The role of the putative catalytic base in the phosphoryl transfer reaction in a protein kinase: first-principles calculations

Protein kinases are important enzymes controlling the majority of cellular signaling events via a transfer of the gamma-phosphate of ATP to a target protein. Even after many years of study, the mechanism of this reaction is still poorly understood. Among many factors that may be responsible for the 1011-fold rate enhancement due to this enzyme, the role of the conserved aspartate (Asp166) has been given special consideration. While the essential presence of Asp166 has been established by mutational studies, its function is still debated. The general base catalyst role assigned to Asp166 on the basis of its position in the active site has been brought into question by the pH dependence of the reaction rate, isotope measurements, and pre-steady-state kinetics. Recent semiempirical calculations have added to the controversy surrounding the role of Asp166 in the catalytic mechanism. No major role for Asp166 has been found in these calculations, which have predicted the reaction process consisting of an early transfer of a substrate proton onto the phosphate group. These conclusions were inconsistent with experimental observations. To address these differences between experimental results and theory with a more reliable computational approach and to provide a theoretical platform for understanding catalysis in this important enzyme family, we have carried out first-principles structural and dynamical calculations of the reaction process in cAPK kinase. To preserve the essential features of the reaction, representations of all of the key conserved residues (82 atoms) were included in the calculation. The structural calculations were performed using the local basis density functional (DFT) approach with both hybrid B3LYP and PBE96 generalized gradient approximations. This kind of calculation has been shown to yield highly accurate structural information for a large number of systems. The optimized reactant state structure is in good agreement with X-ray data. In contrast to semiempirical methods, the lowest energy product state places the substrate proton on Asp166. First-principles molecular dynamics simulations provide additional support for the stability of this product state. The latter also demonstrate that the proton transfer to Asp166 occurs at a point in the reaction where bond cleavage at the PO bridging position is already advanced. This mechanism is further supported by the calculated structure of the transition state in which the substrate hydroxyl group is largely intact. A metaphoshate-like structure is present in the transition state, which is consistent with the X-ray structures of transition state mimics. On the basis of the calculated structure of the transition state, it is estimated to be 85% dissociative. Our analysis also indicates an increase in the hydrogen bond strength between Asp166 and substrate hydroxyl and a small decrease in the bond strength of the latter in the transition state. In summary, our calculations demonstrate the importance of Asp166 in the enzymatic mechanism as a proton acceptor. However, the proton abstraction from the substrate occurs late in the reaction process. Thus, in the catalytic mechanism of cAPK protein kinase, Asp166 plays a role of a "proton trap" that locks the transferred phosphoryl group to the substrate. These results resolve prior inconsistencies between theory and experiment and bring new understanding of the role of Asp166 in the protein kinase catalytic mechanism.     

New insights into the mechanism of the Schiff base formation catalyzed by type I dehydroquinate dehydratase from <Emphasis Type="Italic">S. enterica</Emphasis>

The Schiff base formation catalyzed by type I dehydroquinate dehydratase (DHQD) from Salmonella enterica has been studied by molecular docking, molecular dynamics simulation, and quantum chemical calculations. The substrate locates stably a similar position as the Schiff base intermediate observed in the crystal structure and forms strong hydrogen bonds with several active site residues. This binding mode is different from that of several other Schiff base enzymes. Then, the quantum chemical model has been constructed and the fundamental reaction pathways have been explored by performing quantum chemical calculation. The energy barrier of the previously proposed reaction pathway is calculated to be 30.7 kcal/mol, which is much higher than the experimental value of 14.3 kcal/mol of the whole dehydration reaction by type I DHQD from S. enterica. It means that this pathway is not favorable in energy. Therefore, a new and unexpected reaction pathway has been investigated with the favorable and reasonable energy barrier of 12.1 kcal/mol. The complicated role of catalytic His143 residue has also been elucidated that it mediates two proton transfers to facilitate the reaction. Moreover, the similarity and the difference between these two reaction pathways have been analyzed in detail. The new structural and mechanistic insights may direct the design of the inhibitors of type I dehydroquinate dehydratase as non-toxic antimicrobials, antifungals, and herbicides.     

Active site structure and mechanism of human glyoxalase I-an ab initio theoretical study.

