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Ab initio calculations on trajectories and nonadiabatic transitions in reactions of hydrogen atomic ions with hydrogen molecules
A mechanism for the enhanced splitting detected in the millimeter-wave rotational spectra of the first excited S-S stretching state of HSSH (disulfane) has been studied. The mechanism, which involves a potential coupling between the first excited S-S stretching state and excited torsional states, has been investigated in part by the use of ab initio theory. Based on an ab initio potential surface, coupling matrix elements have been calculated, and the amount of splitting has then been estimated by second-order perturbation theory. The result, while not in quantitative agreement with the measured splitting, lends plausibility to the assumed mechanism.
Density functional theory (DFT) is found to give a better description of the geometries and vibrational frequencies of FeL and FeL(sup +) systems than second order Moller Plesset perturbation theory (MP2). Namely, the DFT correctly predicts the shift in the CO vibrational frequency between free CO and the Sigma(sup -) state of FeCO and yields a good result for the Fe-C distance in the quartet states of FeCH4(+) 4 These are properties where the MP2 results are unsatisfactory. Thus DFT appears to be an excellent approach for optimizing the geometries and computing the zero-point energies of systems containing first transition row atoms. Because the DFT approach is biased in favor of the 3d(exp 7) occupation, whereas the more traditional approaches are biased in favor of the 3d(exp 6) occupation, differences are found in the relative ordering of states. It is shown that if the dissociation is computed to the most appropriate atomic asymptote and corrected to the ground state asymptote using the experimental separations, the DFT results are in good agreement with high levels of theory. The energetics at the DFT level are much superior to the MP2 and in most cases in good agreement with high levels of theory.
Ab initio ionization and thermal equilibrium models are calculated for the winds of O stars using the results of steady state radiation-driven wind theory to determine the input parameters. Self-consistent methods are used for the roles of H, He, and the most abundant heavy elements in both the statistical and the thermal equilibrium. The model grid was chosen to encompass all O spectral subtypes and the full range of luminosity classes. Results of earlier modeling of O star winds by Klein and Castor (1978) are reproduced and used to motivate improvements in the treatment of the hydrogen equilibrium. The wind temperature profile is revealed to be sensitive to gross changes in the heavy element abundances, but insensitive to other factors considered such as the mass-loss rate and velocity law. The reduced wind temperatures obtained in observing the luminosity dependence of the Si IV lambda 1397 wind absorption profile are shown to eliminate any prospect of explaining the observed O VI lambda 1036 line profiles in terms of time-independent radiation-driven wind theory.
High levels of ab initio theory are used to investigate the equilibrium structures, vibrational spectra, and relative energetics of FNO2, cis-FONO, and trans-FONO isomers. FNO2 is determined to be 36.9 +/- 2.5 kcal/mol (0 K) more stable than cis-FONO, which is more stable than trans-FONO by 2.5 +/- 1.0 kcal/mol (0 K). The molecular structure of cis-FONO is shown to have typical F-O and central O-N single bond distances, indicating that cis-FONO has a structure analogous to HONO. The computed vibrational spectrum of cis-FONO is shown to be consistent with IR matrix isolation experiments, including isotopic shifts. The experimentally deduced structure of FONO is shown to be incorrect because one of the vibrational bands included in the normal coordinate analysis is either a combination band or an overtone.
The microwave spectra of five isotopic species of bicyclo (1.1.1) pentanone have been investigated. The rotational constants along with various centrifugal distortion constants for each species have been determined. From the rotational constants, a complete r(s) structure has been determined for the heavy atoms. Analysis of Stark effect measurements has shown the dipole moment to be along the a principal inertial axis with a magnitude of 3.164 (5) D. These results are compared with those obtained by four current theoretical methods: molecular mechanics (MM2), MNDO, and Hartree-Fock ab initio theory with STO-3G and 3-21G basis sets.
A structural characterization is presented for C9, the largest cluster predicted to have a linear ground state. IR laser diode absorption spectroscopy of a supersonic carbon jet is used to measure 51 lines of the nu6 (sigma u) antisymmetric stretch fundamental transition within the linear 1Sigma(g)+ ground electronic state of C9. The measured ground state rotational constant suggests an effective C-C bond length which is in good agreement with ab initio theory and consistent with cumulenic bonding in this cluster.
