Repository of works by Caltech published authors.
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Elements of research misconduct - Wrublewski, Donna; Leonard, Michelle
What do scientists, educators, librarians, and game designers all have in common. In the fall of 2010, this team
at the University of Florida was awarded a grant from the NSF to support Gaming Against Plagiarism (GAP). The
purpose is to develop a self-directed, interactive, online game to educate STEM graduate students to recognize
and avoid plagiarism, including falsification and fabrication of data. GAP's intellectual merit lies in its goal of
training these students in U.S. institutions to function effectively and ethically as authors within multinational
research teams. This talk will discuss the four phases of the game: preliminary content development, design
and development, usability, and...
Engineering Cytochrome P450 for Cyclopropanation - Wang, Z. Jane
The ability to genetically encode catalysts for non-natural chemical reactions will open new routes
to sustainable production of chemicals. In nature, cytochome P450 catalyzes the oxidation of
organic substrates with oxygen to produce epoxides and alcohols. This transformation proceeds
through an iron-oxene complex (Compound I), which is generated in the presence of NAD(P)H
and molecular oxygen. Inspired by this catalytic cycle, we hypothesized that a similar process
could be used to generate an iron-carbenoid specie from diazo compounds that could enable
olefin cyclopropanation. Toward this end, we have been able to evolve a unique serine-heme
ligated cytochrome “P411” that catalyzes formal carbene transfers from diazoesters to olefins...
Natural Product Synthesis: A Platform for Chemical Discovery - Reisman, Sarah E.
Our laboratory has ongoing research programs targeting the chemical syntheses of several
natural products, including members of the epidithiodiketopiperazines, the ent-kauranoids, and
the acutumine alkaloids. The densely packed arrays of heteroatoms and stereogenic centers that
constitute these polycyclic targets challenge the limits of current synthetic methodology. This
seminar will describe our latest progress in both our methodological and target-directed synthesis
High resolution profiling of sulfur and oxygen speciation in microbial mats: Implications for coupling of hydrogen peroxide with sulfur species - Druschel, Greg K.; Kafantaris, Fotios; Orphan, Victoria J.; Houghton, Jennifer; Fike, David A.
Hydrogen sulfide is produced in microbial mats by sulfate reducing bacteria, and diffuses towards the surface
until it is consumed. Cyanobacteria in these mats are able to produce oxygen photochem., and when
subjected to high UV light intensity, can also produce hydrogen peroxide. Microelectrodes have proven to have
sufficient resoln. to resolve the sulfur and oxygen chem. in these mats, demonstrating the links between
these populations of bacteria in modern mats. In sulfur-dominated cyanobacterial mats in several settings, we
have obsd. both high hydrogen sulfide fluxes and the periodic prodn. of significant amts. of hydrogen peroxide
at times of high UV stress using voltammetric Au-amalgam microelectrodes....
Exploring Co(salen) type complexes for use as CO2 reduction catalysts - Hansen, Michelle C.; Kubiak, Clifford P.; Yang, Jenny Y.
Cobalt salen and salophen complexes and their derivs. have been previously studied in many contexts,
including CO_2 binding and redn. to a limited extent. This project studies CO_2 redn. in depth with a breadth of
salen-type ligands and use of glassy carbon working electrodes instead of the previously studied mercury
electrodes. Trends relating redn. potential as well as activity and selectivity to ligand structure will be presented.
Development of CO2-reducing electrocatalysts utilizing non-precious metals supported by pincer ligand scaffolds - Shaffer, David W.; Yang, Jenny Y.
The electrocatalytic redn. of carbon dioxide to form usable fuels such as formate, methanol, or higher-order
hydrocarbons is an ideal method for alternative energy storage. Compared to heterogenous systems, mol.
catalysts are generally more selective, more easily tuned, and allow for detailed mechanistic studies. However, a
catalyst remains to be found which is highly stable, utilizes an earth-abundant metal, and operates at a low
overpotential with a high rate. Late transition metal complexes supported by pincer ligands have been shown
to promote CO_2 insertion into metal-hydride bonds and catalytic CO_2 hydrogenation. Furthermore, efficient and
selective electrochem. redn. of CO_2 to formate has been achieved with a...
Preparation of rapidly initiating ruthenium based olefin metathesis catalysts - Sullivan, Alexandra H.; Keitz, Benjamin K.; Grubbs, Robert H.
Z-selective olefin metathesis ruthenium catalysts are highly sought after, due to their wide applications in
both pharmaceuticals and materials science. A crucial step towards the prepn. of rapidly initiating, Z-selective,
olefin metathesis catalysts was found to be the addn. of sodium pivalate to phosphonium
alkyidene catalyst 1, resulting in the formation of the C-H activated complex 2 after two days of heating. Prepn.
of 2, a close analog to the target catalyst 4, promises that future synthesis of 4 should be facile.
