Browsing by Subject "theoretical chemistry"

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    Charge-dependent non-bonded interaction methods for use in quantum mechanical modeling of condensed phase reactions
    (2015-10) Kuechler, Erich
    Molecular modeling and computer simulation techniques can provide detailed insight into biochemical phenomena. This dissertation describes the development, implementation and parameterization of two methods for the accurate modeling of chemical reactions in aqueous environments, with a concerted scientific effort towards the inclusion of charge-dependent non-bonded non-electrostatic interactions into currently used computational frameworks. The first of these models, QXD, modifies interactions in a hybrid quantum mechanical/molecular (QM/MM) mechanical framework to overcome the current limitations of ‘atom typing’ QM atoms; an inaccurate and non-intuitive practice for chemically active species as these static atom types are dictated by the local bonding and electrostatic environment of the atoms they represent, which will change over the course of the simulation. The efficacy QXD model is demonstrated using a specific reaction parameterization (SRP) of the Austin Model 1 (AM1) Hamiltonian by simultaneously capturing the reaction barrier for chloride ion attack on methylchloride in solution and the solvation free energies of a series of compounds including the reagents of the reaction. The second, VRSCOSMO, is an implicit solvation model for use with the DFTB3/3OB Hamiltonian for biochemical reactions; allowing for accurate modeling of ionic compound solvation properties while overcoming the discontinuous nature of conventional PCM models when chemical reaction coordinates. The VRSCOSMO model is shown to accurately model the solvation properties of over 200 chemical compounds while also providing smooth, continuous reaction surfaces for a series of biologically motivated phosphoryl transesterification reactions. Both of these methods incorporate charge-dependent behavior into the non-bonded interactions variationally, allowing the ‘size’ of atoms to change in meaningful ways with respect to changes in local charge state, as to provide an accurate, predictive and transferable models for the interactions between the quantum mechanical system and their solvated surroundings.
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    Developing a Model Chemistry for Multiconfiguration Pair-Density Functional Theory to Study Photochemistry and Molecular Interactions
    (2021-01) Bao, Jie
    Photochemical reaction, which starts by exciting a system into an electronically excited state, is ubiquitous, for example, in the atmosphere. This has made photochemical reactions a very interesting topic. Multiconfigurational pair-density functional theory (MC-PDFT) is a powerful and efficient method for studying photochemical processes. This method has proved very efficient compared with other wave function methods, such as multi-state complete active space second order perturbation theory (MS-CASPT2), especially for large systems. Successful as MC-PDFT is, there are some limitations that stop MC-PDFT from being applied to studying photochemistry problems. The first limitation is that, like other multireference methods, the performance of MC-PDFT depends on the quality of the reference wave function, which by convention is optimized by an active-space method, such as complete active space self-consistent field (CASSCF). The second limitation is that MC-PDFT is a single-state method that does not include state interaction between reference states. This means that MC-PDFT gives wrong topologies of potential energy surfaces, which are important in studying photochemical reactions. My work is focused on resolving these two limitations. We proposed the ABC scheme and the ABC2 scheme to automatically generate the active space that gives good-quality reference wave functions thus successfully reproducing vertical excitation energies obtained from experiments or high-level calculations. We proposed the extended multi-state PDFT (XMS-PDFT) and compressed-state multi-state PDFT (CMS-PDFT) as two options to introduce state-interaction in pair-density functional theory. Among two methods, XMS-PDFT is more efficient, while CMS-PDFT is more robust. Both methods proved successful in providing correct topologies of potential energy surfaces for a variety of systems.