Computational studies on the sterol-like cyclization of a monodomain class II terpene cyclase.

Recently the first example of a class II terpene cyclase comprised of only a single domain was reported. Class II synthases are a diverse group of enzymes that catalyze exceptionally complex reactions, including the remarkable cyclization of steroids. This discovery of a single-domain enzyme being able to catalyze a steroid-like product contradicted the long-held tenet that complex class II cyclizations required double-domain enzymes. The proposed mechanism for the sterol-like cyclization of a monodomain class II terpene cyclase was studied computationally by using density functional theory (DFT). The complete pathway for the conversion of 5-geranyl-3,4-dihydroxybenzoate to the steroid-like pentacyclic product merosterolic acid A was elucidated. The formation of a tricyclic carbocation intermediate with three cyclohexane rings was found to be a concerted, but asynchronous, cyclization. The formation of the fourth ring proceeds with a low energy activation Friedel-Crafts reaction. Subsequent deprotonation of this pentacyclic system gave as the final product merosterolic acid. The overall conversion was found to be highly exothermic due to the conversion of three C-C double bonds to C-C single bonds.

Computational studies on the cyclization of squalene to the steroids and hopenes.

A review of computational studies of the related biosyntheses of steroids and hopenes reported during the last two decades is presented. Computations in the gas phase and those that include the enzyme are covered. Based on the numerical results conclusions have been drawn about the biosynthetic mechansims of these all important biological reactions.

Biosynthetic Mechanism of Lanosterol: Cyclization.

The remarkable cyclization mechanism of the formation of the 6-6-6-5 tetracyclic lanosterol (a key triterpenoid intermediate in the biosynthesis of cholesterol) from the acyclic 2,3-oxidosqualene catalyzed by oxidosqualene cyclase (OSC) has stimulated the interest of chemists and biologists for over a half century. Herein, the elaborate, state-of-the-art two-dimensional (2D) QM/MM MD simulations have clearly shown that the cyclization of the A-C rings involves a nearly concerted, but highly asynchronous cyclization, to yield a stable intermediate with "6-6-5" rings followed by the ring expansion of the C-ring concomitant with the formation of the D-ring to yield the "6-6-6-5" protosterol cation. The calculated reaction barrier of the rate-limiting step (≈22 kcal mol(-1)) is comparable to the experimental kinetic results. Furthermore all previous experimental mutagenic evidence is highly consistent with the identified reaction mechanism.

The concerted nature of the cyclization of squalene oxide to the protosterol cation.

Concerted A-C ring formation: A concerted, but highly asynchronous, pathway was identified for the formation of rings A-C in the biosynthetic conversion of squalene oxide to the prosterol cation, with ring B being formed in the required boat conformation.

Discovering a uniform functional trade-off of the CBC-type 2,3-oxidosqualene cyclases and deciphering its chemical logic.

Many functionally promiscuous plant 2,3-oxidosqualene cyclases (OSCs) have been found, but complete functional reshaping is rarely reported. In this study, we have identified two new plant OSCs: a unique protostadienol synthase (AoPDS) and a common cycloartenol synthase (AoCAS) from Alisma orientale (Sam.) Juzep. Multiscale simulations and mutagenesis experiments revealed that threonine-727 is an essential residue responsible for protosta-13 (17),24-dienol biosynthesis in AoPDS and that the F726T mutant completely reshapes the native function of AoCAS into a PDS function to yield almost exclusively protosta-13 (17),24-dienol. Unexpectedly, various native functions were uniformly reshaped into a PDS function by introducing the phenylalanine → threonine substitution at this conserved position in other plant and non-plant chair-boat-chair-type OSCs. Further computational modeling elaborated the trade-off mechanisms of the phenylalanine → threonine substitution that leads to the PDS activity. This study demonstrates a general strategy for functional reshaping by using a plastic residue based on the decipherment of the catalytic mechanism.

Concerted, highly asynchronous, enzyme-catalyzed [4 + 2] cycloaddition in the biosynthesis of spinosyn A; computational evidence.

A theoretical study has been carried out on model systems to study a recently reported, (Nature, 2011, 473, 109) biosynthetic, [4 + 2] cycloaddition catalyzed by a stand-alone enzyme (the cyclase SpnF). It was suggested in this paper that SpnF is the first known example of a Diels-Alderase (DA). In the present study, for a model system of the substrate a transition structure was found with density functional calculations (DFT). In addition, the intrinsic reaction coordinate calculations indicated that the transition structure is that of a concerted, but highly asynchronous, DA reaction. Based on the DFT and Møller-Plesset second order calculations the activation energy was estimated to be about 15 kcal mol(-1). The results of a natural population analysis indicated that there is significant charge transfer in the transition state, and it is proposed that possibly the enzyme plays a dual role of not only folding the substrate into the proper conformation for the DA reaction to occur, but also lowering its activation energy by stabilization of the highly polarized transition structure.

Physical constraints on sesquiterpene diversity arising from cyclization of the eudesm-5-yl carbocation.

