Chemistry Commons^™

Solvatochromic Behavior Of 2,7-Disubstituted Sila- And Germafluorenes, Shelby J. Jarrett-Noland, William Mcconnell, Janet Braddock-Wilking, Cynthia M. Dupureur

Educator Preparation & Leadership Faculty Works

Push–pull dyes exhibit intramolecular charge transfer behavior, which due to changes in the dipole moment upon excitation, is the origin of their sensitivity to the environment. Such compounds are of interest as probes for bioimaging and as biosensors to monitor cellular dynamics and molecular interactions. Desirable biological probes absorb in the visible region, have high extinction coefficients, high quantum yield and excellent photostability. Fluorophores with scaffolding that can be used to tune and optimize solvatochromic behavior are of particular interest. Here, we investigate the environmental sensitivity of a small library of highly fluorescent 2,7-disubstituted sila- and germafluorenes. Density functional theory …

Electronic Structure And Molecular Geometries Of Metal Complexes With Dft And Multireference Method, Rina Bhowmick

Dissertations and Theses

Metal complexes are ubiquitous for their diverse applications including catalysis, sensing, medicine, and environmental applications. For effective use of metal complexes, understanding their electronic structure is essential. In most cases, molecules can be represented as a single electron configuration. However, in some cases, especially transition metal and actinide complexes, multireference electronic structures are observed. This is because the valence d (and f) orbitals in metals are often nearly degenerate, leading to close-lying energy states and the subsequently more frequent presence of multiconfigurational electronic structures. The traditional approach to modeling these systems is to use density functional theory to optimize the …

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 …

Computational Materials Chemistry: From Polymer Precursors To Ceramics And High-Pressure Materials, Shariq Haseen

Chemistry & Biochemistry Dissertations - Archive

With advances in computing power, the field of computational chemistry has flourished. Using current computational resources, atomistic simulations of billion atoms and trillions of atoms have been performed. Computational techniques can be used to support experimental investigations into new materials as well as independently predict the existence of new materials. Furthermore, computational techniques are becoming instrumental in investigations. This work is split into two parts. Part I focuses on high-pressure and materials chemistry. We investigate the cristobalite-rutile transformation for SiO2, GeO2, and TiO2, and predict conditions at which cristobalite-GeO2 and cristobalite-TiO2 may be synthesized (Chapter 1), we provide supporting calculations …

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 …

Structural Analysis Of [Ni(Dippe)] Fragment Using Computational Methods, Jennifer L. Sanchez

Theses and Dissertations

The structural analysis of the Nickel (Bisdiisopropylphospino)ethane, also known as [Ni(dippe)H]2, has been heavily studied in our group in collaboration with William D. Jones's group. A computational analysis of the [Ni(dippe)] fragment was performed to determine the structural relationship between the nickel center and its phosphine ligand, due to phosphines having both electronic and steric properties. The reactivity of the Nickel will be most dependent on the dippe ligand. A conformational search generated 244 conformers after a thorough minimization using Molecular Mechanic (MM) calculations where a thorough minimization was performed and then re-minimized using a SEED command until unique conformers …

Computational Study Of The Reactions Of Heteroatomic Compounds On Ceo2, Suman Bhasker Ranganath

LSU Doctoral Dissertations

The mechanisms of ambient-temperature reactions of heteroatomic compounds catalyzed by ceria (CeO₂), an archetypical reducible oxide, for enzyme mimetics, environmental protection, and chemical synthesis are investigated in this dissertation using theoretical methods. CeO₂ is modeled with thermodynamically stable low-index surfaces exposed by commonly studied ceria thin films and nano particles. To understand phosphatase-like dephosphorylation activity, stable adsorption states and surface reactions of model phosphates are examined. Binding of the central P-atom to surface lattice oxygen (O_latt) supplemented by phosphoryl O-Ce interaction is the only stable adsorption state for the un-dissociated molecule. Deprotonation of phosphate monoesters, …

A Theoretical Study Of Co Adsorption On Cu(211) Surface With Coverage Effects, Murat Oluş Özbek

Turkish Journal of Chemistry

CO adsorption on the Cu(211) surface was investigated using energy, geometry and vibrational data, which were produced through periodic DFT computations. Adsorption on the (111) terrace, as well as the previously reported top and bridge sites of the step-edges, was studied at 0.25, 0.33, 0.50, 0.66, 0.75, and 1.00 monolayer (ML) CO coverage. Results showed that up to and including 0.50 ML, on-top or bridge adsorption is preferred on the step-edges. When 0.50 ML is exceeded, top-bridge alternating patterns become feasible on the step edges along with possible shifts towards the terrace. Several feasible patterns were identified at 0.66, 0.75, …