The emission lines observed in many interstellar IR sources at 3.28, 6.2, 7.7, 8.7, and 11.3 microns are theorized to originate from polycyclic aromatic hydrocarbons (PAHs). These assignments are based on analyses of lab IR spectra of neutral PAHs. However, it is likely that in the interstellar medium that PAHs are ionized, i.e., are positively charged. Besides, as pointed out by Allamandola et al., although the IR emission band spectrum resembles what one might expect from a mixture of PAHs, it does not match in details such as frequency, band profile, or relative intensities predicted from the absorption spectra of any known PAH molecule. One source of more information to test the PAH theory is ab initio molecular orbital theory. It can be used to compute, from first principles, the geometries, vibrational frequencies, and vibrational intensities for model PAH compounds which are difficult to study in the lab. The Gaussian 86 computer program was used to determine the effect of ionization on the infrared absorption spectra of several small PAHs: naphthalene and anthracene. A preliminary report is presented of the results of these calculations.
Recent advances in electronic structure theory and the availability of high speed vector processors have substantially increased the accuracy of ab initio potential energy surfaces. The recently developed atomic natural orbital approach for basis set contraction has reduced both the basis set incompleteness and superposition errors in molecular calculations. Furthermore, full CI calculations can often be used to calibrate a CASSCF/MRCI approach that quantitatively accounts for the valence correlation energy. These computational advances also provide a vehicle for systematically improving the calculations and for estimating the residual error in the calculations. Calculations on selected diatomic and triatomic systems will be used to illustrate the accuracy that currently can be achieved for molecular systems. In particular, the F+H2 yields HF+H potential energy hypersurface is used to illustrate the impact of these computational advances on the calculation of potential energy surfaces.
Recent advances in electronic structure theory and the availability of high speed vector processors have substantially increased the accuracy of ab initio potential energy surfaces. The recently developed atomic natural orbital approach for basis set contraction has reduced both the basis set incompleteness and superposition errors in molecular calculations. Furthermore, full CI calculations can often be used to calibrate a CASSCF/MRCI approach that quantitatively accounts for the valence correlation energy. These computational advances also provide a vehicle for systematically improving the calculations and for estimating the residual error in the calculations. Calculations on selected diatomic and triatomic systems will be used to illustrate the accuracy that currently can be achieved for molecular systems. In particular, the F + H2 yields HF + H potential energy hypersurface is used to illustrate the impact of these computational advances on the calculation of potential energy surfaces.
The objective of the present research is to develop a general mathematical model and solution methodologies for analyzing the structural response of thin, metallic shell structures under large transient, cyclic, or static thermomechanical loads. Among the system responses associated with these loads and conditions are thermal buckling, creep buckling, and ratcheting. Thus geometric and material nonlinearities (of high order) can be anticipated and must be considered in developing the mathematical model. A complete, true ab-initio rate theory of kinematics and kinetics for continuum and curved thin structures, without any restriction on the magnitude of the strains or the deformations, was formulated. The time dependence and large strain behavior are incorporated through the introduction of the time rates of metric and curvature in two coordinate systems: fixed (spatial) and convected (material). The relations between the time derivative and the covariant derivative (gradient) were developed for curved space and motion, so the velocity components supply the connection between the equations of motion and the time rates of change of the metric and curvature tensors.
Protonated formaldehyde and protonated methanol are candidate interstellar molecules and models for classes of protonated oxygen compounds. Ab initio molecular orbital theory has been used to compute rotational constants to guide spectroscopic searches both in the laboratory and in space. The ab initio results are empirically correct to account for systematic deficiencies in the theory and zero-point vibrational effects; they are expected to be accurate to about + or - 2 percent. For H2COH(+) the resultant constants are (in GHz) A = 194.3, B = 34.28, and C = 29.14; for H3COH2(+) A = 103.7, B = 21.18, and C = 20.30.
The Wigner-Eisenbud R matrix method has been combined with the frame transformation theory to study electron scattering from molecular systems. The R matrix, calculated at the boundary point of the molecular core radius, has been transformed to the space frame in order to continue the solution of the scattering equations in the outer region where rotational motion of the nuclei is taken into account. This procedure has been applied to a model calculation of thermal energy electron scattering from CO.
