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Open Access Publications from the University of California

Scholarly Works (14 results)

  • Thesis
  • Peer Reviewed
UC Berkeley Electronic Theses and Dissertations (2012)

Femtosecond, angle resolved two photon photoemission spectroscopy is used as a probe of the metal-molecule interface. In four related investigations, monolayer or submonolayer coverages of a molecule are adsorbed onto an Ag(111) surface under ultrahigh vacuum conditions. Studies use a an optically excited electronic probe to investigate to probe the energetic landscape experienced and the response of a molecular adsorbate to an excess charge. Energy levels, electronic population, and band structure reveal molecular structure and mechanisms of dynamic response to an injected charge.

Room temperature ionic liquids (RTIL), consisting of charge separated anions and cations, represent a new and poorly understood class of electrochemical solvents. The mechanism of electron solvation has been proposed to be vastly different at the electrode interface than has been observed in bulk studies. Optical excitation into the RTIL conduction band results in a localized excess charge, as measured by band dispersions. Electron solvation is measured directly as the photoemitted kinetic energy. Solvation by 200-540 meV is found to occur rapidly on the timescale of 350 fs, supporting previous predictions of fast charge solvation at the interface. Further, a previously proposed phase transition is observed between a low temperature ordered phase and high temperature disordered phase. This phase transition, which occurs at 250 K, is quantified by both the change in workfunction and a change in the energy of solvation between the two phases.

The image state is often used as a sensitive probe of molecular films, however, the electronic potential experienced by the image state electron is poorly understood. Theoretical predictions of image state energy in molecular films with a positive electron affinity are often wrong by 1-3 eV, and descriptions of the band structure typically remain limited to a measurement of effective mass. An image state is investigated within a film of metallated phthalocyanines. Phthalocyanines crystallize laying flat on the substrate, with a nearly square unit cell of 14 - 15 Å on a side. Angle resolved measurements into the second Brillouin zone reveal folding of the image state due to interactions with the screened potential energy surface within the molecule. The bandgap, measured to be 150 meV, can be used to estimate the corrugation of the energy landscape. Further, a Kronig Penney model is quantitatively compared to the first several backfolded image bands. Comparision between theory and experiment reveals the effects of the fourfold symmetry of lattice on the image state bandstructure.

The morphology and crystal structure of thin film molecular semiconductors is well known to directly influence the band structure and electronic properties of the material. Further, several morphologies and crystal structures can result from epitaxial growth of a single molecule on a metal surface. Although phase transitions in 2D-atomic systems have been well studied for over 80 years, molecular systems are less well understood due to their larger size and the complex interplay of relatively weak forces that govern the crystalline packing. Three phases of metallated phthalocyanines are studied as a function of substrate temperature and submonolayer coverage. Three phases, the 2D-gas phase, the low temperature commensurate phase, and the high temperature incommensurate phase, are each studied using TPPE and low energy electron diffraction. The image state is found to be an excellent probe of the local crystal structure and local workfunction. Preliminary studies focus on the temperature and coverage dependent energies and intensities of the image state peak in domains of each phase. Temperature dependent studies reveal a pseudo-isosbestic point in the transition from the low temperature commensurate to the high temperature incommensurate phases. Coverage dependence reveals a redshift of the image state with increasing molecular density and decreasing workfunction, and low temperature studies reveal long time scale kinetics of reorganization. Preliminary experimental results are interpreted with the aid of kinetic monte carlo simulations. Further studies will aim to obtain quantitative thermodynamics of these submonolayer coverages.

Two photon photoemission spectrscopy has proven to be a powerful tool for understanding basic surface physics of atomic and molecular systems. In particular, the image state has proven to be a powerful probe of the first 1-2 ML coverage of a molecular system. In order to improve the applicability of TPPE to answer device relevant questions, the technique will need to resolve, identify, and characterize molecularly derived bands and excitonic states. The basic selection rules for metal-molecule charge transfer excitations and exciton formation at a surface are understood, but it is not agreed upon whether hot-electrons or interfacial electronic coupling allow for excitations that break normal selection rules. Further, classical dipole quenching is expected to play a strong role in the exciton lifetimes in molecules adsorbed on metal or semiconductor surfaces, though no TPPE study up to this point has been able to observe the expected distance dependent lifteimes. In this final chapter, selection rules and classical dipole quenching are briefly discussed, and general trends are derived for molecular systems adsorbed on highly oriented metal surfaces. Our work up to this point suggests that selection rules are followed rigourously in molecular adsorbates on Ag(111).

