Research

Latest revision as of 13:39, 25 August 2020

This page reports an overview of the scientific research conducted at C3P. We ask to colleagues who publish results obtained with the aid of the C3P facility to add to the acknowledgements paragraph this line

Computational work has been carried out on the C3P (Computational Chemistry Community in Padua) HPC facility of the Department of Chemical Sciences of the University of Padua.

As a paper citing the C3P facility is published, authors are encouraged to send to c3p.chimica@unipd.it the citation in RIS format. It will be added to the list of publications below.

To keep a summary of the research conducted in the C3P laboratory, we ask account referents to send to c3p.chimica@unipd.it a short description of maximum 300 words, and maximum of 2 figures describing their work. One file per account can be submitted. To keep this page up to date, such a survey of the research activities will be done each year.

The final section of this page is a repository of software tools developed by colleagues and available in the C3P clusters. Developers are encouraged to send to c3p.chimica@unipd.it

• a very short description of the software of maximum 100 words, and maximum 1 figure
• the citation that should appear in publishing results obtained with the software
• the clusters where the software is available
• if applicable, the source code and/or binaries to be distributed

List of publications

2018

• Swamy, V. P.; Thulasiram, H. V.; Rastrelli, F.; Saielli, G. Ion pairing in 1-butyl-3-methylpyridinium halide ionic liquids studied using NMR and DFT calculations. Phys. Chem. Chem. Phys. 2018, 20, 11470-11480.
• Brandiele, R.; Durante, C.; Zerbetto, M.; Vicentini, N.; Kosmala, T.; Badocco, D.; Pastore, P.; Rizzi, G. A.; Isse, A. A.; Gennaro, A. Probing the correlation between Pt-support interaction and oxygen reduction reaction activity in mesoporous carbon materials modified with Pt-N active sites. Electrochem. Acta 2018, 277, 287-300.
• Zerbetto, M.; d'Ortoli T. A.; Polimeno, A.; Widmalm, G. Differential Dynamics at Glycosidic Linkages of an Oligosaccharide as Revealed by ¹³C NMR Spin Relaxation and Stochastic Modeling. Phys. Chem. B 2018, 122, 2287-2294.
• Perazzolo, V.; Brandiele, R.; Durante, C.; Zerbetto, M.; Causin, V.; Rizzi, G. A.; Cerri, I.; Granozzi, G.; Gennaro, A. Density Functional Theory (DFT) and Experimental Evidences of Metal−Support Interaction in Platinum Nanoparticles Supported on Nitrogen- and Sulfur-Doped Mesoporous Carbons: Synthesis, Activity, and Stability. ACS Catal. 2018, 8, 1122-1137.
• Valentini, L. Modeling Dissolution-Precipitation Kinetics of Alkali-Activated Metakaolin. ACS Omega 2018, 3, 18100-18108.
• Todisco, S.; Saielli, G.; Gallo, V.; Latronico, M.; Rizzuti, A.; Mastrorilli, P. ³¹P and ¹⁹⁵Pt solid-state NMR and DFT studies on platinum(I) and platinum(II) complexes Dalton Trans. 2018, 47, 8884-8891.
• Margola, T.; Satoh, K.; Saielli, G. Comparison of the Mesomorphic Behaviour of 1:1 and 1:2 Mixtures of Charged Gay-Berne GB(4.4,20.0,1,1) and Lennard-Jones Particles. Crystals 2018, 8, 371.
• Tähtinen, P.; Guella, G.; Saielli, G.; Debitus, C.; Hnawia, E.; Mancini, I. New Sulfur-Containing Polyarsenicals from the New Caledonian Sponge Echinochalina bargibanti. Mar. Drugs 2018, 16, 382.
• Saielli, G. Computational Spectroscopy of Ionic Liquids for Bulk Structure Elucidation. Adv. Theory Simul. 2018, 1, 1800084.
• Li, S.; Saielli, G.; Wang, Y. Aggregation behavior of dihexadecylviologen bistriflimide ionic liquid crystal in different solvents: influence of polarity and concentration. Phys. Chem. Chem. Phys. 2018, 20, 22730-22738.

2019

• Campeggio, J.; Polimeno, A.; Zerbetto, M. DiTe2: Calculating the diffusion tensor for flexible molecules. J. Comput. Chem. 2019, 40, 697-705.
• Ariai, J.; Saielli, G. "Through-Space" Relativistic Effects on NMR Chemical Shifts of Pyridinium Halide Ionic Liquids. Chem. Phys. Chem. 2019, 20, 108-115.
• Polimeno, A.; Zerbetto, M. Evaluating rotation diffusion properties of molecules from short trajectories. Phys. Chem. Chem. Phys. 2019, 21, 3662-3668.
• Polimeno, A.; Zerbetto, M.; Abergel, D. Stochastic modeling of macromolecules in solution. I. Relaxation processes. J. Chem. Phys. 2019, 150, 184107.
• Polimeno, A.; Zerbetto, M.; Abergel, D. Stochastic modeling of macromolecules in solution. II. Spectral densities. J. Chem. Phys. 2019, 150, 184108.
• Volpato, A.; Zerbetto, M.; Bolzonello, L.; Meneghin, E.; Fresch, B.; Benelli, T.; Giorgini, L.; Collini, E. J. Phys. Chem. C 2019, 123, 10212-10224.

Research at C3P

Software repository

• DiTe2-v1.0: a software for the calculation of the diffusion tensor of flexible molecules. If results are published with DiTe2, please cite: Campeggio, J.; Polimeno, A.; Zerbetto, M. DiTe2: Calculating the diffusion tensor for flexible molecules. J. Comput. Chem. 2019, 40, 697-705.

• C++OPPS-v2.1:calculation of NMR relaxation parameters in fluid phase based on the stochastic description of the relevant coordinates of the system under exam. The program implements the phenomenological two-body model (SRLS - Slowly Relaxing Local Structure, by Polimeno and Freed [Polimeno, A.; Freed J. H. J. Phys. Chem. 1995, 99, 10995]), an extension of the model (TS-SRLS - Two-State SRLS [Zerbetto, M. et al. J. Phys. Chem. B 2012, 116, 13159]) and a molecular model in which it is possible to consider up to two internal torsional degrees of freedom for the internal dynamics [Kotsyubynskyy, D. et al. J. Phys. Chem. B 2012, 116, 14541]. The code is avilable, under the GPL v2.0 licence. If results are published with C++OPPS, please cite: Zerbetto, M.; Polimeno, A.; Meirovitch, E. "C++OPPS, a New Software for the Interpretation of Protein Dynamics from Nuclear Magnetic Resonance Measurements" Int. J. Quantum Chem. 2010, 110, 387.