Spelling suggestions: "subject:"abinitio"" "subject:"initio""
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Gas-phase structures of molecules containing heavy p-block elementsWann, Derek A. January 2005 (has links)
Gas-phase electron diffraction (GED) is the method of choice for determining the structures of molecules containing between two and 100 atoms, free from intermolecular interaction. However, for many molecules it becomes necessary to augment the experimental GED data with information from other sources. The SARACEN method, used routinely at Edinburgh when determining structures, allows computed parameters from ab initio and density functional theory (DFT) calculations to be used as extra data in the GED refinement process. This thesis describes the determinations of the gas-phase structures of molecules that contain heavy p-block elements, including examples from Groups 13, 14, 15 and 16. Each of the compounds studied was solid at room temperature, requiring heating to produce a suitable vapour pressure and vaporisation rate and testing the existing electron diffraction apparatus to its limits. Use was made of a new heated reservoir, recently developed in Edinburgh by a previous PhD student, which has allowed compounds to be studied that were previously inaccessible. The molecules that were studied during the course of this degree are: In(P3C2But2), In(P2C3But3), Sn(P2C2But2), Sb2(C6F6)3, Bi2(C6F6)3, Se(SCH3)2 and Te(SCH3)2. While determining the structures of these molecules, accurate theoretical geometries have been obtained using both ab initio and DFT methods. As a result a better understanding has been achieved of which methods are suitable for use in calculating the structures of molecules with heavy p-block elements. The use of pseudopotentials as opposed to all-electron basis sets proved necessary when performing calculations on such large molecules with heavy atoms. The extent to which these pseudopotentials, especially ones that consider very few electrons to be in the valence shell of an atom, can affect the calculated geometries has been shown to be considerable. In addition, methods being developed to compute vibrational corrections for gas-phase structure determination have been extended to the crystalline phase. Molecular dynamics simulations have been used to derive the effects of vibrations on average nuclear positions, relative to equilibrium positions. The differences, when applied to coordinates obtained experimentally by neutron diffraction yield experimental equilibrium structures.
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Structure, Energetics and Reactions of Bisketenes: An Ab Initio and Density Functional Theory StudyPalmer, Prem 12 1900 (has links)
The effect of varying substituents on structure and energies of bisketenes was studied using ab initio methods. Effect of substituents on ring closing reaction of bisketenes to the corresponding cyclobutenediones was also studied using ab initio methods. One or two of the following substituents were used to study the effect of varying substituents: BH2, CH3, NH2, OH, F, AlH2, SiH3, PH2, SH, Cl. Studies were done at the Hartree-Fock (HF), Møller-Plesset (MP2), and Density Functional Theory (B3LYP) levels of theory using the 6-31G* basis set.
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Development of a new ab-initio method for NMR chemical shifts inSebastiani, Daniel 12 February 2001 (has links)
No description available.
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AB INITIO STUDY OF THE HYDRONIUM RADICAL. PART II. CLUES OF A DEGENERATE30 September 1996 (has links)
No description available.
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New Approaches to Protein Structure PredictionLi, Shuai Cheng 04 November 2009 (has links)
Protein structure prediction is concerned with the prediction of a
protein's three dimensional structure from its amino acid sequence.
Such predictions are commonly performed by searching the possible
structures and evaluating each structure by using some scoring
function. If it is assumed that the target protein structure
resembles the structure of a known protein, the search space can be
significantly reduced. Such an approach is referred to as
comparative structure prediction. When such an assumption is
not made, the approach is known as ab initio structure
prediction. There are several difficulties in devising efficient
searches or in computing the scoring function. Many of these
problems have ready solutions from known mathematical methods.
However, the problems that are yet unsolved have hindered structure
prediction methods from more ideal predictions.
The objective of this study is to present a complete framework for
ab initio protein structure prediction. To achieve this, a new
search strategy is proposed, and better techniques are devised for
computing the known scoring functions. Some of the remaining
problems in protein structure prediction are revisited. Several of
them are shown to be intractable. In many of these cases, approximation
methods are suggested as alternative solutions. The primary issues addressed in this thesis
are concerned with local structures prediction, structure assembly
or sampling, side chain packing, model comparison, and structural
alignment. For brevity, we do not elaborate on these problems here;
a concise introduction is given in the first section of this thesis.
