calculations revealed that DGME stabilized carbamic acid through intermolecular hydrogen bonding interactions, and highly polar ions generated during absorption and uneven charge distribution between ions dominated the phase-change process and increased the water content in the rich phase. Thermodynamic energy barrier calculation showed that the solvent effect of DGME reduced the Gibbs free energy barriers of proton transfer and facilitated reaction progress. 3IL4D3H exhibited excellent cyclic performance with low regeneration energy consumption at 1.77 GJ·t−1. This is the first work to revealing the intrinsic dynamics of carbamic acid formation, and provides a new perspective for the phase-change mechanism of ionic liquid-based biphasic solvent.

Removing the Barrier in O-O Bond Formation Via the Combination of Intramolecular Radical Coupling and the Oxide Relay Mechanism.

The Ru(tda) catalyst has been a major milestone in the development of molecular water oxidation catalysts due to its outstanding performance at neutral pH. The role of the noncoordinating carboxylate group is to act as a nucleophile, donating an oxygen atom to the oxo group, thereby acting as an oxide relay (OR) mechanism for O-O bond formation. A substitution of the carboxylates for phosphonate groups has been proposed, resulting in the Ru(tPaO) catalyst, which has shown even more efficient performance in experimental characterization. In this study, we explore the feasibility of the OR mechanism in the newly reported Ru(tPaO) molecular catalyst. We investigated the catalytic cycle using density functional theory and identified a variation of the OR mechanism that involves radical oxygen atoms in O-O bond formation. We have also determined that the subsequent hydroxide nucleophilic attack is the sole rate-limiting step in the catalytic cycle. All activation free energies are very low, with a free-energy barrier of 2.1 kcal/mol for O-O bond formation and 4.2 kcal/mol for OH- nucleophilic attack.

Water-assisted hydrogenation of aromatics under ambient conditions over Ru catalyst: A combined experimental and computational investigation

Conventional hydrogenation of lignin-derived compounds requires high H2 pressures and temperatures, and yet, achieving the desired conversion and selectivity remains a challenge. Herein, a novel reaction system with a ruthenium catalyst and water as a solvent is developed for the selective hydrogenation of lignin-derived aromatics to corresponding ring-saturated products under ambient conditions (room temperature, and 1 bar H2 pressure). Using a synergistic combination of catalytic experiments, advanced characterization techniques and quantum mechanical simulations, we elucidate that Ru catalyst switches its selectivity from deoxygenation in gas phase to ring hydrogenation in the condensed phase. Water partially dissociates and adsorbs on the catalyst surface as a combination of hydroxyl fragments, H atoms, and physisorbed molecules, and this is critical for Ru to flip its selectivity in the aqueous phase. Experimental results demonstrate a high conversion (>99 %) and >75 % selectivity towards the total hydrogenated products in the presence of water, corroborating the computational results in which kinetic free energy barriers for direct hydrogenation steps reduced to 70 kJ/mol and barrier for direct dehydroxylation increased from 63 kJ/mol to 202 kJ/mol in the case of phenol. Furthermore, H from dissociated water molecules is utilized in the hydrogenation and water also gets regenerated utilizing external hydrogen supply, thus acting as a shuttler for the external hydrogen.

Transesterification of Dimethyl Carbonate with Ethanol Catalyzed by Guanidine: A Theoretical Analysis.

Density-functional theory (DFT) was performed to investigate the mechanistic features of different guanidine-based catalysts, namely, 1,1,3,3-tetramethyl guanidine (TMG) and 1,5,7-triaza-bicyclo-[4.4.0]dec-5-ene (TBD), for the transesterification reaction of dimethyl carbonate (DMC) with ethanol (EtOH). Different possible pathways were suggested in which these catalysts act as either nucleophile or base within a homogeneous system. The DFT results allowed not only the study of the thermochemistry aspects of all elementary reactions featured in the two different activation modes but also the accurate calculation of the free energy barriers for each case. Our findings showed that the catalyzed reaction proceeded through simultaneous activation of DMC and EtOH, facilitated by hydrogen bonding for both catalysts. This feature led to the formation of a stable intermediate with a relatively low free energy barrier. TBD exhibited a potentially more efficient mechanism, owing to its planar structure and dual-activation mode. The free energy barrier of the rate-limiting step, identified as the formation of a zwitterionic complex, then declined by approximately 50% when compared with the reaction without catalysts. Overall, the DFT approach provides good insight into the reactivity of both catalysts and helps to find possibilities for further enhancing the mechanistic features of both catalysts for this type of transesterification reaction.

