Department of Chemistry

Smith's research interests encompass three diverse areas: natural product synthesis, bioorganic chemistry and materials science. To date, more than 90 architecturally complex natural products having significant bioregulatory properties have been prepared in his Laboratory. In addition, Smith, in collaboration with Ralph Hirschmann, has achieved the design and synthesis of non-peptide peptidomimetics of neuropeptideic hormone/transmitters and protease enzyme inhibitors and, also with Stephen Benkovic (Penn State), haptens for the production of catalytic antibodies capable of peptide bond formation. At Monell, in collaboration with Peter Jurs (Penn State), he pioneered the use of computerized pattern recognition techniques for the analysis of primate chemical communication. Collaborative programs at the LRSM include the chemistry and physics of novel liquid crystals and the fullerenes. To date Smith research achievements have been reported in more than 500 peer reviewed publications.

The focus of my research lies with protein nucleic acid assemblies that participate in the replication and maintenance of eukaryotic chromosome ends, called telomeres. Telomeres protect chromosome ends from gradual length erosion, prevent end-to-end fusions and recombination, and promote proper chromosome partitioning during meiosis. Telomere length deregulation and telomerase activation are early and perhaps necessary steps in cancer cell evolution. Furthermore, telomerase and telomere dysfunction are thought to contribute to replicative senescence and programmed cell aging. Despite these fundamental roles in maintaining genome integrity and cell fate, surprisingly little is known about the molecular basis of telomere synthesis by telomerase. We are interested in elucidating the mechanism of telomere replication by telomerase and understand how telomere and telomerase binding proteins regulate telomerase activity and protect chromosome ends. The lab primarily uses structural methods coupled with biophysical and biochemical techniques to study the above systems.

Telomerase Function

Telomere replication is mediated by telomerase, an RNA dependent DNA polymerase structurally similar to retroviral reverse transcriptases and viral RNA polymerases. Biochemical studies on telomerase for more than two decades have provided a wealth of information regarding telomerase function and substrate specificity. Despite this information, the biophysical mechanisms underlying telomerase architecture and function are poorly understood. Our goal is to further elucidate the molecular basis of telomere replication by telomerase using structural and biochemical approaches. The information generated here should provide novel insights into the basic mechanisms of telomere replication and length homeostasis. It will further enrich our understanding of the mechanism of DNA replication by polymerases in general. It will provide a framework to design small molecule inhibitors of telomerase that may be of therapeutic value for cancer and other diseases associated with cellular aging.

Telomerase Regulation

In recent years, a number of factors essential for telomerase regulation and telomere maintenance have been identified. The method by which telomerase and associated regulatory factors physically interact and function with each other to maintain appropriate telomere length is poorly understood. Structural and biochemical characterization of these factors, both in isolation and in complex with one another will facilitate our understanding of how the proper function of these factors impacts telomerase function and cell proliferation.

Projects in the Schelter Group involve inert atmosphere/Schlenk line synthesis of inorganic and organometallic complexes. Rigorous characterization of new compounds is achieved through X-ray crystallography, NMR, FTIR, and UV-Visible absorption spectroscopies, electrochemistry and magnetic susceptibility studies. Current projects are focused on the chemistries and electronic structure effects of the lanthanides, uranium and main group elements

Advanced Rare Earths Separations Chemistry

The rare earth elements: La-Lu, Y and Sc are used in critical renewable energy applications including wind turbine generators and hybrid electric vehicle batteries. These modern applications require pure rare earth elements that must be separated from their composite mineral sources. The Peoples Republic of China currently holds ~97% of the international rare earths market comprising nearly all aspects of the (environmentally taxing) supply chain. To develop other sources of rare earths and reduce the environmental impact of their isolation, there is a clear need for new separations chemistry that reduces the cost of industrial-scale rare earths separations. This project seeks to develop a totally new extractant strategy by harnessing the physicochemical distinctiveness of certain high-value rare earths. New designer rare earth extractants will enable selective separations chemistry for these technologically critical elements.

Capturing Heavy-Fermion Type Electron Correlations in Molecular Complexes

The intermetallic heavy-fermion materials, comprising intermediate valence f-elements such as cerium, are characterized by exotic emergent phenomena including unconventional superconductivity. Recent results on these materials suggest a common energy scale for the emergence of the superconducting state, dependent on the local magnetic interaction of f-moments with conduction electrons. Local electron correlations are also believed to underpin the high Tc superconductivity of other families of materials. Parallel studies in molecular chemistry have begun to show inorganic and organometallic complexes are capable of exhibiting the same type of mixed-valency and correlations found in the heavy-fermion materials.

