Cheminformatics with Invariom String Notation

Breznikar, Rok (author), Urbič, Tomaž (mentor), Dittrich, Birger (comentor)

In this work we gathered reliable 3D information of solid-state structures to provide this information for, in principle, any molecule. The source of this information was a large database of experimental 3D structures, mostly determined using single-crystal X-ray diffraction (SC-XRD). A subset of these structures was also optimised via semiempirical quantum mechanical structure optimisation to get reliable information for hydrogen positions. 3D structure analysis was done by expanding the idea of invarioms and incorporating it in a program called BAERLAUCH via C/C++ code development. The result is a string notation capable of capturing 3D structure of a molecule.

• Language: English
• Keywords: molecular file formats, conformer generation, quantum chemistry
• Work type: Master's thesis/paper
• Typology: 2.09 - Master's Thesis
• Organization: FKKT - Faculty of Chemistry and Chemical Technology
• Year: 2025
• PID: 20.500.12556/RUL-166287
• COBISS.SI-ID: 222892803
• Publication date in RUL: 06.01.2025

Secondary language

• Language: Slovenian
• Title: Kemoinformatika z vrstičnim zapisom Invariom

Abstract

V tej magistrski nalogi smo zbrali zanesljive 3D informacije o strukturah v trdnem stanju, da lahko te informacije zagotovimo za, v principu, katero koli molekulo. Vir teh informacij je bila obsežna zbirka eksperimentalnih 3D struktur, večinoma določenih z uporabo rentgenske difrakcije na monokristalu (SC-XRD). Del teh struktur je bil tudi optimiziran z uporabo semiempirične kvantnomehanske strukturne optimizacije, da smo pridobili zanesljive informacije o položajih vodikovih atomov. Analiza 3D strukture je bila opravljena z razširjanjem ideje o invariomih in njeno vključitvijo v program BAERLAUCH preko razvoja C/C++ kode. Rezultat je vrstični zapis, ki omogoča zajemanje 3D strukture molekule.

• Keywords: zapis molekul, generiranje konformerjev, kvantna kemija