Uriel MorzanCommunity Network Analysis
One of our goals in the Batista lab is to develop methodologies to study complex processes, such as energy or charge transport, in macromolecules. In this context, graph theory provides a powerful theoretical framework to simplify these kinds of problem and extract fundamental properties of the system. Some of the problems that have been investigated with this approach are:  the elucidation of the allosteric mechanism of imidazole glycerol-phosphate synthase (IGPS) and the rationalization of the temperature dependence of its catalytic activity,  the study of the mechanism of CRISPR-Cas9 genome editing activity,  the characterization of the electron transport mechanism in bacterial pili.
Vibrational Relaxation of Molecules on Metalic Surfaces
The simulation of molecular dynamics on metal surfaces is very challenging due to the presence of a variety of quantum and nonadiabatic effects determining their chemical behavior. One of our goals in the Batista group is to develop state of art methodologies to study the surface chemistry of these systems, with a particular focus on the reduction of carbon dioxide.
Atanu AcharyaElectrical Conductivity of Biological Nanowires
Conductive biological nanowire possesses a unique niche in modern biophysical research, both in terms of the mechanism of charge transport and as well as the very long-range nature of them. The electrical conductivity of pili does not require chemical fixation, and the charge transport occurs akin to metal. Recently, it was demonstrated that, introducing two point-mutations (W51W57) significantly increase (∼by three orders of magnitude) the conductivity of the pili and consequently the conductivity of pili become comparable to carbon nanotubes. It is also observed that lowering of pH significantly increase the conductivity of pili independent of point mutations. The origin of such enhancement in conductivity is unknown so far. Introduction of W51W57 mutation and lowering pH also induces significant structural changes in pili assembly leading to contraction of the height by half. In the Batista lab, we investigate the mechanism of conductivity enhancement induced by pH and point mutations using MD simulations and community network analysis (CNA). We hypothesize that the conductivity arises from the arrangement of aromatic amino acids and pH and point-mutations drastically change the structural arrangement of aromatic amino acids. Lower pH and W51W57 mutations bring the aromatic amino acids in a more compact arrangement.
Excited State Dynamics of Photoacids
The acidity of aromatic alcohols significantly increases upon electronic excitations. Thus, aromatic alcohols are more susceptible toward losing a proton from excited electronic state than from ground state. This property of aromatic alcohols is called photoacidity. Naphthol is one such photoacid with dramatically different effects with substitution of the 1- or 2-position of the aromatic ring (i.e., in 1-naphthol (1N) or 2-naphthol (2N), respectively. 1N and 2N have similar acidity in ground state but their photoacidities are strikingly different; 1N is significantly higher photoacidic than 2N. Therefore, the characters of the excited states that stabilizes the respective conjugate bases is quite different. Additionally, the excited state decay [as revealed by time-correlated single-photon counting (TCSPC) measurements of the fluorescence emission and UV-IR experiments] dynamics is much slower in 2N than in 1N. Thus, the excited state lifetime of 2N isomer is much higher than 1N. In Batista lab, we model the excited state decay dynamics of naphthol photoacids in terms of photoinduced electron transfer (PET) from solute to solvent. Our computation shows that the PET rate is slower in 2N by several orders of magnitude leading to the longer lifetime of the excited state. One key factor in our investigation is the application of the state-of-the-art computational technique to characterize the excited states (La and Lb) of naphthol photoacids. Our computation also demonstrates the limitations of TDDFT methods in correctly describing the excited state of naphthol.
Florentina TofoleanuMolecular Dynamics of Proteins
My postdoctoral work is focused on understanding the molecular mechanisms of protein-ligand binding and protein folding by applying computational tools and experimental techniques. I employ molecular dynamics (MD) simulations and free energy calculations to study large molecular systems, such as ion channels, enzymes and amyloid and lipid membrane systems. MD simulations provide details on the protein dynamics, and its modulation by ligand binding or mutationa, giving insights into the allosteric effect and ultimately, its biological function. I use free energy calculations to evaluate protein-ligand binding, and predict which molecules could be used as drugs that inhibit/enhance the protein function. I then test my computational assessments through experiments (isothermal titration calorimetry and fluorescence polarization). My projects require large amounts of computational resources- I use the LoBos and Biowulf supercomputers at the National Institutes of Health, and I have successfully applied for computational resources on the D.E. Shaw Anton2 supercomputer at the Pittsburgh Supercomputing Center.
