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Hydrogen-Deuterium Exchange Mass Spectrometry And Molecular Dynamics Simulations For Studying Protein Structure And Dynamics, Yiming Xiao 2018 The University of Western Ontario

Hydrogen-Deuterium Exchange Mass Spectrometry And Molecular Dynamics Simulations For Studying Protein Structure And Dynamics, Yiming Xiao

Electronic Thesis and Dissertation Repository

Deciphering properties of proteins are essential for human health and aiding in the development of new pharmaceuticals. This dissertation uses hydrogen-deuterium exchange (HDX) mass spectrometry (MS) and molecular dynamics (MD) simulations to study protein dynamics, for improving the understanding of protein folding/unfolding mechanisms, and ligand binding and allosteric regulation.

Chapter 2 uses HDX-MS for probing the conformational dynamics of myoglobin in the presence of N2 bubbles. We propose a dynamic model that reproduces the observed data: “semi-unfolded” “native” “globally unfolded” -> “aggregated”. Chapter 3 focuses on osteoprotegerin (OPG), which hinders bone resorption by inhibiting RANK/RANKL interactions. The dimerization ...


Mechanism Of Protein Charging And Supercharging In Electrospray Ionization: Molecular Dynamics Simulations And Experimental Investigations, Haidy S. Metwally 2018 The University of Western Ontario

Mechanism Of Protein Charging And Supercharging In Electrospray Ionization: Molecular Dynamics Simulations And Experimental Investigations, Haidy S. Metwally

Electronic Thesis and Dissertation Repository

Electrospray ionization mass spectrometry (ESI-MS) is a powerful technique for investigating protein structures, conformations, and interactions. Despite its widespread use, many fundamental aspects of ESI remain poorly understood. In this thesis, we use a combination of molecular dynamics (MD) simulations and experiments to gain insights into the hidden complexities of ESI-MS.

Chapter 2 discusses the topic of salt-induced protein signal degradation. Salts such as NaCl, CsCl, and tetrabutyl ammonium chloride (NBu4Cl) interfere with MS data acquisition, leading to adduct formation and signal suppression. MD simulations provide an explanation for these salt interferences. Signal suppression can be broken down ...


Probing Trapped Extracellular Vesicles By Surface-Enhanced Raman Spectroscopy, Lauren Kaufman 2018 The University of Western Ontario

Probing Trapped Extracellular Vesicles By Surface-Enhanced Raman Spectroscopy, Lauren Kaufman

Electronic Thesis and Dissertation Repository

Extracellular vesicles (EVs) are released by nearly all cell types within the human body and have been found to play important biological roles including cell-to-cell communication, apoptosis and tissue repair. Lacking cellular machinery, these nano-sized vesicles carry functional proteins and nucleic acids from their parent cells, providing insight into biomarkers present in healthy, cancerous and diseased cells. EVs may be isolated from biofluids such as from blood or urine. Their detection and characterization holds extreme potential in developing less invasive disease detection and treatment methods.

In this work, we propose use of lithographic techniques to fabricate platforms to allow for ...


An Overview Of Dynamic Heterogeneous Oxidations In The Troposphere, Elizabeth A. Pillar-Little, Marcelo I. Guzman 2018 University of Kentucky

An Overview Of Dynamic Heterogeneous Oxidations In The Troposphere, Elizabeth A. Pillar-Little, Marcelo I. Guzman

Chemistry Faculty Publications

Due to the adverse effect of atmospheric aerosols on public health and their ability to affect climate, extensive research has been undertaken in recent decades to understand their sources and sinks, as well as to study their physical and chemical properties. Atmospheric aerosols are important players in the Earth’s radiative budget, affecting incoming and outgoing solar radiation through absorption and scattering by direct and indirect means. While the cooling properties of pure inorganic aerosols are relatively well understood, the impact of organic aerosols on the radiative budget is unclear. Additionally, organic aerosols are transformed through chemical reactions during atmospheric ...


