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All Articles in Physical Chemistry

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Investigating The Rotary Mechanism Of Atp Synthase Using Molecular Dynamics Simulations, Angela Marcela Murcia Rios 2019 The University of Western Ontario

Investigating The Rotary Mechanism Of Atp Synthase Using Molecular Dynamics Simulations, Angela Marcela Murcia Rios

Electronic Thesis and Dissertation Repository

F1-ATPase is a motor protein that can use ATP hydrolysis to drive rotation of the central subunit. The γ C-terminal helix constitutes of the rotor tip that is seated in an apical bearing formed by the α3β3 head. It remains uncertain to what extent the γ conformation during rotation differs from that seen in rigid crystal structures. Existing models assume that the entire γ subunit participates in every rotation. Here we develop a molecular dynamics (MD) strategy to model the off-axis forces acting on γ in F1-ATPase. MD runs showed stalling of the ...


High Resolution Near-Infrared/Visible Intracavity Laser Spectroscopy Of Small Molecules, Jack Harms 2019 University of Missouri-St. Louis

High Resolution Near-Infrared/Visible Intracavity Laser Spectroscopy Of Small Molecules, Jack Harms

Dissertations

Intracavity laser spectroscopy has been used to study the electronic structure of several small molecules. The molecules studied as part of this dissertation include germanium hydride (GeH), copper oxide (CuO), nickel chloride (NiCl), platinum fluoride (PtF), platinum chloride (PtCl), and copper hydroxide (CuOH). This work encompasses five peer-reviewed publications and two submitted manuscripts.


Computational Studies Of Alkanol Reaction Pathways On A Srtio3 Perovskite Surface, Kyle R. Mason 2019 University of Tennessee, Knoxville

Computational Studies Of Alkanol Reaction Pathways On A Srtio3 Perovskite Surface, Kyle R. Mason

EURēCA: Exhibition of Undergraduate Research and Creative Achievement

No abstract provided.


Quantitative Analysis Of Iron In Beer Using Cloud Point Extraction, Joshua Rempfer 2019 University of Lynchburg

Quantitative Analysis Of Iron In Beer Using Cloud Point Extraction, Joshua Rempfer

Student Scholar Showcase

Determination of Iron concentration in Apocalypse Ale beer using a preconcentration method coupled with UV-Vis spectroscopy. Samples will be cross checked with MP-AES to ensure precise and accurate results.


Dentin Biomodification Potency Of Proanthocyanidins, David J. Ryker 2019 Taylor University

Dentin Biomodification Potency Of Proanthocyanidins, David J. Ryker

Student Scholarship: Chemistry

No abstract provided.


A Chemical Overview Of Opioid Receptors And Their Agonists, Noah Kuszak 2019 Taylor University

A Chemical Overview Of Opioid Receptors And Their Agonists, Noah Kuszak

Student Scholarship: Chemistry

This work is a brief overview of the three main opioid receptors and some current research of the ways we can change the agonists and how they affect the opioid receptor pathway.


Drug Improvement And Design Involving G-Protein Coupled Receptors, Gabriel Saliba 2019 Taylor University

Drug Improvement And Design Involving G-Protein Coupled Receptors, Gabriel Saliba

Student Scholarship: Chemistry

No abstract provided.


Exploring The Blinking Dynamics Of Eosin Y Photosensitizers For Dye-Sensitized Photocatalysis Using Single-Molecule Spectroscopy, Pauline Lynch 2019 William & Mary

Exploring The Blinking Dynamics Of Eosin Y Photosensitizers For Dye-Sensitized Photocatalysis Using Single-Molecule Spectroscopy, Pauline Lynch

Undergraduate Honors Theses

Dye-sensitized photocatalysis (DSP) is a promising way to harvest solar energy for carbon-neutral fuel production, but a better understanding of how and why it is currently inefficient is necessary. This thesis will delve into the complex excited-state dynamics of Eosin Y (EY), a sensitizer for DSP, on glass substrates. By using single-molecule spectroscopy (SMS) to understand the underlying photophysics at play, we can gain a more complete understanding of the various photophysical events that contribute to inefficient DSP. In particular, SM blinking dynamics give insight into kinetic models.

SM blinking measurements of EY molecules in air and in N2 were ...


