Intramolecular conflict : conformation and self-assembly of architecturally complex macromolecules in solution

The solution behavior of linear polymer chains is well understood, having been the subject of intense study throughout the previous century. As plastics have become ubiquitous in everyday life, polymer science has grown into a major field of study. The conformation of a polymer in solution depends on the molecular architecture and its interactions with the surroundings. Developments in synthetic techniques have led to the creation of precision-tailored polymeric materials with varied topologies and functionalities. In order to design materials with the desired properties, it is imperative to understand the relationships between polymer architecture and their conformation and behavior. To meet that need, this thesis investigates the conformation and self-assembly of three architecturally complex macromolecular systems with rich and varied behaviors driven by the resolution of intramolecular conflicts. First we describe the development of a robust and facile synthetic approach to reproducible bottlebrush polymers (Chapter 2). The method was used to produce homologous series of bottlebrush polymers with polynorbornene backbones, which revealed the effect of side-chain and backbone length on the overall conformation in both good and theta solvent conditions (Chapter 3). The side-chain conformation was obtained from a series of SANS experiments and determined to be indistinguishable from the behavior of free linear polymer chains. Using deuterium-labeled bottlebrushes, we were able for the first time to directly observe the backbone conformation of a bottlebrush polymer which showed self-avoiding walk behavior. Secondly, a series of SANS experiments was conducted on a homologous series of Side Group Liquid Crystalline Polymers (SGLCPs) in a perdeuterated small molecule liquid crystal (5CB). Monodomain, aligned, dilute samples of SGLCP-b-PS block copolymers were seen to self-assemble into complex micellar structures with mutually orthogonally oriented anisotropies at different length scales (Chapter 4). Finally, we present the results from the first scattering experiments on a set of fuel-soluble, associating telechelic polymers. We observed the formation of supramolecular aggregates in dilute (≤0.5wt%) solutions of telechelic polymers and determined that the choice of solvent has a significant effect on the strength of association and the size of the supramolecules (Chapter 5). A method was developed for the direct estimation of supramolecular aggregation number from SANS data. The insight into structure-property relationships obtained from this work will enable the more targeted development of these molecular architectures for their respective applications.

Programming chemical kinetics: engineering dynamic reaction networks with DNA strand displacement

Over the last century, the silicon revolution has enabled us to build faster, smaller and more sophisticated computers. Today, these computers control phones, cars, satellites, assembly lines, and other electromechanical devices. Just as electrical wiring controls electromechanical devices, living organisms employ "chemical wiring" to make decisions about their environment and control physical processes. Currently, the big difference between these two substrates is that while we have the abstractions, design principles, verification and fabrication techniques in place for programming with silicon, we have no comparable understanding or expertise for programming chemistry.

In this thesis we take a small step towards the goal of learning how to systematically engineer prescribed non-equilibrium dynamical behaviors in chemical systems. We use the formalism of chemical reaction networks (CRNs), combined with mass-action kinetics, as our programming language for specifying dynamical behaviors. Leveraging the tools of nucleic acid nanotechnology (introduced in Chapter 1), we employ synthetic DNA molecules as our molecular architecture and toehold-mediated DNA strand displacement as our reaction primitive.

Abstraction, modular design and systematic fabrication can work only with well-understood and quantitatively characterized tools. Therefore, we embark on a detailed study of the "device physics" of DNA strand displacement (Chapter 2). We present a unified view of strand displacement biophysics and kinetics by studying the process at multiple levels of detail, using an intuitive model of a random walk on a 1-dimensional energy landscape, a secondary structure kinetics model with single base-pair steps, and a coarse-grained molecular model that incorporates three-dimensional geometric and steric effects. Further, we experimentally investigate the thermodynamics of three-way branch migration. Our findings are consistent with previously measured or inferred rates for hybridization, fraying, and branch migration, and provide a biophysical explanation of strand displacement kinetics. Our work paves the way for accurate modeling of strand displacement cascades, which would facilitate the simulation and construction of more complex molecular systems.

In Chapters 3 and 4, we identify and overcome the crucial experimental challenges involved in using our general DNA-based technology for engineering dynamical behaviors in the test tube. In this process, we identify important design rules that inform our choice of molecular motifs and our algorithms for designing and verifying DNA sequences for our molecular implementation. We also develop flexible molecular strategies for "tuning" our reaction rates and stoichiometries in order to compensate for unavoidable non-idealities in the molecular implementation, such as imperfectly synthesized molecules and spurious "leak" pathways that compete with desired pathways.

We successfully implement three distinct autocatalytic reactions, which we then combine into a de novo chemical oscillator. Unlike biological networks, which use sophisticated evolved molecules (like proteins) to realize such behavior, our test tube realization is the first to demonstrate that Watson-Crick base pairing interactions alone suffice for oscillatory dynamics. Since our design pipeline is general and applicable to any CRN, our experimental demonstration of a de novo chemical oscillator could enable the systematic construction of CRNs with other dynamic behaviors.

