archives@tulane.edu / Abstract: A search in a research database for “large specific rotation” or anything similar produces few articles. Large specific rotation is not commonly used as an indicator for extraordinary chiroptical response. Alternatively, anisotropy factors obtained from circular dichroism spectra and calculated rotational strengths are more widely used to gauge chiroptical response. To another point, a search for “large chiroptical response” gives few articles that discuss pure organic compounds, and the result list is populated by organometallic clusters, nanostructures, and thin films. A search of the Reaxys database for organic compounds with [α]Ds larger than 1000 revealed that there are about 600, and there are only two that have [α]Ds larger than 10,000.30 We wondered if we could design a compound that would break the record in specific rotation and possess extraordinary chiroptical properties. Guided by time-dependent density functional theory (TD-DFT) calculations, various chiral, polycyclic aromatic compounds (PACs) were chosen as candidates to display extraordinary chiroptical properties, such as high optical rotation, strong circular dichroism, or a high degree of circularly polarized luminescence (CPL). PACs comprise a large class of organic compounds. In addition to synthetic PACs, numerous naturally occurring PACs exist in coal tar and as decomposition products of organic material. Since their pi electrons are delocalized, PACs have interesting and possibly useful electronic properties and a variety of applications. The PACs described in this dissertation, e.g., helical mesobenzanthrones, a cyclophane, are twisted pentacenes are chiral and have interesting optoelectronic properties. TD-DFT was primarily used to predict which compounds had the greatest potential to yield record-breaking specific rotations or other chiroptical properties, and ordinary DFT calculation were used to determine if these compounds had sufficiently high racemization barriers to be resolved at room temperature. With regard to specific rotation, the accuracy of TD-DFT calculations was examined by comparing experimental specific rotations to the calculated values. / 1 / Kelly Jane Dougherty

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Doctor of Philosophy / Department of Chemistry / Christine M. Aikens / Small silver and gold clusters (less than 2 nm) display a discrete absorption spectrum characteristic of molecular systems whereas larger particles display a strong, broad absorption band in the visible. The latter feature is due to the surface plasmon resonance, which is commonly explained by the collective dipolar motion of free electrons across the particle, creating charged surface states. The evolution between molecular properties and plasmon is investigated. Time-dependent density functional theory (TDDFT) calculations are performed to study the absorption spectrum of cluster-size silver and gold nanorods. The absorption spectrum of these silver nanorods exhibits high-intensity longitudinal and transverse modes (along the long and short axis of the nanorod respectively), similar to the plasmons observed experimentally for larger nanoparticles. These plasmon modes result from a constructive addition of the dipole moments of nearly degenerate single-particle excitations. The number of single-particle transitions involved increases with increasing system size, due to the growing density of states available. Gold nanorods exhibit a broader absorption spectrum than their silver counterpart due to enhanced relativistic effects, affecting the onset of the longitudinal plasmon mode. The high-energy, high-intensity beta-peak of acenes also results from a constructive addition of single-particle transitions and I show that it can be assigned to a plasmon. I also show that the plasmon modes of both acenes and metallic nanoparticles can be described with a simple configuration interaction (CI) interpretation. The evolution between molecular absorption spectrum and plasmon is also investigated by computing the density of states of spherical thiolate-protected gold clusters using a charge-perturbed particle-in-a-sphere model. The electronic structure obtained with this model gives good qualitative agreement with DFT calculations at a fraction of the cost. The progressive increase of the density of states with particle size observed is in accordance with the appearance of a plasmon peak. The optical properties of nanoparticles can be tuned by varying their composition. Therefore, the optical behavior of the bimetallic Au[subscript](25-n)Ag[subscript]n(SH)[subscript]18[superscript]- cluster for different values of n using TDDFT is analyzed. A large blue shift of the HOMO-LUMO absorption peak is observed with increasing silver content, in accordance with experimental results.

Phytochromes constitute one of the six well-characterized families of photosensory proteins in Nature. From the viewpoint of computational modeling, however, phytochromes have been the subject of much fewer studies than most other families of photosensory proteins, which is likely a consequence of relevant high-resolution structural data becoming available only in recent years. In this work, hybrid quantum mechanics/molecular mechanics (QM/MM) methods are used to calculate UV-vis absorption spectra of Deinococcus radiodurans bacteriophytochrome. We investigate how the choice of QM/MM methodology affects the resulting spectra and demonstrate that QM/MM methods can reproduce the experimental absorption maxima of both the Q and Soret bands with an accuracy of about 0.15 eV. Furthermore, we assess how the protein environment influences the intrinsic absorption of the bilin chromophore, with particular focus on the Q band underlying the primary photochemistry of phytochromes.

