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Full-Text Articles in Physical Chemistry

Coinage Metal–Sulfur Complexes: Stability On Metal(111) Surfaces And In The Gas Phase, Jiyoung Lee, Theresa L. Windus, Patricia A. Thiel, James W. Evans, Da-Jiang Liu May 2019

Coinage Metal–Sulfur Complexes: Stability On Metal(111) Surfaces And In The Gas Phase, Jiyoung Lee, Theresa L. Windus, Patricia A. Thiel, James W. Evans, Da-Jiang Liu

James W. Evans

We provide a comprehensive theoretical assessment at the level of density functional theory (DFT) of the stability of various coinage metal–sulfur complexes, both in the gas phase and also for the complexes adsorbed on the (111) surface of the same coinage metal. Our primary interest lies in the latter where earlier scanning tunneling microscopy (STM) experiments were interpreted to suggest the existence of adsorbed S-decorated metal trimers, sometimes as a component of more complex adlayer structures. Recent STM studies at 5 K directly observed other isolated adsorbed metal–sulfur complexes. For these adsorbed species, we calculate various aspects of ...


Coinage Metal–Sulfur Complexes: Stability On Metal(111) Surfaces And In The Gas Phase, Jiyoung Lee, Theresa L. Windus, Patricia A. Thiel, James W. Evans, Da-Jiang Liu May 2019

Coinage Metal–Sulfur Complexes: Stability On Metal(111) Surfaces And In The Gas Phase, Jiyoung Lee, Theresa L. Windus, Patricia A. Thiel, James W. Evans, Da-Jiang Liu

Patricia A. Thiel

We provide a comprehensive theoretical assessment at the level of density functional theory (DFT) of the stability of various coinage metal–sulfur complexes, both in the gas phase and also for the complexes adsorbed on the (111) surface of the same coinage metal. Our primary interest lies in the latter where earlier scanning tunneling microscopy (STM) experiments were interpreted to suggest the existence of adsorbed S-decorated metal trimers, sometimes as a component of more complex adlayer structures. Recent STM studies at 5 K directly observed other isolated adsorbed metal–sulfur complexes. For these adsorbed species, we calculate various aspects of ...


Coinage Metal–Sulfur Complexes: Stability On Metal(111) Surfaces And In The Gas Phase, Jiyoung Lee, Theresa L. Windus, Patricia A. Thiel, James W. Evans, Da-Jiang Liu May 2019

Coinage Metal–Sulfur Complexes: Stability On Metal(111) Surfaces And In The Gas Phase, Jiyoung Lee, Theresa L. Windus, Patricia A. Thiel, James W. Evans, Da-Jiang Liu

Theresa Windus

We provide a comprehensive theoretical assessment at the level of density functional theory (DFT) of the stability of various coinage metal–sulfur complexes, both in the gas phase and also for the complexes adsorbed on the (111) surface of the same coinage metal. Our primary interest lies in the latter where earlier scanning tunneling microscopy (STM) experiments were interpreted to suggest the existence of adsorbed S-decorated metal trimers, sometimes as a component of more complex adlayer structures. Recent STM studies at 5 K directly observed other isolated adsorbed metal–sulfur complexes. For these adsorbed species, we calculate various aspects of ...


Characteristics Of Sulfur Atoms Adsorbed On Ag(100), Ag(110), And Ag(111) As Probed With Scanning Tunneling Microscopy: Experiment And Theory, Peter M. Spurgeon, Da-Jiang Liu, Holly Walen, Junepyo Oh, Hyun Jin Yang, Yousoo Kim, Patricia A. Thiel May 2019

Characteristics Of Sulfur Atoms Adsorbed On Ag(100), Ag(110), And Ag(111) As Probed With Scanning Tunneling Microscopy: Experiment And Theory, Peter M. Spurgeon, Da-Jiang Liu, Holly Walen, Junepyo Oh, Hyun Jin Yang, Yousoo Kim, Patricia A. Thiel

Patricia A. Thiel

In this paper, we report that S atoms on Ag(100) and Ag(110) exhibit a distinctive range of appearances in scanning tunneling microscopy (STM) images, depending on the sample bias voltage, VS. Progressing from negative to positive VS, the atomic shape can be described as a round protrusion surrounded by a dark halo (sombrero) in which the central protrusion shrinks, leaving only a round depression. This progression resembles that reported previously for S atoms on Cu(100). We test whether DFT can reproduce these shapes and the transition between them, using a modified version of the Lang–Tersoff–Hamann ...


