The Claisen rearrangement of chorismate to prephenate via the proposed “chair-like” transition state where the atoms involved in the [3, 3]-pericyclic reaction are arranged in a chair configuration.

Active site structures after energy minimization and before dynamics. (A) CHAIR. The interactions between the substrate and the active site residues are the same as those observed in the x-ray structures (10–11). The interactions and distances are (with the values in the initial docked structure given in parentheses): 1) salt bridge between Arg-16 and the side-chain carboxylate with the corresponding distances between the protons of Arg-16 and the oxygens equal to 1.6 Å (2.0–2.3 Å); 2) salt bridge between Lys-168 and the side-chain carboxylate with a distance between the proton of Lys-168 and the oxygen of the carboxylate equal to 1.5 Å (2.5 Å); 3) salt bridge between Arg-157 (H) and the ring carboxylate (O) with distances equal to 1.6 Å (1.9–2.5 Å); 4) hydrogen bond between Glu-246 (H) and the ether oxygen with a distance equal to 1.8 Å (2.3 Å); 5) hydrogen bond between Lys-168 (H) and the ether oxygen with a distance equal to 2.4 Å (2.6 Å); 6) interaction between Thr-242 (H) and the ring carboxylate with a distance equal to 1.7 Å (2.9 Å); 7) interaction between the backbone amide group (H) of Asn-194 and the hydroxyl oxygen with a distance equal to 1.9 Å (2.7 Å); and 8) interaction between Glu-198 and the C₄ hydroxyl proton with a distance equal to 2.0 Å (3.5 Å). The energy minimization of the YCM–CHAIR complex does not lead to a different conformation, although there are some modifications of the structural parameters (see above). R₁ = 2.9 Å, τ₁ = −137°, τ₂ = 87°, τ₃ = 59°, and δ = 25°. (B) DIEQ₁. The substrate is still in DIEQ₁ after the energy minimization. R₁ = 3.7 Å, τ₁ = −70°, τ₂ = 160°, τ₃ = 68°, and δ = −45°. All of the interactions in A exist here, except that the hydroxyl proton is involved in the internal hydrogen bond with the side-chain carboxylate rather than with Glu-198 (8 above). (C) DIAX. The initial orientation of DIAX in the active site is such that the side-chain groups (the carboxylate and ether oxygen) form the observed interactions with the active residues (i.e., 1, 2, 4, and 5). The substrate undergoes a rotation about the C₃—O₇ bond (R₂) toward CHAIR during the minimization, so the conformation is between DIAX and CHAIR. R₁ = 3.6 Å, τ₁ = −145°, τ₂ = 84°, τ₃ = 2°, and δ = 31°. Certain interactions involving the ring carboxylate and the C₄ hydroxyl proton cannot be formed; e.g., Arg-157 interacts only with one of the ring carboxylate oxygens, and the hydroxyl group of Thr-242 is 6 Å away from the oxygen (O_b) of the ring carboxylate.

(A) The internal hydrogen bond between the C₄ hydroxyl proton and the side-chain carboxylate oxygen in the YCM–DIEQ₁ complex monitored as a function of time; the trajectories shown are the ones used to produce Fig. 4B. This figure shows that the hydrogen bond is broken at the same time as the conformation transition from DIEQ₁ to CHAIR occurs at each temperature (compare Fig. 4B). (B) Certain interactions of the ring carboxylate and C₄ hydroxyl group with the active site residues (Arg-157, Thr-242, Glu-198, and Asn-194) in the YCM–DIAX complex as functions of time. The trajectory is the one used to produce Fig. 4C. There are no interactions initially between H of Arg-157 and O_a of the ring carboxylate, between Thr-242 and O_b, and between O_E1 of Glu-198 and the C₄ hydroxyl proton in the YCM–DIAX complex (see Fig. 3C). B shows that these interactions are all formed after 50-ps simulations as the substrate changes from DIAX to CHAIR.

The gas-phase structures of CHAIR, DIEQ₁, DIEQ₂, DIAX, and ex-DIAX obtained from geometry optimization at the B3LYP/6–31G* or HF/6–31G* level (see Table 1); the structures obtained from the semiempirical density functional method (SCC–DFTB) are similar (see Table 1). DIAX was also obtained from solution simulations by using CHAIR as the initial conformation. The values of the structural parameters obtained from the solution simulations are close to those from the HF/6–31G* calculations with bridging water molecules (see Table 1). (A) CHAIR; (B) DIEQ₁; (C) DIEQ₂; (D) DIAX; (E) ex-DIAX.

Motions of CHAIR, DIEQ₁, and DIAX in the active site of YCM as a function of time. (A) CHAIR at 300 K. The motion is monitored by δ (magenta, dashed line) and τ₃ (red, dotted line). No conformational transition occurs, and the substrate remains in the neighborhood of CHAIR (i.e., δ ≈ 30° and τ₃ ≈ 60°). (B) DIEQ₁ at 100 K (blue, dashed line) and 200 K (red, dotted line). The motion is monitored by δ. The substrate changes to CHAIR in about 50 ps at 100 K and 5–10 ps at 200 K, as indicated by the change of δ from negative to positive values. (C) DIAX at 300 K. The motion is monitored by τ₃ (red, dotted line). τ₃ increases from 0° to 50–60° (CHAIR) as a result of the rotation of the ring carboxylate.

The fluctuations of the C₁… C₉ distance (R₁) and the C₃—O₇ distance (R₂) during 2 ps (from 172 to 174 ps) in the active site at 300 K, starting from the minimized structure in Fig. 3A. R₁, blue-solid line; R₂, red-dashed line.