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The quantum mechanical theory of rotational and vibrational transitions in atom-diatom systems is investigated and summarized. The time independent scattering formalism of Arthurs and Dalgarno is used, and the degeneracy-averaged cross section is expressed in terms of the scattering S matrix. The major emphasis is on the solution of the rotationally strongly coupled differential equations. Various methods of solving the scattering equations are examined and some of the inadequacies of these methods are discussed. A strong coupling (SC) approximation, valid for small energy exchange, is introduced and tested numerically on some model problems. A first-order iteration to the SC approximation is presented to improve the SC approximation and to extend the range of validity to cases of larger energy exchange. The SC results are compared with the accurate numerical solution and other approximate methods for some model problems. The comparison clearly demonstrates that the SC approximation is the computationally fastest, reasonably reliable method known for computing rotationally inelastic cross sections.

Methane hydrate has a unique structure that the host water framework forms two kinds of cages, which contain one methane molecule each. Therefore, it has been expected that there may exist three kinds of translational modes of a methane molecule and also the distortion of translational mode of host water molecules compared with normal ice. We need information of the host and guest molecular dynamics over the wide momentum and energy transfer region for studying such dynamics. In this study inelastic neutron measurements were carried under 40 K with MARI spectrometer at ISIS in UK, TAS at JRR-3 and CAT at KENS in Japan. For the methane molecular motion we could confirm its freelike rotation by complementary use of MARI and TAS spectra. After the subtraction of the scattering intensity of the rotation evaluated by the free rotation model from the experimental data, three kinds of translation modes were identified at first experimentally. On the experimental spectra there still remains the excess intensity which could not explain the single mode excitation. The libration mode of the water framework shows the different momentum and energy transfer dependence with those of normal ice. The feature of the libration mode is resemble to ice-IX, that could be considered as a proton ordering of the cage structure appeared in ice-II, VIII and IX.

This research investigates through computational methods whether the physical properties of DNA contribute to its harmonic signature, the uniqueness of that signature if present, and motion of the DNA molecule in water. When DNA is solvated in water at normal 'room temperature', it experiences a natural vibration due to the Brownian motion of the particles in the water colliding with the DNA. The null hypothesis is that there is no evidence to suggest a relationship between DNA's motion and strand length, while the alternative hypothesis is that there is evidence to suggest a relationship between DNA's vibrational motion and strand length. In a similar vein to the first hypothesis, a second hypothesis posits that DNA's vibrational motion may be dependent on strand content. The nature of this relationship, whether linear, exponential, logarithmic or non-continuous is not hypothesized by this research but will be discovered by testing if there is evidence to suggest a relationship between DNA's motion and strand length. The research also aims to discover whether the motion of DNA, when it varies by strand length and/or content, is sufficiently unique to allow that DNA to be identified in the absence of foreknowledge of the type of DNA that is present in a manner similar to a signature. If there is evidence to suggest that there is a uniqueness in DNA's vibrational motion under varying DNA strand content or length, then additional experimentation will be needed to determine whether these variances are unique across small changes as well as large changes, or large changes only. Finally, the question of whether it might be possible to identify a strand of unique DNA by base pair configuration solely from its vibrational signature, or if not, whether it might be possible to identify changes existing inside of a known DNA strand (such as a corruption, transposition or mutational error) is explored. Given the computational approach to this research, the NAMD simulation package (released by the Theoretical and Computational Biophysics Group at the University of Illinois at Urbana-Champaign) with the CHARMM force field would be the most appropriate set of tools for this investigation (Phillips et al., 2005), and will therefore be the toolset used in this research. For visualization and manipulation of model data, the VMD (Visual Molecular Dynamics) package will be employed. Further, these tools may be optimized and/or be aware of nucleic acid structures, and are free. These tools appear to be sufficient for this task, with validated fidelity of the simulation to provide vibrational and pressure profile data that could be analyzed; sufficient capabilities to do what is being asked of it; speed, so that runs can be done in a reasonable period of time (weeks versus months); and parallelizability, so that the tool could be run over a clustered network of computers dedicated to the task to increase the speed and capacity of the simulations. The computer cluster enabled analysis of 30,000 to 40,000 atom systems spending more than 410,000 CPU computational hours of hundreds of nano second duration, experimental runs each sampled 500,000 times with two-femtosecond “frames.” Using Fourier transforms of run pressure readings into frequencies, the simulation investigation could not reject the null hypotheses that the frequencies observed in the system runs are independent on the DNA strand length or content being studied. To be clear, frequency variations were present in the in silicon replications of the DNA in ionized solutions, but we were unable to conclude that those variations were not due to other system factors. There were several tests employed to determine alternative factors that caused these variations. Chief among the factors is the possibility that the water box itself is the source of a large amount of vibrational noise that makes it difficult or impossible with the tools that we had at our disposal to isolate any signals emitted by the DNA strands. Assuming the water-box itself was a source of large amounts of vibrational noise, an emergent hypothesis was generated and additional post-hoc testing was undertaken to attempt to isolate and then filter the water box noise from the rest of the system frequencies. With conclusive results we found that the water box is responsible for the majority of the signals being recorded, resulting in very low signal amplitudes from the DNA molecules themselves. Using these low signal amplitudes being emitted by the DNA, we could not be conclusively uniquely associate either DNA length or content with the remaining observed frequencies. A brief look at a future possible isolation technique, wavelet analysis, was conducted. Finally, because these results are dependent on the tools at our disposal and hence by no means conclusive, suggestions for future research to expand on and further test these hypothesis are made in the final chapter.

