Browsing by Subject "Computational chemistry"

Now showing 1 - 7 of 7
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    Development and testing of a protocol for computational prediction of 1H and 13C NMR chemical shifts and thermochemistry and reaction analysis of benzyne formation and trapping
    (2013-01) Marell, Daniel Joshua
    Elucidating structures of novel compounds and investigation of new reactions are two tasks that experimental organic chemists address on a frequent basis. The pursuit of these objectives can be rigorous and time-consuming. Of the methods employed in elucidating the structure of novel compounds, nuclear magnetic resonance (NMR) is by far the most widely applied. Investigation into new reactions may require any number of techniques to understand the reaction scope, kinetics, optimal conditions, mechanisms, etc. In both cases, the use of computational methods is well-suited to augment the experimentalist's data to guide and understand the system being investigated. A protocol for facilitating computational prediction of NMR chemical shifts was developed. Application to a set of natural products previously evaluated against computed NMR shifts, showed improved accuracy, through analysis of the corrected mean-absolute error (CMAE). The protocol was further employed successfully to aid in analysis of experimental spectra for compounds synthesized by collaborators where multiple diastereomers were possible. Graphing templates were also created to allow for rapid inspection of possible structures without more in-depth statistical analysis. Thermodynamic and mechanistic analysis on the formation and reaction of benzyne was also performed. Thermodynamic restrictions on the ring-size of fused benzynocycloalkanes were investigated. Additionally, analysis of the energetics and transition state geometries for small-molecule trapping (both intra and intermolecular) of benzyne are discussed.
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    Electronic structure and theoretical modeling of UV-Vis-NIR spectra of ferrocene containing tetrazaporphyrins
    (2013-08) Dennison, Richard Michael
    The UV-Vis-NIR spectra of two ferrocene substituted tetraazaporphyrins were analyzed by use of time dependent density functional theory (TDDFT) and polarized continuum model TDDFT (PCM-TDDFT) methods. The TDDFT and PCM-TDDFT calculations were done using four different exchange-correlation functionals (BPW91, BP86, B3LYP, PBE1PBE) with varying amounts of Hartree-Fock exchange included in the functional to find the best agreement between theory and experiment. Once the best agreement was found by comparing experimental spectrum to the PCM-TDDFT calculations, using the B3LYP functional, further calculations were carried out with this functional to assign the electronic transitions that made up the UV-Vis-NIR spectrum and generate the contours of the corresponding molecular orbitals involved. Once assigned, transitions toward the near-IR end of the spectrum (Identified by Region 1; see Figure 12) were found to be predominately metal-to-ligand charge transfer transitions (MLCT) between the iron atoms of the ferrocene substituents and the π* system of the tetraazaporphyrin ring. Transitions toward the UV end of the spectrum (Identified by Region 4; see Figure 12) were found to be predominately π→π* transitions of the tetraazaporphyrin ring. If was also found that the major transitions are fairly mixed in character due to mixed nature of the molecular orbitals involved, containing varying percentages of both tetraazaporphyrin and ferrocene character.
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    Multi-structural and multi-path variational transtition sate thoery. Application to kinetics studies of hydrogen transfer reaction in gas phase.
