#psuchemistry

[portlandstateresearch]

Robert M. Strongin, Martha Sibrian-Vazquez, and Jorge Escobedo, Department of Chemistry faculty, co-authored an article titled, “Altering Fundamental Trends in the Emission of Xanthene Dyes” published in the The Journal of Organic Chemistry.

Fluorescent small molecules enable researchers and clinicians to visualize biological events in living cells, tissues, and organs in real time. Herein, the focus is on the structure and properties of the relatively rare benzo[a]xanthenes that exhibit enhanced steric and electronic interactions due to their annulated structures. Three types of fluorophores were synthesized: (i) pH and solvent dependent seminaphtho-rhodafluors, (ii) pH and solvent independent seminaphthorhodafluors, and (iii) pH-independent but solvent sensitive seminaphthorho-damines. The probes exhibited promising far-red to near-infrared (NIR) emission, large Stoke shifts, broad full width at half maximum (FWHM), relatively high quantum yields and utility in immunofluorescence staining. Deviation of the π-system from planarity due to changes in the fluorophore ionization state resulted in fluorescence properties that are atypical of common xanthene dyes.

[portlandstateresearch]

Steve Richow, chemistry faculty, co-authored “Structure of native lens connexin 46/50 intercellular channels by cryo-EM,” published in the December 2018 issue of Nature.

Abstract: Gap junctions establish direct pathways for cell-to-cell communication through the assembly of twelve connexin subunits that form intercellular channels connecting neighboring cells. Co-assembly of different connexin isoforms produces channels with unique properties and enables communication across cell types. Here we used single-particle cryo-electron microscopy to investigate the structural basis of connexin co-assembly in native lens gap junction channels composed of connexin 46 and connexin 50 (Cx46/50). We provide the first comparative analysis to connexin 26 (Cx26), which—together with computational studies—elucidates key energetic features governing gap junction permselectivity. Cx46/50 adopts an open-state conformation that is distinct from the Cx26 crystal structure, yet it appears to be stabilized by a conserved set of hydrophobic anchoring residues. ‘Hot spots’ of genetic mutations linked to hereditary cataract formation map to the core structural–functional elements identified in Cx46/50, suggesting explanations for many of the disease-causing effects.

[portlandstateresearch]

Ryan Lerud and Shankar Rananavare of Portland State’s Department of Physics and Chemistry co-wrote a paper titled, “Optimizing the Performance of a Commercial Electrochemical Ethylene Sensor via Controlled Ethylene Generation in Situ”, to be published in Sensors and Actuators in February 2019.

Ethylene, which regulates fruit ripening processes in some species, is a molecule of central interest to postharvest researchers and technologists. There is a need for a portable, inexpensive, accurate, and repeatable sensor for infield or storeroom measurements. To help ensure repeatable results, we developed a field calibration protocol for a portable electrochemical gas sensor that combines ethephon (2-chloroethylphosphonic acid) with a buffering agent to release a controlled amount of ethylene gas (1–4 μL/L). The ethephon reaction provides an economical source of standard gas for device calibration. This work addresses device selectivity issues through the use of an inline aqueous trap to remove polar volatile organics (50% reduction, as reported by an electrochemical sensor), interfering with the ethylene detection. A complementary gas chromatographic (GC) assay provided an independent validation of these results. A post-harvest study of ethylene production of apples as detected by the electrochemical sensor illustrates significant improvements in the accuracy and precision of these measurements.

[portlandstateresearch]

Shankar Rananavare, Chemistry faculty member, co-authored “The L Υ Phase of Pulmonary Surfactant,” published in the May 2018 issue of Langmuir.

Abstract: To determine how different components affect the structure of pulmonary surfactant, we measured X-ray scattering by samples derived from calf surfactant. The surfactant phospholipids demonstrated the essential characteristics of the Lγ phase: a unit cell with a lattice constant appropriate for two bilayers; crystalline chains detected by wide angle X-ray scattering (WAXS). The electron density profile, obtained from scattering by oriented films at different relative humidities (70-97%), showed that the two bilayers, arranged as mirror images, each contain two distinct leaflets with different thicknesses and profiles. The detailed structures suggest one ordered leaflet that would contain crystalline chains, and one disordered monolayer likely to contain the anionic compounds, which constitute ~10% of the surfactant phospholipids. The spacing and temperature-dependence detected by WAXS fit with an ordered leaflet composed of dipalmitoyl phosphatidylcholine. Physiological levels of cholesterol had no effect on this structure. Removing the anionic phospholipids prevented formation of the Lγ phase. The cationic surfactant proteins inhibited Lγ structures, but at levels unlikely related to charge. Because the Lγ phase, if arranged properly, could produce a self-assembled ordered interfacial monolayer, the structure could have important functional consequences. Physiological levels of the proteins, however, inhibit formation of the Lγ structures at high relative humidities, making their physiological significance uncertain.

[portlandstateresearch]

Steve Reichow, Chemistry faculty member, co-authored “Multivalency regulates activity in an intrinsically disordered transcription factor,” published in the May 2018 issue of eLife Sciences 7.