The structure of the active site of human glyoxalase I and the reaction mechanism of the enzyme-catalyzed conversion of the thiohemiacetal, formed from methylglyoxal and glutathione, to S-D-lactoylglutathione has been investigated by ab initio quantum chemical calculations. To realistically represent the environment of the reaction center, the effective fragment potential methodology has been employed, which allows systems of several hundred atoms to be described quantum mechanically. The methodology and the active site model have been validated by optimizing the structure of a known enzyme-inhibitor complex, which yielded structures in good agreement with the experiment. The same crystal structure has been used to obtain the quantum motif for the investigation of the glyoxalase I reaction. The results of our study confirm that the metal center of the active site zinc complex plays a direct catalytic role by binding the substrate and stabilizing the proposed enediolate reaction intermediate. In addition, our calculations yielded detailed information about the interactions of the substrate, the reaction intermediates, and the product with the active site of the enzyme and about the mechanism of the glyoxalase I reaction. The proton transfers of the reaction proceed via the two highly flexible residues Glu172 and Glu99. Information about the structural and energetic effect of the protein on the first-shell complex has been attained by comparison of the structures optimized in the local protein environment and in a vacuum. The environment of the zinc complex disturbs the Cs symmetry found for the complex in a vacuum, which suggests an explanation for the stereochemical behavior of glyoxalase I.     

Discovery of the Lanthipeptide Curvocidin and Structural Insights into its Trifunctional Synthetase CuvL

Lanthipeptides are ribosomally-synthesized natural products from bacteria featuring stable thioether-crosslinks and various bioactivities. Herein, we report on a new clade of tricyclic class-IV lanthipeptides with curvocidin from Thermomonospora curvata as its first representative. We obtained crystal structures of the corresponding lanthipeptide synthetase CuvL that showed a circular arrangement of its kinase, lyase and cyclase domains, forming a central reaction chamber for the iterative substrate processing involving nine catalytic steps. The combination of experimental data and artificial intelligence-based structural models identified the N-terminal subdomain of the kinase domain as the primary site of substrate recruitment. The ribosomal precursor peptide of curvocidin employs an amphipathic α-helix in its leader region as an anchor to CuvL, while its substrate core shuttles within the central reaction chamber. Our study thus reveals general principles of domain organization and substrate recruitment of class-IV and class-III lanthipeptide synthetases.     

Electrical properties of polypyrrole/p‐InP structure

The polypyrrole/p‐InP structure has been fabricated by the electrochemical polymerization of the organic polypyrrole onto the p‐InP substrate. The current–voltage (I–V), capacitance–voltage (C–V), and capacitance–frequency (C–f) characteristics of the PPy/p‐InP structure have been determined at room temperature. The structure showed nonideal I–V behavior with the ideality factor and the barrier height 1.48 and 0.69 eV respectively. C–f measurements of the structure have been carried out using the Schottky capacitance spectroscopy technique and it has been seen that there is a good agreement between the experimental and theoretical values. Also, it has been seen that capacitance almost show a plateau up to a certain value of frequency, after which, the capacitance decreases. The higher values of capacitance at low frequencies were attributed to the excess capacitance resulting from the interface states in equilibrium with the p‐InP that can follow the a.c. signal. The interface state density N_ss and relaxation time τ of the structure were determined from C–f characteristics. © 2006 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 44: 1572–1579, 2006     

Electronic Structure and Reactivity of a [1],[1]Disilamolybdenocenophane

The electronic structure of the two‐fold bridged [1],[1]disilamolybdenocenophane has been analyzed by means of density functional theory. As predicted, the relatively high charge at the metal center and, in particular, the highly strained geometry determine a noticeable reactivity towards unsaturated organic substrates. Thus, treatment with the nonpolar reagents 2‐butyne and azobenzene leads to side‐on coordination of the substrate to the metal center, whereas the reaction with polar tert‐butylisonitrile gives a highly unusual structural motif in the form of an ansa‐carbene.     

