Transition State Structures Research Articles

Enhanced Sampling for Free Energy Profiles with Post-Transition-State Bifurcations

We present a strategy to explore the free energy landscapes of chemical reactions with post-transition-state bifurcations using an enhanced sampling method based on well-tempered metadynamics. Obviating the need for computationally expensive density functional theory-level ab initio molecular dynamics simulations, we obtain accurate energetics by utilizing a free energy perturbation scheme and deep learning estimator for the single-point energies of substrate configurations. Using a pair of easily interpretable collective variables, we present a quantitative free energy surface that is compatible with harmonic transition state theory calculations and in which the bifurcations are clearly visible. We demonstrate our approach with the example of the SpnF-catalyzed Diels-Alder reaction, a cycloaddition reaction in which post-transition-state bifurcation leads to the [4+2] as well as the [6+4] cycloadduct. We obtain the free energy landscapes for different stereochemical reaction pathways and characterize the mechanistic continuum between relevant reaction channels without explicitly searching for the pertinent transition state structures.

Bifunctional Iminophosphorane-Catalyzed Enantioselective Nitroalkane Addition to Unactivated α,β-Unsaturated Esters.

Herein we describe the enantioselective intermolecular conjugate addition of nitroalkanes to unactivated α,β-unsaturated esters, catalyzed by a bifunctional iminophosphorane (BIMP) superbase. The transformation provides the most direct access to pharmaceutically relevant enantioenriched γ-nitroesters, utilizing feedstock chemicals, with unprecedented selectivity. The methodology exhibits a broad substrate scope, including β-(fluoro)alkyl, aryl and heteroaryl substituted electrophiles, and was successfully applied on a gram scale with reduced catalyst loading, and, additionally, catalyst recovery was carried out. The formal synthesis of a range of drug molecules, and an enantioselective synthesis of (S)-rolipram were achieved. Additionally, computational studies revealed key reaction intermediates and transition state structures, and provided rationale for high enantioselectivities, in good agreement with experimental results.

Bifunctional Iminophosphorane‐Catalyzed Enantioselective Nitroalkane Addition to Unactivated α,β‐Unsaturated Esters**

AbstractHerein we describe the enantioselective intermolecular conjugate addition of nitroalkanes to unactivated α,β‐unsaturated esters, catalyzed by a bifunctional iminophosphorane (BIMP) superbase. The transformation provides the most direct access to pharmaceutically relevant enantioenriched γ‐nitroesters, utilizing feedstock chemicals, with unprecedented selectivity. The methodology exhibits a broad substrate scope, including β‐(fluoro)alkyl, aryl and heteroaryl substituted electrophiles, and was successfully applied on a gram scale with reduced catalyst loading, and, additionally, catalyst recovery was carried out. The formal synthesis of a range of drug molecules, and an enantioselective synthesis of (S)‐rolipram were achieved. Additionally, computational studies revealed key reaction intermediates and transition state structures, and provided rationale for high enantioselectivities, in good agreement with experimental results.

Modeling Catalyzed Reactions on Metal-Doped Amorphous Silicates: The Case of Niobium-Catalyzed Ethylene Epoxidation

Metal-doped amorphous silicates are promising materials for heterogeneous catalysis because they are easy to make and their properties can be tuned for specific reactions. However, the amorphous nature of the surface makes the characterization difficult, and improvements are based on a trial and error approach. Density functional theory simulations can in principle provide direct structure–property relations, but the sampling of the active site configuration space is not possible via brute force. In this contribution, we use the Nb-catalyzed epoxidation of ethylene as a test reaction to analyze various aspects of the modeling that need to be taken into account for simulations of effective reaction rates. We show that each site can host a variety of transition state structures that represent the same reaction event, but that can differ considerably in reaction barrier. Furthermore, many different sites need to be sampled. We then use machine learning to identify the most important descriptors of the bare active site that correlate directly with the energy barrier. Although our test set is too small for quantitative predictions of reaction rates, we discuss what the important features of a very active site are that can drive the kinetics in the real material.

