{"id":"https://openalex.org/W7220869537","doi":"https://doi.org/10.26434/chemrxiv.15010047/v1","title":"Improved electrostatic machine learning embedding ML/MM scheme for a phosphoryl transfer reaction","display_name":"Improved electrostatic machine learning embedding ML/MM scheme for a phosphoryl transfer reaction","publication_year":2026,"publication_date":"2026-10-07","ids":{"openalex":"https://openalex.org/W7220869537","doi":"https://doi.org/10.26434/chemrxiv.15010047/v1"},"language":"en","primary_location":{"id":"doi:10.26434/chemrxiv.15010047/v1","doi":"https://doi.org/10.26434/chemrxiv.15010047/v1","is_oa":true,"landing_page_url":"https://doi.org/10.26434/chemrxiv.15010047/v1","pdf_url":"https://chemrxiv.org/doi/pdf/10.26434/chemrxiv.15010047/v1","source":{"id":"https://openalex.org/S4393918830","display_name":"ChemRxiv","issn_l":"2573-2293","issn":["2573-2293"],"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":null,"raw_type":"posted-content"},"volume":null,"type":"preprint","indexed_in":["crossref"],"open_access":{"is_oa":true,"oa_status":"green","oa_url":"https://chemrxiv.org/doi/pdf/10.26434/chemrxiv.15010047/v1","any_repository_has_fulltext":true},"authorships":[{"author_position":"first","author":{"id":"https://openalex.org/A5107527948","display_name":"Laetitia Kantin","orcid":"https://orcid.org/0009-0003-0847-2571","observed_orcids":["https://orcid.org/0009-0003-0847-2571"]},"institutions":[{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I204730241","display_name":"Universit\u00e9 Paris Cit\u00e9","ror":"https://ror.org/05f82e368","country_code":"FR","type":"education","lineage":["https://openalex.org/I204730241"]},{"id":"https://openalex.org/I4210094297","display_name":"Laboratoire de Biochimie Th\u00e9orique","ror":"https://ror.org/00nvjgv40","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I204730241","https://openalex.org/I4210094297","https://openalex.org/I4210128300"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Laetitia Kantin","raw_affiliation_strings":["Universit\u00e9 Paris Cit\u00e9, CNRS, Laboratoire de Biochimie Th\u00e9orique, 13 rue Pierre et Marie Curie, Paris, France, 75005"],"raw_orcid":"https://orcid.org/0009-0003-0847-2571","affiliations":[{"raw_affiliation_string":"Universit\u00e9 Paris Cit\u00e9, CNRS, Laboratoire de Biochimie Th\u00e9orique, 13 rue Pierre et Marie Curie, Paris, France, 75005","institution_ids":["https://openalex.org/I1294671590","https://openalex.org/I204730241","https://openalex.org/I4210094297"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5082079166","display_name":"I\u00f1aki Tu\u00f1\u00f3n","orcid":"https://orcid.org/0000-0002-6995-1838","observed_orcids":["https://orcid.org/0000-0002-6995-1838"]},"institutions":[{"id":"https://openalex.org/I16097986","display_name":"Universitat de Val\u00e8ncia","ror":"https://ror.org/043nxc105","country_code":"ES","type":"education","lineage":["https://openalex.org/I16097986"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"I\u00f1aki Tu\u00f1\u00f3n","raw_affiliation_strings":["Departament de Qu\u00edmica F\u00edsica","Universitat de Val\u00e8ncia"],"raw_orcid":"https://orcid.org/0000-0002-6995-1838","affiliations":[{"raw_affiliation_string":"Departament de Qu\u00edmica F\u00edsica","institution_ids":[]},{"raw_affiliation_string":"Universitat de Val\u00e8ncia","institution_ids":["https://openalex.org/I16097986"]}]},{"author_position":"middle","author":{"id":"https://openalex.org/A5039401197","display_name":"Kirill Zinovjev","orcid":"https://orcid.org/0000-0003-1052-5698","observed_orcids":["https://orcid.org/0000-0003-1052-5698"]},"institutions":[{"id":"https://openalex.org/I16097986","display_name":"Universitat de