Molecular Dynamics Simulations of a β-Hairpin Fragment of Protein G by Means of Atom-Bond Electronegativity Equalization Method Fused into Molecular Mechanics (ABEEMσπ/MM)

There are some controversial opinions about the origin of folding β‐hairpin stability in aqueous solution. In this study, the structural and dynamic behavior of a 16‐residue β‐hairpin from B1 domain of protein G has been investigated at 280, 300, 350 and 450 K using molecular dynamics (MD) simulations by means of Atom‐Bond Electronegativity Equalization Method Fused into Molecular Mechanics i.e., ABEEMδπ/MM and the explicit ABEEM‐7P water solvent model. In addition, a 300 K simulation of one mutant having the aromatic residues substituted with alanines has been performed. The hydrophobic surface area, hydrophilic surface area and some structural properties have been used to measure the role of the hydrophobic interactions. It is found that the aromatic residues substituted with alanines have shown an evident destabilization of the structure and unfolding started after 1.5 ns. It is also found that the number of the main chain hydrogen bonds have different distributions through three different simulations. All above demonstrate that the hydrophobic interactions and the main chain hydrogen bonds play an important role in the stability of the folding structure of β‐hairpin in solution. Furthermore, through the structural analyses of the β‐hairpin structures from four temperature simulations and the comparison with other MD simulations of β‐hairpin peptides, the new ABEEMδπ force field can reproduce the structural data in good agreement with the experimental data.     

Substrate‐Selective Catalysis

Substrate selectivity is an important output function for the validation of different enzyme models, catalytic cavity compounds, and reaction mechanisms as demonstrated in this review. In contrast to stereo‐, regio‐, and chemoselective catalysis, the field of substrate‐selective catalysis is under‐researched and has to date generated only a few, but important, industrial applications. This review points out the broad spectrum of different reaction types that have been investigated in substrate‐selective catalysis. The present review is the first one covering substrate‐selective catalysis and deals with reactions in which the substrates involved have the same reacting functionality and the catalysts is used in catalytic or in stoichiometric amounts. The review covers real substrate‐selective catalysis, thus only including cases in which substrate‐selective catalysis has been observed in competition between substrates.     

Enzymatic Hydrolysis of N-Acylated 1-Aminophosphonic Acids

Abstract

Penicillin acylase from E. coli (FC 3.5.1.11) was found to hydrolyse N-phenylacetylated 1-aminoalkylphosphonic acids and their esters. Enzyme preferentially converts the R-form of the substrates: the ratios of the bimolecular rate constants of penicillin acylase-catalysed hydrolysis of R-and S- forms of 1-(N-phenylacetaminol-ethylphosphonic acid and its dimethyl- and diisopropyl- esters are 58000, 2600, 1800; these derivatives were shown to have the greatest values of the catalytic constants for enzymatic hydrolysis of all known substrates of penicillin acylase: 237, 148, and 134 s; corresponding values of Michaelis constants are 3.7×10^?5, 6.8×10^?4, and 6.2×10^?4 M. The kinetics of the enzymatic hydrolysis of 1-(N-phenylacetaminol-ethylphosphonic acid was investigated up to high degrees of conversion. The inhibition of penicillin acylase by high concentrations of the R-form of the substrate (with substrate inhibition constant 0.07 Ml and competitive inhibition by the reaction product phenylacetic acid (K_i=3.5×10_?5 M) was observed. Penicillin acylase was shown to possess quite broad substrate specificity among N-acylated 1-aminoalkylphosphonic acids and was found to be capable of hydrolysing 1-(N-phenylacetaminol-substituted 2-phenylethyl-, 1-phenylmethyl- and 3-methylbutylphosphonic acids with high efficiency and enantioselectivity.     

Low-temperature synthesis of single crystalline Ag2S nanowires on silver substrates

We report on the successful synthesis of silver sulfide (Ag(2)S) nanowires by a simple and mild gas-solid reaction approach. For the nanowire synthesis, a preoxidized silver substrate is exposed to an atmosphere of an O(2)/H(2)S mixture at room temperature or slightly above. The resulting Ag(2)S nanowires are phase pure with a monoclinic crystal structure and have diameters of a few tens of nanometers and lengths up to 100 mum. The influence of reaction conditions on the diameter, length, and morphology of the Ag(2)S nanowires has been studied by a number of structural and spectroscopic techniques. The nanowire growth mechanism on the Ag substrate has been discussed, which is likely characterized by continuous deposition at the tip. Additionally, we demonstrate thinning and cutting of individual Ag(2)S nanowires with electron beams and laser beams, which are potentially useful for nanowire manipulation and engineering.     