A Study Of Silicon And Germanium-Based Molecules In Terms Of Solar Cell Devices Performance, Emi̇ne Taniş

Turkish Journal of Chemistry

Photovoltaic energy sources are increasingly in demand due to the cost of petroleum fuels and concerns about carbon emissions. For this reason, it is important to determine the photovoltaic properties of the compounds that are thought to be suitable for these energy sources. Here, 1,1,2,3,4,5-Hexaphenyl-1H-silole (HPS) and 1,1,2,3,4,5-Hexaphenyl-1H-germole (HPG) compounds that are thought to have excellent photovoltaic properties, electronic and charge transport properties were investigated experimentally and theoretically. The total energies, absorption spectra, Fermi energy (E_fl) and work function (φ), maximum open circuit voltage (V_OC), reorganization energies (λ_e and λ_h), frontier molecular orbital …

An Experimental And Theoretical Analysis Of Supercritical Carbon Dioxide Extraction Of Cu(Ii) And Pb(Ii) Ions In The Form Of Dithizone Bidentate Complexes, Jeton Halili, Avni Berisha

Turkish Journal of Chemistry

For more than five decades, dithizone has been widely used as an analytical reagent. This ligand forms strongly colored complexes with metal ions and this ability to form complexes can be used for extraction/removal of certain metal ions in addition to analytical determination. In static mode, the supercritical carbon dioxide extraction of copper and lead ions from aqueous solutions after complexation by the dithizone ligand is studied (at two different conditions: a) p = 120 bar, T = 30 °C, and b) p = 72 bar, T = 50 °C). The addition of methanol improved the extraction process by modulating …

Theoretical Investigation Of The Co-C Bond Activation In Methylcobalamin And Adenosylcobalamin-Dependent Systems: Mechanistic Insights., Arghya Pratim Ghosh

Electronic Theses and Dissertations

The vitamin B₁₂ derivates, otherwise known as cobalamin (Cbl), are ubiquitous organometallic cofactors. The biologically active forms of Cbl, such as methylcobalamin (MeCbl) and adenosylcobalamin (AdoCbl), act as cofactors in different physiological reactions for both prokaryotes and eukaryotes. A crucial aspect of the Cbl-mediated systems is the activation of the organometallic Co-C bond that plays a critical role in its catalytic activity. One of the most remarkable features of this Co-C bond is its unusual activation in AdoCbl-dependent enzymatic reactions, where a trillion-fold rate acceleration of the Co-C bond cleavage is observed inside the enzyme compared to the isolated …

Tracking The Amide I And Αcoo− Terminal Ν(C=O) Raman Bands In A Family Of L-Glutamic Acid-Containing Peptide Fragments: A Raman And Dft Study, Ashley E. Williams, Nathan I. Hammer, Ryan C. Fortenberry, Dana N. Reinemann

Faculty and Student Publications

The E-hook of β-tubulin plays instrumental roles in cytoskeletal regulation and function. The last six C-terminal residues of the βII isotype, a peptide of amino acid sequence EGEDEA, extend from the microtubule surface and have eluded characterization with classic X-ray crystallographic techniques. The band position of the characteristic amide I vibration of small peptide fragments is heavily dependent on the length of the peptide chain, the extent of intramolecular hydrogen bonding, and the overall polarity of the fragment. The dependence of the E residue’s amide I ν(C=O) and the αCOO− terminal ν(C=O) bands on the neighboring side chain, the length …

Data For: Record Low Ionization Potentials Of Alkali Metal Complexes With Crown Ethers And Cryptands, Alexander I. Boldyrev, Nikolay Tkachenko

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Electronic properties of series of alkali metals complexes with crown ethers and cryptands were studied via DFT hybrid functionals. For [M([2.2.2]crypt)] (M=Li, Na, K) extremely low (1.70–1.52 eV) adiabatic ionization potentials were found. Such low values of ionization energies are significantly lower than those of alkali metal atoms. Thus, the investigated complexes can be defined as superalkalis. As a result, our investigation opens up new directions in the designing of chemical species with record low ionization potentials and extends the explanation of the ability of the cryptates and alkali crown ether complexes to stabilize multiple charged Zintl ions.