    Cover page: Electron Dynamics and Symmetries at the Metal-Molecule Interface Probed by Two Photon Photoemission
    • Article
    • Peer Reviewed
    LBL Publications (2016)
    Molecular solids and polymers can form low-symmetry crystal structures that exhibit anisotropic electron and ion mobility in engineered devices or biological systems. The distribution of molecular orientation and disorder then controls the macroscopic material response, yet it is difficult to image with conventional techniques on the nanoscale. We demonstrated a new form of optical nanocrystallography that combines scattering-type scanning near-field optical microscopy with both optical antenna and tip-selective infrared vibrational spectroscopy. From the symmetry-selective probing of molecular bond orientation with nanometer spatial resolution, we determined crystalline phases and orientation in aggregates and films of the organic electronic material perylenetetracarboxylic dianhydride. Mapping disorder within and between individual nanoscale domains, the correlative hybrid imaging of nanoscale heterogeneity provides insight into defect formation and propagation during growth in functional molecular solids.
      Cover page: Infrared vibrational nanocrystallography and nanoimaging
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      • Peer Reviewed
      UCLA Previously Published Works (2020)
      Much of the electronic transport, photophysical, or biological functions of molecular materials emerge from intermolecular interactions and associated nanoscale structure and morphology. However, competing phases, defects, and disorder give rise to confinement and many-body localization of the associated wavefunction, disturbing the performance of the material. Here, we employ vibrational excitons as a sensitive local probe of intermolecular coupling in hyperspectral infrared scattering scanning near-field optical microscopy (IR s-SNOM) with complementary small-angle X-ray scattering to map multiscale structure from molecular coupling to long-range order. In the model organic electronic material octaethyl porphyrin ruthenium(II) carbonyl (RuOEP), we observe the evolution of competing ordered and disordered phases, in nucleation, growth, and ripening of porphyrin nanocrystals. From measurement of vibrational exciton delocalization, we identify coexistence of ordered and disordered phases in RuOEP that extend down to the molecular scale. Even when reaching a high degree of macroscopic crystallinity, identify significant local disorder with correlation lengths of only a few nanometers. This minimally invasive approach of vibrational exciton nanospectroscopy and -imaging is generally applicable to provide the molecular-level insight into photoresponse and energy transport in organic photovoltaics, electronics, or proteins.
        Cover page: Vibrational exciton nanoimaging of phases and domains in porphyrin nanocrystals
        • Article
        • Peer Reviewed
        Advanced Light Source (2018)
        Optical resonators can enhance light-matter interaction, modify intrinsic molecular properties such as radiative emission rates, and create new molecule-photon hybrid quantum states. To date, corresponding implementations are based on electronic transitions in the visible spectral region with large transition dipoles yet hampered by fast femtosecond electronic dephasing. In contrast, coupling molecular vibrations with their weaker dipoles to infrared optical resonators has been less explored, despite long-lived coherences with 2 orders of magnitude longer dephasing times. Here, we achieve excitation of molecular vibrations through configurable optical interactions of a nanotip with an infrared resonant nanowire that supports tunable bright and nonradiative dark modes. The resulting antenna-vibrational coupling up to 47 ± 5 cm-1 exceeds the intrinsic dephasing rate of the molecular vibration, leading to hybridization and mode splitting. We observe nanotip-induced quantum interference of vibrational excitation pathways in spectroscopic nanoimaging, which we model classically as plasmonic electromagnetically induced scattering as the phase-controlled extension of the classical analogue of electromagnetically induced transparency and absorption. Our results present a new regime of IR spectroscopy for applications of vibrational coherence from quantum computing to optical control of chemical reactions.
          Cover page: Nanoimaging and Control of Molecular Vibrations through Electromagnetically Induced Scattering Reaching the Strong Coupling Regime
          • Article
          • Peer Reviewed
          UC Irvine Previously Published Works (2019)
          ALG11-Congenital Disorder of Glycosylation (ALG11-CDG, also known as congenital disorder of glycosylation type Ip) is an inherited inborn error of metabolism due to abnormal protein and lipid glycosylation. We describe two unrelated patients with ALG11-CDG due to novel mutations, review the literature of previously described affected individuals, and further expand the clinical phenotype. Both affected individuals reported here had severe psychomotor disabilities and epilepsy. Their fibroblasts synthesized truncated precursor glycan structures, consistent with ALG11-CDG, while also showing hypoglycosylation of a novel biomarker, GP130. Surprisingly, one patient presented with normal transferrin glycosylation profile, a feature that has not been reported previously in patients with ALG11-CDG. Together, our data expand the clinical and mutational spectrum of ALG11-CDG.
            Cover page: ALG11-CDG syndrome: Expanding the phenotype.
            • Article
            • Peer Reviewed
            LBL Publications (2020)