Val\u00e8ncia","ror":"https://ror.org/043nxc105","country_code":"ES","type":"education","lineage":["https://openalex.org/I16097986"]}],"countries":["ES"],"is_corresponding":false,"raw_author_name":"Kirill Zinovjev","raw_affiliation_strings":["Departament de Qu\u00edmica F\u00edsica","Universitat de Val\u00e8ncia"],"raw_orcid":"https://orcid.org/0000-0003-1052-5698","affiliations":[{"raw_affiliation_string":"Departament de Qu\u00edmica F\u00edsica","institution_ids":[]},{"raw_affiliation_string":"Universitat de Val\u00e8ncia","institution_ids":["https://openalex.org/I16097986"]}]},{"author_position":"last","author":{"id":"https://openalex.org/A5034203538","display_name":"\u00c9lise Dubou\u00e9-Dijon","orcid":"https://orcid.org/0000-0003-0871-5177","observed_orcids":["https://orcid.org/0000-0003-0871-5177"]},"institutions":[{"id":"https://openalex.org/I1294671590","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73","country_code":"FR","type":"government","lineage":["https://openalex.org/I1294671590"]},{"id":"https://openalex.org/I204730241","display_name":"Universit\u00e9 Paris Cit\u00e9","ror":"https://ror.org/05f82e368","country_code":"FR","type":"education","lineage":["https://openalex.org/I204730241"]},{"id":"https://openalex.org/I4210094297","display_name":"Laboratoire de Biochimie Th\u00e9orique","ror":"https://ror.org/00nvjgv40","country_code":"FR","type":"facility","lineage":["https://openalex.org/I1294671590","https://openalex.org/I204730241","https://openalex.org/I4210094297","https://openalex.org/I4210128300"]}],"countries":["FR"],"is_corresponding":false,"raw_author_name":"Elise Dubou\u00e9 Dijon","raw_affiliation_strings":["Universit\u00e9 Paris Cit\u00e9, CNRS, Laboratoire de Biochimie Th\u00e9orique, 13 rue Pierre et Marie Curie, Paris, France, 75005"],"raw_orcid":"https://orcid.org/0000-0003-0871-5177","affiliations":[{"raw_affiliation_string":"Universit\u00e9 Paris Cit\u00e9, CNRS, Laboratoire de Biochimie Th\u00e9orique, 13 rue Pierre et Marie Curie, Paris, France, 75005","institution_ids":["https://openalex.org/I1294671590","https://openalex.org/I204730241","https://openalex.org/I4210094297"]}]}],"institutions":[],"countries_distinct_count":2,"institutions_distinct_count":4,"corresponding_author_ids":[],"corresponding_institution_ids":[],"apc_list":null,"apc_paid":null,"fwci":null,"has_fulltext":true,"cited_by_count":0,"citation_normalized_percentile":null,"cited_by_percentile_year":null,"biblio":{"volume":null,"issue":null,"first_page":null,"last_page":null},"is_retracted":false,"is_paratext":false,"is_xpac":false,"primary_topic":{"id":"https://openalex.org/T11948","display_name":"Machine Learning in Materials Science","score":0.6669999957084656,"subfield":{"id":"https://openalex.org/subfields/2505","display_name":"Materials Chemistry"},"field":{"id":"https://openalex.org/fields/25","display_name":"Materials Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},"topics":[{"id":"https://openalex.org/T11948","display_name":"Machine Learning in Materials Science","score":0.6669999957084656,"subfield":{"id":"https://openalex.org/subfields/2505","display_name":"Materials Chemistry"},"field":{"id":"https://openalex.org/fields/25","display_name":"Materials Science"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10002","display_name":"Advanced Chemical Physics Studies","score":0.31540000438690186,"subfield":{"id":"https://openalex.org/subfields/3107","display_name":"Atomic and Molecular Physics, and Optics"},"field":{"id":"https://openalex.org/fields/31","display_name":"Physics and Astronomy"},"domain":{"id":"https://openalex.org/domains/3","display_name":"Physical Sciences"}},{"id":"https://openalex.org/T10211","display_name":"Computational Drug Discovery