Physical Chemistry Commons^™

Molecular Dynamics Simulations Of Human Quadruplexes In K+ Solution And The Role Of The Carboxyl Terminus Of Bacteriorhodopsin In Protein Stability, Farah Rezae

Seton Hall University Dissertations and Theses (ETDs)

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Enthalpies Of Mixing Of Water And Alkoxyethanols, John Enriquez

Open Access Theses & Dissertations

Alkoxyethanols [C_mH_2m+1·(OC₂H₄)·OH] (conveniently abbreviated to C_mE₁) are a subgroup of the alkyl poly(ethylene glycol) mono-ethers. They are small relatives of a large number of non-ionic detergents. The thermodynamic properties of their mixing in water have been shown to be good sources of information about the interactions of both hydrophilic and hydrophobic groups with water. Theses alkoxyethanols, or glycol ethers, are the ether derivatives of ethylene glycol where one hydroxyl functional group is substituted for an alkoxy functional group. Our group has already published results for aqueous excess properties …

Development Of Metal-Based Luminescent Probes For Applications In Biomolecular Structure And Dynamics, Ayesha Sharmin

Graduate Student Theses, Dissertations, & Professional Papers

New transition-metal complexes containing luminescent properties have been designed and synthesized for application as structural probes for biomolecules. Potential DNA intercalators, 2- amino-anthracene substituted triosmium clusters, were synthesized by the reactions of 2-aminoanthracene with [Os3(CO)10(CH3CN)2]. The products [Os3(CO)10(μ-η2-(N-C(1))-NH2C14H8)(μ- H)], [Os3(CO)10(μ-η2-(N-C(3))-NHC14H9)(μ-H)], [Os3(CO)9(μ-η2-(N-C(3))-NHC14H8)(μ-H)2] and [Os3(CO)9(μ3-η2-(N-C(3))-NHC10H9)(μ-H)] obtained from this reaction have been structurally characterized by spectroscopic, photophysical and electrochemical techniques. Solid state structures are also reported for the complexes [Os3(CO)10(μ-η2-(N-C(3))-NHC14H9)(μ-H)] and [Os3(CO)9(μ-η2-(N-C(3))-NHC14H8)(μ-H)2]. To investigate bio-macromolecular dynamics on the sub-microsecond-to-microsecond timescale, a series of ruthenium based mono-nuclear metalligand charge-transfer complexes (MLCs) of formula [XRu(CO)(L–L)(L′)2][PF6] (X = H, TFA, Cl; L–L = 2,2′-bipyridyl, 1,10-phenanthroline, 5-amino-1,10-phenanthroline …

Sulfur K-Edge Photo-Fragmentation Of Ethylene Sulfide, Wayne C. Stolte, Gunnar Ohrwall

Chemistry and Biochemistry Faculty Research

We have investigated the photofragmentation properties of the three-membered ring heterocyclic molecule ethylene sulfide or thiirane, C₂H₄S, by time-of-flight mass spectroscopy. Positive ions have been collected as a function of photon energy around the S K ionization threshold. Branching ratios were derived for all detected ions, which are informative of the decay dynamics and photofragmentation patterns of the core-excited species. We present a new assignment of the spectral features around the S K-edge.

Two-Dimensional To Three-Dimensional Structural Transition Of Gold Cluster Au 10 During Soft Landing On Tio 2 Surface And Its Effect On Co Oxidation, Hui Li, Yong Pei, Xiao Cheng Zeng

Xiao Cheng Zeng Publications

We investigate the possible structural transition of a planar Au₁₀ cluster during its soft landing on a TiO₂ (110) surface with or with no oxygen defects. The collision between the gold cluster and the oxide surface is simulated using the Car–Parrinello quantum molecular dynamics method. Both high-speed and low-speed conditions typically implemented in soft-landing experiments are simulated. It is found that under a high-speed condition, the gold cluster Au₁₀ can undergo a sequence of structural transitions after colliding with a defect-free TiO₂ (110) surface. When the TiO₂ (110) surface possesses oxygen vacancies, however, chemical bonds …

Icosahedral B12-Containing Core–Shell Structures Of B80, Hui Li, Nan Shao, Bo Shang, Lan-Feng Yuan, Jinlong Yang, Xiao Cheng Zeng

Xiao Cheng Zeng Publications

Low-lying icosahedral (I_h) B₁₂-containing structures of B₈₀ are explored, and a number of core–shell isomers are found to have lower energy than the previous predicted B₈₀ fullerene. The structural transformation of boron clusters from tubular structure to core–shell structure may occur at a critical size less than B₈₀.

Graphene-Like Bilayer Hexagonal Silicon Polymorph, Jaeil Bai, Hideki Tanaka, Xiao Cheng Zeng

Xiao Cheng Zeng Publications

We present molecular dynamics simulation evidence for a freezing transition from liquid silicon to quasi-twodimensional (quasi-2D) bilayer silicon in a slit nanopore. This new quasi-2D polymorph of silicon exhibits a bilayer hexagonal structure in which the covalent coordination number of every silicon atom is four. Quantum molecular dynamics simulations show that the stand-alone bilayer silicon (without the confinement) is still stable at 400 K. Electronic band-structure calculations suggest that the bilayer hexagonal silicon is a quasi-2D semimetal, similar to a graphene monolayer, but with an indirect zero band gap.

