{"id":"W4404076103","doi":"10.1063/5.0231711","title":"Inferring the existence of hydrogen bonds directly from statistical analysis of molecular dynamics trajectories","year":2024,"lang":"en","type":"article","venue":"The Journal of Chemical Physics","topic":"Crystallography and molecular interactions","field":"Chemistry","cited_by":0,"is_retracted":false,"has_abstract":true,"ca_institutions":"McMaster University","funders":"Alliance de recherche numérique du Canada; Natural Sciences and Engineering Research Council of Canada; Canada Research Chairs","keywords":"Hydrogen bond; Non-covalent interactions; Molecular dynamics; Supramolecular chemistry; Cluster analysis; Laplace operator; Chemical physics; Statistical analysis; Molecule; Statistical physics; Hydrogen; Chemistry; Computer science; Computational chemistry; Physics; Artificial intelligence; Mathematics; Quantum mechanics","routes":{"ca_aff":true,"ca_fund":true,"ca_venue":false,"about_ca":false,"invisible_to_affiliation_only":false},"retraction":null,"screen":null,"direct_labels":[],"prediction":{"model_version":"codex-gemma-dda1882f352a","candidate_categories":[],"consensus_categories":[],"category_scores_codex":[0.0001418485,0.0001127989,0.0003111908,0.00004388829,0.00002515367,0.00001946383,0.0003388827,0.00005075358,0.00005750894],"category_scores_gemma":[0.0000920423,0.0000690433,0.0004004227,0.0004878559,0.0002448944,0.00006159116,0.00005401381,0.0003940368,2.410946e-7],"about_ca_system_candidate":false,"about_ca_system_consensus":false,"about_ca_system_score_codex":0.00004989338,"about_ca_system_score_gemma":0.00007048898,"about_ca_topic_candidate":false,"about_ca_topic_consensus":false,"about_ca_topic_score_codex":0.00008412071,"about_ca_topic_score_gemma":0.000006191789,"domain_scores_codex":[0.9989852,0.00003528467,0.0004353889,0.00008609102,0.000342778,0.0001152431],"domain_scores_gemma":[0.9986098,0.0007258362,0.0002362337,0.0002571412,0.0001267775,0.00004425164],"domain_codex":null,"domain_gemma":null,"domain_candidate":null,"domain_consensus":null,"study_design_codex":"bench_or_experimental","study_design_gemma":"bench_or_experimental","study_design_scores_codex":[0.00005862243,0.00007080024,0.00008933699,0.00004663682,0.002392244,0.00001152894,0.0007682149,0.001585722,0.9903087,0.00363545,0.00002107528,0.001011661],"study_design_scores_gemma":[0.00008104341,0.00001915114,0.0000372361,0.00009882505,0.003164773,0.00001064446,0.0003040666,0.01292097,0.9682127,0.0149831,0.00008753636,0.00007991667],"study_design_candidate":"bench_or_experimental","study_design_consensus":"bench_or_experimental","genre_codex":"empirical","genre_gemma":"empirical","genre_scores_codex":[0.9801354,0.0006493378,0.01784034,0.00008257054,0.00003502672,0.0000175535,0.0002368458,0.000008685039,0.0009942185],"genre_scores_gemma":[0.9995562,0.00003364722,0.0002687908,0.00001503369,0.00007443663,9.385472e-7,0.0000296917,0.0000126599,0.000008639438],"genre_candidate":"empirical","genre_consensus":"empirical","teacher_disagreement_score":0.02209597,"threshold_uncertainty_score":0.2815504,"prediction_status":"machine_predicted_unvalidated"},"machine_scores":{"provisional":true,"baseline":true,"maturity_gate_passed":false,"score_opus":0.009501541065740533,"score_gpt":0.2611311992425568,"score_spread":0.2516296581768163,"validation_status":"score_only:v0-immature-baseline","note":"Baseline scores from an immature model (maturity gate not passed). Scores rank; they never assert a category."}}