Abstract: Biological polymer networks such as mucus, extracellular matrix, nuclear pore complex, and bacterial biofilms, play a critical role in governing the transport of nutrients, biomolecules and particles within cells and tissues. The interactions between particle and polymer chains are responsible for effective selective filtering of particles within these macromolecular networks. This selective filtering is not dictated by steric alone but must use additional interactions such electrostatics, hydrophobic and hydrodynamic effects to control particle transport within biogels. Depending on chemical composition and desired function, biogels use selective filtering to allow some particles to permeate while preventing others from penetrating the biogel. The mechanisms underlying selective filtering are still not well understood yet have important ramifications for a variety of biomedical applications. Controlling these non-steric interactions are critical to understanding molecular transport in vivo as well as for engineering optimized gel-penetrating therapeutics. Fluorescence correlation spectroscopy (FCS) is an ideal tool to study particle transport properties within uncharged and charged polymer solutions. In this dissertation, our research focuses primarily on the role of electrostatics on the particle diffusion behavior within polymer solutions in the semi-dilute and concentrated regimes.

Using a series of charged dye molecules, with similar size and core chemistry but varying net molecular charge, we systematically investigated their diffusion behavior in polymer solutions and networks made up of polysaccharide and proteins. Specifically, we studied in Chapter 3 the probe diffusion in semidilute and concentrated dextran solutions. The hindered diffusion observed in attractive gels is dependent on the probe net charge and shows a dependence on the solution ionic strength. Using a biotinylated probe, we also show evidence of an additional non-electrostatic interaction between the biotin molecule and the dextran polymer chains. In contrast, comparisons to a highly charged, water soluble polyvinylamine (PVAm) semidilute solution shows that all probes, regardless of charge, were highly hindered and a weaker dependence on solution ionic strength was observed. In Chapter 4, we characterized the transport properties of our probe molecules within pure and mixed charge solutions of amino(+)-dextran and carboxymethyl(-)-dextran. We show that these mixed charge polymer solutions still have the potential to be efficient filters for interacting particles even with comparably few attractive interaction sites. By chemical modification of the amino dextran, we also compare these results to those obtained in polyampholytic solutions. Lastly, we investigate the transport properties of both probes and a much larger bovine serum albumin (BSA) protein molecule within liquid-liquid phase separated (LLPS) tau protein in chapter 5. Tau is an intrinsically disordered protein with both positive and negatively charged amino acids. We show that despite having a high local protein concentration, tau droplets are relatively low density and comparable to semi-dilute polymer solutions. Both probe molecules and BSA are observed by FCS to be recruited within the liquid droplet resulting in ~10x fold increase in particle concentration inside the tau droplet compared to outside. Probe transport within the phase separated tau is sensitive to probe net charge and solution ionic strength. Lastly, we show that BSA transport inside the tau droplet can be fairly well described by using Stokes-Einstein adjusted for the experimentally determined microviscosity within the tau droplet.

Keywords: diffusion, biological gels, fluorescence correlation spectroscopy, electrostatic, interaction filtering.

Join the seminar at https://uky.zoom.us/j/9237836600

The Department of Chemistry hosts a Graduation Celebration and Awards Ceremony to recognize the outstanding acheivements of our students on an annual basis. This year's event will be streamed via Facebook. Please join us by clicking here!

We are delighted to recognize the following graduates of our PhD, Masters, and Undergraduate programs:

Abstract:
 

 ClpXP is an Escherichia coli protease that carryout energy-dependent intracellular proteolysis. In recent years, this system has been widely studied due to its importance as a protein regulatory machinery and a virulence factor.  Protein substrates of ClpXP contain degrons with a specific protein sequence. SsrA tag is one of the five degrons known to subject proteins for ClpXP degradation. SsrA is an 11 amino acid peptide added to the C-terminus of nascent polypeptide chains translated from aberrant messenger RNAs lacking stop codons via a process called trans-translation.

ClpXP was known to targets only cytosolic proteins with degrons until recently, AcrB, an E. coli membrane protein was found to be degraded by ClpXP when it is tagged by ssrA peptide, which leads to the speculation that ClpXP is capable of degrading membrane proteins.   However, this speculation was challenged with the finding that ssrA tagging of ProW1−182, a different inner-membrane protein resulted in degradation by AAA+ membrane protease FtSH. We report that the membrane substrates of ClpXP bear long c-terminal cytoplasmic domains while metastable proteins lacking cytoplasmic domains are degraded by FtsH. For instance, ssrA tagged Aquaporin-Z (AqpZ), a stable tetrameric membrane protein lacking a c-terminal cytoplasmic domain is subjected to degradation by neither ClpXP nor FtsH. Nevertheless, when the c-terminus of AqpZ is fused with ssrA tagged Cyan fluorescent protein ClpXP degrades the resulted fusion protein while truncated metastable version, AqpZ 1-155 is degraded by FtSH.