Investigations Into Effects Of Modified Prolines On Cis-Trans Isomers And Polypeptide Secondary Structure & Prediction Of Spectroscopic Properties Of Phthalonitriles For Characterization, Jeffrey Raab

Seton Hall University Dissertations and Theses (ETDs)

Proline is a unique amino acid because it is the only amino acid whose side chain wraps around and bonds back to the peptide backbone. This ring shape helps proteins form conformations which would otherwise not be possible such as hairpin turns. The cis/trans isomerization of the peptide bond between the preceding amino acid (X_aa) and Proline is important in determining how the secondary structure folds. Thus, being able to control the cis/trans isomerization is important when a specific conformation is desired; Proline can be modified to get make the equilibrium shift whichever way is needed. The modifications …

Investigation Of The C—Cn Bond Activation Of Fluorinated Benzonitriles With [Ni(Dmpe)] And Dft Benchmarking Study With [Ni(Dippe)], Dominique C. Gallegos

Theses and Dissertations

Carbon-carbon bond activation has become a rapidly growing area of research due to its extensive range of applications. Despite the significant progress that has been made in this field, the cleavage of kinetically inert and thermodynamically stable C—C σ-bonds under mild homogeneous conditions remains a challenge. The activation is primarily limited to systems in which either relief of strain or aromatization serves as a driving force. A notable exception to this is the oxidative addition of unstrained C—CN bonds of nitriles. In this study, we are looking at the effect of fluoro substituents. We hypothesized …

Computational Study Of Radical Cation Rearrangements, Mi'kayla D. Word

Theses and Dissertations

A radical cation is a molecule that has one unpaired electron that holds a positive charge. The unpaired electron within a radical cation causes the molecule to be reactive. The high reactivity of these species allows for radical cations to be commonly studied experimentally using mass spectrometry and other multi-mass imaging techniques. However, these methods often cannot resolve the reaction mechanisms for these fast reactions. Specifically, radical cation rearrangement mechanisms are particularly unresolved within experiments. For this reason, radical cation rearrangements are computationally investigated to explain complex reaction pathways for processes to understand reactions leading to the initiation of detonation …

Theoretical Investigation Of The Interaction Between The Metal Phthalocyanine [Mpc] A(M = Sc, Ti, And V; A = ?1, 0, And +1) Complexes And Formaldehyde, Nasim Hassani

Turkish Journal of Chemistry

Formaldehyde (FA, CH2O) is one of the toxic volatile organic compounds that cause harmful effects on the human body. In this work, the interaction of FA gas with metal phthalocyanine (MPc) molecules was studied by employing density functional theory calculations. A variety of [MPc] a (M = Sc, Ti, and V; a = -1, 0, and +1) complexes were studied, and the electronic properties, interaction energies, and charge transfer properties of all of the studied molecules were systematically discussed. Among the studied complexes, the Sc and Ti phthalocyanines were more reactive toward the adsorption of FA gas. Moreover, it was …

In Silico Investigation For The Conversion Of Methyl Oleate To Gasoline, Arkanil Roy

Graduate Theses/Dissertations

Petroleum products are found in all walks of life. From the plastic casing on a cell phone to the gasoline that runs most vehicles, a lot is derived from petroleum. Ubiquitous use of petroleum has adversely affected the environment. Toxic substances such as SOx and NOx are released into the atmosphere during the processing and usage of petroleum products, which contributes to global warming. Inevitable oil spills cause devastating effects to marine ecosystems. The rate of regeneration of petroleum is much slower than the rate of usage that would lead to it being exhausted in the recent future. Hence, a …

Crystal Structures Of Two Isostructural Compounds: A Second Polymorph Of Dipotassium Hydrogen Citrate, K2hc6h5o7, And Potassium Rubidium Hydrogen Citrate, Krbhc6h5o7, Diana Gonzalez '20, Joseph T. Golab, Andrew J. Cigler, James A. Kaduk

Student Publications & Research

No abstract provided.

An Atomistic Study Of The Effects On Mechanical Properties And Bonding Interactions Of Carbon Nanofillers In Nylon 6 Nanocomposites, Michael Roth

Dissertations

Polymers have potential for a wide range of applications. The effectiveness of polymers can be further enhanced through the addition of nanofillers that improve thermal, mechanical, and electrical properties of the polymer. Carbon based nanofillers such as carbon nanotube (CNT), graphene, and carbon nanofibre (CNF) are of particular interest due to their high properties and high aspect ratios. However, limited understanding of the governing interactions of these nanofillers with polymers limits the effectiveness of the final nanocomposite.