An Obscured Or Nonexistent Binary Intermetallic, Co7pr17, Its Existent Neighbor Co2pr5, And Two New Ternaries In The System Co/Sn/Pr, Cosn3pr1–X, And Co2–Xsn7pr3, Melissa L. Rhodehouse, Thomas Bell, Volodymyr Smetana, Anja-Verena Mudring, Gerd Meyer 2018 Iowa State University and Ames Laboratory

An Obscured Or Nonexistent Binary Intermetallic, Co7pr17, Its Existent Neighbor Co2pr5, And Two New Ternaries In The System Co/Sn/Pr, Cosn3pr1–X, And Co2–Xsn7pr3, Melissa L. Rhodehouse, Thomas Bell, Volodymyr Smetana, Anja-Verena Mudring, Gerd Meyer

Ames Laboratory Accepted Manuscripts

Four compounds are reported in this study. Co7Pr17 (10, cP96, P213, a = 13.4147(8) Å, Z = 4), either nonexistent or obscured in the Co/Pr phase diagram, has been obtained from a PrBr3 flux. With 29.2 mol % Co, it is close to Co2Pr5 (28.6 mol % Co, 2, C2Mn5 type of structure, mC28, C2/c, a= 16.5471(7) Å, b = 6.5107(3) Å, c = 7.1067(3) Å, β = 96.230(3)°, Z = 4), existent in the Co/Pr phase diagram, produced by arc-melting of a stoichiometric mixture of the metals. The ...


Nascent O2 (A1ΔG, V = 0, 1) Rotational Distributions From The Photodissociation Of Jet‐Cooled O3 In The Hartley Band, Michelle L. Warter, Carolyn E. Gunthardt, Wei Wei, George McBane, Simon W. North 2018 Texas A & M University - College Station

Nascent O2 (A1ΔG, V = 0, 1) Rotational Distributions From The Photodissociation Of Jet‐Cooled O3 In The Hartley Band, Michelle L. Warter, Carolyn E. Gunthardt, Wei Wei, George Mcbane, Simon W. North

Peer Reviewed Articles

We report rotational distributions for the O2 (a 1Δg) fragment from photodissociation of jet‐cooled O3 at 248, 266, and 282 nm. The rotational distributions show a population alternation that favors the even states, as previously reported for a 300 K sample by Valentini et al. (J. Chem. Phys. 86, 6745 (1987)). The alternation from the jet‐cooled precursor is much stronger than that observed by Valentini et al., and in contrast to their observations does not depend strongly on O2 (a 1Δg) vibrational state or photolysis wavelength. The odd/even alternation diminishes ...


Nuclear Magnetic Resonance Studies Of Imidazolium-Based Ionic Liquids And Garnet-Type Li7la3zr2o12, Shen Lai 2018 The Graduate Center, City University of New York

Nuclear Magnetic Resonance Studies Of Imidazolium-Based Ionic Liquids And Garnet-Type Li7la3zr2o12, Shen Lai

All Dissertations, Theses, and Capstone Projects

Advancements in electrochemical energy storage materials are critical in the development and utilization of renewable energy technologies. These advancements involve obtaining a better understanding of electrochemical mechanisms and properties through scientific research towards an improved energy storage technology. Nuclear magnetic resonance (NMR), is a sensitive and selective method to probe particle dynamics (magnetic relaxation, diffusometry, etc.) and material structures (spectroscopy) down to the atomic level. In this work, several NMR techniques are employed to study imidazolium-based ionic liquids and garnet-type inorganic materials. These are being studied due to their potential use as safer alternatives to organic solvent-based electrolytes in lithium-ion ...


