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Research

Scalable Moving-Domain QM/MM methods

We have been working on protocols to obtain self-consistent polarization in the computation of electrostatic properties. Specifically, we aim to obtain an accurate description of electrostatic potentials in proteins and enzymes. The development of these methods is motivated by the importance of incorporating polarization effects in describing molecular interactions, providing first principles detail, and constructing efficient algorithms that scale linearly or quadratically with the size of the macromolecular system.

An open problem in modeling chemical events in QM/MM methods is how to incorporate solvent effects via continuum dielectric models. Considering that many chemical reactions of biological relevance take place near a liquid solution phase, an accurate theoretical treatment of such processes must incorporate a realistic description of environmental effects. We have been working on a scalable method based on a charge density fragmentation of a conductor-like screening model (DDF-COSMO), which can be incorporated into QM/MM and MOD-QM/MM.

 

Polarization effects in protein electrostatics

Recent developments in the biophysical characterization of proteins have provided a means of directly measuring electrostatic fields by introducing a probe molecule to the system of interest and interpreting photon absorption in the context of the Stark effect. To fully account for this effect, the development of accurate atomistic models is of paramount importance. We have been exploring the application of polarization techniques to improve the description of electrostatic in the active site of proteins. This work has relevance in the computation of electric fields to aid the interpretation of Stark shift spectra in protein probes.

 

Molecular Modeling of Monolayer Protected Gold Clusters

Our interest in computation and modeling of biomolecules extends also to the study of nano-materials. A variety of chemically tunable reactions in metallic nanoparticles can be obtained by encapsulation of nanocrystals in alkanethiolate monolayers to form hybrid systems known as monolayer protected clusters (MPCs). Exploiting MPCs for applications in the area of catalysis requires a proper structural and dynamical characterization of the physical properties of the protecting layer. We are interested in a particular type of protecting monolayers, those containing oligopeptides.

 

Study of Spectral Tunning in Invertebrate Visual Rhodopsin

We have a long standing interest in the first events occurring in the vision process of vertebrates. Such processes occur in the active site of rhodopsin proteins, more specifically, by the photo-isomerization of a protonated Schiff base chromophore. Key amino-acids in the active site are responsible of tuning the absorption of a photon to its optimum value. One remarkable aspect of this tuning effect is the recent resolution of the first X-ray structure of an invertebrate rhodopsin (that of squid). The structure reveals a substantially different protein environment than that of vertebrate rhodopsins, and yet absorption occurs at the same wavelength.