Physical Chemistry Commons^™

Using Molecular Dynamics To Study Qs21 Interactions And Penetration Of Lipid-Cholesterol Bilayers, Sarai Guerrero, Mikko Karttunen

Western Research Forum

Saponins have been used as adjuvant agents for decades in vaccines and therapies, but none are as well studied or heavily used as QS-21. This achievement is notwithstanding the fact that QS-21 usage is limited by its stability, toxicity, and scarcity. These shortcomings have only pushed researchers to develop and experiment with artificial recreations of the saponin to harness its unique benefits. A considerable number of research hours have been poured into this topic, but like QS-21 there is a shortcoming here as well. The number of articles that look at QS-21 interactions with the bilayer or the conditions under …

Triplet Population Dynamics And Excited State Relaxation In Chalcogenophene Polymers, Benjamin D. Datko

Chemistry and Chemical Biology ETDs

The conventional understanding of intersystem crossing in multichromophoric conju- gated polymers is usually depicted via a pure electronic model, neglecting contributions of vibrations or conformational order. Obtaining accurate structure-function correlations on spin-conversion processes involving photogenerated singlet excitons to triplet excitons and the excited state dynamics requires sensitivity to the subtle conformational ordering within conjugated polymers. This dissertation seeks to understand the kinetics of multi-exciton singlet-triplet interactions and the excited state relaxation of chalcogen containing (S, Se) conjugated polymers. Utilizing single molecule modulation spectroscopy allows determi- nation of triplet formation of individual conjugated polymer chains and aggregates. This technique resolves triplet-induced …

The Spectroscopic And Computational Exploration Of Sulfur Hydrogen Bonding, Andrew Yoonkeun Lee

Honors Projects

Hydrogen bonds are a subset of non-covalent interactions that occur between X-H — Y, in which X and Y are the very electronegative atoms. In our research, we examine the more unconventional hydrogen bond-like interactions of thiol (SH) containing molecules using vapor-phase infrared (IR) spectroscopy and ab initio computational chemistry. When the SH hydrogen bond donor complexes to a hydrogen bond acceptor, a red shift of the SH stretching mode emerges. An anharmonic oscillator local mode model is applied to the ethanethiol-trimethylamine dimer, and we determine that any IR evidence of dimerization in our experiment is likely obscured by the …

Ab Initio Calculations Of Changes In Sulfur’S Orbital Energies And Sizes With Oxidation State As A Means Of Explaining Hypervalency, Anton V. Taraskin

Honors Projects

The energetics and orbital sizes of sulfur’s valence 3d and fluorine’s valence 2p orbitals were measured using a closed active space self-consistent field calculation to determine the degree of possible bonding available to sulfur’s 3d. It was determined that for orbital energies, the cc-pVXZ and aug sets converged hyperbolically onto a single energy value as X increased and that for both fluorine and sulfur orbital energies scaled down linearly with oxidation state. This resulted in a 0.47 hartree difference between the sulfur 3d and fluorine 2p orbitals at S0.6+ and F-0.1, far exceeding the energy gap between 3p and 2p …

Monolayer Triphosphates Mp3 (M = Sn, Ge) With Excellent Basal Catalytic Activity For Hydrogen Evolution Reaction, Hong-Hui Wu, He Huang, Jie Zhong, Song Yu, Qiaobao Zhang, Xiao Cheng Zeng

Xiao Cheng Zeng Publications

Atomically thin two-dimensional (2D) materials have received intense research interest due to their novel properties and promising applications in nanodevices. By using density functional theory (DFT) calculations, we investigate catalytic activities of several newly predicted two-dimensional (2D) triphosphides GeP₃, SnP₃ and InP₃ monolayers for hydrogen evolution reaction (HER). The calculation results show that GeP₃ and SnP₃ monolayers are active catalysts for HER with suitable free energy of hydrogen adsorption in the basal plane. In particular, the Gibbs free energy of hydrogen adsorption (ΔG_H*) of GeP₃ is 0.024 eV, a value even …

Crystal Structure Of Zymonic Acid And A Redetermination Of Its Precursor, Pyruvic Acid, Dominik Heger, Alexis J. Eugene, Sean R. Parkin, Marcelo I. Guzman

