A Multi-scale Approach to Studying the Complexity in Glutamine Aggregates: Structure, Dynamics and Electronic Properties.

Single amino acid glutamine crystals have recently been shown to exhibit non-aromatic intrinsic fluorescence during their aggregation in aqueous solution. The optical activity of these systems is similar to other complex proteins like amyloids which are involved in various types of neurodegenerative diseases such as Alzheimer and Parkinson. We use a multi-scale atomistic simulation approach to dissect in detail the chemical and structural complexities associated with glutamine crystals. We investigate the ground and excited-state properties of the three different glutamine systems. Our results show that one system that has short hydrogen bonds absorbs light at low energy and is optically brighter, a finding that is consistent with the experimental observation. As a consequence of thermal fluctuations, the proton transfer occurs along the short hydrogen bond. The corresponding free energy profile is characterised by an asymmetric double-well potential. We also investigate the role of the vibrational modes in the excited state. Our results show that the optical properties of glutamine crystals are sensitive to the initial conditions in the ground state and tuned by the collective vibrational modes in the excited state. Different glutamine aggregates differ in terms of their hydrogen bond network. We present a classical versus quantum mechanical analysis of the proton motion along different hydrogen bonds, where we show that the nuclear quantum effects strengthen the short hydrogen bonds and enhance electronic polarisation. Finally, we investigate the coupling of glutamine crystals with the surrounding water by using large scale molecular dynamics simulations. We study the structural and dynamical properties of water near different crystalline surfaces of L-glutamine crystals. Despite having the same molecular composition, water at each surface displays characteristic structural, orientational and dynamical correlations. This behaviour is tuned by how the different chemical groups of the amino-acids make contact with the liquid phase. We show that the binding of glutamine molecules to the crystal surface creates a crowded environment involving pockets of trapped water molecules altering the water dynamics in a highly nontrivial manner suggesting that the solvent dynamics may have important implications on crystal nucleation.