Preliminary attempt to follow the enthalpy of an enzymatic reaction by ab initio computations: Catalytic action of papain

A new theoretical approach to study the enthalpy variations occurring during an enzymatic reaction is presented. The structural modifications of the enzyme–substrate complex along the reaction path are distinguished as macro- and microdeformations. Macrodeformations, which concern primarily the approach of the substrate to the enzyme and the release of the reaction products and arise from nonbonded interactions, are treated with an empirical method for computing the energy of a macromolecule. Microdeformations, which are local displacements driven by variations of the electronic structure and its energy and involve only a limited portion of the complex, are treated with the ab initio SCF-LCAO-MO method. The reaction path is idealized as a sequence of major steps: at each step, first the empirical program REFINE is used to calculate the geometry of the system for that step, then the energy of an appropriate subsystem is computed ab initio with the program IBMOL, using the geometry provided by REFINE and applying small concerted atomic displacements. Thus along the entire reaction path one can obtain an energy profile computed with the ab initio method and compatible with the structure of the whole complex. This approach was applied here to the first steps of the reaction of proteolysis catalyzed by papain. The formation of an ion pair ImH⁺ …S^? between the side chains of residues His-159 and Cys-25 was examined in detail. The results show that the instability of the ion pair decreases by ? 11.5 kcal/mol when the interactions with residues Asn-175 and Ala- 160 are taken into account; the instability is further decreased by ?2 kcal/mol after a partial geometry optimization. The energies of the noncovalent enzyme–substrate complex and of the tetrahedral intermediate were computed, considering N-methyl acetamide (NMA) as model substrate and representing papain with the residues Cys-25, His-159, Gln-19, and Ala-160. The interaction energy of the noncovalent complex is -3.8 kcal/mol, compared to the value of +7.4 kcal/mol for the CH₃S^? -NMA complex. The tetrahedral intermediate is found to be less stable than the noncovalent complex by 27 and 38.5 kcal/mol, respectively, for the papain–NMA and the CH₃S^? -NMA systems. While these rather large energy differences are possibly due to the incorrect geometry of the tetrahedral intermediate and optimization of the structure is required, it appears that the interactions with the various protein residues represent a very important stabilization factor, which lowers the onthalpy variations during the reaction.     

Stereospecific Oxycyanation of Alkenes with Sulfonyl Cyanide

Oxycyanation of alkenes would allow the direct construction of useful β-hydroxy nitrile scaffolds. However, only limited examples of such reactions have been reported, and some problems including limited substrate scope and the lack of diastereocontrol in the case of the oxycyanation of internal alkenes have arisen. We herein report on the intermolecular oxycyanation of alkenes using p-toluenesulfonyl cyanide (TsCN) in the presence of tris(pentafluorophenyl)borane (B(C₆F₅)₃) as a catalyst, affording products that contain a sulfinyloxy group and a cyano group at the vicinal position. The reaction features a stereospecific syn-addition. The reaction also shows a broad substrate scope with good functional group tolerance. Mechanistic investigations by experimental studies and density functional theory (DFT) calculations revealed that the reaction proceeds via an unprecedented stereospecific mechanism through the electrophilic cyanation of alkenes, in which B(C₆F₅)₃ efficiently activates TsCN through the coordination of the cyano group to the boron center.     

A theoretical study on the mechanism of a novel one-carbon unit transfer reaction

The mechanism of one-carbon unit transfer reaction between tetrahydrofolate coenzymes model compound (e.g., benzimidazolium) and Grignard reagent has been investigated employing the DFT and B3LYP/6-31G* levels of theory. Three consecutive reactions leading to major products N,N′-dimethyl-ophenylenediamine and acetone have been proposed and discussed. For these reactions, the structure parameters, vibrational frequencies, and energies for each stationary point have been calculated, and the corresponding reaction mechanism has been given by the potential energy surface, which is drawn according to the relative energies. The calculated results show that the corresponding major products N,N′-dimethyl-ophenylenediamine and acetone are in agreement with experimental findings, which provided a new illustration and guidance for these reactions.     

Generation of an N→B Ladder‐type Structure by Regioselective Hydroboration of an Alkenyl‐Functionalized Quaterpyridine

An unusual reactivity of 2‐(1‐alkenyl)‐pyridines towards hydroboration with 9H‐borabicyclo[3.3.1]nonane (9H‐BBN) has been employed to selectively introduce two borane groups into a conjugated quaterpyridine. Quantitative conversion of the substrate was observed with exclusive regioselectivity. A molecular structure that allows intramolecular N→B coordination was generated. The effect of the ladder formation on the molecular structure and the electronic properties of the conjugated system have been investigated. The synthetic strategy demonstrated herein offers a facile access to N→B ladder‐type structures from readily available substrates, and allows to simultaneously introduce several boron centers under mild conditions.     