Reduced Electronic Spaces For Modeling Donor/Acceptor Interactions, Robert J. Cave, Stephen T. Edwards '06, John A, Kouzelos '07, Marshall D. Newton

All HMC Faculty Publications and Research

Diabatic states for donor (D) and acceptor (A) interactions in electron transfer (ET) processes are formulated and evaluated, along with coupling elements (H_DA) and effective D/A separation distances (r_DA), for reduced electronic spaces of variable size, using the generalized Mulliken Hush model (GMH), applicable to an arbitrary state space and nuclear configuration, and encompassing Robin−Day class III and as well as class II situations. Once the electronic state space is selected (a set of n ≥ 2 adiabatic states approximated by an orbital space based on an effective 1-electron (1-e) Hamiltonian), the charge-localized GMH …

Mechanistic Importance Of Redox Potentials And Conformational Flexibility In Electron-Transferring Flavoproteins, Michael Anthony Swanson

Electronic Theses and Dissertations

The mitochondrial matrix flavoproteins electron transfer flavoprotein (ETF) and electron transfer flavoprotein-ubiquinone oxidoreductase (ETF-QO) are responsible for linking fatty acid β-oxidation with the main mitochondrial respiratory chain. Electrons derived from flavoprotein dehydrogenases are transferred sequentially through ETF and ETF-QO to ubiquinone and then into the respiratory chain via complex III. In this study, the effects of changes in ETF-QO redox potentials on its activity and the conformational flexibility of ETF were investigated.

ETF-QO contains one [4Fe-4S]^2+,1+ and one flavin adenine dinucleotide (FAD). In the porcine protein, threonine 367 is hydrogen bonded to N1 and O2 of the flavin ring …

Elucidating The Structure Of Protein Aggregates By Raman Spectroscopy, Ludmila A. Popova

Legacy Theses & Dissertations (2009 - 2024)

The structures and properties of amyloid fibrils are of considerable interest due to their associations with numerous neurodegenerative diseases such as Alzheimer's disease, Parkinson's disease and transmissible spongiform encephalopaties (prion diseases). Understanding fibrillogenesis at a molecular level requires detailed structural characterization of amyloid fibrils. However amyloid fibrils are difficult objects to study due to their non-crystalline and insoluble nature. These properties make the application of classical tools of structural biology, such as X-Ray crystallography and solution Nuclear Magnetic Resonance spectroscopy, impractical for structural characterization of protein fibrils.

Dynamic Path Bifurcation For The Beckmann Reaction: Observation And Implication, H. Yamataka, M. Sato, H. Hasegawa, Salai Cheettu Ammal

Faculty Publications

The reaction of oximes to amides, known as the Beckmann rearrangement, may undergo fragmentation to form carbocations + nitriles instead of amides when the cations have reasonable stability. The reactions of oxime derivatives of 1-substituted-phenyl-2-propanones and 3-substituted-phenyl-2-butanones in aqueous solvents gave both rearrangement and fragmentation products, the ratio of which was dependent on substituents. Transition state (TS) optimizations and intrinsic reaction coordinate (IRC) calculations for the reaction of 1-phenyl-2-propanone oximes showed that there is a single TS for each substituted compound. The IRC path from the TS either led to a rearrangement product or a fragmentation product depending on the …

Molecular Dynamics Studies Of Simple Model Fluids And Water Confined In Carbon Nanotube, Jun Wang

Department of Chemistry: Dissertations, Theses, and Student Research

Molecular Dynamics (MD) simulation is one of the most important computational techniques with broad applications in physics, chemistry, chemical engineering, materials design and biological science. Traditional computational chemistry refers to quantum calculations based on solving Schrodinger equations. Later developed Density Functional Theory (DFT) based on solving Kohn-Sham equations became the more popular ab initio calculation technique which could deal with ~1000 atoms by explicitly considering electron interactions. In contrast, MD simulation based on solving classical mechanics equations of motion is a totally different technique in the field of computational chemistry. Electron interactions were implicitly included in the empirical atom-based potential …

The Effect Of Ion-Pairing On The Open Circuit Potential Of 3-Mercaptoproprionic Acid Modified Gold Electrodes, Mark Anderson, Alice Harper

Mark R. Anderson

Open circuit potential (OCP) measurement is used to monitor the charge of a monolayer of 3-mercaptopropionic acid. OCP is determined by the concentrations of the reduced and oxidized forms of a redox couple in the solution adjacent to the modified interface. OCP values were monitored in the presence of the one-electron redox couple Fe(CN)63-/4- as a function of solution pH. The OCP measured at basic pHs was different from the acidic OCP due to differences in electrostatic interactions between the interface and the redox species as described by the Nernst equation. The influence of ion-pairing with the monolayer is studied …

Kinetic And Mechanistic Studies Of The Deuterium Exchange In Classical Keto−Enol Tautomeric Equilibrium Reactions, Mark Waner, Michael Nichols

Mark J. Waner

An extension of the classic keto−enol tautomerization of β-dicarbonyl compounds into a kinetic analysis of deuterium exchange is presented. It is shown that acetylacetone and ethyl acetoacetate undergo nearly complete deuterium exchange of the α-methylene carbon when dissolved in methanol-d4. The extent of deuteration may be monitored via NMR spectroscopy as a function of time. A mechanism for deuterium exchange is presented and shown to be consistent with a consecutive first-order process. The data for acetylacetone are consistent with steady-state kinetics, whereas those of ethyl acetoacetate illustrate nonsteady-state behavior, offering an accessible example where students might collect and analyze real …

Cyclohexane Oxidation And Cyclohexyl Hydroperoxide Decomposition By Poly(4-Vinylpyridine-Co-Divinylbenzene) Supported Cobalt And Chromium Complexes, Zeljko D. Cupic

Zeljko D Cupic

No abstract provided.

Interdependence Of In-Cell Xenon Density And Temperature During Rb/129xe Spin-Exchange Optical Pumping Using Vhg-Narrowed Laser Diode Arrays, Nicholas Whiting, Panayiotis Nikolaou, Neil A. Eschmann, Michael J. Barlow, Boyd M. Goodson

Nicholas Whiting