Computational Chemistry Commons^™

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 …

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 …

An Ims-Ms/Md Workflow For Determining Higher Order Structure And Dynamics Of Nucleic Acids, Rebecca D'Esposito

Legacy Theses & Dissertations (2009 - 2024)

Ion mobility spectrometry - mass spectrometry (IMS-MS) has potential for the investigation of structure and dynamics in large biopolymers, which will come to full fruition only with a firmer understanding of how to interpret the experimental data. Numerous studies have employed elements of nucleic acid (NA) secondary structure, such as duplexes and hairpins, to explore the relationships between structure, experimental conditions, and actual observations. When combined with molecular dynamics simulations (MDS), IMS-MS can be effectively employed to perform structural elucidation of biomolecules that are not readily amenable to established techniques employed for structural analysis.

State-Based Biological Communication, Nathan Clement

All Theses

Allostery (1) is the process through which proteins self-regulate in response to various stimuli. Allosteric interactions occur between nonadjacent spatially distant residues (1), and they are exhibited through the correlated motions (2) and momenta of participating residues. The location of allosteric sites in proteins can be determined experimentally but computational methods to predict the location of allosteric sites are being developed as well (2-4, 10). Experimental and computational methodologies for locating allosteric sites can be used to design specific targeted drug delivery (5-6, 19), but these methods have not yet …

Open-Source Workflows For Reproducible Molecular Simulation, Jenny W. Fothergill

Boise State University Theses and Dissertations

We apply molecular simulation to predict the equilibrium structure of organic molecular aggregates and how these structures determine material properties, with a focus on software engineering practices for ensuring correctness. Because simulations are implemented in software, there is potential for authentic scientific reproducibility in such work: An entire experimental apparatus (codebase) can be given to another investigator who should be able to use the same processes to find the same answers. Yet in practice, there are many barriers which stand in the way of reproducible molecular simulations that we address through automation, generalization, and software packaging. Collaboration on and application …

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 …

Exploring Structure-Function Relationship In Small-Molecular Catalysts Using Computational And Experimental Methodologies, Avik Bhattacharjee

Dissertations and Theses

Molecular modeling is a useful tool in the field of catalyst design for various processes. The use of Density Functional Theory (DFT) is routine in almost every discipline of chemistry. This allows for a deeper understanding of a molecular system even in situations where implementation of an experimental technique is unfeasible. However, without the right choice of theory and insufficient description, the model becomes susceptible to produce ambiguous results. This often leads to poor correlation with experimental findings hence an incomplete understanding of the system under study. Hence, to acquire a thorough knowledge of the intricacies involved in a system, …

Calcium Bistriflimide-Mediated Sulfur (Vi)–Fluoride Exchange (Sufex): Mechanistic Insights Toward Instigating Catalysis, Nicholas Ball, Brian Han, Samuel R. Khasnavis, Matthew Nwerem, Michael Bertagna, O Maduka Ogba

Pomona Faculty Publications and Research

We report a mechanistic investigation of calcium bistriflimide-mediated sulfur(VI)–fluoride exchange (SuFEx) between sulfonyl fluorides and amines. We determine the likely pre-activation resting state─a calcium bistriflimide complex with ligated amines─thus allowing for corroborated calculation of the SuFEx activation barrier at ∼21 kcal/mol, compared to 21.5 ± 0.14 kcal/mol derived via kinetics experiments. Transition state analysis revealed: (1) a two-point calcium-substrate contact that activates the sulfur(VI) center and stabilizes the leaving fluoride and (2) a 1,4-diazabicyclo[2.2.2]octane additive that provides Brønsted-base activation of the nucleophilic amine. Stable Ca–F complexes upon sulfonamide formation are likely contributors to inhibited catalytic turnover, and a proof-of-principle redesign …

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 …

Ab Initio Study Of The Rotation Of The C≡C Group In Benzvalyne, Advait Praveen

Honors Theses

For benzvalyne, we have characterized the minima and transition states of the molecule using the B3LYP, MP2, and M06-2X methods and aug-cc-pVTZ basis set. This was done by calculating the energy of the molecule while rotating the alkyne bond contained within it. After the initial rotation, optimized parameters for the molecule are found. Following this, imaginary frequencies were attempted to be found at the local maximum produced by the graph of the Energy v. rotation angle. Should the negative frequencies be found, the energy of the molecule will be characterized by the CCSD (T) method and aug-cc-pVQZ basis sets. This …

Nitro-Aromatic Polymers For Conversion-Style Battery Cathodic Materials, Brady P. Samuelson

Honors Thesis

The development of organic electrode materials in rechargeable batteries has seen a resurgence in recent decades. This spike in interest is mostly due to the increased investments in renewable energy sources, grid-scale energy storage, and the rapid transition to electric vehicles. Current lithium battery cathode materials typically use some form of lithium metal oxide (specific capacity: 272 mAh g^-1 which has problems with limited capacity, thermal runaway, and an unreliable supply chain. Our research group’s solution involves investigating new lightweight, organic redox groups combined with a conductive polymer backbone to serve as a possible replacement for the cathode 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 …