Andrew M. Rappe

Photo: 
First Name: 
Andrew M.
Last Name: 
Rappe
Official Title: 
Blanchard Professor of Chemistry

Physical and Theoretical Chemistry

Additional Titles: 
Professor of Materials Science and Engineering
Co-Director, Pennergy
Contact Information
Office Location: 
264 Cret, Lab: 263, 265, 267, 268 Cret
Email: 
rappe@sas.upenn.edu
Phone: 
(215) 898-8313
Fax: 
(215) 573-2112
Admin Support: 
Education: 
  • B.A. Chemistry and Physics, Summa Cum Laude, Harvard University (1986)
  • ONR Graduate Fellow, Massachusetts Institute of Technology (1986-1989)
  • JSEP Graduate Fellow, Massachusetts Institute of Technology (1990-1992)
  • Ph. D. Physics and Chemistry, Massachusetts Institute of Technology (1992)
  • IBM Postdoctoral Fellow, University of California at Berkeley (1992-1994)
  • Assistant Professor of Chemistry, University of Pennsylvania (1994-2000)
  • Associate Professor of Chemistry, University of Pennsylvania (2000-2006)
  • Professor of Chemistry, University of Pennsylvania (2006-present)
  • NSF CAREER Award (1997-2001)
  • Alfred P. Sloan Foundation Fellow (1998-2000)
  • Dreyfus Teacher-Scholar Award (1999-2004)
Research Interests: 

 

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.

E. James Petersson

Photo: 
First Name: 
E. James
Last Name: 
Petersson
Official Title: 
Associate Professor of Chemistry
Contact Information
Office Location: 
350 N
Email: 
ejpetersson@sas.upenn.edu
Phone: 
215-746-2221
Admin Support: 
Education: 

• A.B. Dartmouth College (1998)

• Ph.D. California Institute of Technology (2005)

• NIH Postdoctoral Fellow, Yale University (2005-2008)

• Searle Scholar (2010)

• Sloan Research Fellow (2012)

• NSF CAREER Award (2012)

• Award for Early Excellence in Physical Organic Chemistry      (2013)

Research Interests: 

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.

Selected Publications: 

Inteins as Traceless Purification Tags for Unnatural Amino Acid Proteins

Batjargal, S.; Walters, C. R.; Petersson, E. J.

J. Am. Chem. Soc. 2015, 137, 1734-1737.

 

Specific Modulation of Protein Activity Through a Bioorthogonal Reaction

Warner, J. B.; Muthusamy, A. K.; Petersson, E. J.

ChemBioChem 2014, 24, 2508-2514.

 

Thioamide-Based Fluorescent Protease Sensors

Goldberg, J. M.; Chen, X. S.; Meinhardt, N.; Greenbaum, D. C.; Petersson, E. J. 

J. Am. Chem. Soc. 2014, 136, 2086-2093.

 

Efficient Synthesis and In Vivo Incorporation of Acridonylalanine, a Fluorescent Amino Acid for Lifetime and Förster Resonance Energy Transfer/Luminescence Resonance Energy Transfer Studies 

Speight, L. C.; Muthusamy, A. K.; Goldberg, J. M.; Warner, J. B.; Wissner, R. F.; Willi, T.; Woodman, B.; Mehl, R. A.; Petersson,     E. J. 

J. Am. Chem. Soc. 2013, 135, 18806-18814.

 

Expressed Protein Ligation at Methionine: N-terminal Attachment of Homocysteine, Ligation, and Masking

Tanaka, T.; Wagner, A. M.; Warner, J. B.; Wang, Y. J.; Petersson, E. J. 

Angew. Chem. Int. Ed. 2013, 52, 6210-6213.

 

Labeling Proteins with Fluorophore/Thioamide FRET Pairs by Combining Unnatural Amino Acid Mutagenesis and Native Chemical Ligation

Wissner, R. F.; Batjargal, S.; Fadzen, C. M.; Petersson, E. J. 

J. Am. Chem. Soc. 2013, 135, 6529-6540.

 

Thioamide Quenching of Fluorescent Probes Through Photoinduced Electron Transfer: Mechanistic Studies and Applications

Goldberg, J. M.; Batjargal, S.; Chen, B. S.; Petersson, E. J. 