This presentation also emphasizes our attempt to unravel the possible effect of proton motive force on the activity of ClpXP. We used Carbonyl cyanide m-chlorophenyl hydrazone (CCCP) to disrupt the proton motive force. Our results suggest that degradation of soluble protein substrates such as GFP-ssrA, MurA-ssrA, Chloramphenicol acetyltransferase ssrA are not affected by CCCP. However, degradation of membrane protein substrates by ClpXP is diminished in the presence of CCCP. We speculate that either the proton motive force or ATP provided from oxidative phosphorylation is essential, or both are important for ClpXP to degrade membrane proteins. 

It has been shown that the TolC is not a good target for inhibition of multidrug efflux of antibiotic-resistant bacteria as the bacterial susceptibility to antibiotics was not affected even when a significant amount of TolC is depleted.  TolC is a membrane protein channel that functions in conjunction with transporters and membrane fusion proteins and provides a pathway to expel antibiotics across the E. coli outer membrane.  AcrAB-TolC multidrug efflux pump is one such example where TolC cooperates with AcrB transporter and AcrA membrane fusion protein.   We report that the depletion of the number of copies of AcrB makes bacteria highly susceptible to antibiotics. We utilized ClpXP degradation system to regulate the copy number of AcrB in the cell. Our results show that AcrB is an excellent target for inhibiting multidrug efflux, and ClpXP is an excellent tool to regulate antibiotic target proteins for research purposes.

Bio: Curtis P. Berlinguette is a Professor of Chemistry and Chemical & Biological Engineering at the University of British Columbia. He is also a CIFAR Program Co-Director and a Principal Investigator at the Stewart Blusson Quantum Matter Institute (SBQMI), and the CEO of Miru Smart Technologies.

Prof. Berlinguette leads a large, interdisciplinary team seeking ways to discover and scale disruptive clean energy materials. His academic group has advanced a range of clean energy applications including CO₂ utilization, next-generation solar cells, and self-driving labs. Prof. Berlinguette also likes to work on high-risk, high-impact clean energy projects like cold fusion. He has authored more than 100 scientific articles and 20 patent applications, and has participated in over 190 invited lectures at leading universities and international conferences. Prof. Berlinguette has been recognized with several awards, including an Alfred P. Sloan Research Fellowship and an NSERC E.W.R. Steacie Memorial Fellowship.

Abstract: The electrochemical conversion of CO₂ by the CO₂ reduction reaction (CO₂RR) is a promising strategy that enables renewable energy to be stored in carbon chemicals and fuels using atmospheric or emitted CO₂. Pilot-scale electrolyzers utilizing gaseous CO₂ feedstocks can mediate high rates of CO₂RR, however, this approach relies on several complex and energy-intensive steps required to produce purified, high-pressure CO₂ from carbon capture. This presentation will focus on the direct conversion of aqueous carbon capture solutions (i.e., those rich in bicarbonate anions) into useful chemicals (i.e., CO) over extended periods of time. I will show how to design an electrolyzer that converts liquid bicarbonate feedstocks into carbon products at comparable rates and greater efficiencies than reactors relying on pressurized CO₂. Our work demonstrates bicarbonate electrolysis as a practical strategy for storing renewable energy in carbon chemicals while bypassing CO₂ separation and pressurization processes in upstream CO₂ capture.

Find details of the event and registration here.

To view a copy of the 2019 abstract booklet, click here.

Note to UK students: Students in CHE 395 planning to graduate or otherwise conclude their research are required to participate in the Poster Session if they have not done so in the past. 

Schedule of Events:
10:00am - Zoom Check-In and Set Up
10:30 - 12:00pm - Group A Presents
1:00pm - 2:30pm - Group B Presents
3:30pm - Awards Presented

Recent winners include students from:

Abstract:

Materials are chemicals that we use every day for tools, tasks, and technology. For most of history, making a material required trial-and-error, synthesizing and testing, a costly endeavor in time and money. With modern computing, not only can the trial-and-error be hastened, but sometimes avoided altogether. The application of a material depends on its properties, which arise from its structure, thus by exploring chemical structure we can predict properties and design materials to suit. One tool to accomplish this is the genetic algorithm (GA), which can build and test chemical structures for a desired property, and then produce new chemical structures through reproduction. Genetic algorithms have been applied to chemistry for 30 years in solving X-ray diffraction patterns, protein folding, and predicting surface structures. Here a GA is applied to solve the structure of Li-Al layered double hydroxide (LDH), given an experimental X-ray diffraction pattern and debate in the literature. The resulting GA can build a wide variety of LDH structures by stacking layers of crystal and molecule together, eventually providing a set of structures that can be used for further quantum mechanical calculations. The GA was then generalized to a wider variety of layered structures, resulting in the development of the Genetic Algorithm for Layered Structures (GALS). GALS is able to generate LDH structures with multiple elements and molecules, structures with different coordinating groups, molecular crystals, and perovskites. Initial results are promising, with testing under a small number of generations showing significant improvements in fitness, and room for generalization down the road.

