Fig. 2: Structural and energetic performance of diffusion and optimal transport generated TS structures.
From: Optimal transport for generating transition states in chemical reactions
a, Cumulative probability for structure r.m.s.d. (left) and absolute energy error (∣ΔETS∣) (right) between the true and generated TS on 1,073 set-aside test reactions. Single-shot OA-ReactDiff39 (blue), 40-shot OA-ReactDiff with recommender (red), single-shot TSDiff38 (green) and React-OT TS (orange) are shown. Both r.m.s.d. and ∣ΔETS∣ are presented in log scale for visibility of the low error regime. b, Reference TS structure, OA-ReactDiff TS sample (red) and React-OT structure (orange) for select reactions. r.m.s.d. and ∣ΔETS∣ for OA-ReactDiff and React-OT structures are shown in text with their corresponding colour. Atoms in the reference TS are coloured as follows: C, grey; N, blue; O, red; H, white. c, Histogram of probability (grey, left y axis) and cumulative probability (blue, right y axis) showing the difference in r.m.s.d. (left) and ∣ΔETS∣ (right) between OA-ReactDiff-recommended and React-OT structures compared with reference TS. Negative Δr.m.s.d. or Δ∣ΔETS∣ suggests that the React-OT structure is of higher quality. A box plot (blue) for Δr.m.s.d. and Δ∣ΔETS∣ is shown above the histogram, correspondingly. A dashed vertical line is shown for no deviation between two structures. d, Inference time in seconds for single-shot OA-ReactDiff (blue), 40-shot OA-ReactDiff with recommender (red) and React-OT (orange). The y axis is presented in log scale for visibility of the extremely low inference time for React-OT. In a and c, the statistics are displayed for 1,073 test reactions, where the median is represented by a solid line, the mean as a dashed line and quarters 1 and 3 as the edges of the box, and the fences correspond to the edges ±1.5 times the interquartile range.