    (2012-07) Yu, Tao
    To use computational methods to study the kinetics of combustion reaction of either alkanes or biofuels, two great challenge issues need to be addressed. The first one is the multi-structure effect, which makes the reactive potential energy surface complex, and requires considering multiple stationary states and multiple reaction paths to calculate the thermal rate. The second issue oringinates from torsional anharmonicity, which causes the harmonic oscillator approximation and normal mode analysis to fail and requires treating the torsions using different models in different temperature regimes. To treat the multi-structural and torsional anharmonicity correctly, we developed the internal-coordinate multi-structural approximation to calculate the partition functions for large molecules. This new method can predict more accurate partition functions for complex molecules in both the low and high temperature ranges. We also developed two new formulations of variational transtition state theory (VTST): multi-structure and multi-path VTST with multi-dimensional tunneling to calculate the thermal rates of hydrogen-transfer reactions in a broad temperature range. These formulations include both multi-structure and torsional anharmonicity effects and a more accurate means to evaluate vairational and tunneling effects using multiple reaction paths in the calculation. The thesis work is presented as four chapters, as follows: Chapter one discusses the theory of the internal-coordinate multi-structural approximation, also called the multi-structure torsional (MS-T) approximation and its application to various molecules. Although this work was mainly contributed by J. Zheng and S. Mielke in our group, the author still would like to present this part in the thesis because this part is one of the fundamentals for the following chapters. Chapter two investigates the thermodynamics properties of two complex molecules, n-hepane and isoheptane, using the MS-T method. The results were compared with experimental data from the API Tables and TRC data sets and with the empirical group additivity method, to further demonstrate the success of the MS-T approximation in calculating the partition functions of large molecules. Chapter three focuses on presenting multi-structure variational transion state theory (MS-VTST) with torsional anhormicity, which includes both multi-structure and torsional anharmonicity effects for reactants, products, and transition states, but uses only the reaction path with the lowest vibrationally adiabatic ground-state potential energy barrier to calculate the variational and tunneling effects. To apply this theory, we studied the thermal rate of the 1,4-hydrogen shift reaction of 1-pentyl radical, and by comparing with experimental data, demonstrated that the MS-VTST rate is more accurate than that obtained by conventional single-structure VTST (SS-VTST). The last chapter, chapter four, extends the MS-VTST method to multi-path VTST (MP-VTST), which includes not only the multi-structure effect, but also the contribution of the variational and tunneling effects of all reaction paths. We applied this formulation to calculate the thermal rate of 1,4-hydrogen shift isomerization of the 2-cyclohexylethyl radical using two reaction paths.
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    Neural Network Potentials for Atomistic Simulations of Reactive Chemistry
    (2024-05) Gordon, Adrian
    Atomistic simulations play an important role in a wide range of chemical investigations, including studies of chemical kinetics. These simulations rely on accurate energies and forces, often obtained through expensive ab initio electronic structure calculations. Recently researchers have explored the use of machine learning models to provide analytical and differentiable potential energy surfaces for use in atomistic simulations. These ML models can provide energies at a fraction of the cost of ab initio methods and are also highly accurate within the chemical space represented in the training data. In this work, we explore methods for data sampling techniques for training datasets used to train ML potentials, specifically to calculate chemical kinetics of the OH+ CH4 hydrogen abstraction reaction. In addition, combined ML and molecular mechanics methods for condensed phase reactions is discussed.
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    Predicting Toxicity and Degradability of Quadricyclane, Fluorocarbon Ethers and their Analogs (1994-1995)
    (University of Minnesota Duluth, 1995) Basak, Subhash C; Lodge, Keith B; Schubauer-Berigan, Joseph
    In a large number of cases, we have to assess the risk of chemicals and predict the toxic potential of molecules in the face of limited experimental data. Structural criteria and functional criteria (if available) are routinely used to estimate the possible hazard posed by a chemical to the environment and ecosystem. Frequently, no biological or relevant physicochemical properties of the chemical species of interest are available to the risk assessor. In the proposed project, we will develop and implement a number of methods of quantifying molecular similarity of chemicals using techniques of computational and mathematical chemistry. Some of the methods are new and will be based on our own research on the theoretical development and implementation of molecular similarity methods. These techniques will be implemented in a user friendly computer environment of the Silicon Graphics workstation. The similarity methods will be used to select analogs of chemicals of interest to the Air Force, viz., QUADRICYCLANE, FLUOROCARBON ETHERS AND THEIR ANALOGS, from databases containing high quality physicochemical data and toxicity endpoints for large number of chemicals. The databases used in the project will come from three sources: a) public domain databases, b) our own in-house databases, and c) databases acquired from commercial vendors. The set of selected analogs, called probe-induced subsets, will be used to: a) develop structure-activity relationships (SAR), and b) carry out ranking of chemicals. Both of these methods will be used to estimate the hazard of the chemicals of interest. A set of chemicals (five to ten) will be chosen for experimental work with the purpose of evaluating and refining computer models. The set will include quadricyclane and fluorocarbon ethers of interest to the Air Force. It will also include a selection of analogs (probe-induced subset) that are readily available, suitable for experimentation, and for which data are lacking. Experiments will be performed to assess the biodegradability and photochemical degradability of the members of the set. Their toxicity will be tested by MicroTox and MutaTox. In cases where significant degradation is observed, the toxicity of the degradation products will also be tested. Direct measurement of the hydrophobicity (octanol-water partition coefficient) will be performed on the members of the set.