The Virial Theorem And Covalent Bonding, George B. Bacskay, Sture Nordholm, Klaus Ruedenberg 2018 University of Sydney

The Virial Theorem And Covalent Bonding, George B. Bacskay, Sture Nordholm, Klaus Ruedenberg

Ames Laboratory Accepted Manuscripts

A long-held view of the origin of covalent binding is based on the notion that electrostatic forces determine the stability of a system of charged particles and that, therefore, potential energy changes drive the stabilization of molecules. A key argument advanced for this conjecture is the rigorous validity of the virial theorem. Rigorous in-depth analyses have however shown that the energy lowering of covalent bonding is due to the wave mechanical drive of electrons to lower their kinetic energy through expansion. Since the virial theorem applies only to systems with Coulombic interaction potentials, its relevance as a foundation of the ...


Building On Nature: Spectroscopic Studies Of Photosynthesis-Inspired Pigments, Fused Light Harvesting Proteins, And Bacterial Reaction Center Mutants, Kaitlyn Faries 2018 Washington University in St. Louis

Building On Nature: Spectroscopic Studies Of Photosynthesis-Inspired Pigments, Fused Light Harvesting Proteins, And Bacterial Reaction Center Mutants, Kaitlyn Faries

Arts & Sciences Electronic Theses and Dissertations

Photosynthesis is the dominant form of solar energy conversion on the planet, making it critical to understand the fundamentals of the process in order to effectively mimic and improve upon it for human energy needs. The initial stages of photosynthesis include light harvesting and chemical conversion of that harvested energy via electron transport, with both of these stages relying on pigments (or chromophores) such as chlorophyll and specific protein architectures for the processes. In this work, the fundamental underpinnings of photosynthetic light harvesting and electron transport are explored via spectroscopy of various photosynthetic systems with altered natural pigments and proteins ...


Instrumentation For Cryogenic Dynamic Nuclear Polarization And Electron Decoupling In Rotating Solids, Faith Joellen Scott 2018 Washington University in St. Louis

Instrumentation For Cryogenic Dynamic Nuclear Polarization And Electron Decoupling In Rotating Solids, Faith Joellen Scott

Arts & Sciences Electronic Theses and Dissertations

Dynamic nuclear polarization (DNP) increases the sensitivity of nuclear magnetic resonance (NMR) using the higher polarization of electron radical spins compared to nuclear spins. The addition of electron radicals for DNP to the sample can cause hyperfine broadening, which decreases the resolution of the NMR resonances due to hyperfine interactions between electron and nuclear spins. Electron decoupling has been shown to attenuate the effects of hyperfine coupling in rotating solids. Magic angle spinning (MAS) DNP with electron decoupling requires a high electron Rabi frequency provided by a high-power microwave source such as a frequency-agile gyrotron. This dissertation describes the development ...


Materials Characterization By Dynamic Nuclear Polarization Enhanced Solid-State Nmr Spectroscopy, Aaron Rossini 2018 Iowa State University and Ames Laboratory

Materials Characterization By Dynamic Nuclear Polarization Enhanced Solid-State Nmr Spectroscopy, Aaron Rossini

Chemistry Publications

High-resolution solid-state NMR spectroscopy is a powerful tool for the study of organic and inorganic materials because it can directly probe the symmetry and structure at nuclear sites, the connectivity/bonding of atoms and precisely measure inter-atomic distances. However, NMR spectroscopy is hampered by intrinsically poor sensitivity, consequently, the application of NMR spectroscopy to many solid materials is often infeasible. High-field dynamic nuclear polarization (DNP) has emerged as a technique to routinely enhance the sensitivity of solid-state NMR experiments by one to three orders of magnitude. This perspective gives a general overview of how DNP enables advanced solid-state NMR experiments ...