Comparative studies on parallel and antiparallel duplex and triplex DNA

Parallel strand models for base sequences d(A)(10). d(T)(10), d(AT)(5) . d(TA)(5), d(G(5)C(5)). d(C(5)G(5)), d(GC)(5) . d(CG)(5) and d(CTATAGGGAT). d(GATATCCCTA), where reverse Watson-Crick A-T pairing with two H-bonds and reverse Watson-Crick G-C pairing with one H-bond or with two H-bonds were adopted, and three models of d(T)(14). d(A)(14). d(T)(14) triple helix with different strand orientations were built up by molecular architecture and energy minimization. Comparisons of parallel duplex models with their corresponding B-DNA models and comparisons among the three triple helices showed: (i) conformational energies of parallel AT duplex models were a little lower, while for GC duplex models they were about 8% higher than that of their corresponding B-DNA models; (ii) the energy differences between parallel and B-type duplex models and among the three triple helices arose mainly from base stacking energies, especially for GC base pairing; (iii) the parallel duplexes with one H-bond G-C pairs were less stable than those with two H-bonds G-C pairs. The present paper includes a brief discussion about the effect of base stacking and base sequences on DNA conformations. (C) 1997 Academic Press Limited.

One-pot synthesis and characterization of hyperbranched poly(ester-amide)s from commercially available dicarboxylic acids and multihydroxyl secondary Amines

A convenient and cost-effective strategy for synthesis of hyperbranched poly(ester-amide)s from commercially available dicarboxylic acids (A(2)) and multihydroxyl secondary amine (CB2) has been developed. By optimizing the conditions of model reactions, the AB(2)-type intermediates were formed dominantly during the initial reaction stage. Without any purification, the AB(2) intermediate was subjected to thermal polycondensation in the absence of any catalyst to prepare the aliphatic and semiaromatic hyperbranched poly(ester-amide)s bearing multi-hydroxyl end-groups.

Study of morphology and phase diagram of the H-shaped (AC)B(CA) ternary block copolymers using self-consistent field theory

By using a combinatorial screening method based on the self-consistent field theory (SCFT) for polymer systems, the micro-phase morphologies of the H-shaped (AC)B(CA) ternary block copolymer system are studied in three-dimensional (3D) space. By systematically varying the volume fractions of the components A, B, and C, six triangle phase diagrams of this H-shaped (AC)B(CA) ternary block copolymer system with equal interaction energies among the three components are constructed from the weaker segregation regime to the strong segregation regime, In this study, thirteen 3D micro-phase morphologies for this H-shaped ternary block copolymer system are identified to be stable and seven 3D microphase morphologies are found to be metastable.

Facile syntheses and characterization of hyperbranched poly(ester-amide)s from commercially available aliphatic carboxylic anhydride and multihydroxyl primary amine

A new method for synthesis of novel hyperbranched poly(ester-amide)s from commercially available AA' and CBx type monomers has been developed on the basis of a series of model reactions. The hyperbranched poly(ester-amide)s with multihydroxyl end groups are prepared by thermal polycondensation of carboxyl anhydrides (AA') and multihydroxyl primary amine (CBx) without any catalyst and solvent. The reaction mechanism in the initial stage of polymerization was investigated with in situ H-1 NMR. In the initial stage of the reaction, primary amino groups of 2-amino-2-ethyl-1,3-propanediol (AEPO) or tris(hydroxymethyl)aminomethane (THAM) react rapidly with anhydride, forming an intermediate which can be considered as a new AB(x) type monomer. Further self-polycondensation reactions of the AB. molecules produce hyperbranched polymers. Analysis using H-1 and C-13 NMR spectroscopy revealed the degree of branching of the resulting polymers ranging from 0.36 to 0.55. These hyperbranched poly(ester-amide)s contain configurational isomers observed by C-13 and DEPT C-13 NMR spectroscopy, possess high molecular weights with broad distributions and display glass-transition temperatures (T(g)s) between 7 and 96 degreesC.

A self-consistent field theory study on the morphologies of linear ABCBA and H-shaped (AB)(2)C(BA)(2) block copolymers

By using a combinatorial screening method based on the self-consistent field theory, we investigate the equilibrium morphologies of linear ABCBA and H-shaped (AB)(2)C(BA)(2) block copolymers in two dimensions. The triangle phase diagrams of both block copolymers are constructed by systematically varying the volume fractions of blocks A, B, and C. In this study, the interaction energies between species A, B, and C are set to be equal. Four different equilibrium morphologies are identified, i.e., the lamellar phase (LAM), the hexagonal lattice phase (HEX), the core-shell hexagonal lattice phase (CSH), and the two interpenetrating tetragonal lattice phase (TET2). For the linear ABCBA block copolymer, the reflection symmetry is observed in the phase diagram except for some special grid points, and most of grid points are occupied by LAM morphology. However, for the H-shaped (AB)(2)C(BA)(2) block copolymer, most of the grid points in the triangle phase diagram are occupied by CSH morphology, which is ascribed to the different chain architectures of the two block copolymers. These results may help in the design of block copolymers with different microstructures.