Unravelling the anchoring effects of Hd-Graphene for lithium‑sulfur batteries: A first-principles calculation

For the widespread commercialization of lithium‑sulfur (LiS) batteries, the identification of anchoring materials capable of effectively mitigating the shuttle effect is of paramount importance. This study is centered around examining the adsorption characteristics of lithium polysulfides (S8 and Li2Sn, n = 1, 2, 4, 6, 8), as well as investigating the sulfur reduction reaction (SRR), and the decomposition mechanisms of Li2S on the pristine and defective Hd-Graphene monolayers. These investigations were carried out using first-principles calculations. The results reveal that the adsorption energies of polysulfides to the electrolytes (DOL and DME) are lower compared to that on the substrates. The moderate anchoring strength (0.8–2.0 eV) between polysulfides and the monolayer can effectively suppress the shuttle effect. Additionally, the Gibbs free energy barrier for SRR on the substrate is determined to be about 0.68 eV. The dissociation energy barrier of Li2S on Hd-Graphene is about 1.54 eV. Lower energy barriers indicate favorable reaction kinetics, leading to improved discharging and charging efficiency. Based on these findings, Hd-Graphene is predicted to be a promising anchoring material for LiS batteries.

Micro-macro consistency in multiscale modeling: Score-based model assisted sampling of fast/slow dynamical systems.

A valuable step in the modeling of multiscale dynamical systems in fields such as computational chemistry, biology, and materials science is the representative sampling of the phase space over long time scales of interest; this task is not, however, without challenges. For example, the long term behavior of a system with many degrees of freedom often cannot be efficiently computationally explored by direct dynamical simulation; such systems can often become trapped in local free energy minima. In the study of physics-based multi-time-scale dynamical systems, techniques have been developed for enhancing sampling in order to accelerate exploration beyond free energy barriers. On the other hand, in the field of machine learning (ML), a generic goal of generative models is to sample from a target density, after training on empirical samples from this density. Score-based generative models (SGMs) have demonstrated state-of-the-art capabilities in generating plausible data from target training distributions. Conditional implementations of such generative models have been shown to exhibit significant parallels with long-established-and physics-based-solutions to enhanced sampling. These physics-based methods can then be enhanced through coupling with the ML generative models, complementing the strengths and mitigating the weaknesses of each technique. In this work, we show that SGMs can be used in such a coupling framework to improve sampling in multiscale dynamical systems.

Mechanisms of glycine formation in cold interstellar media: a theoretical study.

The possibility of the formation of glycine (Gly) from fundamental gas molecules in cold interstellar media was studied using quantum chemical methods, transition state theory and microcanonical molecular dynamics simulations with surface hopping dynamics (NVE-MDSH). This theoretical study emphasized five photochemical pathways in the lowest singlet-excited (S 1) state, thermochemical processes after non-radiative S 1→S 0 relaxations, and photo-to-thermal energy conversion in the NVE ensemble. The optimized reaction pathways suggested that to generate a reactive singlet dihydroxy carbene (HOCOH) intermediate, photochemical pathways involving the H2O…CO van der Waals and H2O-OC hydrogen bond precursors (Ch (1)_Step (1)) possess considerably lower energy barriers than the S 0 state pathways. The Gibbs free energy barriers (∆G ǂ ) calculated after the non-radiative S 1 →S 0 relaxations indicated higher spontaneous temperatures (T s) for the formation of the HOCOH intermediate (Ch (1)_Step (1)) than for Gly formation (Ch (1)_Step (2) and Ch (4)). Although the termolecular reaction in Ch (4) possesses a low energy barrier, and is thermodynamically favourable, the high exothermic S 1 →S 0 relaxation energy leads to the separation of the weakly associated H2O…CH2NH…CO complex into single molecules. The NVE-MDSH results also confirmed that the molecular processes after the S 1 →S 0 relaxations are thermally selective, and because the non-radiative S 1 →S 0 relaxation temperatures are exceedingly higher than T s, the formation of Gly on consecutive reaction pathways is non-synergistic with low yields and several side products. Based on the theoretical results, photo-to-thermal control strategies to promote desirable photochemical products are proposed. They could be used as guidelines for future theoretical and experimental research on photochemical reactions.

