Computational Chemistry Commons^™

Application Of Computational Biophysics Techniques To Characterize Cell Membrane-Associated Events, Kyle Billings

Graduate Theses, Dissertations, and Problem Reports (ETD)

Cell membranes are crowded environments which can modulate protein structure-function relationships through interaction with lipids, other proteins, carbohydrate structures and so on. This work focuses the impact of the membrane environment on two varieties of peptides: Microbial rhodopsin proteins, and cyclic peptides.

Life on Earth is dependent on the ability of plants and microbes to harness sunlight for energy production. Their ability to transform light into carbohydrates requires tailor-made machinery, and for a wealth of microorganisms, microbial rhodopsin proteins (MR) are critical for maintaining the concentration gradients used to produce the energy molecule Adenosine triphosphate (ATP). The central retinal molecule …

Translating Chemistry, Structure, And Processing To The Solid-State Morphology And Function Of Organic Semiconductors Through Computational Modeling And Simulations, Chamikara D. Karunasena

Theses and Dissertations--Chemistry

The immense synthetic design space and material versatility have driven the exploration and development of organic semiconductors (OSC) over several decades. While many OSC designs focus on the chemistries of the molecular or polymer building blocks, a priori, multiscale control over the solid-state morphology is required for effective application of the active layer in a given technology. However, molecular assembly during solid-state formation is a complex function interconnecting the building block chemistry and the processing environment. Insufficient knowledge as to how these aspects engage, especially at the atomistic and molecular scales, has so far limited the ability to predict …

Developing And Deploying Data-Driven Tools For Accelerated Design Of Organic Semiconductors, Vinayak Bhat

Theses and Dissertations--Chemistry

Organic semiconductors have gained widespread attention due to their potential applications in flexible, low-cost, lightweight electronics, energy storage and generation technologies, and sensing applications. However, developing new organic semiconductors with improved performance remains a significant challenge due to the vast chemical space of possible molecular and materials structures. Furthermore, the high cost and time-consuming nature of experimental synthesis and characterization hinder the rapid discovery of new materials. To overcome these challenges, this dissertation presents a data-driven approach to organic semiconductor discovery. The primary focus of this work is the development of data-driven tools, namely machine learning models, to predict critical …

Water-Soluble Palladium, Copper, And Nickel Catalysts And Their Formation In Ligand-Free Suzuki-Miyaura Cross-Coupling Reactions, Priya Karna

Theses and Dissertations--Chemistry

Transition-metal catalyzed Suzuki-Miyaura (SM) cross coupling is a powerful synthetic method for constructing carbon-carbon and carbon-heteroatom bonds in designing organic compounds, agrochemicals, pharmaceuticals, and precursors for materials. However, the nature of catalysis and identity of the transition metal catalysts used in these reactions remain under debate or unknown. This dissertation reports the studies of three metals: Pd, Cu, and Ni. Pd-nanocluster catalysts and their formation in ligand-free SM reactions with Pd(II) nitrate as a precatalyst was investigated. The catalysts are water-soluble neutral Pd tetramer and trimer in their singlet electronic states as identified by UV-Vis absorption spectroscopy and are formed …

First Principles Calculations To Investigate Surface And Catalytic Properties Of Materials For Green Energy Generation, Keerthan Raghavendra Rao

Theses and Dissertations--Chemistry

Climate change due to greenhouse gas build up in the earth’s atmosphere is an existential threat to humanity. To mitigate climate change, a significant shift from fossil fuels is necessary. Over the years, several renewable energy sources like solar, wind, geothermal etc. have been explored with the aim providing carbon-free energy. In this work, we focus on using density functional theory (DFT) methods to investigate key functional properties of materials of interest for applications in solar cells and catalytic conversion for energy generation. We show geometric effects of carboxylic acid binding on a transition metal surface to impact the deoxygenation …

Quantum Computations And Molecular Dynamics Simulations: From The Fundamentals Of Antimicrobial Resistance To Neurological Diseases, Angel Tamez