This project will generalize the requirements for emergence of Kondo-like phenomena in magnetically-dilute molecular complexes. New materials will be synthesized from fundamental units of electron correlation to three-dimensional molecular phases.

Exploring the Inverse Trans Influence in the Chemistry of Uranium

Antithetical to the trans influence in transition metal chemistry, which results in a weakening of metal-ligand bonds trans to strongly-bound groups, is the inverse trans influence in the chemistry of the actinides. Semi-core p-orbital mixing with valence d- or f-orbitals gives rise to the influence, however, the presence of both orbital types in the actinide valence shell precludes its simple description. The large thermodynamic stability of the ubiquitous linear, trans-dioxo uranyl cation, UO22+ is one important consequence of this influence.

This project will develop new complexes in varying geometries and coordination environments to systematically study the inverse trans influence in the structural chemistry of uranium. These results will have direct relevance to the bio-remediation of actinide contaminated ground waters, for which the thermodynamic driving force of the influence plays an important role.

Computationally designed protein complex containing a nonbiological cofactor, designed and studied in collaboration with the DeGrado and Therien groups in the Department of Chemistry. On the left is the computationally designed protein scaffold (magenta) and two abiotic porphyrin cofactors (yellow). On the right is a model of the computationally designed sequence and structure.

Our research interests involve theoretical chemistry, particularly as it applies to biopolymers, macromolecules, condensed phases, and disordered systems. We are developing computational methods for understanding and designing molecular sytems having many physical and chemical degrees of freedom. Molecular simulation techniques are used both to study molecular systems in detail and to test and illustrate our theories. 

A current thrust of the group involves developing computational tools for understanding the properties of protein sequences consistent with a chosen three-dimensional structure. The group works closely with experimental groups at Penn and at other universities; some group members are involved in joint theoretical/experimental projects. Recent projects involve the design of soluble and membrane bound proteins, discerning the origins of conservation in naturally occurring proteins, biomolecular simulation, and the design of nonbiological folding molecules.

My research group creates and uses new theoretical and computational approaches to study complex systems in materials science, condensed-matter physics, and physical chemistry.

We look for new phenomena that occur when different components are brought together. For example, we examine molecules adsorbing on metal surfaces, in order to understand the effect of surface composition and structure on preferred adsorption sites, dissociation pathways, and vibrational dynamics. We also study how the compositions of oxide solid solutions lead to Angstrom-scale chemical structure, nanometer scale structural disorder, and long-range ferroelectric and piezoelectric properties. These studies find real-world applications in catalysis, corrosion, SONAR, fuel cells and other important technologies. Whenever possible, we model systems analytically, in order to extract general principles and simple pictures from complex systems. We recently derived general expressions for the vibrational lifetimes of molecules on surfaces, revealing the dependence of lifetime on molecular coverage and arrangement. Our recent exploration of quantum stress fields has helped to link chemical and mechanical effects in materials.

We are constantly developing methods for computing new properties, and for making quantum-mechanical calculations more accurate and more efficient. We tailor computational algorithms to maximize performance on modern computing platforms such as Beowulf clusters. Wherever possible, we also model systems analytically, in order to extract general principles and simple pictures from complex systems. This combination of theoretical and computational tools enables us to identify new phenomena in complex systems, like multicenter bonds between methyl radicals and the rhodium surface. ( See figure below )

Converting the 5d wavefunction of gold to a smoother pseudowavefunction results in a dramatic reduction in the required basis set size for converged calculations.

Protein motion underlies both proper function and disease in biological systems. Many signaling and transport proteins require complex rearrangements for function, and some proteins, such as amyloids, misfold into toxic conformations. Studying these protein motions not only aids our understanding of diverse biological phenomena, it also contributes to an important fundamental problem in biochemistry: understanding how motions propagate from one end of a protein to another. The Petersson laboratory is developing tools to address questions of how dynamic proteins mediate communication and how the cellular environment catalyzes protein misfolding, from detailed in vitro folding studies to modeling protein motion in living cells. These tools include novel chromophores, which we synthesize and incorporate into proteins through unnatural amino acid mutagenesis and synthetic protein ligation.

