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Updated: Feb 24, 2026

Optimization of the Ugi Reaction Using Parallel Synthesis and Automated Liquid Handling
Published on: November 11, 2008
Automated Generation of Reaction Complexes for Double-Ended Transition State Searches
Wen-Jie Fu1, Da-Bao Li1, Chen-Ming Xue1
1College of Environment and Resources, Guangxi Normal University, Guilin 541004, China.
Abstract:
Double-ended transition state (TS) search algorithms require reliable reactant and product geometries, which are often difficult to obtain. Here, we introduce Orienta, a lightweight tool that rapidly generates plausible reactant and product complexes by predicting atom connection orientations based on steric minimization principles inspired by VSEPR theory. Validation on a suite of 13 bimolecular reactions demonstrated that the generated complexes reliably support TS searches using NEB method. In addition, Orienta can generate adsorption and surface reaction orientations for clusters and periodic systems, showing excellent agreement with DFT-optimized structures. Despite certain limitationsincluding its inability to handle reactions that do not involve bond breaking or formation, such as intramolecular rotationsOrienta reduces the need for manual intervention and is capable of providing an effective front-end for fully automated double-ended TS searches. Orienta can be obtained at github.com/atomsos/orienta.
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