Structure And Thermodynamics Of Polyglutamine Peptides And Amyloid Fibrils Via Metadynamics And Molecular Dynamics Simulations, Riley Workman 2018 Duquesne University

Structure And Thermodynamics Of Polyglutamine Peptides And Amyloid Fibrils Via Metadynamics And Molecular Dynamics Simulations, Riley Workman

Electronic Theses and Dissertations

Aggregation of polyglutamine (polyQ)-rich polypeptides in neurons is a marker for nine neurodegenerative diseases. The molecular process responsible for the formation of polyQ fibrils is not well understood and represents a growing area of study. To enable development of treatments that could interfere with aggregation of polyQ peptides, it is crucial to understand the molecular mechanisms by which polyQ peptides aggregate into fibrils. Many experimental techniques have been employed to probe polyQ aggregation, however, observations from these studies have not lead to a unified understanding of the properties of these systems, instead yielding competing, fragmented theories of polyQ aggregation ...


Mechanistic Studies Of Reducible Metal Oxides As Hydrodeoxygenation Catalysts, Akbar Mahdavi Shakib 2018 University of Maine

Mechanistic Studies Of Reducible Metal Oxides As Hydrodeoxygenation Catalysts, Akbar Mahdavi Shakib

Electronic Theses and Dissertations

Hydrodeoxygenation of phenol to benzene using ruthenium supported titania catalysts strongly varies depending on the support crystal structure and preparation conditions. Here, we performed spectroscopic characterization of titania supports to identify the surface impurities common to commercial and synthesized titania samples using a variety of spectroscopic methods. Sulfate impurities were detected for the commercial anatase samples and a procedure for their elimination was proposed so that inactive catalysts gained reactivity. Surface hydroxyls of different TiO2 samples (anatase, rutile, and pyrogenic) were identified using diffuse reflectance infrared Fourier transform spectroscopy (DRIFTS) experiments performed on vigorously cleaned surfaces and a facet-specific assignment ...


Spatial Distribution Of Organic Functional Groups Supported On Mesoporous Silica Nanoparticles (2): A Study By 1h Triple-Quantum Fast-Mas Solid-State Nmr, Takeshi Kobayashi, Dilini Singappuli-Arachchige, Igor I. Slowing, Marek Pruski 2018 Ames Laboratory

Spatial Distribution Of Organic Functional Groups Supported On Mesoporous Silica Nanoparticles (2): A Study By 1h Triple-Quantum Fast-Mas Solid-State Nmr, Takeshi Kobayashi, Dilini Singappuli-Arachchige, Igor I. Slowing, Marek Pruski

Chemistry Publications

The distribution of organic functional groups attached to the surface of mesoporous silica nanoparticles (MSNs) via co-condensation was scrutinized using 1D and 2D 1H solid-state NMR, including the triple-quantum/single-quantum (TQ/SQ) homonuclear correlation technique. The excellent sensitivity of 1H NMR and high resolution provided by fast magic angle spinning (MAS) allowed us to study surfaces with very low concentrations of aminopropyl functional groups. The sequential process, in which the injection of tetraethyl orthosilicate (TEOS) into the aqueous mother liquor was followed by dropwise addition of the organosilane precursor, resulted in deployment of organic groups on the surface, which were ...


Cation-Π Interactions Of Selected Alkali Metal Ions With Two Benzene Rings Connected Through Linear Chains, Nouf Alshamrani 2018 Clark Atlanta University

Cation-Π Interactions Of Selected Alkali Metal Ions With Two Benzene Rings Connected Through Linear Chains, Nouf Alshamrani

Electronic Theses & Dissertations Collection for Atlanta University & Clark Atlanta University

Quantum chemical calculations at M06-2X/6-311+G(2d,2p) level were employed to examine the structures, dissociation energies and vibrational spectra of complexes formed by Li+, Na+ and K+ with diphenylmethane, 1,2-diphenylethane, 1,3-diphenylpropane, [2.2]paracyclophane and [3.3]paracyclophane molecules. The effect of heteroatom substitution in the connecting chains of 1,3-diphenylpropane and [3.3]paracyclophane molecules on the binding affinity of cations with ligands was also included in this study. The complexes of [3.3] paracyclophane based molecules seem to have weak cation-pi interactions with metal ions Na+ and K+ when they were placed between two ...