RRNA methylation by Spb1 regulates the GTPase activity of Nog2 during 60S ribosomal subunit assembly

Biogenesis of the large ribosomal (60S) subunit involves the assembly of three rRNAs and 46 proteins, a process requiring approximately 70 ribosome biogenesis factors (RBFs) that bind and release the pre-60S at specific steps along the assembly pathway. The methyltransferase Spb1 and the K-loop GTPase Nog2 are essential RBFs that engage the rRNA A-loop during sequential steps in 60S maturation. Spb1 methylates the A-loop nucleotide G2922 and a catalytically deficient mutant strain (spb1D52A) has a severe 60S biogenesis defect. However, the assembly function of this modification is currently unknown. Here, we present cryo-EM reconstructions that reveal that unmethylated G2922 leads to the premature activation of Nog2 GTPase activity and capture a Nog2-GDP-AlF4− transition state structure that implicates the direct involvement of unmodified G2922 in Nog2 GTPase activation. Genetic suppressors and in vivo imaging indicate that premature GTP hydrolysis prevents the efficient binding of Nog2 to early nucleoplasmic 60S intermediates. We propose that G2922 methylation levels regulate Nog2 recruitment to the pre-60S near the nucleolar/nucleoplasmic phase boundary, forming a kinetic checkpoint to regulate 60S production. Our approach and findings provide a template to study the GTPase cycles and regulatory factor interactions of the other K-loop GTPases involved in ribosome assembly.

Prediction of transition state structures of gas-phase chemical reactions via machine learning

The elucidation of transition state (TS) structures is essential for understanding the mechanisms of chemical reactions and exploring reaction networks. Despite significant advances in computational approaches, TS searching remains a challenging problem owing to the difficulty of constructing an initial structure and heavy computational costs. In this paper, a machine learning (ML) model for predicting the TS structures of general organic reactions is proposed. The proposed model derives the interatomic distances of a TS structure from atomic pair features reflecting reactant, product, and linearly interpolated structures. The model exhibits excellent accuracy, particularly for atomic pairs in which bond formation or breakage occurs. The predicted TS structures yield a high success ratio (93.8%) for quantum chemical saddle point optimizations, and 88.8% of the optimization results have energy errors of less than 0.1 kcal mol−1. Additionally, as a proof of concept, the exploration of multiple reaction paths of an organic reaction is demonstrated based on ML inferences. I envision that the proposed approach will aid in the construction of initial geometries for TS optimization and reaction path exploration.

High-throughput ab initio reaction mechanism exploration in the cloud with automated multi-reference validation.

Quantum chemical calculations on atomistic systems have evolved into a standard approach to studying molecular matter. These calculations often involve a significant amount of manual input and expertise, although most of this effort could be automated, which would alleviate the need for expertise in software and hardware accessibility. Here, we present the AutoRXN workflow, an automated workflow for exploratory high-throughput electronic structure calculations of molecular systems, in which (i) density functional theory methods are exploited to deliver minimum and transition-state structures and corresponding energies and properties, (ii) coupled cluster calculations are then launched for optimized structures to provide more accurate energy and property estimates, and (iii) multi-reference diagnostics are evaluated to back check the coupled cluster results and subject them to automated multi-configurational calculations for potential multi-configurational cases. All calculations are carried out in a cloud environment and support massive computational campaigns. Key features of all components of the AutoRXN workflow are autonomy, stability, and minimum operator interference. We highlight the AutoRXN workflow with the example of an autonomous reaction mechanism exploration of the mode of action of a homogeneous catalyst for the asymmetric reduction of ketones.

