Chemistry Commons^™

Dissociation Of Singly And Multiply Charged Nitromethane Cations: Femtosecond Laser Mass Spectrometry And Theoretical Modeling, G. L. Gutsev, S. L. Mcpherson, Hugo A. López Peña, Derrick Ampadu Boateng, L. G. Gutsev, B. R. Ramachandran, Katharine M. Tibbetts

Chemistry Publications

Dissociation pathways of singly- and multiply charged gas-phase nitromethane cations were investigated with strong-field laser photoionization mass spectrometry and density functional theory computations. There are multiple isomers of the singly charged nitromethane radical cation, several of which can be accessed by rearrangement of the parent CH3–NO2 structure with low energy barriers. While direct cleavage of the C–N bond from the parent nitromethane cation produces NO2+ and CH3+, rearrangement prior to dissociation accounts for fragmentation products including NO+, CH2OH+, and CH2NO+. Extensive Coulomb explosion in fragment ions observed at high laser intensity indicates that rapid dissociation of multiply charged nitromethane cations …

Mechanism Of Nickel Phyllosilicate Formation By Laser Ablation In Liquid, Mallory G. John, Katharine M. Tibbetts

Chemistry Publications

No abstract provided.

High-Pressure Infiltration−Expulsion Of Aqueous Nacl In Planar Hydrophobic Nanopores, S. Zamfir, F. Moucka, D. Bratko

Chemistry Publications

Pressure-driven permeation of water in a poorly wettable material results in a conversion of mechanical work into surface free energy representing a new form of energy storage, or absorption. When water is replaced by a concentrated electrolyte solution, the storage capacity of a nanoporous medium becomes comparable to high-end supercapacitors. The addition of salt can also reduce the hysteresis of the infiltration/expulsion cycle. Our molecular simulations provide a theoretical perspective into the mechanisms involved in the process, and underlying structures and interactions in compressed nanoconfined solutions. Specifically, we consider aqueous NaCl in planar confinements of widths of 1.0 nm and …

From Neutral Aniline To Aniline Trication: A Computational And Experimental Study, G. L. Gutsev, H. A. López Peña, S. L. Mcpherson, Derrick Ampadu Boateng, B. R. Ramachandran, L. G. Gutsev, Katharine M. Tibbetts

Chemistry Publications

We report density functional theory computations and photoionization mass spectrometry measurements of aniline and its positively charged ions. The geometrical structures and properties of the neutral, singly, doubly, and triply positively charged aniline are computed using density functional theory with the generalized gradient approximation. At each charge, there are multiple isomers closely spaced in total energy. Whereas the lowest energy states of both neutral and cation have the same topology C₆H₅–NH₂, the dication and trication have the C₅NH₅–CH₂ topology with the nitrogen atom in the meta and para positions, …

Development Of Supported Pd-Based Catalysts For Carbon-Carbon Cross-Coupling And Oxidation Reactions, Mrinmoy Das

Theses and Dissertations

Heterogeneous catalysts are a crucial part of chemistry used for various chemical synthesis stages, pharmaceutical, and environmental applications. The use of nanoparticles or rather nanocatalysts enhances the heterogeneous catalytic applications. Both chemical and physical methods can be used to synthesize nanocatalysts. Chemical synthesis methods require comparatively fewer instruments and can easily synthesize a large amount of nanocatalysts. Nevertheless, chemical synthesis methods require reducing agents and solvents that can be toxic or harmful materials. They often need harsh reaction conditions as well, like high temperature and pressure. On the other hand, physical synthesis methods often require complex instrument setup, but their …

Discerning The Spectroscopic Properties And Chemical Reactivity Of Bioinspired Metallocomplexes, Ashley K. Forney

Theses and Dissertations

In Nature, metalloenzymes catalyze a variety of thermodynamically demanding reactions with remarkable performance under mild, physiological conditions. This innate ability is a driving force for the development of nature inspired, synthetic analogues that are robust and can catalyze a variety of organic transformations. This work involves the successful syntheses of four coordinate, bioinspired complexes, [M^II(n-DOB)] (M = Ni, Co, and Cu; n = 12 and 13), which have been characterized by NMR, ESI-MS, UV/Vis, EPR, and CV. Spectroscopic evidence presents the generation of reactive metal-(di)oxygen species that display amphoteric reaction behavior, making these rarities among inorganic oxidants. These …

Detection Of Biomolecules Via Ocp Measurements Using Npg Electrodes, Borkat Ullah