Methods","score":0.005200000014156103,"subfield":{"id":"https://openalex.org/subfields/3002","display_name":"Drug Discovery"},"field":{"id":"https://openalex.org/fields/30","display_name":"Pharmacology, Toxicology and Pharmaceutics"},"domain":{"id":"https://openalex.org/domains/1","display_name":"Life Sciences"}}],"keywords":[{"id":"https://openalex.org/keywords/phosphoryl-transfer","display_name":"phosphoryl transfer","score":0.8370000123977661},{"id":"https://openalex.org/keywords/rna-cleavage","display_name":"RNA cleavage","score":0.9769999980926514},{"id":"https://openalex.org/keywords/equivariant-neural-networks","display_name":"equivariant neural networks","score":0.7490000128746033},{"id":"https://openalex.org/keywords/active-learning-machine-learning","display_name":"active learning (machine learning)","score":0.5870000123977661},{"id":"https://openalex.org/keywords/umbrella-sampling","display_name":"umbrella sampling","score":0.7049999833106995},{"id":"https://openalex.org/keywords/free-energy-profiles","display_name":"free energy profiles","score":0.7910000085830688},{"id":"https://openalex.org/keywords/energy-decomposition-analysis","display_name":"energy decomposition analysis","score":0.3499999940395355},{"id":"https://openalex.org/keywords/query-by-committee","display_name":"query-by-committee","score":0.5299999713897705}],"concepts":[{"id":"https://openalex.org/C41608201","wikidata":"https://www.wikidata.org/wiki/Q980509","display_name":"Embedding","level":2,"score":0.5995000004768372},{"id":"https://openalex.org/C173523689","wikidata":"https://www.wikidata.org/wiki/Q215589","display_name":"Dipole","level":2,"score":0.5059999823570251},{"id":"https://openalex.org/C41008148","wikidata":"https://www.wikidata.org/wiki/Q21198","display_name":"Computer science","level":0,"score":0.504800021648407},{"id":"https://openalex.org/C89464430","wikidata":"https://www.wikidata.org/wiki/Q849516","display_name":"Metastability","level":2,"score":0.49970000982284546},{"id":"https://openalex.org/C11413529","wikidata":"https://www.wikidata.org/wiki/Q8366","display_name":"Algorithm","level":1,"score":0.3986999988555908},{"id":"https://openalex.org/C48044578","wikidata":"https://www.wikidata.org/wiki/Q727490","display_name":"Scalability","level":2,"score":0.3785000145435333},{"id":"https://openalex.org/C186370098","wikidata":"https://www.wikidata.org/wiki/Q442787","display_name":"Energy (signal processing)","level":2,"score":0.36739999055862427},{"id":"https://openalex.org/C121332964","wikidata":"https://www.wikidata.org/wiki/Q413","display_name":"Physics","level":0,"score":0.36320000886917114},{"id":"https://openalex.org/C121864883","wikidata":"https://www.wikidata.org/wiki/Q677916","display_name":"Statistical physics","level":1,"score":0.35760000348091125},{"id":"https://openalex.org/C117626034","wikidata":"https://www.wikidata.org/wiki/Q26336","display_name":"Electrostatics","level":2,"score":0.32420000433921814},{"id":"https://openalex.org/C184720557","wikidata":"https://www.wikidata.org/wiki/Q7825049","display_name":"Topology (electrical circuits)","level":2,"score":0.32420000433921814},{"id":"https://openalex.org/C168900304","wikidata":"https://www.wikidata.org/wiki/Q171407","display_name":"Valence (chemistry)","level":2,"score":0.3206999897956848},{"id":"https://openalex.org/C185592680","wikidata":"https://www.wikidata.org/wiki/Q2329","display_name":"Chemistry","level":0,"score":0.3100000023841858},{"id":"https://openalex.org/C77618280","wikidata":"https://www.wikidata.org/wiki/Q1155772","display_name":"Scheme (mathematics)","level":2,"score":0.3070000112056732},{"id":"https://openalex.org/C41999313","wikidata":"https://www.wikidata.org/wiki/Q489328","display_name":"Molecular