Striking Stabilization Effect of Spinel Cobalt Oxide Oxygen Evolution Electrocatalysts in Neutral pH by Dual‐Sites Iron Incorporation

Developing stable and efficient nonprecious‐metal‐based oxygen evolution catalysts in the neutral electrolyte is a challenging but essential goal for various electrochemical systems. Particularly, cobalt‐based spinels have drawn a considerable amount of attention but most of them operate in alkali solutions. However, the frequently studied Co–Fe spinel system never exhibits appreciable stability in nonbasic conditions, not to mention attract further investigation on its key structural motif and transition states for activity loss. Herein, we report exceptional stable Co–Fe spinel oxygen evolution catalysts (~30% Fe is optimal) in a neutral electrolyte, owing to its unique metal ion arrangements in the crystal lattice. The introduced iron content enters both the octahedral and tetrahedral sites of the spinel as Fe2+ and Fe3+ (with Co ions having mixed distribution as well). Combining density functional theory calculations, we find that the introduction of Fe to Co3O4 lowers the covalency of metal‐oxygen bonds and can help suppress the oxidation of Co2+/3+ and O2−. It implies that the Co–Fe spinel will have minor surface reconstruction and less lattice oxygen loss during the oxygen evolution reaction process in comparison with Co3O4 and hence show much better stability. These findings suggest that there is still much chance for the spinel structures, especially using reasonable sublattices engineering via multimetal doping to develop advanced oxygen evolution catalysts.

Ab Initio Metadynamics Simulations of Hexafluoroisopropanol Solvent Effects: Synergistic Role of Solvent H-Bonding Networks and Solvent-Solute C-H/π Interactions.

The solvent effects in Friedel-Crafts cycloalkylation of epoxides and Cope rearrangement of aldimines were investigated by using ab initio molecular dynamics simulations. Explicit molecular treatments were applied for both reactants and solvents. The reaction mechanisms were elucidated via free energy calculations based on metadynamics simulations. The results reveal that both reactions proceed in a concerted fashion. Key solvent-substrate interactions are identified from the structures of transition states with explicit solvent molecules. The remarkable promotion effect of hexafluoroisopropanol solvent is ascribed to the synergistic effect of H-bonding networks and C-H/π interactions with substrates.

A Useful Classification of Organic Reactions Based on the Flux of the Electron Density

A useful classification of polar organic reactions in Forward Electron Density Flux (FEDF) and Reverse Electron Density Flux (REDF), based on the unambiguously analysis of the direction of the flux of the global electron density transfer (GEDT) at the transition state structures (TSs), has been recently proposed (RSC Adv. 2020, 10, 15394) within the Molecular Electron Density Theory. Further, non-polar reactions have been classified as Null Electron Density Flux (NEDF) (Eur. J. Org. Chem. 2020, 5938). This classification allows characterizing the nucleophilic/electrophilic species participating in polar reactions. Analysis of the electronic chemical potential m, and the electrophilicity w and nucleophilicity N indices, defined within Conceptual DFT, at the ground state (GS) of the reagents also permits to establish this classification of polar reactions.

The importance of nuclear dynamics in reaction mechanisms of acetylene cyclotrimerization catalyzed by Fe+-compounds

The reaction mechanism of transition metal-catalyzed [2 + 2 + 2] cyclotrimerization of three acetylenes to form benzene consists of multiple steps, including the generation of a metallacyclopentadiene intermediate through the coupling of two acetylenes and subsequent [4 + 2] cycloaddition. Using quantum chemical calculations, we show that acetylene cyclotrimerization catalyzed by Fe+–L-type compounds (where L represents the ligands F−, Cl−, OH−, SH−, NC−, NH3, H2O, and cyclopentadienyl anion) can occur via a concerted single-step mechanism, where the reactant complex (C2H2)3–Fe+–L is directly connected to the C6H6–Fe+–L product complex via a single intrinsic reaction coordinate (IRC) path with one transition state. We then performed trajectory calculations, starting from concerted transition state structures with small kinetic energies, to confirm the efficient formation of benzene via this single-step mechanism. Interestingly, we found that many of the trajectories exhibited non-IRC dynamics—the trajectories did not directly lead to the formation of the benzene product, but to that of the C2H2–Fe+–L–C4H4 intermediate; in contrast, direct benzene formation predominantly occurred for the compounds comprising the ligands F− and NC−. Thus, we report that nuclear dynamics play an important role in determining the cyclotrimerization reaction mechanism, and that the properties of the potential energy surface depend on the ligand molecule.

How Do Self-Interaction Errors Associated with Stretched Bonds Affect Barrier Height Predictions?

