Naslov
Samoudruživanje nukleinskih baza poboljšanim uzorkovanjem MD: razumijevanje biološke tvari iz perspektive molekulskih gradivnih blokova
(Nucleobase Assemblies via Enhanced- sampling MD: Understanding Biological Matter From Its Molecular Building Blocks)

Autori
Ostojić, Tea ; Stolar, Tomislav ; Užarević, Krunoslav ; Meštrović, Ernest ; Grisanti, Luca

Vrsta, podvrsta i kategorija rada
Sažeci sa skupova, sažetak, znanstveni

Izvornik
Simpozij studenata doktorskih studija PMF-a : knjiga sažetaka = 6th Faculty of Science PhD student symposium / Schneider, Petra ; Đaković, Marijana ; Korać, Petra ; Lukić, Aleksandar ; Marušić-Paloka, Eduard ; Novak, Predrag ; Pezelj, Đurđica ; Pikelj, Kristina ; Smolčić, Vernesa - Zagreb : Prirodoslovno-matematički fakultet Sveučilišta u Zagrebu, 2022, 278-279

ISBN
978-953-6076-93-2

Skup
6. Simpozij studenata doktorskih studija PMF-a = 6th Faculty of Science PhD Student Symposium

Mjesto i datum
Zagreb, Hrvatska, 23.04.2022. - 24.04.2022

Vrsta sudjelovanja
Poster

Vrsta recenzije
Domaća recenzija

Ključne riječi
samoudruživanje ; nukleinske baze ; molekularna dinamika
(self-assembly, nucleobases, molecular dynamics)

Sažetak
The properties of molecular systems, such as aggregates in solutions or molecular crystals, are controlled by interactions between the molecular units. In this context, an example is optical properties. The evolution of the optical responses from the isolated molecule to a supramolecular assembly and large crystal is directly connected to the interactions between the units, which in turn depends on the structural key feature of the soft matter [1]. With the aim of assessing the properties of (biological) material, we have focused on the structural properties of nucleobases assemblies in water. Besides, nucleobases and their specific base pairing is the paradigm of molecular recognition in nature [2]. The hypothesis, in the context of prebiotic chemistry, focuses on the selection operated by nature, in terms of their structural properties, but also in respect of their stability under UV light. Modeling techniques can help in understanding the relationship between these elements from a fundamental and microscopic perspective. The computational prediction of the molecular assemblies structure is not an easy task and we must rely on the usage of enhanced sampling techniques. We have explored the formation of N- mer (N = 2- 8) assemblies in water by combining metadynamics with classical potential. We have biased two collective variables defined as coordination numbers for π- stacking and Watson Crick hydrogen bonding [3]. Our preliminary results show the crucial role of these two collective variables for obtaining the structure and properties of nucleobase assemblies.

Izvorni jezik
Hrvatski, engleski

Znanstvena područja
Kemija

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