Assembly of Linked Nanocrystal Colloids by Reversible Covalent Bonds

The use of dynamically bonding molecules designed to reversibly link solvent-dispersed nanocrystals (NCs) is a promising strategy to form colloidal assemblies with controlled structure and macroscopic properties. In this work, tin-doped indium oxide NCs are functionalized with ligands that form reversible covalent bonds with linking molecules to drive assembly of NC gels. We monitor gelation using small angle X-ray scattering and characterize how changes in the gel structure affect infrared optical properties arising from the localized surface plasmon resonance of the NCs. The assembly is reversible because of the designed linking chemistry, and we disassemble the gels using two strategies: addition of excess NCs to change the ratio of linking molecules to NCs and addition of a capping molecule that displaces the linking molecules. The assembly behavior is rationalized using a thermodynamic perturbation theory to compute the phase diagram of the NC–linking molecule mixture. Coarse-grained molecular dynamics simulations reveal the competition between loop and bridge linking motifs essential for understanding NC gelation. This combined experimental, computational, and theoretical work provides a platform for controlling and designing the properties of reversible colloidal assemblies that incorporate NC and solvent compositions beyond those compatible with other contemporary (e.g, DNA-based) linking strategies.We would like to acknowledge the UT Mass Spectrometry Facility for their instrumental help and the UT NMR facilities for equipment use and assistance: NIH Grant Number 1 S10 OD021508-01. This work was primarily supported by the National Science Foundation through the Center for Dynamics and Control of Materials: an NSF Materials Research Science and Engineering Center (NSF MRSEC) under Cooperative Agreement DMR-1720595. This work was also supported by NSF Graduate Research Fellowships DGE-1610403 (M.N.D. and S.V.), an Arnold O. Beckman Postdoctoral Fellowship (Z.M.S.), NSF (CHE- 1905263), and the Welch Foundation (F-1848 and F-1696). E.V.A. acknowledges support from the Welch Regents Chair (F-0046). We acknowledge the Texas Advanced Computing Center (TACC) at The University of Texas at Austin for providing HPC resources.Center for Dynamics and Control of Material

The emerging landscape of single-molecule protein sequencing technologies

Single-cell profiling methods have had a profound impact on the understanding of cellular heterogeneity. While genomes and transcriptomes can be explored at the single-cell level, single-cell profiling of proteomes is not yet established. Here we describe new single-molecule protein sequencing and identification technologies alongside innovations in mass spectrometry that will eventually enable broad sequence coverage in single-cell profiling. These technologies will in turn facilitate biological discovery and open new avenues for ultrasensitive disease diagnostics.This Perspective describes new single-molecule protein sequencing and identification technologies alongside innovations in mass spectrometry that will eventually enable broad sequence coverage in single-cell proteomics.</p

Mechanistic, Synthetic and Theoretical Studies of High Valent Metallacycles and metal Alkylidenes

The primary focus of this thesis is on the mechanism of olefin metathesis and ring opening metathesis polymerizations. In addition, several reactions of metal alkylidenes and metallacycles which are not traditionally viewed as part of the olefin metathesis reaction are presented. Olefin metathesis involves the 2+2 cycloaddition of metal alkylidenes with olefins and the 2+2 cycloreversion of metallacyclobutanes. These reactions are becoming common place in organometallic reaction mechanisms and join the traditional oxidative additions, reductive eliminations, ligand substitutions, intramolecular insertions, nucleophilic attacks on coordinated ligands and ligand fluxtionalities as the commonly sited organometallic reactions. A current goal of organometallic chemistry is to understand the influence of oxidation state, electron count, ligand sterics, ligand electronics and substituent effects upon each of these reactions. The knowledge of mechanisms is essential to be able to understand and rationally manipulate chemical processes. The knowledge also allows for the capability to catagorize mechanistic theories as an organizing device for understanding organometallic chemistry as a whole. Organometallic chemistry, however, is not easily catagorized due to the large complexity of bonding types and structures that inorganic chemistry produces. The work in this thesis has utilized some techniques of physical organic chemistry to study mechanisms and reactive intermediates. These techniques include kinetics, substituent effects, isotope effects, stereochemical studies and theoretical calculations. Organic chemistry has greatly benefited from the advent and subsequent development of the pericyclic theory for the understanding of covalent bonding, frontier orbitals and symmetry. These same notions have met with various levels of success in organometallic chemistry. The success of theoretical studies in organometallic systems very often depends upon the level of electron correlation and the extent to which the exchange integrals are calculated. The theory presented in this thesis utilizes a fully ab initio method with electron correlation. The structure of organometallic complexes is examined as a function of the nodal planes of the individual metal ligand bonds and their influence on the bonding of other ligands within the same complex. In addition, reactivity of the complexes are probed as a function of the symmetry and energy of the bonding and empty orbitals. In chapter one, data and speculations relating to the mechanism of cleavage of titanocene metallacyclobutanes is presented. The reactive intermediate is postulated to be a titanocene methylidene-olefin adduct. Chapter two further expands upon these mechanistic studies by presenting the kinetics and polydispersities of the ring opening metathesis polymerizations of slightly strained olefins. Chapter three presents work which utilizes ab initio electronic structure theory calculations to determine the energetics of the 2+2 cycloaddition of molybdenum alkylidene and imido complexes with olefins. In chapters 4, 5 and 6, reactivity different than the normal cycloadditions of metal alkylidenes and cycloreversions of metallacycles is examined. In chapter 4, an electron transfer mechanism for the reaction of titanocene methylidene with activated halides is presented. Chapter 5 discusses the reactivity of titanocene methylidene with inorganic carbonyls. The titanocene methylidene does not perform methylene transfer as is seen with organic carbonyls, but instead, the resultant oxametallacycle rearranges to yield a titanocene ketene complex. Finally, in chapter six, ab initio electronic structure theory calculations are again presented. They are used to explore the interconversion of a metallacyclobutadiene to a metallatetrahedrane. The two complexes are found to be energetically similar due to a balance between the strength of σ and π bonds and the role of strain and resonance effects. Each chapter was written as an individual study and thus includes an Abstract, Introduction, Results and Discussion section and a Summary or Conclusion. Thus, this thesis presents work that attempts to add a little more knowledge to the mechanistic and theoretical understanding of organometallic reaction mechanisms.</p

