Browsing by Subject "Potential energy surfaces"
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Item Kinetics and dynamics of adsorption on single crystal semiconductor and metal surfaces(2001-08) Reeves, Christopher Thomas; Mullins, C. B.Item The performance of the non-iterative and iterative triples corrected EOMIP-CCSD in characterizing stationary points of excited state potential energy surfaces(2002) Saeh, Jamal Carlos; Stanton, John (John F.)Item Quantum mechanical studies of weakly bound molecular ions(Texas Tech University, 2002-12) Chang, Daniel Ta-JenThe study of weakly bound complexes constitutes an active field of research. High-resolution experimental spectra are necessary to provide precise measurements of the intermolecular forces of these systems. Analogously, highly accurate quantum calculations are required to correctly describe weak intermolecular forces such as dispersion and induction. In this work, theoretical studies of three molecular ions, He3, Li-(H2), and LiH~, are described where each ion is weakly bound to their respective He^-|- He, Li~ +- H2, and LiH + -e - limits. For He3+, an analytical global ground state potential energy surface is developed from high quality ab initio calculations. The linear symmetric global minimum is found to be consistent with previous ab initio results (r^ = 2.340 a.u, and Dg = 0.175 eV). Numerical determination of the bound rovibrational levels reveals that (1) the ZPE is highly anharmonic, (2) a large number of banding states (v2 < 6) is supported, and (3) two quanta of pure asymmetric stretch (f 3 = 2) is not seen in our calculations implying that this state may be unbound. In the second study, an analytical potential energy surface is developed from high quality ab initio calculations for the electrostatic region of the Li~ -f H2 interaction. The Li~(H2) electrostatic complex is found to have a linear minimum energy structure with a De of 64.44 cm~-^ and numerical determinations of the bound levels indicate a Do of only ~7 cm~-^ for Li~(para-H2) and a considerably larger D0 of ~22 cm^-1 for Li-(ortho-B.2). Altogether, the Li-(para-H2) interaction is predicted to support 11 bound levels, whereas the Li~(ortho-H2) interaction is predicted to support 28 bound levels. Analogous results for the D2 and HD isotopomers are also reported. Finally, the photoelectron spectra of LiH" and LiD~ are determined from a first principles theoretical treatment. Satisfactory simulation of the experimental photoelectron spectra is accomplished by assuming a non-Boltzmann distribution of the anion vibrational levels and the discrepancy between the experimental (920 ± 80 cm-1) and theoretical (1176.1 cm~^) values of we of LiH- is resolved by a reassignment of the hot band transition region of the photoelectron spectrum.Item Simulation methodology for the kinetics of solid state atomic systems(2015-08) Duncan, Juliana Rebecca; Henkelman, Graeme; Makarov, Dmitrii E; Stanton, John F; Ganesan, Venkat; Elber, Ron; Hwang, Gyeong SA major challenge in computational chemistry and solid-state atomic systems is overcoming the limitations of molecular dynamics (MD) simulations by utilizing alternative methods to efficiently calculate the rate of chemical reactions and diffusion events. The focus of my dissertation is the following: 1) development of new methods to overcome the time scale limitations of MD; 2) greater understanding of the failures of current methods; and 3) application of the current methods to solid-state atomic systems. Harmonic transition state theory (HTST) is a powerful approximation within the transition state theory (TST) framework that reduces the problem of capturing reaction rates to indentifying the lowest energy first order saddle points. In this work, the biased gradient squared descent (BGSD) saddle point finding method is introduced. BGSD first converts all critical points into global minima by transforming the PES into the gradient squared landscape. A biasing term is added to stabilize critical points at a specified energy levels and destabilize other critical points. BGSD is shown to be competitive with the dimer method in terms of force evaluations required to find a set of low-energy saddle points around a reactant minimum. We use adaptive kinetic Monte Carlo simulations to investigate the transformation of a topologically