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TITLE:  Seeking a plausible prebiotic solution (and solvent) for the origin of RNA 

ABSTRACT:  The RNA World remains a popular and influential hypothesis in origins of life research. However, prebiotic chemists are still lacking a plausible prebiotic synthesis for RNA. We are investigating the possibility that RNA was preceded by a polymer that would have assembled more easily than RNA (i.e., pre-RNA), and that non-aqueous solvents could have facilitated prebiotic nucleic acid synthesis and replication. In support of these theories, recent experiments have revealed alternative nucleobases that readily form nucleosides with ribose, a property not observed with the nucleobases of extant RNA. Alternative solvents have also been identified that allow nucleoside phosphorylation from water-insoluble minerals, as well as the polymerase-free transfer of information from long nucleic acid duplexes.

Abstract:

Proteins are intrinsically dynamic. By undergoing motions on a wide range of time and length scales, they are able to bind substrates, regulate their own activities, and transmit information over considerable distances. In this talk, I will discuss multiple projects in our group that utilize conventional and enhanced sampling molecular dynamics simulations to probe these dynamical properties for a diverse array of systems. Our results reveal atomic-scale details about how seemingly minor protein modifications can influence molecular motions and interactions and, by working closely with our experimental collaborators, help to discern the molecular mechanisms of biomolecular complexes.

METAL OXIDE NANOSTRUCTURES FOR ELECTRONICS AND ENERGY APPLICATIONS: ENDOWING "INTELLIGENCE" THROUGH PHASE TRANSFORMATIONS

Scaling ceramics and metals to nanoscale dimensions substantially alters their phase stabilities and phase diagrams with tremendous consequences for the manifestation of unique physical phenomena. Such new physical phenomena that oftentimes have no parallels in the bulk can be utilized to fabricate novel functional materials with applications for logic circuitry, "smart windows", photocatalysis, and electrochemical energy storage. In this talk, I will focus on our recent results on the influence of finite size and doping on the metal-insulator phase transitions of the binary vanadium oxide VO₂. We have achieved substantial tunability of the critical transition temperature between -20 and 70°C through control of dimensionality, morphology, and dopant concentration in hydrothermally prepared single-crystalline VO₂ nanostructures. The tunability of the phase diagram portends applications of these materials as dynamically switchable glazings for energy efficient windows (smart windows!). I will further discuss colossal metal—insulator switching recently discovered in M_xV₂O₅ bronze phases, platforms for photocatalysis that exploit the tunabilty of the band structure within these compounds, and the interplay between structure and chemical bonding for intercalation of Li and Mg-ions within V₂O₅ and the implications therein for novel battery architectures.

Keywords: smart windows, phase transformations, vanadium oxides

References:

1) K. E. Pelcher, C. C. Milleville, L. Wangoh, S. Chauhan, M. R. Crawley, L. F. J. Piper, D. F. Watson, and S. Banerjee, Integrating β-Pb_0.33V₂O₅ Nanowires with CdSe Quantum Dots: Towards Nanoscale Heterostructures with Tunable Interfacial Energetic Offsets, ÌÇÐÄvlog¹Ù·½Èë¿Ú of Materials 2015, 27, 2468-2479.

2) P. M. Marley, G. A. Horrocks, K. E. Pelcher, and S. Banerjee, Transformers: The Changing Phases of Low-Dimensional Vanadium Oxide Bronzes, Chemical Communications 2015, 51, 5181-5198.

3) P. M. Marley, T. A. Abtew, K. E. Farley, G. A. Horrocks, R. V. Dennis, P. Zhang, and S. Banerjee, Emptying and Filling a Tunnel Bronze, Chemical Science 2015, 6, 1712-1718.

4) G. A. Horrocks, S. Singh, M. F. Likely, G. Sambandamurthy, S. Banerjee, Scalable Hydrothermal Synthesis of Free-Standing VO₂ Nanowires in the M1 Phase, ACS Applied Materials and Interfaces 2014, 6, 15726-15732.

5) P. M. Marley, S. Singh, T. A. Abtew, C. Jaye, D. A. Fischer, P. Zhang, G. Sambandamurthy, S. Banerjee, Electronic Phase Transitions of δ-Ag_xV₂O₅ Nanowires: The Interplay between Geometric and Electronic Structure, Journal of Physical ÌÇÐÄvlog¹Ù·½Èë¿Ú C 2014, 118, 21235–21243.

Abstract: Sulfur is a constituent atom in two naturally occurring amino acids, namely, methionine and cysteine. It has been well established that in many proteins and enzymes the non-covalent interactions involving sulfur atom in these two amino acids play important role in lending them their intrinsic structures and also in enzymatic catalysis. These interactions have been interchangeably categorized as either as generic non-covalent interactions or specifically hydrogen bonding interactions. However, in many instances their structural properties do not necessarily confirm to those of the conventional hydrogen bonds. We have been investigating the spectroscopic and electronic structure properties of sulfur centered non-covalent contacts using a variety of laser spectroscopic techniques in gas phase and have been able to show that they satisfy all the criteria of hydrogen bonding interaction. We have also determined the dissociation energies of OH---S hydrogen bonded complexes using a combination of the ZEKE photoelectron spectroscopy and photo-fragmentation spectroscopy. In this talk I will present some of these results.

