Implicit solvation using the superposition approximation applied to many-atom solvents with static geometry and electrostatic dipole
| dc.contributor.author | Mattson, Max Atticus, author | |
| dc.contributor.author | Krummel, Amber T., advisor | |
| dc.contributor.author | McCullagh, Martin, advisor | |
| dc.contributor.author | Szamel, Grzegorz, committee member | |
| dc.contributor.author | Prieto, Amy, committee member | |
| dc.contributor.author | Krueger, David, committee member | |
| dc.date.accessioned | 2020-06-22T11:53:52Z | |
| dc.date.available | 2022-06-15T11:53:52Z | |
| dc.date.issued | 2020 | |
| dc.description.abstract | Large-scale molecular aggregation of organic molecules, such as perylene diimides, is a phenomenon that continues to generate interest in the field of solar light-harvesting. Functionalization of the molecules can lead to different aggregate structures which in turn alter the spectroscopic properties of the molecules. To improve the next generation of perylene diimide solar cells a detailed understanding of their aggregation is necessary. A critical aid in understanding the spectroscopic properties of large-scale aggregating systems is molecular simulation. Thus development of an efficient and accurate method for simulating large-scale aggregating systems at dilute concentrations is imperative. The Implicit Solvation Using the Superposition Approximation model (IS-SPA) was originally developed to efficiently model nonpolar solvent–solute interactions for chargeless solutes in TIP3P water, improving the efficiency of dilute molecular simulations by two orders of magnitude. In the work presented here, IS-SPA is developed for charged solutes in chloroform solvent. Chloroform is the first solvent model developed for IS-SPA that is composed of more than one Lennard-Jones potential. Solvent distribution and force histograms were measured from all-atom explicit-solvent molecular dynamics simulations, instead of using analytic functions, and tested for Lennard-Jones sphere solutes of various sizes. The level of detail employed in describing the 3-dimensional structure of chloroform is tested by approximating chloroform as an ellipsoid, spheroid, and sphere by using 3-, 2-, and 1-dimensional distribution and force histograms respectively. A perylene diimide derivative, lumogen orange, was studied for its unfamiliar aggregation mechanism in chloroform and tetrahydrofuran solvents via Fourier-transform infrared and 2dimensional infrared spectroscopies as well as all-atom explicit-solvent molecular dynamics simulations and quantum mechanical frequency calculations. Molecular simulations identified two categories of likely aggregate dimer structures: the expected -stack structure, and a less familiar edge-sharing structure where the most highly charged atoms of the perylene diimide core are strongly interacting. Quantum mechanical vibrational frequency calculations were performed for various likely dimer aggregate structures identified in molecular simulation and compared to experimental spectroscopic results. The experimental spectra of the aggregating system share qualities with the edge-sharing dimer frequency calculations however larger aggregate structures should be tested. A violanthrone derivative, violanthrone-79 (V-79), was studied for its differing aggregation mechanisms in chloroform and tetrahydrofuran solvents via Fourier-transform infrared and 2dimensional infrared spectroscopies as well as all-atom explicit-solvent molecular dynamics simulations and quantum mechanical frequency calculations. The -stacking aggregate structure of V-79 is supported by all methods used, however, the type of -stacking orientations are different between the two solvents. Chloroform supports parallel -stacked aggregates while tetrahydrofuran supports anti-parallel -stacked aggregates which show differing vibrational energy delocalization between the aggregated molecules. The publications in chapters 3 and 4 demonstrate the power of combining experimental spectroscopy and computational methods like molecular dynamics simulations and quantum mechanical frequency calculations, however, they also show how having larger simulations with multiple solute molecules are needed. This is why developing IS-SPA to be used for these simulations is necessary. Further developments to IS-SPA are discussed regarding the importance of various symmetries of chloroform and the subsequent dimensionalities of the histograms used to describe its distribution and Lennard-Jones force. Two methods for describing the Coulombic forces of chloroform solvation are discussed and tested on oppositely charged Lennard-Jones sphere solutes. The radially symmetric treatment fails to capture the Coulombic forces of the spherical solute system from all-atom explicit-solvent molecular dynamics simulations. A dipole polarization treatment is presented and tested for the charged spherical solute system which better captures the Coulombic forces measured from all-atom explicit-solvent molecular dynamics simulations. Additional considerations for the improvement of IS-SPA and the developments in this work are presented. The dipole polarization approximation outlined in chapter 5 assumes that each chloroform is a static dipole, allowing the dipole magnitude to fluctuate as well as polarize is a more physically rigorous approximation that will likely improve the accuracy of Coulombic forces in IS-SPA. A novel method, drawn from the knowledge gained studying chloroform, for the efficient modeling of new solvent types including flexible solvent molecules in IS-SPA is discussed. | |
| dc.format.medium | born digital | |
| dc.format.medium | doctoral dissertations | |
| dc.identifier | Mattson_colostate_0053A_15987.pdf | |
| dc.identifier.uri | https://hdl.handle.net/10217/208571 | |
| dc.language | English | |
| dc.language.iso | eng | |
| dc.publisher | Colorado State University. Libraries | |
| dc.relation.ispartof | 2020- | |
| 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 | implicit | |
| dc.subject | superposition | |
| dc.subject | solvation | |
| dc.subject | dipole | |
| dc.title | Implicit solvation using the superposition approximation applied to many-atom solvents with static geometry and electrostatic dipole | |
| dc.type | Text | |
| dcterms.embargo.expires | 2022-06-15 | |
| dcterms.embargo.terms | 2022-06-15 | |
| 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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