closed packed (TCP) structure to a cubic phase in molybdenum. Molybdenum is one refractory element added to nickel-based superalloys to improve properties of the material for high-temperature applications. However, when the concentrations of refractory elements are too high TCP phases can form and degrade properties of the material. This study is a first step towards an atomistic description of the transformation of TCP phases to cubic phases. A successful method for accelerating MD simulations is Voter's hyperdynamics approach, which adds a non-negative bias potential to the system's potential energy surface (PES). A novel bias potential is introduced which utilizes a machine learning technique and constructs the bias potential based off of the distance to the ridge. The bias potential is shown to produce boost factors, or computational acceleration, that scale well with dimensionality. HTST does a remarkably good job of capturing reaction rates at low temperatures. However, as the temperature increases results generated by HTST can di ffer from direct MD rates by an order of magnitude. The successes and failures of HTST to capture reactions rates are investigated with the goal of inspiring increased accuracy at less cost than other existing methods.Item Theoretical and experimental studies of some unusual potential energy surfaces and pseudopericyclic reactions(2006-05) Sadasivam, Dhandapani V.; Birney, David M.; Li, Guigen; Bartsch, Richard A.Transition states are central to our understanding of the mechanism of reactions; especially in organic chemistry. This dissertation is aimed at understanding some unique transition states and energy surfaces. Both theoretical and experimental methods are used in this dissertation. Tetrazines undergo inverse electron demand Diels-Alder reactions. UV and stopped-flow spectrophotometric studies were undertaken to study the rate of Diels-Alder cycloadditions with N,N-dipropynylamine. For the cycloaddition of 3,6-diphenyl-1,2,4,5-tetrazine the ?G‡ is 19.2 ± 1.0 kcal/mol and for 3,6-dimethyl dicarboxylate -1,2,4,5-tetrazine, ?G‡ is 11.5 ± 1.2 kcal/mol. These results were consistent with the DFT (density functional theory) calculations carried out at (B3LYP/6-31G(d,p) + ZPVE) level. Study of these revealed two interesting features of the calculated energy surfaces. First, there might be no barrier for the loss of nitrogen from the bicyclic intermediate; which in turn makes it a transition state. Thus there are two sequential transition states; one for the addition of a dienophile to tetrazine and the other for the loss of nitrogen from the bicyclic structure. This study extends Berson’s correlation of activation energy with reaction energy in pericyclic reactions to significantly lower barriers. Second, the additions of a dienophile to the pyridazines lead to an interesting and unique energy surface, which we termed "a corner". An extension of sequential transition states to energy surfaces for chemical reactions that might have transition structures or states that are monkey saddles or higher order saddles (three or more valleys converging at a point) were also studied. At the transition structure, such a surface has second derivatives of the energy that are equal to zero and thus two frequencies that are equal to zero. These do not have the imaginary frequency associated with a one-dimensional saddle point. The Diels-Alder reactions between nitrogen and tetrazines were studied as possible reactions with monkey saddle transition states. Computationally, we have shown that these reactions go through a monkey saddle transition states at some levels of theory. For 12-annulene, a D3 conformation is calculated to be a monkey saddle transition structure at the BH&HLYP/3-21G level. For the addition of iodide to COI2, the C3v structure is calculated to be a monkey saddle transition state at the RHF/3-21G level. A theoretical study (B3LYP and G3MP2B3) of the dimerization of thioformylketene was performed. Four pathways, two [4 + 2] pathways and one [4 + 4] pathway with thioformylketene and one [4 + 2] pathway involving thioformylketene and thietone were also considered. Interestingly, the [4 + 4] pathway with thioformylketene had the lowest barrier among all dimerizations. The geometry of the transition state is unusual, with the forming bonds in the plane of the ketene. This reaction is best interpreted as pseudopericyclic reaction. The electrocyclic ring closure of a vinylogous form of an ?