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Design of Molecules and Materials for Applications in Clean Energy, Catalysis and Molecular Machines Through Quantum Mechanics, Molecular Dynamics and Monte Carlo Simulations


Mendoza-Cortes, Jose Luis (2012) Design of Molecules and Materials for Applications in Clean Energy, Catalysis and Molecular Machines Through Quantum Mechanics, Molecular Dynamics and Monte Carlo Simulations. Dissertation (Ph.D.), California Institute of Technology. doi:10.7907/PQ74-HK88.


We use a multiparadigm, multiscale strategy based on quantum mechanics (QM), first-principles QM-based molecular mechanics (MD) and grand canonical Monte Carlo (GCMC) to rationally design new molecules and materials for clean energy (H2 and CH4 storage), catalysis (O2 evolution, metal organic complexes) and molecular architectures (rotaxanes, hydrogels). This thesis is organized in seven chapters and shows that it is crucial to understand the scale of the system to be studied, the insight obtained can be used to rationally design new molecules and materials for desirable applications; as well as to guide and complement experimental studies. Chapter 1 discusses the specific details of the proposed methodology, including the theoretical underpinning of each modeling paradigm, potential limitations, and how we use these for in silico characterization and design optimization. Chapter 2 covers the structure prediction and characterization of metal-organic complex arrays (MOCA) through QM and force-field-based molecular mechanics. The methodology is inspired by the approach used for enzymatic systems, considering that experimentally determining their three-dimensional structure remains an open challenge. Chapter 3 describes the use of transition state theory for the calculation of reaction rates in polymer hydrogel network formation. This enables the determination of optimum concentrations for polymerization reactions and preparation of coarse-grained force elds. Chapter 4 describes the work performed on Stoddard's rotaxane dumbbells, where we explained origin for the template-directed synthesis through QM-derived free energies. We also give a consistent explanation for the role of the counter anion. Chapter 5 presents the simulation results for a tetranuclear cluster model for O2 evolution, based on CaMn304 and Mn4O4 clusters. We demonstrate how to calculate their oxidation potentials and propose new molecular designs that resemble the oxygen evolution complex (OEC) both structurally and electronically. Chapter 6 presents our findings for CH4 storage. Using a second-order Moller-Plesset perturbation theory force field and GCMC we propose a framework for optimal delivery. Chapter 7 presents our designed materials for hydrogen storage and the validation of our methodology against experimental results. We based our predictions in QM and GCMC calculations through the development of our own first-principles vdW force eld. Our results demonstrate novel frameworks capable of achieving the DOE energy density target for 2015. Finally, we show the generalization of adsorption phenomena for any porous material based on topological constraints.

Item Type:Thesis (Dissertation (Ph.D.))
Subject Keywords:Clean energy; hydrogen storage; methane storage; oxygen evolution; molecular machines; quantum mechanics; molecular dynamics; Monte Carlo
Degree Grantor:California Institute of Technology
Division:Engineering and Applied Science
Major Option:Materials Science
Thesis Availability:Public (worldwide access)
Research Advisor(s):
  • Goddard, William A., III
Thesis Committee:
  • Goddard, William A., III (chair)
  • Fultz, Brent T.
  • Agapie, Theodor
  • Greer, Julia R.
  • Johnson, William Lewis
Defense Date:17 May 2012
Non-Caltech Author Email:mendozajoseluis (AT)
Record Number:CaltechTHESIS:05292012-220632933
Persistent URL:
Default Usage Policy:No commercial reproduction, distribution, display or performance rights in this work are provided.
ID Code:7091
Deposited By: Jose Mendoza Cortes
Deposited On:31 May 2012 16:08
Last Modified:03 Oct 2019 23:56

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