Doctor of Philosophy / Department of Chemistry / Christine M. Aikens / The remarkable optical and luminescence properties of noble metal nanoparticles (with diameters < 2 nm) attract researchers due to potential applications in biomedicine, photocatalysis, and optoelectronics. Extensive experimental investigations on luminescence properties of thiolate-protected gold and silver nanoclusters during the past decade have failed to unravel their exact photoluminescence mechanism. Herein, density functional and time-dependent density functional theory (DFT and TDDFT) calculations are performed to elucidate electronic-level details of several such systems upon photoexcitation. Multiple excited states are found to be involved in photoemission from Au₂₅(SR)₁₈– nanoclusters, and their energies agree well with experimental emission energies. The Au₁₃ core-based excitations arising due to electrons excited from superatom P orbitals into the lowest two superatom D orbitals are responsible for all of these states. The large Stokes shift is attributed to significant geometrical and electronic structure changes in the excited state. The origin of photoluminescence of Ag₂₅(SR)₁₈– nanoclusters is analogous to their gold counterparts and heteroatom doping of each cluster with silver and gold correspondingly does not affect their luminescence mechanism. Other systems have been examined in this work to determine how widespread these observations are. We observe a very small Stokes shift for Au₃₈(SH)₂₄ that correlates with a relatively rigid structure with small bond length changes in its Au₂₃ core and a large Stokes shift for Au₂₂(SH)₁₈ with a large degree of structural flexibility in its Au₇ core. This suggests a relationship between the Stokes shift of gold−thiolate nanoparticles and their structural flexibility upon photoexcitation. The effect of ligands on the geometric structure and optical properties of the Au₂₀(SR)₁₆ nanocluster is explored. Comparison of the relative stability and optical absorption spectra suggests that this system prefers the [Au₇(Au₈SR₈)(Au₃SR₄)(AuSR₂)₂] structure regardless of whether aliphatic or aromatic ligands are employed. The real-time (RT) TDDFT method is rapidly gaining prominence as an alternative approach to capture optical properties of molecular systems. A systematic benchmark study is performed to demonstrate the consistency of linear-response (LR) and RT-TDDFT methods for calculating the optical absorption spectra of a variety of bare gold and silver nanoparticles with different sizes and shapes.

abstract: The absorption spectra of metal-centered phthalocyanines (MPc's) have been investigated since the early 1960's. With improved experimental techniques to characterize this class of molecules the band assignments have advanced. The characterization remains difficult with historic disagreements. A new push for characterization came with a wave of interest in using these molecules for absorption/donor molecules in organic photovoltaics. The use of zinc phthalocyanine (ZnPc) became of particular interest, in addition to novel research being done for azaporphyrin analogs of ZnPc. A theoretical approach is taken to research the excited states of these molecules using time-dependent density functional theory (TDDFT). Most theoretical results for the first excited state in ZnPc are in only limited agreement with experiment (errors near 0.1 eV or higher). This research investigates ZnPc and 10 additional porphyrin analogs. Excited-state properties are predicted for 8 of these molecules using ab initio computational methods and symmetry breaking for accurate time- dependent self-consistent optimization. Franck-Condon analysis is used to predict the Q-band absorption spectra for all 8 of these molecules. This is the first time that Franck-Condon analysis has been reported in absolute units for any of these molecules. The first excited-state energy for ZnPc is found to be the closest to experiment thus far using a range-separated meta-GGA hybrid functional. The theoretical results are used to find a trend in the novel design of new porphyrin analog molecules. / Dissertation/Thesis / Doctoral Dissertation Materials Science and Engineering 2014

Doctor of Philosophy / Department of Chemistry / Christine M. Aikens / Gold and silver particles with dimensions less than a nanometer possess unique characteristics and properties that are different from the properties of the bulk. They demonstrate a non–zero HOMO–LUMO gap that can reach up to 3.0 eV. These differences arise from size quantization effects in the metal core due to the small number of atoms. These nanoparticles have attracted great interest for decades both in fundamental and applied research. Small gold clusters protected by various types of ligands are of interest because ligands allow obtaining gold nanoclusters with given sizes, shapes and properties. Three main families of organic ligands are usually used for stabilization of gold nanoclusters: phosphine ligands, thiolate ligands and DNA. Usually, optical properties of these NPs are studied using optical absorption spectroscopy. Unfortunately, sometimes this type of spectrum is poorly resolved and tends to appear very similar for different complexes. In these cases, circular dichroism (CD) and magnetic circular dichroism (MCD) spectroscopy can be applied. However, the interpretation of experimental CD and MCD spectra is a complicated process. In this thesis, theoretically simulated CD and MCD spectra were combined with optical absorption spectra to study optical activity for octa– and nona– and undecanuclear gold clusters protected by mono– and bidentate phosphine ligands. Additionally, optical properties of bare and DNA protected silver NPs were studied. Theoretical CD spectra were examined to learn more about the origin of chirality in chiral organometallic complexes, and to contribute to the understanding of the difference in chiroptical activity of gold clusters stabilized by different phosphine ligands and DNA–stabilized silver clusters. Furthermore, optical properties of the small centered gold clusters Au₈(PPh₃)₈²⁺ and Au₉(PPh₃)₈³⁺ were examined by optical absorption and MCD spectra using TDDFT. Theoretical MCD spectra were also used to identify the plasmonic behavior of silver nanoparticles. These results showed that CD and MCD spectroscopy yield more detailed information about optical properties and electronic structure of the different chemical systems than optical absorption spectroscopy alone. Theoretical simulation of the CD and MCD spectra together with optical absorption spectra can be used to assist in the understanding of empirically measured CD and MCD and provide useful information about optical properties and electronic structure.

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Time-dependent density functional theory calculations have been carried out to determine the complex first-order hyperpolarizability in the two-photon resonance region of the molecule IDS-Cab. Calculations show that three strongly absorbing states, in the ultraviolet region, are separated to the extent that no significant interference of the imaginary parts of the tensor elements of the first-order hyper-polarizability occurs. Consequently, and in contrast to experimental findings [27], no reduced imaginary parts of the first-order hyperpolarizability in the two-photon resonant region can be seen.