Foto del docente

Andrea Bottoni

Alma Mater Honorary Professor

Alma Mater Studiorum - Università di Bologna

Adjunct professor

Department of Chemistry "Giacomo Ciamician"

Research

Keywords: molecular dynamics asymmetric catalysis Enzyme catalysis QM methods Computational chemistry hybrid QM/MM methods organometallic reactions Reaction mechanisms

1. Implementation of new “software” suitable to describe large molecular systems, in particular enzyme or conventional organic and organometallic reactions where a bulk of solvent molecules is explicitly described. This “software” is based on a hybrid quantum-mechanical(QM)/molecular mechanics (MM) approach.

2. Theoretical Study and Computational Modeling of Organic and Organometallic Reactions.

The aim of these studies is: (a) To determine the mechanism of synthetically important reactions in both industry and academic laboratories. (b) To recognize the “active species” involved in metal-catalyzed or metal-mediated processes. (c) To understand the specific role played by the metal. These studies are performed by means of QM (DFT, MSCSCF, CI, Moller-Plesset, Coupled Cluster) and hybrid QM/MM methods.

3. Computational Modeling of Biochemical Reactions.

The mechanism of important biological reactions is investigated by means of QM, MM and QM/MM methods. In particular, reactions involving enzymes and metal-enzymes are examined. Our aim is to define a strategy that allows to obtain reliable model-systems to simulate the behavior of important biological processes. This strategy is based either on a conventional investigation of the potential energy surface or molecular dynamics techniques.

1. Implementation of new “software” suitable to describe large molecular systems, in particular enzyme or conventional organic and organometallic reactions where a bulk of solvent molecules is explicitly described. This “software” is based on a hybrid quantum-mechanical(QM)/molecular mechanics (MM) approach.

COBRAM code, obtained within this project, links together several QM and MM codes commercially available. It makes possible an effective investigation of enzyme systems by partitioning the whole system in different regions. The innermost region (in general the smallest one) is described at the QM level. It includes the active site residues playing a key-role in the catalysis (breaking and forming of new bonds) and the substrate portion directly involved in the process. The other regions are described at the MM level. These regions are treated at different level of accuracy in the geometry optimization and/or molecular dynamics procedures. The type of algorithms used makes very effective the usage of this code which has been demonstrated to be competitive with respect to similar codes now available.

2. Theoretical Study and Computational Modeling of Organic and Organometallic Reactions.

The aim of these studies is: (a) To determine the mechanism of synthetically important reactions in both industry and academic laboratories. (b) To recognize the “active species” involved in metal-catalyzed or metal-mediated processes. (c) To understand the specific role played by the metal. These studies are performed by means of QM (DFT, MSCSCF, CI, Moller-Plesset, Coupled Cluster) and hybrid QM/MM methods.

Carbonylation, metathesis, cyclopropanation, ketone reductions catalyzed by transition metals such as Cu, Zn, Pd, Pt, Rh are investigated.

3. Computational Modeling of Biochemical Reactions.

The mechanism of important biological reactions is investigated by means of QM, MM and QM/MM methods. In particular, reactions involving enzymes and metal-enzymes are examined. Our aim is to define a strategy that allows to obtain reliable model-systems to simulate the behavior of important biological processes. This strategy is based either on a conventional investigation of the potential energy surface or molecular dynamics techniques. The mechanism of action of biologically important enzyme are under investigation. For instance: racemase, glutaminyl cyclase, anhydrase, endonucleases, glucosylase, DNA repair proteins.