Chemistry Faculty Publications

The structure of zymonic acid (systematic name: 4-hy­droxy-2-methyl-5-oxo-2,5-di­hydro­furan-2-carb­oxy­lic acid), C₆H₆O₅, which had previously eluded crystallographic determination, is presented here for the first time. It forms by intra­molecular condensation of parapyruvic acid, which is the product of aldol condensation of pyruvic acid. A redetermination of the crystal structure of pyruvic acid (systematic name: 2-oxo­propanoic acid), C₃H₄O₃, at low temperature (90 K) and with increased precision, is also presented [for the previous structure, see: Harata et al. (1977). Acta Cryst. B33, 210–212]. In zymonic acid, the hy­droxy­lactone ring …

The Investigation Of Methylidyne Radical (Ch) Reactions With Furan, 2-Methylfuran, And 2,5-Dimethlyfuran And The Photoionization And Photodissociation Of Valeric Acid, Erica Carrasco

Master's Theses

This thesis presents the combustion study of three furanic compounds using synchrotron radiation coupled with multiplexed photoionization mass spectrometry at 298 K. The experiments were performed at the Chemical Dynamics Beamline 9.0.2 at the Advanced Light Source of the Lawrence Berkeley National Laboratory. The reactions of the three furanic compounds with methylidyne (CH) radicals were analyzed based on their photoionization spectra and kinetic profiles.

Additionally, the unimolecular dissociation of valeric acid was also studied and presented in this work using the double imaging photoelectron photoion spectrometry (i2PEPICO) coupled with synchrotron radiation from the VUV beamline. The experiments were carried out …

Synchrotron Photoionization Study Of 2,5-Dimethylfuran Oxidation Initiated By O(3p) Atoms, And Computational Studies Of Superalkali Species: Li3f2, Heejune Park

Master's Theses

This thesis presents the experimental study of a 2,5-dimethylfuran oxidation reaction initiated by atomic oxygen (O(³P)) and the theoretical investigation of superalkalis properties. The experiments were performed at the Chemical Dynamics Beamline 9.0.2 of the Advanced Light Source (ALS) located at the Lawrence Berkeley National Laboratory in Berkeley, CA. The first chapter discusses world energy consumption and progress towards new sustainable energy sources, mainly focusing on biofuels, along with a basic description of combustion. A description of the superalkalis and a brief history of synchrotron radiation are also presented in Chapter 1. Chapter 2 describes the components of …

Defect Chemistry And Ion Intercalation During The Growth And Solid-State Transformation Of Metal Halide Nanocrystals, Bo Yin

McKelvey School of Engineering Graduate Student Theses & Dissertations

Abstract of the Dissertation

Defect Chemistry and Ion Intercalation During the Growth and Solid-State Transformation of Metal Halide Nanocrystals

Semiconductor metal halides as light-sensitive materials have applications in multiple areas, such as photographic film, antibacterial agents and photocatalysts. One focus of this dissertation is to achieve novel morphologies of ternary silver bromoiodide (AgBr1-xIx, 0

For the silver halide system, we demonstrate that the anion composition of AgBr1-xIx nanocrystals determines their shape through the introduction of twin defects as the nanocrystals are made more iodide-rich. AgBr1-xIx nanocrystals grow as single-phase, solid solutions with the rock salt crystal structure for anions compositions …

Pressure-Induced Phase Transition In 1,3,5-Triamino-2,4,6-Trinitrobenzene (Tatb), Brad A. Steele, Samantha M. Clarke, Matthew P. Kroonblawd, I-Feng W. Kuo, Philip F. Pagoria, Sergey N. Tkachev, Jesse S. Smith, Sorin Bastea, Laurence E. Fried, Joseph M. Zaug, Elissaios Stavrou, Oliver Tschauner

Geoscience Faculty Research

Determining the unreacted equation of state of 1,3, 5-triamino-2,4,6-trinitrobenzene (TATB) is challenging because it exhibits low crystal symmetry and low X-ray scattering strength. Here, we present the first high-pressure single-crystal X-ray diffraction (SXD) study of this material. Our SXD results reveal a previously unknown transition to a monoclinic phase above 4 GPa. No abrupt change of the volume occurs but the compressibility changes. Concomitant first principles evolutionary crystal structure prediction USPEX calculations confirm this transition and show that it involves a pressure-induced in-plane shift of the layers of TATB molecules with respect to the ambient-pressure phase.