Elucidating Daptomycin's Antibacterial Efficacy: Insights into the Tripartite Complex with Lipid II and Phospholipids in Bacterial Septum Membrane.

This study elucidated the mechanism of formation of a tripartite complex containing daptomycin (Dap), lipid II, and phospholipid phosphatidylglycerol in the bacterial septum membrane, which was previously reported as the cause of the antibacterial action of Dap against gram-positive bacteria via molecular dynamics and enhanced sampling methods. Others have suggested that this transient complex ushers in the inhibition of cell wall synthesis by obstructing the downstream polymerization and cross-linking processes involving lipid II, which is absent in the presence of cardiolipin lipid in the membrane. In this work, we observed that the complex was stabilized by Ca2+-mediated electrostatic interactions between Dap and lipid head groups, hydrophobic interaction, hydrogen bonds, and salt bridges between the lipopeptide and lipids and was associated with Dap concentration-dependent membrane depolarization, thinning of the bilayer, and increased lipid tail disorder. Residues Orn6 and Kyn13, along with the DXDG motif, made simultaneous contact with constituent lipids, hence playing a crucial role in the formation of the complex. Incorporating cardiolipin into the membrane model led to its competitively displacing lipid II away from the Dap, reducing the lifetime of the complex and the nonexistence of lipid tail disorder and membrane depolarization. No evidence of water permeation inside the membrane hydrophobic interior was noted in all of the systems studied. Additionally, it was shown that using hydrophobic contacts between Dap and lipids as collective variables for enhanced sampling gave rise to a free energy barrier for the translocation of the lipopeptide. A better understanding of Dap's antibacterial mechanism, as studied through this work, will help develop lipopeptide-based antibiotics for rising Dap-resistant bacteria.

Pt-O-Ce interaction enhanced by Al substitution to promote the acetone degradation through accelerating the breaking of C[sbnd]C bond in acetic acid intermediate

The reaction rate of volatile organic compounds (VOCs) oxidation is controlled by the rate-limiting step in the total reaction process. This study proposes a novel strategy, by which the rate-limiting step of acetone oxidation is accelerated by enhanced chemical bond interaction with more electrons transfer through Al-substituted CeO2 loaded Pt (Pt/Al-CeO2). Results indicate that the rate-limiting step in the process of acetone oxidation is the decomposition of acetic acid. Al substitution enhances the Pt-O-Ce interaction that transfers more electrons from Pt/Al-CeO2 to acetic acid, promoting the breaking of its CC bond with a lower free energy barrier. Attributing to these, the reaction rate of Pt/Al-CeO2 is 13 times as high as that of Pt/CeO2 and its TOFPt value is 11 times as high as that of Pt/CeO2 at 150 °C. Moreover, the CO2 selectivity of Pt/Al-CeO2 also increases by 22 %. This work establishes the relationship between Pt-O-Ce interaction and acetone oxidation that provides novel perspectives on the development of efficient materials for VOCs oxidation.

Molecular Mechanism for Regioselectivity of P450-BM3 Monooxygenase Towards Stearic Acid Hydroxylation

Hydroxy stearic acid is an important raw material for the synthesis of biobased materials, and the hydroxylation at different positions showed different properties. With the catalysis of P450-BM3 monooxygenase, (ω - 1)-Hydroxy stearic acid was generated, which is a precursor of macrocyclic musk. Experimental results have shown that the L188Q mutant can increase the yield of (ω - 1)-Hydroxy stearic acid by more than three times, but the reason and underlying molecular mechanism are still unclear. In this study, molecular dynamics (MD) simulations were conducted to study the structural characteristics of the P450-BM3 wild type and its three mutants (F87V, L188Q, and F87V-L188Q) in combination with stearic acid. The MD simulation results showed significant changes in the interactions between the three mutants and the carboxyl- and terminal-end of stearic acid. The results of the Molecular mechanics-Poisson-Boltzmann surface area (MMPBSA) binding free energies indicated that the L188Q mutant showed the most stable binding with the stearic acid. Finally, the H-abstraction free energy barriers of L188Q and wild type systems were calculated to study the regioselectivity, and the results indicated that the L188Q mutant shown a significant advantage in the hydroxylation of stearic acid at the ω - 1 position. Our research results not only explain molecular mechanism for regioselectivity of P450-BM3 towards stearic acid hydroxylation, but also provide some useful ideas for the synthesis of biobased materials from hydroxy fatty acids.