Ion Pair Catalyst - Pentanidinium

In this account, we further describe our already developed N-sp² hybrid guanidinium as an efficient phase-transfer catalyst and ion pair catalysis based on N-sp² hybrid pentanidinium and its application in some new reactions. The sp³ hybrid quaternary ammonium salt has a tetrahedral structure, which means that three sides of it can be effectively steric, allowing the remaining side to be close to the substrate. However, the sp² hybrid ammonium salt allows the substrate to form ion pairs from both directions respectively, so it is a greater challenge to control the stereoselectivity of the reaction. Van der Waals forces, such as hydrogen bonds and interactions, have been used to make electrophiles approach from a certain direction, leading to a higher enantioselectivity. Based on the above idea, we designed an N-sp² hybrid phase-transfer catalyst, pentanidinium. Pentanidinium has five conjugated nitrogen atoms, one of which has a formal positive charge, which is necessary for it to become an ion pair catalyst. We have confirmed that pentanidinium can catalyze α-hydroxylation of 3-substituted-2-oxindoles, Michael addition of 3-alkyloxindoles with vinyl sulfone, and alkylation reactions of sulfenate anions and dihydrocoumarins, desymmetrization of pro-chiral sulfinate to afford enantioenriched sulfinate esters. Pentanidinium with side chain structure changes can also be catalyzed efficiently with enantioconvergent halogenophilic nucleophilic substitution, including azidation and thioesterification. In the reaction catalyzed by pentanidinium, it always attracts us with the advantages of low catalytic load and good enantioselectivity.     

Wetting and dynamics of structured liquid films

The stability of a sufficiently thin, supported, homopolymer film against the development of local thickness fluctuations which can become amplified, eventually leading to structural destabilization of the film, is typically determined by long and short‐range intermolecular forces. In A‐B diblock copolymers, the connectivity between the blocks, the preferential attraction of one block to an external interface, combined with an incompatibility between the A‐B segments, the situation is very different. Two cases, largely dictated by χN, wher χ is the Flory‐Huggins interaction parameter and N is the degree of polymerization, can arise in thin copolyme films. When χN is large, thin films exhibit comparatively stable topographical structures, where the dimensions of the topographies normal to the substrate reflect a natural length‐scale associated with phase separation in the material. In the other situation, where χN is sufficiently small, the copolymer bulk structure is homogeneous. An ordered structure can be induced into the otherwise compositionally homogeneous structure in the vicinity of a substrate. Here, depending on film thickness, a series of transient and stable topographies can develop. Wetting, early stage structural destabilization dynamics leading to the formation of droplets, and late stage coarsening of the droplets are discussed. © 2003 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 41: 2219–2235, 2003     

Photochromic Inorganic/Organic Self-Assembled Superlattice Films

Phosphotungstic acid (PW₁₂) and 1,10-diaminodecane (1,10-DAD) molecules have been alternatively assembled on 3-aminopropyltriethyoxysilane modified quartz or silicon substrate to form multicomposite mutilayer thin films by the molecular deposition technique. Thus-obtained films were characterized by UV-visible, XRD, X-ray reflection (XRR), and XPS spectra. Results show that the layer-by-layer self-assembly of PW₁₂ and 1,10-DAD leads to a well-ordered superlattice-layered structure with a d-spacing of 3.19 nm, which exhibits extremely exciting photochromic properties. Based on the experimental data, a presumable interlayer structural model has also been suggested.     

