1102 Natural Sciences 2
University of California, Irvine,
California, 92697-2025 ::
phone (949) 824-4097 ::
fax (949) 824-8571
Research Highlights
 | The Promise of Phage Display: Customized Affinity and Specificity In this months issue of Analytical Chemistry, Greg Weiss and Reg Penner report the creation of biosensors that exploit virus particles - prepared using the methods of phage display - to detect particular target molecules in solution.[ link ] |
 | Seeing is Believing: Single Palladium Complexes Wouldn’t it be incredible to image catalytic reactions at the single molecule level? In order to examine the steps of a mechanism, one would simply look. In a recent issue of Organometallics, Prof. Suzanne A. Blum and coworkers report the single-molecule fluorescence microscopy imaging of individual palladium(II) complexes. These experimental results lay the fundamental groundwork for studying organometallic reaction chemistry at the single-molecule level. |
 | Polyketide ring mystery solved In the April 8, 2008 issue of the Proceedings of National Academy of Sciences, Prof. Sheryl Tsai and coworkers report the crystal structure and chemical biology of the aromatase/cyclase domain from the aromatic polyketide synthase. Microbes are thought to produce polyketides by first making a long-chain linear polyketone then bending and folding it to produce the polyaromatic molecule. But precisely how they accomplished this feat of origami was a mystery. The UCI researchers showed that the aromatase/cyclase contains a C-shaped cavity perfectly configured for housing a long-chain linear polyketone, and the pocket shape is key to the highly specific first and second ring cyclizations. By subtly changing aspects of the active site they will be able to control the size and shape of the polyketide, resulting in the formation of new drugs. [ link ] |
 | Coupled protein and water dynamics: what a coincidence! In a Communication in the April 9, 2008 edition of the Journal of the American Chemical Society, Prof. Doug Tobias and collaborators in Europe report a study of the dynamics of protein molecules and their hydration shells using a combination of neutron scattering experiments with selective deuteration and molecular dynamics simulations. The results firmly establish and explain, for the first time, the direct coupling between soluble protein and water dynamics suggested by many previous experimental and theoretical investigations. [ link ] |
 | Chemistry professors discuss ion effects in Science paper Chemistry professors Doug Tobias and John Hemminger have an invited perspectives paper in the journal Science on Friday, Feb. 29, titled, "The Hofmeister Series: Getting More Specific about Specific Ion Effects." Different types of salt have predictable effects on a wide variety of chemical phenomena. For example, salt solutions containing fluoride ions tend to precipitate proteins, while salt solutions containing iodide ions dissolve them. These "specific ion effects" have been known for more than a century, but their molecular mechanism continues to evade scientists. This Science paper reviews recent progress toward unraveling specific ion effects, including research from the AirUCI Environmental Molecular Sciences Institute.[ link ] |
 | Phosphatase Activation by an Inhibitor Analog The current issue of Chemistry & Biology features an article, highlighted on the journal cover, reporting the design and synthesis of a small molecule that activates protein phophatase-1 (PP-1). The activity of PP-1 is normally controlled by a wide variety of binding proteins, each containing a consensus sequence (RVXF) recognized by a regulatory site on PP-1. Tappan and Chamberlin (pp. 167–174) demonstrate that a small molecule mimic of this regulatory consensus sequence activates PP-1 in two ways, despite the fact that its structure is, paradoxically, an analog of the well-known microcystin family of potent inhibitors.[ link ] |
 | Nanoprecipitation-induced current oscillations in a single nanopore In a recent publication in Nature Nanotechnology, Prof. Craig Martens of the UCI Chemistry Department, Prof. Zuzanna Siwy of the UCI Physics Department, and coworkers show how to induce current oscillations in a single nanopore [Nature Nanotechnology 3, 51 - 57 (2008)]. In strongly soluble salt solutions these systems act as molecular current rectifiers. When traces of sparingly soluble species, such as CaHPO4 are present, the systems undergo an intriguing transformation from DC current flow (a) to quasiperiodic current oscillations (b) when a critical membrane voltage is reached. This transition corresponds to negative differential resistance on the current-voltage (I-V) curve. The authors show how voltage-induced precipitation and re-dissolution inside the nanopore underlie the ion current oscillations. The behavior of these nonlinear systems is very sensitive to experimental conditions. The frequency of oscillation is tunable from a fraction of Hz to tens of Hz. The authors also discuss possible application of these nonlinear oscillating systems to the building a single pore-based chemical sensor. [ link ] |