The Recognition of Viologen Derivatives in Water by N-Alkyl Ammonium Resorcinarene Chlorides

Three water-soluble N-alkyl ammonium resorcinarene chlorides decorated with terminal hydroxyl groups at the lower rims were synthesized and characterized. The receptors were decorated at the upper rim with either terminal hydroxyl, rigid cyclohexyl, or flexible benzyl groups. The binding affinities of these receptors toward three viologen derivatives, two of which possess an acetylmethyl group attached to one of the pyridine nitrogens, in water were investigated via 1H NMR spectroscopy, fluorescence spectroscopy, and isothermal titration calorimetry (ITC). ITC quantification of the binding process gave association constants of up to 103 M-1. Analyses reveal a spontaneous binding process which are all exothermic and are both enthalpy and entropy driven.peerReviewe

Modeling Boronic Acid Based Flourescent Saccharide Sensors: Computational Investigation of d-Fructose Binding to Dimethylaminomethylphenylboronic Acid (DMPBA)

Designing organic saccharide sensors for use in aqueous solution is a non-trivial endeavor. Incorporation of hydrogen bonding groups on a sensor’s receptor unit to target saccharides is an obvious strategy, but not one that is likely to ensure analyte-receptor interactions over analyte-solvent or receptor-solvent interactions. Phenylboronic acids are known to reversibly and covalently bind saccharides (diols in general) with highly selective affinity in aqueous solution. Therefore, recent work has sought to design such sensors and understand their mechanism for allowing fluorescence with bound saccharides. In past work, binding orientations of several saccharides were determined to dimethylaminomethylphenylboronic acid (DMPBA) receptors with an anthracene fluorophore, however the binding orientation of D-fructose to such a sensor could not be determined. In this work, we investigate the potential binding modes by generating 20 possible bidentate and six possible tridentate modes between fructose and DMPBA, a simplified receptor model. Gas phase and implicit solvent geometry optimizations, with a myriad functional/basis set pairs, were carried out to identify the lowest energy bidentate and tridentate binding modes of D-fructose to DMPBA. An interesting hydrogen transfer was observed during selected bidentate gas phase optimizations, this transfer suggests a strong sharing of the hydrogen atom between the boronate hydroxyl and amine nitrogen

Assembly of Linked Nanocrystal Colloids by Reversible Covalent Bonds

The use of dynamically bonding molecules designed to reversibly link solvent-dispersed nanocrystals (NCs) is a promising strategy to form colloidal assemblies with controlled structure and macroscopic properties. In this work, tin-doped indium oxide NCs are functionalized with ligands that form reversible covalent bonds with linking molecules to drive assembly of NC gels. We monitor gelation using small angle X-ray scattering and characterize how changes in the gel structure affect infrared optical properties arising from the localized surface plasmon resonance of the NCs. The assembly is reversible because of the designed linking chemistry, and we disassemble the gels using two strategies: addition of excess NCs to change the ratio of linking molecules to NCs and addition of a capping molecule that displacesthe linking molecules. The assembly behavior is rationalized using a thermodynamic perturbation theory to compute the phase diagram of the NC–linking molecule mixture. Coarse-grained molecular dynamics simulations reveal the competition between loop and bridge linking motifs essential for understanding NC gelation. This combined experimental, computational, and theoretical work provides a platform for controlling and designing the properties of reversible colloidal assemblies that incorporate NC and solvent compositions beyond those compatible with other contemporary (e.g, DNA-based) linking strategies.</div