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Showing 1 to 16 of 16 for “"Partial charges"”.
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Application of Ab Initio Calculations and Molecular Dynamics to Collagen and Brome Mosaic Virus
… this thesis, we have calculated ab initio atomic partial charges for proteins of collagen and the brome mosaic virus (BMV) capsid. These proteins contain from 1000-3000 atoms and efficient and accurate ab initio quantum modeling methods have only become more recently available for systems of this …
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Synthesis of coordination complexes and the use of X-ray diffraction data towards the development of refinement of occupancy of spherical atoms (ROSA), a new approach for the determination of atomic partial charges
… mimics and (2) experimentally determine partial atomic charges in molecules to better understand development toward molecular discovery. Inspired by reactive small molecule iron catalysts, a chiral pyridyl amine-based ligand, (R)-1-(pyridin-2-ylmethyl)pyrrolin-2-yl)methanol, was …
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Computational Study of Metal-Organic Frameworks for Gas Adsorption Applications
… as quantum mechanics and molecular simulations. Partial charges are used to model the adsorbate-MOF electrostatic interaction and are traditionally calculated using quantum mechanics, which is highly accurate but computationally expensive. Calculating highly accurate partial charges is costly and …
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Empirical Nanotube Model: Applications to Water Channels and Nano -Oscillators
… through nanotubes. In the proposed model, atomic partial charges are calculated from a quantum chemistry approach, and the polarizability of the nanotube is modeled through a self-consistent tight-binding method. The suitability of the model is demonstrated through studies of a nanotube water …
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A Description of the Electrostatic Interactions of Fluorophores With Polar Solvents Based on A Gaussian Distribution of Interaction Energies (Danca, Prodan)
… in the ground and excited states arise from partial charges localized on specific parts of the molecule. These charges are considered to be monopoles which interact independently with solvent dipoles. The orientation of a solvent dipole with respect to each monopole is given by the Langevin …
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Empirical Nanotube Model: Applications to Water Channels and Nano-Oscillators
… through nanotubes. In the proposed model, atomic partial charges are calculated from a quantum chemistry approach, and the polarizability of the nanotube is modeled through a self-consistent tight-binding method. The suitability of the model is demonstrated through studies of a nanotube water …
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Towards Ion Channel Based Nanofluidic Devices: Simulations of Water and Electrolyte Transport in Nanotubes and Channels
… devices. Effects of nanoscale confinement and partial charges, that stem from quantum calculations, are investigated in silica slit channels filled with 1 M KCl at the point of zero charge. Oscillations in concentration profiles of K+ and Cl- ions give rise to an electroosmotic flow in the …
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Theory and Applications of Fluctuating-Charge Models
… more familiar variables that represent atomic partial charges. This allows us to formulate a unified theoretical framework for fluctuating-charge models and topological charge descriptors. We also demonstrate the important role of charge screening effects in obtaining correct size extensivity …
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Semi-Empirical Studies on Electronic Properties and Applications of Carbon Nanotubes
… of the nanotube polarization effect and atomic partial charges in determining the energetics of the system, which may facilitate understanding and controlling the electronic behavior of carbon nanotubes in biological applications.
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Spectra at speed: neural force fields for IR spectroscopy in ionic liquids
… estimated from arbitrary, method-dependent partial charges. In this work, we address these challenges for a prototypical IL. First, for an isolated ion pair, we develop a hybrid framework combining Deep Potential (DP) and Deep Wannier (DW) models to predict potential energy, forces, and …
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Thermodynamics of Buried Water in Protein Cavities and Revised Algorithms for Introducing Polarizability to Molecular Dynamics Simulations
… time steps. The fluctuating charge model treats partial charges as variables which are propagated using Lagrangian dynamics. A coordinate transform to normal mode charge variables is applied to the TIP4P-FQ model of water to decrease the coupling between the atomic and charge degrees of freedom.
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Exploring Molecular Systems From Chemical Physics To Biochemistry Using Classical And Quantum Mechanics
… restraining procedure to generate atom-centered partial charges for use in molecular dynamics simulations using the AMBER force field. The parameters will allow AMBER and other similar force fields method users to incorporate modified nucleosides into their classical simulations. Chapters 7 and 8 …
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Exploration of Toll-like Receptor 7 and 8 Agonists as Potential Vaccine Adjuvants
… compounds, confirming the critical role of partial charges in determining biological activity (Chapter 6). Molecular conjugation of TLR7/8 agonists to hyaluronic acid (HA) was evaluated to enhance selective and targeted delivery of vaccine construct to draining lymph nodes while limiting …
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Development of Novel High Temperature Mixed Matrix Membranes (MMMs) for Oil Sands Wastewater Treatment
… association of charged groups and increase their partial charges, thus promote higher inter-molecular interactions, resulting in well-connected polymer network. Moreover, the performance of modified membrane was examined at high temperatures (i.e., 25, 50, 70 and 90oC). Overall, high temperatures …
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Vibrational spectroscopy and density functional theory calculations, a powerful approach for the characterization of pharmaceuticals and new organometallic complexes
… The total electron density of molecules and the partial charges situated on selected atoms, which were determined theoretically by NPA, allowed us to establish the probability of different atoms acting as an adsorptive site for the metal surface. Moreover, a closer examination of the calculated …
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WETTING TRANSITIONS AT NANOSTRUCTURED SURFACES
… and hydrophobic carbon cages. Even adding partial charges to hydrophilic confinement did not make a big effect on results compared to hydrophobic case. These findings are suggesting that in highly symmetric confinement water molecules do not care about the type of interaction with the wall …