Comparing the morphology and phase diagram of H-shaped ABC block copolymers and linear ABC block copolymers

By using a combinatorial screening method based on the self-consistent field theory (SCFT) for polymers, we have investigated the morphology of H-shaped ABC block copolymers (A(2)BC(2)) and compared them with those of the linear ABC block copolymers. By changing the ratios of the volume fractions of two A arms and two C arms, one can obtain block copolymers with different architectures ranging from linear block copolymer to H-shaped block copolymer. By systematically varying the volume fractions of block A, B, and C, the triangle phase diagrams of the H-shaped ABC block copolymer with equal interactions among the three species are constructed. In this study, we find four different morphologies ( lamellar phase ( LAM), hexagonal lattice phase ( HEX), core-shell hexagonal lattice phase (CSH), and two interpenetrating tetragonal lattice (TET2)). Furthermore, the order-order transitions driven by architectural change are discussed.

A Monte Carlo simulation for the micellization of ABC 3-miktoarm star terpolymers in a selective solvent

We have used Monte Carlo simulation to study the micellization of ABC 3-miktoarm star terpolymers in a selective solvent (good to A segment, bad to B and C segments). The simulation results reveal that the self-assembled morphology is determined by the block length, molecular architecture, terpolymer concentration and insolubility of insoluble block in the solvent. In dilute solution, symmetric terpolymers (N-B = N-C = 30) tend to aggregate into a novel wormlike pearl-necklace structure linked by an alternating arrangement of B and C spheres, whereas the asymmetric terpolymers (NB = 10, NC = 50) are likely to aggregate into spherical or cylindrical micelles (formed by C blocks) connected with some small B spheres, when the concentration of terpolymer is relatively low (chain number is 100). However, when the concentration of terpolymer is relatively high (chain number is 250), the symmetric terpolymers tend to aggregate into a netlike structure linked by an alternation of B and C spheres, whereas the asymmetric terpolymers are likely to aggregate into wormlike micelles (formed by C blocks) connected with some of small spheres (formed by B blocks). Moreover, when the insolubility of insoluble block in the solvent is weak, the insoluble blocks aggregate into some incompact micelles.

Synthesis and characterization of hyperbranched aromatic poly(ether imide)s

The four AB(2) monomers, N-[3- or 4-bis(4-hydroxyphenyl)toluoyl]-4-chlorophthalimide and N-{3- or 4-[1,1-bis(4-hydroxyphenyl)]ethylphenyl}-4-chlorophthalimides, were prepared and used for synthesis of hyperbranched poly(ether imide)s bearing hydroxyl end groups. These hyperbranched poly(ether imide)s had moderate molecular weights with broad distributions and showed glass-transition temperatures (Tgs) between 177 and 230 degreesC. The thermogravimetric analytic measurement revealed the decomposition temperature at 5% weight-loss temperatures (T-d(5%)) ranging from 240 to 281 degreesC. Analysis using H-1 NMR spectroscopy revealed the four types of hyperbranched poly(ether imide)s to have similar degrees of branching (ca. 60%). These polymers were modified by acylation or nucleophilic substitution reaction at the hydroxyl end groups. The conversion effectiveness depended on the type of modification reaction, modifier, and reaction conditions. The thermal stability and solubility of hyperbranched poly(ether imide)s were improved by the modification of the end groups.

Synthesis and characterization of hyperbranched aromatic poly(ester-imide)s

The synthesis and characterization of hyperbranched aromatic poly(ester-imide)s are described. A variety of AB(2) monomers, N-[3- or 4-bis(4-acetoxyphenyl)toluoyl]-4-carboxyl-phthalimide and N-{3- or 4-[1,1-bis(4-acetooxyphenyl)]ethylphenyl}-4-carboxy phthalimides were prepared starting from condensation of nitrobenzaldehydes or nitroacetophenones with phenol and used for synthesis of hyperbranched poly(ester-imide)s containing terminal acetyl groups by transesterification reaction. These hyperbranched poly(ester-imide)s were produced with weight-average molecular weight of up to 6.87 g/mol. Analysis of H-1 NMR and C-13 NMR spectroscopy revealed the structure of the four hyperbranched poly(ester-imide)s. These hyperbranched poly(ester-imide)s exhibited excellent solubility in a variety of solvents such as N,N-dimethylacetamide, dimethyl sulfoxide, and tetrahydrofuran and showed glass-transition temperatures between 217 and 255 degreesC. The thermogravimetric analytic measurement revealed the decomposition temperature at 10% weight-loss temperature (T-d(10)) ranging from 365 to 416 degreesC in nitrogen.

