Chemistry Department - University of Florida

Svetlana V Kilina, Los Alamos National Lab, NM.

skilina@u.washington.edu

Simulations of electronic properties of disordered and self assembled soft materials: disordered polyfluorenes and DNA adsorbed on metallic and carbon nanotube surfaces

The idea of harnessing the molecular building blocks to assemble nanometer-scale devices promises the fascinating applications ranging from electronic to medical ones. Advances in atomic-scale experimental imagining and manipulation techniques, e.g., STM, AFM, dip-pen lithography, and ultrafast spectroscopy, pave the way to control the transport in such electronic devices, where all elements are parts of a single molecular-macro-assembly. Yet, the fundamental understanding of the underlying physics and chemistry of such complex structures lag the experiments. We use a combination of ab initio techniques, such as Density Functional Theory (DFT), with classical force field (FF) calculations to predict and to explain experimental results on transport properties of several molecular composites and disordered materials. Among the considered systems are: i) Adsorbed DNA strands on metallic surfaces. Here the unique STM spectra of bases promise fast sequencing of DNA. To interpret experimental results, we simulate tunneling spectra and identify the underlying electronic features of each DNA bases adsorbed on Cu(111) surface. Our simulations reveal that cytosine and guanine, having large dipole moments, interact strongly with the substrate through chemisorption, while thymine and adenine, having smaller dipole moments, are weakly physisorbed on Cu. The observed diversity of the geometrical and electronic structures of the nucleobases on the Cu substrate provides guidelines for interpreting DNA tunneling microscopy spectra, and shows perfect agreement of the simulation with available dI/dV measurements. ii) DNA strands wrapping around carbon nanotubes (CNT). We focus on structural relaxation and uncaging of DNA molecules in a presence of a CNT. Simulated structures coincide with recently resolved STM images of these systems. iii) Amorphous conjugated polymers, e.g. polyfluorenes (PFO). We have found that electronic and optical properties of this system are affected by disorder and intra-chain conformational changes: the electron traps are induced by changes in intra-chain configuration, while hole traps originate from inter-chain correlations. Our quantum-classical numerical approach allows to describe extended complex systems on a quantum mechanical level and opens a new prospective for understanding of transport properties in bio- and conjugated polymers, interacting with each other or with inorganic substrates.

Host: Micha

Ryan Rodgers, National High Magnetic Field Laboratory, Tallahassee

Petroleomics: Chemistry from the Underworld

The continued depletion of light sweet crude oil reserves and rapid growth of developing countries has shifted global oil markets to heavier crude oils. The lost/decreased production of light sweet oils is compensated for by increased production of heavy crude oils and opportunity materials such as oil sands / bitumen. Although abundant, these unconventional or previously undesirable petroleum resources are rich in heteroatom containing species such as nitrogen, oxygen and sulfur and as a result pose significant production, refining and upgrading challenges. The analysis of heavy crude oil has largely been limited to bulk characterization and chromatographic techniques due to the immense chemical complexity of the crude oils. However, it is information on this wealth of chemical compositional complexity that holds the greatest potential for non-incremental gains in enhanced recovery and more efficient processing of heavy crude oils. First reported in 1974, FT-ICR mass spectrometry now offers the highest mass resolution and mass accuracy. At sub-ppm mass accuracy, it becomes possible to determine a unique elemental composition, CcHhNnOoSs, for each of up to 50,000 resolved peaks in a single mass spectrum. That capability has spawned the field of "petroleomics," namely, correlation (and ultimately prediction) of the properties and behavior of petroleum and its products from detailed chemical composition. Moreover, as a separation technique, FT-ICR offers 200x higher "peak capacity" than any single-stage wet chemical separation method (GC, LC, gels, etc.)--thus, it is often possible to analyze samples directly without prior treatment. Here we report the detailed analysis of complex petroleum derived samples in order to highlight the strengths of FT-ICR mass spectrometry as well as class specific information that can be determined by a combination of common ionization techniques (ElectroSpray and Atmospheric Pressure PhotoIonization). Recent results obtained from the 14.5T FT-ICR Mass Spectrometer at the National High Magnetic Field Laboratory will be presented.

rodgers@magnet.fsu.edu
http://www.magnet.fsu.edu/scientificdivisions/icr/overview.html

Host: Eyler

October 16

Carlos Simmerling, Department of Chemistry, State University of New York, Stony Brook, NY

carlos.simmerling@sunysb.edu
http://comp.chem.sunysb.edu/

Atomic-level simulations of complex biomolecular systems

Experimental methods have been highly successful in determining 3-dimensional biomolecular structures. However, most approaches provide only time- or ensemble-averaged data, making it much more difficult to study the dynamic and energetic aspects of biological systems. Atomic-resolution simulations are highly complementary to experiments, and can provide data with unparalleled resolution in time and space. Due to the long timescales of biologically relevant events, as well as the complexity of the energy function, accurate and precise simulations remain highly computationally challenging. This seminar will highlight recent progress in both areas by the Simmerling lab, illustrating how energy functions that have been trained on simple peptide models can be used for the study of much more complex systems. Examples include studies of the dynamic behavior and drug binding in HIV-1 protease and the modeling of new enzyme inhibitors for the treatment of tuberculosis.