physics","level":1,"score":0.2903999984264374},{"id":"https://openalex.org/C30475298","wikidata":"https://www.wikidata.org/wiki/Q909554","display_name":"Computational physics","level":1,"score":0.28769999742507935},{"id":"https://openalex.org/C98576551","wikidata":"https://www.wikidata.org/wiki/Q841798","display_name":"Electric potential energy","level":3,"score":0.2784999907016754},{"id":"https://openalex.org/C84551667","wikidata":"https://www.wikidata.org/wiki/Q155640","display_name":"Potential energy","level":2,"score":0.2736000120639801},{"id":"https://openalex.org/C59593255","wikidata":"https://www.wikidata.org/wiki/Q901663","display_name":"Molecular dynamics","level":2,"score":0.26589998602867126},{"id":"https://openalex.org/C171036898","wikidata":"https://www.wikidata.org/wiki/Q256355","display_name":"Equivariant map","level":2,"score":0.2599000036716461},{"id":"https://openalex.org/C147597530","wikidata":"https://www.wikidata.org/wiki/Q369472","display_name":"Computational chemistry","level":1,"score":0.25760000944137573},{"id":"https://openalex.org/C186060115","wikidata":"https://www.wikidata.org/wiki/Q30336093","display_name":"Biological system","level":1,"score":0.2556000053882599}],"mesh":[],"locations_count":1,"locations":[{"id":"doi:10.26434/chemrxiv.15010047/v1","doi":"https://doi.org/10.26434/chemrxiv.15010047/v1","is_oa":true,"landing_page_url":"https://doi.org/10.26434/chemrxiv.15010047/v1","pdf_url":"https://chemrxiv.org/doi/pdf/10.26434/chemrxiv.15010047/v1","source":{"id":"https://openalex.org/S4393918830","display_name":"ChemRxiv","issn_l":"2573-2293","issn":["2573-2293"],"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":null,"raw_type":"posted-content"}],"best_oa_location":{"id":"doi:10.26434/chemrxiv.15010047/v1","doi":"https://doi.org/10.26434/chemrxiv.15010047/v1","is_oa":true,"landing_page_url":"https://doi.org/10.26434/chemrxiv.15010047/v1","pdf_url":"https://chemrxiv.org/doi/pdf/10.26434/chemrxiv.15010047/v1","source":{"id":"https://openalex.org/S4393918830","display_name":"ChemRxiv","issn_l":"2573-2293","issn":["2573-2293"],"is_oa":false,"is_in_doaj":false,"is_core":false,"listed_in":[],"host_organization":null,"host_organization_name":null,"host_organization_lineage":[],"host_organization_lineage_names":[],"type":"repository"},"license":"cc-by","license_id":"https://openalex.org/licenses/cc-by","version":"acceptedVersion","is_accepted":true,"is_published":false,"raw_source_name":null,"raw_type":"posted-content"},"sustainable_development_goals":[],"study_designs":[],"awards":[{"id":"https://openalex.org/G3693125636","display_name":null,"funder_award_id":"ANR-11-LABX-0011","funder_id":"https://openalex.org/F4320322892","funder_display_name":"Centre National de la Recherche Scientifique"},{"id":"https://openalex.org/G5883419531","display_name":"Multiscale Simulations to Unveil the Role of Divalent Cations in Ribozyme Catalysis","funder_award_id":"ANR-22-CE29-0004","funder_id":"https://openalex.org/F4320320883","funder_display_name":"Agence Nationale de la Recherche"},{"id":"https://openalex.org/G879526358","display_name":"Centre d'analyse de syst\u00e8mes complexes dans les environnements complexes","funder_award_id":"ANR-11-EQPX-0008","funder_id":"https://openalex.org/F4320320883","funder_display_name":"Agence Nationale de la Recherche"},{"id":"https://openalex.org/G8924954789","display_name":"Dynamique des membranes transductrices d'\u00e9nergie : biog\u00e9n\u00e8se et organisation supramol\u00e9culaire.","funder_award_id":"ANR-11-LABX-0011","funder_id":"https://openalex.org/F4320320883","funder_display_name":"Agence Nationale de la Recherche"}],"funders":[{"id":"https://openalex.org/F4320320883","display_name":"Agence Nationale de la