Owing to their extraordinary photophysical properties, carbon dots (CDs) have found applications across various fields, including bioimaging, sensing, and environmental research. Despite huge application potential, the fabrication of CDs still lacks the desired control at the molecular level, and precise structural regulation towards property-tailored CDs remains elusive. The mechanistic details of nucleation, growth, and carbonization processes leading to CDs are still unknown, with key thermodynamic and kinetic parameters yet to be revealed. Herein, we performed quantum chemical calculations of explicitly micro-hydrated reaction systems to thoroughly explore the mechanism of a prototypical reaction of citric acid and ethylenediamine. The theoretical results showed activation barriers and thermodynamics along the reaction pathway, thus helping identify key heterocyclic intermediates and cyclization products. The cyclization and condensation reactions were further simulated via a reactive molecular dynamics protocol, suggesting potential growth scenarios and generating plausible structures for further exploration of the polymerization and carbonization processes. The theoretical calculations were cross-validated with NMR and MALDI-TOF measurements. The data obtained provide a comprehensive deterministic insight into the initial stages of CD formation, revealing new reaction intermediates and pathways, and rationally predicting the formation of specific structural arrangements of premature CDs. The presented deterministic approach represents an important step towards rational bottom-up design of these unique fluorescence systems.

Department of Biochemistry Faculty of Science Palacký University Olomouc Šlechtitelů 27 779 00 Olomouc Czech Republic

Department of Chemical and Geological Sciences University of Cagliari 1 09042 Monserrato Italy

Department of Chemistry Faculty of Natural Sciences Matej Bel University Tajovského 40 974 01 Banská Bystrica Slovak Republic

Department of Materials Science and Engineering and Center for Functional Photonics City University of Hong Kong 83 Tat Chee Avenue Kowloon Hong Kong SAR 999077 China

Department of Organic Chemistry Faculty of Natural Sciences Comenius University Bratislava 84215 Slovakia

Department of Physics University of Cagliari 1 09042 Monserrato Italy

IT4Innovations VSB Technical University of Ostrava 17 listopadu 2172 15 708 00 Ostrava Poruba Czech Republic

Nanotechnology Centre Centre for Energy and Environmental Technologies VŠB Technical University of Ostrava 17 listopadu 2172 15 708 00 Ostrava Poruba Czech Republic

Regional Centre of Advanced Technologies and Materials The Czech Advanced Technology and Research Institute Palacký University Olomouc Šlechtitelů 27 779 00 Olomouc Czech Republic

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