Theses and Dissertations

In sensing application nanoporous gold (NPG) has attracted much attention. NPG is prepared by dealloying Au:Ag alloys. Characterization was done using scanning electron microscopy (SEM), X-ray photoelectron spectroscopy (XPS), and cyclic voltammetry (CV). In this work, the open circuit potential (OCP) of ferricyanide, cysteine, uric acid, and ascorbic acid was measured in phosphate buffer solution (PBS) and biofouling solution containing bovine serum albumin (BSA) at pH 7.4. OCP measurement has been hindered due to biofouling and surface passivation on the metal electrodes. By the use of the NPG electrodes, electrochemical activity can be maintained. From the OCP measurement of cysteine, …

Redox-Active Porous Organic Materials For Electrochemical Energy Storage Applications, K. Shamara Weeraratne

Theses and Dissertations

As the demand for renewable energy technologies grows, so does the need for cheaper, more efficient rechargeable batteries to store the energy. While lithium-ion battery (LIBs) technology is well established, it suffers from limited lithium supplies. Furthermore, the highly toxic transition metals used in the electrodes places a huge burden on the environment. Therefore, replacing lithium with more economical sodium metal in rechargeable batteries (i.e. sodium-ion batteries, SIBs) has garnered considerable attention. Despite the fact that sodium and lithium share similar electrochemical properties, which may cause the transition from lithium to sodium easier, the larger ionic radius of Na^{+ …}

Solid Phase Extraction And High-Precision Mass Spectrometry Analysis Methods For Crassostrea Virginica Metabolome, Alyssa Darling

Theses and Dissertations

Metabolomics is the rapidly-growing field which focuses on the endpoints of biological processes, and has the capability to provide a snapshot of an organisms’ interaction with their environment on a molecular scale. The objective of the experiment herein was to develop a standard metabolic extraction technique coupled with ultrahigh-precision analytical tools to build a global metabolic pathway of the keystone species Crassostrea virginica. To achieve this, C. virginica whole-body samples were extracted using acetonitrile and methanol, then split into a dehydrated group and a diluted group. Following reversed-phase solid phase extraction (RP-SPE) of both groups, metabolites were identified using …

Synthesis And The Genetic Encoding Of Novel Lysine Post-Translational Modifications, Sahan A. Galbada Liyanage

Theses and Dissertations

Post-translational modifications (PTMs) play a significant role in regulating cell signaling and regulating the inner cellular environment. The study of PTMs and their primary biological functions is critical for the development of new medicines targeting the pathways and biomolecules responsible for the PTMs.

Previous studies revealed the direct coupling of the β -hydroxybutyryl lysine (K_BHB) modification with the gene expression. K_BHB in histone proteins links metabolism to epigenetics and gene expression and enables to study in-depth, how cell metabolism controls the gene expression and vice versa. Similar novel histone modification, K_Lac, attracts a special interest …

Open Ensemble Modeling Of Confined Electrolytes, Serban Zamfir

Theses and Dissertations

The main purpose of my study was to work towards better understanding the behavior of salt solutions in nanoconfinements and its causes. To this end I have developed an in-house C++ code that can perform notoriously challenging open ensemble Monte Carlo molecular simulations, calculate relevant thermodynamic and extract structural information about each system. I use this code in my first project which deals with the intrusion/extrusion of aqueous NaCl into a nanopore open to a pressurized bulk environment. For my second project, I study the effect of explicitly accounting for intramolecular polarization and accompanying multi-body interactions on the uptake, structure, …

Temporal Behavior Of The Individual Soft Microparticles: Understanding The Detection By Particle Impact Electrochemistry, Junaid Ahmed, Julio C. Alvarez

Graduate Research Posters

Emerging progress of the Particle Impact Electrochemistry (PIE) technique has opened a novel field of detection and characterization of many analyte particles. 1 PIE comprises detection of changes in current when collisions of individual micro or nanoparticles are linked with an electrochemical event at the surface of an ultramicroelectrode (UME). 2 Being a rapid, low cost, and analyzing of one analyte at a time, PIE is widely used to characterize the shape, size distribution, and catalytic activity of nanoparticles. 2-5 To explore the scope of PIE for the detection of soft microparticles (absence of crystalline structure), ferrocene (Fc) trapped toluene-in-water …