Electronic Theses and Dissertations

Biophysical phenomena are modeled using a combination of quantum and classical methods to interpret and supplement three distinct and diverse problems in this dissertation. In the first project, decarboxylation reactions are ubiquitous across chemical and biological disciplines, yet the origin of non-catalytic solvent effects remains elusive. Specific solvent structure and energetics have not been well described for the monoanion of malonate, nor corrected from the gas-phase charge-assisted intramolecular hydrogen bond model known as “pseudochair”. In the aqueous phase, a low-lying energy conformer known as the “orthogonal conformation” is computed to be preferred by a three-water cluster of hydrogen bonding over …

Hydrogen Bonding In Small Model Peptides; The Dft And Mp2 Study, Gracie Smith, Martina Kaledin

Symposium of Student Scholars

Formamide is a small model compound for the study of the peptide bond. The peptide bond links amino acids together, specifies rigidity to the protein backbone, and includes the essential docking sites for hydrogen-bond-mediated protein folding and protein aggregation, namely, the C=O acceptor and the N-H donor parts. Therefore, the infrared C=O (amide-I) and N-H (amide-A) vibrations provide sensitive and widely used probes into the structure of peptides. This computational chemistry work, we study hydrogen bonds in formamide dimer isomers. We evaluate the accuracy of the density functional theory (DFT) and many-body perturbation theory to the 2^nd order (MP2) …

Turning Ligands On Their Side: Computational Investigation Into The Binding Of N2o And N2 In Transition Metal Complexes, Cole Donald

Electronic Theses and Dissertations

Common greenhouse gas nitrous oxide (N₂O) is a thermodynamically potent and environmentally benign oxidant, making it a desirable target for metal center activation. Unfortunately, N₂O is a poor ligand for transition metals due to its weak sigma-donating and pi-accepting properties; as a result, few transition metal complexes capable of interacting with N₂O have been found. As the primary source of all nitrogen in organisms, abundant gas dinitrogen (N₂) is a crucially important tiny molecule and an essential part of daily existence. However, due to its inertness, it has limited practical uses in …

Perfect Polar Alignment Of Parallel Beloamphiphile Monolayers: Synthesis, Characterization, And Crystal Architectures Of Unsymmetrical Phenoxy-Substituted Acetophenone Azines, Harmeet Bhoday, Michael Lewis, Steven P. Kelley, Rainer Glaser

Chemistry Faculty Research & Creative Works

It remains a great challenge to achieve polar order in organic molecular crystals because anti-parallel alignment of side-by-side molecules is intrinsically preferred. We have addressed this problem with a rational design that focuses on the polar stacking of parallel beloamphiphile monolayers (PBAMs) with strong lateral quadrupole-quadrupole attractions. We employ arene-arene interactions as lateral synthons. The first successes were achieved with unsymmetrical donor (X), acceptor (Y) substituted acetophenone azines which form polar PBAMs with double T-contacts between the azines. Near-perfect alignment was achieved with the methoxy series of (MeO, Y)-azines with Y=Cl, Br, I. Here, we report on the synthesis, the …

Helium Nanodroplets As An Efficient Tool To Investigate Hydrogen Attachment To Alkali Cations, Siegfried Kollotzek, José Campos-Martínez, Massimiliano Bartolomei, Fernando Pirani, Lukas Tiefenthaler, Marta I. Hernández, Teresa Lázaro, Eva Zunzunegui-Bru, Tomás González-Lezana, José Bretón, Javier Hernández-Rojas, Olof E. Echt, Paul Scheier

Faculty Publications

We report a novel method to reversibly attach and detach hydrogen molecules to positively charged sodium clusters formed inside a helium nanodroplet host matrix. It is based on the controlled production of multiply charged helium droplets which, after picking up sodium atoms and exposure to H₂ vapor, lead to the formation of Na_m⁺(H₂)_n clusters, whose population was accurately measured using a time-of-flight mass spectrometer. The mass spectra reveal particularly favorable Na⁺(H₂)_n and Na₂⁺(H₂)_n clusters for specific “magic” numbers of attached hydrogen molecules. …