Results from these studies prompted the development of several
programs, forming a utility suite for ab initio protein
structure prediction. Due to the general usefulness of these
programs, some of them are released with open source licenses to
benefit the community.
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New Approaches to Protein Structure PredictionLi, Shuai Cheng 04 November 2009 (has links)
Protein structure prediction is concerned with the prediction of a
protein's three dimensional structure from its amino acid sequence.
Such predictions are commonly performed by searching the possible
structures and evaluating each structure by using some scoring
function. If it is assumed that the target protein structure
resembles the structure of a known protein, the search space can be
significantly reduced. Such an approach is referred to as
comparative structure prediction. When such an assumption is
not made, the approach is known as ab initio structure
prediction. There are several difficulties in devising efficient
searches or in computing the scoring function. Many of these
problems have ready solutions from known mathematical methods.
However, the problems that are yet unsolved have hindered structure
prediction methods from more ideal predictions.
The objective of this study is to present a complete framework for
ab initio protein structure prediction. To achieve this, a new
search strategy is proposed, and better techniques are devised for
computing the known scoring functions. Some of the remaining
problems in protein structure prediction are revisited. Several of
them are shown to be intractable. In many of these cases, approximation
methods are suggested as alternative solutions. The primary issues addressed in this thesis
are concerned with local structures prediction, structure assembly
or sampling, side chain packing, model comparison, and structural
alignment. For brevity, we do not elaborate on these problems here;
a concise introduction is given in the first section of this thesis.
Results from these studies prompted the development of several
programs, forming a utility suite for ab initio protein
structure prediction. Due to the general usefulness of these
programs, some of them are released with open source licenses to
benefit the community.
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noneHuang, Ya-Yao 04 July 2002 (has links)
none
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An ab-initio analysis of bimetallic oligoaniline molecular junctionsWang, Michael Wei-Lueng 17 September 2007 (has links)
The electron transport characteristics of Oligoaniline molecular junctions
terminated with thiol-ends are analyzed with the density functional theory and the
Green's function approach. The molecular junction consists of an Oligoaniline molecule
attached to metal electrodes at each end. By applying an electric field, the molecule
conducts a current that depends on either the molecular conformation or the ionization
state. Ab initio optimization methods are performed on various Oligoaniline systems to
analyze how different conformational changes are associated with different
conductivities. The density functional theory and Green's function are used to calculate
the density of states, transmission probability functions, and current-voltage calculations
for each Oligoaniline system to complement the results from the molecular analysis. An
inelastic tunneling spectrum analysis is also performed through frequency calculations to
examine the different characteristics of each conducting state. Molecular orbits of each
conformation was used to investigate further the relation between structure and electrical
properties of the molecular junction. The combined results from the different
calculations provided insight into the possible mechanisms for electron transfer
throughout the junction.
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High-accuracy ab initio thermochemistry : application to hydrocarbonsFerguson, Michael Eric 08 October 2013 (has links)
This work focuses on an examination of the high-accuracy extrapoloated ab initio thermochemistry (HEAT) protocol of determining molecular atomization energies. The HEAT protocol does not utilize experimental data or empirical scaling effects. The accuracy of the approach is tested via comparison to ATcT data, and all molecules fall within 1 kcal/mol of accepted values. There are several important points to note about this treatment: namely, that we have used atomic natural orbital (ANO) basis sets for the calculation of the zero point energy and that we have made determinations for larger molecules than previously done with HEAT. The molecules in this paper were chosen to provide benchmark numbers for the homodesmotic reaction heirarchy as described by Wheeler et al.[3] The relative accuracy of the approach is considered, as well as a discussion of possible remaining sources of error. / text
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Many-body effects in interionic interactionsDomene, Carmen January 2000 (has links)
No description available.
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