Thermodynamics of guest-host interaction in TMAAI-ordered porous silica system - Wu, Di; Hwang, Sonjong; Zones, Stacey I.; Navrotsky, Alexandra
Mol. level guest-host interactions in inorg. frameworks play crucial roles in many scientific/engineering
applications, ranging from drug delivery and geol. mineral pptn. in the presence of org. matter. In order to seek
insights into detailed chem. of guest-host interactions, we investigated the phase evolution and energetics of
confinement of a rigid org. guest TMAAI (N,N,N-trimethyl-1-adamantammonium iodide) in inorg. porous
silica with various pore sizes (0.8 nm to 20.0 nm). HF calorimetry was employed to measure the enthalpies of
guest-host interaction. The values vary from -56 to -175 kJ/mol of TMAAI. Phase evolution inside the
nanopores was investigated by X-ray diffraction, IR, TG-DSC and solid-state NMR. The...
Symmetry breaking charge transfer processes of zinc dipyrrin complexes - Trinh, Cong; Kirlikovali, Kent; Das, Saptaparna; Bradforth, Stephen E.; Ener, Maraia E.; Gray, Harry B.; Djurovich, Peter I.; Thompson, Mark E.
Photoinduced charge transfer (CT) via symmetry breaking (SB) processes plays a crucial role in
photosynthetic reaction center of biol. systems. In such systems, which contain two or more identical and sym.
chromophores, CT process from one to another chromophore occurs upon photo-excitation, thus breaking the
symmetry. It is of great interest to apply SBCT processes in org. photovoltaics (OPV) and related systems.
For application to OPVs, it is desirable for compds. that undergo SB processes to have absorption in the visible
spectrum. The most well-documented compds. for SB phenomenon, such as bianthryl derivs., do not absorb
visible light. Herein we present study on Zinc Dipyrrin complexes,...
New electrocatalysis for dioxygen reduction and water oxidation - Mayer, James; Barnett, Shoshanna; Blacquiere, Johanna; Carver, Colin; Matson, Benjamin; Pegis, Michael; Rodriguez, Carlos; Wasylenko, Derek; Yang, Jenny Y.
Electrocatalysis is key to the efficient interconversion of elec. and chem. energies, an important component of future energy
technologies. We have developed new electrocatalysts for the oxygen redn. reaction (ORR), incorporating proton relays in the
second coordination sphere. Iron-tetrakis(2-carboxyphenyl)porphyrin chloride is an active, stable, and unusually selective ORR
electrocatalyst in acidic acetonitrile, reducing O_2 almost entirely to H_2O rather than H_2O_2. The related tetrakis(2-pyridyl)
porphyrin complex is also a relatively selective ORR electrocatalyst in acidic water, despite the long distance between the
pyridyl nitrogen atoms and the iron center. The role of the proton relays, and now complexes with flexible tripodal ligands and
pendent tertiary amines,...
Biomimetic camouflage inspired by cephalopods - Phan, Long; Walkup, Ward G.; Gorodetsky, Alon A.
Cephalopods are known as the chameleons of the sea - they can alter their skin's coloration, pattern, texture,
and reflectivity to blend into the surrounding environment. Despite much research effort, there are few known
strategies (natural or artificial) for emulating the unique dynamic reflectivity and coloration of cephalopods.
We have developed an approach to the fabrication of stimuli-responsive cephalopod-inspired thin films with
emergent optical properties. We have furthermore enhanced the properties of such films through a synergistic
combination of bioconjugate chem., bottom up self-assembly, and top down nanofabrication. Our findings hold
significant implications for the development of reconfigurable biomimetic camouflage coatings.
Highly sensitive and rapid detection of carbon nanotube-based biosensors using immune binding reaction - Kim, Ji Won; Kim, Yeonsuk; Woo, Soohyun; Chung, David S.; Ahn, Curie; Chung, Sung-Jae
The field effect transistor (FET) based on a network of single-walled carbon nanotubes (SWCNTs) that can
perform sensitive and selective real-time monitoring of target analytes are tremendously valuable for various
sensing applications. Here carbon nanotube-field effect transistors (CNT-FETs) were functionalized with
antibody-binding fragments as a receptor, and the binding event of specific target antigen onto the fragments
was detected by monitoring the gating effect caused by the charges of the target antigen. We were able to
lower the detection limit to a protein concn. of 100 ng/mL, without cutting antibody or labeling the target
proteins. Our results show that there is good correlation between the two...
DNA-mediated oxidation of transcription factor p53: Dependence upon DNA sequence and cysteine residues - Schaefer, Kathryn N.; Geil, Wendy M.; Barton, Jacqueline K.
Transcription factor p53 controls many cellular processes in response to cellular stress. As a redox-active
protein, p53 binds DNA in its reduced state and dissocs. upon oxidn. Transcription factor p53 can be
directly oxidized via DNA-mediated charge transport (DNA-CT). The ability of certain consensus sites to be
responsive to DNA-CT induced oxidn. of p53 correlates to the oxidn. potential of the consensus sequence
nucleobases. Greater p53 oxidative dissocn. is obsd. from consensus sequences contg. purine sequences with
low oxidn. potential; a guanine triplet is far more favorable to conduct DNA-CT to p53 than an adenine triplet.
