{"id":975,"date":"2014-06-28T22:51:27","date_gmt":"2014-06-29T02:51:27","guid":{"rendered":"http:\/\/titan.chem.uottawa.ca\/?page_id=975"},"modified":"2025-06-18T14:50:30","modified_gmt":"2025-06-18T18:50:30","slug":"software","status":"publish","type":"page","link":"http:\/\/titan.chem.uottawa.ca\/?page_id=975","title":{"rendered":"Software & Datasets"},"content":{"rendered":"

All of our software can be found on the lab’s GitHub page<\/a><\/strong>.<\/p>\n

\n

MOSAEC-DB – DATASET<\/h2>\n

\"\"<\/p>\n

MOSAEC-DB<\/strong> is a database of high-fidelity experimental MOF structures ready for simulation using improved processing and structural error analysis algorithms. It currently contains >100K structures as is updated the CSD is updated. Structural errors found<\/a> in many other experimental databases have been screened for and removed.<\/p>\n

Reference<\/strong>: Gibaldi, M.; Kapeliukha, A.; White, A.; Luo, J.; Mayo, R.A.; Burner, J.; Woo, T.K.\u00a0 \u201cMOSAEC-DB: A comprehensive database of experimental metal-organic frameworks with verified chemical accuracy suitable for molecular simulations\u201d, Chemical Science<\/em>,\u00a02025<\/strong>,\u00a016<\/em>, 4085-4100.\u00a0\u00a0link<\/a><\/p>\n

Download<\/strong>: Currently, the database can be obtained from the CCDC website. link<\/a><\/p>\n

\n

ARC-MOF –\u00a0DATASET<\/h2>\n

\"\"<\/p>\n

ARC-MOF<\/strong>\u00a0 is a curated database (>200K) of experimentally characterized and computer-generated MOFs ready for computation. Importantly, structural errors that are seen<\/a> in many other databases have been screened for and removed in this database.\u00a0 The structures also include DFT derived partial atomic charges for us in simulation.\u00a0 ARC-MOF was featured in the journal Chemistry of Materials<\/em> highlights of 2023<\/a>.<\/p>\n

Reference<\/strong>: Burner, J.; Luo, J.; White, A.; Mirmiran, A,; Kwon, O.; Boyd, P.G.; Maley, S.; Gibaldi, M.; Simrod, S.;\u00a0 Ogden, V.; Woo, T.K.* \u201c<\/span>ARC-MOF: A Diverse Database of Metal-Organic Frameworks with DFT-Derived Partial Atomic Charges and Descriptors for Machine Learning<\/span>\u201c,\u00a0Chemistry of Materials<\/em>,\u00a02023<\/strong>,\u00a035<\/em>,\u00a0<\/span><\/span>900\u2013916. link<\/a>\u00a0<\/span><\/p>\n

Download: <\/strong>link<\/a><\/p>\n

\n

HEALED SBUs for MOF construction<\/h2>\n

\"Abstract<\/p>\n

HEALED SBUs: <\/strong>are a set of SBUs (structural building units) or linkers for building MOFs that have been manually inspected for structural errors.\u00a0 Structural errors found<\/a> in many computer generated MOF databases likely have their origin in the source SBU’s that were used.<\/p>\n

Reference<\/strong>: Gibaldi, M.;\u00a0<\/span>Kwon, O.; White, A.;\u00a0<\/span>Burner, J.;\u00a0<\/span>Woo, T.K.*\u00a0<\/span>\u201cThe\u00a0<\/span>HEALED<\/span>\u00a0SBU<\/span>\u00a0l<\/span>ibrary of <\/span>chemically<\/span>\u00a0realistic<\/span>\u00a0building blocks<\/span>\u00a0for construction of hypothetical metal<\/span>\u2013<\/span>organic frameworks\u201d,\u00a0ACS Applied Materials and Interfaces,<\/em>\u00a02022<\/strong>,\u00a014<\/em><\/span>, 43372\u201343386<\/span>.\u00a0 link<\/a><\/span><\/p>\n

Download<\/strong>: link<\/a><\/p>\n

\n

MOSAEC – Metal Oxidation State Analysis structural Error Checker<\/h2>\n

\"\"<\/a><\/p>\n

MOSAEC is the first generalized method to compute the metal oxidation states of a structure (molecular or periodic) ‘as-given’. In this way it can be used to detect structural errors when an unknown or impossible metal oxidation state is determined.<\/p>\n

Reference<\/strong>: White, A.; Gibaldi, M.; Burner, J.; Mayo, R.A.;\u00a0 Woo, T.K.* \u201cHigh structural error rates in MOF databases used in data driven workflows identified via a novel metal oxidation state-based method\u201d,\u00a0Journal of the American Chemical Society<\/em>, in press.\u00a0\u00a0link<\/a><\/p>\n