Determinations Of Proton Affinities Of Methylated Cysteine And Serine Homologs, Danielle Long 2019 William & Mary

Determinations Of Proton Affinities Of Methylated Cysteine And Serine Homologs, Danielle Long

Undergraduate Honors Theses

Non-protein amino acids (NPAAs) are of interest to study for their potential to be incorporated into peptides and proteins, as well as for understanding their structure-energetics relationships. Studying these amino acids’ thermochemical properties such as their acidity and basicity allow for elucidation of the structure and bonding characteristics of these molecules. By examining these molecules in the gas-phase in mass spectrometers, we are able to determine their intrinsic thermodynamic properties without solvation effects. These thermochemical properties, in part, determine the structure, function and bonding of the molecules.

This study focused on determining the proton affinities of methylated cysteine and serine ...


Ligand-Protein Binding Of Cantharidin And Norcantharidin On Hsf1: A Docking Study, Daniel Coyle 2019 La Salle University

Ligand-Protein Binding Of Cantharidin And Norcantharidin On Hsf1: A Docking Study, Daniel Coyle

HON499 projects

Previous research provides experimental evidence that cantharidin acts as an inhibitor of HSF1 in cancer cells whereas the similar norcantharidin exhibits no inhibitory activity on HSF1. This computational study utilized Autodock to suggest both binding site(s) and binding energies of cantharidin and norcantharidin on HSF1. This study found cantharidin to consistently bind stronger than norcantharidin in the same area on HSF1 when assuming a rigid protein structure.


Corrosion Studies On Lightweight Automotive Alloys: The Effect Of Microstructure And Fundamental Mechanisms, Wilfred J. Binns 2019 The University of Western Ontario

Corrosion Studies On Lightweight Automotive Alloys: The Effect Of Microstructure And Fundamental Mechanisms, Wilfred J. Binns

Electronic Thesis and Dissertation Repository

Owing to their excellent strength-to-weight ratio and low density, magnesium alloys have the potential to significantly reduce the weight of automobiles leading to decreased emissions and greater range for electrical vehicles. However, the practicality of magnesium alloys for automotive and aerospace applications is severely hindered by their poor corrosion resistance in aqueous environments. Despite intensive research effort, the underlying mechanism(s) responsible for this poor corrosion resistance remains elusive. Further complicating the situation is the presence of secondary microstructures which are necessary for desirable physical properties but lead to microgalvanic coupling which exacerbates the poor corrosion resistance of magnesium alloys ...


Control Strategies For Multi-Evaporator Vapor Compression Cycles, Sunderlin D. Jackson 2019 Air Force Institute of Technology

Control Strategies For Multi-Evaporator Vapor Compression Cycles, Sunderlin D. Jackson

Theses and Dissertations

Next-generation military aircraft must be able to handle highly transient thermal loads that exceed the ability of current aircraft thermal subsystems. Vapor compression cycle systems are a particular refrigeration technology that is an attractive solution for dealing with this challenge, due primarily to their high efficiency. However, there are several barriers to realizing the benefits of vapor cycles systems for controlling thermal loads in military aircraft. This thesis focuses on addressing the challenge of controlling vapor cycles in the presence of highly transient evaporator heat loads. Specifically, a linear quadratic regulator (LQR) is designed for a simple vapor cycle system ...


The Effects Of Reactant Concentration And Air Flow Rate In The Consumption Of Dissolved O2 During The Photochemistry Of Aqueous Pyruvic Acid, Alexis J. Eugene, Marcelo I. Guzman 2019 University of Kentucky

The Effects Of Reactant Concentration And Air Flow Rate In The Consumption Of Dissolved O2 During The Photochemistry Of Aqueous Pyruvic Acid, Alexis J. Eugene, Marcelo I. Guzman

Chemistry Faculty Publications

The sunlight photochemistry of the organic chromophore pyruvic acid (PA) in water generates ketyl and acetyl radicals that contribute to the production and processing of atmospheric aerosols. The photochemical mechanism is highly sensitive to dissolved oxygen content, [O2(aq)], among other environmental conditions. Thus, herein we investigate the photolysis (λ ≥ 305 nm) of 10–200 mM PA at pH 1.0 in water covering the relevant range 0 ≤ [O2(aq)] ≤ 1.3 mM. The rapid consumption of dissolved oxygen by the intermediate photolytic radicals is monitored in real time with a dissolved oxygen electrode. In addition, the rate ...


Recycling Aluminum, Steffani Burwitz, Kristin M. Roe, Matthew L. Miller, Madhav P. Nepal, Larry B. Browning, P. Troy White 2019 West Central High School, Humboldt, SD

Recycling Aluminum, Steffani Burwitz, Kristin M. Roe, Matthew L. Miller, Madhav P. Nepal, Larry B. Browning, P. Troy White

iLEARN Teaching Resources

Students will investigate and compare the energy cost to produce aluminum products from aluminum ore and recycled aluminum. Students will perform an electrolysis activity to reinforce the idea that recycling metal requires less energy than mining and refining metals from their original source in the earth.