Nontraditional Hydrogen Bonding In Asymmetric Lewis Acid Catalysis, Brandon Vernier

Electronic Theses and Dissertations

In the field of asymmetric induction, there is a shift from the synthesis of reaction

specific chiral auxiliaries towards a broader mechanistic approach. Our approach is to

develop a theory of asymmetric catalyst design from first principles. The Diels-Alder

reaction of 2-methacrolein and 1,3-cyclopentadiene in the presence of 15 mole % lmenthoxy

aluminum dichloride, reported by Koga, achieved the (S)-exo-Diels-Alder

cycloadduct with 72% ee (0% ee Endo for acrolein). The dramatic change from 72% to 0%

ee is a significant fact that has been overlooked in practical organic synthesis.

In the first phase of this work, the conformational landscape of …

Engineering Multifunctional And Morphologically Diverse Polymer Brush Surfaces, Cassandra M. Reese

Dissertations

The combination of surface-initiated polymerization (SIP) and post-polymerization (PPM) serves as a powerful approach to fabricate complex, multifunctional polymer films, which can be precisely tuned for desired surface engineering applications. Careful manipulation of PPM parameters such as reaction conditions, the tethered brush parameters, and the physical properties of the unbound post-modifier greatly influence the depth of penetration of the post-modifier and the polymer brush compositional heterogeneity. This dissertation focuses on engineering polymer brush surfaces with multifunctional chemistries and tunable morphologies by investigating the PPM parameters that dictate the distribution of post-modifiers on grafted polymer brush surfaces.

The first chapter of …

Hartree-Fock Implementation For Pedagogical & Research Purposes, Gary Zeri, Jerry Larue

Student Scholar Symposium Abstracts and Posters

Often during the process of innovation and scientific advancement, experimentation is the key to increasing the current knowledge of body. Unfortunately, experimentation can often require extended periods of time as well as monetary resources to perform. The use of computational chemistry can increase the rate of scientific advancement by simulating experimental results, allowing researchers to focus on experiments whose computational counterparts show the greatest promise. Students new to the sciences are often not exposed to these methods due to their complexities. The purpose of this project is to implement the Hartree-Fock method, one type of computational chemistry method, whose programming …

Peptide Mediated Co-Assembly Of Porphyrin: Towards Sustainable Biomaterials For Light Harvesting And Catalysis, Wsm Nadeesha K. Wijerathne

Dissertations, Theses, and Capstone Projects

The diverse molecular functions of naturally occurring biomaterials designed from proteins are fundamentally based on a set of conserved building blocks, namely the 20 gene coded amino acids. The supramolecular structures and functions of proteins dictates by the self-assembly, where the complexity of proteins arise from a large number of amino acids. Generation of biomimetic systems that resemble the structures and functions of proteins is of great interest yet challenging due to the tremendous complexity of the natural systems. It is important to investigate alternative strategies to design much simpler systems that exhibit the same or similar function as proteins. …

Preparation And Characterization Of Ruthenium-Gold Raman-Active Catalytic Surfaces, Thang Nguyen

Student Scholar Symposium Abstracts and Posters

Heterogeneous reactions at the gas-solid interface play a major role in many important industrial and environmental processes. These reactions typically rely on metal surfaces, to act as a catalyst between gas phase reactants and products. The catalysts lower the transition state barrier in the formation of the products. The mechanisms of reactions on catalysts is often not fully known due to the difficulty of observing the bond breakage and formation between gaseous molecules at the interface. One method in which the catalytic mechanism can be studied is by using Raman Spectroscopy. However, one drawback of this method is the fact …

Experimental And Computational Study On Magnetic Nanowires Of Layered Titanates, Caleb Layne Heath