Recherche","ror":"https://ror.org/00rbzpz17"},{"id":"https://openalex.org/F4320322892","display_name":"Centre National de la Recherche Scientifique","ror":"https://ror.org/02feahw73"},{"id":"https://openalex.org/F4320326256","display_name":"Grand \u00c9quipement National De Calcul Intensif","ror":"https://ror.org/0010d1q40"},{"id":"https://openalex.org/F4320335598","display_name":"Agencia Estatal de Investigaci\u00f3n","ror":"https://ror.org/003x0zc53"}],"has_content":{"pdf":true,"grobid_xml":true},"content_urls":{"pdf":"https://content.openalex.org/works/W7220869537.pdf","grobid_xml":"https://content.openalex.org/works/W7220869537.grobid-xml"},"referenced_works_count":1,"referenced_works":["https://openalex.org/W622472563"],"related_works":["https://openalex.org/W4399091017","https://openalex.org/W4416674740","https://openalex.org/W6957946773","https://openalex.org/W4396665490","https://openalex.org/W4407999286","https://openalex.org/W7127078992","https://openalex.org/W7203495320","https://openalex.org/W7134968171","https://openalex.org/W7202091562","https://openalex.org/W4403319715"],"abstract_inverted_index":{"The":[0,72,116,158],"promise":[1],"of":[2,19,23,53,204],"hybrid":[3],"machine":[4],"learning/molecular":[5],"mechanics":[6],"(ML/MM)":[7],"simulations":[8,150],"is":[9,26,59,84],"to":[10,27,63,200],"provide":[11],"QM/MM-quality":[12],"free":[13],"energy":[14,100],"profiles":[15],"at":[16],"a":[17,50,64,75,87,93,171],"fraction":[18],"the":[20,24,30,33,37,43,98,103,114,133,155,162,179,186,201],"cost.":[21],"One":[22],"challenges":[25],"accurately":[28],"treat":[29],"interaction":[31],"between":[32],"ML":[34,45],"subsystem":[35],"and":[36,109],"MM":[38],"environment.":[39],"Here":[40],"we":[41],"test":[42],"Electrostatic":[44],"Embedding":[46],"(EMLE)":[47],"scheme":[48],"on":[49],"minimal":[51],"model":[52],"RNA":[54],"cleavage":[55],"in":[56,91,151],"water,":[57],"which":[58,92],"already":[60],"challenging":[61],"due":[62,199],"doubly":[65],"charged":[66],"reactant":[67],"dissociating":[68],"into":[69],"two":[70],"anions.":[71],"original":[73],"scheme,":[74],"MACE":[76],"potential":[77],"embedded":[78],"by":[79,113,120,130],"an":[80,195],"independent":[81],"EMLE":[82],"model,":[83,198],"compared":[85],"with":[86,102,127,208],"new":[88],"EMLE\u2013MACE":[89,159],"architecture,":[90],"single":[94,139],"equivariant":[95],"network":[96],"predicts":[97],"gas-phase":[99],"together":[101],"atomic":[104],"charges,":[105],"valence":[106],"widths,":[107],"polarizabilities":[108],"static":[110,180,187],"dipoles":[111,181],"required":[112],"embedding.":[115],"models":[117],"were":[118,142],"trained":[119,197],"active":[121],"learning":[122],"against":[123],"M06-2X/def2-":[124],"TZVP":[125],"data,":[126],"structures":[128],"selected":[129],"query-by-committee":[131],"from":[132],"ML/MM":[134],"dynamics":[135],"itself.":[136],"About":[137],"1500":[138],"point":[140],"calculations":[141],"sufficient":[143],"for":[144,194],"stable":[145],"100":[146],"ps":[147],"umbrella":[148],"sampling":[149,168],"73":[152],"windows":[153],"along":[154],"reaction":[156],"pathway.":[157],"profile":[160,165],"reproduces":[161],"reference":[163],"DFT/MM":[164],"within":[166],"its":[167],"error,":[169],"including":[170],"metastable":[172],"pentacoordinate":[173],"intermediate.":[174],"Energy":[175],"decomposition":[176],"shows":[177],"that":[178],"are":[182],"essential:":[183],"without":[184],"them":[185],"error":[188,203],"stays":[189],"above":[190],"chemical":[191],"accuracy":[192],"even":[193],"ideally":[196],"irreducible":[202],"approximating":[205],"electron":[206],"density":[207],"spherical":[209],"atoms.":[210]},"counts_by_year":[],"updated_date":"2026-11-04T10:54:05.112534","created_date":"2026-10-08T00:00:00"}