Browsing by Subject "Computational chemistry"
Now showing 1 - 4 of 4
Results Per Page
Sort Options
Item Development of accurate and efficient models for biological molecules(2011-12) Wu, Johnny Chung; Ren, PengyuThe abnormal expression or function of biological molecules, such as nucleic acids, proteins, or other small organic molecules, lead to the majority of diseases. Consequently, understanding the structure and function of these molecules through modeling can provide insight and perhaps suggest treatment for diseases. However, biologically relevant molecular phenomenon can vary vastly in the nature of their interactions and different classes of models are required to accommodate for this diversity. The objective of this thesis is to develop models for small molecules, amino acid peptides, and nucleic acids. A physical polarizable molecular mechanics model is described to accurately represent small molecules and single atom ions and applied to predict experimentally measurable thermodynamic properties such as hydration and binding free energies. A novel physical coarse-grain model based on Gay-Berne potentials and electrostatic multipoles has been developed for short peptides. The fraction of residues that adopt the alpha-helix conformation agrees with all-atom molecule dynamics results. Finally, a statistically-derived model based on sequence comparative sequence alignments is developed and applied to improve folding accuracy of RNA molecules.Item Materials design via tunable properties(2012-05) Pozun, Zachary David; Henkelman, Graeme; Rossky, Peter J.; Chelikowsky, James R.; Makarov, Dmitrii E.; Mullins, Charles B.In the design of novel materials, tunable properties are parameters such as composition or structure that may be adjusted in order to enhance a desired chemical or material property. Trends in tunable properties can be accurately predicted using computational and combinatorial chemistry tools in order to optimize a desired property. I present a study of tunable properties in materials and employ a variety of algorithms that ranges from simple screening to machine learning. In the case of tuning a nanocomposite membrane for olefin/paraffin separations, I demonstrate a rational design approach based on statistical modeling followed by ab initio modeling of the interaction of olefins with various nanoparticles. My simplified model of gases diffusing on a heterogeneous lattice identifies the conditions necessary for optimal selectivity of olefins over paraffins. The ab initio modeling is then applied to identify realistic nanomaterials that will produce such conditions. The second case, [alpha]-Fe₂O₃, commonly known as hematite, is potential solar cell material. I demonstrate the use of a screened search through chemical compound space in order to identify doped hematite-based materials with an ideal band gap for maximum solar absorption. The electronic structure of hematite is poorly treated by standard density functional theory and requires the application of Hartree-Fock exchange in order to reproduce the experimental band gap. Using this approach, several potential solar cell materials are identified based on the behavior of the dopants within the overall hematite structure. The final aspect of this work is a new method for identifying low-energy chemical processes in condensed phase materials. The gap between timescales that are attainable with standard molecular dynamics and the processes that evolve on a human timescale presents a challenge for modeling the behavior of materials. This problem is particularly severe in the case of condensed phase systems where the reaction mechanisms may be highly complicated or completely unknown. I demonstrate the use of support vector machines, a machine-learning technique, to create transition state theory dividing surfaces without a priori information about the reaction coordinate. This method can be applied to modeling the stability of novel materials.Item Rovibrational spectroscopy calculations using a Weyl-Heisenberg wavelet basis and classical phase space truncation(2006-08) Lombardini, Richard Luzi; Poirier, Bill; Glab, Wallace; Gibson, Thomas; Gellene, GregNew basis set methods are examined regarding quantum mechanical calculations of energy levels and wave functions of bound systems. The first method (I) involves compact orthogonal wavelets as the basis set which is subsequently truncated using the guidance of a classical phase space picture of the system. In this dissertation, the first application of this technique to a real molecular system (neon dimer) is presented, and many of the technical details are developed for its use on any arbitrary system. Although in many respects, neon dimer represents a "worst-case scenario" for the method, it is still competitive with another state-of-the-art scheme applied to the same system. The second method (II) greatly improves the computed accuracies of the first through the introduction of phase space region operators, which increase the efficiency K/N of the basis set, where N is the number of basis functions needed to calculate K energy eigenvalues to a given level of accuracy. For one model system, the absolute error of the computed energy levels is reduced by nearly 4 orders of magnitude, as compared to method I. Finally, a new parallel algorithm for matrix diagonalization (method III) is introduced, which uses a modified subspace iteration method. The new method exhibits great parallel scalability, making it possible to determine many thousands of accurate eigenvalues for sparse matrices of order N approximately N ~ 106 or larger.Item Spectroscopic and theoretical investigation of selected cyclic and bicyclic molecules in their ground and excited electronic states(2009-05-15) Rishard, Mohamed Zuhair MohamedThe structures, vibrational frequencies, and potential energy functions of several molecules in their ground and excited electronic states were determined using various spectroscopic and theoretical methods. High-level ab initio and density functional theory (DFT) calculations were utilized to investigate the previously reported structures and vibrational spectra of 1,3- disilacyclobutane (13DSCB) and its 1,1,3,3-d4 (13DSCB-d4) isotopomer. These calculations confirmed the finding from earlier microwave work that the CSiC angles of the 13DSCB ring are unexpectedly larger than the SiCSi angles. The calculated vibrational spectra using density functional theory agreed well with the experimental data and showed CH2 modes to have unusually low values. The calculations also confirmed that the individual molecules in the vapor phase are puckered whereas in the solid they become planar. The one-dimensional potential energy surfaces (PESs) for the ring inversion vibration of 2-cyclohexen-1-one and its 2,6,6-d3 isotopomer in its ground and singlet S1(n,?*) electronic states were determined using ultraviolet cavity ringdown spectroscopy (CRDS). The CRDS data allowed several of the quantum states of the ring inversion vibration to be determined for both the ground and excited electronic states, and the data were fit very well with PESs with high barriers to inversion. The infrared and Raman spectra and DFT calculations were utilized to complete a vibrational assignment of 2CHO and 2CHO-d3. A remarkable agreement was seen between the experimental and calculated spectra. The fluorescence excitation spectra (FES) and the single-vibronic level fluorescence (SVLF) spectra of jet-cooled 1,4-dihydronaphthalene (14DHN) were acquired to determine its ring-puckering potential energy function for the ground and singlet S1(?,?*) electronic states. Ultraviolet, infrared, and Raman spectra were also recorded to complement the analysis. The potential energy functions showed that the molecule is planar in both the ground and S1(?,?*) states. A complete vibrational assignment was carried out for 14DHN using the infrared and Raman data and aided by DFT calculations. The ab intio calculations carried out on 2-methyl-2-cyclopenten-1-one (2MCP) showed that the molecule can have 3 different conformers. Infrared and Raman spectra of the liquid-phase molecule were recorded and analyzed to complement the theoretical calculations.