Department of Chemistry

In my research group, we use a combination of analytical theory and numerical simulation to study problems in soft matter physics ranging from jamming in glassforming liquids, foams and granular materials, to biophysical self-assembly in actin structures and other systems. The idea of jamming is that slow relaxations in many different systems, ranging from glassforming liquids to foams and granular materials, can be viewed in a common framework. For example, one can define jamming to occur when a system develops a yield stress or extremely long stress relaxation time in a disordered state. According to this definition, many systems jam. Colloidal suspensions of particles are fluid but jam when the pressure or density is raised. Foams and emulsions (concentrated suspensions of deformable bubbles or droplets) flow when a large shear stress is applied, but jam when the shear stress is lowered below the yield stress. Even molecular liquids jam as temperature is lowered or density is increased this is the glass transition. We have been testing the speculation that jamming has a common origin in these different systems, independent of the control parameter varied. On the biophysical side, our research has been motivated recently by the phenomenon of cell crawling. When a cell crawls, its cytoskeleton--a network of filaments (primarily composed of the protein actin) that maintains the mechanical rigidity of the cell and gives the cell its shape--must reorganize in structure. This reorganization is accomplished via polymerization, depolymerization and branching of actin filaments, as well as by crosslinking the filaments together with "linker" proteins. The morphology of the resulting structure is of special interest because it determines the mechanical properties of the network. We are developing dynamical descriptions that capture morphology. In addition, we are exploring models for how actin polymerization gives rise to force generation at the leading edge.

Criegee intermediates: Research in the Lester laboratory is currently focused on the photo-induced chemistry of Criegee intermediates.  Alkene ozonolysis is a primary oxidation pathway for alkenes emitted into the troposphere and an important mechanism for generation of atmospheric OH radicals, particularly in low light conditions, urban environments, and heavily forested areas.  Alkene ozonolysis proceeds through Criegee intermediates, R1R2COO, which eluded detection until very recently.  In the laboratory, the simplest Criegee intermediate, CH2OO, and methyl-substituted Criegee intermediates, CH3CHOO and (CH3)2COO, have now been generated by an alternative synthetic route and detected by VUV photoionization.  This laboratory has further shown that UV excitation of the Criegee intermediates on a strong π*←π transition induces photochemistry, which involves multiple coupled excited state potentials and yields both O3P and O1D products.  This group has also demonstrated that IR excitation of methyl-substituted Criegee intermediates in the CH stretch overtone region initiates unimolecular decay.  The latter enables direct examination of the hydrogen transfer reaction leading to OH products, which is a key non-photolytic source of OH radicals in the atmosphere.

Hydrogen trioxide radical: This laboratory obtained the first infrared spectrum of the hydrogen trioxide (HOOO) radical, an intermediate invoked in the H + O3 and O + HO2 atmospheric reactions as well as the efficient vibrational relaxation of OH radicals by O2. There had been much debate in the literature as to whether HOOO is stable or metastable with respect to the OH + O2 limit, as well as the relative stability of the cis and trans conformers. We have characterized the geometric structure, vibrational frequencies, and stability of the cis and trans conformers of HOOO and its deuterated analog. In particular, by measuring the OH product state distribution following IR excitation of HOOO, we have directly determined the stability of trans-HOOO and shown that is much greater than prior estimates. As a result, HOOO may act as temporary sink for OH radicals and be present in measurable concentrations in the Earth's atmosphere. The experimental stability indicates that 25% of the OH radicals in the vicinity of the tropopause may be bound to O2, rather than free OH radicals. Studies of combination bands in the fundamental OH stretch region reveal nearly all other vibrational modes of trans- and cis-HOOO.  We have subsequently derived a torsional potential from our spectroscopic data to obtain the relative stability of the cis and trans conformers and isomerization barrier, which are critical for atmospheric modeling of HOOO. 

