Physical Chemistry Commons^™

Resolving The Three-Dimensional Rotational And Translational Dynamics Of Single Molecules Using Radially And Azimuthally Polarized Fluorescence, Oumeng Zhang, Weiyan Zhou, Jin Lu, Tingting Wu, Matthew D. Lew

Electrical & Systems Engineering Publications and Presentations

We report a radially and azimuthally polarized (raPol) microscope for high detection and estimation performance in single-molecule orientation-localization microscopy (SMOLM). With 5000 photons detected from Nile red (NR) transiently bound within supported lipid bilayers (SLBs), raPol SMOLM achieves 2.9 nm localization precision, 1.5° orientation precision, and 0.17 sr precision in estimating rotational wobble. Within DPPC SLBs, SMOLM imaging reveals the existence of randomly oriented binding pockets that prevent NR from freely exploring all orientations. Treating the SLBs with cholesterol-loaded methyl-β-cyclodextrin (MβCD-chol) causes NR’s orientational diffusion to be dramatically reduced, but curiously NR’s median lateral displacements drastically increase from 20.8 to …

Spectroscopic Properties Relevant To Astronomical And Laboratory Detection Of Mch And Mch+ (M = Al, Mg), Vincent J. Esposito, Tarek Trabelsi, Joseph S. Francisco

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

New spectroscopic parameters have been calculated to aid in the laboratory and observational detection of AlCH, AlCH⁺, MgCH, MgCH⁺, and their deuterated analogs. All species exist in linear geometry except for AlCH+, which exhibits a bent structure. Rotational frequencies have been calculated and the transition with maximum intensity is discussed for three temperature regions present in space: 100 K for a central circumstellar envelope (CSE), 30 K for an outer CSE, and 3 K indicative of the interstellar medium. Pertinent frequencies range from 25 to 250 GHz, depending on the species. At 30 K, the most …

Inhibitors Of Alpha-Synuclein Aggregation, Jemil Ahmed

Electronic Theses and Dissertations

Alpha-Synuclein (αS) – a neuronal, disordered, presynaptic protein – aggregates into amyloid fibrils and accumulates in the substantia nigra pars compacta of Parkinson's Disease (PD) patients. The aggregation and accumulation of αS amyloid fibrils leads to death of dopaminergic neurons; a hallmark of PD. Although it’s not clear why αS aggregates, prior studies have found that intrastriatal injection of fibril alone is sufficient to cause PD pathology in mouse and non-human primates models. These observations implicate αS as a therapeutic target against PD.

Unfortunately, there are three caveats when attempting to target αS. First, αS is a neuronal protein expressed …

Using Powder Diffraction To Give Insight Into Structures Of Ir2(Diisocyanomenthane)4x2 [Dimen] (X = Cl; Pf6; Bph4), Mairead Brownell

Scripps Senior Theses

Ir2(dimen)42+ (dimen = 1,8-diisocyanomenthane) has been studied extensively as model compound to better understand catalysis of photochemical reactions. Although Ir2(dimen)42+ has been used primarily to observe the photophysical changes of metal-metal transitions, it gives great insight into the transitions that allow other d8-d8 metal complexes to undergo photochemical processes and generate hydrogen gas. The large visible range by which Ir2(dimen)42+ (1) can be electronically excited in solution is indicative of its two solution phase ground states, which interestingly have been hypothesized to resemble two unique packing structures observed in the powder state. In this study, the powder diffraction patterns of …

Electronic Structure Of Early Transition Metal Complexes Supported By Pyridine Polypyrrolide Ligands, Dylan Connor Leary

Graduate Theses, Dissertations, and Problem Reports (ETD)

A thorough study of photoluminescent molecules involving the pyridine polypyrrole(ide) ligand platform has been conducted. A detailed analysis on speciation of the proligand H₂(^MesPDP^Ph) (H₂^MesPDP^Ph = 2,6-bis(5-mesityl-3-phenyl-1H-pyrrol-2-yl)-pyridine) and its dilithium salt Li₂(^MesPDP^Ph) revealed temperature- and solvent-dependent effects. These molecules, along with the hydrochloric acid adduct [H₃(^MesPDP^Ph)]Cl were found to exhibit short-lived photoluminescence in both tetrahydrofuran and benzene solution. These findings confirm the hypothesis that heavy-atom involvement is crucial for the favorable photophysical properties observed for the Zr(PDP)_{2 …}

