This dissertation describes a tight-binding technique that treats the dynamics of electrons and ions simultaneously. The main features are a generalized Hellmann- Feynman theorem, a standard, time-dependent, self-consistent-field description and the interaction picture. The time-dependence is incorporated by using Peierls Substitution. We also apply the velocity-Verlet algorithm to predict the motion of the ions. We first test the validity of this semi-empirical tight-binding approach on several smaller systems including ethylene, 2-butene, and stilbene. The cis-trans isomerization is modeled and in each case the results agree well with those obtained from other computational and empirical methods. Next, we use the tight-binding model to simulate the photoisomerization of the retinal molecule from its cis to trans form. The results are comparable to those obtained from experiments. The vibrational frequencies for retinal obtained using the force-constant techniques in this model agree well with those obtained from Fourier transform methods and a standard software. The cis-trans isomerization takes 217.91 fs to complete with a field strength of 1.0 gauss·cm, which is comparable to 200 fs reported from experiments. The isomerization depends on the strength of the vector potential, the time-step of the simulation and also the wavelength of the light. Using different parameters the isomerization takes place in 1-2 ps which is within the range reported from experimentation. The present semi-empirical technique provides an excellent compromise between computationally-prohibitive first principles methods and approximate empirical methods to model the motion of electrons and ions in a large molecule like retinal.

No description available.

Thesis (Ph.D.)--Washington State University, May 2006. / Includes bibliographical references.

Thesis (Ph. D.)--University of Canterbury, 2006. / Typescript (photocopy). Includes bibliographical references. Also available via the World Wide Web.

In the past two decades, a number of artificial molecular motors have been constructed using organic molecules as components which can perform unidirectional motion. Among the best-known examples are the light-activated molecular rotary motors synthesized and analyzed in B. L. Feringa's lab. Yet there is limited understanding of the photoisomerization and thermal isomerization processes that control the speed and energy conversion efficiency of these molecular devices. The present thesis work aims at: 1) developing a computational methodology to provide the atomic and electronic details that allow for quantitative descriptions of light-activated molecular motion, 2) improving the understanding of the physical principles governing photo- and thermal-isomerization processes in specific molecular systems, and 3) proposing a new strategy of molecule design to assist experimental investigations. A key component in our methodology is the calculation of the potential energy surface (PES) spanned by collective atomic coordinates using ab initio quantum mechanical methods. This is done both for the electronic ground state, which is relatively straightforward, and for the photo-excited state, which is more involved. Once the PES is known, classical statistical mechanical methods can be used to analyze the dynamics of the slow variables from which information about the rotational motion can be extracted. Calculation of the PES is computationally expensive if one were to sample the very high dimensional space of the atomic coordinates. A new method, based on the torque experienced by individual atoms, is developed to capture key aspects of the intramolecular relaxation in terms of angular variables associated with the rotational degrees of freedom. The effectiveness of the approach is tested on specific light-driven molecular rotary motors that were successfully synthesized and analyzed in previous experiments. Finally, based on the experience accumulated in this study, a new molecular rotary motor driven by visible light is proposed to reach MHz rotational frequency.

Thesis (Ph. D.)--University of Chicago, Dept. of Chemistry, March 2003. / Includes bibliographical references. Also available on the Internet.

Thesis (Ph. D.)--Ohio State University, 2007. / Title from first page of PDF file. Includes bibliographical references (p. 185-221).

Chapter 1 describes an introduction to the area of organocatalysis and delineates previous work within the Smith group on the use of isothioureas in asymmetric catalysis. Chapter 2 showcases a one-pot isothiourea-catalysed Michael addition-lactamisation using cheap and readily available starting materials (carboxylic acids) and easily prepared α,β-unsaturated ketimines via an ammonium enolate intermediate to give dihydropyridinones with high diastereo- and enantioselectivity (typically >90:10 dr, up to 99% ee). The resultant dihydropyridinones can be successfully derivatised into multiple products without erosion of stereointegrity. In chapter 3 the same concept has also been applied to the synthesis of planar molecules by using (phenylthio)acetic acid as a suiTable ammonium enolate precursor. Generation of an ammonium enolate using an achiral isothiourea (DHPB) and reaction with α,β-unsaturated trifluoromethyl ketones allows an isothiourea-mediated Michael addition / lactonisation / thiophenol elimination cascade reaction for the formation of 4,6-disubstituted and 3,4,6-trisubstituted 2-pyrones in good to excellent yields (61-99%). Notably this method allows low catalyst loadings of 1% to be used. The methodology has successfully been applied to the synthesis of a COX-2 inhibitor and a wide range of derivatisations has been performed, giving valuable aromatic and heteroaromatic products containing the trifluoromethyl motif. In chapter 4 a novel N- to C-sulfonyl migration of dihydropyridinones via photoisomerisation is investigated. The scope and limitations of this process is investigated and the process is shown to proceed without compromising the diastereo- or enantiomeric purity of the starting material, giving 5-sulfonyl products in good to excellent yields (67-95%). Mechanistic crossover has indicated that this migration includes an intermolecular step, while EPR studies provided evidence of its radical nature.

This dissertation describes the synthesis of novel, small molecule building blocks and the phenomena that are revealed when they are studied in unusual environments. Chapter 1 is divided into two sections, serving as introductions for chapters 2-3 and 4-5 respectively. The first section introduces the scanning tunneling microscope break junction (STM-BJ) as a new environment for reaction chemistry. Chapter 2 describes a truly single molecule reaction in which azobenzenes are formed in the STM-BJ one molecule at a time. Chapter 3 describes an electrostatically driven Ullmann coupling reaction of biphenyl iodides in the STM-BJ. In contrast to the reaction described in chapter 2, this reaction occurs throughout the solution in the presence of an electric field that surrounds the nanoelectrodes. The second half of chapter 1 provides a primer on the photoisomerization of azobenzenes, a class of small molecule dyes whose unique photochromic profile and switchable properties have been exploited across a wide range of fields. Chapter 4 introduces azobenzenes as photoswitchable ligands on superatomic clusters. Chapter 5 details the phenomenon and mechanism of white light driven rolling of Cu(I) isocyanoazobenzene crystals. Finally, chapter 6 is a self-contained research project. It details an organocatalytic O₂-coupled oxidation platform that capitalizes on the capacity of hydrazines to undergo rapid autoxidation to diazenes.

No description available.