2023 Poster Abstracts

Poster #3: Uncovering the Driving Forces Controlling Ion Diffusion in Carbon Dioxide-Expanded Electrolytes

Elizabeth R. Bartlett, Ashley K. Borkowski, Christian K. Nilles, James D. Blakemore, and Ward H. Thompson

Department of Chemistry, University of Kansas

Elevated levels of atmospheric carbon dioxide (CO₂) resulting from human activities have triggered various adverse environmental consequences. This challenge has spurred the development of innovative technologies designed to transform excess gaseous CO₂, which is typically inert, into more usable species. Within the realm of electrochemical CO₂ conversion, efficiency is constrained by CO₂ concentration and solution conductivity. A recent advancement in this field involves the use of CO₂-expanded electrolytes (CXEs), which leverage electrochemical CO₂ conversion at high concentrations of CO₂ within non-aqueous electrolyte systems. However, experimental studies of CXEs have demonstrated that solution conductivity declines at high CO₂ pressures. Using molecular dynamics simulations, we aimed to elucidate the properties and behaviors of the system on the molecular level which contribute to the loss of solution conductivity.

From molecular dynamics simulations, a number of energetic and dynamical properties were calculated, including diffusion coefficients, activation energies of diffusion, and shear viscosity. Analyzing these properties of the CXE system components across a range of CO₂ pressures has provided insights into the molecular driving forces at play. As CO₂ is introduced, ion-ion interactions become increasingly prominent. Simultaneously, the diffusion of ions and the acetonitrile solvent accelerates, despite the presence of higher activation energies, thus underscoring the crucial role played by activation entropy in the diffusion process.

Poster #4: Understanding Hydrolysis Energy on Amorphous Silica Surface

Shreyaa Brahmachari and Marco Caricato

Department of Chemistry, University of Kansas

Amorphous silicates are widely used as support in heterogeneous catalysis due to their tunable structure and large surface area. The bulk of silica is composed of SiO₄ tetrahedral units that form siloxane rings of different sizes. In this project, cluster models composed of siloxane cages are used in modelling the silica surfaces to study the energetics of the hydrolysis reaction on amorphous silica. To quantify the variation of hydrolysis energy with the structural parameters of the unfunctionalized site, we use the random forest regression model to determine the most important descriptor that correlates with the functionalization energy. Observing all the different combinations of descriptors, the lowest average root mean square error is seen for a two-descriptor set composed of r^L (longest Si-O bond at the site) and θ^P_diff (difference between the smallest and largest peripheral angles). However, modelling large clusters is computationally expensive. Thus, for a quantitative simulation of the reaction we attempt to produce minimal models of the site of functionalization that mimic the results of the large clusters.

Poster #8:  Towards Accurate Modelling of Solute – Silica Interactions Using Ab Initio-Assisted Forcefields

Sahan M. Godahewa¹, Thanuja Jayawardena¹, Ward H. Thompson¹, and Jeffery A. Greathouse²

¹Department of Chemistry, University of Kansas and ²Nuclear Waste Disposal Research & Analysis Department, Sandia National Laboratories

Silica, being the most abundant material in the earth’s crust, offers a wide array of interesting applications based on the interactions between its surface and different types of solute molecules. The significance of these applications spans from geochemistry to catalysis. The difficulty in accurate modelling of interactions at silica interfaces motivates the development of forcefields that can describe the surface phenomena to a further extent. In this work, a recently developed silica-DDEC potential was further improved to model the interactions between CO₂ and cristobalite silica as a benchmark system. The Lennard-Jones parameters were optimized to reproduce the extensive dispersion-corrected periodic density functional theory calculations. The Locus of this work is to expand its application for use in molecular dynamic simulations, aiming to further validate structural and dynamical properties of CO₂ other organic molecules in aqueous solutions at silica interfaces. SNL is managed and operated by NTESS under DOE NNSA contract DE-NA0003525.

Poster #9: An Optimized Force Field for Silica-Water Interfaces

Thanuja Jayawardena¹, Sahan M. Godahewa¹, Ward H. Thompson¹, and Jeffery A. Greathouse²

¹Department of Chemistry, University of Kansas and ²Nuclear Waste Disposal Research & Analysis Department, Sandia National Laboratories

Given the significance of water-silica interfaces in numerous geochemical applications, it is crucial to have a force field that accurately describes their attributes. This can enable long timescale and large lengthscale modeling studies of mineral-fluid interfaces, including in microporous and mesoporous materials. While significant effort has been focused on the development of accurate silica force fields, much less attention has been paid to descriptions of liquids at the interface. In this work, the parameters for water-silica interactions are explicitly optimized to reproduce the results of density functional theory (DFT)calculations. The recently developed silica-DDEC force field, which was designed to reproduce the electrostatic interactions near the silica interface, is used as a starting point so that the focus is on modification of the Lennard-Jones parameters. DFT interaction energies of a single water molecule near a hydroxylated cristobalite surface were used to optimize the force field parameters. The force field is validated by analyzing the structural and dynamical properties of water at the interface. The prospects for applying this approach to aqueous solutions, including electrolytes, is discussed.SNL is managed and operated by NTESS under DOE NNSA contract DE-NA0003525.