From Evaluating The Performance Of Approximations In Density Functional Theory To A Machine Learning Design, Pedram Tavazohi

Graduate Theses, Dissertations, and Problem Reports (ETD)

Density-functional theory (DFT) has gained popularity because of its ability to predict the properties of a large group of materials a priori. Even though DFT is exact, there are inaccuracies introduced into the theory due to the approximations in the exchange-correlation (XC) functionals. Over the 50 years of its existence, scientists have tried to improve the design of the XC functionals. The errors introduced by these functionals are not consistent across all types of solid-state materials. In this project, a high throughput framework was utilized to compare the theoretical DFT predictions with the experimental results available in the Inorganic Crystal …

Self-Assembly Of Black Cumin Oil-Based Nanoemulsion On Various Surfactants: A Molecular Dynamics Study, Aulia Fikri Hidayat, Taufik Muhammad Fakih

Makara Journal of Science

Black cumin is commonly used as traditional medicine due to its wide range of pharmacological potential. Black cumin oil (BCO) was often prepared as nanoemulsion to improve its solubility, stability, and bioavailability. This study was conducted to investigate the molecular behavior as well as structural evolution of BCO-surfactant systems during self-assembly micellization using molecular dynamics (MD) simulations. Several BCO constituents and variations of surfactants were employed to model BCO-surfactant systems. 50 ns of MD simulations were performed to elucidate their evolution of structures and physicochemical properties during formation. Results showed that BCO-tween20 and BCO-lecithin were able to form spherical-shaped micelles …

A Nanoscale Shape-Discovery Framework Supporting Systematic Investigations Of Shape-Dependent Biological Effects And Immunomodulation, Wei Zhang, Hender Lopez, Luca Boselli, Paolo Bigini, André Perez-Potti, Zengchun Xie, Valentina Castagnola, Qi Cai, Camila P. Silveira, Joao M. De Araujo, Laura Talamini, Nicolò Panini, Giuseppe Ristagno, Martina B. Violatto, Stéphanie Devineau, Marco P. Monopoli, Mario Salmona, Valeria A. Giannone, Sandra Lara, Kenneth A. Dawson, Yan Yan

Articles

Since it is now possible to make, in a controlled fashion, an almost unlimited variety of nanostructure shapes, it is of increasing interest to understand the forms of biological control that nanoscale shape allows. However, a priori rational investigation of such a vast universe of shapes appears to present intractable fundamental and practical challenges. This has limited the useful systematic investigation of their biological interactions and the development of innovative nanoscale shape-dependent therapies. Here, we introduce a concept of biologically relevant inductive nanoscale shape discovery and evaluation that is ideally suited to, and will ultimately become, a vehicle for machine …

Splashing Of Large Helium Nanodroplets Upon Surface Collisions, Paul Martini, Simon Albertini, Felix Laimer, Miriam Meyer, Michael Gatchell, Olof E. Echt, Fabio Zappa, Paul Scheier

Faculty Publications

In the present work we observe that helium nanodroplets colliding with surfaces can exhibit splashing in a way that is analogous to classical liquids. We use transmission electron microscopy and mass spectrometry to demonstrate that neutral and ionic dopants embedded in the droplets are efficiently backscattered in such events. High abundances of weakly bound He-tagged ions of both polarities indicate a gentle extraction mechanism of these ions from the droplets upon collision with a solid surface. This backscattering process is observed for dopant particles with masses up to 400 kilodaltons, indicating an unexpected mechanism that effectively lowers deposition rates of …

Discovery Of An Olivine-Type Lithium Manganese Thiophosphate, Limnps4,: Via A Building Block Approach, Srikanth Balijapelly, Kartik Ghosh, Aleksandr V. Chernatynskiy, Amitava Choudhury

Physics Faculty Research & Creative Works

An olivine-type orthothiophospate LiMnPS4 has been synthesized for the first time through a building block approach by reacting preformed ternary lithium thiophospate with MnCl2. Diffuse reflectance measurements show an optical band gap of 2.36 eV, which is further confirmed by DFT calculations. Irreversible weak ferromagnetic ordering and metamagnetism are verified through preliminary magnetic measurements.