Density functional theory (DFT) suffers from self-interaction errors (SIEs) that generally result in the underestimation of chemical reaction barrier heights. This is commonly attributed to the tendency of density functional approximations to overstabilize delocalized densities that typically occur in the stretched bonds of transition state structures. The Perdew-Zunger self-interaction correction (PZSIC) and locally scaled self-interaction correction (LSIC) improve the prediction of barrier heights of chemical reactions, with LSIC giving better accuracy than PZSIC on average. These methods employ an orbital-by-orbital correction scheme to remove the one-electron SIE. In the context of barrier heights, this allows an analysis of how the self-interaction correction (SIC) for each orbital contributes to the calculated barriers using Fermi-Löwdin orbitals (FLOs). We hypothesize that the SIC contribution to the reaction barrier comes mainly from a limited number of orbitals that are directly involved in bond-breaking and bond-making in the reaction transition state. We call these participant orbitals (POs), in contrast to spectator orbitals (SOs) which are not directly involved in changes to the bonding. Our hypothesis is that ΔETotalSIC ≈ ΔEPOSIC, where ΔETotalSIC is the difference in the SIC corrections for the reactants or products and the transition state. We test this hypothesis for the reaction barriers of the BH76 benchmark set of reactions. We find that the stretched-bond orbitals indeed make the largest individual SIC contributions to the barriers. These contributions increase the barrier heights relative to LSDA, which underpredicts the barrier. However, the full stretched-bond hypothesis does not hold in all cases for either PZSIC or LSIC. There are many cases where the total SIC contribution from the SOs is significant and cannot be ignored. The size of the SIC contribution to the barrier height is a key indicator. A large SIC correction is correlated to a large LSDA error in the barrier, showing that PZSIC properly gives larger corrections when corrections are needed most. A comparison of the performance of PZSIC and LSIC shows that the two methods have similar accuracy for reactions with large LSDA errors, but LSIC is clearly better for reactions with small errors. We trace this to an improved description of reaction energies in LSIC.

Do-It-Yourself 5-Color 3D Printing of Molecular Orbitals and Electron Density Surfaces

This report outlines an approach for preparing 5-color 3D printed plastic models of molecular orbitals and electron density surfaces using a hobby-grade 3D printer. Instructions are provided for preparing 3D orbital and electron density surface (EDS) models using solid or mesh representations in ground state and transition state structures. We show that the information content of 3D orbital and surface models can be enhanced with text annotation, bisection, strut and dashed bond placement, and composite orbital-EDS model constructions. Example prints illustrate orbital concepts in organic and inorganic chemistry, such as the ethyl cation (σ–p hyperconjugation), methane (hybridization and C–H bonding), ethane (σ–σ* hyperconjugation in the staggered and eclipsed conformations), 2-hydroxytetrahydropyran (the anomeric effect/n−σ* hyperconjugation), the water dimer (hydrogen bonding/n−σ* overlap), ethylene, 1,3-butadiene, and benzene (π molecular orbitals), Re2Cl82–, and U2(COT)2 (metal–metal quadruple bonds). Transition state models illustrate orbital interactions in the SN2 reaction of cyanide with methyl, ethyl, and isopropyl chloride and in a hydroboration reaction of BH3 with propene. Composite EDS models of methyl and isopropyl chloride (for exploring their relative reactivities as SN2 electrophiles) and methylcyclohexane (visualizing 1,3-diaxial interactions) are described. Student perceptions of a multicolor 3D orbital print used in an introductory organic chemistry laboratory course are reported.

Theoretical Mechanistic Investigation of the Dynamic Kinetic Resolution of N-Protected Amino Acid Esters using Phase-Transfer Catalysts.

A detailed theoretical mechanistic investigation on the dynamic kinetic resolution of N-protected amino acid esters using phase-transfer catalysts is described. Semiautomatic exhaustive conformation search of transition state (TS)-like structures were carried out using the ConFinder program and the pseudo-TS conformational search (PTSCS) method. This conformational search method successfully provided reasonable TS structures for determining the stereoselectivity in the asymmetric base hydrolysis of hexafluoroisopropyl (HFIP) esters as well as the racemization mechanism. Furthermore, the independent gradient model (IGM) analysis of the TS structures suggested that the H-bonding interactions with the oxyanion hole and π-stacking interactions are the common important features of the proposed TS structures that determine the stereoselectivity.

