Hsu, Jun-WeiJun-WeiHsuSHIANG-TAI LIN2026-01-082026-01-082025-11-2515499618https://www.scopus.com/record/display.uri?eid=2-s2.0-105022724339&origin=resultslisthttps://scholars.lib.ntu.edu.tw/handle/123456789/735172Clathrate hydrates are crystalline inclusion compounds with relevance to global climate mitigation, energy resource development, and carbon capture and storage (CCS) technologies, owing to their high volumetric gas density and thermodynamic stability under moderate pressure–temperature conditions. The fundamental building blocks of hydrate crystals are polyhedral cages formed by hydrogen-bonded water molecules. Accurate identification of these cage structures in molecular simulations is critical for investigating the mechanisms of hydrate nucleation and growth. In this work, we introduce a novel open-source algorithm, TRACE (Topological Ring and Additive-Coordinated Cage Explorer), designed to detect and classify structural motifs, such as rings, cups, and both complete and incomplete cages, formed during hydrate nucleation in molecular dynamics simulations. A distinguishing feature of TRACE is its capability to include additives (e.g., hydrate formation promoters or inhibitors) in the cage identification process, making it particularly well-suited for investigating additive effects on hydrate formation. We validate TRACE by analyzing CO2hydrate systems in the presence of urea, a known kinetic promoter. The algorithm enables the tracking of structural evolution and allows for the quantification of cage statistics, lifetimes, urea retention times, and nucleation kinetics via mean first-passage time (MFPT) analysis. By bridging structural and kinetic information, TRACE provides new insights into additive-modulated nucleation pathways and offers a robust tool for characterizing microstructural development in clathrate hydrate formation.truejournal article10.1021/acs.jctc.5c014592-s2.0-105022724339