Global ETD Search
Search theses and dissertations gathered from participating repositories worldwide. Every result links back to the library that holds it. No account is needed.
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Showing 1 to 14 of 14 for “"atomic charges"”.
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Fast, efficient generation of high-quality atomic charges
… quickly and efficiently generates high-quality atomic charges for organic molecules suitable for computer simulations in the solution phase. The concept of the AM1-BCC charge model is to produce atomic charges that emulate the HF/6-31G* electrostatic potential (ESP). Underlying electronic …
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Development of a force field with condensed phase consistent charges for N,N' - dialkylimidazolium room temperature ionic liquids
… the effects that the linear scaling of partial atomic charges on nonpolarisable force fields from a reference potential has on the structure and dynamics of the room temperature ionic liquids (RTILs) 1-butyl-3-methylimidazolium tetraflouroborate [C4MIM][BF4] and 1-butyl-3-methylimidazolium …
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A Computational Study on 18+δ Organometallics
… of bond angles, bond distances, natural atomic charges and IR vibrational frequencies were compared with the available experimental parameters. The differences between the 19- and 18-electron systems have been analyzed. The results reveal that the 19th electron is mostly distributed over …
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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 synthesized with …
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Development of pharmacophore and CoMFA studies for sigma2 receptor ligands
… the geometry optimization and electrostatic charges for each molecule. CoMFA maps were developed using SYBYL ver. 7.2 to compare the electrostatic and steric properties of each calculation and molecule. With "leave-one-out" cross validation, the numbers of optimal components was determined. …
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Pharmacophore derivation using discotech and comparison of semi-emperical, AB initio and density functional CoMFA studies for sigma 1 and sigma 2 receptor-ligands
… with the pharmacophore, derived using DISCOtech. Atomic charges were calculated using AMl, HF/3-21G*, B3LYP/3-21G*, MP2/3-21G* methods in Gaussian 98. The CoMFA Maps that were developed using Sybyl 6.9 were compared on steric and electrostatic field differences. With leaveone-out cross validation …
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Development of pharmacophore and comfa study of rigid and flexible sigma 2 receptor ligands
… ligands. The geometries and electrostatic charges of all molecules were calculated using various levels of calculations. The geometry optimization and electrostatic charges of all 26 molecules were performed by using semiemprical AM1, ab initio HF/6-31G* and density functional B3LYP/6-31G* …
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Application of molecular mechanics polarization to fragment based drug design.
… After running the MD simulations for 200ns with atomic charges generated from the polarization the results we found were quite interesting. Some ligands would be trapped in their binding site but would fluctuate quite readily such as 2GVV. Some ligands showed that despite low RMSD they would be …
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Exploring relaxation of magnetization in paramagnetic molecules
… a strong correlation between the partial atomic charges on the ligands and the effective barrier of magnetization. Based on this discovery, we proposed a new design strategy for paramagnetic molecules with large effective barrier of magnetization. Our study highlighted the important role …
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Predicting the Hydration Free Energy of Small Alkanes and Alcohols from Custom, Electronic Structure-Based Force Fields
… water. </p> <p>A new method for computing static charges of atomic nuclei is derived, which offers a simple and physically sound method that can be used to investigate charge transfer in model systems and generate atomic charges for use in simulations. </p> <p>Formulae used to calculate HFEs and …
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Molecular Dynamics and Quantum Chemistry Studies of the Protein Bacteriorhodopsin
… by explicitly including all protein partial atomic charges into the electronic Hamiltonian. The calculations are applied to an ensemble of bacteriorhodopsins generated by molecular dynamics simulations using a CHARMM force field with special parameters for retinal torsions. Spectral …
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Molecular pharmacology of an insect GABA receptor
… to determine the dipole separation distances and atomic charges. Computational calculations and functional experiments revealed that agonists require a charged ammonium and an anionic centre, with the most potent agonists having a dipole separation distance of ~5 Å. I made a homology model of the …
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Understanding the ATP hydrolysis mechanism in myosin using computer simulation techniques
… (NUCS) was developed which scales the partial atomic charges on the molecular mechanical atoms so as to optimally reproduce electrostatic interaction energies between groups of protein atoms and the QM region as determined from an initial continuum solvent analysis with a simple Coulomb …
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Speeding up electrostatic computations for molecular dynamics
… is approximated by a much smaller number of charges. For nearby components, the HCP uses the full set of atomic charges. For large structures the HCP can be several orders of magnitude faster than the exact pairwise O(<i>n</i>²) all-atom computation. For a representative set of structures, …