Research

10 - April - 2021

The research  in the Quantum Chemistry and Molecular Modeling group is focused on describing molecular phenoma using methods from molecular dynamics simulations and ab initio quantum chemistry through cutting edge software and computing infrastructures.  Some of our research lines are:

CO2 fixation with enzymes:

Carbon dioxide is one of the most abundant greenhouse gases associated with global warming. One of the main goals to reduce global warming’s adversary effects is to reduce its emission and develop alternative methods to transform this gas into valuable compounds. Nature can fix approximately 400 gigatons of this gas efficiently with enzymes as RUBISCO. In our group, we use computational reaction dynamics to study how enzymes catalyze this chemical reaction or induce CO2 binding. We apply molecular dynamics simulations with well-parameterized force fields to study the enzyme dynamics and the CO2 binding process. The carboxylation reaction, where CO2 is bound to the substrate, is addressed with electronic structure methods within the QM/MM approach to identify specific substrate-enzyme interactions contributing to the catalysis. In collaboration with our experimental collaborators at Prof. Erb’s group at Max-Planck Institute in Germany, we aim to rational design new, more efficient CO2 fixing enzymes.

Molecular interactions in condensed phases:

Condensed phases involve the interplay of many types of interactions between molecules, and the study of their dynamics with computer simulations requires efficient computational models that describe them. In our group, we develop new force fields based on an atomic representation of the molecular system to address binding affinity and kinetics of host-guest systems or organic molecules (drugs) to proteins. We use the Atom-In-Molecules approach to obtain non-bonded force field parameters from electronic structure calculations, which we combine with the bonding parameters of the Openforce field initiative. The new force fields are validated by comparing our simulation results with experimental hydration free energies and binding free energies. This project is carried out in close collaboration with Dr. David Mobley at UC Irvine, EEUU Prof. Verstraelen in Ghent, Belgium and Dr. Paul Ayers in Mcmaster University, Canada.

Astrochemistry:

Understanding the chemistry of the interstellar medium is key for various astrophyiscal processes like star formations or  Astrobiology.  In our group we apply electronic structure and density functional theory methods in order to obtain highly accurate estimates of binding energies of small molecules on interstellar icy mantels. The data we produce is an important parameter for astrochemical models which predict the abundance of different interstellar molecules over time. We also use the binding energy data and icy-grain mantel models to study ice catalyzed chemical reactions.  Our approach is very data intensive which is why we use modern server architectures to store and access the QC data. In that line, to make the data more accessible, we have a QCFractal server instance, which is a  platform to compute, store, organize, and share large-scale quantum chemistry data.  This research line is in close collaboration with Dr. Stefano Bovino from the Computational Astrochemistry group @ UdeC.  

Stereoselective Polymerization: 

The synthesis of biodegradable polymers is a thriving research field considering the ever growing amounts of synthetic plastics that end up in the oceans every year.  In this line of research we try to theoretically predict stereoselective reaction paths for novel catalyzed of ring-opening polymerization that lead to the biodegradable PLA (poly-lactide).  We use a systematic approach that allow to find all possible pathways for a given stereoselective path and predict the tacticity of the resulting polymer by studying not only the initiation phase but also the propagation phase of the polymerization.  In order to be able to accurately compute these large systems we use a combination DFT validated with more accurate wavefunction methods.