Solvation Of Large Polycyclic Aromatic Hydrocarbons In Helium: Cationic And Anionic Hexabenzocoronene, Miriam Kappe, Florent Calvo, Johannes Schöntag, Holger F. Bettinger, Serge Krasnokutski, Martin Kuhn, Elisabeth Gruber, Fabio Zappa, Paul Scheier, Olof E. Echt

Faculty Publications

The adsorption of helium on charged hexabenzocoronene (Hbc, C₄₂H₁₈), a planar polycyclic aromatic hydrocarbon (PAH) molecule of D_6h symmetry, is investigated by a combination of high-resolution mass spectrometry and classical and quantum computational methods. The ion abundance of He_nHbc⁺ complexes versus size n features prominent local anomalies at n = 14, 38, 68, 82, and a weak one at 26, indicating that for these “magic” sizes the helium evaporation energies are relatively large. Surprisingly, mass spectra of anionic He_nHbc^– complexes feature a different set of anomalies, namely at …

Adsorption Of Helium And Hydrogen On Triphenylene And 1,3,5-Triphenylbenzene, Bergmeister Bergmeister, Kollotzek Kollotzek, Florent Calvo, Elisabeth Gruber, Fabio Zappa, Paul Scheier, Olof E. Echt

Faculty Publications

The adsorption of helium or hydrogen on cationic triphenylene (TPL, C₁₈H₁₂), a planar polycyclic aromatic hydrocarbon (PAH) molecule, and of helium on cationic 1,3,5-triphenylbenzene (TPB, C₂₄H₁₈), a propeller-shaped PAH, is studied by a combination of high-resolution mass spectrometry and classical and quantum computational methods. Mass spectra indicate that He_nTPL⁺ complexes are particularly stable if n = 2 or 6, in good agreement with the quantum calculations which show that for these sizes the helium atoms are strongly localized on either side of the central carbon ring for n = …

Understanding Dynamics Of Polymers Under Confinement: A Molecular Dynamics And Neutron Scattering Study, Supun Samindra Kamkanam Mohottalalage

All Dissertations

The current study probes the structure, dynamics, and rheological behavior of associating polymers including ionomers in melts and solutions as well as conjugated polymers confined into nanoparticles, using molecular dynamics (MD) simulations and neutron scattering techniques. The study focuses on two families of associative polymers, ion containing macromolecules and conjugated polymers.

Polymers that consist of ionizable groups along their backbone found uses in a broad range of applications. Examples include light weight energy storage and generation systems, and biomedical applications, where the polymers act as ion exchange membranes, and actuators. The ionic groups tend to form clusters that are in …

Evaluation Of The Energetic Factors In Crystalline Pharmaceuticals Using Solid-State Density Functional Theory And Low-Frequency Vibrational Spectroscopy, Margaret P. Davis

Dissertations - ALL

Due to the importance of maintaining stable and effective pharmaceutical solid doses, it is critical to study the variety of solid forms that active pharmaceutical ingredients can adopt including polymorphs, hydrates, and cocrystals. In this work, low-frequency vibrational spectroscopies and rigorous quantum mechanical simulations are combined to provide a new technique for characterizing and investigating pharmaceutically relevant polymorphs, hydrates, and cocrystals as well as a series of model cocrystals. Low-frequency spectra in the sub-200 cm-1 range provide not only unique and characteristic spectra for all of the systems explored here but, along with X-ray structural parameters, they offer a way …

Application Of Numerical Simulation Method In Periodic Pulse Reverse Electroplating Through Hole, Yuan-Hang Zhang, Mao-Zhong An, Pei-Xia Yang, Jin-Qiu Zhang

Journal of Electrochemistry

The upgrade of the fifth generation (5G) communication technology increases the number of communication backplane layers and the aspect ratio of through holes on the board, making it more difficult to use traditional direct current deposition for interconnection. Direct current electrodeposition is more prone to uneven coating in the hole, resulting in poor contact between the coating and components, and open circuit. This has a serious impact on the stability of printed circuit board. The periodic pulse reverse plating method can significantly improve the uniformity of high aspect ratio through-hole plating and improve the production quality of through-hole plating through …

