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Full-Text Articles in Physical Sciences and Mathematics

Optimizing Protocols For Carbohydrate Nmr Chemical Shift Computations, Michael Trent Kemp Mar 2016

Optimizing Protocols For Carbohydrate Nmr Chemical Shift Computations, Michael Trent Kemp

USF Tampa Graduate Theses and Dissertations

The spectroscopic analysis of cellulose is experimentally challenging while computationally accessible with recent developments in NMR code. However, prior to using density functional theory to calculate the NMR chemical shifts of cellulose, smaller, sugar-like molecule systems need to be benchmarked against experimental values. The quantum mechanical / molecular mechanical (QM/MM) calculations presented herein utilize six test systems: ethanol, pyridine, pyrrolidine, pyrrole, myo-inositol and scyllo-inositol in conjunction with the reference tetramethylsilane used to scale the calculated isotropic shielding tensors to relative chemical shifts. The effect of solvent on calculated NMR chemical shifts has also been investigated with regard to quantity of …

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From Dye Sensitized Solar Cells To Organic Field Effect Transistors: A Computational Investigation Into The Structural And Electronic Properties Of Novel Phthalocyanines, Patrick J. Dwyer Dec 2015

From Dye Sensitized Solar Cells To Organic Field Effect Transistors: A Computational Investigation Into The Structural And Electronic Properties Of Novel Phthalocyanines, Patrick J. Dwyer

Seton Hall University Dissertations and Theses (ETDs)

Phthalocyanines (Pc) have gained intense research attention in many diverse application areas due to their highly tunable electronic and structural properties through modification of the molecular periphery and metal center. Throughout this work a series of novel perfluoro-isopropyl substituted MPc have been investigated through theoretical methods. First, the synthetic mechanisms of these Pcs will be explored to gain insight into the experimentally observed Pc product distribution. By examining the electronic structure and formation energies of the various Pc precursors, we explain the product distribution as well as propose the formation of additional Pcs, which were not currently believed to form. …

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Quantum Calculations Of Aldol Condensation In Acidic Zeolites, Angela N. Migues Nov 2015

Quantum Calculations Of Aldol Condensation In Acidic Zeolites, Angela N. Migues

Doctoral Dissertations

We have used Density Functional Theory to model the mixed aldol condensation reaction catalyzed by acidic zeolites. We have studied the convergence of barriers for the keto-enol tautomerization of acetone in cluster models of HZSM-5 and HY ranging in size from 3-37T. A key finding was that activation barriers for keto-enol tautomerization of acetone in both zeolites (~20 kcal/mol) are significantly higher than those for the condensation reaction between the acetone enol and formaldehyde in 11T cluster models of HZSM-5 and HY. Moreover we found that three zeolite clusters of HZSM-5, similarly sized but including different structural features of the …

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Computational Studies On Bimetallic Catalysis And X-Ray Absorption Spectroscopy, Sayakkarage R. G. Fernando Jan 2015

Computational Studies On Bimetallic Catalysis And X-Ray Absorption Spectroscopy, Sayakkarage R. G. Fernando

LSU Doctoral Dissertations

Computational studies are very important to gain an insight into reaction mechanisms and in interpreting and understanding complicated experimental observations. This report contains a discussion on computational studies performed on bimetallic catalysis and on X-ray absorption spectroscopy of insulators. The viability of a bimetallic rhodium and cobalt catalysts for industrially important hydroformylation and aldehyde-water shift catalysis (AWS) is discussed. Density functional theory (DFT) studies were used for bimetallic catalysis and time-dependent DFT studies were used for excited state dynamics. These studies were performed using Gaussian 09 package and NWChem. Hydroformylation is experimentally performed in acetone and 30% water/acetone systems and …

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Computational Studies For Optimization And Design Of Extracting Agents For Separation Of Lanthanides And Actinides, Deborah Andrea Penchoff Dec 2014

Computational Studies For Optimization And Design Of Extracting Agents For Separation Of Lanthanides And Actinides, Deborah Andrea Penchoff

Doctoral Dissertations

Rare earths and actinides are of great interest given their varied applications in energy conversion and storage, such as in catalysis and batteries, and for advanced technological applications related to optical and magnetic properties (including electronics and automotive), amongst others. Many of the rare earth elements are considered endangered species due to their unique properties which have no clear alternatives that will maintain performance for important applications. The optimal approach is to find readily available alternatives for critical materials to ensure a certain standard of living and quality of life for future generations, but it is very likely that reusing …

