Development and application of conformational methodologies: eliciting enthalpic global minima and reaction pathways
| dc.contributor.author | Allison, Joseph T., author | |
| dc.contributor.author | Rappé, Anthony, advisor | |
| dc.contributor.author | Strauss, Stephen, committee member | |
| dc.contributor.author | Levinger, Nancy, committee member | |
| dc.contributor.author | Shores, Matthew, committee member | |
| dc.contributor.author | Slayden, Richard, committee member | |
| dc.date.accessioned | 2007-01-03T05:57:09Z | |
| dc.date.available | 2016-01-31T06:30:24Z | |
| dc.date.issued | 2014 | |
| dc.description.abstract | The information granted by assembling the global minimum and low-enthalpy population of a chemical species or ensemble can be utilized to great effect across all fields of chemistry. With this population, otherwise impossible tasks including (but not limited to) reaction pathway characterization, protein folding, protein-ligand docking, and constructing the entropy to characterize free energy surfaces becomes a reasonable undertaking. For very small systems (single molecule with 1-3 torsions) generating the low-enthalpy population is a trivial task. However as the system grows, the task exponentially increases in difficulty. This dissertation will detail the two sides of this problem, generating the low-energy population of larger and more complex species and then utilizing those populations to garner a greater understanding of their systems. The first discussion describes a new model, Surface Editing Molecular Dynamics (SEMD), which aids in accelerating conformational searching by removing minima from the potential energy surface by adding Gaussian functions. Accompanying this new method are a multitude of new tools that can be utilized to aid in molecular dynamics simulations. The first of these tools, named CHILL, performs a projection of unproductive degrees of freedom from the molecular dynamics velocity to smooth atomic motions without artificially constraining those degrees of freedom. Another tool, Conjugate Velocity Molecular Dynamics (CVMD), rigorously generates a list of productive velocities via the biorthogonalization of local modes with a vector representation of previously explored conformational minima. In addition to these tools, a new description of distance in torsional space was developed to provide a robust means of conformational uniqueness. With each of these tools working in concert, the global minimum and associated low-enthalpy population of conformations have been obtained for various benchmark species. The second section discusses the application of conformational searching and the subsequent electronic structure calculations to characterize the reaction pathway for the ruthenium tris(2,2'-bipyridine) photocatalyzed [2+2] cycloaddition of aromatically substituted bis(enones). The APFD hybrid density functional is used along with a 6-311+g* basis and a PCM solvent model. The reaction is computed to proceed through a rate-limited formation of a cyclopentyl intermediate. Lithium tetrafluoroborate is found to facilitate initial bis(enone) reduction as well as final product distribution. In addition, aromatic substituents are found to impact both initial reduction and final product distribution. | |
| dc.format.medium | born digital | |
| dc.format.medium | doctoral dissertations | |
| dc.identifier | Allison_colostate_0053A_12727.pdf | |
| dc.identifier.uri | http://hdl.handle.net/10217/88409 | |
| dc.language | English | |
| dc.language.iso | eng | |
| dc.publisher | Colorado State University. Libraries | |
| dc.relation.ispartof | 2000-2019 | |
| dc.rights | Copyright and other restrictions may apply. User is responsible for compliance with all applicable laws. For information about copyright law, please see https://libguides.colostate.edu/copyright. | |
| dc.subject | conformational searching | |
| dc.subject | surface editing | |
| dc.subject | photocatalysis | |
| dc.subject | molecular dynamics | |
| dc.subject | Cycloheptadecane | |
| dc.subject | Bis(enone) | |
| dc.title | Development and application of conformational methodologies: eliciting enthalpic global minima and reaction pathways | |
| dc.type | Text | |
| dcterms.embargo.expires | 2016-01-31 | |
| dcterms.embargo.terms | 2016-01-31 | |
| dcterms.rights.dpla | This Item is protected by copyright and/or related rights (https://rightsstatements.org/vocab/InC/1.0/). You are free to use this Item in any way that is permitted by the copyright and related rights legislation that applies to your use. For other uses you need to obtain permission from the rights-holder(s). | |
| thesis.degree.discipline | Chemistry | |
| thesis.degree.grantor | Colorado State University | |
| thesis.degree.level | Doctoral | |
| thesis.degree.name | Doctor of Philosophy (Ph.D.) |
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