We present revised measurements of the static electric dipole polarizabilities of K, Rb, and Cs based on atom interferometer experiments presented in [Phys. Rev. A 2015, 92, 052513] but now re-analyzed with new calibrations for the magnitude and geometry of the applied electric field gradient. The resulting polarizability values did not change, but the uncertainties were significantly reduced. Then, we interpret several measurements of alkali metal atomic polarizabilities in terms of atomic oscillator strengths f(ik), Einstein coefficients A(ik), state lifetimes tau(k), transition dipole matrix elements D-ik, line strengths S-ik, and van der Waals C-6 coefficients. Finally, we combine atom interferometer measurements of polarizabilities with independent measurements of lifetimes and C-6 values in order to quantify the residual contribution to polarizability due to all atomic transitions other than the principal ns-np(J) transitions for alkali metal atoms.

Free energy calculations for the transfer of a water molecule from the pure liquid to an interior cavity site in a protein are presented. Three different protein cavities, in bovine pancreatic trypsin inhibitor (BPTI), the I106A mutant of lysozyme, and in the I76A mutant of barnase, represent very different environments for the water molecule, one which is polar, forming four water-protein hydrogen bonds, and two which are more hydrophobic, only forming one or two water-protein hydrogen bonds. The calculations give very different free energies for the different cavities, with only the polar BPTI cavity predicted to be hydrated. The corresponding entropies for the transfer to the interior cavities are calculated as well and show that the transfer to the polar cavity is significantly entropically unfavorable while the transfer to the non-polar cavity is entropically favorable. For all proteins an analysis of the fluctuations in the positions of the protein atoms shows that the addition of a water molecule makes the protein more flexible. This increased flexibility appears to be due to an increase length and weakened strength of protein-protein hydrogen bonds near the cavity. Similar free energy studies are performed on the three proteins at high pressure, 3 kbar. As in the 1 atm studies BPTI is the only protein that should be hydrated at 3 kbar, however the protein free energy changes appear to be not strongly dependent on the number of hydrogen bonds available. Changes in protein structure and flexibility are analyzed in an attempt to more fully understand the changes proteins undergo prior to pressure induced denaturation. These changes can help understand the forces at work in the last stages of protein folding. The role of interior water in this process is also analyzed. Changes to the fluctuating charge algorithm that handles polarizability in molecular dynamics simulations were performed to allow for longer time steps. The fluctuating charge model treats partial charges as variables which are propagated using Lagrangian dynamics. A coordinate transform to normal mode charge variables is applied to the TIP4P-FQ model of water to decrease the coupling between the atomic and charge degrees of freedom.

<p>The main purpose of this thesis is to implement the Gauss--Legendre quadrature for the dispersion coefficient. This has been done and can be now be made with different number of points. The calculations with this implementation has shown that the relativistic impact on helium, neon, argon and krypton is largest for krypton, that has the highest charge of its nucleus. It was also seen that the polarizability of neon as a function of the imaginary angular frequency decreases monotonically from a static value.</p>

<p>This work presents first-principles calculations of long-range intermolecular dispersion energies between two atoms or molecules as expressed in terms of the C₆ dipole-dipole dispersion coefficients. In a series of publications, it has been shown by us that the complex linear polarization propagator method provides accurate <em>ab initio</em> and first-principles density functional theory values of the C₆ dispersion coefficients in comparison with those reported in the literature. The selected samples for the investigation of dispersion interactions in the electronic ground state are the noble gases, <em>n</em>-alkanes, polyacenes, azabenzenes, and C₆₀. It has been shown that the proposed method can also be used to determine dispersion energies for species in their respective excited electronic states. The C₆dispersion coefficients for the first <em>π</em> → <em>π*</em> excited state of the azabenzene molecules have been obtained with the adopted method in the multiconfiguration self-consistent field approximation. The dispersion energy of the <em>π</em> → <em>π*</em> excited state is smaller r than that of the ground state. It is found that the characteristic frequencies ω₁ defined in the London approximation of <em>n</em>-alkanes vary in a narrow range and that makes it possible to construct a simple structure-to-property relation based on the number of -bonds for the dispersion interaction in these saturated compounds. However, this simple approach is not applicable for the interactions of the <em>π</em>-conjugated systems since their characteristic frequencies <em>ω</em>₁ vary strongly depending on the systems.</p> / Report code: LIU-TEK-LIC-2006:2

The main purpose of this thesis is to implement the Gauss--Legendre quadrature for the dispersion coefficient. This has been done and can be now be made with different number of points. The calculations with this implementation has shown that the relativistic impact on helium, neon, argon and krypton is largest for krypton, that has the highest charge of its nucleus. It was also seen that the polarizability of neon as a function of the imaginary angular frequency decreases monotonically from a static value.