Abstract:  Metal-halide perovskites (MHPs), with formula ABX₃ (A = methylammonium, formamidinium, or Cs⁺; B = Sn²⁺ or Pb²⁺; and X = Cl^-, Br^-, or I^-) are versatile and attractive materials because of their tunable optical and electronic properties. These optical and electronic properties include tunable direct band gaps, high absorption coefficients, low exciton binding energies, relatively high electron and hole mobilities, narrow emission line-widths, and high photoluminescence (PL) quantum yields (Φ_PL). Much of the initial excitement around organic metal-halide perovskites focused on their application in photovoltaics (PVs) based on thin polycrystalline films, whereas colloidal metal-halide perovskite nanocrystals (NCs) are now a subject of intense interest due to their highly desirable emission properties and low rate of non-radiative recombination for light emitting applications. However, both polycrystalline MHP thin films and their NC counterparts suffer from poor stability and are highly moisture sensitive. In this talk, facile and rapid anion exchange and surface modification routes of MHP NCs will be discussed using alkyltrichlorosilane, alkanethiols, and alkanethiol-aluminum trihalide combinations. In addition, similar approaches are employed to modify solution processed MHP thin films for fabricating efficient and stable photovoltaic devices.

Rapid anion exchange and surface modification reactions with MHP NCs readily proceed via coupling and/or hydrolysis reactions of the surface ligands at room temperature. Both NCs, thin films, and thin film-based PV devices demonstrate significantly enhanced performance and stability upon surface modification. It is shown that alkyltrichlorosilanes (RSiCl₃) can be used as Cl^- sources for rapid anion exchange with host CsPbBr₃ NCs during hydrolysis of alkytrichlorosilanes in the colloidal dispersion of CsPbBr₃ NCs. Hydrolysis of alkyltrichlorosilanes leads to the formation of siloxane coated CsPbCl₃ NCs with significantly improved Φ_PL of up to 12% and improved long-term stability. In another study of surface modification, dodecanethiol modification of CsPbBr₃ NCs is demonstrated to significantly enhance the stability and Φ_PL of CsPbBr₃ NCs, with Φ_PL of near 100%. This surface modification can be expedited through exposure to UV light, which also induces thiol-ene reactions.  A mixture of dodecanethiol (DDT) and AlX₃ (X = Cl, Br, I) can be used to increase the applicability of alkanethiol treatment to all NC compositions.  Here, DDT and AlX₃ (X = Cl, Br, I) treatment transforms CsPbCl₃ nanocubes into 4-15 monolayer thick CsPbX₃ nanoplates (NPs) with high Φ_PL (up to 47% and 65% for violet and blue emitting NPs, respectively, near 100% for green emitting NPs, and 81% for red emitting NPs) while maintaining good long-term stability at room temperature. NC modifications do not directly translate to their thin film counterparts because of variations in surface properties. However, with some ligand engineering, thiol derived surface ligand modified polycrystalline Cs_0.15FA_0.85PbI₃ photovoltaics show power conversion efficiency of near 17% with enhanced stability. These findings will help pave the way towards efficient and stable future optoelectronic devices.

Abstract: To meet increasingly stringent automotive emissions standards, further improvements in catalytic converter design are necessary. Current automotive catalyst systems are effective at eliminating emission of nitrogen oxides (NOx) once the catalyst reaches operational temperature (~200 °C). NOx emitted at lower catalyst temperatures now comprises most of the NOx released during a typical test cycle. Referred to as “the cold start problem” this issue has come to the forefront of automotive catalyst development, as mitigating these emissions is necessary to further reduce automotive emissions. Passive NOx adsorbers present an appealing solution to the cold start problem, these being a class of materials that chemisorb exhaust components such as NOx, carbon monoxide (CO) and hydrocarbons at near-ambient temperatures, and then desorb these compounds once the downstream catalyst has reached operational temperature. An effective passive NOx adsorber must have several properties: high NOx adsorption at near-ambient temperatures, near-complete NOx desorption at temperatures within the operational range, high thermal stability, and resistance to automotive exhaust components at high temperatures.

Pd-exchanged zeolites have shown promise for deployment as Passive NOx adsorbers, though much remains to be understood about their adsorption chemistry and deactivation. In-situ Diffuse Reflectance Infrared Fourier Transform Spectroscopy (DRIFTS) provides a convenient probe of adsorbed species, most automotive exhaust components possessing IR-active chemical bonds. By examining the evolution of IR bands under various pretreatments and adsorbates, the overall Pd-speciation and adsorptive zeolite sites of each material can be characterized, and the identities of IR bands can be deduced. In this work, microreactor-MS analysis of the adsorption and desorption behavior of these materials was also examined, these results being coupled with in-situ DRIFTS temperature programmed desorption (TPD) to correlate desorption events with specific adsorbed species.