Adsorption Of Helium On A Charged Propeller Molecule: Hexaphenylbenzene, Siegfried Kollotzek, Florent Calvo, Serge Krasnokutski, Fabio Zappa, Paul Scheier, Olof E. Echt

Faculty Publications

Physisorption on planar or curved graphitic surfaces or aromatic rings has been investigated by various research groups, but in these studies the substrate was usually strictly rigid. Here we report a combined experimental and theoretical study of helium adsorption on cationic hexaphenylbenzene (HPB), a propeller-shaped molecule. The orientation of its propeller blades is known to be sensitive to the environment, with substantial differences between the molecule in the gas phase and in the crystalline solid. Mass spectra of He_nHPB⁺, synthesized in helium nanodroplets, indicate enhanced stability for ions containing n = 2, 4, 14, 28, 42, …

The Profound Photophysical Effects Of Organic Chromophore Connectivity And Coupling, David J. Walwark Jr

Nanoscience and Microsystems ETDs

Through-bond and through-space interactions between chromophores are shown to have wide-ranging effects on photophysical outcomes upon light absorption in organic molecules. In collapsed poly(3-hexylthiophene), through-space coupling creates hybrid chromophores that act as energy sinks for nearby excitons and favorable sites for molecular oxygen to dock. Upon excitation with visible light the highly-coupled chromophores react with the docked oxygen and subsequently do not quench nearby excitons as efficiently. In tetramer arrays of perylene diimide chromophores the central moiety through-bond connectivity is synthesized in two variants which exhibit vastly different single-molecule blinking behavior and theoretically-predicted electronic transition character. In the more-connected tetramer …

Single-Molecule Localization Microscopy Of 3d Orientation And Anisotropic Wobble Using A Polarized Vortex Point Spread Function, Tianben Ding, Matthew D. Lew

Electrical & Systems Engineering Publications and Presentations

Within condensed matter, single fluorophores are sensitive probes of their chemical environments, but it is difficult to use their limited photon budget to image precisely their positions, 3D orientations, and rotational diffusion simultaneously. We demonstrate the polarized vortex point spread function (PSF) for measuring these parameters, including characterizing the anisotropy of a molecule’s wobble, simultaneously from a single image. Even when imaging dim emitters (∼500 photons detected), the polarized vortex PSF can obtain 12 nm localization precision, 4°–8° orientation precision, and 26° wobble precision. We use the vortex PSF to measure the emission anisotropy of fluorescent beads, the wobble dynamics …

Bridging The 12-6-4 Model And The Fluctuating Charge Model, Pengfei Li

Chemistry: Faculty Publications and Other Works

Metal ions play important roles in various biological systems. Molecular dynamics (MD) using classical force field has become a popular research tool to study biological systems at the atomic level. However, meaningful MD simulations require reliable models and parameters. Previously we showed that the 12-6 Lennard-Jones nonbonded model for ions could not reproduce the experimental hydration free energy (HFE) and ion-oxygen distance (IOD) values simultaneously when ion has a charge of +2 or higher. We discussed that this deficiency arises from the overlook of the ion-induced dipole interaction in the 12-6 model, and this term is proportional to 1/r …

Awegnn: Auto-Parametrized Weighted Element-Specific Graph Neural Networks For Molecules., Timothy Szocinski, Duc Duy Nguyen, Guo-Wei Wei

Mathematics Faculty Publications

While automated feature extraction has had tremendous success in many deep learning algorithms for image analysis and natural language processing, it does not work well for data involving complex internal structures, such as molecules. Data representations via advanced mathematics, including algebraic topology, differential geometry, and graph theory, have demonstrated superiority in a variety of biomolecular applications, however, their performance is often dependent on manual parametrization. This work introduces the auto-parametrized weighted element-specific graph neural network, dubbed AweGNN, to overcome the obstacle of this tedious parametrization process while also being a suitable technique for automated feature extraction on these internally complex …