Spectroscopy of Cold Trapped Ions – Fundamentals and Chemical Applications

Christopher J. Johnson, Stony Brook University

In the last 10 years, advances in ion sources for mass spectrometry, laser spectroscopy of gaseous ions, and temperature controlled ion traps have been combined to make it possible to record electronic and vibrational spectra of essentially any chemical system that can be analyzed by mass spectrometry.  This has led to fundamental advances in cluster chemistry and spectroscopy as well as applications in catalytic mechanisms, biomolecular structure and solvation, and atmospheric chemistry, to name a few.  I will discuss the development of these spectroscopic methods and the current state-of-the-art.  Examples of the application of this technology to address questions in vibrational spectroscopy of systems with large-amplitude motion and the mechanism of atmospheric new particle formation will be presented.  Finally, I will give a look ahead at planned advances in speed, sensitivity, and complexity of systems amenable for study using these techniques.

Virus Based Nanotechnology and Nanotechnology Based on Viruses

Abstract:  Nature long ago solved problems plaguing contemporary chemists with polydispersity and controlled synthesis at the nanoscale. The biological production and proliferation of viruses—each viral particle identical to the last—is unsurpassed in terms of both output and quality control relative to anything humans can accomplish today at such a scale. Our research program reengineers viruses for a palate of purposes, from drug delivery to materials fabrication to a test-bed for new bioconjugation reactions. I will be presenting several projects in our group that illustrate the power of chemical virology from an organic/materials chemist’s perspective with applications in medicinal science as well as material science.

Bio: Dr Jeremiah Gassensmith earned his B. Sc. (Hons in ÌÇÐÄvlog¹Ù·½Èë¿Ú) degree under the tutelage of Professor Joseph Gajewski at Indiana University and his Ph.D. from Professor Bradley D Smith at the University of Notre Dame, where he studied the synthesis of sterically shielded near-infrared luminescent dyes. After his PhD, he traveled to Northwestern University to learn under Professor Sir J. Fraser Stoddart. At Northwestern, he investigated a diverse array of topics, including gas sequestration by cyclodextrin based metal-organic frameworks. He joined the faculty at the University of Texas at Dallas in August 2013. He’s the author of 30 scientific articles, has a book chapter, and two US patents. Check out his website () or his twitter account (@gassensmith)!

Light-driven P450 enzymes

 

Lionel Cheruzel¹ , lionel.cheruzel@sjsu.edu

¹ ÌÇÐÄvlog¹Ù·½Èë¿Ú, San Jose State University, San Jose, California, United States

Cytochrome P450s are unique heme thiolate enzymes that catalyze the regio and stereoselective functionalization of unactivated C-H bonds in a wide range of substrates, using molecular dioxygen, two protons, and two electrons provided by a reductase domain. As an alternative approach to deliver the necessary electrons and perform P450 reactions upon visible light excitation, we have developed hybrid P450 enzymes contain a Ru(II)-diimine photosensitizer covalently attached to strategically positioned non-native cysteine residues of P450 heme domains. High photocatalytic activity (i.e. high total turnover numbers and initial reaction rates) could be achieved in the hydroxylation of natural long-chain fatty acid substrates. The crystal structure of an efficient hybrid enzyme reveals that the photosensitizer is ideally positioned to deliver electrons to the active site utilizing the natural electron transfer pathway. A combination of rational and directed evolution approaches has been used to develop the next generation of hybrid enzymes showing enhanced photocatalytic activity towards a wide range of non-natural substrates.

Statistics of Battery Failure

Steve Harris

Lawrence Berkeley Lab

The battery community, implicitly or explicitly, usually takes failure to be deterministic rather than statistical.  This means that there should be a function (model) which predicts a single value for life as a function of critical parameters such as C-rate, temperature, electrode properties, etc.  Variability is rarely explicitly discussed, but when it is, it is further assumed that any variability in life is Gaussian and that with sufficiently close control of the appropriate parameters, the variability can be always be reduced.  In this talk I will make the case that battery failure is intrinsically statistical, which means that there is no single function (model) that predicts the lifetime of a battery, just as there is no model that can predict lifetime of a person or a gear.  On the other hand, as I will show with standard statistical methods, it is possible to predict the time-evolution of the distribution of lifetimes with considerable accuracy using capacity vs cycle data.  Furthermore, the analysis offers a way to qualitatively classify the type of degradation that the cells are undergoing.

Professor Emeritus Jame Flesher from the ÌÇÐÄvlog¹Ù·½Èë¿Ú's Deparetment of Pharmacology will present his seminar titled Structure, Function, and Carcinogenicity of Oxidized Metabolites of Methylated and non-Methylated Polynuclear Hydrocarbons.

Abstract:

The Unified Theory of PAH Carcinogenicity accommodates the activities of methylated and non-methylated polycyclic aromatic hydrocarbons (PAHs) and states that substitution of methyl groups on meso-methyl substituted PAHs with hydroxy, acetoxy, chloride, bromide or sulfuric acid ester groups imparts potent cancer producing properties. It incorporates specific predictions from past researchers on the mechanism of carcinogenesis by methyl-substituted hydrocarbons, including (1) requirement for metabolism to an ArCH2X type structure where X is a good leaving group and (2) biological substitution of a meso-methyl group at the most reactive center in non-methylated hydrocarbons. The Theory incorporates strong inferences of Fieser: (1) The mechanism of carcinogenesis involves a specific metabolic substitution of a hydrocarbon at its most reactive center and (2) Metabolic elimination of a carcinogen is a detoxifying process competitive with that of carcinogenesis and occurring by a different mechanism. According to this outlook, chemical or biochemical substitution of a methyl group at the reactive meso-position of non-methylated hydrocarbons is the first step in the mechanism of carcinogenesis for most, if not all, PAHs and the most potent metabolites of PAHs are to be found among the meso methyl-substituted hydrocarbons. Some PAHs and their known or potential metabolites and closely related compounds have been tested in rats for production of sarcomas at the site of subcutaneous injection and the results strongly support the specific predictions of the Unified Theory.