 | Tubular self-embracing tripeptide superstructures with the same sense of chirality as the folded arms of Foyatier's Spartacus Tripeptides attached to (R,R)-1,2-diaminocyclohexanes self-assemble into tubular superstructures in which each peptide strand folds over and under the other, reminiscent of Spartacus's folded arms, with the same sense of chirality! Thus is born a new class of non-cyclic "self-embracing" peptides held together by intra- and interstrand H-bonds.[ link ] |
 | Chemistry and Biology of the Aeruginosin Family of Serine Protease Inhibitors Different phyla and different oceans are sources of linear peptides in the aeruginosin family which comprise a central hydroxy- (or dihydroxy-) octahydroindole carboxamide core unit onto which unusual amino acids are appended. The aeruginosins exhibit varying degrees of inhibitory activity against serine proteases, including factor II (thrombin) and factor VIIa of the blood coagulation cascade. In their Review on page 1202 ff., S. Hanessian et al. provide an overview of the chemical and biological properties of the aeruginosins as well as the natural sources of these compounds, their total syntheses, and structure revisions.[ link ] |
 | Polymorphism in Br2 Clathrate Hydrates On the cover of the Journal of Physical Chemistry A is the article reporting polymorphism in bromine clathrate hydrates, discovered by the Janda and Apkarian groups, through micro-Raman spectroscopy on single crystals. One of the first discovered clathrates, Br2-clathrate hydrates have played a central role in our understanding of the stability of clathrates, and more generally, of solid solutions. The stacking of the Archimedean polyhydra of water, through hydrogen bonds, allows for a very large number of ways to tile 3-D space. Yet, not all possible structures are realized. Identifying the units that acquire special stability has been a challenge, which is in good part resolved by the report.[ link ] |
 | Bimetallic Catalysis in the Synthesis of Highly Substituted Olefins In a recent publication in the Journal of the American Chemical Society, Professor Blum and graduate students Yili Shi, Sonja Peterson, and Walter Haberaecker show that a gold/palladium bimetallic system catalyzes the synthesis of tri- and tetra-substituted olefins with high stereo- and regiocontrol. The unique reactivity produced by the bimetallic system is consistent with a gold Lewis acid that promotes back bonding of palladium into the alkyne substrate to initiate reactivity. |
 | Spherical, Monodisperse, Functional Bridged Polysilsesquioxane Nanoparticles In one of the most-accessed papers published in Nano Letters, Ken Shea and his graduate student Mariya Khiterer report a general method for the synthesis of uniform functional hybrid nanoparticles. Spherical bridged polysilsesquioxane nanoparticles are prepared utilizing microemulsion technology. The electrochemically active charged nanoparticles are being utilized in solid state electrochromic devices and as carriers for polyanions such as DNA. Nano Letters, 2007, 7, 2684-2687[ link ] |
 | Umpolung Allylation Reactions In one of the most-accessed papers in Organometallics, Professor Jarvo and graduate students Nick Barczak and Robin Grote report umpolung reactions of allylpalladium complexes. Neutral bidentate N-heterocyclic carbene ligands are sufficiently electron donating to impart nucleophilic character to allylpalladium complexes and promote attack on aldehydes. They have also demonstrated that these complexes catalyze allylation reactions, important transformations for natural product synthesis. [ link ] |
 | Novel Cyclophane Catalyst for Valuable Materials A “Holy Grail” in olefin polymerization catalysis field is to discover transition metal catalysts that can efficiently copolymerize polar olefins. In a Communication to J. Amer. Chem. Soc. that is currently in press, Professor Guan and his graduate student Chris Popeney, and former postdoctoral fellow Drexel Camacho, have reported a cyclophane-based Pd(II) complex that is highly efficient in incorporating polar olefins like acrylates. Furthermore, low temperature NMR studies have revealed a unique mechanistic origin for the increased efficiency for polar olefin incorporation. [ link ] |
 | Interfacial Velocity-Dependent Plasmon Damping in Colloidal Metallic Nanoparticles On the cover of the Journal of Physical Chemistry C, Vol. 111, Apkarian and Corn groups, in collaboration with Newport Corporation report that “the interfacial velocity-induced electrophoretic potential leads to plasmon damping in colloidal nanoparticles”.[ link ] |
 | A New Class of Macrocyclic Receptors In an article in the Journal of the American Chemical Society, Professor James Nowick and his students report a new class of macrocycles based on iota-peptides. The macrocycles bind guests such as steroids and demonstrate that synthetic peptides containing a few large man-made amino acids can mimic the functions of large proteins.[ link ] |