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Speciation Behavior Of Americium Higher Oxidation States For The Separation Of Americium From Curium, Catherine Lynn Riddle Aug 2014

Speciation Behavior Of Americium Higher Oxidation States For The Separation Of Americium From Curium, Catherine Lynn Riddle

UNLV Theses, Dissertations, Professional Papers, and Capstones

Several countries are currently expanding the use of nuclear energy as a method for the safe generation of carbon free energy and a number are evaluating starting up a nuclear power program. Closed fuel cycle technologies may be key to waste reduction and a sustainable nuclear energy future and to support the development of more efficient fuel cycles, the investigation of the chemical properties of key actinides is at the forefront of separations research. In this work the characterization of higher oxidation states of americium (Am) has been performed using spectroscopic methods. Americium in the formal oxidation state of Am(V) …

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First-Principles Study Of The Electric Field Effect On The Water-Adsorbed Rutile Titanium Dioxide Surface, Abraham L. Hmiel Jan 2014

First-Principles Study Of The Electric Field Effect On The Water-Adsorbed Rutile Titanium Dioxide Surface, Abraham L. Hmiel

Legacy Theses & Dissertations (2009 - 2024)

TiO2 is a semiconducting material that has been used extensively in many industrial applications, and recently has become a candidate for photocatalytic water splitting, fuel cell anode support materials, sensors, and other novel nanodevices. The interface of TiO2 with water, historically well-studied but still poorly understood, presents a ubiquitous environmental challenge towards the ultimate practical usefulness of these technologies. Ground-state density functional theory (DFT) calculations studying the characteristics of molecular adsorption on model surfaces have been studied for decades, showing constant improvement in the description of the energetics and electronic structure at interfaces. These simulations are invaluable in the …

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Zinc Environment In Proteins: The Flexible And Reactive Core Of Hiv-1 Ncp7 And The Inhibitory Site Of Caspase-3, A. Gerard Daniel Dec 2013

Zinc Environment In Proteins: The Flexible And Reactive Core Of Hiv-1 Ncp7 And The Inhibitory Site Of Caspase-3, A. Gerard Daniel

Theses and Dissertations

Zinc is an essential cofactor of several proteins. The roles of zinc in these proteins are classified as catalytic, structural or regulatory. Zinc present in structural sites is considered to be a chemically inert, static structural element. On the contrary, previous studies on a C2H2 type zinc finger model compound and the C3H type HIV-1 NCp7 C-terminal zinc knuckle have shown that zinc at these sites can undergo coordination sphere expansion under the influence of a Pt based electrophile. The pentacoordination observed around zinc in these experiments raises an important question: are the structural zinc motifs found in the proteins …

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Molecular Dynamics Simulations Using Advanced Sampling And Polarizable Force Fields, Tugba Kucukkal Dec 2013

Molecular Dynamics Simulations Using Advanced Sampling And Polarizable Force Fields, Tugba Kucukkal

All Dissertations

Molecular dynamics (MD) simulations were carried out for aqueous dipeptides, water over self-assembled monolayer (SAM) surfaces, and the nicotinic acetylcholine receptor (nAChR) ion channel. The main goal is to use advanced methods to increase the accuracy of molecular dynamics simulations while seeking solutions to problems relevant to chemistry, biophysics and materials science. In addition, activation energies of several cyclodimerization reactions were studied quantum mechanically. The simulations of the aqueous dipeptides and SAM surfaces involve modeling and detailed analysis of interfacial water, which is of interest to a range of fields from biology to materials science. For example, water has a …

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Binding Energies And Solvation Of Organic Molecular Ions, Reactions Of Transition Metal Ions With, And Plasma Discharge Ionization Of Molecular Clusters, Isaac Kwame Attah May 2013

Binding Energies And Solvation Of Organic Molecular Ions, Reactions Of Transition Metal Ions With, And Plasma Discharge Ionization Of Molecular Clusters, Isaac Kwame Attah