Download<\/strong>: link<\/span><\/a><\/p>\n

\n

MEPO-ML<\/h2>\n

\"\"<\/a><\/p>\n

MEPO-ML<\/strong> is a machine learning model to rapidly generate DFT quality partial atomic charges for atomistic simulations of MOFs.\u00a0 MEPO-ML was trained on a dataset of over 40 million DFT computed partial atomic charges.<\/p>\n

Reference<\/strong>: Luo, J.; Said, O.B.; Xie, P.; Gibaldi, M.; Burner, J.; Pereira, C.; Woo, T.K.* \u201cMEPO-ML: a robust graph attention network model for rapid generation of partial atomic charges in metal-organic frameworks\u201d,\u00a0npj Computational Materials<\/em>\u00a02024<\/strong>, 10, 224.\u00a0link<\/a><\/p>\n

News<\/strong>:\u00a0 June 2025 – a new model has been trained with more experimental MOFs taken from MOSAEC-DB<\/p>\n

Download<\/strong>: link\u00a0\u00a0<\/a><\/p>\n

\n

SAMOSA<\/h2>\n

\"\"<\/a><\/p>\n

SAMOSA<\/strong> (Structural Activation <\/span>via Metal Oxidation State Analysis) is a algorithm to prepare experimental MOF crystal structures\u00a0 for atomistic simulation that incorporates ligand charge and metal oxidation state considerations when computationally removing solvent from the structures.<\/span><\/p>\n

Reference<\/strong>: Gibaldi, M.;\u00a0 Kapeliukha, A.; White, A.; Woo, T.K.* \u201cIncorporation of ligand charge and metal oxidation state considerations into the computational solvent removal and activation of experimental crystal structures preceding molecular simulation\u201d,\u00a0Journal of Chemical Information and Modeling<\/em>,\u00a02025<\/strong>\u00a065<\/em>, 275-287.\u00a0\u00a0link<\/a><\/p>\n

Download<\/strong>: link\u00a0\u00a0<\/a><\/p>\n

\n

REPEAT<\/h2>\n

REPEAT <\/b>is the first method to extract electrostatic potential fitted partial atomic charges from periodic DFT calculations.<\/p>\n

Reference<\/strong>: \u00a0Campa\u00f1\u00e1, C.; Mussard, B.; Woo, T.K.\u201dElectrostatic Potential Derived Atomic Charges for Periodic Systems Using a Modified Error Functional: REPEAT Charges\u201d\u00a0Journal of Chemical Theory and Computation<\/em>,2009<\/strong>,\u00a05<\/em>, 2866-2878.\u00a0 lin<\/a>k<\/p>\n

Download<\/strong>: link\u00a0\u00a0<\/a><\/p>\n

\n

All of our software can be found on the lab\u2019s\u00a0GitHub page<\/a><\/strong>.<\/p>\n

 <\/p>\n

 <\/p>\n","protected":false},"excerpt":{"rendered":"

All of our software can be found on the lab’s GitHub page. MOSAEC-DB – DATASET MOSAEC-DB is a database of high-fidelity experimental MOF structures ready for simulation using improved processing and structural error analysis algorithms. It currently contains >100K structures as is updated the CSD is updated. Structural errors found in many other experimental databases […]<\/p>\n","protected":false},"author":1,"featured_media":1669,"parent":485,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"template-full-width.php","meta":{"footnotes":""},"class_list":["post-975","page","type-page","status-publish","has-post-thumbnail","hentry"],"_links":{"self":[{"href":"http:\/\/titan.chem.uottawa.ca\/index.php?rest_route=\/wp\/v2\/pages\/975","targetHints":{"allow":["GET"]}}],"collection":[{"href":"http:\/\/titan.chem.uottawa.ca\/index.php?rest_route=\/wp\/v2\/pages"}],"about":[{"href":"http:\/\/titan.chem.uottawa.ca\/index.php?rest_route=\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"http:\/\/titan.chem.uottawa.ca\/index.php?rest_route=\/wp\/v2\/users\/1"}],"replies":[{"embeddable":true,"href":"http:\/\/titan.chem.uottawa.ca\/index.php?rest_route=%2Fwp%2Fv2%2Fcomments&post=975"}],"version-history":[{"count":57,"href":"http:\/\/titan.chem.uottawa.ca\/index.php?rest_route=\/wp\/v2\/pages\/975\/revisions"}],"predecessor-version":[{"id":3179,"href":"http:\/\/titan.chem.uottawa.ca\/index.php?rest_route=\/wp\/v2\/pages\/975\/revisions\/3179"}],"up":[{"embeddable":true,"href":"http:\/\/titan.chem.uottawa.ca\/index.php?rest_route=\/wp\/v2\/pages\/485"}],"wp:featuredmedia":[{"embeddable":true,"href":"http:\/\/titan.chem.uottawa.ca\/index.php?rest_route=\/wp\/v2\/media\/1669"}],"wp:attachment":[{"href":"http:\/\/titan.chem.uottawa.ca\/index.php?rest_route=%2Fwp%2Fv2%2Fmedia&parent=975"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}