Recovery Of High Specific Activity Molybdenum-99 From Accelerator-Induced Fission On Low-Enriched Uranium For Technetium-99m Generators, M. Alex Brown, Nathan Johnson, Artem V. Gelis, Milan Stika, Anna G. Servis, Alex Bakken, Christine Krizmanich, Kristin Shannon, Peter Kozak, Amanda Barnhart, Chad Denbrock, Nicolas Luciani, Terry Grimm, Peter Tkac

Chemistry and Biochemistry Faculty Research

A new process was developed to recover high specific activity (no carrier added) 99Mo from electron-accelerator irradiated U3O8 or uranyl sulfate targets. The process leverages a novel solvent extraction scheme to recover Mo using di(2-ethylhexyl) phosphoric acid following uranium and transuranics removal with tri-n-butyl phosphate. An anion-exchange concentration column step provides a final purification, generating pure 99Mo intended for making 99Mo/99mTc generators. The process was demonstrated with irradiated uranium targets resulting in more than 95% 99Mo recovery and without presence of fission products or actinides in the product.

Characterizing The Vibrational Spectra Of Hydrogen Bonded Systems With Molecular Dynamics Simulations And Quantum Chemical Methods, Dalton Boutwell

Master of Science in Chemical Sciences Theses

We apply and assess the utility of DMD for the purpose of investigating complex spectral features in N₂H⁺···OC, N₂D⁺···OC, C₂O₄H^-, C₂O₄D^- and (HCOOH)₂. The proton transfer as a vibrational motion consists of diffuse qualities that can be accounted for with classical and quantum chemical analyses. Classical approaches yield a wealth of information about vibrational spectra at a reduced cost, as in the case of previously investigated N₄H⁺. The isoelectronic N₂H⁺···OC has …

Β -Technetium: An Allotrope With A Nonstandard Volume-Pressure Relationship, Emily Siska, Dean Smith, Christian Childs, Daniel Koury, Paul M. Forster, Keith V. Lawler, Ashkan Salamat

Chemistry and Biochemistry Faculty Research

We report the synthesis and structure of the second allotrope of technetium, β-Tc. Transformative pathways are accessed at extreme conditions using the laser-heated diamond anvil cell and confirmed with in situ synchrotron x-ray diffraction and Raman spectroscopy. β-Tc is fully recoverable to ambient conditions, although counter to our DFT calculations predicting a face-centered-cubic lattice, we observe a tetragonal structure (I4/mmm) that exhibits further tetragonal distortion with pressure. β-Tc has an expanded volume relative to the hcp ground state phase, that when doped with nitrogen has an unexpected volume lowering. Such anomalous behavior is possibly indicative of a rare electronic phase …

Complexes With Atomic Gold Ions: Efficient Bisligand Formation, Felix Duensing, Elisabeth Gruber, Paul Martini, Marcelo Goulart, Michael Gatchell, Bilal Rasul, Olof E. Echt, Fabio Zappa, Masoomeh Mahmoodi-Darian, Paul Scheier

Faculty Publications

Complexes of atomic gold with a variety of ligands have been formed by passing helium nanodroplets (HNDs) through two pickup cells containing gold vapor and the vapor of another dopant, namely a rare gas, diatomic molecule (H₂, N₂, O₂, I₂, P₂), or various polyatomic molecules (H₂O, CO₂, SF₆, C₆H₆, adamantane, imidazole, di-cyclopentadiene, and fullerene). The doped HNDs were irradiated by electrons; ensuing cations were identified in a high-resolution mass spectrometer. Anions were detected for benzene, di-cyclopentadiene, and fullerene. For most …

Colossal Density-Driven Resistance Response In The Negative Charge Transfer Insulator Mns2, Dylan Durkee, Nathan Dasenbrock-Gammon, G. Alexander Smith, Elliot Snider, Dean Smith, Christian Childs, Simon A.J. Kimber, Keith V. Lawler, Ranga P. Dias, Ashkan Salamat