Theses and Dissertations

In this dissertation, different approaches have been employed to address the quest of understanding the formation and growth mechanisms of carbon-containing molecular ions with relevance to astrochemistry. Ion mobility mass spectrometry and DFT computations were used to investigate how a second nitrogen in the pyrimidine ring will affect the formation of a covalent bond between the benzene radical cation and the neutral pyrimidine molecule, after it was shown that a stable covalent adduct can be formed between benzene radical cation and the neutral pyridine. Evidence for the formation of a more stable covalent adduct between the benzene radical cation and …

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Applications Of Density Functional Theory In Materials Science And Engineering, Manuel Alvarado Jan 2012

Applications Of Density Functional Theory In Materials Science And Engineering, Manuel Alvarado

Open Access Theses & Dissertations

Density Functional Theory (DFT) is a powerful tool that can be used to model various systems in materials science. Our research applies DFT to two problems of interest. First, an organic/inorganic complex dye system known as a Mayan pigment is modeled to determine chemical binding sites, verifying each model with physical data such as UV/Vis spectra. Preliminary studies on palygorskite-based mayan pigments (mayacrom blue, mayacrom purple) show excellent agreement with experimental studies when using a dimer dye geometry binding with tetrahedrally-coordinated aluminum impurity sites in palygorksite. This approach is applied to a sepiolite-based organic/inorganic dye system using thioindigo attached to …

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Density Functional Theory Calculations On Hydrated Dimethylarsinic Acid And Iron Oxide Clusters, Adrian Adamescu Jan 2012

Density Functional Theory Calculations On Hydrated Dimethylarsinic Acid And Iron Oxide Clusters, Adrian Adamescu

Theses and Dissertations (Comprehensive)

Dimethylarsinic Acid (DMA) or (CH3)2AsO2H is an important organoarsenical compound detected in arsenic speciation studies of environmental samples and synthesized during pyrolysis of oil shale. DMA was used historically as a herbicide on large agricultural fields and can be detected in the leachates of landfills rich in waste containing arsenic such as glass, alloys, and semiconductors, as well as biologically pre-treated municipal solid waste. Under certain soil conditions DMA can become bio-available and has the potential to be recycled to more toxic inorganic forms of arsenic. Bioavailability of DMA is largely controlled by the …

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Computational Investigation Of The Bioactive Selenium Compounds Ebselen And Selenious Acid, Sonia Antony Apr 2011

Computational Investigation Of The Bioactive Selenium Compounds Ebselen And Selenious Acid, Sonia Antony

Chemistry & Biochemistry Theses & Dissertations

Selenium, a toxic element, is required in trace quantities for the proper functioning of biological systems. The experimental mechanistic study of the reactions of ebselen and selenious acid is difficult due to complexity of the reaction mixtures and the presence of short-lived intermediates. Computational modeling of the reactivity of these species can give us an insight into their mechanisms, but the process is complicated by proton exchanges associated with the mechanistic steps. In gas phase modeling, this may be corrected to a certain level using the solvent assisted proton exchange (SAPE) method. SAPE is a modeling technique that mimics solvent …

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15N Solid-State Nmr Detection Of Flavin Perturbation By H-Bonding In Models And Enzyme Active Sites, Dongtao Cui Jan 2010

15N Solid-State Nmr Detection Of Flavin Perturbation By H-Bonding In Models And Enzyme Active Sites, Dongtao Cui

University of Kentucky Doctoral Dissertations

Massey and Hemmerich proposed that the different reactivities displayed by different flavoenzymes could be achieved as a result of dominance of different flavin ring resonance structures in different binding sites. Thus, the FMN cofactor would engage in different reactions when it had different electronic structures. To test this proposal and understand how different protein sites could produce different flavin electronic structures, we are developing solid-state NMR as a means of characterizing the electronic state of the flavin ring, via the 15N chemical shift tensors of the ring N atoms. These provide information on the frontier orbitals. We propose that …

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Quantum Chemical Investigations Of Nucleophilic Aromatic Substitution Reactions And Acid Dissociations Of Aliphatic Carboxylic Acids, David Henry Schory Jan 2009

Quantum Chemical Investigations Of Nucleophilic Aromatic Substitution Reactions And Acid Dissociations Of Aliphatic Carboxylic Acids, David Henry Schory