Mechanisms of reactions of the frustrated Lewis pairs (FLPs) with carbon dioxide (CO2) and hydrogen (H2) are studied by using quantum chemical modelling. FLPs are relatively novel chemical systems in which steric effects prevent a Lewis base (LB) from donating its electron pair to a Lewis acid (LA). From the main group of the periodic table, a variety of the electron pair donors and acceptors can create an FLP and the scope of the FLP chemistry is rapidly expanding at present. Representative intermolecular FLPs are phosphines and boranes with bulky electron-donating groups on phosphorus and bulky electron-withdrawing groups on boron – e.g., the tBu3P/B(C6F5)3 pair. The intramolecular FLPs feature linked LB and LA centers in one molecule. Investigations of the FLP reaction mechanisms were carried out using the transition state (TS) and the potential energy surface (PES) calculations plus the Born-Oppenheimer molecular dynamics (BOMD) as an efficient and robust implementation of general ab initio molecular dynamics scheme. In BOMD simulations, quantum and classical mechanics are combined. The electronic structure calculations are fully quantum via the density functional theory (DFT). Molecular motion at finite (non-zero) temperature is explicitly accounted for at non-quantized level via Newton’s equations. Due to recent advancements of computers and algorithms, one can treat fairly large macromolecular systems with BOMD and even include significant portion of the first solvation shell surrounding a large reacting complex in the molecular model. Main results are as follows. It is shown that dynamics is significant for understanding of FLP chemistry. The multiscale nature of motion – i.e., light molecules such as CO2 or H2 versus a pair of heavy LB and LA molecules – affects the evolution of interactions in the reacting complex. Motion which is perpendicular to the reaction coordinate was found to play a role in the transit of the activated complex through the TS-region. Regarding the heterolytic cleavage of H2 by tBu3P/B(C6F5)3 FLP simulated in gas phase and with explicit solvent, it was found that (i) the reaction path includes shallow quasi-minima “imbedded” in the TS-region, and (ii) tBu3P/B(C6F5)3 are almost stationary while proton- and hydride-like fragments of H2 move toward phosphorous and boron respectively. For binding of CO2 by tBu3P/B(C6F5)3 FLP, it was found that (i) the reacting complex can “wander” along the “potential energy wall” that temporarily blocks the path to the product, and (ii) the mechanism can combine the concerted and two-step reaction paths in solution. The discovered two-step binding of CO2 by tBu3P/B(C6F5)3 FLP involves solvent-stabilized phosphorus-carbon interactions (dative bonding). These and other presented results are corroborated and explained using TS and PES calculations. With computations of observable characteristics of reactions, it is pointed out how it could be possible to attain experimental proof of the results. / <p>At the time of the doctoral defense, the following paper was unpublished and had a status as follows: Paper 6: Accepted.</p><p> </p>

The identification and quantification of atoms, molecules, or ions concentrations in gaseous samples are in great demand for medical, environmental, industrial, law enforcement and national security applications. These applications require in situ, high-resolution, non-destructive, sensitive, miniature, inexpensive, rapid detection, remotely accessed, real time and continuously operating chemical sensing devices. The aim of this work is to design a miniature optical sensing device that is capable of detecting and measuring chemical species, compatible with being integrated into a large variety of monitoring systems, and durable enough to be used under extreme conditions. The miniature optical sensor has been realized by employing technologies from the optical communication industry and spectroscopic methods and techniques. Fused silica capillary tubing along with standard communication optical fibers have been utilized to make miniature gas sensor based on near-infrared spectroscopy for acetylene gas detection. In this work, the basic principles of infrared spectroscopy are reviewed. Also, the principle of operation, fabrication, testing, and analysis of the proposed sensor are discussed in details. / Master of Science