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    Predicting Toxicity and Degradability of Quadricyclane, Fluorocarbon Ethers and their Analogs (1996-1997)
    (University of Minnesota Duluth, 1997) Basak, Subhash C; Lodge, Keith B; Schubauer-Berigan, Joseph
    In a large number of cases, we have to assess the risk of chemicals and predict the toxic potential of molecules in the face of limited experimental data. Structural criteria and functional criteria (if available) are routinely used to estimate the possible hazard posed by a chemical to the environment and ecosystem. Frequently, no biological or relevant physicochemical properties of the chemical species of interest are available to the risk assessor. In the proposed project, we will develop and implement a number of methods of quantifying molecular similarity of chemicals using techniques of computational and mathematical chemistry. Some of the methods are new and will be based on our own research on the theoretical development and implementation of molecular similarity methods. These techniques will be implemented in a user friendly computer environment of the Silicon Graphics workstation. The similarity methods will be used to select analogs of chemicals of interest to the Air Force, viz., QUADRICYCLANE, FLUOROCARBON ETHERS AND THEIR ANALOGS, from databases containing high quality physicochemical data and toxicity endpoints for large number of chemicals. The databases used in the project will come from three sources: a) public domain databases, b) our own in-house databases, and c) databases acquired from commercial vendors. The set of selected analogs, called probe-induced subsets, will be used to: a) develop structure-activity relationships (SAR), and b) carry out ranking of chemicals. Both of these methods will be used to estimate the hazard of the chemicals of interest. A set of chemicals (five to ten) will be chosen for experimental work with the purpose of evaluating and refining computer models. The set will include quadricyclane and fluorocarbon ethers of interest to the Air Force. It will also include a selection of analogs (probe-induced subset) that are readily available, suitable for experimentation, and for which data are lacking. Experiments will be performed to assess the biodegradability and photochemical degradability of the members of the set. Their toxicity will be tested by MicroTox and MutaTox. In cases where significant degradation is observed, the toxicity of the degradation products will also be tested. Direct measurement of the hydrophobicity (octanol-water partition coefficient) will be performed on the members of the set.
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    Toward Simulation of Complex Reactive Systems: Development and Application of Enhanced Sampling Methods
    (2018-03) Fetisov, Evgenii
    redictive modeling of fluid phase and sorption equilibria for reacting systems presents one of the grand challenges in the field of molecular simulation. Difficulties in the study of such systems arise from the need (i) to accurately model both strong, short-ranged interactions leading to the formation of chemical bonds and weak interactions representing the environment, and (ii) to sample the range of time scales involving frequent molecular collisions, slow diffusion, and infrequent reactive events. This thesis showcases some of my efforts in developing and applying advanced simulation methods to a variety of important systems. Chapters 2 and 3 describe how a novel Monte Carlo method (reactive first principles Monte Carlo or RxFPMC) can be used to overcome some limitations of existing methods for simulation of reactive systems. Chapter 4 shows how advanced sampling techniques in combination with sophisticated interatomic potentials can be used to elucidate nucleation pathways. Chapters 5 and 6 manifest how first principles simulations can be leveraged to understand liquid structure of novel complex solvents as well as reactive processes in such solvents. Finally, the last chapter discusses the use of smart sampling algorithms to study chemisorption of mixed ligands on nanoparticles.