IR action spectrum of cis- and trans-HOOO in the OH overtone region (left), and fraction of atmospheric OH predicted to exist as HOOO (right).

Dynamical signatures of quenching: Collisional quenching of electronically excited OH A2Σ+ radicals has been extensively investigated because of its impact on OH concentration measurements in atmospheric and combustion environments. Yet little is known about the outcome of these events, except that they facilitate the efficient removal of OH population from the excited A2Σ+ electronic state by introducing nonradiative decay pathways. The quenching of OH A2Σ+ by H2 and D2 has emerged as a benchmark system for studying the nonadiabatic processes that lead to quenching. Theoretical calculations indicate that a conical intersection funnels population from the excited to ground electronic surfaces. Our studies examined the Doppler profiles for the H/D-atom products of reactive quenching, which show that most of the excess energy results in vibrational excitation of ‘hot’ water products. Our work also focused on characterizing the nonreactive quenching process, where OH X2Π products are generated with a remarkably high degree of rotational excitation and lambda-doublet specificity. The OH quantum state distribution directly reflects the anisotropy and A′ symmetry of the conical intersection region. We also demonstrated for H2 and D2 collision partners that reaction accounts for nearly 90% of the quenched products.  These distinctive dynamical signatures of passage through a conical intersection region have sparked intense theoretical interest in this system.

We gratefully acknowledge financial support from the National Science Foundation under Grant No. NSF CHE-1362835 and the Chemical Sciences, Geosciences and Biosciences Division, Office of Basic Energy Sciences, Office of Science, U.S. Department of Energy under Grant No. DE-FG02-87ER13792.

The central theme of research in my laboratory is the rational design of new methods and catalysts for use in organic synthesis. As well as using traditional screening and development approaches, we employ several novel computational tools for the discovery and optimization of new reagents and catalysts. These new synthetic methods comprise the key steps in our total synthesis strategies to a variety of important pharmaceutical agents and natural products.

Asymmetric Oxidative C-C Bond Forming Reactions: The development of chiral catalysts for oxidative C-C bond formation is a major focus in our laboratory. In addition to the substantial potential for developing biomimetic synthetic approaches to a variety of natural products, such transformations are appealing in that C-H bonds are directly transformed to C-C bonds with an inexpensive oxidant, molecular oxygen. 

To this end, we developed 1,5-diaza-cis-decalin copper complexes, the catalysts of choice for the oxidative asymmetric biaryl coupling of 2-naphthol derivatives. Study of the mechanism has allowed the development of new reaction methods as well as couplings of highly functionalized 2-naphthols. With this ability, we have completed the first asymmetric synthesis of the natural product nigerone. The first total syntheses of the complex natural products cercosporin and hypocrellin have also been accomplished. These structurally novel compounds display promising photodynamic therapy profiles in cancer treatment. Future goals include exploiting the oxidative biaryl coupling method in the synthesis of chiral bisanthraquinone and naphthodianthrone natural products.

Reactions of α-Ketoesters and Derivatives: We have described bifunctional salen-derived catalysts that contain electronically decoupled Lewis acid and Lewis base sites. This electronic decoupling permits generation of optimally active catalysts as both the Lewis acid and Lewis base can be maximized without quenching each other. These catalysts are particularly effective for the very difficult asymmetric alkylation of α-ketoesters and α-iminoesters to yield α-hydroxy and α-amino acid adducts in enantiomerically pure form. Further studies with α-iminoesters have revealed an umpolung addition pathway allowing addition of nucleophiles to imine nitrogens. We have exploited this reactivity pattern to develop a three-component coupling that generates highly functionalized α-amino acid derivatives.