The biogenic origins of complex cyclic terpenes derive from the interplay of enzymes and the intrinsic reactivity of carbocation species at major branch-points along intramolecular cyclization pathways to ultimately determine the distribution of terpene skeletal types in nature. Solanaceous plants biosynthesize chemical defense compounds, largely derived from the eremophilane and spirovetivane-type sesquiterpenes. These hydrocarbon skeletons share a common biogenic origin, stemming from alternative Wagner-Meerwein rearrangements of the eudesm-5-yl carbocation during the cyclization of farnesyl pyrophosphate (FPP) catalyzed by sesquiterpene synthases. While the spirojatamane skeleton shares the same carbocation intermediate, this class of sesquiterpenes has not been reported in the Solanaceae and is exceedingly rare in nature. To investigate the physical basis for alternative rearrangements of the eudesm-5-yl carbocation, we carried out quantum mechanics (QM) analyses to calculate the allowable conformations, energies, and transition states linking conformers of the eudesm-5-yl carbocation to the eremophilene, spirovetivane, and spirojatamane skeletons. Additionally, we conducted parallel investigations on simplified decalin carbocation systems to examine the contribution of ring substituents to allowable conformations and rearrangement pathways. Our study reveals that ring substituents expand the conformational space accessible to the eudesm-5-yl carbocation while sterically blocking rearrangements in certain contexts. From our analysis, we define a conformational threshold for each possible rearrangement based on dihedral angles describing transition state geometry. Further, our calculations indicate that methylene migration rearrangements leading to spiro compounds are thermodynamically dominant in the eudesm-5-yl and simpler decalin carabocation systems. Interestingly, the theoretical abundance of sesquiterpene skeletal types arising from the intrinsic reactivity of the eudesm-5-yl carbocation stands in sharp contrast to their currently known natural abundance. The implications of these results for the catalytic tragectories catalyzed by sesquiterpene synthases are discussed.

Compelling computational evidence for the concerted cyclization of the ABC rings of hopene from protonated squalene.

The long-standing question of what is the nature of the cyclization of squalene to form tetracyclic and pentacyclic triterpenes has been addressed computationally. Using the DFT method with an intrinsic reaction coordinate calculation, we find that the first three rings of protonated squalene were formed without the intermediacy of mono- or bicyclic carbocations. The cyclization, calculated in the gas phase, proceeds in a highly asynchronous, concerted reaction to yield the tricyclic, tertiary carbocation with a 5-membered C ring. The fourth double bond of squalene is not properly oriented for the ring expansion of the C ring in concert with the formation of the 5-membered ring.

Lewis acid-catalyzed one-pot, three-component route to chiral 3,3'-bipyrroles.

3,3'-Bipyrroles 3 could be synthesized using a double Michael addition reaction involving diaroyl acetylene 1 and the appropriate 1,3-dicarbonyls 2 using ammonium acetate as a nitrogen source. The axial chirality of bipyrrole was anticipated from the X-ray crystal structure and DFT calculations and confirmed by separating the racemates on a chiral column and subsequent CD spectra of the enantiomers. The absolute configuration of the enantiomers was achieved by theoretical CD spectra calculation using the ZINDO method.

Role of the antenna in tissue selective probes built of lanthanide-organic chelates.

The role of the antenna in the process of the host sensitized luminescence of the DOTA cage coordinated with the Eu ion is investigated. The analysis of the optimal geometries of DOTA modified by several antennas is based on the results of density functional theory (DFT) calculations. The physical environment of the luminescence center (the lanthanide ion) is illustrated by charge density maps and described by the values of the crystal field parameters directly evaluated. The conclusions derived from this theoretical analysis support earlier observations that antennas attached to the cage play the sole role of harvesting and transferring the energy to the lanthanide ion, whereas the cage perturbs the symmetry of the environment of the lanthanide ion, giving rise to the sensitized luminescence. The implications of the separation of the two parts of the organic chelate, cage and antenna, are discussed within the theoretical models of the energy transfer and of forced f <--> f electric dipole transitions.

The rearrangement of fluorenylideneallene oxide. A DFT study.

[reaction: see text] Density functional calculations indicate that the rearrangement of fluorenyl allene oxide to the spiro fluorenyl cyclopropanone proceeds through the reactive intermediate fluorenyl oxyallyl. The calculated energetics of this conversion are in agreement with that observed experimentally. The spiro fluorenyl cyclopropanone was calculated to have a low activation energy for its conversion to fluorene and carbon monoxide.

Formation of the C ring in the lanosterol biosynthesis from squalene.

[reaction: see text] Ab initio calculations were performed on a cyclohexane derivative to elucidate the mechanism of the formation of the five-membered C ring in the biosynthesis of lanosterol from squalene. A conformational analysis of the side chain containing the double bond indicated that the conformer that should give rise to the cyclized C ring is not a minimum on the potential surface. Consequently, it is suggested that it is very likely that C-ring formation occurs in concert with formation of the A and B rings.

Concerted nature of AB ring formation in the enzymatic cyclization of squalene to hopenes.

