Polyhomologation is a powerful method to prepare polyethylene-based materials with controlled molecular weight, topology and composition. This dissertation focuses on the discovery of new synthetic routes to prepare polyethylene-based macromolecular architectures by combining polyhomologation with highly orthogonal and efficient linking reactions such as Diels Alder, copper-catalyzed azide-alkyne cycloaddition (CuAAC), and Glaser. Taking advantage of functionalized polyhomologation initiators, as well as of the efficient coupling chemistry, we were able to synthesize various types of polymethylene (polyethylene)-based materials with complex architectures including linear co/terpolymers, graft terpolymers, and tadpole copolymers. In the first project, a facile synthetic route towards well-defined polymethylene-based co/terpolymers, by combining the anthracene/maleimide Diels–Alder reaction with polyhomologation, is presented. For the synthesis of diblock copolymers the following approach was applied: (a) synthesis of α-anthracene-ω-hydroxy-polymethylene by polyhomologation using tri (9 anthracene-methyl propyl ether) borane as the initiator, (b) synthesis of furan-protected-maleimide-terminated poly(ε-caprolactone) or polyethylene glycol and (c) Diels–Alder reaction between anthracene and maleimide-terminated polymers. In the case of triblock terpolymers, the α-anthracene-ω-hydroxy polymethylene was used as a macroinitiator for the ring-opening polymerization of D, L-lactide to afford an anthracene-terminated PM-b-PLA copolymer, followed by the Diels–Alder reaction with furan-protected maleimide-terminated poly (ε-caprolactone) or polyethylene glycol to give the triblock terpolymers. The synthetic methodology is general and potentially applicable to a range of polymers. The coupling reaction applied in the second project of this dissertation was copper-catalyzed “click” cycloaddition of azides and alkynes (CuAAC). Novel well-defined polyethylene-based graft terpolymers were synthesized via the “grafting onto” strategy by combining nitroxide-mediated radical polymerization (NMP), polyhomologation and copper(I)-catalyzed azide–alkyne cycloaddition (CuAAC). Three steps were involved in this approach: (a) synthesis of alkyne-terminated polyethylene-b-poly(ε-caprolactone) (PE-b-PCL-alkyne) block copolymers (branches) by esterification of PE-b-PCL-OH with 4-pentynoic acid; the PE-b-PCL-OH was obtained by polyhomologation of dimethylsulfoxonium methylide to afford PE-OH, followed by ring opening polymerization of ε-caprolactone using PE-OH as a macroinitiator (b) synthesis of random copolymers of styrene (St) and 4-chloromethylstyrene (4-CMS) with various CMS contents, by nitroxide-mediated radical copolymerization (NMP), and conversion of chloride to azide groups by reaction with sodium azide (NaN3) (backbone) and (c) “click” linking reaction to afford the PE-based graft terpolymers. This method opens up new routes for the creation of polyethylene-based graft terpolymers by a combination of polyhomologation, NMP and CuAAC. The third project deals with the synthesis of polyethylene-based tadpole copolymer (c-PE)-b-PSt. Cyclic polymers represent a class of understudied polymer architecture mainly due to the synthetic challenges. Within this dissertation, a new method was reported for the synthesis of cyclic polymers in exceptionally high purity and yield. The main approaches to synthesize macrocycles are based on the end-to-end ring-closure (coupling) of homo difunctional linear precursors under high dilution. Our process relies on the preparation of well-defined linear α, ω-dihydroxy polyethylene and a bromide group at the middle of the chain through polyhomologation of ylide using functionalized initiator, followed by ATRP of styrene monomer. The two hydroxyl groups were transformed into alkyne groups, via esterification reaction, followed by Glaser reaction between terminal alkynes to afford the tadpole-shaped copolymers with PE ring and PSt tail. In Our PhD research, we also studied the self-assembly properties of the amphiphilic copolymers PM-b-PEG in aqueous solution by DLS, Cryo-TEM, and AFM. Furthermore, the critical micelle concentration (CMC) was estimated from the intensity of the pyrene emissions by the fluorescence technique. All the findings presented in this dissertation are emphasizing the utility of polyhomologation for the synthesis of well-defined polyethylene-based complex macromolecular architectures, almost impossible through other kind of polymerization including the catalytic polymerization of ethylene.

Proteins that have been modified by attaching them to a surface or to a polyethylene glycol (PEG) molecule can see many uses in therapeutics and diagnostics -- these unique proteins are called protein devices. Current techniques can perform these functionalizations at a specific residue on the protein, but what remains is identifying what happens to protein structure when mutated, and where to perform the attachment. Both of these issues can be examined using molecular dynamic (MD) simulations. Currently, simulations of the unnatural amino acid (uAA) mutations necessary for protein device functionalization cannot be executed, and full-protein screens of all possible protein device models have never been attempted. Results from this dissertation first employs a new model for simulating PEGylated protein devices building off of previous studies that explore where to attach functional groups. Next, many current assumptions in the community regarding ideal attachment sites are examined. Some of these factors include primary chain location, amino acid type, solvent accessibility, and secondary structure. The focus then turns to novel tertiary structure factors that could influence how well attachment locations affect overall protein device stability. The usefulness of each factor is analyzed to show what factors provided the best predictive power for a site's performance in the screen. A general heuristic is given that could aid in future screens of other protein devices to reduce compute time and quickly identify sites for experimental examination. To explore uAA mutation effects on protein structure, parameters are developed for linear moiety R-groups present in these novel amino acids. The CHARMM and CGenFF force fields currently lack parameters for most linear-angle molecular moieties. This work proposes a method that (1) develops CHARMM parameters for four small molecules that contain terminal azido and alkynyl groups using ffTK, (2) addresses linearity issues, and (3) validates ffTK results via in silico MD simulation. Dihedral analysis examines the linear-angle-containing dihedrals and compares methods for the moiety parameterization. Next, the small molecule parameters are combined with CGenFF to generate parameters for unnatural amino acid MD simulation in a protein. Finally, validation confirms the parameters derived in this work to appropriately simulate unnatural amino acids and small molecules with azido and alkynyl groups.