Computer-Aided Design of Chiral Auxiliaries and Catalysts:Diastereo- and enantioselective chemical reactions are essential components for the efficient synthesis of complex chiral targets. We have generated several computational tools to assist researchers in designing and optimizing chiral catalysts including database searching and functionality mapping. In addition, we have developed semi-empirical quantum mechanical quantitative structure selectivity (QSSR) relationships for accurate and precise enantiomeric excess predictions of chiral catalysts. In one example, we correlated the structures of various beta-amino alcohol catalysts to their enantioselectivities in the asymmetric addition of diethylzinc to benzaldehyde. With our method the selectivities of new catalysts were also calculated. Subsequent chemical synthesis and analysis of the new catalysts indicated that the model was very useful and easily distinguished catalysts of low, moderate, and high selectivity. 

Investigations carried out in our laboratory encompass a wide range of interests in synthetic organic chemistry including heterocyclic and medicinal chemistry.

Current efforts are in the following areas: (1) synthesis and chemistry of five-membered heterocycles and natural products containing such units; (2) synthesis and chemistry of fungal metabolites; (3) synthesis and chemistry of cyclopeptide alkaloids; (4) synthesis of biologically important depsipeptides; (5) synthesis of novel ninhydrins; (6) synthesis of anti- angiogenic agents.

1. Utilization of D-ribonolactone and other sugars as precursors in the synthesis of several structurally challenging molecules is currently underway in our laboratory.
2. The synthesis of naturally occurring fungal metabolites containing a common hexasubstituted aromatic ring but different side chains such as colletochlorin D, ascofuranone and ascochlorin are another area of interest. The biological activities of those natural products range from high hypolipidemic action to anticancer and antiprotozoan activity.
3. Cyclopeptide alkaloids are natural products found in many plant families. A broad program aimed at developing methodology for the synthesis of the most commonly found thirteen- and fourteen-membered ring cyclopeptide alkaloids is currently underway. Sanjoin, used in Chinese folk medicine is one of our targets. Other antitumor cyclic peptides provenient from plants, the astins, are also under investigation.
4. Didemnins are a new class of depsipeptides isolated from a Carribean tunicate of the family Didemnidae, a species of the genus Trididemnum. These cyclic peptides have shown highly active antiviral and antitumor agents. The synthetic studies carried out in our laboratory have produced synthetic and spectral evidence for the absolute configuration of the asymmetric centers of the hydroxyisovalerylpropionyl (HIP) unit of the macrocycle, thereby requiring a revision of the original stereochemistry. The stereocontrolled total synthesis of these natural products has already been accomplished. The synthesis of several beta-turn mimics and constrained analogs are under investigation. Because of a broad program to develop efficient synthetic routes to the didemnins, other cyclodepsipeptides have been chosen as the next targets. The choice of these compounds was not only based on their relationship to didemnins but also on previous synthetic studies of products originating from polyketide biosynthesis, and earlier investigations of carbohydrates.
5. Novel ninhydrins are being synthesized as reagents for the detection of amino acids.
6. We have found that sulfated beta-cyclodextrin mimicked heparin advantageously. This effective synthetic product is of utmost importance in the control of angiogenesis and has other important applications in medicine. This recent discovery uncovers a new class of anti-angiogenic agents, consisting of a hydrophilic carrier and a hydrophobic angiostat, and offers a unique opportunity for the development of chemical technologies which will have important applications in the bio- and medical sciences. We are therefore continuing these studies with several goals in mind. We are investigating new and more effective carriers, we are designing single species that contain both the angiostat and carrier, and we are looking for new and more effective angiostats.
7. 

Identification, characterization and optimization of chemical probes of biological systems; Identification of novel agents to treat neurodegenerative diseases such as Alzheimer's Disease; Design of novel chemical libraries to probe biological systems.

The focus of our research is to study how proteins fold from random or quasi-random coils to their biologically functional conformations. We are particularly interested in the kinetic aspects of the folding mechanisms. Novel laser spectroscopic methods are being used and developed to study the early folding events and folding intermediates.