Enzyme Kinetics Features of the Representative Engineered Recombinants of Chondroitinase ABC I.

Chondroitinase ABC I (cABC I) from Proteus vulgaris is an important enzyme in medicinal biotechnology due to its ability to help axon regeneration after spinal cord injury. Its practical application involves solving several problems at the molecular and cellular levels. Structurally, most residues at the C-terminal domain of cABC I are arranged as organized strands, and only a small fraction of residues have helical conformation. The structural and functional features of modified residues on two specific helix fragments have previously been reported. The single mutant M889K has been combined with L679S and L679D mutants to make enzyme variants containing simultaneously modified helix. Here, the pH stability and temperature-based analysis of the transition state structure for the catalysis reaction were investigated. We found that double mutant L679D/M889K is the better choice to use in physiological conditions due to its higher pH stability at physiological pH as well as its different optimum temperature as compared with the (wild-type) WT protein. According to Arrhenius's analysis, the values of the Gibbs free energy of the transition state (∆G#) are not changed upon mutation. However, the relative contribution and absolute values of the enthalpy and entropy change to the total value of ∆G#, varied between the WT and mutants.

Understanding the mechanism and regio- and stereo selectivity of [3 + 2] cycloaddition reactions between substituted azomethine ylide and 3,3,3-trifluoro-1-nitroprop-1-ene, within the molecular electron density theory.

The selectivity and the nature of the molecular mechanism of the [3 + 2] cycloaddition (32CA) reaction between 2-(dimethylamino)-1H-indene-1,3(2H)-dione (AY11) and trans(E)-3,3,3-trifluoro-1-nitroprop-1-ene(FNP10) has been studied, in which the molecular electron density theory using density functional theory methods at the MPWB1K/6-31G(d) computational level was used. Analysis of the global reactivity indices permits us to characterize FNP10 as a strong electrophile and AY11 as a strong nucleophile. Four reactive pathways associated with the ortho/meta regioselective channels and endo/exo stereoselective approaches modes have been explored and characterized in the gas phase and in the benzene solvent. The analysis of the relative energies associated with the different reaction pathways indicates that the 32CA reactions of the azomethine ylide (AY) with the nitroalkene (FNP) is meta regioselective with high endo stereoselectivity. This result is in good agreement with the experimental observations. electron localization function topological analysis of the most favored reactive pathways allows for characterizing the mechanism of this 32CA reactions as a non-concerted two-stage one-step mechanism. Finally, non-covalent interactions and quantum theory of atoms in molecule analyses at the meta/endo transition state structure indicate that the presence of different several weak interactions, namely, CF and NH contributed in favoring the formation of a meta-endo cycloadduct.

Adaptive Electric Fields Embedded Electrochemical Barrier Calculations.

Electrochemical interfaces are grand canonical ensembles of varying electrons. Simulating them by standard first-principles methods is a challenging task, since the number of electrons (or charge) is fixed in the calculation. Under the constant charge framework, we developed a constant potential simulation method realized by adding an adaptive electric field to a charge neutral system. Electric field is the controlling variable. In addition, we defined an internal reversible hydrogen electrode potential (ϕIRHE), which can ensure the model independence of our method. To validate our method, the reaction energies of some electrochemical reactions are calculated, the results are comparable with the computational hydrogen electrode model and experiments. At last, the evolution of transition state structures and charge transfer coefficients of some electrochemical reactions on Ag(111) surface were discussed by our method.

The Malaprade reaction mechanism for ethylene glycol oxidation by periodic acid based on density functional theory (DFT).