J. Am. Chem. Soc. 2013, 135, 18651-18658.

Virgil Percec

Photo: 
First Name: 
Virgil
Last Name: 
Percec
Official Title: 
P. Roy Vagelos Professor of Chemistry

Organic, Supramolecular and Macromolecular Chemistry

Contact Information
Office Location: 
4003 IAST, Lab: 4160 IAST
Email: 
percec@sas.upenn.edu
Phone: 
(215) 573-5527
Fax: 
(215) 573-7888
Admin Support: 
Education: 
  • B.S. 1969 Department of Organic and Macromolecular Chemistry, Polytechnic Institute of Jassy, Romania
  • Ph.D. 1976 Institute of Macromolecular Chemistry, Jassy, Romania
  • Postdoctoral July-August 1981 Hermann Staudinger Hause, University of Freiburg, Germany
  • Postdoctoral September 1981 - March 1982 Institute of Polymer Science, University of Akron, U.S.A.
Research Interests: 

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.

Christopher B. Murray

Photo: 
First Name: 
Christopher B.
Last Name: 
Murray
Official Title: 
Richard Perry University Professor of Chemistry and Materials Science and Engineering

Nanoscale and Inorganic Materials Chemistry

Contact Information
Office Location: 
347N (Chem 73) & 322 (LRSM) MSE
Email: 
cbmurray@sas.upenn.edu
Phone: 
(215) 898-0588
Admin Support: 
Education: 
  • 1985-1988 B.Sc. Honors Chemistry, Summa cum Laude, St. Mary's University, Halifax N.S., Canada
  • 1989 Rotary International Fellow, University of Auckland, New Zealand
  • 1990-1995 Ph.D. Physical Chemistry, Massachusetts Institute of Technology, Cambridge, MA
  • 1995- 2000 Member of research staff, IBM Corp., T. J. Watson Research Center. Established a program in the preparation and characterization of nanomaterials and devices.
  • 2000 - 2006 Manager of the Nanoscale materials and devices department leading development of nanomaterials and exploring self-organizing phenomena for applications in IT.
  • 2007- University of Pennsylvania: Richard Perry University Professor of Chemistry and Materials Science and Engineering.
Research Interests: 

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. 

Other Affiliations: 

Gary A. Molander

Photo: 
First Name: 
Gary A.
Last Name: 
Molander
Official Title: 
Hirschmann-Makineni Professor of Chemistry and Department Chair
Contact Information
Office Location: 
4001 IAST
Email: 
gmolandr@sas.upenn.edu
Phone: 
(215) 573-8604
Fax: 
(215) 573-7165
Twitter: 
@molandergroup
Admin Support: 
Research Interests: 

 

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.

Ronen Marmorstein

Photo: 
First Name: 
Ronen
Last Name: 
Marmorstein
Official Title: 
Professor, Department of Biochemistry and Biophysics Investigator, Abramson Family Cancer Research Institute

Biological Chemistry

Additional Titles: 
Wistar Institute Professor of Chemistry
Contact Information
Office Location: 
BRB II/III, Room 454
Email: 
marmor@mail.med.upenn.edu
Phone: 
215-898-7740
Fax: 
215-746-5511
Education: 
  • B.S. University of California at Davis (1984)
  • M.S. University of Chicago (1989)
  • Ph.D. University of Chicago (1989)
  • Postdoctoral Fellow, Harvard University (1989-1994)
Research Interests: 

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.

