School of Molecular Sciences


Seminar schedules

All Seminars are on Fridays at 1:30PM in Biodesign B (BDB) Auditorium B105, unless otherwise stated.

Previous Seminars


John Peters
Washinton State University  
The diverse catalytic reactivity of hydrogenases reveals a simple model for tuning catalytic bias in oxidation-reduction catalysis

Hydrogenases display a wide range of catalytic rates and biases in reversible hydrogen gas oxidation catalysis. The interactions of the iron-sulfur containing catalytic site with the local protein environment are thought to contribute to differences in catalytic reactivity, but this has not been demonstrated. The microbe Clostridium pasteurianum produces three [FeFe]-hydrogenases that differ in their “catalytic bias” exerting a disproportionate rate acceleration in one direction or the other spanning a remarkable six orders of magnitude. The combination of high-resolution structural work, biochemical analyses, and computational modeling indicate that protein secondary interactions directly influence the relative stabilization/destabilization of different oxidation states of the active site metal cluster. This selective stabilization or destabilization of different oxidation states can promote preferentially hydrogen oxidation or proton reduction and represent a simple yet elegant model for how a protein catalytic site can confer catalytic bias.
Host: Anne Jones

Jean-François Masson
Université de Montréal  
Plasmonic nanobiosensors: From therapeutic drugs and environmental monitoring to optophysiology of living cells

This presentation will provide an overview of our research activities in plasmonic nanobiosensing. Our research lies in the areas of plasmonic materials, low-fouling surface chemistry and instrumental design for biosensing. This presentation will focus on applying these concepts for several classes of sensors for monitoring biomolecules, therapeutic drugs, pheromones and for environmental contaminants. We have developed a SPR and LSPR sensing platform based on a small and portable instrument that can be field-deployed. In the first example, this SPR chip was integrated with a RDX-selective molecularly imprinted polymer to detect RDX at ppb levels directly in natural waters. The system was deployed to a Canadian army base for monitoring the level of RDX in proximity of training grounds. This system was tested on several trips in different environmental conditions and results were in good agreement with HPLC performed in a laboratory. Clinical sensing in crude biofluids is a common challenge to different biosensing platforms. To prevent nonspecific adsorption of serum, a series of peptide monolayers were synthesized and tested in crude serum. Based on this, competition assays were validated for therapeutic drug quantitation, such as methotrexate with the SPR sensors. The methotrexate assay was tested at a local hospital and was cross-validated with the current state-of-the-art FPIA analyzer commercially available. Lastly, we are currently exploring the concept of optophysiology using plasmonic nanopipettes for monitoring living cell secretion events. Due to the lack of analytical techniques for detecting metabolites near living cells, developing tools to monitor cell secretion events remains a challenge to overcome in chemical analysis. Plasmonic nanopipettes were developed based on the decoration of patch clamp nanocapillaries with Au nanoparticles. The plasmonic nanopipette is thus competent for dynamic SERS measurements in the liquid environment near cells. This nanobiosensor was tested with the detection of small metabolites near living cells and of neurotransmitters released by neurons.
Host: Mark Hayes

Paul Braun
University of Illinois at Urbana-Champaign.  
High Energy and Power Density Electrodeposited Lithium and Sodium Battery Electrodes

Electrodeposition of electrode materials has the potential to grow anode and cathode materials with unprecedented energy and power densities for both Li-ion and Na-ion rechargeable batteries and to broaden the scope of available electrode form factors. I will present our work on the electrodeposition of high performance silicon and tin-based Na and Li-ion anodes and LiCoO2, NaCoO2, LiMn2O4, and Al-doped LiCoO2-based Na and Li-ion cathodes. The electrolytically active materials were formed either as solid films, or where significant volume changes upon cycling are present, as a 3D mesostructured film. The capacities are near-theoretical, and in the case of the electroplated oxides, the crystallinities and electrochemical capacities are comparable, or in some cases, even better than powders synthesized at much higher temperatures. Time permitting, I will also discuss some of our recent work on the fundamentals of energy transport in redox-active materials for flow batteries.
Host: Neal Woodbury

Jun Wang
University of Arizona  
Medicinal Chemistry and Pharmacology of Antivirals

Host: Wei Liu

Kit Bowen
Johns Hopkins  
Adventures in Anion Photoelectron Spectroscopy

Host: Scott Sayres

Thom LaBean
NC State University  
Engineering Biomolecular Assembly for Medical Applications

The ability to design and program complex molecular interactions between synthetic biomolecules (especially polynucleotides and polypeptides) has led to a revolution in artificial nanomaterials capable of self-assembly. For example, DNA-based nanotech entails the design of artificial nucleotide sequences capable of self-assembling into desired geometric shapes, patterns, and architectures with nanometer-scale precision. These synthetic DNA nanostructures have been shown useful for organizing other materials including inorganic nanoparticles (metals and semiconductors), nucleic acid aptamers, and even carbon nanostructures. We are working with DNA self- and directed-assembly to expand our molecular assembly toolbox for use in a wide variety of applications, especially in nanoelectronics and medicine. One promising recent development is a chemically modified RNA origami-based anticoagulant [See Ref. 1 and schematic below] with potential to treat complex, life-threatening conditions such as disseminated intravascular coagulation (DIC).
Host: Nicholas Stephanopoulos

Victor Batista
Yale University  
Studies of Natural and Artificial Photosynthesis