Heparan Sulfate. A Ligand For Coordination Compounds., Eric Ginsburg

Theses and Dissertations

Heparan sulfate (HS), a type of glycosaminoglycan (GAG), has been identified as a ligand for interactions with polynuclear platinum complexes (PPCs). HS is involved in numerous biological processes, and often considered to be extracellular DNA. PPCs interact with HS through the formation of a “sulfate clamp”, where multiple anionic sulfate groups cluster around the cationic PPC. The masking of HS results in the inhibition of enzymatic activity, protein-HS interactions, and other biological processes. PPCs use HS proteoglycans as an method of cellular internalization. By targeting sulfated-GAGs, PPCs can offer precision medicine not currently observed with the FDA approved platinum therapies. …

Electrocatalytic Cathodes For Advanced Lithium–Sulfur Batteries, Ahmed Abdelkader

Theses and Dissertations

Energy demands are anticipated to increase in the next decades with the consumption of fossil fuels predicted to grow from the current levels. This will place an enormous burden on the non–renewable reserves of our energy sources and add to the preexisting environmental crisis with the emission of greenhouse gases like carbon dioxide (CO₂). Electrical energy storage (EES) is considered one of the most crucial needs of modern society to circumvent this crisis and potential applications include electric vehicles and devices, as well as storage systems for solar and wind sources.Lithium–ion batteries (LIBs) have proven to be …

Three Studies Of Research-Based Pedagogy In Physical Chemistry: Development Of A Zno Thin Film Experiment, Analysis Of Student Discourse By Graph Theory And Cognitive Engagement, Building A Physical Chemistry Faculty Network., Dilhara Liyanage

Theses and Dissertations

Three research projects, each focusing on a different aspect, development of a ZnO thin film experiment, student’s cognitive engagement behavior, and building of a faculty network, are presented in this dissertation.

In the first project, a physical chemistry laboratory experiment was developed to answer the question, “How do electrons move in a solid?”. The experiment structure follows the POGIL-PCL (Process Oriented Guided Inquiry Learning - Physical Chemistry Laboratory) model. Students begin by using the PhET “Quantum Bound States” animation to compare energy levels for single atoms to energy levels of a lattice containing many potential wells, and they incorporate that …

Synthesis Of Supported Metal Nanoparticles On High Surface Area Supports For Application In Energy Conversion And Heterogeneous Catalysis, Nazgol Norouzi

Theses and Dissertations

Precise control of metal nanoparticles’ size, composition, and dispersity over high surface area supports are highly desirable to address current challenges in energy storage and conversion as well as catalytic processes involving precious metals. Therefore, developing viable synthetic routes that enable new catalytic systems derived from inexpensive transition metals or limited use of precious metals is vital for clean energy applications such as fuel cells and rechargeable batteries or affordable drugs in the pharmaceuticals arena. In addition to metal components of heterogeneous catalysts, the catalyst support is an integral part of catalyst design as it can impart both physical stability …

Fabrication And Characterization Of Multicomponent Gradients Containing Weakly Acidic And Basic Functional Groups, Kallol Roy

Theses and Dissertations

Multicomponent synthetic chemical gradients containing amine (NH₂) and carboxylic acid (COOH) groups have been prepared on the silanol (Si-OH) containing a base-layer substrate by the controlled-rate infusion (CRI) method. The spatial variation of weakly acidic COOH and basic NH₂ functional groups on weakly acidic Si-OH surface was created in such a way that the two antagonist groups at high concentrations were in close proximity (aligned gradient) and were separated (opposed gradient). The difference in concentration of different components (acid, base, or silanol) along the length of aligned or opposed resulted in significantly different physicochemical properties …

Structure, Morphology And Composition-Property Elucidation Of Ni–Mo And Ni−Mo−P Nanocrystals For Water Splitting Reactions And Group Iv Alloy And Silicate Nanocrystals For Visible To Near Ir Optoelectronics, Ebtesam Hassan Abuelenein Eladgham

Theses and Dissertations

Abstract

Structure, Morphology and Composition-Property Elucidation of Ni–Mo and Ni−Mo−P Nanocrystals for Water Splitting Reactions and Group IV Alloy and Silicate Nanocrystals for Visible to Near IR Optoelectronics

by

Ebtesam Hassan Abuelenein Eladgham

A dissertation submitted in partial fulfillment of the requirements for the degree of Doctor of Philosophy at Virginia Commonwealth University.