Morphological Study of Tetra-n-Butylammonium Bromide Semi-Clathrate Hydrate in Confined Space

Tetra-n-butylammonium Bromide (TBAB) finds extensive use in diverse applications. An in-depth investigation into the effects of the formation conditions on TBAB hydrate is necessary to optimize the application process. This work focuses on examining the influence of the mass concentration of TBAB solution and the cooling rate on TBAB hydrate formation through optical microscopy and Raman spectroscopy. The TBAB hydrate formation process occurs in a confined space created by an optical sheet with a 0.03 mm deep groove. Four TBAB solutions of 13. 8 wt%, 18 wt%, 32 wt%, and 40 wt% are investigated, and the supercooling required for hydrate nucleation increases with concentration at a cooling rate of 0.5 K/min. Notably, Type A TBAB hydrate preferentially forms in all of the solutions, although type B hydrate is thermodynamically stable in the two dilute solutions. At a larger cooling rate of 2 K/min, two distinct crystal growth patterns are observed: one controlled by mass transfer and the other regulated by heat transfer. Increasing the cooling rate not only alters the optical morphology, but also reduces the supercooling due to a decrease in the Gibbs free energy barrier caused by a larger temperature gradient. This is beneficial for practical applications as it helps to alleviate the supercooling degree.

Enhanced Adsorption Response of pH-Sensitive Peptides: The Role of Membrane Acidity.

pH-sensitive peptides bind and traverse lipid membranes in response to changes in pH. They can be used to target tumors and other acidic tissues. We investigate the influence of acidic lipids on the pH-driven adsorption of recently synthesized peptides. Using a statistical-thermodynamic theory that takes into account the acid-base chemistry of peptides and lipids, we find that the presence of acidic lipids amplifies changes in peptide surface concentration when transitioning from high to low pH. We study cyclic and linear peptides, containing tryptophan, glutamic acid, and arginine residues, examining their behavior in both neutral and acidic membranes. Membrane binding consistently results from the shallow insertion of tryptophan residues with hydrophilic residues facing the aqueous solution. Regardless of the pH, the peptide's geometry predominantly determines the orientation and distribution of residues. Notably, we find that not only the extent of adsorption is pH-sensitive but also the underlying adsorption mechanism: it is barrier-free at low pH but hindered by a large free energy barrier at high pH. Hence, under more acidic conditions, pH-sensitive peptides show facilitated adsorption both kinetically and thermodynamically.

Oxygen-vacancy-enriched MgO/carbon composite as a highly efficient electrocatalyst for phenazine/dihydrophenazine redox reaction of aqueous phenazine redox flow battery

Phenazine derivatives are attractive anolyte redox-active species in aqueous redox flow batteries (ARFBs). Unfortunately, they typically suffer from sluggish reaction kinetics, resulting in poor rate capability and inferior energy efficiency, especially under high current densities. Herein, we report a composite of MgO and Ketjen black carbon (MgO/KB) that can serve as a low-cost ARFB electrocatalyst to significantly improve the redox reaction kinetics of phenazine derivatives. The MgO/KB composite catalyst exhibits excellent catalytic performance, with an area-specific resistance (ASR) of 1.54 and 1.11 Ω/cm2 for the charge and discharge processes, respectively, as well as improved energy efficiency, capacity utilization, and durability in practical ARFB applications. Detailed research confirms that the oxygen vacancies within the MgO promote electron transfer and enhance catalytic activity for the electrochemical reaction of phenazine derivatives. Using density functional theory (DFT) calculations, we unveil that the underlying catalytic enhancement mechanism stems from a low free energy barrier of the rate-determining step (RDS) on oxygen-vacancy-enriched MgO for the oxidation reaction of dihydro-phenazine derivative. These findings will guide the design of highly active electrocatalysts for organic ARFBs.