Enhanced Acidity Of Acetic And Pyruvic Acids On The Surface Of Water, Alexis J. Eugene, Elizabeth A. Pillar, Agustín J. Colussi, Marcelo I. Guzman 2018 University of Kentucky

Enhanced Acidity Of Acetic And Pyruvic Acids On The Surface Of Water, Alexis J. Eugene, Elizabeth A. Pillar, Agustín J. Colussi, Marcelo I. Guzman

Chemistry Faculty Publications

Understanding the acid–base behavior of carboxylic acids on aqueous interfaces is a fundamental issue in nature. Surface processes involving carboxylic acids such as acetic and pyruvic acids play roles in (1) the transport of nutrients through cell membranes, (2) the cycling of metabolites relevant to the origin of life, and (3) the photooxidative processing of biogenic and anthropogenic emissions in aerosols and atmospheric waters. Here, we report that 50% of gaseous acetic acid and pyruvic acid molecules transfer a proton to the surface of water at pH 2.8 and 1.8 units lower than their respective acidity constants ...


Infra-Red Microwave Spectra, Overtones, Degeneracy And Thermal Populations All In One Diagram, Carl W. David 2018 University of Connecticut

Infra-Red Microwave Spectra, Overtones, Degeneracy And Thermal Populations All In One Diagram, Carl W. David

Chemistry Education Materials

An old drawing, which had an error in it, is re-presented (corrected) for understanding the relationships in diatomic vibrational-rotational interactions at the introductory level.


Synthetic And Theoretical Studies For Cyclization Reactions To Form C-C And C-N Bonds, Nicholas Jentsch 2018 The University of Southern Mississippi

Synthetic And Theoretical Studies For Cyclization Reactions To Form C-C And C-N Bonds, Nicholas Jentsch

Dissertations

Natural product total synthesis provides an alternative method for obtaining medicinally relevant compounds in a more efficient process with higher yields than what nature can provide. Natural products pose significant synthetic challenges due to the unique heterocyclic skeletons with fused and spirocyclic ring systems. Therefore, it is paramount to develop efficient reaction methodologies targeting substructures such as cyclic ureas and spiro[4.5]decanes which are prominent among marine natural products and Lycopodium alkaloids, respectively. Presented here is a compilation of research seeking to develop synthetic methods for the construction of cyclic moieties such as those previously mentioned. The objectives ...


Pnnl Dark Matter Bubble Chamber, Ryan Robinson 2018 STAR Program

Pnnl Dark Matter Bubble Chamber, Ryan Robinson

STAR (STEM Teacher and Researcher) Presentations

The Pacific Northwest National Laboratory (PNNL) prototype bubble chamber is intended to address issues encountered with the current PICO dark matter search detectors and improve the functionality of future experimental designs. The PNNL bubble chamber accomplishes this with a simplified interface between the hydraulic pressure controls and the target vessel and altering the standard chamber design such that it can be easily exchanged and replaced with vessels of various sizes and materials for testing purposes. The chamber itself is a glass vessel which houses perfluorobutane and holds the target fluid above room temperature and atmospheric pressure. The target fluid becomes ...


Modern Electronic Structure Theory: The Search For Chemical Accuracy, Jonathan Prince 2018 Boise State University

Modern Electronic Structure Theory: The Search For Chemical Accuracy, Jonathan Prince

Boise State University Theses and Dissertations

Electronic structure theory has progressed significantly within the last few decades, venturing far from the early days of the Hartree-Fock self-consistent field method. Modern electronic structure theory focuses on compound methods, which operate under the idea that we can take a lower level of theory computation (typically, a result from Hartree-Fock, Configuration Interaction, Coupled Cluster or Moller-Plesset perturbation theory) and add in higher level of the theory corrections such as extrapolations to the infinite basis set limit, as well as, relativistic effects.

Using the Gaussian-n, Complete Basis Set and Weizmann compound methods, we were able to provide theoretical evidence to ...


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