Graduate Theses and Dissertations

The intricate nanostructures of layered titanates are unique among nanomaterials due to their easy and inexpensive syntheses. These nanomaterials have been proven valuable for use in industries as varied as energy, water treatment, and healthcare, and can be produced at industrial scales using already existent equipment. They have complex morphology, and surface structure well suited to chemical modification and doping. However, there is a longstanding debate on their lattice structure after the doping. There is a long-unmet need to understand, using both experimental and simulation methods, how dopants alter the clay-like layered crystal structure and associated physical and chemical properties. …

Electrochemical Analysis And Sensing Preface, Yi-Tao Long, Yang Tian

Journal of Electrochemistry

No abstract provided.

Surface-Enhanced Infrared Absorption Spectroscopy- Surface Sensitive In Situ Label-Free Spectroelectrochemistry, Lie Wu, Jian-Long Sun, Xiu-E Jiang

Journal of Electrochemistry

Surface-enhanced infrared absorption spectroscopy (SEIRAS), especially in attenuated total reflectance (ATR) mode, taking advantages of surface-enhancement and near-field optical effect of enhancing substrate, is a ultra-sensitive infrared spectroscopy, which could achieve surface-selected detection at a sub-monolayer level. Since the enhancing substrate could simultaneously serve as a working electrode, ATR-SEIRAS is a readily surface-sensitive in situ label-free spectroelectrochemistry technique. With the advantages of small influence from metal species on enhancement effect, good potential reversibility of spectra, simple surface selection rule and sensitivity to polar molecules, ATR-SEIRAS has been widely applied in the fields of orientation analysis and species identification of interfacial …

High-Efficiency Nitrite Sensor Based On Cop Nanowire Array, Fu-Ling Zhou, Xiao-Li Xiong, Xu-Ping Sun

Journal of Electrochemistry

Nitrite has a negative impact on the environment and human health. The long-term consumption of nitrite-containing foods has a carcinogenic risk. Therefore, the analysis and detection of nitrite are important. It is of great significance to develop high-efficiency electrocatalysts to achieve high sensitivity and selectivity for nitrite detection. The cobalt phosphide nano-array (CoP/TM) was obtained by hydrothermal and low-temperature phosphating. The electrochemical test results show that the constructed CoP/TM was a highly efficient electrochemical reduction nitrite catalyst with the excellent sensing performance and response time less than 3 s, as well as the linear detection range of 1.0 μmol·L^{-1 …}

Preparation And Capacitive Property Of Two-Dimensional Multilayer Ti3C2TX-Mxene/Ppy-Nw Composite Material, Lu Chen, Xuan Jian, Min He, Mi-Mi Zhang, Xiao-Die Chen, Lou-Jun Gao, Zhen-Hai Liang

Journal of Electrochemistry

In this paper, the two-dimensional multilayered Ti₃C₂T_x-MXene was obtained by hydrofluoric acid etching method on the bulk phase material MAX(Ti₃AlC₂) substrate. The two-dimensional multilayered Ti₃C₂T_x-MXene/PPy-NW composite electrode materials were successfully prepared by combining the one-dimensional polypyrrole nanowires (PPy-NW) with two-dimensional multilayered Ti₃C₂T_x-MXene. The morphologies and compositions of the synthetic materials were characterized by scanning electron microscopy (SEM), X-ray diffraction (XRD), Fourier transform infrared spectroscopy (FTIR) and X-ray photoelectron spectroscopy (XPS). Electrochemical tests showed that Ti₃C_{2 …}

In Situ/Operando Visualization Of Electrode Processes In Lithium-Sulfur Batteries: A Review, Shuang-Yan Lang, Xin-Cheng Hu, Rui Wen, Li-Jun Wan

Journal of Electrochemistry

Lithium-sulfur (Li-S) batteries have been regarded as one of the most promising candidates for the next-generation energy storage devices. Fundamental understanding of the structure and evolution processes at electrode-electrolyte interfaces is essential to the further development. In this review, we summarize recent advances in the interfacial observations by means of various in situ/operando visualization techniques, including scanning probe microscopy (SPM), electron microscopy (EM), X-ray microscopy (XRM) and optical microscopy (OM). The real-time investigation provides important evidence for the morphology and component changes including S/Li₂S transformation, polysulfide dissolution on cathodes and Li/solid electrolyte interphase (SEI) evolution on anodes, which …