Fast events in protein folding

Understanding how folding proceeds at early time is apparently essential to the elucidation of the entire folding mechanism. To access and characterize the early folding events requires a fast initiation method and a probe that has structural specificity. Our general approach is to use novel laser-induced temperature-jump and fast-mixing techniques to initiate refolding/unfolding on nanosecond or microsecond timescales, and use time-resolved infrared and fluorescence spectroscopies to probe the subsequent folding dynamics and structural ordering along the folding/unfolding pathways. This approach provides not only fast time resolution, but also the necessary structural sensitivity, since both infrared and fluorescence are well-established conformation probes. Recent works involve the study of the helix-coil transition, helix-helix interaction, and ß-sheet formation. 

Single-molecule study of protein conformation dynamics

Recently, a new view of the kinetics of protein folding has emerged based on the new conceptual framework of statistical mechanical models, replacing the pathway concept with the broader notion of rugged energy landscapes. The heterogeneity in folding kinetics therefore can be realized as a result of the motions of an ensemble of protein conformations on the rugged energy hypersurface that is biased towards the native state, analogous to parallel diffusion-like processes. Studying folding dynamics statistically using single-molecule techniques will provide unique information regarding a protein's folding energy landscape, which may not be obtained by conventional ensemble studies since the conventional measurements of molecular dynamics in the condensed phase represent only averages over large numbers of molecules and events. Currently, confocal fluorescence spectroscopy and microscopy are being used to study protein spontaneous fluctuation and folding dynamics at single-molecule level. 

From a knowledge of the interactions among molecules, it is possible in principle to predict the structure and the thermodynamic properties of materials as well as the dynamics of molecular processes. The overall objective of our research program is twofold: to evaluate the potential energies of intermolecular interactions for various systems as accurately as possible and to study by means of statistical mechanics the influence of these potentials of intermolecular force on the structure and properties of macroscopic systems.

Our group is interested to study the effect of nano-confinement on structure, dynamics and other properties of materials. Materials behave differently on surfaces, interfaces or small length scales compared to their bulk properties.  Understanding such differences are crucial in many technological applications where materials are constrained in nanometer size spaces, such as organic electronics, polymer applications and drug delivery. One can take advantage of such difference to produce novel materials, such as exceptionally stable glasses or harvest light for various applications. In biological systems, most of the dynamics happens in nanometer size proximity of surfaces and interfaces, and understanding the properties in confinement is a key in predicting function. We focus our efforts on understanding the origins of such modified properties on a fundamental level as well as possible application of such phenomena in producing novel materials or experimental tools. For more details please see our website at:

 http://web.sas.upenn.edu/fakhraaigroup/research/

Enhanced Mobility at the Surface of Polymeric and Organic Glasses: 

We study the properties of glasses at the air/glass interface. Our studies show that below the glass transition temperature, where the bulk of the material is in an out of equilibrium state, the interfacial dynamics are many orders of magnitude faster that the bulk dynamics. As a result a layer close to the interface maintains equilibrium properties. We study the dynamics of this layer, its thickness, and its effect on the properties of the underlying glass. The interfacial layer can strongly modify properties of amorphous materials in nanometer length scales. They also allow one to produce near-equilibrium structures at temperatures well below bulk glass transition temperature, through physical vapor deposition.

Exceptionally Stable Glasses: 

The enhanced mobility of the interfacial layer allows us to produce near-equilibrium glasses at temperatures well below the bulk glass transition temperature, Tg, by means of physical vapor deposition (PVD). Exceptionally stable glasses are formed when the substrate temperature during PVD is maintained just below the glass transition temperature. We study the morphology and the kinetics of PVD films during formation and their relationship to the final properties of the stable glass. These studies provide information on mechanisms of rapid aging below Tg and stable glass formation. We also investigate exceptional material properties of these glasses and the role of the chemical structure in these properties such as the optical birefringence and electronic properties.