Extraction Of Acids And Bases From Aqueous Phase To A Pseudoprotic Ionic Liquid, Nikolas Patsos, Karin Lewis, Francesco Picchioni, Mark N. Kobrak 2019 University of Groningen

Extraction Of Acids And Bases From Aqueous Phase To A Pseudoprotic Ionic Liquid, Nikolas Patsos, Karin Lewis, Francesco Picchioni, Mark N. Kobrak

Publications and Research

We report experiments on the extraction of acids and bases from an aqueous phase to a pseudoprotic ionic liquid phase consisting of an equimolar mixture of trihexylamine and octanoic acid. We observed the extraction of a wide range of acids and bases, and investigated the mechanism of extraction in detail. Our results confirmed the observation of the Hofmeister effect in these systems reported in our previous work, where the extent of the extraction of copper salts was significantly influenced by the interactions between extracted inorganic anions and the organic phase. Our results further demonstrated that the organic layer served as ...


Fundamental Limits Of Measuring Single-Molecule Rotational Mobility, Oumeng Zhang, Matthew D. Lew 2019 Washington University in St Louis

Fundamental Limits Of Measuring Single-Molecule Rotational Mobility, Oumeng Zhang, Matthew D. Lew

Electrical & Systems Engineering Publications and Presentations

Various methods exist for measuring molecular orientation, thereby providing insight into biochemical activities at nanoscale. Since fluorescence intensity and not electric field is detected, these methods are limited to measuring even-order moments of molecular orientation. However, any measurement noise, for example photon shot noise, will result in nonzero measurements of any of these even-order moments, thereby causing rotationally-free molecules to appear to be partially constrained. Here, we build a model to quantify measurement errors in rotational mobility. Our theoretical framework enables scientists to choose the optimal single-molecule orientation measurement technique for any desired measurement accuracy and photon budget.


Solvation Thermodynamic Mapping In Computer Aided Drug Design, Steven Ramsey 2019 The Graduate Center, City University of New York

Solvation Thermodynamic Mapping In Computer Aided Drug Design, Steven Ramsey

All Dissertations, Theses, and Capstone Projects

The displacement of water from surfaces upon biomolecular recognition and association makes a significant contribution to the free energy changes of these processes. We therefore posit that accurate characterization of local structural and thermodynamic molecular water properties can improve computational model accuracy and predictivity of recognition and association processes. In this thesis, we discuss Solvation Thermodynamic Mapping (STM) methods that we have developed using inhomogeneous fluid solvation theory (IST) to better characterize active site water structural and thermodynamic properties on protein surfaces and the open source tools that we have developed, GIST-CPPTRAJ and SSTMap, which implement these methods which we ...


Manori Perera And Problems For Automobiles During Sub-Zero Temperatures, Eric Stock 2019 WGLT, Illinois State University

Manori Perera And Problems For Automobiles During Sub-Zero Temperatures, Eric Stock

Interviews for WGLT

Eric Stock,WGLT Radio, spoke to Professor of Chemistry Manori Perera about the hazards that sub-zero temperatures create for automobiles.


The Van Der Waals Fluid’S Liquid Vapor Coexistence Locus, Using Maxima/Gnuplot, Carl W. David 2019 University of Connecticut

The Van Der Waals Fluid’S Liquid Vapor Coexistence Locus, Using Maxima/Gnuplot, Carl W. David

Chemistry Education Materials

The Maxima/Gnuplot code for plotting the van der Waals locus of liquid and vapor molar volumes as a function of pressure and temperature (all reduced) is presented.


Protein Conformations In The Gas Phase Probed By Mass Spectrometry And Molecular Dynamics Simulations, Maryam Bakhtiari 2019 The University of Western Ontario

Protein Conformations In The Gas Phase Probed By Mass Spectrometry And Molecular Dynamics Simulations, Maryam Bakhtiari

Electronic Thesis and Dissertation Repository

Mass Spectrometry (MS) has been revolutionized by the ability to produce intact gaseous protein ions by electrospray ionization (ESI). The question to what extent these ions retain solution-like conformations under “native” ESI conditions remains a matter of debate. Traditional high-resolution structure determination techniques only report on proteins in the condensed phase. For this reason, MD simulations play an important role in exploring the behavior of gas phase proteins. In this research, mobile and non-mobile proton MD simulations along with mass spectrometry data at 300 K in both positive and negative ion mode indicated that native-like conformations were largely retained. Surface ...


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