Advisor: Indika U Arachchige

Associate Professor, Department of Chemistry

Nanomaterials have gained a great attention because of their unique physical properties with size intermediate between molecular materials and extended solids. They have a large surface to volume ratio and display size tunable physical properties that was not …

Metal-Oxide Nanostructures Fabricated From Reactive Laser Ablation In Liquid, Mallory G. John

Theses and Dissertations

The development of metal-oxide nanostructures is a growing area due to their applications in diverse fields spanning energy conversion and storage, chemical manufacturing, and en- vironmental technology. This interest in catalytically active nanomaterials has prompted the synthesis and investigation of highly functionalized nanoparticles (NPs), including core- shell, silicate-stabilized, and bi- and multi-metallic nanocomposites. While wet-chemical synthesis methods of metal-oxide nanostructures have led to several morphologies, compositions, and shapes, these syntheses often require high temperatures, toxic solvents or reducing agents, and long reaction times.

Laser synthesis and processing of colloids (LSPC) encompasses both ‘top down’ and ‘bottom up’ approaches to synthesize …

Investigation Into The Reaction Profile Of A Bioinspired Nickel Complex, Denver Heitger

Theses and Dissertations

Metal complexes that can activate natural oxidants like H₂O₂ and O₂ have become a key research topic in many labs in hope of mimicking nature, by generating a bioinspired complex that can perform unique chemistry through green processes. To prepare the perfect catalyst, this has lead scientists to explore numerous avenues, including the use of both natural and artificial oxidants, to tease apart the reaction pathway taking place. A ligand system dear to the Lucas Lab (13-DOB) has been metalated with nickel, a cheap and earth abundant transition metal. Our bioinspired metal-(di)oxygen adducts can be formed …

Probing Vibrational Wave Packets In Organophoshorous Molecules Using Femtosecond Time-Resolved Mass Spectrometry (Ftrms), Derrick Ampadu Boateng

Theses and Dissertations

The study of organophosphorus and nitroaromatic compounds is essential due to their suitability as models for understanding the dynamics of radiation induce damage to DNA sugar-phosphate backbone, and the detection of chemical warfare agents as well as nitroaromatic explosives (such as TNT). The ultrafast dynamics of these polyatomic radicals were studied using femtosecond time-resolved mass spectrometry (FTRMS), a versatile method that is capable of monitoring the ultrafast dynamics of rapid dissociation in the gas phase after the removal of an electron. The method uses a technique called pump-probe, which makes use of two time-delayed laser pulses. In this work, the …

Towards A Greener Route To Blockbuster Statin Drugs: Harnessing The Power Of Biocatalysis And Integrating Cross-Coupling Catalysis In The Synthesis Of Rosuvastatin, Chanaka M. Amarasekarage

Theses and Dissertations

As global and political awareness about green and sustainable practices sharpens in the face of dramatic climate change and environmentally detrimental practices, one attractive approach is to harness the catalytic potential of enzymes. Thus influenced, our efforts focused on the development of an innovative chemoenzymatic route to widely prescribed Blockbuster statin drugs, specifically rosuvastatin. In this work, we engineered novel deoxyribose phosphate aldolase (DERA) variants via rationally designed site-directed mutagenesis to accept non-natural, less polar substrate, acrolein, along with acetaldehyde. Several of new mutants displayed elevated tolerance towards aldehydes and showed effective incorporation of acrolein into the unprecedented enzymatically-derived chiral …

Investigations Of Graphene-Supported Single-Atom Catalyst Model Ions In The Gas Phase, Michael Borrome

Theses and Dissertations

Recent developments in heterogeneous catalysis has led to the conception of single-atom catalysts (SACs), a class of catalysts based on isolated metal atoms anchored to a support scaffold. SACs are often much more reactive and can offer better selectivity when compared to nano-scale catalysts. In order to realize the full potential of SACs, a sound understanding of the underlying catalytic mechanisms is required. However, surface analysis tools can become less effective in studying catalytic mechanisms at the atomic scale. Mass spectrometry has proven to be a robust technique for studying organometallic catalytic mechanisms at the single-molecule level. Using mass spectrometry, …

Mechanistic Study Of C-H Activation By Iridium Complexes, Rozalie S G Corea

Theses and Dissertations

C-H activation is considered the “holy grail” of chemistry. Remote, selective C-H activation has many applications such as modifying precursors, adding complexity to molecules, and modifying pre- existing structures in a reduced number of steps. Previous work by Swift and Gronert identified an iridium(III) phenanthroline complex that can activate C-H bonds of cyclohexane. The objective of this dissertation is to study the mechanism and regioselectivity of this complex in common precursors, namely 1-butanol, 1-methoxybutane and butyl acetate.