Proteins that have been modified by attaching them to a surface or to a polyethylene glycol (PEG) molecule can see many uses in therapeutics and diagnostics -- these unique proteins are called protein devices. Current techniques can perform these functionalizations at a specific residue on the protein, but what remains is identifying what happens to protein structure when mutated, and where to perform the attachment. Both of these issues can be examined using molecular dynamic (MD) simulations. Currently, simulations of the unnatural amino acid (uAA) mutations necessary for protein device functionalization cannot be executed, and full-protein screens of all possible protein device models have never been attempted. Results from this dissertation first employs a new model for simulating PEGylated protein devices building off of previous studies that explore where to attach functional groups. Next, many current assumptions in the community regarding ideal attachment sites are examined. Some of these factors include primary chain location, amino acid type, solvent accessibility, and secondary structure. The focus then turns to novel tertiary structure factors that could influence how well attachment locations affect overall protein device stability. The usefulness of each factor is analyzed to show what factors provided the best predictive power for a site's performance in the screen. A general heuristic is given that could aid in future screens of other protein devices to reduce compute time and quickly identify sites for experimental examination. To explore uAA mutation effects on protein structure, parameters are developed for linear moiety R-groups present in these novel amino acids. The CHARMM and CGenFF force fields currently lack parameters for most linear-angle molecular moieties. This work proposes a method that (1) develops CHARMM parameters for four small molecules that contain terminal azido and alkynyl groups using ffTK, (2) addresses linearity issues, and (3) validates ffTK results via in silico MD simulation. Dihedral analysis examines the linear-angle-containing dihedrals and compares methods for the moiety parameterization. Next, the small molecule parameters are combined with CGenFF to generate parameters for unnatural amino acid MD simulation in a protein. Finally, validation confirms the parameters derived in this work to appropriately simulate unnatural amino acids and small molecules with azido and alkynyl groups.

Successful enzyme catalysis depends on many noncovalent interactions between the enzyme, cofactors, and substrate that poise the system to access a productive transition state. Motions on a variety of timescales contribute to this, but some controversy exists surrounding the role of ultrafast dynamics on catalysis. Site-specific 2D IR spectroscopy using probes of vibrational dynamics provides the opportunity to explore ultrafast motions in an enzyme active site owing to the technique’s spatial and temporal resolution. In this work, a series of aryl-azide vibrational labels were assessed using a variety of 2D IR techniques for their sensitivity to solvent and energy transfer processes, and their ability to be adapted to experiments in biomacromolecules. One of these labels, 4-azido-N-phenylmaleimide, is a substrate analog for the promiscuous ene-reductase from Pyrococcus horikoshii (PhENR). The label was covalently attached in two orientations in the enzyme active site, occupying the same position as native substrates based on X-ray crystallography and molecular dynamics simulations. FTIR and 2D IR spectroscopy were used to identify close-lying conformational states based on the strong anharmonic coupling of the label, revealing that the active site itself modulates the probe’s internal vibrational coupling. More commonly used analogous aryl-nitrile labels, however, were not sensitive to such small structural and lineshape changes. This demonstrates the importance of thoughtful label design to maximize the amount of information that can be gleaned from 2D IR studies. Using the methods herein—both spectroscopic and biochemical—provides a strategy for probing ultrafast motions that could possibly be catalytically relevant.

This thesis focuses on developing a new photocoupling surface, base on polyallyamine (PAAm), to increase the efficiency of the photocoupling agent perfluorophenyl azide (PFPA) in the immobilization of nanoparticles, carbohydrates and graphene. Extensive studies have been carried out in our lab on the covalent immobilization of polymers and graphene using PFPA-functionalized surfaces. Here we show that PAAm-based PFPA surface can be used to efficiently immobilize not only graphene and polymers but also nanomaterials and small molecules. This was accomplished by first silanizing silicon wafers with PFPA-silane followed by attaching a thin film of PAAm by UV radiation. Treating the PAAm surface with N-hydroxysuccinimide-derivatized PFPA (PFPA-NHS) yielded the PAAm-PFPA surface. The functionalized surfaces were characterized by ellipsometry (layer thickness), contact angle (surface tension), and ATR-FTIR. The PAAm surface was further characterized by determining the density of amino groups on the surface. The PAAm-PFPA surfaces were subsequently used to covalently immobilize polymers, nanomaterials, carbohydrates and graphene by a simple procedure of coating the molecules or materials on the PAAm-PFPA surface followed by UV irradiation. The resulting surfaces were characterized using ellipsometry, AFM, optical microscopy. The attached carbohydrates were further evaluated using lectins, i.e., carbohydrate-binding proteins.

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