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.