 | Vibrational Spectroscopy of the Photoactive Yellow Protein (PYP): Theory and Experiment of Intermediates of the Photocycle In an article currently in press in J. Am. Chem. Soc., R. B. Gerber and graduate student Yemi Adesokan, in collaboration with the experimental group of Richard Mathies and co-workers at UC Berkeley, were able to compute with high accuracy vibrational frequencies of the major intermediates of the Photoactive Yellow Protein (PYP) photocycle. The calculations use ab initio potentials and employs an algorithm that goes beyond the harmonic approximation. The results are an important step forward for first-principles calculations of vibrational spectroscopy of biological chromophores, including of short lived intermediates. Insight into the evolution of the potential surface along the reaction path is also obtained.[ link ] |
 | Single Molecule Circuits for Chemical Biology A research team led by Philip Collins (Dept. of Physics and Astronomy) and Gregory Weiss (Dept. of Chemistry) has developed a new technique for making single-molecule electronic circuits with a protein attached. This research was published in the journal Science.[ link ] |
 | Structure-Based Organic Synthesis of Drug Prototypes Professor Stephen Hanessian is the author of a joint article between UC Irvine and the University of Montreal , which will appear in the December issue of ChemMedChem . Hanessian will direct the new ChemBioPharm graduate program in pharmaceutical sciences starting in 2007. [ link ] |
 | Structure and Chemistry of Aqueous Interfaces Professors Doug Tobias and Barbara Finlayson-Pitts along with AirUCI international collaborator, Professor Pavel Jungwirth of the Academy of Sciences of the Czech Republic, edited a special issue of Chemical Reviews on the "Structure and Chemistry of Aqueous Interfaces." In this issue, Jungwirth and Tobias review their theoretical development and experimental validation of a new view of ion solvation at the air-water interface and its implications for the chemistry of aqueous particles in the atmosphere. [ link ] |
 | Organic Aerosol Particles Chewed up by Sunlight In a recent paper featured on the cover of the June issue of Physical Chemistry Chemical Physics, the Nizkorodov group describes photochemistry of oxidized organic monolayers on quartz nanoparticles. This study is a part of the group’s ambitious endeavor to understand the role of solar radiation in atmospheric chemistry of organic aerosol particles. [ link ] |
 | Surface Enzyme Chemistry and SPR Imaging Professor Rob Corn and his group have been working to develop the method of surface plasmon resonance imaging (SPRI) for a variety of biosensing applications, with recent efforts focusing on achieving greater specificity and sensitivity from the SPRI measurements by coupling the surface bioaffinity process to an enzymatic transformation such as ligation or polymerase extension. For more information, please see the feature article "Creating Advanced Multifunctional Biosensors with Surface Enzymatic Transformations" by Hye Jin Lee, Alastair W. Wark, and Robert M. Corn in Langmuir, Vol. 22, pages 5241-5250 (2006). [ link ] |
 | Virus Electrodes for Universal Biodection In a collaboration between the laboratories of Greg Weiss and Reg Penner , a prototype of a biosensor based on the attachment of virus particles to a gold electrode has been developed. The attached virus particles are engineered using phage display to recognize and bind both an antibody and a prostate cancer marker called PSMA. Exposure of the virus-coated electrode to either of these molecules caused an increase in both the mass of the surface, and its electrical resistance. Concentrations of PSMA down to 120 nM were detectable at this biosensor. The advantage of this approach, in principle, is that viruses can be engineered using phage display to recognize and bind virtually any molecule.[ link ] |
 | Proteins, Pronto A Nature press release highlights research from the Shaka group. In their recent JACS Communication, (128, 4508-4509 (2006) the group has found a quick and clean method to go from a gene to a protein NMR spectrum in under five hours, using a cell-free protein production system called Expressway, that is manufactured by Invitrogen Corporation in Carlsbad. |
 | Protein Recognition As part of their molecular imprinting program, the Shea group has recently developed a family of "plastic antibodies" for protein recognition. ("Selective Protein Capture by Epitope Imprinting" H. Nishino, C.-S. Huang, K. J. Shea, Angewandte Chemie, 2006, 45 2392-2396). |
 | New Annulation Reaction In a recent JACS Communication [Bolla et al., J. Am. Chem. Soc. 2005, 127, 16044], the Rychnovsky group reports a new annulation reaction that generates tetrahydropyran rings as single diastereomers from unsaturated ketones and enol ether alkenes. The reaction is stereoselective and should be useful for synthesizing natural products containing tetrahydropyran rings. |
 | The Chemistry department is a major participant in the ACS 40th Western Regional Meeting, "Water, Water, Everywhere!?!", which is being held January 22-25, 2006 in Orange, California. A symposium on Gas Clathrate Hydrates, organized by the Collaborative Research Center on the topic is headed by Kenneth Janda . Reginald Penner will preside over a symposium on Advances in Nanotechnology: Low Dimensional Materials in Chemical Analysis. Iota Sigma Pi will be hosting a table representing the department.