The first facet of this dissertation focuses on determining the dominating interactions between pristine CNT and graphene with nylon 6 monomer and the …

Computational Modeling Of Photolysis And Catalysis Reactions In Vitamin B12-Dependent Enzymes., Abdullah Al Mamun

Electronic Theses and Dissertations

Vitamin B₁₂ is a complex organometallic molecule, the derivatives of which such as adenosylcobalamin (AdoCbl) and methylcobalamin (CH₃Cbl) act as a cofactor in numerous enzymatic reactions. These two biologically active cofactors contain a unique organometallic Co-C σ bond. Important feature of this Co-C bond is that it can be activated by both thermally and photolytically inside the enzymatic environment as well as in the solution. In the case of enzymatic reactions where AdoCbl molecule act as a cofactor, the cleavage of the Co-C bond constitutes the key catalytic step. The most intriguing features of this cleavage is …

Computational Quantum Study Of Intermediates Formed During The Partial Oxidation Of Melatonin, Oladun Oladiran

Electronic Theses and Dissertations

Melatonin is a neurohormone produced by the pineal gland in the brain. It functions as an antioxidant to scavenge free radicals. Free radicals are reactive species; they often oxidize the cells leading to oxidative stress which may lead to severe health complications. Reaction of melatonin with free radicals is known to be stepwise, as such the stability of the intermediates can be examined. Thus, the possibility of using melatonin as an in vivo spin trap can be determined. Spin traps allow characterization of unstable radical species using electron spin resonance spectroscopy. In this research, ab initio quantum chemistry techniques were …

Water-Mediated Peptide Bond Formation In The Gas Phase: A Model Prebiotic Reaction, George C. Shields, Ariel Gale, Tuguldur T. Odbadrakh, Tyler Ball

Chemistry Publications

The emergence of life on the prebiotic Earth must have involved the formation of polypeptides, yet the polymerization of amino acids is thermodynamically unfavorable under biologically relevant aqueous conditions because amino acids are zwitterions in solution and because of the production of a water molecule through a condensation reaction. Many mechanisms for overcoming this thermodynamic unfavorability have been proposed, but the role of gas phase water clusters has not been investigated. We present the thermodynamics of the water-mediated gas phase dimerization reaction of glycine as a model for the atmospheric polymerization of amino acids prior to the emergence of biological …

Design Of Novel Substituted Phthalocyanines; Synthesis And Fluorescence, Dft,Photovoltaic Properties, Mehmet Sali̇h Ağirtaş, Derya Güngördü Solğun, Ümi̇t Yildiko, Abdullah Özkartal

Turkish Journal of Chemistry

The 4-(2-[3,4-dimethoxyphenoxy] phenoxy) phthalonitrile was synthesized as the starting material of new syntheses. Zinc, copper, and cobalt phthalocyanines were achieved by reaction of starting compound with Zn(CH3COO)2, CuCl2, and CoCl2 metal salts. Basic spectroscopic methods such as nuclear magnetic resonance electronic absorption, mass and infrared spectrometry were used in the structural characterization of the compounds. Absorption, excitation, and emission measurements of the fluorescence zinc phthalocyanine compound were also investigated in THF. Then, structural, energy, and electronic properties for synthesized metallophthalocyanines were determined by quantum chemical calculations, including the DFT method. The bandgap of HOMO and LUMO was determined to be …

Synthesis, Optical, And Structural Properties Of Bisphenol-Bridgedaromatic Cyclic Phosphazenes, Bünyemi̇n Çoşut, Burcu Topaloğlu Aksoy, Süreyya Oğuz Tümay, Ahmet Şenocak, Serkan Yeşi̇lot

Turkish Journal of Chemistry

Phenoxy- and naphthoxy-substituted bisphenol-bridged cyclic phosphazenes were synthesized in 2 steps and their thermal, photophysical, and electrochemical properties were investigated. The structures of the cyclic phosphazene compounds were determined by ESI-MS mass spectrometry and $^{1}$H, $^{13}$C, and $^{31}$P NMR spectroscopies. The photophysical studies of phenoxy- and naphthoxy-substituted bridged cyclophosphazenes were investigated by means of absorption and fluorescence spectroscopies in different solvents. Thermal and electrochemical properties of the target compounds were also studied. Furthermore, the excimer emissions through intramolecular interactions in solution and in solid state were investigated by fluorescence spectroscopy and the theoretical calculations were performed in detail using DFT.

