engleski

Hydrogen Bonding vs. π-stacking Interactions in Nucleobase Assemblies via Enhanced-Sampling MD

Properties of interacting molecular frameworks, such as aggregates in solutions or molecular crystals, are controlled by intermolecular interactions. For instance, the evolution of optical responses from an isolated molecule to a supramolecular assembly and large crystal arises from interactions that take place between the units, which in turn depend on the structural key feature of the soft matter. In the family of biological materials, DNAs and RNAs building blocks are among the most fascinating. Nucleobases and their specific base pairings are the paradigm of molecular recognition in nature. In the context of prebiotic chemistry, the hypothesis focuses on the selection operated by nature, in terms of their structural characteristics, but also in respect of their stability under light. Modeling techniques can help in examining and understanding the relations between all these elements, both from a fundamental and microscopic perspective. We have focused on the structural properties of nucleobases assemblies in water with a two-fold aim: i) exploring the structural patterns that govern the self-assembly ii) establishing the relevant structures necessary to predict their optical properties. The computational prediction of the molecular assemblies structure is quite a demanding task and one must rely on the usage of enhanced sampling techniques. We have explored the formation of N-mer (N = 2–16) assemblies in the water by employing metadynamics with classical potential. The AMBER99 RNA force field was reparameterized in a way to avoid artifacts due to the overestimation of base-stacking propensities. We have biased two collective variables defined as coordination numbers for π-stacking and Watson Crick hydrogen bonding. Our preliminary results show the crucial role of these two collective variables for obtaining the structure and properties of nucleobase assemblies.

hydrogen bonding ; stacking intertactions ; enhanced-sampling MD

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