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 | Saccharide-peptide hybrid copolymers as highly functional biomaterials, is the new design concept introduced by Professor Zhibin Guan, published online September 15, in Angewandte Chemie International Edition. The novelty of the demonstrated concept, and its promise as a flexible approach for the synthesis of biomaterials with tailored properties has already been recognized in Chemical Engineering News (C&EN) and the international press.
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 | In the April 28 and May 12 issues of the Journal of Physical Chemistry B, Professor Doug Tobias and collaborators (including former UCI postdoc Professor Pavel Jungwirth of the Academy of Sciences of the Czech Republic, and former UCI graduate students Professor Heather Allen of Ohio State University and Dr. Liem Dang of Pacific Northwest National Laboratory) published three articles reporting combined theoretical and spectroscopic studies of the structure of the surfaces of aqueous electrolyte solutions (acid, base, and salts of atomic and molecular ions).
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 | Surfaces of Ionic Solutions Differ from the Bulk In the January 28, 2005 issue of Science Magazine, the Hemminger group and collaborators at Lawrence Berkeley National Lab report ambient pressure X-ray photoelectron spectroscopy measurements that confirm theoretical predictions of enhanced halogen ion concentrations at the air-water interface of alkali halide solutions. |
 | October 6, 2004. Irwin (Ernie) Rose received the 2004 Nobel Prize in Chemistry today for the discovery of ubiquitin-mediated protein degradation. At age 78, Ernie continues to work in the laboratory and is focusing his efforts on mechanistic enzymology. "I had the privilege of collaborating with Ernie a couple of years ago on a project involving the mechanism of methyl glyoxalate synthetase", says UCI Chemistry Professor James Nowick. Ernie had postulated the intermediacy of the never-before-observed molecule 2-hydroxypropenal in the methylglyoxal synthetase reaction and had hints of its existence from UV spectroscopic studies. "We used the UCI Chemistry Department's state-of-the-art NMR facility to prove that this molecule was forming. Observing a compound that contains only three carbon atoms, yet had never been seen before, felt like discovering a new planet in the solar system", adds Nowick. Drs. Rose and Nowick published this work in the Journal of the American Chemical Society in 2002. Nowick comments: "Ernie Rose is the consummate scientist. He is enthralled by the problems upon which he is working and loves the pursuit of new knowledge through research. After discovering ubiquitin-mediated protein degradation, which ultimately led to his Nobel Prize, Ernie did not rest on his laurels, but rather moved on to new problems and challenges. He continues to work in the laboratory and is focusing his efforts on mechanistic enzymology. When I finally got through to him this morning, after the Nobel Prize was announced, Ernie said that he was looking forward to coming to UCI this afternoon to perform mass spectrometric experiments in the UCI Chemistry Department's world-class mass spectrometry facility." [ link ] |
 | In this structure of engrailed homeodomain (left) binding to DNA (right), key residues for DNA recognition, as determined by shotgun scanning performed by Ken Sato and Aron Levin of the Weiss laboratory, are highlighted in yellow. [ link ] |