-oxoketenes ((6Z)-6-(3-oxoallylidene)cyclohexa-2,4-dienone) was studied theoretically at B3LYP/6-31G(d,p) level. The dienone cyclizes without a barrier. Constrained optimization, NBO (natural bonding orbital) analysis, NICS (nucleus independent chemical shift) values were determined to understand and classify the nature of the reaction as either a pericyclic / pseudopericyclic or possibly both. Finally, generation and trapping of ?-oxoketenes using novel synthetic methods were also attempted.Item Theoretical and experimental studies of some unusual potential energy surfaces and pseudopericyclic reactions(Texas Tech University, 2006-05) Sadasivam, Dhandapani V.; Birney, David M.; Li, Guigen; Bartsch, Richard A.Transition states are central to our understanding of the mechanism of reactions; especially in organic chemistry. This dissertation is aimed at understanding some unique transition states and energy surfaces. Both theoretical and experimental methods are used in this dissertation. Tetrazines undergo inverse electron demand Diels-Alder reactions. UV and stopped-flow spectrophotometric studies were undertaken to study the rate of Diels-Alder cycloadditions with N,N-dipropynylamine. For the cycloaddition of 3,6-diphenyl-1,2,4,5-tetrazine the ?G‡ is 19.2 ± 1.0 kcal/mol and for 3,6-dimethyl dicarboxylate -1,2,4,5-tetrazine, ?G‡ is 11.5 ± 1.2 kcal/mol. These results were consistent with the DFT (density functional theory) calculations carried out at (B3LYP/6-31G(d,p) + ZPVE) level. Study of these revealed two interesting features of the calculated energy surfaces. First, there might be no barrier for the loss of nitrogen from the bicyclic intermediate; which in turn makes it a transition state. Thus there are two sequential transition states; one for the addition of a dienophile to tetrazine and the other for the loss of nitrogen from the bicyclic structure. This study extends Berson’s correlation of activation energy with reaction energy in pericyclic reactions to significantly lower barriers. Second, the additions of a dienophile to the pyridazines lead to an interesting and unique energy surface, which we termed "a corner". An extension of sequential transition states to energy surfaces for chemical reactions that might have transition structures or states that are monkey saddles or higher order saddles (three or more valleys converging at a point) were also studied. At the transition structure, such a surface has second derivatives of the energy that are equal to zero and thus two frequencies that are equal to zero. These do not have the imaginary frequency associated with a one-dimensional saddle point. The Diels-Alder reactions between nitrogen and tetrazines were studied as possible reactions with monkey saddle transition states. Computationally, we have shown that these reactions go through a monkey saddle transition states at some levels of theory. For 12-annulene, a D3 conformation is calculated to be a monkey saddle transition structure at the BH&HLYP/3-21G level. For the addition of iodide to COI2, the C3v structure is calculated to be a monkey saddle transition state at the RHF/3-21G level. A theoretical study (B3LYP and G3MP2B3) of the dimerization of thioformylketene was performed. Four pathways, two [4 + 2] pathways and one [4 + 4] pathway with thioformylketene and one [4 + 2] pathway involving thioformylketene and thietone were also considered. Interestingly, the [4 + 4] pathway with thioformylketene had the lowest barrier among all dimerizations. The geometry of the transition state is unusual, with the forming bonds in the plane of the ketene. This reaction is best interpreted as pseudopericyclic reaction. The electrocyclic ring closure of a vinylogous form of an ?-oxoketenes ((6Z)-6-(3-oxoallylidene)cyclohexa-2,4-dienone) was studied theoretically at B3LYP/6-31G(d,p) level. The dienone cyclizes without a barrier. Constrained optimization, NBO (natural bonding orbital) analysis, NICS (nucleus independent chemical shift) values were determined to understand and classify the nature of the reaction as either a pericyclic / pseudopericyclic or possibly both. Finally, generation and trapping of ?-oxoketenes using novel synthetic methods were also attempted.