Computational Chemistry Commons^™

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 …

Computer Simulation Of The Light Absorption Band Of The Jumping Spider Isorhodopsin, Noah Zoldak

Honors Projects

In order to simulate the photoisomerization of the 9-cis Jumping Spider Isorhodopsin (JSiR-1) it is necessary to first simulate its light-absorption band. Here we report on the absorption band simulated using protein models constructed using the advanced Automatic Rhodopsin Modeling (a-ARM) program. A population of S₀ models was created and the corresponding S₀ to S₁ transitions were determined for each member of the resulting population. The calculation resulted in a Gaussian plot showing that the wavelength of the absorption maximum of 560 nm (a violet color) that is consistent, but red-shifted, with respect the experimentally observed value.

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) …

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 …

Turning Density Functional Theory Calculations Into Molecular Mechanics Simulations : Establishing The Fluctuating Density Model For Rna Nucleobases, Christopher A. Myers

Legacy Theses & Dissertations (2009 - 2024)

Molecular mechanics (MD) simulations and density functional theory (DFT) have been the backbone of computational chemistry for decades. Due to its accuracy and computational feasibility, DFT has become the go-to method for theoretically predicting interaction energies, polarizability, and other electronic properties of small molecules at the quantum mechanical level. Although less fundamental than DFT, molecular mechanics (MM) algorithms have been just as influential in the fields of biology and chemistry, owing their success to the ability to compute measurable, macroscopic quantities for systems with tens of thousands to hundreds of thousands of atoms at a time. Nevertheless, MD simulations would …

First-Principles Study Of Doping Effects On Ferroelectricity And On Rashba Spin Splitting, Zegnet Yimer Muhammed

Graduate Theses and Dissertations

In this dissertation, we have thoroughly studied the effect of chemical and charge dopingon ferroelectrics (PbTiO3 and BaTiO3) and Rashba type semiconductor (BiTeI). In the first project, We investigate the polar instability and soft modes in electron-doped PbTiO3 using linear-response density functional calculations. Because, metallicity and ferroelectric-like polar distortion are mutually non-compatible, and their coexistence in the same system is an intriguing subject of fundamental interest in the field of structure phase transition. However, it is unclear what mechanism may extend the limit of metallicity that allows polar distortion. We find that ferroelectric instability can remarkably sustain up to an …

Computational And Experimental Investigations Of Alkali Cation Interactions At The Rutile – Water Interface, Isaac Johnston

All Dissertations

Overall, the objective of this dissertation was to investigate the degree of sorption for the alkali cations on rutile to ascertain the impact of different cation properties, such as ion size and charge density, on sorption mechanics as well as probe how the ion may alter the surface – aqueous interface. Initial molecular dynamic simulations and batch experiments showed minimal surface sorption for any alkali cation at relatively low concentrations while simultaneously suggesting the enthalpy of deprotonation shifts slightly in the presence of the alkali cations at different ionic strengths. The cations are likely causing small reorientations of the near-surface …

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 …

Using Molecular Dynamics Simulations To Decipher Mechanistic Details Of Biomolecular Processes Of Biology And Biotechnology Oriented Applications, Adithya Polasa

Graduate Theses and Dissertations

Researchers in chemistry and biology often utilize computer simulations, in conjunction with experimental data, to model and predict the structures, energies, kinetics, processes, and functions of the systems that are their focus of study, ranging from single molecules to whole viruses. Here, we use molecular dynamics (MD) techniques to gain a deeper understanding of biomolecular processes in biology and biotechnology-oriented applications. Using a mixture of equilibrium and non-equilibrium MD simulations, this work describes the insertion process of YidC at the atomic level. In order to better comprehend the insertion process, several docking models of YidC-Pf3 in the lipid bilayer were …

Elucidation Of Active Site And Mechanism Of Metal Catalysts Supported In Nu-1000, Hafeera Shabbir

All Dissertations

Advances in extraction of shale oil and gas has increased the production of geographically stranded natural gas (primarily consisting of methane (C1) and ethane (C2)) that is burned on site. A potential utilization strategy for shale gas is to convert it into fuel range hydrocarbons by catalytic dehydrogenation followed by oligomerization by direct efficient catalysts. This work focuses on understanding metal cation catalysts supported on metal-organic framework (MOF) NU-1000 that will actively and selectively do this transformation under mild reaction conditions, while remaining stable to deactivation (via metal agglomeration or sintering). I built computational models validated by experimental methods to …

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. …

Biomimetic Modifications Of A Feni Hydrogenase Bridging Cys Residue Ligand, Madeline Kesner, Meghan Mcgreal

Annual Symposium on Biomathematics and Ecology Education and Research

No abstract provided.