Recycling Aluminum, Steffani Burwitz, Kristin M. Roe, Matthew L. Miller, Madhav P. Nepal, Larry B. Browning, P. Troy White May 2019

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

Madhav Nepal

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.


Characteristics Of Sulfur Atoms Adsorbed On Ag(100), Ag(110), And Ag(111) As Probed With Scanning Tunneling Microscopy: Experiment And Theory, Peter M. Spurgeon, Da-Jiang Liu, Holly Walen, Junepyo Oh, Hyun Jin Yang, Yousoo Kim, Patricia A. Thiel May 2019

Characteristics Of Sulfur Atoms Adsorbed On Ag(100), Ag(110), And Ag(111) As Probed With Scanning Tunneling Microscopy: Experiment And Theory, Peter M. Spurgeon, Da-Jiang Liu, Holly Walen, Junepyo Oh, Hyun Jin Yang, Yousoo Kim, Patricia A. Thiel

Chemistry Publications

In this paper, we report that S atoms on Ag(100) and Ag(110) exhibit a distinctive range of appearances in scanning tunneling microscopy (STM) images, depending on the sample bias voltage, VS. Progressing from negative to positive VS, the atomic shape can be described as a round protrusion surrounded by a dark halo (sombrero) in which the central protrusion shrinks, leaving only a round depression. This progression resembles that reported previously for S atoms on Cu(100). We test whether DFT can reproduce these shapes and the transition between them, using a modified version of the Lang–Tersoff–Hamann ...


Preparation And Characterization Of Ruthenium-Gold Raman-Active Catalytic Surfaces, Thang Nguyen May 2019

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 ...


Hartree-Fock Implementation For Pedagogical & Research Purposes, Gary Zeri, Jerry Larue May 2019

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 ...


Computational Studies Of Small Molecule Activation In Catylsis And Green Chemistry, Alexa N. Griffith Ms. May 2019

Computational Studies Of Small Molecule Activation In Catylsis And Green Chemistry, Alexa N. Griffith Ms.

Chancellor’s Honors Program Projects

No abstract provided.


Neurological Disease Detection Using Surface Enhanced Spatially Offset Raman Spectroscopy (Sesors), Taylor D. Payne May 2019

Neurological Disease Detection Using Surface Enhanced Spatially Offset Raman Spectroscopy (Sesors), Taylor D. Payne

Chancellor’s Honors Program Projects

No abstract provided.


Spatial Encoding With Single-Sided Nmr, Madeline Brass May 2019

Spatial Encoding With Single-Sided Nmr, Madeline Brass

Undergraduate Honors Theses

Single-sided NMR is an important non-invasive, non-destructive technique used to characterize molecules. Specifically, single-sided NMR has applications in biomedicine, elastomers, solid polymers, moisture in porous media, and cultural heritage. Single-sided magnets can be used to analyze T2 relaxation to gauge the relative motion of molecules in the sample. However, the are few methods to characterize heterogeneous samples with single-sided NMR. Most experiments take one set of data for the entire sample regardless if the sample is heterogeneous or homogeneous. New methods to spatially encode with single-sided NMR were explore and characterized based on their advantages and disadvantages. These methods include ...


Characterizing Flame-Resistant Polymers Using Single-Sided Nmr, Anna Tsutsui May 2019

Characterizing Flame-Resistant Polymers Using Single-Sided Nmr, Anna Tsutsui

Undergraduate Honors Theses

Many commonly used polymers are inherently flammable. Manufacturers have been able to make polymers more flame-resistant by incorporating additives in polymer matrices. Current testing methods of these materials are destructive. As a result, there is a lack of data that can characterize the long-term effects of thermal exposure on these materials. This study presents single-sided NMR as an alternative technique to characterize the physical properties of these materials before and after thermal exposure. From single-sided NMR, this study finds that it is possible to characterize the molecular behavior of flame-resistant polymers and that additives cause no significant physical change to ...