Insights Into Molecular Recognition And Reactivity From Molecular Simulations Of Protein-Ligand Interactions Using Md And Qm/Mm, Jerrano L. Bowleg

Theses and Dissertations

In this thesis, we have employed two computational methods, molecular dynamics (MD) and hybrid quantum mechanics/molecular mechanics (QM/MM) MD simulations with umbrella sampling (US), to gain insights into the molecular mechanism governing the molecular recognition and reactivity in several protein-ligand complexes. Three systems involving protein-ligand interactions are examined in this dissertation utilizing well-established computational methodologies and mathematical modeling. The three proteins studied here are acetylcholinesterase (AChE), butyrylcholinesterase (BChE), and peptidyl-prolyl cis-trans isomerase NIMA-interacting 1 (PIN1). These enzymes are known to interact with a variety of ligands. AChE dysfunction caused by organophosphorus (OP) chemicals is a severe hazard since AChE is …

A Study Of Cannabigerolic Acid And Its Derivatives Via Raman Spectroscopy And Density Functional Theory, Trevor Wolfe

Honors Theses

The cannabinoids are a class of molecules endogenous to the cannabis plant. Their scientific relevance has increased in recent years due to the mercurial legal status of marijuana across the United States. Some of the most known are cannabidiol (CBD), δ9-tetrahydrocannabinol (δ9-THC), and δ8-THC due in large part to their widespread use, especially in states where marijuana and related products are legal. However, cannabigerolic acid (CBGA) is arguably the most important cannabinoid; it is enzymatically converted into other acidic cannabinoids, which subsequently undergo non-enzymatic processes (isomerization, thermal decarboxylation, oxidation, etc.) to synthesize further cannabinoids. Although there is a wealth of …

Computational Investigations Into Astrochemical Inorganic Oxides, Ammonia Borane, And Genetic Algorithms, E. Michael Valencia

Honors Theses

The formulations of quantum mechanics in the early 1900s were exciting theoretical discoveries, but were not practical to apply until the advent of computers and the subsequent computational methods in 1951. With the introduction of tractable simplifications, procedures such as Hartree-Fock allowed for determination of properties of non-trivial systems. Presently, huge leads of computational power have allowed for extremely precise, quantitative work that can be applied to the human body, synthesis, or even astrochemical processes. This thesis presents works concerning 1) the history of quantum mechanics; 2) a brief primer on computational chemistry and its methods; 3) inorganic oxides in …

Computational And Spectroscopic Studies Of New Sulfur-Containing Dipole-Bound Anions, Nicholas Allen Kruse

Honors Theses

Sulfur and Nitrogen are essential ingredients in both life-supporting and light-harvesting molecules. Their presence also usually leads to the delocalization of electrons and large dipole and quadrupole moments. Such molecules are sometimes able to form negative ions through the electrostatic binding of an excess electron. These so-called multipole-bound (dipole-bound, quadrupole-bound, etc.) anions have been shown to be important in radiation damage in biology and electron transport processes. Here, we present our recent computational and experimental results studying the creation of new multipole-bound anions.

Theoretical Studies Of Benzoquinone Reactivity In Acidic And Basic Environments, Natali Majoras

Honors Theses

Quinones are a class of organic compounds containing a six-membered unsaturated ring with two carbonyl groups. They are biologically relevant mostly due to their ability to participate in redox reactions. Prior experiments in our lab showed that quinones can induce protein modifications that are pH dependent. In an acidic environment the modifications were less significant than in a basic environment. Previous computational studies have also been carried out to model, in neutral solutions, the reaction between various quinones and various amines. Various amine groups are used as a model for the amino group of lysine to represent protein modification. The …

Multi-Scale Simulation Revealing The Decomposition Mechanism Of Electrolyte On Lithium Metal Electrode, Yan-Yan Zhang, Yue Liu, Yi-Ming Lu, Pei-Ping Yu, Wen-Xuan Du, Bing-Yun Ma, Miao Xie, Hao Yang, Tao Cheng