            Infrared (IR) spectroscopy has evolved into a powerful analytical technique to probe molecular and lattice vibrations, low-energy electronic excitations and correlations, and related collective surface plasmon, phonon, or other polaritonic resonances. In combination with scanning probe microscopy, near-field infrared nano-spectroscopy and -imaging techniques have recently emerged as a frontier in imaging science, enabling the study of complex heterogeneous materials with simultaneous nanoscale spatial resolution and chemical and quantum state spectroscopic specificity. Here, we describe synchrotron infrared nano-spectroscopy (SINS), which takes advantage of the low-noise, broadband, high spectral irradiance, and coherence of synchrotron infrared radiation for near-field infrared measurements across the mid- to far-infrared with nanometer spatial resolution. This powerful combination provides a qualitatively new form of broadband spatio-spectral analysis of nanoscale, mesoscale, and surface phenomena that were previously difficult to study with IR techniques, or even any form of micro-spectroscopy in general. We review the development of SINS, describe its technical implementations, and highlight selected examples representative of the rapidly growing range of applications in physics, chemistry, biology, materials science, geology, and atmospheric and space sciences.
              Cover page: Synchrotron infrared nano-spectroscopy and -imaging
              • Article
              • Peer Reviewed
              UC Davis Previously Published Works (2021)
              The mitotic spindle is resilient to perturbation due to the concerted, and sometimes redundant, action of motors and microtubule-associated proteins. Here, we utilize an inducible ectopic microtubule nucleation site in the nucleus of Saccharomyces cerevisiae to study three necessary steps in the formation of a bipolar array: the recruitment of the γ-tubulin complex, nucleation and elongation of microtubules (MTs), and the organization of MTs relative to each other. This novel tool, an Spc110 chimera, reveals previously unreported roles of the microtubule-associated proteins Stu2, Bim1, and Bik1, and the motors Vik1 and Kip3. We report that Stu2 and Bim1 are required for nucleation and that Bik1 and Kip3 promote nucleation at the ectopic site. Stu2, Bim1, and Kip3 join their homologs XMAP215, EB1 and kinesin-8 as promoters of microtubule nucleation, while Bik1 promotes MT nucleation indirectly via its role in SPB positioning. Furthermore, we find that the nucleation activity of Stu2 in vivo correlates with its polymerase activity in vitro. Finally, we provide the first evidence that Vik1, a subunit of Kar3/Vik1 kinesin-14, promotes microtubule minus end focusing at the ectopic site.
                Cover page: Microtubule-associated proteins and motors required for ectopic microtubule array formation in Saccharomyces cerevisiae
                • Article
                LBL Publications (2008)
                  Cover page: The Ultrafast Dynamics of Image Potential State Electrons at the Dimethylsulfoxide/Ag(111) Interface
                  • Article
                  • Peer Reviewed
                  UC Davis Previously Published Works (2018)
                  Phosphorylation modulates many cellular processes during cell cycle progression. The yeast centrosome (called the spindle pole body, SPB) is regulated by the protein kinases Mps1 and Cdc28/Cdk1 as it nucleates microtubules to separate chromosomes during mitosis. Previously we completed an SPB phosphoproteome, identifying 297 sites on 17 of the 18 SPB components. Here we describe mutagenic analysis of phosphorylation events on Spc29 and Spc42, two SPB core components that were shown in the phosphoproteome to be heavily phosphorylated. Mutagenesis at multiple sites in Spc29 and Spc42 suggests that much of the phosphorylation on these two proteins is not essential but enhances several steps of mitosis. Of the 65 sites examined on both proteins, phosphorylation of the Mps1 sites Spc29-T18 and Spc29-T240 was shown to be critical for function. Interestingly, these two sites primarily influence distinct successive steps; Spc29-T240 is important for the interaction of Spc29 with Spc42, likely during satellite formation, and Spc29-T18 facilitates insertion of the new SPB into the nuclear envelope and promotes anaphase spindle elongation. Phosphorylation sites within Cdk1 motifs affect function to varying degrees, but mutations only have significant effects in the presence of an MPS1 mutation, supporting a theme of coregulation by these two kinases.
                    Cover page: Key phosphorylation events in Spc29 and Spc42 guide multiple steps of yeast centrosome duplication
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                    • Peer Reviewed
                    UC San Francisco Previously Published Works (2014)
                    The use of in vivo Förster resonance energy transfer (FRET) data to determine the molecular architecture of a protein complex in living cells is challenging due to data sparseness, sample heterogeneity, signal contributions from multiple donors and acceptors, unequal fluorophore brightness, photobleaching, flexibility of the linker connecting the fluorophore to the tagged protein, and spectral cross-talk. We addressed these challenges by using a Bayesian approach that produces the posterior probability of a model, given the input data. The posterior probability is defined as a function of the dependence of our FRET metric FRETR on a structure (forward model), a model of noise in the data, as well as prior information about the structure, relative populations of distinct states in the sample, forward model parameters, and data noise. The forward model was validated against kinetic Monte Carlo simulations and in vivo experimental data collected on nine systems of known structure. In addition, our Bayesian approach was validated by a benchmark of 16 protein complexes of known structure. Given the structures of each subunit of the complexes, models were computed from synthetic FRETR data with a distance root-mean-squared deviation error of 14 to 17 Å. The approach is implemented in the open-source Integrative Modeling Platform, allowing us to determine macromolecular structures through a combination of in vivo FRETR data and data from other sources, such as electron microscopy and chemical cross-linking.
                      Cover page: Determining Protein Complex Structures Based on a Bayesian Model of in Vivo Förster Resonance Energy Transfer (FRET) Data*
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