Browse all Theses and Dissertations

Quantum chemical analysis was used to examine nucleophilic aromatic substitution reactions of fluorinated benzophenones, diphenyl sulfones, and triphenylphosphine oxides. Some experimental results for these compounds were contrary to conventional wisdom, which holds that calculated atomic charges for the aromatic sites and 13C-NMR and 19F-NMR chemical shifts should allow prediction of the preferred sites for aromatic substitution. Density functional theory (B3LYP/6-31+G*//RM1) and semi-empirical (RM1) quantum chemical calculations were employed to study the intermediates in the reaction pathways in order to identify the preferred paths for aromatic substitution. In most cases studied para substitution pathways had the lower energy intermediates …

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Hydrogenase Inhibition By O2: Density Functional Theory/Molecular Mechanics Investigation, Daniela Dogaru Jan 2008

Hydrogenase Inhibition By O2: Density Functional Theory/Molecular Mechanics Investigation, Daniela Dogaru

ETD Archive

[Fe-Fe]-hydrogenases are enzymes that reversibly catalyze the reduction of protons to molecular hydrogen, which occurs in anaerobic media. In living systems, [Fe-Fe]-hydrogenases shift the reversible reaction towards H2 formation. The [Fe-Fe]-hydrogenase H-cluster is the active site, which contains two iron atoms (Fep-Fed, i.e., proximal and distal iron). Because most experimental and theoretical investigations confirm that the structure of di-iron air inhibited species is FepII-FedII-O-O-H-, O2 has to be prevented from binding to Fed in all di-iron subcluster oxidation states in order to retain a catalytically active enzyme. By understanding the catalytic processes of metalloenzymes, researches are enabled to produce an …

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A Theoretical Study For The Reactivation Of O2 Inhibited [Fe-Fe]-Hydrogenase, Stefan Motiu Jan 2008

A Theoretical Study For The Reactivation Of O2 Inhibited [Fe-Fe]-Hydrogenase, Stefan Motiu

ETD Archive

The current investigation presents a reactivation pathway of the exogenously inhibited H-cluster (viz., by O2, or OH-, which metabolizes to H2O), for both vacuum and aqueous enzyme phase. The H-cluster is the catalytic site of [Fe-Fe]-hydrogenase, with the latter extracted from Desulfovibrio desulfuricans (Dd) bacteria. It consists of proximal iron, Fep, and distal Fed subunit, [Fep-Fed], which is bridged by di(thiomethyl)amine (DTMA) ligand, and a proximal cubane subunit, [Fe4-S4]2+p. [Fep-Fed] is coordinated by two cyanides (CN-), two terminal carbonyls (COt), and a bridging carbonyl (COb)*. An Fe atom from [Fe4-S4]2+p connects Fep through a cysteinyl sulfur (of Cys382). Density functional …

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Ab Initio Molecular Dynamics Simulations Of Methylaluminoxane (Mao) Synthesis By Hydrolysis Of Trimethylaluminum, Lacramioara Negureanu Jan 2006

Ab Initio Molecular Dynamics Simulations Of Methylaluminoxane (Mao) Synthesis By Hydrolysis Of Trimethylaluminum, Lacramioara Negureanu

LSU Doctoral Dissertations

MAO is the co-catalyst in the metallocene catalytic systems, which are widely used in single site olefin polymerization due to their high stereoselectivity. To date, the precise structure of MAO, the particular compound or compounds catalytically active in MAO, have eluded researchers. MAO, a white amorphous powder, is not a good sample for a direct spectroscopic characterization, and its NMR spectra are broad and almost featureless. Many structural models have been proposed but none are generally accepted. In the first part of this work the MAO formation mechanism was addressed. Molecular dynamics simulations at MP2 configuration interaction theory level have …

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Potential Energy Surface Around The Tropylium Ion., Kenneth Wayne Bullins Aug 2005

Potential Energy Surface Around The Tropylium Ion., Kenneth Wayne Bullins

Electronic Theses and Dissertations

The formation of the tropylium ion, C7H7+, in the mass spectrum of toluene is a chemical process that has been studied extensively in the past. The advances in computational power of personal computers have made the investigation of the pathway to form this ion and its subsequent decomposition feasible at a fairly high level of theory. The calculations that we performed were at the HF/6-31G (d, p) and the B3LYP/6-311++G (2d) levels. This work will show areas of the potential energy surface around the highly symmetric tropylium ion to give a glance of possible mechanisms …

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