Host: Roitberg

October 23

no seminar

October 30

Timothy Cross, Department of Chemistry and National High Magnetic Field Laboratory, Florida State University, Tallahassee, FL.

cross@magnet.fsu.edu
website

The Balance of Molecular Interactions in Membrane Proteins:
Characterizations by Solid State NMR Spectroscopy

Structural biologists have been slow to appreciate the implications of the heterogeneous membrane protein environment and the significant difference in the amino acid composition for transmembrane domains of integral membrane proteins. In the low dielectric interior of the membrane where water is scarce and the amino acids sidechains are predominately hydrocarbon the intra-helical hydrogen bonds are strengthened and the inter-helical interactions are dominated by non-specific van der Waals interactions and other weak electrostatic interactions that permit multiple conformations and large amplitude dynamics. Such a scenario has multiple implications for membrane protein stability and function. Long range dipolar interactions influence free energy profiles for ion conduction through channels. Ions are dehydrated for passage through channels in a step-wise fashion. Binding sites may permit considerable dynamics thereby allowing ions to retain considerable entropy. Charges are delocalized as extensively as possible including through the use of low barrier hydrogen bonds, and controlling water accessibility appears to be important for functional regulation. Solid state NMR is one of the few technologies that permit characterizations of these proteins in a liquid crystalline lipid bilayer environment.

Host: Bowers

Sophia Hayes, Department of Chemistry & Center for Materials Innovation, Washington University, St. Louis, MO 63130

hayes@wustl.edu
http://www.chemistry.wustl.edu/

Optically-pumped NMR of semiconductors: probing the band structure and defect sites in GaAs

It is possible to orient electron spins in semiconductors by irradiating them with circularly polarized light near the bandgap, Eg. The extent to which the electrons can be oriented depends on the details of the band structure, relaxation processes, and various other external factors. By changing the photon energy of the laser, different parts of the band structure may be accessed. Coupling between the oriented electrons and nuclear spins results in enhanced NMR signals, termed “optically-pumped NMR” (OPNMR). Measurements of the intensity of OPNMR signals in semiconductors have been found to depend sensitively on the photon energy and the helicity of light for optical pumping. We have measured two sample thicknesses, where the maximum intensity of the OPNMR signals were observed well below Eg, and this maximum shifted to higher photon energies for thinner samples. In the range of photon energies for which the maximum OPNMR signals are obtained, there is little or no hyperfine shift of the OPNMR resonance. Hyperfine shifts with the largest magnitude are recorded for photon energies at or above the bandgap. Additionally, at a given photon energy, asymmetric OPNMR signals were observed, with sigma+ light producing a more intense emissive signal than the corresponding absorptive signal coming from sigma– light. We have developed simulations to explain the intensity dependence and the hyperfine shifts of 69/71Ga OPNMR signals as a function of laser photon energy, which I will discuss in detail in this talk.

Host: Bowers

Ka Yee C. Lee, Department of Chemistry, The Institute for Biophysical Dynamics & The James Franck Institute, The University of Chicago, Chicago, IL 60637

kayeelee@uchicago.edu
http://leelab.uchicago.edu/

Poking and Sealing Holes: Interactions of Antimicrobial Peptides and Poloxamers with Lipid Membrane

The cell membrane acts as a barrier, controlling the transport of molecules into and out of the cell. When the structural integrity of the membrane is compromised, so does its barrier function. In this talk, we examine how the membrane barrier function can be compromised by antimicrobial peptides, and how leakage of intracellular materials from a structurally damaged cell membrane can be arrested by triblock copolymers. Antimicrobial peptide is a class of peptide innate to various organisms and function as a defense agent against harmful microorganisms by means of membrane disordering. Despite their enormous biomedical potentials, progress towards developing them into therapeutic agents has been hampered by a lack of understanding of their mechanism of action. A class triblock copolymer of the form poly(ethylene oxide)-poly(propylene oxide)-poly(ethylene oxide)(PEO-PPO-PEO) has been shown to help seal electroporated cell membranes, arresting the leakage of intracellular materials of the damaged cell. However, the interaction mechanism between the cell membrane and poloxamer is still unclear. Using a variety of model systems and biophysical techniques, we have examined the targeting selectivity as well as the membrane disruption mechanism of antimicrobial peptide protegrin-1, and have explored the sealing capability of poloxamer 188.

