Chemistry

The Isayev lab works at the interface of theoretical chemistry, pharmaceutical sciences and computer science. In particular, we are using molecular simulations and artificial intelligence (AI) to solve hard problems in chemistry. We are working towards the acceleration of molecular discovery by the combination of AI, informatics and high-throughput quantum chemistry. We also focus on both generative and predictive ML models for chemical and biological data. Details on specific projects can be found below.

Accelerating computational chemistry with deep learning: We are developing fully transferable deep learning potentials for molecular and materials systems. Such atomistic potentials are highly accurate compared to reference QM calculations at speeds 107faster. Neural network potentials are shown to accurately represent the underlying physical chemistry of molecules through various test cases including chemical reactions, kinetics, thermochemistry, structural optimization, and molecular dynamics simulations.

Materials informatics: Material informatics is a rapidly emerging data- and knowledge-driven approach for the identification of novel materials for a range of applications, including solar energy conversion. As the proliferation of high-throughput methods in chemical sciences is increasing the wealth of data in the field, the gap between accumulated-information and derived knowledge widens. We address the issue of scientific discovery in chemical and biological databases by introducing novel analytical approaches based on large-scale data mining and machine learning.

De Novo molecular design: The de novo molecular design problem involves generating novel molecular structures or focused molecular libraries with desirable properties. It solves a so-called inverse design problem. We develop artificial intelligence method that enables the design of chemical libraries with the desired physicochemical and biological properties or both.

Understanding binding and structural properties of nanostructures that have important implications for increasing storage capacity in molecular electronics, minimizing high temperature destabilizing effects in energy systems, and maintaining bioactivity of bound molecules in biosensors are topics of interest in the group.  DNA origami nano technology, scanning microscopy (SEM and AFM), and electrochemistry are applicable techniques.

Our research involves the design and synthesis of novel hybrid inorganic-organic-biomolecule materials and studying, understanding, and precisely controlling their structures and properties. This research encompasses organic and inorganic synthesis, coordination chemistry, solid-state chemistry, biomolecule assembly, and nanoparticle synthesis and assembly.  We are particular motivated by applications related to the porosity of metal-organic framework materials (e.g. gas storage and separations) and the unique collective plasmonic properties of peptide-nanoparticle assemblies.

Our research focuses on fundamental science and engineering questions motivated by the creation of materials on the nanometer scale (1 nm=10-9 m). Our research themes include the synthesis, characterization, and applications of nanoparticles (typically 1-100 nm in size). We are developing chemical methods for synthesizing well defined nanoparticles, including atomically precise nanoclusters, shape- and size-controlled nanocrystals, hybrid nano-architectures, and inorganic/polymer nanocomposites. In-depth characterizations of the physical and chemical properties of nanoparticles and self-assembled nanomaterials are carried out with microscopy and spectroscopy techniques, such as electron microscopy, atomic force microscopy, X-ray crystallography, steady-state and ultrafast spectroscopies, etc. We also develop applications of nanoparticles in areas of catalysis, optics, chemo- and bio-sensing, and photovoltaics, etc.

Raúl Hernández Sánchez's research group is interested in combining supramolecular, inorganic, and materials chemistry to synthesize functional systems that bridge the gap between nanoscale materials and molecular chemistry. Their research is focused on developing new synthetic methodologies to access well-defined nanometer-sized clusters where they can investigate surface structure-function relationships relevant in catalytic and magnetic materials. Other efforts in the Hernández Sánchez (HS) group are aimed at designing and synthesizing structural analogues of carbon nanotubes where exquisite control of the resulting framework allows for properties manipulation.

Students in the HS group will engage in synthetic chemistry and develop familiarity with a range of spectroscopic, electrochemical, crystallographic and magnetic techniques. While rooted in synthetic chemistry, research in the HS group will interface with materials, organic, theory, and physical chemistry.

Saxena Group is focused on developing Fourier Transform electron spin resonance and its application to otherwise inaccessible problems in biophysics. The coupling of electron spin angular momentum to its environment—as revealed by the ESR spectrum—provides rich information about the electronic, structural and dynamical properties of the molecule. Saxena group creates the methods that measure the precise distance between two units in a protein, in order to determine their folding patterns and conformational dynamics. These ESR Spectroscopic Rulers— based on multiple quantum coherences and double resonance experiments—are unique in that they resolve distances in the 1-16 nm length scale even on bulk amorphous materials. Much of this work is based on the use of first-principles theory to develop new experimental protocols and to analyze experimental results.

His group continues to develop applications of these spectroscopic rulers that range from capturing the essence of structural changes - such as misfolding - in proteins, to measuring the atomic-level details of ion-permeation in a ligand gated ion-channel. The main projects of his group include:

• Pulsed ESR methods to measure distance constraints in systems containing paramagnetic metals
• Measurement of structural and dynamical determinants of the protein-DNA interactions and functional dynamics in pentameric ligand gated ion-channels.
• Application of the spectroscopic ruler to measure and predict global structures of nanostructured materials.
• Role of metals in aggregation of Amyloid-β peptide.