A general mechanism of the Malaprade oxidative carbon-carbon bond cleavage reaction of α-glycol in the presence of periodic acid has been proposed on the basis of density functional theory (DFT) computations. Ethylene glycol and periodic acid, both in their neutral forms, have been studied as noble substrate representatives in model reactions. The proposed reaction mechanism has been constructed based on and compared with previously published experimental kinetic, spectroscopic and temperature and pH-dependent studies. In the presented theoretical mechanistic considerations, four alternative molecular transformations have been analyzed from thermodynamic and kinetic points of view. Theoretically, the predicted activation energy barriers have been compared with experimental ones published elsewhere. The presented minimum energy pathway (MEP) unveiled the shape and conformation of the intermediate and transition state structures. The three-step reaction process involves the formation of a seven-membered quasi-ring assisted by an intramolecular hydrogen-bond intermediate structure forming one I-O bond (IC1_B), a cyclic ester intermediate forming two I-O bonds (IC2_C) and the final products formed at the two very last stages (HIO3, water and two formaldehyde molecules). The computed and energetically the most favourable reaction landscape proposed in this work uniforms and refines the mechanistic proposition given by Criegee for Malaprade type of reactions and further gives a detailed molecular understanding of the reaction rate and atomic connections en route the transformation. The molecular geometries of all stationary points (intermediate and transition state structures) lying on the potential energy hypersurface have been optimized at the four alternative DFT levels under the solvation model based on the density approximation: B3PW91, CAM-B3LYP, BMK, ωB97XD. The 6-311+G(2d,p) basis set for C, O, and H atoms and both the full (DGDZVP) and Ahlrichs-Weigend1 (def2-TZVP) basis sets for iodine atoms were used during the computations.

Exploring mechanochemical reactions at the nanoscale: theory versus experiment.

Mechanochemical reaction pathways are conventionally obtained from force-displaced stationary points on the potential energy surface of the reaction. This work tests a postulate that the steepest-descent pathway (SDP) from the transition state to reactants can be reasonably accurately used instead to investigate mechanochemical reaction kinetics. This method is much simpler because the SDP and the associated reactant and transition-state structures can be obtained relatively routinely. Experiment and theory are compared for the normal-stress-induced decomposition of methyl thiolate species on Cu(100). The mechanochemical reaction rate was calculated by compressing the initial- and transition-state structures by a stiff copper counter-slab to obtain the plots of energy versus slab displacement for both structures. The reaction rate was also measured experimentally under compression using a nanomechanochemical reactor comprising an atomic-force-microscopy (AFM) instrument tip compressing a methyl thiolate overlayer on Cu(100) (the same system for which the calculations were carried out). The rate was measured from the indent created on a defect-free region of the methyl thiolate overlayer, which also enabled the contact area to be measured. Knowing the force applied by the AFM tip yields the reaction rate as a function of the contact stress. The result agrees well with the theoretical prediction without the use of adjustable parameters. This confirms that the postulate is correct and will facilitate the calculation of the rates of more complex mechanochemical reactions. An advantage of this approach, in addition to the results agreeing with the experiment, is that it provides insights into the effects that control mechanochemical reactivity that will assist in the targeted design of new mechanochemical syntheses.

Dissociative photoionization ofm-xylene

The photoionization and dissociative photoionization of m-xylene (C8H10) were researched by using synchrotron radiation vacuum ultraviolet (SR-VUV) and supersonic expanding molecular beam reflectron time-of-flight mass spectrometer (RFTOF-MS) system. The photoionization efficiency spectra (PIEs) of parent ion C8H10+ and main fragment ions C8H9+ and C7H7+ were observed, and the ionization energy (IE) of m-xylene and appearance energies (AEs) of main fragment ions C8H9+ and C7H7+ were determined to be 8.60±0.03 eV, 11.76±0.04 eV and 11.85±0.05 eV, respectively. Structures of reactant, transition states (TSs), intermediates (INTs), and products involved in two dominant dissociation channels were optimized at the B3LYP/6-311++G(d,p) level, and the relative energies were calculated at the G3 level. Based on the results, two major dissociative photoionization channels, C7H7++CH3 and C8H9++H were calculated at the B3LYP/6-311++G(d,p) level. On the basis of theoretical and experimental results, the dissociative photoionization mechanisms of m-xylene were proposed. The C–H or C–C bond dissociation and hydrogen migration are the main processes in the dissociation channels of m-xylene cation.