Other Affiliations: 

Sally Mallory

Photo: 
First Name: 
Sally
Last Name: 
Mallory
Official Title: 
Senior Lecturer

Organic Chemistry

Additional Titles: 
Director, Organic Chemistry Laboratory
Research Associate, Bryn Mawr College
Contact Information
Office Location: 
443 N
Email: 
smallory@sas.upenn.edu
Phone: 
(215) 898-5429
Admin Support: 
Education: 
  • Bryn Mawr College, A.B. (1959); M.A. (1960); Ph. D. (1963)
  • Research Associate (1963-77)
  • Yale University, Lecturer (1977-80)
  • Philadelphia Organic Chemists' Club, Chairman-elect (1975-76) and Chairman (1976-77)
  • Bryn Mawr College, Visiting Research Fellow (1986- )
  • University of Pennsylvania, Provost's Award for Distinguished Teaching (1989)
  • University of Pennsylvania, Department of Chemistry, Undergraduate Advisory Board, Excellence in Teaching Award (1996-97)
  • Inter-American Photochemical Society, elected Fellow of the Society (2005)
  • University of Pennsylvania, School of Arts and Sciences, Dean's Award for Distinguished Teaching by Affiliated Faculty (2007)
  • Award for Excellence in Undergraduate Teaching in Chemical Science, American Chemical Society, Philadelphia Section (2010)
Research Interests: 

Mechanistic and synthetic organic photochemistry; NMR studies of through-space spin-spin coupling, magnetic anisotropy, substituent effects, and structural effects on spin relaxation rates.

Ponzy Lu

Photo: 
First Name: 
Ponzy
Last Name: 
Lu
Official Title: 
Professor of Chemistry
Contact Information
Office Location: 
352N, Lab: 312N
Email: 
ponzy@sas.upenn.edu
Phone: 
215-898-4863
Research Interests: 

Since the lac operon has been the paradigm for gene regulatory systems, our efforts have been focused on obtaining structural information on the repressor operator complex. To this end, a series of DNA binding domain fragments and variants have been cloned and expressed for solution multinuclear multidimensional NMR analysis, both as proteins and protein DNA complexes. In collaboration with M. Lewis of the Department of Biochemistry and Biophysics, the three-dimensional structures of (1) lac repressor alone, (2) lac repressor with inducer, and (3) complexes of intact tetrametic lac repressor, and operator DNA have been solved. 

An interesting result from our group is the solution structure of A-tract DNA. This variation from the average B form has been studied for two decades. Several X-ray structures by other groups have been not consistent with the body of solution properties of this family of DNA sequences. Our NMR solution structure shows that the bend In the helix axis is actually 90 degrees away from the bend plane in the crystal structures. The variation of nucleic acid structures as a function of sequence and solvent conditions is an important consideration. In related experiments, we have exploited the use of fluorescence depolarization of bound ethidium bromide to investigate hydrodynamic size and shape of RNA structures, e.g., tetraloops and ribozymes. These issues have also become important as we are finding variations in mRNA accessibility to antisense probes.

In collaboration with the late Alan Gewirtz we demonstrated that anti-sense oligonucleotides actually find their complementary sequences in the cell.

Andrea J. Liu

Photo: 
First Name: 
Andrea J.
Last Name: 
Liu
Official Title: 
Hepburn Professor of Physics
Additional Titles: 
Professor of Chemistry
Contact Information
Office Location: 
2N30, David Rittenhouse Laboratory
Email: 
ajliu@physics.upenn.edu
Phone: 
(215) 573-7374
Fax: 
(215) 898-2010
Education: 

Ph.D., Cornell University (1989)
B.A., University of California, Berkeley (1984)

Research Interests: 

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.

Marsha I. Lester

Photo: 
First Name: 
Marsha I.
Last Name: 
Lester
Official Title: 
Edmund J. Kahn Distinguished Professor

Physical Chemistry, Molecular Structure and Dynamics

Additional Titles: 
Editor, The Journal of Chemical Physics
Contact Information
Office Location: 
262 T, Lab: 236- 39N
Email: 
milester@sas.upenn.edu
Phone: 
(215) 898-4640
Fax: 
(215) 573-2112
Admin Support: 
Education: 
  • B.A. Douglass College, Rutgers University (1976)
  • Ph.D. Columbia University (1981)
  • NSF Postdoctoral Fellow, AT&T Bell Laboratories (1981-82)
Honors and Awards
  • Editor-in-Chief, The Journal of Chemical Physics (2009-present)
  • Member, National Academy of Sciences (2016)
  • Francis P. Garvan-John M. Olin Medal, American Chemical Society (2014)
  • Fellow, American Academy of Arts and Sciences (2008)
  • Bourke Lectureship, Faraday Division of the Royal Society of Chemistry (2005)
  • Visiting Miller Research Professor, Berkeley (2003)
  • Guggenheim Fellowship (2002-03)
  • Fellow of the American Physical Society (1993), the American Association for the Advancement of Science (1997), and the American Chemical Society (2010)
  • Alfred P. Sloan Research Fellow (1987)
  • Camille and Henry Dreyfus Young Faculty Award (1982), Teacher-Scholar Award (1986)
Research Interests: 

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.