This work presents first-principles calculations of long-range intermolecular dispersion energies between two atoms or molecules and of electronic circular dichroism spectra of chiral molecules. The former is expressed in terms of the C6 dipole-dipole dispersion coefficients Δε, and the latter is given in terms of the extinction coefficient. In a series of publications, the complex linear polarization propagator method has been shown to be a powerful tool to provide accurate ab initio and first-principles density functional theory results. This was the case not only for the C6 dispersion coefficients but also for the electronic circular dichroism at an arbitrary wavelength ranging from the optical to the X-ray regions of the spectrum. The selected samples for the investigation of dispersion interactions in the electronic ground state are the noble gases, n-alkanes, polyacenes, azabenzenes, alkali-metal clusters, and C60. It is found that the values of C6 for the sodium-cluster-to-fullerene interactions are well within the error bars of the experiment. The proposed method can also be used to determine dispersion energies for species in their respective excited electronic states. The C6 dispersion coefficients for the first π → π* excited state of the azabenzene molecules have been obtained with the adopted method in the multiconfiguration self-consistent field approximation. The dispersion energy of the π → π* excited state is smaller than that of the ground state. It is found that the characteristic frequencies ω1 defined in the London approximation of n-alkanes vary in a narrow range which makes it possible to construct a simple structure-to-property relationship based on the number of π-bonds for the dispersion interaction in these saturated compounds. However, this simple approach is not applicable to the interactions of the π-conjugated systems since, depending on the systems, their characteristic frequencies ω1 can vary greatly. In addition, an accomplishment of calculations of the electronic circular dichroism spectra in the near-edge X-ray absorption has been demonstrated.

Although current classical force fields describe homogeneous single-componentsystems fairly well, they do not represent the response of an individual molecule's electronic structure to its local environment with enough detail to reliably predict atomic motions in interfacial regions such as a solvation structure or liquid surface.Since most chemical processes of non-trivial interest involve two or more dissimilar molecules interacting at a short distance, molecular models must accurately simulate the interactions between different molecular species as well as bulk behavior in order to provide useful information. Results from two simulation studies are presented to illustrate both the utility of current point-charge electrostatics models in liquid structure determination and the critical importance of modeling induction effects in liquid water.

No description available.

Thesis (Ph. D.)--University of Washington, 1999. / Vita. Includes bibliographical references (p. 115-123).

abstract: This thesis develops molecular models for electron transport in molecular junctions and intra-molecular electron transfer. The goal is to identify molecular descriptors that afford a substantial simplification of these electronic processes. First, the connection between static molecular polarizability and the molecular conductance is examined. A correlation emerges whereby the measured conductance of a tunneling junction decreases as a function of the calculated molecular polarizability for several systems, a result consistent with the idea of a molecule as a polarizable dielectric. A model based on a macroscopic extension of the Clausius-Mossotti equation to the molecular domain and Simmon’s tunneling model is developed to explain this correlation. Despite the simplicity of the theory, it paves the way for further experimental, conceptual and theoretical developments in the use of molecular descriptors to describe both conductance and electron transfer. Second, the conductance of several biologically relevant, weakly bonded, hydrogen-bonded systems is systematically investigated. While there is no correlation between hydrogen bond strength and conductance, the results indicate a relation between the conductance and atomic polarizability of the hydrogen bond acceptor atom. The relevance of these results to electron transfer in biological systems is discussed. Hydrogen production and oxidation using catalysts inspired by hydrogenases provides a more sustainable alternative to the use of precious metals. To understand electrochemical and spectroscopic properties of a collection of Fe and Ni mimics of hydrogenases, high-level density functional theory calculations are described. The results, based on a detailed analysis of the energies, charges and molecular orbitals of these metal complexes, indicate the importance of geometric constraints imposed by the ligand on molecular properties such as acidity and electrocatalytic activity. Based on model calculations of several intermediates in the catalytic cycle of a model NiFe complex, a hypothetical reaction mechanism, which very well agrees with the observed experimental results, is proffered. Future work related to this thesis may involve the systematic analysis of chemical reactivity in constrained geometries, a subject of importance if the context of enzymatic activity. Another, more intriguing direction is related to the fundamental issue of reformulating Marcus theory in terms of the molecular dielectric response function. / Dissertation/Thesis / Doctoral Dissertation Chemistry 2015