Investigation into self-assembled monolayers of a polyether dendron thiol: Chemisorption, kinetics, and patterned surface

Different sizes of Frechet-type dendrons with a thiol group at the focal point were synthesized, well characterized, and used as building blocks for the preparation of self-assembled monolayers (SAMs) on metal surfaces. From the studies of the kinetic process of dendron thiol self-assembling on gold, it is shown that the dendron thiol assembling proceeds with different adsorption rates depending on the assembly time. In contrast to normal alkanethiols forming highly molecular structures on metal surfaces, the SAMs of polyether dendron form patterned surfaces with nanometer-sized features and in long-range order. It is found that the patterned stripes are closely related to the size of the dendron, and the patterned stripes can be improved by thermal annealing.

Rapid synthesis of polyester dendrimers

Aryl polyester dendrimers and dendrons have been prepared by using 'branched monomer strategies', in which the surface and the focal point of the multi-branched monomer have been protected with two different kinds of protective group. The protective group for the focal point was stable during deprotection of the surface. Different wedges could be attached to the multi-branched monomers to form large dendrons whilst active dendrons could be attached to different cores to form various dendrimers with different wedges and different cores.

Expression of muscle-related genes and two MyoD genes during amphioxus notochord development

The notochord is one of the diagnostic features of the phylum Chordata. Despite the similarities in the early morphogenetic patterns of the notochords of various chordates, they are strikingly distinct from one another at the histological level. The amphioxus notochord is one example of an evolutionary novelty because it is made up of muscle cells. Our previous expressed sequence tag analysis, targeting messenger RNAs expressed in the adult amphioxus notochord, demonstrated that many muscle-related genes are expressed there. To characterize amphioxus notochord cells and to gain insights into the myogenic program in the notochord, we determined the spatial and temporal expression patterns of these muscle-related genes during amphioxus development. We found that BbNA1 (notochord actin), Amphi-Trop I (troponin I), Amphi-TPmyosin (tropomyosin), Amphi-MHC2 (myosin heavy chain), Amphi-nMRLC (notochord-specific myosin regulatory light chain), AmphinTitin/MLCK (notochord-specific titin/myosin light chain kinase), Amphi-MLP/CRP3 (muscle LIM protein), and Amphi-nCalponin (notochord-specific calponin) are expressed with characteristic patterns in notochord cells, including the central cells, dorsally located cells, and ventrally located cells, suggesting that each notochord cell has a unique molecular architecture that may reflect its function. In addition, we characterized two MyoD genes (Amphi-MyoD1 and Amphi-MyoD2) to gain insight into the genetic circuitry governing the formation of the notochord muscle. One of the MyoD genes (Amphi-MyoD2) is expressed in the central notochord cells, and the coexistence of Amphi-MyoD2 transcripts along with the Amphi-MLP/CRP3 transcripts implies the participation of Amphi-MyoD2 in the myogenic program in the notochord muscle.

Neighboring Group-Controlled Hydrolysis: Towards “Designer” Drug Release Biomaterials

To give the first demonstration of neighboring group-controlled drug delivery rates, a series of novel, polymerizable ester drug conjugates was synthesized and fully characterized. The monomers are suitable for copolymerization in biomaterials where control of drug release rate is critical to prophylaxis or obviation of infection. The incorporation of neighboring group moieties differing in nucleophilicity, geometry, and steric bulk in the conjugates allowed the rate of ester hydrolysis, and hence drug liberation, to be rationally and widely controlled. Solutions (2.5 x 10-5 mol dm-3) of ester conjugates of nalidixic acid incorporating pyridyl, amino, and phenyl neighboring groups hydrolyzed according to first-order kinetics, with rate constants between 3.00 ( 0.12 10-5 s -1 (fastest) and 4.50 ( 0.31 10- 6 s-1 (slowest). The hydrolysis was characterized using UV-visible spectroscopy. When copolymerized with poly(methyl methacrylate), free drug was shown to elute from the resulting materials, with the rate of release being controlled by the nature of the conjugate, as in solution. The controlled molecular architecture demonstrated by this system offers an attractive class of drug conjugate for the delivery of drugs from polymeric biomaterials such as bone cements in terms of both sustained, prolonged drug release and minimization of mechanical compromise as a result of release. We consider these results to be the rationale for the development of 'designer' drug release biomaterials, where the rate of required release can be controlled by predetermined molecular architecture.