The creation of enzymes capable of catalyzing any desired chemical reaction is a grand challenge for computational protein design. Using new algorithms that rely on hashing techniques to construct ...active sites for multistep reactions, we designed retro-aldolases that use four different catalytic motifs to catalyze the breaking of a carbon-carbon bond in a nonnatural substrate. Of the 72 designs that were experimentally characterized, 32, spanning a range of protein folds, had detectable retroaldolase activity. Designs that used an explicit water molecule to mediate proton shuffling were significantly more successful, with rate accelerations of up to four orders of magnitude and multiple turnovers, than those involving charged side-chain networks. The atomic accuracy of the design process was confirmed by the x-ray crystal structure of active designs embedded in two protein scaffolds, both of which were nearly superimposable on the design model.
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Alarming: Multiple sources of errors in DFT energetics of CC bond‐forming reactions were investigated by evaluating structural transformations in Diels–Alder reactions: conversion of π into σ bonds ...and changes in conjugation, hyperconjugation, and branching interactions. A startling overestimation of the π to σ bond conversion is found with most methods, a central problem to all reactions involving addition of π bonds (electrocyclic processes, ene, aldol).
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Computational studies have led to models to understand some classic and contemporary asymmetric reactions involving organocatalysts. The Hajos−Parrish−Eder−Sauer−Wiechert reaction and intermolecular ...aldol reactions as well as Mannich reactions and oxyaminations catalyzed by proline and other amino acids, and Diels−Alder reactions catalyzed by MacMillan's chiral amine organocatalysts have been studied with density functional theory. Quantitative predictions for several new catalysts and reactions are provided.
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A comparison of previously proposed models of the CC bond‐forming step of the title reaction with density functional methods indicate that the most favored one involves an enamine intermediate ...undergoing a concerted aldol cyclization with proton transfer from the proline carboxylic acid group (see structure). This step is equal in energy to the intramolecular deprotonation leading to the enamine, and both are partially rate‐determining steps.
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The effects of different amino acid catalysts and substrate substituents on the stereoselectivity of the title reactions have been studied with the aid of density functional theory methods. ...Experimental data available in the literature have been compiled. B3LYP/6-31G(d) calculations match the general experimental trends and provide useful insights into the origins of the variations in stereoselectivities. Acyclic primary amino acids allow a greater conformational flexibility in the aldol transition states compared with proline. This makes them poorer enantioselective catalysts with triketone substrates with a methyl ketone side chain. The steric repulsion upon substitution at the terminal methyl group increases the energy difference between anti- and syn-chairs with primary amino acid catalysts and, consequently, the stereoselectivities. Proline, in contrast, is a poor catalyst for the latter reactions because the substituent's steric bulkiness raises the activation energy of the favored C−C bond-forming pathway.
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The archetypical proline-catalyzed intramolecular aldol reaction, the Hajos-Parrish-Eder-Sauer-Wiechert reaction, has served as a model reaction for the mechanistic study of the ever-growing class of ...proline-catalyzed conversions. Experimental measurements of the 13C kinetic isotope effects for this reaction show conclusively that carbon−carbon bond formation is not rate-limiting.
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The design of active sites has been carried out using quantum mechanical calculations to predict the rate-determining transition state of a desired reaction in presence of the optimal arrangement of ...catalytic functional groups (theozyme). Eleven versatile reaction targets were chosen, including hydrolysis, dehydration, isomerization, aldol, and Diels−Alder reactions. For each of the targets, the predicted mechanism and the rate-determining transition state (TS) of the uncatalyzed reaction in water is presented. For the rate-determining TS, a catalytic site was designed using naturalistic catalytic units followed by an estimation of the rate acceleration provided by a reoptimization of the catalytic site. Finally, the geometries of the sites were compared to the X-ray structures of related natural enzymes. Recent advances in computational algorithms and power, coupled with successes in computational protein design, have provided a powerful context for undertaking such an endeavor. We propose that theozymes are excellent candidates to serve as the active site models for design processes.
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Quantum mechanical optimizations of theoretical enzymes (theozymes), which are predicted catalytic arrays of biological functionalities stabilizing a transition state, have been carried out for a set ...of nine diverse enzyme active sites. For each enzyme, the theozyme for the rate‐determining transition state plus the catalytic groups modeled by side‐chain mimics was optimized using B3LYP/6–31G(d) or, in one case, HF/3–21G(d) quantum mechanical calculations. To determine if the theozyme can reproduce the natural evolutionary catalytic geometry, the positions of optimized catalytic atoms, i.e., covalent, partial covalent, or stabilizing interactions with transition state atoms, are compared to the positions of the atoms in the X‐ray crystal structure with a bound inhibitor. These structure comparisons are contrasted to computed substrate–active site structures surrounded by the same theozyme residues. The theozyme/transition structure is shown to predict geometries of active sites with an average RMSD of 0.64 Å from the crystal structure, while the RMSD for the bound intermediate complexes are significantly higher at 1.42 Å. The implications for computational enzyme design are discussed.
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Complete saturation of a single six-membered ring on fullerene C60 has been achieved. The critical step in this first synthesis of a fully characterized 1,2,3,4,5,6-hexaadduct consisted of a ...remarkable double 5-exo-trig addition of alkoxyl radicals promoted by lead tetraacetate. Two possible opening pathways (2 + 2 + 2 retrocycloadditions) for the newly synthesized compound were explored using quantum mechanical calculations. We found that the oxa bridges in the hexaadduct prevent ring opening through the retro2 + 2 + 2 mechanism due to the high activation barrier and endothermicity of the reaction.
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The addition of diazomethane and diazoethane to (5S,SS)- and (5R,SS)-5-ethoxy-3-p-tolylsulfinylfuran-2(5H)-ones (1a and 1b) and their 4-methylderivatives (2a and 2b) proceeded in almost quantitative ...yields and complete regioselectivity. The observed π-facial selectivity is determined by the configurations at both C-5 and the sulfinyl group, the later being the most important. The syn adducts were almost exclusively obtained from 1a and 2a in apolar solvents but the π-facial selectivity was strongly decreased in more polar solvents. On the other hand, the major adducts from 1b and 2b were the anti ones and such predominance was slightly increased with solvent polarity. The exo-selectivity was complete in all the cases except for the anti approach to compounds 2a (in polar solvents) and 2b. The role of the sulfinyl group in this behavior was inferred by comparison of these results with those obtained in reactions of diazoalkanes with 5-methoxyfuran-2(5H)-one (3). Steric interactions seem to be the main ones responsible for the observed exo selectivity of reactions with diazoethane, but electronic factors, which can be modulated by the solvent, are also significant in the π-facial selectivity control. DFT computational methods are able to correctly predict the reactivity, regioselectivity, and π-facial selectivity exhibited by 5-alkoxyfuranones as well as their changes with the solvent polarity. A C−H···O hydrogen bond, involving the oxygen atom of the 5-alkoxy group at dipolarophiles and the endo-hydrogen atom at dipoles, seems to play a key role in the electronic interactions influencing the stereochemical course of these reactions.
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