{"id":{"repo_id":"cambridge","oai_identifier":"oai:www.repository.cam.ac.uk:1810/369353"},"canonical_url":"https://search.dev.ndltd.org/etd/cambridge/oai:www.repository.cam.ac.uk:1810/369353","repository":{"repo_id":"cambridge","name":"Cambridge University","base_url":"https://api.repository.cam.ac.uk/server/oai/request"},"display":{"title":"Diamond Energy - A systematic conformation searching method","abstract":"Fully understanding the properties of molecules requires a good knowledge of all low-energy conformations. A python program, Diamond Energy, was developed based on an assumption that the structures of local minima are similar to a diamond lattice. These conformers could be found by calculations with integer arithmetic and evaluated with simple energy equations. Both of these should speed up systematic searching. Test results on alkane showed that Diamond Energy was able to do systematic conformational searching for acyclic alkanes exhaustively, accurately and very fast. The scope of the program’s application was extended beyond acyclic alkanes to include six-membered rings, and then further extended to include saccharides. This extension was facilitated by the development of an automatic pipeline for searching suitable energy evaluation parameters when introducing new atom types. Finally, using the large quantity of data generated by the Diamond Energy test process, a machine learning pipeline was applied and fed with Diamond Energy data. This made it possible to explore the geometry distribution of diamond lattice framework and help to improve the conformational searching process.","abstract_html":"Fully understanding the properties of molecules requires a good knowledge of all low-energy conformations. A python program, Diamond Energy, was developed based on an assumption that the structures of local minima are similar to a diamond lattice. These conformers could be found by calculations with integer arithmetic and evaluated with simple energy equations. Both of these should speed up systematic searching. Test results on alkane showed that Diamond Energy was able to do systematic conformational searching for acyclic alkanes exhaustively, accurately and very fast. The scope of the program’s application was extended beyond acyclic alkanes to include six-membered rings, and then further extended to include saccharides. This extension was facilitated by the development of an automatic pipeline for searching suitable energy evaluation parameters when introducing new atom types. Finally, using the large quantity of data generated by the Diamond Energy test process, a machine learning pipeline was applied and fed with Diamond Energy data. This made it possible to explore the geometry distribution of diamond lattice framework and help to improve the conformational searching process.","abstract_has_math":false,"creators":["Wei, Mengman"],"institution":"University of Cambridge","degree_name":"Doctor of Philosophy (PhD)","degree_level":"Doctoral","degree_discipline":null,"degree_department":null,"school":null,"contributors":[],"advisors":["Goodman, Jonathan"],"committee_chairs":[],"committee_members":[],"year":2024,"date_issued":"2024-01-05","date_published":"2024-01-05","updated_at":"2026-07-22T22:23:57Z","subjects":["Cheminformatics","Conformation Searching","Diamond Lattice","Systematic Search","Tree Searching"],"languages":["eng"],"rights":[],"rights_urls":["https://www.repository.cam.ac.uk/bitstreams/353f4d43-6c08-4177-bc26-b06d5318d259/download","https://creativecommons.org/licenses/by/4.0/"],"identifier_entries":[]},"links":{"outbound_url":"https://doi.org/10.17863/CAM.109200","outbound_label":"DOI","outbound_source":"dc:identifier.doi"},"metadata_groups":[{"id":"people","label":"People","entries":[{"key":"dc:contributor.advisor","label":"Advisor","values":["Goodman, Jonathan"]},{"key":"dc:creator","label":"Author","values":["Wei, Mengman"]}]},{"id":"academic_context","label":"Academic Context","entries":[{"key":"dc:date.issued","label":"Date","values":["2024-01-05"]},{"key":"dc:publisher.institution","label":"Dc Publisher Institution","values":["University of Cambridge"]},{"key":"dc:relation.isreferencedby.uri","label":"Dc Relation Isreferencedby URI","values":["https://www.repository.cam.ac.uk/handle/1810/369353"]},{"key":"dc:type","label":"Dc Type","values":["Thesis"]},{"key":"dc:type.qualificationlevel","label":"Dc Type Qualificationlevel","values":["Doctoral"]},{"key":"dc:type.qualificationname","label":"Dc Type Qualificationname","values":["Doctor of Philosophy (PhD)"]}]},{"id":"subjects_keywords","label":"Subjects and Keywords","entries":[{"key":"dc:subject","label":"Dc Subject","values":["Cheminformatics","Conformation Searching","Diamond Lattice","Systematic Search","Tree Searching"]}]},{"id":"language_rights","label":"Language and Rights","entries":[{"key":"dc:language","label":"Dc Language","values":["eng"]},{"key":"dc:rights","label":"Dc Rights","values":["https://www.repository.cam.ac.uk/bitstreams/353f4d43-6c08-4177-bc26-b06d5318d259/download","https://creativecommons.org/licenses/by/4.0/"]}]},{"id":"identifiers","label":"Identifiers","entries":[{"key":"dc:identifier.doi","label":"DOI","values":["https://doi.org/10.17863/CAM.109200"]},{"key":"dc:identifier.uri","label":"Identifier URI","values":["https://www.repository.cam.ac.uk/bitstreams/5ebd4782-743d-432e-957d-4fedf5518aae/download"]}]},{"id":"additional","label":"Additional Metadata","entries":[{"key":"dc:description.abstract","label":"Abstract","values":["Fully understanding the properties of molecules requires a good knowledge of all low-energy conformations. 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