Poster #10: Ultrafast Solution-Phase Norrish Photochemistry of Heterocyclic Cyclobutanones: Effect of 3-Oxo, 3-Aza, and 3-Thio Substitutions

Daniel R. Johnson¹, Manvendra Singh², Zarko Boskovic², and Christopher G. Elles¹

¹Department of Chemistry and ²Department of Medicinal Chemistry, University of Kansas

Non-linear spectroscopies have revolutionized many areas of material and life sciences. For example, the microscopy technique based on two-photon absorption (2PA) and emission enables super-resolution bioimaging. 2PA can provide complementary (and sometimes more detailed) information about electronic structure relative to one-photon absorption (1PA). The combination of theory and experiment can advance our understanding of the relationship between the molecular structure and the non-linear optical properties of the materials. Because of the experimental difficulties with measuring 2PA spectra and theoretical challenges with computing higher-order molecular properties, our knowledge of the 2PA processes is rather limited. In this talk, I will present our investigation on the 2PA spectra for several prototypical molecules (ethylene, toluene, cis- and trans-stilbene, and phenanthrene). The choice of stilbene and phenanthrene is motivated by their potential applications as molecular switches, which stimulated recent experimental studies by Elles and coworkers. Ethylene and toluene can be viewed as building blocks of stilbene. We employ the recently developed implementation for calculating 2PA cross-sections using equation-of-motion coupled-cluster wave functions with single and double substitutions (EOM-CCSD). We also analyze the electronic structure of the states that give rise to dominant features in the 2PA spectra using wave function analysis tools. We compare the computed 2PA spectra with the 1PA ones as well as with the experimentally measured ones (for stilbene and phenanthrene). We also investigate the effects of details of computational protocols on the computed spectra.

Norrish type I cleavage is initiated by a forbidden π* ← n UV excitation in cyclobutanone, a model system to physical chemists. In the gas phase, the reaction leads to two distinct product channels differentiated by number of carbon atoms, C2 and C3. While solution phase reaction products are known, the ultrafast reaction and the rate of formation of products is not understood. Here, we studied the ultrafast behavior of cyclobutanone in solution, and the consequence of S, O, and N-substitution, on the ultrafast time scale via electronic spectroscopy, supported by theoretical calculations and kinetic modeling. In heteroatom structures C-X-C product, analogous to C3 channel of CB, is stabilized by the heteroatom, and formation was observed on distinct timescales: direct formation due to ballistic motion (~100 fs) and delayed via thermalized channel (~100 ps). Direct formation occurs due to excitation above a C-C cleavage barrier on S₁, while slow formation is due to a fraction of population thermalizing before the barrier. The thermally excited initial product cools and blue shifts in ~4 ps to a long-lived state. Cyclobutanone photoproduct is formed on two similar time scales, but decays to zero in 1 ps. Kinetic and spectral components shared by all four structures indicate that the initial C3 product is shared between all four species, and the product formation observed in cyclobutanone is that of the C3 channel. 

Poster #15:  Selective Ethanol Dehydrogenation over Oxide-Supported Cu Nano-Islands

Lindsey N. Penland, Theresa Read, Darya M. Moiny, Jenyn Pinkley, and Rachael G. Farber

Department of Chemistry, University of Kansas

Oxide supported metal nanoparticles are commonly used heterogeneous catalysts for high selectivity product formation. Acetaldehyde, an industrially relevant petrochemical feedstock, is currently produced via oxidative dehydrogenation of alcohols over noble-metal catalysts. This approach is inherently expensive due to necessary post-production separation methods. A more cost-effective, efficient, and selective approach is non-oxidative dehydrogenation of ethanol over oxide supported Cu nanoparticles which eliminates the need for a separation step. While it is thought that the Lewis acid site strength of the oxide support influences product selectivity, there is not a thorough understanding of the atomistic reaction mechanism, structural features, or chemical and electronic properties driving this selective ethanol dehydrogenation.

Using TiO₂ anatase, ZrO₂/Pt₃Zr (001), and Nb(100) single crystals as oxide supports for Cu metal nano-islands, we will use a combination of in situ ultra-high vacuum (UHV) surface science techniques to elucidate the effect of Lewis acid site strength on the selective dehydrogenation of ethanol to acetaldehyde. First, we will develop preparation methods for Cu/TiO₂, Cu/ZrO₂, and Cu/(3×1)-O Nb(100) substrates. Then, initial ethanol adsorption on the model catalyst surface will be understood before studying the ethanol dehydrogenation pathway to form acetaldehyde. Auger electron spectroscopy (AES), temperature programmed desorption (TPD) and low energy electron diffraction (LEED) will be used to understand the surface composition, reaction products, and long-range surface structure of the model catalyst following substrate formation, ethanol adsorption, and acetaldehyde formation. Spatially resolved low-temperature scanning tunneling microscopy (LT-STM) and scanning tunneling spectroscopy (STS) will reveal the real-space structural and electronic features leading to observed catalytic performance. These fundamental mechanistic studies will contribute to the current understanding of how structural, chemical, and electronic properties drive selective chemical transformations over complex heterogeneous catalyst surfaces.