Unmasking quantum effects in the surface thermodynamics of fluid nanodrops.

The focus of our study is an in-depth investigation of the quantum effects associated with the surface tension and other thermodynamic properties of nanoscopic liquid drops. The behavior of drops of quantum Lennard-Jones fluids is investigated with path-integral Monte Carlo simulations, and the test-area method is used to determine the surface tension of the spherical vapor-liquid interface. As the thermal de Broglie wavelength, λB, becomes more significant, the average density of the liquid drop decreases, with the drop becoming mechanically unstable at large wavelengths. As a consequence, the surface tension is found to decrease monotonically with λB, vanishing altogether for dominant quantum interactions. Quantum effects can be significant, leading to values that are notably lower than the classical thermodynamic limit, particularly for smaller drops. For planar interfaces (with infinite periodicity in the direction parallel to the interface), quantum effects are much less significant with the same values of λB but are, nevertheless, consequential for values representative of hydrogen or helium-4 at low temperatures corresponding to vapor-liquid coexistence. Large quantum effects are found for small drops of molecules with quantum interactions corresponding to water, ethane, methanol, and carbon dioxide, even at ambient conditions. The notable decrease in the density and tension has important consequences in reducing the Gibbs free-energy barrier of a nucleating cluster, enhancing the nucleation kinetics of liquid drops and of bubble formation. This implies that drops would form at a much greater rate than is predicted by classical nucleation theory.

A weak coupling mechanism for the early steps of the recovery stroke of myosin VI: A free energy simulation and string method analysis.

Myosin motors use the energy of ATP to produce force and directed movement on actin by a swing of the lever-arm. ATP is hydrolysed during the off-actin re-priming transition termed recovery stroke. To provide an understanding of chemo-mechanical transduction by myosin, it is critical to determine how the reverse swing of the lever-arm and ATP hydrolysis are coupled. Previous studies concluded that the recovery stroke of myosin II is initiated by closure of the Switch II loop in the nucleotide-binding site. Recently, we proposed that the recovery stroke of myosin VI starts with the spontaneous re-priming of the converter domain to a putative pre-transition state (PTS) intermediate that precedes Switch II closing and ATPase activation. Here, we investigate the transition from the pre-recovery, post-rigor (PR) state to PTS in myosin VI using geometric free energy simulations and the string method. First, our calculations rediscover the PTS state agnostically and show that it is accessible from PR via a low free energy transition path. Second, separate path calculations using the string method illuminate the mechanism of the PR to PTS transition with atomic resolution. In this mechanism, the initiating event is a large movement of the converter/lever-arm region that triggers rearrangements in the Relay-SH1 region and the formation of the kink in the Relay helix with no coupling to the active site. Analysis of the free-energy barriers along the path suggests that the converter-initiated mechanism is much faster than the one initiated by Switch II closure, which supports the biological relevance of PTS as a major on-pathway intermediate of the recovery stroke in myosin VI. Our analysis suggests that lever-arm re-priming and ATP hydrolysis are only weakly coupled, so that the myosin recovery stroke is initiated by thermal fluctuations and stabilised by nucleotide consumption via a ratchet-like mechanism.

Chemical reaction process and dynamic characteristics of urea pyrolysis products in inhibiting gas explosion

During the coal mining process, gas explosions pose significant hazards, causing casualties and property losses. In order to develop new types of inhibitors for gas explosions, this paper explores the reaction mechanisms of urea pyrolysis products NH3 and HNCO inhibiting gas explosions based on density functional theory (DFT), transition state theory, and grand canonical ensemble Monte Carlo method (GCMC). It analyzes the reaction processes and kinetic characteristics of urea pyrolysis products with key radicals and gas molecules involved in explosions from a microscopic dynamic perspective. The results show that urea pyrolysis products exhibit good inhibition effects on active radicals involved in explosion reactions·NH3 and HNCO show stronger van der Waals forces in electrostatic attraction towards O2 and *H, respectively, and faster rate advantages in reaction rate constants. The lower Gibbs free energy barrier indicates higher reaction activity of pyrolysis products, thereby diluting the concentration of key radicals involved in explosion reactions and effectively inhibiting explosion key elementary reactions (R32, R38, R53, R57, R156, and R170). This study provides new insights into the microscopic inhibition mechanism of urea pyrolysis products on gas explosions, offering a new approach for designing more targeted modified inhibitors, which helps reduce the hazards of gas explosions during coal mining and provides scientific support and technical guidance for safe coal mining production.