Chemistry and Biochemistry Faculty Research

A reversible density driven insulator to metal to insulator transition in high-spin MnS2 is experimentally observed, leading with a colossal electrical resistance drop of 108 ω by 12 GPa. Density functional theory simulations reveal the metallization to be unexpectedly driven by previously unoccupied S22- σ3p∗ antibonding states crossing the Fermi level. This is a unique variant of the charge transfer insulator to metal transition for negative charge transfer insulators having anions with an unsaturated valence. By 36 GPa the emergence of the low-spin insulating arsenopyrite (P21/c) is confirmed, and the bulk metallicity is broken with the system returning to an …

Quantum Transport Of The 2d Surface State In A Nonsymmorphic Semimetal, Xue Liu, Jin Hu, Jiang Wei, Chunlei Yue, Sergey V. Erohin, Yanglin Zhu, Abin Joshy, Jinyu Liu, Ana M. Sanchez, David Graf, Pavel B. Sorokin, Zinqiang Mao

Physics Faculty Publications and Presentations

In a topological semimetal with Dirac or Weyl points, the bulk-boundary correspondence principle predicts a gapless edge mode if the essential symmetry is still preserved at the surface. The detection of such topological surface state has been considered as the fingerprint prove for crystals with nontrivial topological bulk band. On the contrary, it has been proposed that even with symmetry broken at the surface, a new surface band can emerge in nonsymmorphic topological semimetals. The symmetry reduction at the surface lifts the bulk band degeneracies and produces an unusual “floating” surface band with trivial topology. Here, we first report quantum …

A Theoretical Study Of Synchronous Proton Transfer In (Hf)N, (H2O) N, And (Hcl) N Where N = 3, 4, 5, Johnny Yang

Honors Theses

For (HF)_n, (H₂O)_n, and (HCl)_n (n = 3 − 5), we have rigorously characterized the structures for the minima and transition states for synchronous proton transfer (SPT) with the CCSD(T) method and aug-cc-pVTZ basis set. The electronic barrier heights (∆E^†) associated with these transition states have also been computed with the explicitly correlated CCSD(T)-F12 method and the aug-cc-pVQZ-F12 basis set (abbreviated aQZ-F12). (HCl)_n (n = 3 − 5) SPT transition states have not been previously identified to the best of our knowledge, and they have been found …

Photochemistry Of Nh2No2 And Implications For Chemistry In The Atmosphere, Vincent J. Esposito, Tarek Trabelsi, Joseph S. Francisco

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

Recent studies have indicated that nitramide (NH₂NO₂) may be formed more plentifully in the atmosphere than previously thought, while also being a missing source of the greenhouse gas nitrous oxide (N₂O) via catalyzed isomerization. To validate the importance of NH₂NO₂ in the Earth’s atmosphere, the ground and first electronic excited states of NH₂NO₂ were characterized and its photochemistry was investigated using multireference and coupled cluster methods. NH₂NO₂ is non-planar and of singlet multiplicity in the ground state while exhibiting large out-of-plane rotation in the triplet …

Sf6+: Stabilizing Transient Ions In Helium Nanodroplets, Simon Albertini, Stefan Bergmeister, Felix Laimer, Paul Martini, Elisabeth Gruber, Fabio Zappa, Milan Ončák, Paul Scheier, Olof E. Echt

Faculty Publications

There are myriads of ions that are deemed too short-lived to be experimentally accessible. One of them is SF₆⁺. It has never been observed, although not for lack of trying. We demonstrate that long-lived SF₆⁺ can be formed by doping charged helium nanodroplets (HNDs) with sulfur hexafluoride; excess helium is then gently stripped from the doped HNDs by collisions with helium gas. The ion is identified by high-resolution mass spectrometry (resolution m/Dm = 15000), the close agreement between the expected and observed yield of ions that contain minor sulfur isotopes, and collision-induced dissociation …

Direct Detection Of 5-Mev Protons By Flexible Organic Thin-Film Devices, Ilaria Fratelli, Andrea Ciavatti, Enrico Zanazzi, Laura Basiricò, Massimo Chiari, Laura Fabbri, John E. Anthony, Alberto Quaranta, Beatrice Fraboni