Poster #16:  Insights into How Chaperone Net Charge and Sequence Pattering Influence Nucleic Acid Folding

Gabrielle M. Perkins¹, Parnian Arafi², and Erik D. Holmstrom^1,3 

¹Department of Molecular Biosciences, ²Department of Undergraduate Biology, and ³Department of Chemistry, University of Kansas

Nucleic acid folding chaperone (NAFC) proteins help NAs adopt complex secondary and tertiary structures by transiently interacting with NA molecules. Some NAFCs can function as biomolecular counterions to the polyanionic phosphate backbone, thereby screening electrostatic repulsions and lowering the energic barrier between unfolded and folded NA states. To explore the fundamental principles associated with how NAFCs assist folding, we systematically “re-build” NAFCs from their smallest cationic constituents (e.g., ammonium→ Lys→ polyK₁₀→ NAFC). Using single-molecule FRET, we have begun to uncover sequential aspects of NAFCs that contribute to their chaperoning function, such as net cationic charge and charge distribution. We show that increasing counterion charge systematically decreases the ^appK_d over several orders of magnitude and that an optimal net charge exists for decreasing the folding free energy barrier (deltadeltaG). We compare these observations from polypeptide chaperones to the behavior of biological NAFCs (e.g., protamine, H1, and HCV nucleocapsid protein). 

Poster #19:  Insights into the Isoenergetic Monomeric Structures of the Hepatitis C Virus 3'X RNA

Parker D. Sperstad¹ and Erik D. Holmstrom^1,2 

¹Department of Molecular Biosciences and ²Department of Chemistry, University of Kansas

The hepatitis C virus 3ʹX RNA is a highly conserved, 98-nt sequence at the 3ʹ terminus of the genome with two isoenergetic conformations. These two conformations differ in the base paring in the first 55-nt and are notably distinguished by the organization of a palindromic 16-nt sequence called the dimer linkage sequence (DLS) that is responsible for genome dimerization. One conformation, DLSa, is a single stem-loop and presents the DLS in the apical loop. Conversely, the second conformation, DLSb, is a two stem-loop conformation that buries the dimer initiating bases in a stem. Here, we monitored the conformational status of monomeric 3ʹX RNA using single-molecule FRET to further understand which conformation is formed at any given time or under a given set of conditions and how they might interconvert. We have observed the two monomeric conformations with their relative abundances dictated by either solution conditions or nucleotide deletions.

Poster #20:  Expanding Differential Ion Mobility Separations into the MegaDalton Range

Tobias P. Worner¹, Hayden A. Thurman², Alexander A. Makarov¹, Alexandre A. Shvartsburg²

¹Thermo Fisher Scientific, Bremen, Germany and ²Department of Chemistry and Biochemistry, Wichita State University

Along with mass spectrometry (MS), ion mobility separations (IMS) continuously advance to ever larger biomolecules. The emergence of electrospray ionization (ESI) and native MS had enabled the IMS/MS analyses of proteins up to ~100 kDa in 1990s and protein complexes and viruses up to ~10 MDa since 2000s. Differential IMS (FAIMS) capturing the high-field ion mobility is substantially orthogonal to linear IMS based on the absolute low-field mobility and offers exceptional resolution, unique selectivity, and steady filtering compatible with slower analytical methods such as the electron transfer or ozone-induced dissociation. However, the associated MS stages have limited FAIMS to ions with m/z < 8,000 and mass under ~300 kDa. Here we integrate high-definition FAIMS with bisinusoidal waveform of 1 MHz frequency at UD up to 4.6 kV (ED up to 25 kV/cm) with the Thermo Q-Exactive Orbitrap UHMR mass spectrometer with m/z range to 80,000, enabling FAIMS/MS analyses of “native” MDa-size species. In the initial assessment, the oligomers of monoclonal antibody Adalimumab/Humira (148 kDa) were size-selected up to at least nonamers (1.3 MDa with m/z up to ~17,000). All signal was at positive compensation voltages with cubic dependence on the dispersion voltage, indicating the regular FAIMS process with no dipole alignment and thus low dipole moments below 400 Debye as previously found for native protein complexes up to ~150 kDa. That is consistent with the preserved compact geometries and diminished charge density. The m/z limit of current platform extends fourfold above the explored range, allowing studies of yet larger macromolecules.