The cyclization of the A-B rings of squalene to hopene is studied computationally (DFT). A transition structure is found for a concerted, asynchronous pathway for the formation of chair-chair decalin carbocation. The computationally derived conformer leading to this asynchronous transition structure is remarkably similar to the analogous region of 2-azasqualene encapsulated by squalene-hopene cyclase recently reported by Schulz. A concerted A-B ring closure is likely to occur in the cyclization of squalene to hopene. [structure--see text]

Aromaticity of butalene and its homologues.

[structure: see text] The aromaticity of a series of fused cyclobutadiene systems is discussed in terms of their resonance energies. While there is considerable variation in their resonance energies per pi electron, all members of the series are calculated to be antiaromatic, though to a lesser degree than the parent cyclobutadiene.

On the stability of large [4n]annulenes.

[reaction: see text] The stabilization energies (B3LYP/6-31G) of planar [4n]annulenes, evaluated by a new indene-isoindene isomerization method (see Abstract graphic), reveal that all 4n pi-electron rings larger than the energetically unfavorable cyclobutadiene are only slightly destabilized by the pi-electron interactions. Cyclooctatetraene prefers the "tub" conformation because of strain effects. Generally, the antiaromatic character of the larger systems with 4n pi-electrons is revealed best by their magnetic properties rather than by their energies.

Structural elucidation of cisoid and transoid cyclization pathways of a sesquiterpene synthase using 2-fluorofarnesyl diphosphates.

Sesquiterpene skeletal complexity in nature originates from the enzyme-catalyzed ionization of (trans,trans)-farnesyl diphosphate (FPP) (1a) and subsequent cyclization along either 2,3-transoid or 2,3-cisoid farnesyl cation pathways. Tobacco 5-epi-aristolochene synthase (TEAS), a transoid synthase, produces cisoid products as a component of its minor product spectrum. To investigate the cryptic cisoid cyclization pathway in TEAS, we employed (cis,trans)-FPP (1b) as an alternative substrate. Strikingly, TEAS was catalytically robust in the enzymatic conversion of (cis,trans)-FPP (1b) to exclusively (>/=99.5%) cisoid products. Further, crystallographic characterization of wild-type TEAS and a catalytically promiscuous mutant (M4 TEAS) with 2-fluoro analogues of both all-trans FPP (1a) and (cis,trans)-FPP (1b) revealed binding modes consistent with preorganization of the farnesyl chain. These results provide a structural glimpse into both cisoid and transoid cyclization pathways efficiently templated by a single enzyme active site, consistent with the recently elucidated stereochemistry of the cisoid products. Further, computational studies using density functional theory calculations reveal concerted, highly asynchronous cyclization pathways leading to the major cisoid cyclization products. The implications of these discoveries for expanded sesquiterpene diversity in nature are discussed.

Thermal [1,5] hydrogen sigmatropic shifts in cis,cis-1,3-cyclononadienes probed by gas-phase kinetic studies and density functional theory calculations.

The kinetics of gas-phase thermal [1,5] hydrogen shifts interconverting the five isomeric mono-deuterium-labeled cis,cis-1,3-cyclononadienes have been followed at four temperatures from 240 to 287 degrees C. The activation parameters found were Ea = 37.1 +/- 0.8 kcal/mol, log A = 11.6 +/- 0.3, DeltaH++ = 36.0 +/- 0.8 kcal/mol, and DeltaS++ = -9.0 +/- 0.3 eu. Density functional theory based calculations have provided geometries and energies for the ground-state cyclononadiene conformational isomers, for the transition states linking one to another, and for the transition states for [1,5] hydrogen shifts responsible for isomerizations among the five labeled dienes. A generalized formulation of the Winstein-Holness equation is presented and applied to the complex system, one that involves 11 ground-state conformers, 10 transition states separating them, and five transition states for [1,5] hydrogen shifts. The value for the empirical Ea derived from calculated mole fractions of ground-state conformers and calculated energies for specific ground-state conformers and [1,5] hydrogen shift transition structures was 37.5 kcal/mol, in excellent agreement with the experimentally obtained activation energy. The significance of conformational options in various ground states and transition structures for the [1,5] hydrogen shifts is considerable, an inference that may well have general applicability.

Cycloheptatrienyl oxyallyl. An observable oxyallyl?

Density functional calculations have been carried out for cycloproylidene-, cyclopentylidene-, and tropyllideneallene oxides (7-9) and the reaction pathway for their conversion to the corresponding oxyallyls (10-12) and cyclopropanones (13-15) in order to probe the electronic structure of the intermediate oxyallyls. All three oxyallyls were found to be stabilized with respect to their allene oxides in comparison to the unsubstituted allene oxide and oxyallyl. For 7 and 9 the stabilization can be attributed to the zwitterionic character of the oxyallyls, while for 8 the stabilization can be attributed to its diradical character. This suggests that oxyallyl is capable of "adapting" to its local environment. Calculations predict that oxyallyl 12 should be an observable intermediate in the absence of nucleophiles, since it is calculated to be of lower energy than either the allene oxide 9 or the cyclopropanone 15.