Fluorescent Sensing Platform For Low-Cost Detection Of Cu$^{\Mathbf{2+}}$ By Coumarin Derivative: Dft Calculation And Practical Application In Herbal And Black Tea Samples, Tahi̇r Savran, Abdurrahman Karagöz, Şükri̇ye Ni̇han Karuk Elmas, Duygu Aydin, Furkan Özen, Kenan Koran, Fatma Nur Arslan, Ahmet Orhan Görgülü, İbrahi̇m Yilmaz

Turkish Journal of Chemistry

A fluorogenic probe based on a coumarin-derivative for Cu$^{2+}$ sensing in CH$_{3}$CN/H$_{2}$O media (v/v, 95/5, 5.0 \textmu M) was developed and applied in real samples. 3-(4-chlorophenyl)-6,7-dihydroxy-coumarin (MCPC) probe was obtained by synthetic methodologies and identified by spectral techniques. The probe MCPC showed remarkable changes with a ``turn-off'' fluorogenic sensing approach for the monitoring of Cu$^{2+}$ at 456 nm under an excitation wavelength of 366 nm. The response time of the probe MCPC was founded as only 1 min. The detection limit of the probe MCPC was recorded to be 1.47 nM. The binding constant and possible stoichiometric ratio (1:1) values …

Quantum Chemical Pka Estimation Of Carbon Acids, Saturated Alcohols, And Ketones Via Quantitative Structure-Activity Relationships, Corey Adam Baldasare

Browse all Theses and Dissertations

Acid dissociation constants, often expressed as pKa values, afford vital information with regards to molecular behavior in various environments and are of significance in fields of organic, inorganic, and medicinal chemistry. Several quantitative structure-activity relationships (QSARs) were developed that correlate experimental pKas for a given class of compounds with a descriptor(s) calculated using density functional theory at the B3LYP/6-31+G** level utilizing the CPCM solvent model. A set of carbon acids provided a good final QSAR model of experimental aqueous pKas versus ΔEH2O (R2 = 0.9647) upon removal of three aldehydes as outliers. A study of saturated alcohols offered a final …

On Comparison Of Luminescence Properties Of La2zr2o7 And La2hf2o7 Nanoparticles, Santosh K. Gupta, Maya Abdou, Partha Sarathi Ghosh, Jose P. Zuniga, Ezhilarasan Manoharan, Hyeongjun Kim, Yuanbing Mao

School of Integrative Biological & Chemical Sciences (Formerly Dept. of Chemistry)

Unveiling the underlying mechanisms of properties of functional materials, including the luminescence differences among similar pyrochlores A2B2O7, opens new gateways to select proper hosts for various optoelectronic applications by scientists and engineers. For example, although La2Zr2O7 (LZO) and La2Hf2O7 (LHO) pyrochlores have similar chemical compositional and crystallographic structural features, they demonstrate different luminescence properties both before and after doped with Eu3+ ions. Based on our earlier work, LHO‐based nanophosphors display higher photo‐ and radioluminescence intensity, higher quantum efficiency, and longer excited state lifetime compared to LZO‐based nanophosphors. Moreover, under electronic O2−→Zr4+/Hf4+ transition excitation at 306 nm, undoped LHO nanoparticles (NPs) …

Exploration Of Nucleic Acid Hydrogran Bonding Using Molecular Mechanics And Dft Calculations, Simi Kaur

Biological Sciences

Many recent theoretical and experimental techniques have been developed to probe the structurefunction relationships of complex biomolecules. The roles of RNAs are dependent upon various intricate structural motifs and interactions, including hairpins, pseudoknots, long range territory contacts, bulges and internal loops, that are not easily captured by these methods. We had previously developed an enhanced replica exchange molecular dynamics method that incorporated secondary structure information in the form of distance restraints in order to effectively overcome kinetic barriers and sample conformational space. In several structures, restrained RNA base pairs near large bulges displayed a preference for stacking over hydrogen bonding …

Computational Design And Analysis Of Molecular Ethylene Oligomerization Catalysts, Doo Hyun Kwon

Theses and Dissertations

Linear alpha olefins (LAOs) are key petrochemical precursors for the synthesis of larger polymers, detergents, plasticizers, and lubricants. Most catalytic ethylene oligomerization processes generate a wide distribution of LAO carbon chain lengths. A major ongoing industrial challenge is to develop homogeneous catalysts that result in selective and tunable ethylene oligomerization to 1-hexene and 1-octene alkenes. Quantum mechanical calculations coupled with rapidly advancing technology have enabled the ability to calculate small molecule systems with high accuracy. Employing computational models to advance from empirical to quantitative prediction of product selectivities has become an active area of exploration. In this work, we demonstrate …