Abstract: The transcription factor ASCIZ (ATMIN, ZNF822) has an unusually high number of recognition motifs for the product of its main target gene, the hub protein LC8 (DYNLL1). Using a combination of biophysical methods, structural analysis by NMR and electron microscopy, and cellular transcription assays, we developed a model that proposes a concerted role of intrinsic disorder and multiple LC8 binding events in regulating LC8 transcription. We demonstrate that the long intrinsically disordered C-terminal domain of ASCIZ binds LC8 to form a dynamic ensemble of complexes with a gradient of transcriptional activity that is inversely proportional to LC8 occupancy. The preference for low occupancy complexes at saturating LC8 concentrations with both human and Drosophila ASCIZ indicates that negative cooperativity is an important feature of ASCIZ-LC8 interactions. The prevalence of intrinsic disorder and multivalency among transcription factors suggests that formation of heterogeneous, dynamic complexes is a widespread mechanism for tuning transcriptional regulation.

[portlandstateresearch]

Mark Woods, Chemistry faculty member, co-authored “ParaCEST Agents Encapsulated in Reverse Nano-Assembled Capsules (RACs): How Slow Molecular Tumbling Can Quench CEST Contrast,” published in the April 2018 issue of Frontiers in Chemistry 6.

Abstract: Although paraCEST is a method with immense scope for generating image contrast in MRI, it suffers from the serious drawback of high detection limits. For a typical discrete paraCEST agent the detection limit is roughly an order of magnitude higher than that of a clinically used relaxation agent. One solution to this problem may be the incorporation of a large payload of paraCEST agents into a single macromolecular agent. Here we report a new synthetic method for accomplishing this goal: incorporating a large payload of the paraCEST agent DyDOTAM3+ into a Reverse Assembled nano-Capsule. An aggregate can be generated between this chelate and polyacrylic acid (PAA) after the addition of ethylene diamine. Subsequent addition of polyallylamine hydrochloride (PAH) followed by silica nanoparticles generated a robust encapsulating shell and afforded capsule with a mean hydrodynamic diameter of 650 ± 250 nm. Unfortunately this encapsulation did not have the effect of amplifying the CEST effect per agent, but quenched the CEST altogether. The quenching effect of encapsulation could be attributed to the effect of slowing molecular tumbling, which is inevitable when the chelate is incorporated into a nano-scale material. This increases the transverse relaxation rate of chelate protons and a theoretical examination using Solomon Bloembergen Morgan theory and the Bloch equations shows that the increase in the transverse relaxation rate constant for the amide protons, in even modestly sized nano-materials, is sufficient to significantly quench CEST.

[portlandstateresearch]

Hayden Winter, Elena Christopher-Allison, and Andrea Goforth, Chemistry Department, co-authored “Aerobic method for the synthesis of nearly size-monodisperse bismuth nanoparticles from a redox non-innocent precursor,” published in the February 2018 issue of Nanotechnology 29(15).

Abstract: Herein, we report an aerobic synthesis method to produce bismuth nanoparticles (Bi NPs) with average diameters in the range 40-80 nm using commercially available bismuth triiodide (BiI₃) as starting material; the method uses only readily available chemicals and conventional laboratory equipment. Furthermore, size data from replicates of the synthesis under standard reaction conditions indicate that this method is highly reproducible in achieving Bi NP populations with low standard deviations in the mean diameters. We also investigated the mechanism of the reaction, which we determined results from the reduction of a soluble alkylammonium iodobismuthate precursor species formed in situ . Under appropriate concentration conditions of iodobismuthate anion, we demonstrate that burst nucleation of Bi NPs results from reduction of Bi³⁺ by the coordinated, redox non-innocent iodide ligands when a threshold temperature is exceeded. Finally, we demonstrate phase transfer and silica coating of the Bi NPs, which results in stable aqueous colloids with retention of size, morphology, and colloidal stability. The resultant, high atomic number, hydrophilic Bi NPs prepared using this synthesis method have potential for application in emerging X-ray contrast and X-ray therapeutic applications.

[portlandstateresearch]

Dean Atkinson, Chemistry faculty, co-authored “Using spectral methods to obtain particle size information from optical data: applications to measurements from CARES 2010,” in the April 2018 issue of ATMOSPHERIC CHEMISTRY AND PHYSICS 18(8).

Abstract: Multi-wavelength in situ aerosol extinction, absorption and scattering measurements made at two ground sites during the 2010 Carbonaceous Aerosols and Radiative Effects Study (CARES) are analyzed using a spectral deconvolution method that allows extraction of particle-size-related information, including the fraction of extinction produced by the fine-mode particles and the effective radius of the fine mode. The spectral deconvolution method is typically applied to analysis of remote sensing measurements. Here, its application to in situ measurements allows for comparison with more direct measurement methods and validation of the retrieval approach. Overall, the retrieved fine-mode fraction and effective radius compare well with other in situ measurements, including size distribution measurements and scattering and absorption measurements made separately for PM1 and PM10, although there were some periods during which the different methods yielded different results. One key contributor to differences between the results obtained is the alternative, spectrally based definitions of fine and coarse modes from the optical methods, relative to instruments that use a physically defined cut point. These results indicate that for campaigns where size, composition and multi-wavelength optical property measurements are made, comparison of the results can result in closure or can identify unusual circumstances. The comparison here also demonstrates that in situ multi-wavelength optical property measurements can be used to determine information about particle size distributions in situations where direct size distribution measurements are not available.