Theoretical and computational chemistry
Molecular modeling; in silico characterization; molecular dynamics and reactivity; quantum and statistical methods; computational spectroscopy.
Listed here below you can check the groups developing this research area's activities.
Molecular Recognition and Catalysis
Giulia Licini (giulia.licini@unipd.it); Cristiano Zonta (cristiano.zonta@unipd.it); Manuel Orlandi ( manuel.orlandi@unipd.it).
The Molecular Recognition and Catalysis group is interested in all aspects of selective catalytic transformations and molecular recognition. Our research is centered on the design, discovery, and study of new catalytic systems that catalyze fundamentally useful organic reactions. These include, in particular Lewis Acid catalysis, oxidations, and new stereoselective transformations. In addition, we apply the tools of physical-organic chemistry tools to gain insights into the transition structure geometries and molecular recognition events that control reactivity and selectivity.
The following topics are currently under investigation in our laboratories:
1. Activation of Small Molecules (CO2, O2, H2O2); 2. Mimics of Physiologically Important Metallo-Enzymes (haloperoxidases, ligninperoxidases); 3. New Approaches to Catalyst Design and Recycling in Green Chemistry; 4. Self-Assembled Molecular Cages and Catalysis in Confined Spaces; 5. Probes for Enantiomeric Excess Determination; 6. Development of New Stereoselective C-C Bond Forming Reactions.
- Concentration-Independent Stereodynamic g-Probe for Chiroptical Enantiomeric Excess Determination, J. Am. Chem. Soc., 2017, 139, 15616–15619, DOI: 10.1021/jacs.7b09469.
- Triggering Assembly and Disassembly of a Supramolecular Cage, J. Am. Chem. Soc., 2017, 139, 6456–6460 DOI: 10.1021/jacs.7b02341.
- Vanadium(V) Catalysts with High Activity for the Coupling of Epoxides and CO2: Characterization of a Putative Catalytic Intermediate, ACS Catalysis, 2017, 7, 2367–2373, DOI: 10.1021/acscatal.7b00109.
– Efficient Vanadium-Catalyzed Aerobic C−C Bond Oxidative Cleavage of Vicinal Diols, Adv. Synth. Catal., 2018, 360, 3286-3296. DOI: 10.1002/adsc.201800050.
– A Diastereodynamic Probe Transducing Molecular Length into Chiroptical Readout, J. Am. Chem. Soc., 2019, 141, 11963-11969. DOI: 10.1021/jacs.9b04151.
Nanostructures & (Bio)molecules Modeling
Stefano Corni (stefano.corni@unipd.it); Agostino Migliore (agostino.migliore@unipd.it)
The group develops and applies multiscale computational methods to describe hybrid systems, such as organic and biological molecules interacting with inorganic nanoparticles. The methods used range from ab initio atomistic calculations (also on quantum computers) and classical molecular dynamics to classical and quantum electrodynamics. The main research topics are:
-ultrafast spectroscopy and optical properties of molecules close to plasmonic nanostructures & in solution.
-the quantum nature of plasmonics excitations at the nanoscale.
-charge and energy transfer in (bio)molecules and in nanoscale structures
-the interactions of inorganic surfaces and nanoparticles with proteins.
The group is currently funded by EU H2020 and HE projects in which light-biomolecule interactions play a major role.
- Strong coupling between localized surface plasmons and molecules by coupled cluster theory, Nano Letters, 2021, 21, 6664-6670
- The physical origin of a photon-number parity effect in cavity quantum electrodynamics, Results in Physics, 2021, 30, 104690
- Charge transfer between [4Fe4S] proteins and DNA is unidirectional. Implications for biomolecular signaling, Chem, 2019, 5, 122-137
- Manipulating azobenzene photoisomerization through strong light–molecule coupling, Nature Communications, 2018, 9, 4688-9
- How to Identify Plasmons from the Optical Response of Nanostructures, ACS Nano, 2017, 11, 7321–7335.
Soft Matter Theory
Prof. Alberta Ferrarini (alberta.ferrarini@unipd.it); Dr. Francesco Avanzini (francesco.avanzini@unipd.it)
We use and develop statistical mechanical theories and computer simulations to reach a microscopic understanding of equilibrium and nonequilibrium properties of Soft Matter. Different methods and techniques, suitable to bridge different time and length scales, are employed and developed to address questions of interest to biophysics and materials science.
Research topics:
- Chirality propagation across length scales in self-assembling systems (polymers, nucleic acids, supramolecular aggregates);
- Elastic, rheological and thermodynamic properties of soft matter systems (lipid membranes, liquid crystals, polyelectrolytes, colloids, emulsions and gels);
- Nonequilibrium chemical processes and self-organization at different scales.
Publications:
Modeling of minimal systems based on ATP-Zn coordination for chemically fueled self-assembly, Phys. Chem. Chem. Phys. 2023, 25, 6102.
Spontaneous twisting of achiral nematic rods, Phys. Rev. Lett. 2023, 130, 1.
Helical inclusions in phospholipid membranes: lipid adaptation and chiral order, J. Phys. Chem. Lett. 2019, 10, 5629.
Circuit Theory for Chemical Reaction Networks, Phys. Rev. X 2023, 13, 021041
Deficiency, Kinetic Invertibility, and Catalysis in Stochastic Chemical Reaction Networks, J. Chem. Phys. 2023, 158, 204108
updated September 26th, 2023
Theoretical Chemistry
Prof. Antonino Polimeno (antonino.polimeno@unipd.it); Prof. Barbara Fresch (barbara.fresch@unipd.it); Dr. Diego Frezzato (diego.frezzato@unipd.it); Prof. Laura Orian (laura.orian@unipd.it); Prof. Mirco Zerbetto (mirco.zerbetto@unipd.it)
At TCG we develop theoretical models and computational simulations of molecular properties and reactivity. We address a wide range of physical chemistry topics, from magnetic and optical spectroscopies to the design of functional molecular structures using molecular dynamics, quantum-statistical and stochastic thermodynamics methods. We investigate also novel approaches, like machine learning techniques and quantum technologies, for theoretical and computational chemistry. Current research subjects are:
- coarse-grained description of biomolecules and supramolecular systems
- deterministic and stochastic kinetics in chemical reaction networks
- computer-guided rational design of bio inspired molecules and catalysts for applications to health and sustainability
- design of quantum nanodevices for molecular logic
- models of quantum dynamics and spectroscopic response
- Strategies to simulate dephasing-assisted quantum transport on digital quantum computers. New Journal of Physics 2022, 24, 023039.
- Effect of methylmercury binding on the peroxide reduction potential of cysteine and selenocysteine. Inorg. Chem. 2021, 60, 4646-4656.
- Stochastic modelling of C-13 NMR spin relaxation experiments in oligosaccharides. Molecules 2021, 26, 2418
- Sensitivity analysis of the reaction occurrence and recurrence times in steady-state biochemical networks. Math. Biosci. 2021, 333, 108518
- Parameter free evaluation of SN2 reaction rates for halide substitution in halometane. Phys. Chem. Chem. Phys. 2022, 24, 7474.
updated April 6th, 2022