This characteristic property was studied in vitro by EMSA and...
Sugar rearrangements mediated by Lewis acidic molecular sieves in liquid media - Gounder, Rajamani; Davis, Mark E.
Monosaccharide and disaccharide isomerization and epimerization reactions are catalyzed by Lewis acidic sites
(M = Sn, Ti, Zr) isolated in silica-based heterogeneous solids, with selectivity and stereochem. specificity that are
inaccessible to sugar rearrangements involving enolate intermediates catalyzed by bases. Such selectivity and
specificity reflect the ability of electrophilic Lewis acid centers to coordinate with oxygenated sugar functional
groups and to subsequently mediate intramol. rearrangements of specific H and C atoms, the mechanistic
details of which are probed using D and ^(13)C isotopically-labeled reactants. Here, we discuss recent progress in
understanding the influence of: (i) heteroatom and solvent identity on active site structures and reaction
Anything BUT overlooked: Librarians teaching scientific communication skills at the University of Florida - Wrublewski, Donna T.; Buhler, Amy; Gonzalez, Sara; Johnson, Margeaux
Over the past 7 years, faculty science librarians at the University of Florida have developed and taught a
three-credit Honors program course entitled "Discovering Research and Communicating Science". The goal of
this course is to prep. students (primarily freshmen) to begin undergraduate research, and thus teaches the
ancillary skills often overlooked in advanced electives: searching and evaluating scientific literature, prepg. a
scientific poster, and writing scientific abstrs. and papers. Guest researchers visit throughout the semester to
expose students to undergraduate research opportunities and talk about success in research and other
professional opportunities. This talk will discuss the motivation, organization, and ongoing development of the
course over its...
Phototropic growth control of nanoscale pattern formation in photoelectrodeposited Se-Te films - Sadtler, Bryce; Burgos, Stanley P.; Batara, Nicolas A.; Beardslee, Joseph A.; Atwater, Harry A.; Lewis, Nathan S.
Photoresponsive materials that adapt their growth rates dynamically to the local incident electromagnetic field
would provide a remarkable route to the synthesis of complex three-dimensional mesoscale structures via
feedback between illumination and the morphol. that develops in response to the optical excitation. We report
the spontaneous development of ordered, complex nanoscale lamellar patterns in electrodeposited seleniumtellurium
(Se-Te) alloy films that are grown under uniform illumination on unpatterned substrates in an isotropic
electrolyte soln. These inorg. nanostructures exhibited phototropic growth in which lamellar stripes grew
towards the incident light source, adopted an orientation parallel to the light polarization direction, and showed
an increased growth rate with increasing light...
Plasmoelectric potentials in colloidal Ag and Au nanoparticles - Sheldon, Matthew; Brown, Ana; Atwater, Harry
The resonant plasmonic properties of metallic nanostructures depend strongly on charge carrier d. While
researchers have reported shifts of the resonant absorption frequency of plasmonic nanostructures due to
electrostatically induced changes of charge d., the converse -the dependence of charge d. and electrostatic
potential on optical absorption- has been largely overlooked. Here, we report a theor. framework and provide
exptl. evidence for a 'plasmoelec. effect', a newly described mechanism for generating electrochem. potentials
in plasmonic nanostructures via narrowband absorption. A simple thermodn. model shows that, unlike the more
familiar thermoelec. or photovoltaic effects, the magnitude and sign of the plasmoelec. potential depends on the
frequency difference between...
First principles-based methods for chemical mechanisms in advanced batteries and energy storage materials - Goddard, William A.; Nielsen, Robert J.; Merinov, Boris V.
Advances in theor. chem. and supercomputers are making it practical to consider first principles (de novo)
predictions of new materials for batteries and energy storage. Our approach is to start with accurate
quantum mechanics on which we build a hierarchy of models each based on the results of more fundamental
methods but coarsened to make practical the consideration of much larger length and time scales. The
connection this multi-paradigm multi-scale hierarchy back to quantum mechanics enables the application of first
principles to the coarse levels essential for practical simulations of complex systems. We will highlight some
recent advances in methodol. such as: PBE-lg and XYGJ-OS quantum...
First principle study on the mechanism of O2 activation by Pt(II) monomethyl complex - Liu, Wei-Guang; Sberegaeva, Anna; Nielsen, Robert; Goddard, William A.; Vedernikov, Andrei N.
The Shilov system is the first successful case to activate methane C-H bonds and convert it to Me derivs. In this system, the
kinetics of the oxidn. of Pt(II) is important because the oxidn. competes with the protonolysis of Pt(II)-Me complex, the
reverse reaction of C-H activation. Several oxidants, such as Pt(IV), chlorine, hydroperoxide and Cu(I) are effective. However,
the direct utilization of dioxygen as stoichiometric oxidant without electron-transfer reagent is not achieved yet. Vedernikov et al
demonstrated that Pt(II) monomethyl complex with facially chelating ligands such as di(2-pyridine)methanesulfonate ligand
(dpms) contg. the semilabile sulfonate donor facilitates the kinetics of oxygen activation, making it an...