Redox and Conformational Equilibria and Dynamics of Cytochrome c at High Electric Fields

Cytochrome c (Cyt‐c) adsorbed in the electrical double layer of the Ag electrode/electrolyte interface has been studied by stationary and time‐resolved surface‐enhanced resonance Raman spectroscopy to analyse the effect of strong electric fields on structure and reaction equilibria and dynamics of the protein. In the potential range between +0.1 and ?0.55 V (versus saturated calomel electrode), the adsorbed Cyt‐c forms a potential‐dependent reversible equilibrium between the native state B1 and a conformational state B2. The redox potentials of the bis‐histidine‐coordinated six‐coordinated low‐spin and five‐coordinated high‐spin substates of B2 were determined to be ?0.425 and ?0.385 V, respectively, whereas the additional six‐coordinated aquo‐histidine‐coordinated high‐spin substate was found to be redox‐inactive. The redox potential for the conformational state B1 was found to be the same as in solution in agreement with the structural identity of the adsorbed B1 and the native Cyt‐c. For all three redox‐active species, the formal heterogeneous electron transfer rate constants are small and of the same order of magnitude (3–13 s^?1), which implies that the rate‐limiting step is largely independent of the redox‐site structure. These findings, as well as the slow and potential‐dependent transitions between the various conformational (sub‐)states, can be rationalized in terms of an electric field‐induced increase of the activation energy for proton‐transfer steps linked to protein structural reorganisation. Further increasing the electric field strength by shifting the electrode potential above +0.1 V leads to irreversible structural changes that are attributed to an unfolding of the polypeptide chain.     

Theoretical investigation on dual fluorescence and intramolecular charge transfer of 5-phenyl-5H-phenanthridin-6-one

Quantum-chemical calculations with the time-dependent density function theory (TDDFT) have been carried out for 5-phenyl-5H-phenanthridin-6-one (PP). For this molecule, dual fluorescence and in- tramolecular charge transfer (ICT) were experimentally observed. The B3LYP functional with 6-311 G (2d, p) basis set has been used for the theoretical calculations. The solvent effects have been described within the polarizable continuum model (PCM). Ground-state geometry optimization reveals that the phenyl/phenanthridinone dihedral angle equals 90.0°, a nearly perpendicular structure. Vertical ab- sorption energy calculations characterize the lower singlet excited states both in gas phase and in solvents. It can be found that the lower excited states have locally excitation (LE) feature. Through constructing the potential energy curves of both isolated and solvated systems describing the LE→ICT reaction and fluorescence emission, we obtain the enthalpy difference ΔH between the LE and ICT states, energy barrier Ea, and energy difference δEFC, indicating the structural changes taking place during the ICT reaction. Potential curve and calculated emission energies for both isolated and sol- vated systems show a dual fluorescence phenomenon, consisting of a LE emission band and a red-shifted ICT band. Our calculations including the solvent effects indicate that the dual fluorescence is brought about by the change in molecular structure connected with the planarization of the twisted N-phenylphenanthridinone during the ICT reaction.     

Two‐Dimensional Infrared Spectroscopy Reveals the Structure of an Evans Auxiliary Derivative and Its SnCl4 Lewis Acid Complex

Determining the structure of reactive intermediates is the key to understanding reaction mechanisms. To access these structures, a method combining structural sensitivity and high time resolution is required. Here ultrafast polarization‐dependent two‐dimensional infrared (P2D‐IR) spectroscopy is shown to be an excellent complement to commonly used methods such as one‐dimensional IR and multidimensional NMR spectroscopy for investigating intermediates. P2D‐IR spectroscopy allows structure determination by measuring the angles between vibrational transition dipole moments. The high time resolution makes P2D‐IR spectroscopy an attractive method for structure determination in the presence of fast exchange and for short‐lived intermediates. The ubiquity of vibrations in molecules ensures broad applicability of the method, particularly in cases in which NMR spectroscopy is challenging due to a low density of active nuclei. Here we illustrate the strengths of P2D‐IR by determining the conformation of a Diels–Alder dienophile that carries the Evans auxiliary and its conformational change induced by the complexation with the Lewis acid SnCl₄, which is a catalyst for stereoselective Diels–Alder reactions. We show that P2D‐IR in combination with DFT computations can discriminate between the various conformers of the free dienophile N‐crotonyloxazolidinone that have been debated before, proving antiperiplanar orientation of the carbonyl groups and s‐cis conformation of the crotonyl moiety. P2D‐IR unequivocally identifies the coordination and conformation in the catalyst–substrate complex with SnCl₄, even in the presence of exchange that is fast on the NMR time scale. It resolves a chelate with the carbonyl orientation flipped to synperiplanar and s‐cis crotonyl configuration as the main species. This work sets the stage for future studies of other catalyst–substrate complexes and intermediates using a combination of P2D‐IR spectroscopy and DFT computations.