Nowadays the availability of large computational power along with the development of powerful computational tools and techniques allow us to disclose, at atomic scale, the complexity of chemical systems, including biomolecules and organic materials. In particular, Molecular Dynamics (MD) simulations and Density Functional Theory (DFT) calculations can act as an artificial microscope unveiling the dynamic behavior, the structural properties and mechanisms of the matter at a molecular level of detail. Moreover, machine learning techniques can exploit the large availability of experimental data allowing us to build highly predictive models.
The presentation will be focused on five different case studies, framed in this context: i) use of MD simulations to shed light on the role of two key residues regulating the water permeation in a protein named Aquaporin 4 (AQP4) [1]; ii) MD and DFT simulations applied to the study of the morphological and charge transport properties of the organic polymers P3HT and PBTTT, employed as active materials in organic thin film transistors (OTFT)[2,3]; iii) a theoretical investigation of the effects of different self-assembled monolayers (SAMs) on the structure of OTFT [4]; iv) a combined DFT/MD study aimed at shedding light on atomic mechanisms behind the functioning of an innovative single molecule molecular sensor [5] and v) the use of machine learning methods to build algorithms able to predict the potential toxicity and biological activity of small organic molecules. [6,7]
References:
[1] D. Alberga, O. Nicolotti, G. Lattanzi, G.P. Nicchia, A. Frigeri, F. Pisani, V. Benfenati, G.F. Mangiatordi, A new gating site in human aquaporin-4: Insights from molecular dynamics simulations, Biochimica et Biophysica Acta (BBA)-Biomembranes. 1838 (2014) 3052–3060
[2] D. Alberga, G.F. Mangiatordi, L. Torsi, G. Lattanzi, Effects of annealing and residual solvents on amorphous P3HT and PBTTT Films, The Journal of Physical Chemistry C. 118 (2014) 8641–8655.
[3] D. Alberga, A. Perrier, I. Ciofini, G.F. Mangiatordi, G. Lattanzi, C. Adamo, Morphological and charge transport properties of amorphous and crystalline P3HT and PBTTT: insights from theory, Physical Chemistry Chemical Physics. 17 (2015) 18742–18750.
[4] D. Alberga, G.F. Mangiatordi, A. Motta, O. Nicolotti, G. Lattanzi, Effects of different self-assembled monolayers on thin-film morphology: a combined DFT/MD simulation protocol, Langmuir. 31 (2015) 10693–10701.
[5] E. Macchia, K. Manoli, B. Holzer, C. Di Franco, M. Ghittorelli, F. Torricelli, D. Alberga, G.F. Mangiatordi, G. Palazzo, G. Scamarcio, others, Single-molecule detection with a millimetre-sized transistor, Nature Communications. 9 (2018) 1–10.
[6] D. Alberga, D. Trisciuzzi, K. Mansouri, G.F. Mangiatordi, O. Nicolotti, Prediction of acute oral systemic toxicity using a multifingerprint similarity approach, Toxicological Sciences. 167 (2019) 484–495.
[7] D. Alberga, D. Trisciuzzi, M. Montaruli, F. Leonetti, G.F. Mangiatordi, O. Nicolotti, A new approach for drug target and bioactivity prediction: the multifingerprint similarity search algorithm (MuSSeL), Journal of Chemical Information and Modeling. 59 (2018) 586–596.