hrvatski

Samoudruživanje nukleinskih baza poboljšanim uzorkovanjem MD: razumijevanje biološke tvari iz perspektive molekulskih gradivnih blokova

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.

samoudruživanje ; nukleinske baze ; molekularna dinamika

nije evidentirano

engleski

Nucleobase Assemblies via Enhanced- sampling MD: Understanding Biological Matter From Its Molecular Building Blocks

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.

self-assembly, nucleobases, molecular dynamics

nije evidentirano