A pair of zeolite frameworks of similar Si/Al ratio but differing pore size were examined, Beta zeolite (BEA) and Chabazite (CHA) representing a medium- and small-pore framework, respectively. The effect of Pd-loading on BEA was examined, as well as the various deactivation pathways and active sites of each material.

KEYWORDS: Passive NOx Adsorber, Automotive Catalysis, Environmental Catalysis, Palladium, Zeolite, DRIFTS

Abstract: Application of organic electronics have increased significantly over the past two decades. Organic materials can be used in flexible devices with cheaper cost of fabrication, yet in most cases the devices suffer from poor performance and stability. Investigating doping mechanism, charge transport and charge transfer in such materials can help us to understand the origin of these issues and later resolve them. In this dissertation, organic materials are used in three different device structures to investigate charge transport and charge transfer. Chemically doped pi-conjugated polymers are promising materials to be used in thermoelectric (TE) devices, yet their application is limited by their low performance. Blending two polymers is a simple way to change the properties of the TE devices. Here we used a simple analytical model to calculate TE properties of polymer blend by taking into account for energetic disorder, energetic offset between two polymers and localization length which proposed TE performance of polymer blend can exceed the individual ones at specific blends of two polymers. We showed these improvements are achievable by experimentally testing TE properties of selected polymer blends. Further, to investigate the doping mechanism in polymers, we used organic electrochemical transistors to investigate the effect of anion size on polaron delocalization and the thermoelectric properties of single polymers. This device structure allowed us to control the charge carrier concentration with minimizing the effects on the film morphology.

In organic photovoltaics (OPVs), upon fluorination of donor molecules the performance of device increases in most cases. So, we investigated the charge transfer state energy between the electron donor anthradithiophene (ADT) and the electron acceptor C60 upon halogenation of the ADT molecule. Interfacial energetics and charge transfer state energies between donor and acceptor are crucial to performance of these devices. We probe interfacial energetics of donor/acceptor interfaces with Ultraviolet photoelectron spectroscopy (UPS) charge transfer state energies with sensitive External Quantum Efficiency (EQE) setup both in bilayer and bulk heterojunction device structure. These measurements coupled with DFT calculations allowed us to explain the effects of halogenation on the OPV devices characteristics. Investigating charge transfer states energies, charge transport and doping mechanism in organic materials allow us to improve the performance of organic based electronics and also propose new applications for these family of materials.

Abstract: Organic metal halide perovskites are promising materials for various optoelectronic device applications such as light emitting diodes (LED) and photovoltaic (PV) cells. Perovskite solar cells (PSCs) have shown dramatic increases in power conversion efficiency over the previous ten years, far exceeding the rate of improvement of all other PV technologies. PSCs have attracted significant attention due to their strong absorbance throughout the visible region, high charge carrier mobilities, color tunability, and ability to make ultralight weight devices. However, organic metal halide perovskites still face several challenges. For example, their environmental stability issue must be overcome to enable widespread commercialization. Meeting this challenge involves material and interface development and optimization throughout the whole PV device stack. Fundamental understanding of the optical properties, electrical properties, interfacial energetics, and device physics is key to overcome current challenges with PSCs. In this dissertation, we report a new family of triarylaminoethynyl silane molecules as hole transport layers (HTLs), which are in part used to investigate how the PV performance depends on the ionization energy (IE) of the HTL and provide a new and versatile HTL material platform. We found that triarylamoniethynyl silane HTLs show comparable PV performance to the state-of-the art HTLs and demonstrated that different processing conditions can influence IE of methylammonium lead iodide (MAPbI3).

Surface ligand treatment provides a promising approach to passivate defect states and improve the photoluminescence quantum yield (PLQY), charge-carrier mobilities, material and device stability, and photovoltaic (PV) device performance of PSCs. Numerous surface treatments have been applied to PSC thin films and shown to passivate defect states and improve the PLQY and PV performance of PSCs, but it is not clear which surface ligands bind to the surface and to what extent. As surface ligands have the potential to passivate defect states, alter interface energetics, and manipulate material and device stability, it is important to understand how different functional groups interact with the surfaces of PSC thin films. We investigate a series of ligand binding groups and systematically probe the stability of the bound surface ligands, how they influence energetics, PLQYs, film stability, and PV device performance. We further explore ligand penetration and whether surface ligands prefer to remain on the surface or penetrate into the perovskite. Three variations of tail groups including aryl groups with varying extents of fluorination, bulky groups of varying size, and linear alkyl groups of varying length are examined to probe ligand penetration and the impact on material stability.