Selected Publications: 

Y. Fang, F. Liu, V. P. Barber, S. J. Klippenstein, A. B. McCoy, and M. I. Lester, “Communication: Real time observation of unimolecular decay of Criegee intermediates to OH radical products”, J. Chem. Phys. 144, 061101 (2016).

 

N. M. Kidwell, H. Li, X. Wang, J. M. Bowman, and M. I. Lester, “Unimolecular dissociation dynamics of vibrationally activated CH3CHOO Criegee intermediates to OH radical products”, Nat. Chem., 8, 509-14 (2016).


H. Li, Y. Fang, N. M. Kidwell, J. M. Beames, and M. I. Lester, “UV photodissociation dynamics of the CH3CHOO Criegee intermediate: Action spectroscopy and velocity map imaging of O-atom products”, J. Phys. Chem. A. 119, 8328-37 (2015).

 

F. Liu, J. M. Beames, A. S. Petit, A. B. McCoy, and M. I. Lester, “Infrared-driven unimolecular reaction of CH3CHOO Criegee intermediates to OH radical products”, Science 345, 1596-1598 (2014).

 

J. H. Lehman and M. I. Lester, “Dynamical outcomes of quenching: Reflections on a conical intersection”, Ann. Rev. Phys. Chem. 65, 537-55 (2014).


J. H. Lehman, H. Li, J. M. Beames and M. I. Lester, “Communication: Ultraviolet photodissociation dynamics of the simplest Criegee intermediate CH2OO”, J. Chem. Phys. 139, 141103 (2013).

 

J. M. Beames, F. Liu, L. Lu, and M. I. Lester, “Ultraviolet spectrum and photochemistry of the simplest Criegee intermediate CH2OO”, J. Am. Chem. Soc. (Communication) 134, 20045-48 (2012).

 

J. H. Lehman, M. I. Lester, and D. H. Yarkony, “Reactive quenching of OH A2Σ+ by O2 and CO: Experimental and nonadiabatic theoretical studies of H- and O-atom product channels”, J. Chem. Phys. 137, 094312 (2012).

 

J. M. Beames, F. Liu, M. I. Lester, and C. Murray, “Communication: A new spectroscopic window on hydroxyl radicals using UV+VUV resonant ionization”, J. Chem. Phys. 134, 241102 (2011). 

 

J. M. Beames, M. I. Lester, C. Murray, M. E. Varner, and J. F. Stanton, “Analysis of the HOOO Torsional Potential”, J. Chem. Phys. 134, 044304 (2011). 

 

C. Murray, E. L. Derro, T. D. Sechler, and M. I. Lester, “Weakly bound molecules in the atmosphere – a case study of HOOO”, Acc. Chem. Res. 42, 419-427 (2009). 

 

E. L. Derro, T. D. Sechler, C. Murray, and M. I. Lester, “Observation of combination bands of the HOOO and DOOO radicals using infrared action spectroscopy”, J. Chem. Phys. 128, 244313 (2008). 

 

B. A. O’Donnell, E. X. J. Li, M. I. Lester, and J. S. Francisco, “Spectroscopic identification and stability of the intermediate in the OH + HONO2 reaction”, Proc. Natl. Acad. Sci. 105, 12678-12683 (2008). 

 

I. M. Konen, I. B. Pollack, E. X. J. Li, M. I. Lester, M. E. Varner, and J. F. Stanton, "Infrared overtone spectroscopy and unimolecular decay dynamics of peroxynitrous acid", J. Chem. Phys. 122, 094320 (2005). 

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