Pablo VidelaUnderstanding molecule-interface interactions: SFG of proteins, catalysts and hydrocarbons
Understanding the interaction of molecules with interfaces is of fundamental importance since a lot of processes are controlled by the particular way the molecule and surface ‘talk’ to each other. For example, the catalytic efficiency for the reduction of CO2 to CO by surface-immobilized Rhenium complexes crucially depends on the particular crystal face of the substrate used, whereas the stability of molecules of environmental importance, such as terpenes or carbamates, varies depending on particular surface-molecule interactions. One of the main focus of the group is to unravel how the underlying substrate-adsorbate interactions modulated the orientation, energetics and reactivity of different molecules at interfaces using a variety of computational methods ranging from Molecular Dynamics simulations to Quantum Mechanics calculations. Since a lot of the experimental information of substrate-molecule interactions come from surface-specific spectroscopies such as Sum Frequency Generation (SFG), the development of theoretical models to simulate and interpret the different spectral features of the SFG spectra is an active research area of the group. By combining electronic structure calculations with computational modelling, we have simulated both 1D-SFG and 2D-SFG for rigid and flexible molecules on different interface environment, providing insight into the interpretation of congested experimental spectral signals and disentangling the influence of surface interactions in determining molecular structure, orientation and ordering at the interfaces. This project involves an active collaboration with different experimental groups: Elsa Yan , Clifford Kubiak , Tianquan Lian , Poul Petersen , Luis Vellarde , Franz Geiger .
Kenny JungMy research is focused on two fronts. The first is the development of novel quantum-classical mappings for the description of non-adiabatic dynamics. The other area of focus is to generalize and extend semi-classical methods for the simulation of nonlinear spectroscopy.
Adam MatulaElectron Transport Simulations
My research in the Batista group focuses on understanding electron transport in real-world systems. As part of the solar group collaboration (Robert Crabtree and Gary Brudvig of the Yale Chemistry department as well as Antoni Llobet, Schmuttenmaer) I use DFT calculations and an extended Hückel electron dynamics technique to study interfacial electron transfer in dye-sensitized solar cells (DSSCs) and photoelectrochemical cells. I have also studied electron transport and rectification effects through single molecules in gold junctions via DFT-NEGF calculations, identifying a key pathway through which directional charge transport behavior can be induced. Finally, via collaboration with researchers at the National University of Singapore (Venkatesan) I worked to explain charge transport effects in a new class of robust organic memristors.
Subhajyoti (Subha) ChaudhuriSubha studies excited state charge transfer processes in systems ranging from naphthol photoacids to bacterial pili. His previous work focused on designing computational models to study the effects of vibronic coupling on electron transfer rates. At present he is working on implementing alternative clustering algorithms to obtain accurate partial charges on atoms.
Krystle ReissNatural Water Oxidation and Oxygen Evolution
My research primarily consists of the study of the oxygen-evolving complex (OEC) of photosystem II. The sole producer of molecular oxygen found in nature, the OEC is a unique metal complex composed of four highly charged manganese centers held together by a network of μ-oxo bridges and protein residues. While a fascinating system in itself, our ultimate goal is to use the OEC to create synthetic mimics for renewable fuel production. Our primary tools for studying this complex system are two-layer QM/MM models, which take advantage of the low cost of molecular mechanics (MM) for the large protein layer while saving expensive quantum mechanics (QM) for the much smaller OEC. With these model systems in hand, we can calculate IR spectra, S-state transitions, EXAFS, and other properties that can be matched to real world experiments. We are also working to build parameters for a fully classical OEC that can be implemented in molecular dynamics simulations to compliment the more static QM/MM models. We work closely with several experimental groups, both at Yale and beyond, meeting weekly to discuss results and ongoing projects.
Ray KellyCO2 reduction catalysts
We are interested in surface-immobilized catalysts which display enhanced activity for the reduction of CO2. We simulate sum frequency generation spectra of these systems to understand the orientation of the catalyst on the solid surface. This work is done in collaboration with the experimental groups of Tianquan Lian at Emory University and Clifford Kubiak at the University of California, San Diego.
Catalysis on Metal Surfaces
Additionally, we are working to understand catalysis on metal surfaces. In particular, we are investigating hydride transfer reactions of unsaturated hydrocarbons with tertiary amines on noble metal surfaces. This work is a collaboration with the experimental groups of Gary Haller at Yale and Eszter Baráth at Technische Universität München.
Jessica FreezeMachine Learning
Current research involves using machine learning (ML) for the prediction of chemical properties including catalyst screening. Additionally, the development of new methods for applying ML techniques to chemistry is being explored.
Destruction of waterways through nitrafication from fertilizer run off presents a current and pressing problem. Designing catalysts to oxidize ammonia to nitrogen gas may be a solution. Efficient design of these catalysts and understanding their mechanisms will assist in these goals.