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Theoretical simulation of prebiotic chemical processes is an invaluable tool for probing the phenomenon of the evolution of life. Using computational and modeling techniques and guided by analogies from present day systems, we seek to understand the emergence of the genetic apparatus, enzymatic catalysis and protein synthesis under prebiotic conditions. Modeling of the ancestral aminoacyl-tRNA-synthetases (aRS) may provide important clues to the emergence of the genetic code and the protein synthetic machinery. The minimal structural requirements for the catalysis of tRNA aminoacylation are being explored. A formation of an aminoacyl adenylate was studied in the framework of ab initio molecular orbital theory. The role of individual residues in the vicinity of the TyrRS active site was examined, and the effect of all possible amino acids substitutions near the active site was examined. A formation of aminoacyl tRNA was studied by the molecular modeling system SYBYL with the high resolution crystallographic structures of the present day tRNA, aRS's complexes. The ultimate goal is to propose a simple RNA segment that is small enough to be build in the primordial chemical environment but maintains the specificity and catalytic activity of the contemporary RNA enzyme. To understand the mechanism of ribozyme catalyzed reactions, ab initio and semi-empirical (ZINDO) programs were used to investigate the reaction path of transphosphorylation. A special emphasis was placed on the possible catalytic and structural roles played by the coordinated magnesium cation. Both the inline and adjacent mechanisms of transphosphorylation were studied. The structural characteristics of the target helices, particularly a possible role for the G-T pair, is also studied by a molecular dynamics (MD) simulation technique.
Ab initio molecular orbital theory has been used to determine the equilibrium geometries, rotational constants, and rotational spectra of four isoelectronic molecules. Two of these, HOCO(plus) and HOCN, are candidate interstellar molecules. The other two, HNCO and HN3, have known rotational constants. Theoretical rotational constants and spectra for the two unknown species were corrected with the mean experimental to theoretical ratios from the two known species. This procedure resulted in predicted frequencies of 83.75 plus or minus 0.2 GHz for the 4(04) to 3(03) transition in HOCN and 85.08 plus or minus 0.2 GHz for the same transition in HOCO(plus). These are the central lines of triplets whose other members are the 4(14) to 3(13) and 4(13) to 3(12) transitions. The triplet splittings were predicted to be 0.36 plus or minus 0.01 GHz for HOCN and 0.33 plus or minus 0.01 GHz for HOCO(plus). These results indicate that HOCO(plus) is a better candidate for the source of a series of lines reported by Thaddeus, Guelin, and Linke than is HOCN.
A number of molecular species on the H3CO(+) energy hypersurface is examined. Ab initio molecular orbital theory is used to determine the structures and relative energetics of the two isomers of HCO(+) and HOC(+) together with the affinity of CO for protonation at either end. The proton affinities of H2 and H2CO are also examined. The calculations are performed using large basis sets and include the effects of electron correlation. The calculated vibrational frequencies are used to correct for zero point energy differences. The results show that the proton affinities of H2 and CO to form HOC(+) are within 1 kcal of each other. The calculations demonstrate that there is no thermodynamic driving force to form HOC(+) in collisions of H3(+) with CO, and that the formation of HCO(+) in such collisions is very exoergic. A plausible mechanism is suggested to explain the differences observed between the laboratory and the interstellar medium.
The discovery of cyclopropenylidene in space suggests that other C3H2 isomers may be present, and a tentative detection of one such isomer, propargylene (HCCCH), has been reported. Ab initio molecular orbital theory has been used to characterize five low-lying, metastable isomers of cyclopropenylidene. Extended calculations including the electron correlation energy, show that the lowest in energy is singlet propadienylidene, followed by propargylene; the singlet and triplet of the latter are too close in energy to allow an assignment of the ground state; triplet propadienylidene is at a significantly higher energy. Rotational frequencies computed to an expected accuracy of + or - 1 -2 percent do not confirm the tentative detection of propargylene in space, although the discrepancy between theory and the observation is not so great as to unequivocally rule out this possibility.