Host: Fanucci

December 4

Christopher Boxe, Jet Propulsion Laboratory, Pasadena, California

Christopher.Boxe@jpl.nasa.gov

Surface Chemistry and Physics: Implications for Terrestrial Polar Science and Planetary Science

Field measurements have only recently unearthed the discovery that the terrestrial polar snowpack is one of the most photochemically active environments on Earth. Due to the strong feedback between the sunlit snowpack and the air over it, such chemistry in the terrestrial polar regions is now recognized to strongly influence the overlying atmospheric boundary layer and potentially the free troposphere due to mixing. It is becoming more accepted that iodine chemistry, intimately linked to NO_x chemistry, plays a major role in controlling ozone concentrations in the overlying boundary layer. In addition, iodine forms aerosols and contributes to the transformation of elemental mercury to its reactive form. Considering that polar tropospheric ozone exhibits a large radiative forcing, iodine forms aerosols, and reactive mercury is detrimental to the polar ecosystems, it is imperative to understand the source of iodine and NO_x. An overview covering laboratory results, which elucidates the properties of ice as a reaction medium, and provides the framework (i.e., the surface chemistry and physics) for the creation of the first multi-phase model for the polar regions, CON-AIR (Condensed Phase to Air Transfer Model) will be presented. This model accounts for the measured iodine and NO_x in the terrestrial polar boundary layer. These model simulations have implications for: 1) being available as a tool for the atmospheric science community to perform additional modeling, laboratory, and field studies relevant to the dynamic interplay of the polar boundary layer and the snowpack; 2) the influence of heterogeneous surface photochemistry on overlying gas phase chemistry of planetary bodies with tenuous atmospheres; and 3) carrying out laboratory and modeling investigations relevant to planetary surfaces (e.g., Mars, Europa, and interstellar clouds) to study the possible formation and chemistry of life forming molecules.

December 11

Oleg Matveev, Department of Chemistry, University of Florida

oleg@chem.ufl.edu

A Novel Multipass Optical System

Multipass optical systems (MOS) are broadly used in absorption, Raman, fluorescence, and ionization laser spectroscopy and also in Raman lasers, laser amplifiers and optical parametric oscillators [1]. Traditional MOS are not universally applicable. Depending on the optical task, sometimes rather complicated types of MOS have to be designed with specialized optical elements, primarily mirrors. This work describes a simpler and more universal MOS design allowing to create either all beams focused or after minor modification homogeneous illumination of areas with practically any heights (H+h), widths (W) and lengths (see Fig.1). Figure.1 a) shows one of the focusing MOS configuration using four (A, B, C, and D) right angle prisms and two convex lenses. For simplicity, only first 11 passes are pictured. In Fig.1 b) matrixes are depicted showing where and in what order the beams are crossing the prisms surfaces. Here, also for simplicity, only first 40 crosses are shown. By removing the lenses, placing the prism B on the top of A, and shifting prisms C and D vertically, homogeneous illumination by 20 laser beams and 40 passes of the area between prisms surfaces can be created.

Simulations of various modifications of the new MOS design have been performed using OptiLab 522 optical design software (Science Lab Software, CA, USA). A remarkable feature of the novel MOS is its ability, in some cases, to provide confined beams in the illuminated areas with a number of passes limited only by the reflection losses on the optical surfaces. Another interesting simulation with one of the convex lenses replaced by a concave one, produced a sort of telescope. In this case the beams become “compressed”, providing nearly homogeneous illumination in a small area with laser radiation of much higher irradiance. Preliminary experiments have been performed using a planar MOS with two simple focusing lenses. A cuvette with various liquid organic solutions was illuminated by CW 50 mW 532 nm laser, and Raman scattering was detected using CD 2000 digital spectrometer (Ocean Optics Inc., Dunedin, FL, USA). When using two 10 and 12 mm right angle prisms, MOS provided 8 passes. Because the lenses had not been corrected for aberrations and the surfaces lacked antireflection coatings the Raman signal was enhanced only threefold. With an optimized system much larger enhancements are expected.

Reference
[1] S. M. Chernin, J. Mod. Opt. 48, (2001) 619-632.