Rate limiting step precedes C-C bond formation in the archetypical proline-catalyzed intramolecular aldol reaction.

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 (13)C kinetic isotope effects for this reaction show conclusively that carbon-carbon bond formation is not rate-limiting.

De novo computational design of retro-aldol enzymes.

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 retro-aldolase 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.

Quantum mechanical design of enzyme active sites.

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.

How similar are enzyme active site geometries derived from quantum mechanical theozymes to crystal structures of enzyme-inhibitor complexes? Implications for enzyme design.

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 A from the crystal structure, while the RMSD for the bound intermediate complexes are significantly higher at 1.42 A. The implications for computational enzyme design are discussed.

Approaches to open fullerenes: a 1,2,3,4,5,6-hexaadduct of C60.

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 retro[2 + 2 + 2] mechanism due to the high activation barrier and endothermicity of the reaction.

Theoretical studies of stereoselectivities of intramolecular aldol cyclizations catalyzed by amino acids.

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.

Theory of asymmetric organocatalysis of Aldol and related reactions: rationalizations and predictions.

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.

The role of steric and electronic interactions in the stereocontrol of the asymmetric 1,3-dipolar reactions of 5-ethoxy-3-p-(S)-tolylsulfinylfuran-2(5H)-ones with diazoalkanes: theoretical calculations and experimental evidences.

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 pi-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 pi-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 pi-facial selectivity control. DFT computational methods are able to correctly predict the reactivity, regioselectivity, and pi-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.

1,3-dipolar cycloaddition of 2-dialkylaminothioisomünchnones with aliphatic aldehydes: synthesis of beta-lactams and thiiranes, structure elucidation, and rationale for chemoselective fragmentation of cycloadducts.

A series of highly funtionalized beta-lactams and thiiranes can be generated on treatment of 1,3-thiazolium-4-olates (thioisomünchnones) with aliphatic aldehydes. Although in some cases a variety of products have been obtained, the present paper now provides a mechanistic rationale to explain the product distribution based on stereoelectronic effects. Thus, ring fragmentation of the initial [3+2] cycloadduct is essentially dictated by the electronic character of the aryl substituent on the nitrogen atom of the parent thioisomünchnone. However, further evolution of such cycloadducts into beta-lactams or thiiranes is governed by steric effects to a large extent. Evidence for such interactions has been obtained by computing PM3-optimized diastereomeric transition structures in the reaction of a thioisomünchnone with a chiral aliphatic aldehyde.

Conformation of secondary amides. A predictive algorithm that correlates DFT-calculated structures and experimental proton chemical shifts.

The magnetic deshielding caused by the amido group on CON-CHalpha protons of secondary amides can easily be correlated with DFT-based structures at the B3LYP/6-31G level of theory via a novel algorithm that refines previous models, such as the classical McConnell equation. The shift is given by delta = a + 2.16 cos2(alpha - 35)/d, where alpha denotes the virtual dihedral angle resulting from linking the carbonyl and the alpha-carbons and d is the distance (A) between the shifted proton and the carbonyl oxygen. Notably, in this equation a is a parameter that can be optimized for different solvents, namely, CDCl3, DMSO-d6, and D2O. For the development of these correlations, the preferential conformation of amides is taken from the optimized structures in the gas phase obtained at the DFT level. The deshielding on anti and gauche protons in both rotamers of (Z)-acetamides and E/Z isomers of formamides has been evaluated. This methodology has proved to be highly reliable, allowing us to discard ab initio or DFT conformational arrangements when shifts calculated by the above-mentioned equation differ from the experimental values. Thus, the anti disposition between the CHalpha proton and the N-H bond appears to be the more stable conformation of simple amides. For amides bearing only one proton at Calpha, a local syn minimum can equally be characterized. The rotational barriers around the CON-alkyl bond along with the pyramidalization of the amido group have also been reassessed. As the conformation is taken away from anti or local syn minima, the nonplanarity of the amido group appears to increase.