Our research group is involved in the elaboration of synthetic methods, strategies and architectural concepts, as well as in the understanding of the fundamental principles that govern the rational design and synthesis of complex molecular, macromolecular, and supramolecular nonbiological systems that exhibit biological functions. Biological systems are employed as models to develop the synthetic architectural motifs and to control their self-assembly and self-organization during the creation of ordered systems. Our research strikes a balance among a diversity of interrelated disciplines, such as organic, bioorganic, macromolecular, and supramolecular synthesis and catalysis, seeking to understand, mimic, and extend Nature's solutions to the design of synthetic functional nanosystems. 

Hierarchical folding, supramolecular chirality, nonbiological ionic and electronic channels and nanowires, nanostructured supramolecular membranes, externally regulated drug release mechanisms, enzyme-like catalytic systems, and self-interrupted organic and macromolecular synthesis are examples of new concepts that are under investigation. Central to the capacity of biological molecules to perform critical functions is their ability to form highly organized and stable 3-D structures using a combination of molecular recognition processes. Therefore, the combinatorial libraries of synthetic building blocks required in our strategies consist of combinations of macrocyclic, dendritic, and other primary sequences that are able to fold into well-defined conformations and also contain all the information required to control and self-repair their secondary, tertiary, and quaternary structure at the same level of precision as in biological molecules. To what extent the delicate balance between the structures and functions evolved in Nature during billions of years can be transplanted to synthetic molecules is a fascinating question.

Towards these goals, we also develop new synthetic methods for the formation of carbon-carbon and carbon-heteroatom bonds using metal-catalyzed homo- and cross-coupling, radical, and various ionic and ion-radical reactions. Living and non-statistically self-interrupted polymerization methods are elaborated based on these organic reactions. The design of the internal structure of complex single molecules and the elucidation of the reactivity principles induced by the controlled environment confined within a single molecule or supramolecule are actively pursued. This research involves collaborations with structural and computational chemists and biochemists.

Our research focuses on Materials Chemistry with full participation in both the departments of Chemistry in the School of Arts and Sciences (SAS) and in the Department of Materials Science and Engineering in the School of of Engineering and Applied Sciences (SEAS).

Many collective phenomena in inorganic materials have natural length scales between 1 and 50 nm. Thus size control nanometer sized crystals or "nanocrystals" allows materials properties to be engineered. Nanocrystals display new mesoscopic phenomena found in neither bulk nor molecular systems. For example, the electronic, optical and magnetic properties semiconductors and magnetic nanocrystals strongly depend on crystallite size. Excited by the potential of these nanocrystal materials our mode of operation has been to develop leading synthetic methods and to push the resulting materials toward technology demonstrations. We try to blend the perspective of academic chemistry and materials science with technological perspective that I developed in over a decade of work in industrial research. We hope this mix of influences will help to align opportunities for applications with broader understanding of nanomaterials. Materials chemistry that embraces and harnesses these principles of self-assembly is at the frontier of materials science and become one of its cornerstones within our generation. Key challenges to the advance of this field will be met by advancing synthetic design, improved analytical tools and perhaps through forethought of environmental health and safety issues. Share in efforts to meet these challenges and thus influence the evolution of both materials science and chemistry. 

The central theme of the Molander group's research is the development of new synthetic methods and their application to the synthesis of organic molecules. The group's focus is to expand and improve the Suzuki coupling reaction for organoboron compounds. Robust, air- and water-stable potassium organotrifluoroborates (R-BF3K), are employed to carry out couplings under relatively mild conditions using non-toxic components.

Greener Routes to Standard Reagents

The preparation of aryl- and heteroaryl potassium trifluoroborate and trihydroxyborate salts has been modified to take advantage of atom-economical boron sources, such as bis-boronic acid (BBA) and tetrakis(dimethylamino)diboron, which allow low catalyst loading and relatively mild reaction conditions. Reactive boronic acid species are generated, and subsequent coupling reactions with these substrates allow greener access to biaryl products.

Improving Transformations with More Robust Reagents

Organotrifluoroborates allow installation of functional groups within a molecule in the place of an existing carbon-boron bond. This allows one to prepare or purchase a simple, functionalized organotrifluoroborate and to elaborate the structure, drawing on the reactivity of the boron species. Some of the transformations carried out to date in this way are outlined below, highlighting the ability to install a cyclopropyl, hydroxymethyl, or nitroso functional group using potassium trifluoroborates.

Novel Reagents and Transformations

Some methods have been developed for the synthesis of novel reagents containing alkyltrifluoroborates, namely potassium aminomethyl-, hydroxymethyl-, and a-alkoxyalkyltrifluoroborates. The synthesis of these structures is outlined below with their applications in cross coupling illustrated.