Journal of Electrochemistry

Lithium metal is considered as an ideal anode material for next-generation high energy density batteries with its high specific capacity and low electrode potential. However, the high activity of lithium metal can lead to a series of safety issues. For example, lithium metal will continuously react chemically with the electrolyte, forming unstable the solid electrolyte (SEI) films. In addition, lithium dendrites can be formed during cycling, which can puncture the SEI film and cause short circuits in the battery. These drawbacks greatly hinder the commercial application of lithium metal. To solve the above problems, it is important to understand the …

Synthesis And Characterization Of A Novel Reaction-Based Azaborine Fluorescent Probe Capable Of Selectively Detect Carbon Monoxide Based On Palladium-Mediated Carbonylation Chemistry, Samuel Moore, Carl Jacky Saint-Louis

Symposium of Student Scholars

Azaborines are fascinating compounds because they possess valuable properties such as photochemical stability, have high molar absorption coefficient and high fluorescent quantum yields, as well as large Stokes shifts and tunable absorption/emission spectra. Here, we designed, synthesized, and will examine a novel reaction-based azaborine fluorescent probe capable of selectively detect carbon monoxide (CO) based on palladium-mediated carbonylation chemistry. This novel azaborine fluorescent probe will exhibit high selectivity for CO and display a robust turn-on fluorescent response in the presence of CO in aqueous buffer solution.

Ketal-Azaborine Versus Ketal-Azaborine With A Spacer: Structural Effects On The Photophysical Properties Of Tunable Heteroaromatic Polycyclic Chromophores, Albert Campbell, Janiyah Riley, Samuel Moore, Albert Campbell

Symposium of Student Scholars

Flat-structured heteroaromatic polycyclic compounds with extended conjugated π-systems such as azaborines are in high demand in the material and imaging technology markets because of their unique features such as simultaneous tunability of fluorescence color and intensity. We have designed, synthesized, and investigated a series of novel conjugated thermally stable ketal-azaborine chromophores that contain a phenyl ring as a spacer between electronic moieties and the ketal-azaborine core as easily tunable high-luminescent organic materials. We investigated the impact of the phenyl spacer on the ketal-azaborine unit. We examined the structural effects on their photophysical properties by incorporating electron –donating and –withdrawing substituents …

Azaborine Versus Azaborine With A Spacer: Structural Effects On The Photophysical Properties Of Tunable Azaborine Chromophores, Kaia Ellis, Janiyah Riley, Lyric Gordon, Janiyah Riley

Symposium of Student Scholars

Azaborines are fascinating compounds because of their valuable and interesting optical properties making them suitable to be utilized in many optoelectronic devices. We have designed, synthesized, and investigated a series of novel conjugated thermally stable azaborine chromophores by incorporating a phenyl ring as a spacer linking the chromophore to different electronic moieties as easily tunable high-luminescent organic materials. We investigated the effect of the phenyl spacer on the azaborine unit. The substituent effects of different electronic moieties were investigated by the insertion of electron –withdrawing and –donating moieties to the phenyl spacer. We examined the role of the electron –donating …

Computer Simulation Of Raman Spectra And Mode Assignment: Application To Methane, Oluwaseun Omodemi, Ciara Tyler, Martina Kaledin

Symposium of Student Scholars

This work uses driven molecular dynamics (DMD) method, in conjunction with an analytic PES calculated using MP2/aug-cc-pVDZ energies to identify and assign Raman vibrational modes of methane. Recently, a new linearized approach was proposed for the Polarizability Tensor Surfaces (PTS) that yields a unique solution to the least-squares fitting problem and provides a competitive level of accuracy compared to the non-linear PTS model. We used the previously reported B3LYP/6-31+G(d) molecular geometries for CH₄ and generated a new PTS at the MP2/aug-cc-pVDZ level of theory. The performance of the linearly parametrized functional form for the CH₄ PTS is examined. …

Unraveling Molecular Mechanisms Of Antibiotic Resistance Through Multiscale Simulations And Explainable Machine Learning, Zilin Song