Experimental and theoretical insights regarding the cycloaddition reaction of carbohydrate-based 1,2-diaza-1,3-butadienes and acrylonitrile. A model case for the behavior of chiral azoalkenes and unsymmetric olefins.

A series of carbohydrate-based tetrahydropyridazines are prepared by the hetero-Diels-Alder reaction of the chiral 1,2-diaza-1,3-butadienes 1 and 2 with acrylonitrile. Reactions are regiospecific, and the observed diastereoselection is consistent with a preferred attack to the Re face of the heterodiene unit, as the chiral sugar placed at C4 does largely protect the opposite Si face. The stereochemistry of the major cycloadduct 4 has been firmly established by an X-ray crystallographic study that, in addition, reveals a conformation placing the cyano group in axial orientation. Cycloadducts such as 9 and 11, in which the axial cyano group and the carbohydrate moiety exhibit a cis relationship, undergo a facile E2 elimination that relieves the steric congestion. A detailed computational study is reported to provide better insight into the factors that influence this asymmetric cycloaddition. A DFT study (B3LYP/6-31G) on a reduced model does correctly predict the regiochemistry observed experimentally, while the facial diastereoselection is modeled at a semiempirical (PM3) level on the parent reagents, thereby accounting for the steric factor provided by the chiral substituent. The calculations also indicate that the axial orientation of the cyano group can be rationalized in terms of a stabilizing anomeric effect.

Novel acid-catalyzed rearrangement of tetrahydro-1,2,3,4-tetrazines: unexpected formation of glycosazones.

The present contribution discloses a simple and unexpected acid-catalyzed cleavage of tetrahydrotetrazines leading to 1,2-bis(hydrazones). Incorporation of a chiral fragment derived from carbohydrates enables the rapid preparation of glycosazones, a family of compounds employed by Emil Fischer to elucidate the configuration of sugars. In addition, a mechanistic proposal accounts for experimental observations.

Cyclic vinyl p-tolyl sulfilimines as chiral dienophiles: Diels-Alder reactions with furan and acyclic dienes.

The dienophilic behavior of the sulfilimine 2, synthesized from (Z)-3-p-tolylsulfinylacrylonitrile 1, in its Diels-Alder reactions with furan and acyclic dienes has been investigated. A complete pi-facial selectivity for 2, opposite to that observed from its precursor 1, is the main feature of all these cycloadditions. Moreover, the high exo selectivity observed in reactions of 2 with furan (not observed for 1) contrasts with the almost complete endo selectivity with other cyclic and acyclic dienes. Additionally, the opposite regioselectivities obtained for 2 with Dane's diene and 1-substituted butadienes (not observed for 1) are also noteworthy. This behavior allows dienophiles 1 and 2 to be considered as complementary precursors from a synthetic point of view.

Cyclic vinyl p-tolyl sulfilimines as chiral dienophiles: theoretical study on the stereoselectivity, Lewis acid catalysis, and solvent effects in their Diels-Alder reactions.

The theoretical study reported in the present work deals with chiral cyclic vinyl sulfilimines and their reactivity as dienophiles in [4 + 2] cycloaddition reactions, using B3LYP/6-31G(d)//AM1 and B3LYP/6-31G(d)//B3LYP/6-31G(d) model chemistries. Consideration of Lewis acid catalysis, illustrated by BF(3), decreases the activation energies of the cycloaddition process while the charge transfer from the diene to the sulfilimine is augmented. The [4 + 2] cycloaddition reactions of sulfilimines with both furan and cyclopentadiene occur in the gas phase with endo stereoselectivity, which is more pronounced with the latter diene. Endo-exo energy differences in the gas phase with the B3LYP/6-31+G(d)//B3LYP/6-31+G(d), B3LYP/6-31G(d)//B3LYP/6-31G(d), and B3LYP/6-31G(d)//AM1 model chemistries are almost the same. Solvent effects are responsible for the inversion of the stereoselectivity in the reactions of sulfilimines with furan because of the great difference in the dipole moments in endo and exo approaches.