Novel Emergent Optical Properties in Disordered Nanoparticle Clusters: 

Using simple synthetic routs we can produce dielectric core-gold shell nanoparticles decorated with randomly packed nanoparticles of various shapes and sizes. Spiky nanoparticles are a good example of such nanoparticles. Broadband and tunable structure of spiky gold nanoshells makes them ideal for various applications such as enhanced Raman scattering, temperature and index sensing and sensors for biological and light harvesting applications. Exceptional properties, such as higher order quadrupoloar scattering and magnetic dipole plasmons in these nanoparticles are due to inherent disorder in their structure and random packing arrangements. We explore optical properties of these nanoshells, using various theoretical and experimental tools. We also develop new techniques that allow us to study properties of meta materials formed from these types of particles.

Surface Mediated Self-assembly of Amyloid Aggregrates: 

Surface self-assembly provides an alternative pathway for amyloid aggregation that is not available in bulk solutions. We us high-resolution atomic force microscopy and other imaging techniques to study the adhesion and diffusion of peptides on various surfaces and their role in facilitating amyloid fibril formation through self-assembly routs. We also use our exceptional capabilities in high-resolution imaging to study the conformation of amyloids formed under various conditions in aqueous conditions.

Our lab is developing chemical and biophysical tools to study and manipulate complex biological systems. Projects span many areas of synthetic organic, inorganic, and biophysical chemistry; molecular, cell, and developmental biology; and bioengineering. We are particularly interested in developing new technologies for biomolecular imaging and the fabrication of functional bio-nanomaterials.

Hyperpolarized 129Xe Biosensors for Early Cancer Detection

Molecular imaging technologies hold great promise for early cancer diagnosis and intervention. Our goal is to develop new reagents that extend the capabilities of magnetic resonance imaging (MRI) for monitoring multiple cancer markers simultaneously in vivo. 129Xe has found increasing use for biological imaging applications, due to its biological compatibility (xenon is an anesthetic at high concentrations), hyperpolarizability (this enhances signals 1,000-fold), and high affinity for organic cages such as cryptophanes. The chemical shift of 129Xe varies by a remarkable 200 ppm, depending on its molecular environment: Thus, a 129Xe atom encapsulated inside a cryptophane is a sensitive reporter of perturbations outside the cage. Based on this principle, our lab is generating new biosensors that will identify biomarkers associated with cancers of the breast, lungs, brain, and pancreas. The long-range goal of this project is to use MRI to detect aberrant proteins that cause cancer in humans, years before the formation of a tumor.

Ferritin Templates for Nanoparticle Synthesis and Assembly

The goal of this project is to use ferritin proteins as templates for synthesizing and assembling inorganic nanoparticles with nanometer precision. Ferritins contain 24 four-helix bundle subunits that self-assemble to create a large central cavity. We have made water-stable, 10-12-nm gold and silver nanoparticles inside ferritin (gray sphere). Particles are fully characterized using facilities at the UPenn Laboratory for Research on the Structure of Matter (LRSM). We are functionalizing the surface of these ferritin-metal nanoparticles for sensing and nano/biomaterials applications. We are also performing computational protein design, in collaboration with the Saven lab, to mutate residues inside the ferritin cavity to enhance their metal-binding properties. Methods for organizing ferritin metal nanoparticles in 2- and 3-dimensions are being developed, in order to build very small conducting circuits. 

Laser-Activated Chemical Biology: Controlling Genes with Light

The goal of this project is to develop methods for turning genes "on" and "off" with light inside neurons and developing zebrafish embryos with high spatial and temporal control. As a first step, we have developed methods for incorporating a photoactive blocking group in the middle of a DNA or RNA oligonucleotide. In one application, we modulated primer extension by DNA polymerase (KF) using UV light. Photoactivation was monitored using a fluorescent reporter. We are now developing methods to control protein translation by the ribosome using similarly caged RNA. Blocking groups mask the messenger RNA start codon, and are designed to prevent translation until photocleavage. We will control complex gradients of proteins involved in cell signaling during zebrafish development and wound healing, using a state-of-the-art UV confocal microscope in the lab.