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 …

Probing Mechanisms Of Binding And Allostery In The Sars-Cov-2 Spike Omicron Variant Complexes With The Host Receptor: Revealing Functional Roles Of The Binding Hotspots In Mediating Epistatic Effects And Communication With Allosteric Pockets, Gennady M. Verkhivker, Steve Agajanian, Ryan Kassab, Keerthi Krishnan

Mathematics, Physics, and Computer Science Faculty Articles and Research

In this study, we performed all-atom MD simulations of RBD–ACE2 complexes for BA.1, BA.1.1, BA.2, and BA.3 Omicron subvariants, conducted a systematic mutational scanning of the RBD–ACE2 binding interfaces and analysis of electrostatic effects. The binding free energy computations of the Omicron RBD–ACE2 complexes and comprehensive examination of the electrostatic interactions quantify the driving forces of binding and provide new insights into energetic mechanisms underlying evolutionary differences between Omicron variants. A systematic mutational scanning of the RBD residues determines the protein stability centers and binding energy hotpots in the Omicron RBD–ACE2 complexes. By employing the ensemble-based global network analysis, we …

Interpretable Machine Learning Models For Molecular Design Of Tyrosine Kinase Inhibitors Using Variational Autoencoders And Perturbation-Based Approach Of Chemical Space Exploration, Keerthi Krishnan, Ryan Kassab, Steve Agajanian, Gennady M. Verkhivker

Mathematics, Physics, and Computer Science Faculty Articles and Research

In the current study, we introduce an integrative machine learning strategy for the autonomous molecular design of protein kinase inhibitors using variational autoencoders and a novel cluster-based perturbation approach for exploration of the chemical latent space. The proposed strategy combines autoencoder-based embedding of small molecules with a cluster-based perturbation approach for efficient navigation of the latent space and a feature-based kinase inhibition likelihood classifier that guides optimization of the molecular properties and targeted molecular design. In the proposed generative approach, molecules sharing similar structures tend to cluster in the latent space, and interpolating between two molecules in the latent space …

In Silico Evaluation Of The Antimalarial Potential Of The Phytoconstituents Of The Azadirachta Indica Plant, Areh E.T., Atolani O., Kambizi L

Al-Bahir

Background and Objectives: Malaria, a parasitic protozoan disease caused primarily by Plasmodium falciparum, has killed millions of people in Africa, particularly those with meager or no access to orthodox medical facilities and therapies. Extracts from the Azadirachta indica (neem) plant is believed to possess antimalaria properties among the locals that rely on herbs. Numerous in - vivo studies have suggested the antimalarial properties of neem extract and phytochemicals. This study employs an in - silico method through molecular docking techniques to provide insight while adding credence to the antimalarial potential of phytochemicals of neem plants as claimed …

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 = …

Design Of Multi-Principal Element Materials Using A Combination Of First-Principles Calculations And Machine Learning, Zhaohan Zhang

McKelvey School of Engineering Graduate Student Theses & Dissertations

Multiple-principal element materials, including alloys (MPEAs), oxides and other compounds combine several elements on a sub-lattice, which increases the configurational entropy and contributes to their thermodynamic stability. The vast combinatorial design space of multi-principal element materials gives rise to diverse microstructures and unprecedent combination of properties. It also poses a challenge—how to rapidly screen MPEAs with stability and properties for targeted applications. Furthermore, fundamental composition-structure-property relationships in MPEAs are currently missing. In this dissertation, I have used MPEAs as a representative system and investigated the role of chemical composition on their phase-stability and mechanical properties. With a combination of first-principles …

Theory Of Aqueous Solvation: Uninterrupted, Cyclic Hydrogen-Bonding Essential For Accurate Keto-Enol Energies And Grotthuss Tautomerism Of Acetone, Mark Recznik

Electronic Theses and Dissertations

Keto-enol tautomerization (KET) is a fundamental process impacting a range of molecular phenomena in organic and biochemistry. However, the accurate computation of solution-phase KET energies remains a challenge, even for prototypical acetone.

In Part I, keto-enol tautomers of acetone were incorporated into solvent clusters that interact via uninterrupted, cyclic hydrogen-bonding (UCHB) networks. An empirical model was created to predict accurate KET energies, E_taut, of simple carbonyl compounds. Based on the availability of experimental data and structural simplicity, acetone was selected as a prototype. A discrete-continuum strategy was employed – accounting simultaneously for local noncovalent interactions and bulk-phase effects …

Advanced Insights Regarding Both Micro- And Macro-Molecules In Various Environments: Showcasing The Local Mode Theory As A Powerful Tool., Alexis A. A. Delgado

Chemistry Theses and Dissertations

A majority of the research featured in my dissertation has involved the derivation of direct quantitative measures of intrinsic strength from quantum chemical calculations of molecular systems. In my works I applied Local Vibrational Mode Theory (LVMT) to 1) transform normal modes to local modes, via the elimination of all mode-mode coupling, to obtain local mode force constants (i.e. direct measures of intrinsic strength), 2) in combination with the Unified Reaction Valley Approach, unravel detailed information about bond breaking/formation processes that occur along a reaction, and 3) decompose individual normal modes into percentages of local mode contributions. This dissertation encompasses …