Coinage Metal–Sulfur Complexes: Stability On Metal(111) Surfaces And In The Gas Phase, Jiyoung Lee, Theresa L. Windus, Patricia A. Thiel, James W. Evans, Da-Jiang Liu Apr 2019

Coinage Metal–Sulfur Complexes: Stability On Metal(111) Surfaces And In The Gas Phase, Jiyoung Lee, Theresa L. Windus, Patricia A. Thiel, James W. Evans, Da-Jiang Liu

Chemistry Publications

We provide a comprehensive theoretical assessment at the level of density functional theory (DFT) of the stability of various coinage metal–sulfur complexes, both in the gas phase and also for the complexes adsorbed on the (111) surface of the same coinage metal. Our primary interest lies in the latter where earlier scanning tunneling microscopy (STM) experiments were interpreted to suggest the existence of adsorbed S-decorated metal trimers, sometimes as a component of more complex adlayer structures. Recent STM studies at 5 K directly observed other isolated adsorbed metal–sulfur complexes. For these adsorbed species, we calculate various aspects of ...


Heavy-Atom Tunneling In The Planar Bond Shifting Of [16]Annulene, Philip Lampkin, Jon Shezaf Apr 2019

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 ...


Photoelectrochemical Oxidative Homocoupling Of 1-(2-Thienyl)Pyrene, Austin Dobrecevich Apr 2019

Photoelectrochemical Oxidative Homocoupling Of 1-(2-Thienyl)Pyrene, Austin Dobrecevich

Carroll College Student Undergraduate Research Festival

In this project the goal is to begin research on a more sustainable form of energy. The sun’s energy is harnessed in many different ways, and we are trying to use this energy to synthesize a storable fuel. Using the sun’s energy, we can make a monomer dimerize, then this product can be collected, and is stable. This dimer can then be reacted to produce the monomer, and the reaction energy can be harnessed. Then the reaction scheme can begin again. This reaction is all done with a transparent semiconductor, a fluid containing the monomer, and light. The ...


Site Specific Photoinitiated Release Of Bromothymol Blue, Alexander Hoffman, Taryn Stewart, Keaton Brady, Samantha Mundel Apr 2019

Site Specific Photoinitiated Release Of Bromothymol Blue, Alexander Hoffman, Taryn Stewart, Keaton Brady, Samantha Mundel

Carroll College Student Undergraduate Research Festival

Delivery of pharmaceutical drugs to specific sites of the body would be beneficial for the treatment of cancer and other major ailments which affect singular areas of the body. There are promising possibilities being studied to determine their efficacy. Here is presented the investigation of the photoinitiated release of an indicator, acting as a drug, from a vesicle into an environment containing a reactant. In this experiment, spiropyran was integrated into Dipalmitoylphosphatitylcholine (DMPC) and 1’,3’,3’-Trimethylspiro[chromene-2,2’-indoline] (spiropyran) are the components of the carrier vesicles that surround bromothymol blue (BTB) in the sodium bicarbonate solution. Spiropyran ...


Investigating The Rotary Mechanism Of Atp Synthase Using Molecular Dynamics Simulations, Angela Marcela Murcia Rios Apr 2019

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 ...


Computational Studies Of Alkanol Reaction Pathways On A Srtio3 Perovskite Surface, Kyle R. Mason Apr 2019

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 Apr 2019

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.


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

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.


Determinations Of Proton Affinities Of Methylated Cysteine And Serine Homologs, Danielle Long Apr 2019

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 ...


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

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 ...


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

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 ...


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 Mar 2019

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 Mar 2019

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.


Fundamental Limits Of Measuring Single-Molecule Rotational Mobility, Oumeng Zhang, Matthew D. Lew Feb 2019

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.


Role Of Structure And Oxidation States In The Passivation Of Stainless Steel By Chromium, Suman Bhasker Ranganath, Collin D. Wick, B. R. Ramachandran Feb 2019

Role Of Structure And Oxidation States In The Passivation Of Stainless Steel By Chromium, Suman Bhasker Ranganath, Collin D. Wick, B. R. Ramachandran

B. Ramu Ramachandran

The early stages of the oxidation of stainless steel is studied using first principles density functional theory calculations. A Monte Carlo approach was used to efficiently identify the most probable low energy structures in the high-dimensional configuration space. The composition, structure, and oxidation states of the atoms in the oxide layers were analyzed by atomic density profiles, nearest neighbor distribution, and Bader charge analysis. The results suggest that the passivation of steel by chromium is largely due to its high preference for the Cr3+ oxidation state with 6 oxygen neighbors.  In contrast, iron is more susceptible to oxygen penetration because ...


Solvation Thermodynamic Mapping In Computer Aided Drug Design, Steven Ramsey Feb 2019

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 ...


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

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 Jan 2019

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 ...