Advanced Electrochemical Strategy For In Vivo Detection Of Electrochemically Inactive Molecules, Qi Zhou, Li-Min Zhang, Yang Tian

Journal of Electrochemistry

Development of efficient electrochemical strategies for in vivo analysis of electrochemically inactive molecules in brain is significant for understanding and studying their molecular mechanism and roles playing in brain and brain diseases. This review gives a brief introduction on the advanced in vivo electrochemical sensor for detection of non-redox active molecules from three aspects: 1) The selection and design of specific molecules are highly desirable to develop electrochemical sensors with high selectivity for measuring electrochemical inactive molecules through converting specific chemical reaction involved by target to electric signal; 2) The analysis based on ion current rectification occurred at spatial confined …

Recent Progress Of Electrochemiluminescence Sensors Based On Electrically Heated Electrode, Hui-Fang Zhang, Yi-Ting Chen, Fang Luo, Zhen-Yu Lin, Guo-Nan Chen

Journal of Electrochemistry

Electrochemiluminescence (ECL) has broad application in the fields of environmental monitoring and biological analysis due to its intrinsic advantages such as excellent versatility, good detection sensitivity, and high specificity. The intensity of ECL can be influenced by temperature variation in the ECL quantum efficiency and the rate of electrochemical reaction. However, traditional temperature control is commonly realized through bulk solutions heating, which is complicated and unfavorable for detection when the volatile and thermally unstable materials existed. In order to address these problems, electrically heated electrodes are used to adjust the temperature desired. The major character of this technique lies in …

Application Of Nanomaterials In The Detection Of Volatile Organic Compounds In Exhaled Breath For Cancer Diagnosis, Wan-Qiao Bai, Xue-Zhi Qiao, Tie Wang

Journal of Electrochemistry

Volatile organic compounds (VOCs) generated in human body can reflect one’s health state, and numerous diseases are identified by some VOCs biomarkers. More recently, analyses of VOCs biomarkers from exhaled breath have turned into a research frontier worldwide because it offers a noninvasive way for diseases diagnosis. Various kinds of nanomaterials are used to enhance the performance of sensing techniques, and play an essential role in miniaturization detection. In this review, several kinds of nanomaterials (metallic, metal oxide, carbon-based, composites and MOFs-based materials) used in various VOCs detection methods, especially in VOCs sensors are summarized. Learning from the successful utilization …

Sensitive And Reusable Electrogenerated Chemiluminescence Aptasensor Fabricated By Electrochemically Double Covalent Coupling Method For The Detection Of Cocaine, Xiao-Feia Wang, Tinga Zhang, Bing Wang, Hong-Lan Qi, Cheng-Xiao Zhang

Journal of Electrochemistry

A double covalent coupling method based on click chemistry and diazonium chemistry was developed for the fabrication of a sensitive and reusable electrogenerated chemiluminescence (ECL) aptasensor. As a proof-of-concept, cocaine was chosen as a model target, and a specific aptamer was chosen as a recognition molecule element, while ruthenium complex derivative (Ru1) as an ECL signal compound. The ECL aptasensor was fabricated by electrochemically diazotizing a phenylazide on the surface of a glassy carbon electrode, and then, coupling the alkyne functionalized Ru1-labeled cocaine aptamer through click chemistry. The ECL aptasensor was facilely used to determine cocaine in the range from …

Sensitive Photoelectrochemical Assay Of Nucleic Acids Based On Catalytic Hairpin Assembly And Ru(Nh3)63+, Ya-Min Fu, Xiao-Xia Yan, Xiao-Hua Zhang, Jin-Hua Chen

