Chemical Physics and Physical Chemistry

Mark Johnson, Yale; Physical Seminar - CANCELED

Thu, 2012-11-01 09:00 - 10:30

Location: Carolyn Hoff Lynch Room

Adam Wasserman, Purdue; Physical Seminar

Thu, 2012-10-11 09:00 - 10:30

Location: Carolyn Hoff Lynch Room

Connie Roth, Emory; Physical Seminar

Thu, 2012-10-04 09:00 - 10:30

Location: Carolyn Hoff Lynch Room

Michael R. Topp

Photo: 
First Name: 
Michael R.
Last Name: 
Topp
Official Title: 
Professor of Chemistry

Physical Chemistry 

Contact Information
Office Location: 
249 N, Lab: 240 N
Email: 
mrt@sas.upenn.edu
Phone: 
(215) 898-4859
Admin Support: 
Education: 
  • B.Sc. Sheffield University (1966) - Haworth Medal winner
  • Ph.D. University College London and the Royal Institution of Great Britain (1969)
  • Member of Technical Staff, Bell Labs, (1969-71)
  • IBM Research Fellow, Pembroke College, Oxford (1971-73)
Research Interests: 

Conformational Relaxation in Isolated Molecular Clusters

When molecules become electronically excited, the rearrangement of electronic charge can precipitate many types of relaxation processes. To probe details of such events, one can employ isolated molecular clusters consisting of only a few hydrogen-bonded molecules. One particularly interesting case is the cluster involving a Coumarin 151 molecule bonded to a water dimer. Two different structures have been identified in the ground state, as shown below.

 

 

Recent experiments have shown that the species shown on the left here is unstable in the excited state, and relaxes to that shown on the right on a picosecond or nanosecond time scale depending on the available energy. This corresponds to movement of the water dimer by ~10Å from one side of the molecule to another, following and yet the activation energy is only 60 cm-1. Such conformational changes have been studied by a combination of fluorescence and infrared double resonance techniques in conjunction with ionization and mass resolution.

 

Hydrogen-Bonded Molecular Dimers

 

Hydrogen-bonded dimers present important opportunities to study short-range intermolecular interactions, including modification of the electronic structure, and corelated proton or hydrogen atom transfer. Molecules such as the dimer of 4-Amino-N-methylphthalimide, shown here, reveal dramatic changes in their infrared spectra between the ground and excited states. The simple ground-state ground-state infrared spectrum reflects the high symmetry of the ground state. On the other hand, the much more complex excited-state spectrum shows evidence for a loss of symmetry resulting from changes in the acid-base properties of NH2 and >C=O groups, which may result in proton transfer across the intermolecular hydrogen bonds. These types of strongly bonded dimers are different from many other dimer systems studied so far, because both their electronic and vibrational spectra are highly structured, despite the large increase in binding energy upon electronic excitation. Femtosecond-domain experiments are planned, to follow in real time the changes in vibrational spectra, which will provide further insights into the reasons for their complexity in the excited state.

 

 

Ultrafast Electronic Relaxation of Hydrogen-Bonded Molecules Studied by Femtosecond Pump-Probe Spectroscopy

 

Femtosecond pump-probe experiments allow us to observe the time evolution of the first events following pulsed laser excitation, including motions in the first coordination shell of a hydrogen-bonded molecule in fluid solution. New pump-probe experiments involving the detection of ultrashort-lived fluorescence have explored spectroscopic changes of aminophthalimide molecules in hydrogen-bonding solvents on a time scale more than 10 times faster than existing data for fluorescence Stokes shifts. Both fluorescence upconversion and pump-probe methods are being used to investigate ultrafast energy transfer processes in complex molecules, in collaboration with the Regional Laser and Biomedical Technology Laboratories at Penn.

Joseph Subotnik

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First Name: 
Joseph
Last Name: 
Subotnik
Official Title: 
Edmund J. and Louise W. Kahn Endowed Term Professor of Chemistry

Physical and Theoretical Chemistry

Contact Information
Office Location: 
268 Cret wing
Email: 
subotnik@sas.upenn.edu
Phone: 
215-746-7078
Admin Support: 
Education: 

B.A. Harvard University, 2000

Physics and Math (summa cum laude)


Ph.D.  UC Berkeley, 2006  Biophysics

 

NSF International Research Fellow (2007 -2009), Tel-Aviv

Postdoctoral Fellow, Northwestern University (2009-2010)

Research Interests: 

Research in the Subotnik group focuses on the intersection of static quantum chemistry methods (especially for excited states) with nonadiabatic dynamics methods (specifically surface hopping). The focus is quantifying electron transfer, energy transfer, and electronic relaxation. Applications are to almost all photo-induced processes!

