{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,23]],"date-time":"2026-10-23T19:45:29Z","timestamp":1792784729056,"version":"4.5.0"},"reference-count":50,"publisher":"American Chemical Society (ACS)","issue":"41","license":[{"start":{"date-parts":[[2026,9,30]],"date-time":"2026-09-30T00:00:00Z","timestamp":1790726400000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-029"},{"start":{"date-parts":[[2026,9,30]],"date-time":"2026-09-30T00:00:00Z","timestamp":1790726400000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-037"},{"start":{"date-parts":[[2026,9,30]],"date-time":"2026-09-30T00:00:00Z","timestamp":1790726400000},"content-version":"stm-asf","delay-in-days":0,"URL":"https:\/\/doi.org\/10.15223\/policy-045"}],"funder":[{"name":"National Natural Science Foundation of China (NSFC)","award":["52104045"],"award-info":[{"award-number":["52104045"]}],"id":[{"id":"https:\/\/ror.org\/01h0zpd94","id-type":"ROR","asserted-by":"crossref"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,10,15]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:p>Order parameters are essential for molecular dynamics structures of crystalline water, as they provide quantitative measures of phase change. Yet conventional descriptors cannot directly resolve water-ring connectivity, face adjacency, or cage closure. Here, we develop the Graph-guided Ring Overlap Workflow (GROW) algorithm and its open-source implementation, Shell Quant Qualifier (SQQ), to connect molecular coordinates with cage and phase topology. SQQ constructs hydrogen-bond or oxygen\u2013oxygen water graphs, identifies chordless rings as faces, and reconstructs cages by expanding connected face sets along exposed edges. Since GROW tests branches without predefining the final face arrangement, it can distinguish standard cages, uncommon cage compositions, and isomers that share the same face counts. SQQ maps cage occupancy, face-sharing clusters, hydrate domains, and phase boundaries while preserving the molecular identities behind each result. Tests on standard, perturbed, and periodically translated sI, sII, and sH crystals recover the expected network edges, cage types, and cage\u2013water assignments. Comparisons on a hydrate-growth trajectory show close population agreement with GRADE and TRACE when graph definitions and ring ranges are aligned, while examples explain differences caused by recognition rules. In the benchmark, SQQ completed the system containing more than one million waters within 3 min. Through its Python and C++ engine, SQQ provides an end-to-end workflow for multiframe cage detection, phase analysis, visualization, and traceable structural reporting.<\/jats:p>","DOI":"10.1021\/acs.jpca.6c05769","type":"journal-article","created":{"date-parts":[[2026,10,1]],"date-time":"2026-10-01T01:01:31Z","timestamp":1790816491000},"page":"8187-8199","source":"Crossref","is-referenced-by-count":0,"title":["SQQ: Python Joint\nToolkit for Water-Shell Topology\nAnalysis"],"prefix":"10.1021","volume":"130","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-1882-9920","authenticated-orcid":true,"given":"Jiangtao","family":"Pang","sequence":"first","affiliation":[{"name":"Chinese Academy of Sciences , , ,","place":["Wuhan, P. R. China, 430071"]},{"name":"University of Chinese Academy of Sciences , ,","place":["Beijing, P. R. China, 100049"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Quan","family":"Sun","sequence":"additional","affiliation":[{"name":"Wuhan University , , ,","place":["Wuhan, P. R. China, 430079"]},{"name":"Wuhan University , , ,","place":["Wuhan, P. R. China, 430223"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"316","published-online":{"date-parts":[[2026,9,30]]},"reference":[{"issue":"7788","key":"2026101508072698700_cit1","doi-asserted-by":"publisher","first-page":"60","DOI":"10.1038\/s41586-019-1853-4","article-title":"Atomic Imaging\nof the Edge Structure and Growth of a Two-Dimensional Hexagonal Ice","volume":"577","author":"Ma","year":"2020","journal-title":"Nature"},{"issue":"1","key":"2026101508072698700_cit2","doi-asserted-by":"publisher","DOI":"10.1038\/s41467-024-52131-w","article-title":"Effect of Ion-Specific Water Structures\nat Metal Surfaces on Hydrogen Production","volume":"15","author":"Tian","year":"2024","journal-title":"Nat.