Computational investigation of uracil dimers in water and the role of classical potentials

Ostojić, Tea; Ovčar, Juraj; Hassanali, Ali; Grisanti, Luca (2025) Computational investigation of uracil dimers in water and the role of classical potentials. Physical Chemistry Chemical Physics, 27 (22). pp. 11869-11878. ISSN 1463-9076

PDF - Published Version - article Available under License Creative Commons Attribution Non-commercial. Download (2MB)

Abstract

Nucleobases possess a marked tendency to establish hydrogen bonds – a structural trait at the base of the storage of biological information. It is crucial to understand what is the impact on this intermolecular interaction when free nucleobases are moved to aqueous media. In this work, we present a systematic investigation of the thermodynamics of uracil dimers in explicit water solvent. We employ well-tempered metadynamics simulations to generate a reliable free energy surface and classify all low-energy states. We perform detailed structural analysis of the relevant dimer configurations. The results obtained with different force fields are compared and a methodological assessment of the force fields accuracies are presented.

Item Type:	Article
Uncontrolled Keywords:	nucleobases; molecular dynamics; aqueous solution; metadynamcis; absorption; free energy
Subjects:	NATURAL SCIENCES > Chemistry > Theoretical Chemistry
Divisions:	Theoretical Physics Division
Projects:	Project title Project leader Project code Project type Hibridno modeliranje pobuđenih stanja u novim molekularnim materijalima: od optičkih svojstava do dinamike ekscitona-HYMO4EXNOMOMA Luca Grisanti IP-2020-02-7262 HRZZ
Depositing User:	Lorena Palameta
Date Deposited:	24 Jun 2025 09:48
URI:	http://fulir.irb.hr/id/eprint/9864
DOI:	10.1039/d4cp04238g

Actions (login required)

View Item