Skip to main content
eScholarship
Open Access Publications from the University of California

Scholarly Works (4 results)

  • Thesis
  • Peer Reviewed
UC Riverside Electronic Theses and Dissertations (2016)

The research in this thesis illustrates how chemical shift (CS) and chemical shift anisotropy (CSA) give a detailed view into atomic and molecular structure. Through the collaborative approach of NMR crystallography, utilizing solid-state NMR, x-ray diffraction, and computational methods a deeper understanding of crystal structure and systematic motion is formed. This thesis in constructed in a linear fashion as to shown how more detailed information can be obtained via more complex methods, culminating in the application of all the methods presented within to describe the structure and mechanism of expansion of a the novel anthracene system 9-tertbutylantrhacene ester (9TBAE).

Utilizing the CS, which provides information about the local electronic structure, directed questions such as the structure or arrangement of atoms can be answered. In this thesis problems in which the CS is used to provide detailed information about the location or inclusion of specific atoms in a molecule’s crystal structure will be presented. As crystallographic information for structures with greater complexity is required, the CS alone may be unable to differentiate between multiple similar structures, requiring a method that provides even greater detail of the local electronic environment.

The CSA is capable of providing this greater detail by quantifying a molecule’s discrete orientations in the magnetic field. Obtaining CSA values is non-trivial, requiring the application of pulse sequences with significantly greater complexity than those required to obtain the isotropic CS. Utilizing the approaches of slow spinning, a modified TOSS-t1-DeTOSS sequence, and xCSA, CSA principle components are obtained for increasingly complex systems.

The presentation of these methods culminates in their application on 9TBAE to elucidate not only the molecular structure, but also the mechanism of expansion when 9TBAE nanorods are photoreacted. The data obtained shows the generation of new lattice orientations within the nanorod, and based on these observations, the nanorods expand not due to a change in the volume of the unit cell, but rather due to a rotation of the unit cells. These results demonstrated while most photomechanical materials rely on the generation of a mixed phase bimorph structure, reconfiguration of the product phase can likewise generate a large mechanical response.

    Cover page: Solid-State NMR Spectroscopy, Anisotropic Interactions, and the Elucidation of Molecular StructureCreative Commons 'BY' version 4.0 license
    • Article
    • Peer Reviewed
    UC Riverside Previously Published Works (2016)
    The performance of fragment-based ab initio(1)H, (13)C, (15)N and (17)O chemical shift predictions is assessed against experimental NMR chemical shift data in four benchmark sets of molecular crystals. Employing a variety of commonly used density functionals (PBE0, B3LYP, TPSSh, OPBE, PBE, TPSS), we explore the relative performance of cluster, two-body fragment, and combined cluster/fragment models. The hybrid density functionals (PBE0, B3LYP and TPSSh) generally out-perform their generalized gradient approximation (GGA)-based counterparts. (1)H, (13)C, (15)N, and (17)O isotropic chemical shifts can be predicted with root-mean-square errors of 0.3, 1.5, 4.2, and 9.8 ppm, respectively, using a computationally inexpensive electrostatically embedded two-body PBE0 fragment model. Oxygen chemical shieldings prove particularly sensitive to local many-body effects, and using a combined cluster/fragment model instead of the simple two-body fragment model decreases the root-mean-square errors to 7.6 ppm. These fragment-based model errors compare favorably with GIPAW PBE ones of 0.4, 2.2, 5.4, and 7.2 ppm for the same (1)H, (13)C, (15)N, and (17)O test sets. Using these benchmark calculations, a set of recommended linear regression parameters for mapping between calculated chemical shieldings and observed chemical shifts are provided and their robustness assessed using statistical cross-validation. We demonstrate the utility of these approaches and the reported scaling parameters on applications to 9-tert-butyl anthracene, several histidine co-crystals, benzoic acid and the C-nitrosoarene SnCl2(CH3)2(NODMA)2.
      Cover page: Benchmark fragment-based 1 H, 13 C, 15 N and 17 O chemical shift predictions in molecular crystals
      • Article
      • Peer Reviewed
      UC Riverside Previously Published Works (2016)
      Carbanionic intermediates play a central role in the catalytic transformations of amino acids performed by pyridoxal-5'-phosphate (PLP)-dependent enzymes. Here, we make use of NMR crystallography-the synergistic combination of solid-state nuclear magnetic resonance, X-ray crystallography, and computational chemistry-to interrogate a carbanionic/quinonoid intermediate analogue in the β-subunit active site of the PLP-requiring enzyme tryptophan synthase. The solid-state NMR chemical shifts of the PLP pyridine ring nitrogen and additional sites, coupled with first-principles computational models, allow a detailed model of protonation states for ionizable groups on the cofactor, substrates, and nearby catalytic residues to be established. Most significantly, we find that a deprotonated pyridine nitrogen on PLP precludes formation of a true quinonoid species and that there is an equilibrium between the phenolic and protonated Schiff base tautomeric forms of this intermediate. Natural bond orbital analysis indicates that the latter builds up negative charge at the substrate Cα and positive charge at C4' of the cofactor, consistent with its role as the catalytic tautomer. These findings support the hypothesis that the specificity for β-elimination/replacement versus transamination is dictated in part by the protonation states of ionizable groups on PLP and the reacting substrates and underscore the essential role that NMR crystallography can play in characterizing both chemical structure and dynamics within functioning enzyme active sites.
        Cover page: NMR Crystallography of a Carbanionic Intermediate in Tryptophan Synthase: Chemical Structure, Tautomerization, and Reaction Specificity
        • Article
        • Peer Reviewed
        UC Riverside Previously Published Works (2021)
        Crystals composed of photoreactive molecules represent a new class of photomechanical materials with the potential to generate large forces on fast timescales. An example is the photodimerization of 9-tert-butyl-anthracene ester (9TBAE) in molecular crystal nanorods that leads to an average elongation of 8%. Previous work showed that this expansion results from the formation of a metastable crystalline product. In this article, it is shown how a novel combination of ensemble oriented-crystal solid-state NMR, X-ray diffraction, and first principles computational modeling can be used to establish the absolute unit cell orientations relative to the shape change, revealing the atomic-resolution mechanism for the photomechanical response and enabling the construction of a model that predicts an elongation of 7.4%, in good agreement with the experimental value. According to this model, the nanorod expansion does not result from an overall change in the volume of the unit cell, but rather from an anisotropic rearrangement of the molecular contents. The ability to understand quantitatively how molecular-level photochemistry generates mechanical displacements allows us to predict that the expansion could be tuned from +9% to -9.5% by controlling the initial orientation of the unit cell with respect to the nanorod axis. This application of NMR-assisted crystallography provides a new tool capable of tying the atomic-level structural rearrangement of the reacting molecular species to the mechanical response of a nanostructured sample.
          Cover page: Bridging photochemistry and photomechanics with NMR crystallography: the molecular basis for the macroscopic expansion of an anthracene ester nanorod
          Top