\nCommun."},{"issue":"6879","key":"2026101508072698700_cit3","doi-asserted-by":"publisher","first-page":"409","DOI":"10.1038\/416409a","article-title":"Molecular Dynamics\nSimulation of\nthe Ice Nucleation and Growth Process Leading to Water Freezing","volume":"416","author":"Matsumoto","year":"2002","journal-title":"Nature"},{"issue":"6964","key":"2026101508072698700_cit4","doi-asserted-by":"publisher","first-page":"353","DOI":"10.1038\/nature02135","article-title":"Fundamental\nPrinciples and Applications of Natural Gas Hydrates","volume":"426","author":"Sloan","year":"2003","journal-title":"Nature"},{"issue":"6603","key":"2026101508072698700_cit5","doi-asserted-by":"publisher","first-page":"315","DOI":"10.1126\/science.abo0823","article-title":"Visualizing Eigen\/Zundel\nCations and Their Interconversion in Monolayer Water on Metal Surfaces","volume":"377","author":"Tian","year":"2022","journal-title":"Science"},{"key":"2026101508072698700_cit6","doi-asserted-by":"crossref","first-page":"331","DOI":"10.1007\/978-94-015-7658-1_21","volume-title":"Intermolecular Forces","author":"Berendsen","year":"1981"},{"issue":"5940","key":"2026101508072698700_cit7","doi-asserted-by":"publisher","first-page":"249","DOI":"10.1038\/306249a0","article-title":"Molecular Layering of Water at Surfaces\nand Origin\nof Repulsive Hydration Forces","volume":"306","author":"Israelachvili","year":"1983","journal-title":"Nature"},{"key":"2026101508072698700_cit8","article-title":"Clathrate Hydrates\nof Natural Gases","volume-title":"Chemical industries","author":"Sloan","year":"2008","edition":"3"},{"issue":"8","key":"2026101508072698700_cit9","doi-asserted-by":"publisher","first-page":"4477","DOI":"10.1016\/j.petsci.2026.06.013","article-title":"One Hundred\nGrand Challenges in Petroleum Science","volume":"23","author":"Xiao","year":"2026","journal-title":"Pet.\nSci."},{"issue":"43","key":"2026101508072698700_cit10","doi-asserted-by":"publisher","first-page":"13796","DOI":"10.1021\/jp107269q","article-title":"Nucleation Pathways\nof Clathrate\nHydrates: Effect of Guest Size and Solubility","volume":"114","author":"Jacobson","year":"2010","journal-title":"J. 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U.S.A."},{"issue":"1","key":"2026101508072698700_cit33","doi-asserted-by":"publisher","first-page":"177","DOI":"10.1111\/j.1749-6632.1994.tb38833.x","article-title":"Computer Simulation of the Crystal Growth and Dissolution\nof Natural Gas Hydrates","volume":"715","author":"Ba\u0301ez","year":"1994","journal-title":"Ann. N.Y. Acad. Sci."},{"issue":"1\u20132","key":"2026101508072698700_cit34","doi-asserted-by":"publisher","first-page":"326","DOI":"10.1016\/0378-3812(95)02903-6","article-title":"Simulations\nof the Methane Hydrate\/Methane\nGas Interface near Hydrate Forming Conditions Conditions","volume":"116","author":"Rodger","year":"1996","journal-title":"Fluid Phase Equilib."},{"issue":"16","key":"2026101508072698700_cit35","doi-asserted-by":"publisher","DOI":"10.1063\/1.4871898","article-title":"Two-Component Order\nParameter for Quantifying Clathrate Hydrate Nucleation and Growth","volume":"140","author":"Barnes","year":"2014","journal-title":"J. Chem. Phys."},{"issue":"20","key":"2026101508072698700_cit36","doi-asserted-by":"publisher","DOI":"10.1063\/1.4996132","article-title":"Nucleation Mechanism\nof Clathrate Hydrates of Water-Soluble\nGuest Molecules","volume":"147","author":"DeFever","year":"2017","journal-title":"J. Chem. Phys."},{"key":"2026101508072698700_cit37","doi-asserted-by":"publisher","DOI":"10.1016\/j.jcis.2025.137812","article-title":"The Secret Role of\nWater\u2019s Structure near Surfaces\nin Ice Formation","volume":"698","author":"Sun","year":"2025","journal-title":"J. Colloid Interface Sci."},{"issue":"25","key":"2026101508072698700_cit38","doi-asserted-by":"publisher","DOI":"10.1039\/c1cp20070d","article-title":"Using the Face-Saturated\nIncomplete Cage Analysis to Quantify the Cage Compositions and Cage\nLinking Structures of Amorphous Phase Hydrates","volume":"13","author":"Guo","year":"2011","journal-title":"Phys. Chem. Chem. Phys."