Jeffery G. Saven

Photo: 
First Name: 
Jeffery G.
Last Name: 
Saven
Official Title: 
Professor of Chemistry

Biological and Theoretical Physical Chemistry

Contact Information
Office Location: 
266 Cret, Lab 261 Cret
Email: 
saven@sas.upenn.edu
Phone: 
215-573-6062
Fax: 
215-573-2112
Admin Support: 
Education: 
  • BA, New College of Florida
  • PhD, Columbia University & University of Wisconsin
  • NSF Postdoctoral Fellow in Chemistry, University of Illinois, Urbana-Champaign, 1993-1995. Postdoctoral Research Associate, University of Illinois, Urbana-Champaign, 1995-1997
Research Interests: 

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.

Andrew M. Rappe

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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.

Andrea J. Liu

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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
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: 

M. I. Lester and S. J. Klippenstein, “Unimolecular decay of Criegee intermediates to OH radical products: Prompt and thermal decay processes”, Acc. Chem. Res. 51, 978-985 (2018).

 

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). 

Feng Gai

Photo: 
First Name: 
Feng
Last Name: 
Gai
Official Title: 
Edmund J. and Louise W. Kahn Endowed Term Professor of Chemistry
Contact Information
Office Location: 
254N
Email: 
gai@sas.upenn.edu
Phone: 
(215) 573-6256
Education: 

 

  • B.S. Peking University (1983)
  • M.S. Peking University (1986)
  • Ph.D. Iowa State University (1994)
  • Lecturer, Tsinghua University (1986-89)
  • Postdoctoral Research Associate, Harvard University (1994-97)
  • Director’s Postdoctoral Fellow, Los Alamos National Laboratory (1997-99)
Research Interests: 

 

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. 

Selected Publications: 

 

S. Mukherjee, P. Chowdhury and F. Gai, “Infrared study of the effect of hydration on the amide I band and aggregation properties of helical peptides,” J. Phys. Chem. B 2007, 111, 4596.

 

Y. Xu, P. Purkayastha, and F. Gai, “Nanosecond folding dynamics of a three-stranded beta-sheet,” J. Am. Chem. Soc. 2006, 128, 15836.

 

M. R. Bunagan, L. Cristian, W. F. DeGrado, and F. Gai, “Truncation of a cross-linked GCN4-p1 coiled-coil leads to ultrafast folding,” Biochemistry 2006, 45, 10981.

 

D. Du, and F. Gai, “Understanding the folding mechanism of alpha-helical hairpin. Biochemistry 2006, 45, 13131.

 

M. J. Tucker, J. Tang, and F. Gai, “Probing the kinetics of membrane-mediated helix folding,” J. Phys. Chem. B 2006, 110, 8105.

 

M. J. Tucker, R. Oyola, and F. Gai, “Conformational distribution of a 14-residue peptide in solution: a FRET study,” J. Phys. Chem. B 2005, 109, 4788.

 

D. G. Du, Y. J. Zhu, C-Y. Huang, and F. Gai, “Understanding the key factors that control the rate of -hairpin folding,” Proc. Natl. Acad. Sci. USA 2004, 101, 15915.

 

Y. J. Zhu, D. O. V. Alonso, K. Maki, C-Y Huang, S. J. Lahr, V. Daggett, H. Roder, W. F. DeGrado, and F. Gai, “Ultrafast folding of alpha3D, a de novo designed three-helix bundle protein,” Proc. Natl. Acad. Sci. USA 2003, 100, 15486.

 

Z. Getahun, C-Y. Huang, T. Wang, B. D. León, W. F. DeGrado, and F. Gai, “Using nitrile-derivatized amino acids as infrared probes of local environment,” J. Am. Chem. Soc. 2003, 125, 405.

 

C.-Y. Huang, Z. Getahun, Y. J. Zhu, J. W. Klemke, W. F. DeGrado, and F. Gai, “Helix formation via conformation diffusion search,” Proc. Natl. Acad. Sci. USA 2002, 99, 2788.

Department of Chemistry

231 S. 34 Street, Philadelphia, PA 19104-6323

215.898.8317 voice | 215.573.2112 fax | web@chem.upenn.edu

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