Mechanistic investigations of the water-splitting reaction are fundamentally informed by structural studies of the oxygen-evolving complex (OEC) of photosystem II (PSII) and biomimetic catalytic complexes. Many physical techniques have provided important insights into the OEC structure and function, including X-ray diffraction (XRD) and extended X-ray absorption fine structure (EXAFS) spectroscopy as well as mass spectrometry (MS), electron paramagnetic resonance (EPR) spectroscopy, and Fourier transform infrared spectroscopy applied in conjunction with mutagenesis studies. However, experimental studies have yet to yield consensus as to the nature of the reaction mechanism responsible for oxygen evolution. Computational modeling studies, including density functional (DFT) theory combined with quantum mechanics/molecular mechanics (QM/MM) hybrid methods for explicitly including the influence of the surrounding protein provide powerful modeling tools to explore reaction mechanisms for the fully ligated OEC within PSII and examine whether they are maximally consistent with experimental data. The computational models are useful for rationalizing spectroscopic and crystallographic results and for building a complete structure-based mechanism of water-splitting as described by the intermediate oxidation states of oxomanganese complexes. This talk summarizes our recent advances in studies of water oxidation catalyzed by the OEC of PSII and biomimetic catalysts for artificial photosynthesis.
Host: Ana Moore

Jeff Hartgerink
Rice University  
Self-assembly of collagen triple helices and b-sheet nanofiber hydrogels: applications in peptide design

Host: Nicholas Stephanopoulos
6:30 PM
PSH 153
Stephen Boxer
Stanford University  
GFP - the Green Revolution Continues

Bioluminescence has fascinated scientists since ancient times – the green fluorescence from agitated jellyfish is an example and this comes from Green Fluorescent Protein (GFP). Since the discovery in the mid-1990’s that GFP can be expressed in essentially any organism, GFPs have become indispensable tools as genetically encoded fluorescent reporters. A bewildering array of variants has been developed leading to a wide pallet of colors and photo-switching characteristics that are essential for super-resolution microscopy. Our lab was involved in early studies of excited state properties of GFP that led to the discovery that the GFP chromophore is a photoacid – this has many consequences for further protein design and is related to the natural function of this unusual protein. Beyond applications in imaging, GFPs are a wonderful model system for probing the spectroscopic and functional consequences of the interaction between a prosthetic group and the protein surrounding it. I will discuss several examples related to photoisomerization of the chromophore. (1) We have systematically altered the electrostatic properties of the GFP chromophore in a photo-switchable variant using amber suppression to introduce electron-donating and -withdrawing groups to the phenolate ring. The contributions of sterics and electrostatics can be evaluated quantitatively and used to demonstrate how electrostatic effects bias the pathway of chromophore isomerization. (2) Split GFPs are made from protein fragments whose reassembly leads to a fluorescent readout. By chance, we discovered that split -strands can be photo- dissociated, i.e. split GFP is a genetically encoded caged protein. The mechanism of this unusual process will be discussed along with possible applications as optogenetic tools.
Host: Neal Woodbury

Steven Boxer
Stanford University  
Electric Fields and Enzyme Catalysis

We have developed the vibrational Stark effect to probe electrostatics and dynamics in organized systems, in particular in proteins where vibrational probes can report on functionally important electric fields. The strategy involves deploying site-specific vibrational probes whose sensitivity to an electric field is measured in a calibrated external electric field. Once calibrated, these probes, typically nitriles or carbonyls, can be used to probe changes in electric field due to mutations, ligand binding, pH effects, light-induced structural changes, etc. We can also obtain information on absolute fields by combining vibrational solvatochromism and MD simulations, checked by the vibrational Stark effect calibration. This frequency-field calibration can be applied to quantify functionally relevant electric fields at the active site of enzymes. Using ketosteroid isomerase as a model system, we correlate the field sensed at the bond involved in enzymatic catalysis with the rate of the reaction it catalyzes, including variations in this rate in a series of mutants and variants using non-canonical amino acids. This provides the first direct connection between electric fields and function: for this system electrostatic interactions are a dominant contribution to catalytic proficiency. Using the vibrational Stark effect, we can now consistently re-interpret results already in the literature and provide a framework for parsing the electrostatic contribution to catalysis in both biological and non-biological systems. Extensions of this approach to other classes of enzymes, to effects of electrostatics on pathways of photoisomerization in proteins, and to the evolutionary trajectories of enzymes responsible for antibiotic resistance will be described if time permits.
Host: Neal Woodbury

Elena Galoppini
Rutgers University Newark  
Synthetic Design of Porphyrin/Metal Oxide Semiconductor Interfaces for Solar Energy Applications: the influence of surface dipoles

The exchange of charges between photo-excited molecules and a metal oxide semiconductor such as TiO2 or ZnO is a process of great importance for solar energy conversion research on photovoltaics, artificial photosynthesis, and photocatalysis. Molecular design of chromophore-linker-anchor compounds plays an important role to control, at the molecular level, charge transfer at hybrid organic-inorganic systems and to gain a fundamental understanding of these important interfaces. The talk will address several aspects of molecular design that our group has focused on, including ways to control the energy level alignment between the LUMO and HOMO of Zinc Tetraphenylporphyrin (ZnTPP) chromophores and the conduction band of TiO2 or ZnO surfaces through the presence of permanent dipoles built in the linker unit.
Host: Ana Moore

Milica Radisic
University of Toronto  

Host: Steve Presse

Derek Pratt
University of Ottawa  

Host: Sid Hecht

Emily Pentzer
Texas A&M University  

Host: Anne Jones

Leslie Schoop
Princeton University  

Host: Christina Birkel

Visitation weekend: No seminar


Justin Sambur
Colorado State University  

Host: Gary Moore

Lian Yu
University of Wisconsin - Madison  

Host: Ranko Richert

Spring Break


Kim See

Host: Christina Birkel

Matthew S. Sigman
University of Utah  

Host: Anne Jones

Paul Weiss
Eyring lecture

Host: Neal Woodbury



Claudia Turro
Ohio State University  

Host: Gary Moore

Sheryl L. Wiskur
University of South Carolina  

Host: Ryan Trovitch