Journal of Electrochemistry

A simple “signal-on” photoelectrochemical (PEC) sensing platform for sensitive assay of nucleic acids was developed by coupling catalytic hairpin assembly (CHA) signal amplification strategy with Ru(NH₃)₆³⁺. Herein, cadmium sulfide (CdS) was deposited on the TiO₂/indium tin oxide (ITO) electrode by a method of successive ionic layer adsorption and reaction (SILAR), serving as one kind of photoelectric material to broaden absorption range of TiO₂ and to improve the photoelectric conversion efficiency. Thereafter, the capture DNA (C-DNA) was immobilized on the CdS/TiO₂/ITO electrode. Simultaneously, Au-hairpin DNA probe 1 (Au-HP1) and hairpin DNA …

A Facile Strategy For Two-Step Fabrication Of Gold Nanoelectrode For In Vivo Dopamine Detection, Li-Hao Guan, Chao Wang, Wang Zhang, Yu-Lu Cai, Kai Li, Yu-Qing Lin

Journal of Electrochemistry

In vivo monitoring neurochemicals with microelectrode is invasive and the damage to brain tissue may inevitably cause disturbance signals physiologically to the measurement. It is of great importance to reduce the electrode size and to decrease the damage. This study demonstrates a novel nanoelectrode preparation methodology for in vivo monitoring dopamine (DA) fluctuation in the living brain of rats with high dependability. The fabrication process of the gold nanoelectrode involving a few minutes consists of only two steps: 1) growing gold nanoseeds on surface of tip of glassy capillary by ion sputtering; 2) wet depositing a continuous conductive gold film …

Graphene-Like Secondary-Laser-Etched Polyimide Film Decorated With CuXO Nanocomposites: A Novel Electrode Substrate For Non-Enzymatic Glucose Sensors, Wan-Lin Dai, Zhi-Wei Lu, Jian-Shan Ye

Journal of Electrochemistry

In this work, a novel electrode substrate with graphene-like surface and Cu_xO nanocomposites derived from secondary-laser-etched polyimide (SLEPI) film was synthesized and applied in non-enzymatic glucose detection for the first time. Characterizations indicate that the as-prepared SLEPI/Cu_xO film electrode (SLEPI/Cu_xO-FE) possessed huge surface area, plentiful active sites and excellent electrocatalytic performance. The obtained sensor exhibited the high sensitivity and selectivity for glucose determination with a linear range of 0.05 mmol·L^-1 to 3 mmol·L^-1 and a detection limit of 1.72 μmol·L^-1 (S/N=3), which provides a simple, flexible and low-cost electrochemical sensor for …

Preparation And Electrocatalytic Oxygen Reduction Performance Of Self-Doped Sludge-Derived Carbon, Ya-Li Ye, Wei-Ming Feng, Ge Li, Zhen-Chao Lei, Chun-Hua Feng

Journal of Electrochemistry

The development of low-cost, high-performance cathode catalysts is critical for practical application of fuel cells. Here, the N, P-doped porous graphene-like carbon with outstanding oxygen reduction reaction (ORR) performance was synthesized by pyrolysis of surplus sludge, which functioned as a self-doped, self-activated, and self-templated precursor by acclimation with continuous feedings of phenol. The results show that the amounts of microorganisms were enriched after acclimation, with increasing contents of N, P, Fe, as well as C atoms. The increasing pyrolysis temperature resulted in the formation of an ordered graphitic structure, however, the excessively high temperature induced the drop in the amounts …

Heavy-Atom Tunneling In The Planar Bond Shifting Of [16]Annulene, Philip Lampkin, Jon Shezaf

Creative Activity and Research Day - CARD

Mid-sized annulenes are known to undergo rapid π-bond shifting. Given that heavy­atom tunneling plays a role in planar bond shifting of cyclobutadiene, we computationally explored the contribution of heavy­ atom tunneling to the planar bond shifting in the major (CTCTCTCT) and minor (CTCTTCTT) isomers of [16]annulene. (U)M06-2X/cc-pVDZ calculations yield bond-shifting barriers of ca. 10 kcal/mol. The results also reveal extremely narrow barrier widths, suggesting a high probability of tunneling for these bond-shifting reactions. Rate constants were calculated using canonical variational transition state theory (CVT) as well as with small curvature tunneling (SCT) contributions, via direct dynamics. For the major isomer, …