Chemistry Theses and Dissertations

Pathogen resistance to β-lactam antibiotics compromises effective treatments of superbug infections. One major source of β-lactam resistance is the bacterial production of β-lactamases, which could effectively hydrolyze β-lactam drugs. In this thesis, the hydrolysis of various β-lactam antibiotics by class A serine-based β-lactamases (ASβLs) were investigated using hybrid Quantum Mechanical / Molecular Mechanical (QM/MM) minimum energy pathway (MEP) calculations and explainable machine learning (ML) approaches. The TEM-1/benzylpenicillin acylation reaction with QM/MM chain-of-states reaction pathways was firstly revisited. I proposed two decomposition methods for energy contribution analysis based on perturbing ML regression models. Both methods were shown to be model implementation …

The Effect Of Fluorinated Substitution Of Meso Phenyl Porphyrins On Porphyrin Basicity, Harsh Chheda, Rushi Patel, Maria Ballester Ph.D., Victor Castro Ph.D.

Chemistry and Physics Faculty Proceedings, Presentations, Speeches, Lectures

The protonation of meso-Tetra(2,3,4-trifluoromethylphenyl) porphyrin (TF) and meso-Tetra(pentafluorophenyl) porphyrin (PF) will be studied through UV vis spectroscopy. Protonation is achieved by titration of each porphyrin in toluene with trifluoroacetic acid (TFA). The presence of a wavelength shift from the free base Soret to the protonated Soret will indicate the formation of a dication. The data from the UV spectra will be used to calculate the pKa values associated with each porphyrin. Based on the results, the average pKa for TF upon protonation was 2.07, while the average pKa for PF was 1.36 over four trials. A greater acidic value for …

Recent Advances In Electrochemical Kinetics Simulations And Their Applications In Pt-Based Fuel Cells, Ji-Li Li, Ye-Fei Li, Zhi-Pan Liu

Journal of Electrochemistry

Theoretical simulations of electrocatalysis are vital for understanding the mechanism of the electrochemical process at the atomic level. It can help to reveal the in-situ structures of electrode surfaces and establish the microscopic mechanism of electrocatalysis, thereby solving the problems such as electrode oxidation and corrosion. However, there are still many problems in the theoretical electrochemical simulations, including the solvation effects, the electric double layer, and the structural transformation of electrodes. Here we review recent advances of theoretical methods in electrochemical modeling, in particular, the double reference approach, the periodic continuum solvation model based on the modified Poisson-Boltzmann …

A Beginners’ Guide To Modelling Of Electric Double Layer Under Equilibrium, Nonequilibrium And Ac Conditions, Lu-Lu Zhang, Chen-Kun Li, Jun Huang

Journal of Electrochemistry

In electrochemistry, perhaps also in other time-honored scientific disciplines, knowledge labelled classical usually attracts less attention from beginners, especially those pressured or tempted to quickly jam into research fronts that are labelled, not always aptly, modern. In fact, it is a normal reaction to the burden of history and the stress of today. Against this context, accessible tutorials on classical knowledge are useful, should some realize that taking a step back could be the best way forward. This is the driving force of this article themed at physicochemical modelling of the electric (electrochemical) double layer (EDL). We begin the exposition …

Phenanthrene: Establishing Lower And Upper Bounds To The Binding Energy Of A Very Weakly Bound Anion, Elisabeth Gruber, Siegfried Kollotzek, Stefan Bergmeister, Fabio Zappa, Milan Ončák, Paul Scheier, Olof E. Echt

Faculty Publications

Quite a few molecules do not form stable anions that survive the time needed for their detection; their electron affinities (EA) are either very small or negative. How does one measure the EA if the anion cannot be observed? Or, at least, can one establish lower and upper bounds to their EA? We propose two approaches that provide lower and upper bounds. We choose the phenanthrene (Ph) molecule whose EA is controversial. Through competition between helium evaporation and electron detachment in He_nPh^- clusters, formed in helium nanodroplets, we estimate the lower bound of the vertical detachment energy …