The studies were carried out in the gas phase on a modified mass spectrometer. Selectively deuterated alcohol, ether and ester were used to …

One-Step Femtosecond Laser Ablation Synthesis Of Sub-3 Nm Gold Nanoparticles Stabilized By Silica, Mallory G. John, Katharine M. Tibbetts

Chemistry Publications

No abstract provided.

Conserved Vibrational Coherence In The Ultrafast Rearrangement Of 2-Nitrotoluene Radical Cation, Derrick Ampadu Boateng, Mi'kayla D. Word, Lavrenty Gutsev, Puru Jena, Katharine M. Tibbetts

Chemistry Publications

2-Nitrotoluene (2-NT) is a good model for both photolabile protecting groups for organic synthesis and the military explosive 2,4,6-trinitrotoluene (TNT). In addition to the direct C−NO2 bond-cleavage reaction that initiates detonation in TNT, 2-NT undergoes an H atom attack reaction common to the photolabile 2-nitrobenzyl group, which forms the aci-nitro tautomer. In this work, femtosecond pump−probe measure- ments with mass spectrometric detection and density functional theory (DFT) calculations demonstrate that the initially prepared vibrational coherence in the 2-NT radical cation (2- NT+) is preserved following H atom attack. Strong-field adiabatic ionization is used to prepare 2-NT+, which can overcome a …

Single-Step Fret-Based Detection Of Femtomoles Dna, Kumar Sapkota, Anisa Kaur, Caleb Donkoh-Moore, Soma Dhakal

Chemistry Publications

Sensitive detection of nucleic acids and identification of single nucleotide polymorphism (SNP) is crucial in diagnosis of genetic diseases. Many strategies have been developed for detection and analysis of DNA, including fluorescence, electrical, optical, and mechanical methods. Recent advances in fluorescence resonance energy transfer (FRET)-based sensing have provided a new avenue for sensitive and quantitative detection of various types of biomolecules in simple, rapid, and recyclable platforms. Here, we report single-step FRET-based DNA sensors designed to work via a toehold-mediated strand displacement (TMSD) process, leading to a distinct change in the FRET efficiency upon target binding. Using single-molecule FRET (smFRET), …

Anisotropic Structure And Dynamics Of Water Under Static Electric Fields, M. Shafiei, M. Von Domaros, D. Bratko, A. Luzar

Chemistry Publications

We study the structure and dynamics of water subject to a range of static external electric fields, using molecular dynamics simulations. In particular, we monitor the changes in hydrogen bond kinetics, reorientation dynamics, and translational motions of water molecules. We find that water molecules translate and rotate slower in elec- tric fields, because the tendency to reinstate the aligned orientation reduces the prob- ability of finding a new hydrogen bond partner and hence increases the probability of reforming already ruptured bonds. Furthermore, dipolar alignment of water mole- cules with the field results in structural and dynamic anisotropies even though the …

Homologous Recombination Under The Single-Molecule Fluorescence Microscope, Dalton R. Gibbs, Soma Dhakal

Chemistry Publications

Homologous recombination (HR) is a complex biological process and is central to meiosis and for repair of DNA double-strand breaks. Although the HR process has been the subject of intensive study for more than three decades, the complex protein–protein and protein–DNA interactions during HR present a significant challenge for determining the molecular mechanism(s) of the process. This knowledge gap is largely because of the dynamic interactions between HR proteins and DNA which is difficult to capture by routine biochemical or structural biology methods. In recent years, single-molecule fluorescence microscopy has been a popular method in the field of HR to …

Single-Molecule Analysis Of I-Motif Within Self-Assembled Dna Duplexes And Nanocircles, Anoja Megalathan, Bobby D. Cox, Peter D. Wilkerson, Anisa Kaur, Kumar Sapkota, Joseph E. Reiner, Soma Dhakal

Chemistry Publications

The cytosine (C)-rich sequences that can fold into tetraplex structures known as i-motif are prevalent in genomic DNA. Recent studies of i-motif–forming sequences have shown increasing evidence of their roles in gene regulation. However, most of these studies have been performed in short single-stranded oligonucleotides, far from the intracellular environment. In cells, i-motif–forming sequences are flanked by DNA duplexes and packed in the genome. Therefore, exploring the conformational dynamics and kinetics of i-motif under such topologically constrained environments is highly relevant in predicting their biological roles. Using single-molecule fluorescence analysis of self-assembled DNA duplexes and nanocircles, we show that the …