The laboratory uses a broad range of molecular, biochemical and biophysical research tools centered around X-ray crystal structure determination to understand the mechanism of chromatin recognition and assembly and post-translational histone and protein modification in the regulation of gene expression; and kinase signaling pathways. The laboratory is particularly interested in gene regulatory proteins and their upstream signaling kinases that are aberrantly regulated in cancer and age-related metabolic disorders such as type II diabetes and obesity, and the use of high-throughput small molecule screening and structure-based design strategies towards the development of protein-specific small-molecule probes to be used to further interrogate protein function and for development into therapeutic agents.

Chromatin recognition and assembly and histone modification in gene regulation. DNA within the eukaryotic nucleus is compacted into chromatin containing histone proteins and its appropriate regulation orchestrates all DNA-templated reactions such as DNA transcription, replication, repair, mitosis, and apoptosis. Among the many proteins that regulate chromatin, the proteins that recognize DNA, assemble chromatin, called histone chaperones, and that modify the histones through the addition or removal of functional groups such as acetyl, methyl or phosphate play important roles. We are studying the DNA binding proteins p53, FoxO and the Gal4 family; the histone chaperones HIRA, Asf1, Vps75 and their associated factors; and the family of histone acetyltransferase (HAT) and histone deacetylase (HDAC) enzymes. We are particularly interested in how DNA binding proteins navigate the recognition of their cognate DNA targets, how histone chaperones coordinate the assembly of distinct chromatin complexes correlated with different DNA regulatory processes, and how histone modification enzymes link catalysis to their substrate specific activities for their respective biological activities. More recently, we have been studying how the binding of accessory and regulatory protein subunits regulates the various activities of these proteins and in some cases we are developing small molecule protein specific inhibitors.

Enzymes associated with aging and age-related disorders.Sirtuin enzymes are NAD+-dependent histone and protein deactylases and/or ADP-ribotransferases that have been implicated in the regulation of gene expression, cellular aging, adipogenesis, type II diabetes and several neurodegenerative disorders. We have determined the structure of these enzymes in several liganded forms and have developed novel small molecule sirtuin inhibitors. Together with associated biochemical studies, these studies have provided insights into the mode of catalysis and substrate-specific recognition by this protein family and have illuminated new avenues for small molecule effector design. We are currently working towards understanding the factors that distinguish different sirtuin proteins and how the functions of these proteins are modulated by other protein factors. We are also pursuing structure/function studies of other proteins that are implicated in aging and age-related disorders.

Tumor suppressors and oncoproteins. We are carrying out biochemical and structural studies on the tumor suppressor proteins pRb, p53 and p300/CBP, both alone and in complex with their relevant protein targets. We are also interested in the mode of inactivation of these tumor suppressors by the viral oncoproteins E7 and E6 from human papillomavirus (HPV), the etiological agent for cervical cancer, and Adenovirus (Ad) E1A. We are also combining structural studies with small molecule screening to prepare small molecule HPV-E7 and for HPV-E6 inhibitors. Most recently we have begun to exploit structure-based design strategies to develop inhibitors of oncogenic kinases, such as PI3K, BRAF and PAK1 implicated in melanoma and other cancers. Our goal for these studies is to derive functional and structural information that will lead to the design of small molecule compounds that may have therapeutic applications.

Tumor suppressors and viral oncoproteins- We are pursuing biochemical and structural studies on the tumor suppressor proteins p18INK4c, pRb, p53 and p300/CBP, both alone and in complex with their relevant protein targets. The activity of pRb is inhibited by several known DNA viral oncoproteins, including human papillomavirus (HPV) E7, the etiological agent for cervical cancer, and Adenovirus (Ad) E1A. We have most recently characterized the binding properties of pRb to HPV-E7 and Ad-E1a and are now determining their structures both alone and in complex with pRb. Our goal for these studies is to derive functional and structural information that will lead to the design of small molecule compounds that may have clinical applications against cancer.

Protein-DNA recognition- As a model to understand sequence-specific DNA recognition by transcriptional regulatory proteins, we are studying the structure and function of three families of DNA binding proteins, the fungal specific Zn2Cys6 binuclear cluster proteins, the higher eukaryotic Ets proteins and p53. We have determined several structures of these proteins either alone or in complex with their associated DNA targets and are continuing to use these proteins as a model to understand DNA recognition by protein and protein complexes. With regard to p53, we are studying its unique mode of DNA recognition and are developing structure-based strategies for the repair of tumor-derived p53 mutations.