Simultaneous Interface Engineering and Phase Tuning of CeO2-Decorated Catalysts for Boosted Oxygen Evolution Reaction.

Heterogeneous catalysts have attracted extensive attention among various emerging catalysts for their exceptional oxygen evolution reaction (OER) capabilities, outperforming their single-component counterparts. Nonetheless, the synthesis of heterogeneous materials with predictable, precise, and facile control remains a formidable challenge. Herein, a novel strategy involving the decoration of catalysts with CeO2 is introduced to concurrently engineer heterogeneous interfaces and adjust phase composition, thereby enhancing OER performance. Theoretical calculations suggest that the presence of ceria reduces the free energy barrier for the conversion of nitrides into metals. Supporting this, the experimental findings reveal that the incorporation of rare earth oxides enables the controlled phase transition from nitride into metal, with the proportion adjustable by varying the amount of added rare earth. Thanks to the role of CeO2 decoration in promoting the reaction kinetics and fostering the formation of the genuine active phase, the optimized Ni3FeN/Ni3Fe/CeO2-5% nanoparticles heterostructure catalyst exhibits outstanding OER activity, achieving an overpotential of just 249mV at 10mAcm-2. This approach offers fresh perspectives for the conception of highly efficient heterogeneous OER catalysts, contributing a strategic avenue for advanced catalytic design in the field of energy conversion.

Solution Ionic Strength Can Modulate Functional Loop Conformations in E. coli Dihydrofolate Reductase.

The observation of multiple conformations of a functional loop (termed M20) in the Escherichia coli dihydrofolate reductase (ecDHFR) enzyme triggered the proposition that large-scale motions of protein structural elements contribute to enzyme catalysis. The transition of the M20 loop from a closed conformation to an occluded conformation was thought to aid the rate-limiting release of the products. However, the influence of charged species in the solution environment on the observed M20 loop conformations, independent of charged ligands bound to the enzyme, had not been considered. Molecular dynamics simulations of ecDHFR in model CaCl2 solutions of varying molar ionic strengths IM reveal a substantial free energy barrier between occluded and closed M20 loop states at IM exceeding the E. coli threshold (∼0.24 M). This barrier may facilitate crystallization of ecDHFR in the occluded state, consistent with ecDHFR structures obtained at IM exceeding 0.3 M. At lower IM (≤0.15 M), the M20 loop can explore the occluded state, but prefers an open/partially closed conformation, again consistent with ecDHFR structures. Our findings caution against using ecDHFR structures obtained at nonphysiological ionic strengths in interpreting catalytic events or in structure-based drug design.

Density Functional Theory Study on the Mechanism of Nickel-Catalyzed 3,3-Dialkynylation of 2-Aryl Acrylamides Via Double Vinylic C-H Bond Activation.

The mechanisms of Ni-catalyzed 3,3-dialkynylation of 2-aryl acrylamide have been investigated by using density functional theory calculations. The result shows that this reaction includes double alkynylation, which involves sequential key steps of vinylic C-H bond activation, successive oxidative addition, and reductive elimination, with the second C-H bond activation being the rate-determining step. C-H and N-H bond activation occurs via the concerted metalation-deprotonation mechanism. The calculations show that no transition state exists in the first reductive elimination process, and a negative free energy barrier in the second reductive elimination process though a transition state is identified, indicating that the nickel-catalyzed vinylic C(sp2)-C(sp) bond formation does not require activation energy. Z-E isomerization is the prerequisite for the second alkynylation. In addition, our spin-flip TDDFT (SF-TDDFT) computational result discloses that the actual process of Z-E isomerization occurs on the potential energy surface of the first excited singlet state S1.