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Understanding Solvation Environments in Chemical Systems

Basdogan, Yasemin (2020) Understanding Solvation Environments in Chemical Systems. Doctoral Dissertation, University of Pittsburgh. (Unpublished)

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Molecular level understanding and characterization of solvation environments is often needed across chemistry, biology, and engineering. In many cases, the explicit interactions between molecules with nearby solvents are crucial for molecular-scale understanding. Toward practical modelling of local solvation effects of any solute in any solvent, we developed a general, all-QM, cluster-continuum approach. This approach uses a global optimization procedure to identify low energy molecular clusters with different numbers of explicit solvent molecules and then employs a machine learning algorithm with the help of the Smooth Overlap of Atomic Positions (SOAP) kernel to quantify the similarity between different low-energy solvent environments. From these data, we use a sketch-map non-linear dimensionality reduction technique to obtain a visual representation of the similarity between solvent environments in differently sized microsolvated clusters. After studying the evolution of the local solvation environment around the molecules, we systematically explore reaction pathways using Growing String Method. Without needing either dynamics simulations or a prior knowledge of the local solvation structure, this procedure was used to calculate reaction energies, solvation free energies and barrier heights in solvated systems. We now use this approach to model reaction mechanisms in more complicated reaction environments that are relevant for renewable fuels and chemicals. We reliably predict hydrogenation pathways and calculate barrier heights under electrochemical environments. This approach can be used to study physically significant solvation environments in any solvated system where the solvent molecules affects the quantum level nature of reaction mechanisms.


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Item Type: University of Pittsburgh ETD
Status: Unpublished
CreatorsEmailPitt UsernameORCID
Basdogan, Yaseminyaseminbasdogan@gmail.comyab160000-0002-2071-9675
ETD Committee:
TitleMemberEmail AddressPitt UsernameORCID
Thesis AdvisorKeith, John A.jakeith@pitt.edujakeith0000-0002-6583-6322
Committee MemberJohnson, J. Karlkarlj@pitt.edukarlj
Committee MemberJordan, Kenneth D.jordan@pitt.edujordan
Committee MemberWilmer, Christopher E.wilmer@pitt.eduwilmer0000-0002-7440-5727
Date: 30 July 2020
Date Type: Publication
Defense Date: 3 January 2020
Approval Date: 30 July 2020
Submission Date: 23 March 2020
Access Restriction: No restriction; Release the ETD for access worldwide immediately.
Number of Pages: 130
Institution: University of Pittsburgh
Schools and Programs: Swanson School of Engineering > Chemical Engineering
Degree: PhD - Doctor of Philosophy
Thesis Type: Doctoral Dissertation
Refereed: Yes
Uncontrolled Keywords: Solvation, Molecules, Solvent Cluster Chemistry, Reaction Mechanisms and Catalysis
Date Deposited: 30 Jul 2020 18:21
Last Modified: 30 Jul 2020 18:21

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