Chemistry Faculty Publications

The direct detection of 5-MeV protons by flexible organic detectors based on thin films is here demonstrated. The organic devices act as a solid-state detector, in which the energy released by the protons within the active layer of the sensor is converted into an electrical current. These sensors can quantitatively and reliably measure the dose of protons impinging on the sensor both in real time and in integration mode. This study shows how to detect and exploit the energy absorbed both by the organic semiconducting layer and by the plastic substrate, allowing to extrapolate information on the present and past …

Complex Fluid Dynamics: Chemo-Hydrodynamics Driven By Autocatalytic Reaction Fronts, Matthew Walter Eskew

Dissertations and Theses

Chemo-hydrodynamics generated from reaction-diffusion-convection processes of autocatalytic chemical systems are extensively studied for their applications in modeling complex systems. Compared to the more extensively studied autocatalytic systems, chlorite-tetrathionate and chlorite-trithionate, the chlorite-thiourea systems is relatively unexplored. Compared to the two previous systems, chlorite-thiourea has more straightforward chemical kinetics. To narrow the gap between chlorite-thiourea and the other systems a combination of experimental study and numerical simulation were employed to quantify this system.

Compared to established literature, experiments were performed at five orders of magnitude lower concentration of indicator, minimizing confounding effects of indicator on hydrodynamic motion. To accurately image the …

Non-Adiabatic Quantum Interference In The Ultracold Li + Lina → Li2+ Na Reaction, Brian K. Kendrick, Hui Li, Ming Li, Svetlana Kotochigova, James F.E. Croft, Naduvalath Balakrishnan

Chemistry and Biochemistry Faculty Research

Electronically non-adiabatic effects play an important role in many chemical reactions. However, how these effects manifest in cold and ultracold chemistry remains largely unexplored. Here for the first time we present from first principles the non-adiabatic quantum dynamics of the reactive scattering between ultracold alkali-metal LiNa molecules and Li atoms. We show that non-adiabatic dynamics induces quantum interference effects that dramatically alter the ultracold rotationally resolved reaction rate coefficients. The interference effect arises from the conical intersection between the ground and an excited electronic state that is energetically accessible even for ultracold collisions. These unique interference effects might be exploited …

Electronic Transitions In Rb2+ Dimers Solvated In Helium, Simon Albertini, Paul Martini, Arne Schiller, Harald Schöbel, Elham Ghavidel, Milan Ončák, Olof E. Echt, Paul Scheier

Faculty Publications

We have measured depletion spectra of the heteronuclear (⁸⁵Rb⁸⁷Rb⁺) dimer cation complexed with up to 10 He atoms. Two absorption bands are observed between 920 and 250 nm. The transition into the repulsive 1²Sigma_u⁺ state of HeRb₂⁺ gives rise to a broad feature at 790 nm (12650 cm^–1); it exhibits a blueshift of 98 cm^–1 per added He atom. The transition into the bound 1 ²Pi_u state of HeRb₂⁺ reveals vibrational structure with a band head at < 15522 cm^–1, a harmonic …

Determination Of The Rydberg Constant From The Emission Spectra Of H And He+, Kyle D. Shaffer

Ramifications

Abstract

In this experiment, the Rydberg constants for the hydrogen atom and He⁺ were determined by analysis of the emission spectra of Hand He, respectively, in comparison to the principal quantum numbers of each transition. Using both a hydrogen and then a helium atomic lamp attached to a 0.5 m grating spectrometer and a photomultiplier detector (PMT), a change in voltage detected by the PMT can be paired with a corresponding wavelength passing through the spectrometer from each emission peak in the visible to ultraviolet range. The peaks acquired from this change in voltage were analyzed to find their …

Computational Modelling Enables Robust Multidimensional Nanoscopy, Matthew D. Lew

Electrical & Systems Engineering Publications and Presentations

The following sections are included:

• Present State of Computational Modelling in Fluorescence Nanoscopy

• Recent Contributions to Computational Modelling in Fluorescence Nanoscopy

• Outlook on Computational Modelling in Fluorescence Nanoscopy

• Acknowledgments

• References