},{"key":"2026101508072698700_cit39","doi-asserted-by":"publisher","first-page":"385","DOI":"10.1016\/j.cpc.2019.06.004","article-title":"GRADE: A Code to\nDetermine Clathrate Hydrate Structures","volume":"244","author":"Mahmoudinobar","year":"2019","journal-title":"Comput.\nPhys. Commun."},{"issue":"4","key":"2026101508072698700_cit40","doi-asserted-by":"publisher","first-page":"1282","DOI":"10.1021\/acs.jpcb.0c08964","article-title":"Iterative\nCup Overlapping: An Efficient\nIdentification Algorithm for Cage Structures of Amorphous Phase Hydrates","volume":"125","author":"Hao","year":"2021","journal-title":"J. Phys. Chem. B"},{"issue":"1","key":"2026101508072698700_cit41","doi-asserted-by":"publisher","first-page":"699","DOI":"10.1515\/ntrev-2022-0044","article-title":"HTR: An Ultra-High\nSpeed Algorithm for Cage Recognition of Clathrate Hydrates","volume":"11","author":"Liu","year":"2022","journal-title":"Nanotechnol. Rev."},{"issue":"36","key":"2026101508072698700_cit42","doi-asserted-by":"publisher","DOI":"10.1088\/1361-648X\/ad52df","article-title":"HTR+: A Novel Algorithm\nfor Identifying Type and Polycrystal of Gas Hydrates","volume":"36","author":"Shi","year":"2024","journal-title":"J. Phys.: Condens. Matter"},{"issue":"22","key":"2026101508072698700_cit43","doi-asserted-by":"publisher","first-page":"11436","DOI":"10.1021\/acs.jctc.5c01459","article-title":"TRACE: A Topological\nAlgorithm for Detecting Additive-Coordinated\nHydrate Cages","volume":"21","author":"Hsu","year":"2025","journal-title":"J. Chem. Theory Comput."},{"issue":"1","key":"2026101508072698700_cit44","doi-asserted-by":"publisher","DOI":"10.1038\/s42004-021-00539-6","article-title":"Open Questions\non Methane Hydrate Nucleation","volume":"4","author":"Guo","year":"2021","journal-title":"Commun. 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Technol."},{"key":"2026101508072698700_cit47","unstructured":"Volkova, E.\n          \n          Molecular Dynamics\nModeling of Kaolinite Particles Aggregates and Their Interaction with\nAmorphous Glass Surfaces; PhD Thesis; KAUST Research Repository, 2022. 10.25781\/KAUST-3YKX4."},{"issue":"24","key":"2026101508072698700_cit48","doi-asserted-by":"publisher","first-page":"9093","DOI":"10.1021\/acs.jctc.3c01120","article-title":"Quantifying the Relevance of Long-Range\nForces for Crystal Nucleation in Water","volume":"19","author":"Zhao","year":"2023","journal-title":"J. Chem.\nTheory Comput."},{"issue":"1","key":"2026101508072698700_cit49","doi-asserted-by":"publisher","first-page":"694","DOI":"10.1016\/j.petsci.2023.08.027","article-title":"New Insights\ninto the Deposition of Natural Gas Hydrate on Pipeline Surfaces: A\nMolecular Dynamics Simulation Study","volume":"21","author":"Zhang","year":"2024","journal-title":"Pet. Sci."},{"key":"2026101508072698700_cit50","doi-asserted-by":"publisher","DOI":"10.1016\/j.clay.2024.107400","article-title":"New Insight into Methane Hydrate\nFormation at Clay-Geofluid Interface in Natural Kaolinite-Stacking\nSediments","volume":"255","author":"Pang","year":"2024","journal-title":"Appl. Clay Sci."}],"container-title":["The Journal of Physical\nChemistry A"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/pubs.acs.org\/doi\/pdf\/10.1021\/acs.jpca.6c05769","content-type":"application\/pdf","content-version":"vor","intended-application":"unspecified"},{"URL":"https:\/\/pubs.acs.org\/jpcafh\/article-pdf\/130\/41\/8187\/68720524\/acs.jpca.6c05769.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/pubs.acs.org\/jpcafh\/article-pdf\/130\/41\/8187\/68720524\/acs.jpca.6c05769.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,10,15]],"date-time":"2026-10-15T12:30:10Z","timestamp":1792067410000},"score":1,"resource":{"primary":{"URL":"https:\/\/pubs.acs.org\/jpcafh\/article\/130\/41\/8187\/5443037\/SQQ-Python-Joint-Toolkit-for-Water-Shell-Topology"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,9,30]]},"references-count":50,"journal-issue":{"issue":"41","published-online":{"date-parts":[[2026,9,30]]},"published-print":{"date-parts":[[2026,10,15]]}},"URL":"https:\/\/doi.org\/10.1021\/acs.jpca.6c05769","relation":{},"ISSN":["1089-5639","1520-5215"],"issn-type":[{"value":"1089-5639","type":"print"},{"value":"1520-5215","type":"electronic"}],"subject":[],"published":{"date-parts":[[2026,9,30]]}}}