Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemical Engineering, 2008. / Includes bibliographical references. / The goal of this work was to develop a detailed understanding of carbon-nitrogen (C-N) bond-forming reactions of amines carried out in supercritical and expanded-liquid carbon dioxide (CO2) media. Key motivations behind this study were the importance of nitrogen-containing compounds in the pharmaceutical and fine chemical industries and a growing commercial interest in utilizing environmentally-friendly syntheses and processing with cost-efficient, green solvents. The thermodynamics and reaction engineering characteristics associated with the synthesis of several model C-N bond-forming reactions were examined both experimentally and theoretically. Operating conditions and engineering correlations were identified that will facilitate process scale-up and potential commercialization of these and other fundamentally-important CO2-based processes. Amine chemistry in CO2-based media was complicated by the facility of nucleophilic amines to react with carbon dioxide to form carbamic acids, which sometimes interfered with desired reaction pathways. Experimental observations and a complimentary ab initio quantum chemical calculation study revealed that carbamic acid formation was suppressed when adding bulky N-substituents to primary amines and when operating at low pressures and/or high temperatures. With a firm understanding of amine-CO2 chemistry, we developed a synthetic protocol that produced classes of pharmacologically-significant nitrogen heterocycles known as tetrahydroisoquinolines and tetrahyrdo-carbolines. Our method involved (1) the in situ carbamation of amines from their reaction with carbon dioxide and a dialkyl carbonate and (2) the Pictet-Spengler cyclization of these carbamates by their reaction with an aldehyde in the presence of acid. The conversion of amines to their carbamate derivatives offered suitable N-protection against carbamic acid formation. / (cont.) For nearly all reactions studied, the Pictet-Spengler step proceeded nearly quantitatively. The efficiency of amine carbamation via the CO2/dimethyl (cont) carbonate (DMC) reaction system was highly sensitive to process operating conditions. Phase behavior, amine conversion, and carbamate yield and selectivity all varied appreciably with temperature, pressure, and amine feed concentration. For example at 130 oC, carbamate selectivity increased from 50 to 75% with increasing pressure up to the mixture critical pressure of the CO2/DMC binary system (P, mixco2/DMC ). Selectivity decreased to 55% for ... mix of the entire reaction system (P,mixsystem). Above Pmixsytem,, selectivity increased to 80%. At 105 bar, decreasing temperature from 150 to 100 oC led to an increase in carbamate selectivity by 25%. Finally, decreasing the amine feed concentration from 4 to 1 M resulted in an increase in carbamate selectivity by 30%. Mixture critical pressures (Pc,mix) and liquid-phase densities, species concentrations, and volume expansion were measured for the CO2/DMC system over a wide range of operating conditions. Importantly, we developed an equation-of-state (EOS) model and several empirical engineering correlations that were used to predict vapor-liquid equilibrium properties in P-T-xi regimes for which data were not available. Deviations from experimental data and empirical correlations were typically less than 9%. Pmix CO2/DMC data were measured for 37 < T < 150 oC and were correlated well by a third-order polynomial. Liquid-phase carbon dioxide concentration ([CO2]I) varied linearly with pressure for 37 to 100 oC. Liquid-phase volume expansion (AV/) measured for the same temperature range increased exponentially with increasing pressure. Maximum-possible values of [C02]1 and AVI decreased with increasing temperature. [CO211 was 2 to 4 times larger than that of pure CO2 when compared at the same Tand P. / (cont.) We also developed and optimized a practical and high atom-economy C02-based synthetic protocol that afforded amides via the amination of ketenes generated in situ from the thermolysis of 1-alkynyl ethers. A variety of amines, 1-alkynyl ethers, and ketenes participated efficiently in the reaction and produced amides in yields comparable to those of conventional solvents. Experimental phase partitioning observations agreed well with EOS-based predictions and aided in the determination of process operating conditions. Amide yield varied in the order secondary > branched-primary > primary amines, which suggested that carbamic acid formation may have diminished reaction efficiency. t-butoxy-substituted 1-alkynyl ethers produced ketenes at rates faster than ethoxy-substituted ethers and allowed for a considerable reduction in operating temperature. Extension of the amide synthesis protocol to an intramolecular variant that afforded lactams resulted in a significant decrease in selectivity when compared to conventional solvents. We suspected that multi-phasic behavior led to this discrepancy and were able to increase selectivity by 25% using CO2/co-solvent mixtures. Finally, an ab initio quantum chemical kinetic model was developed and was capable of qualitatively predicting observed amide formation dynamics. Product selectivity and amine consumption rate predictions, for example, agreed well with experimental data. / by Rocco P. Ciccolini. / Ph.D.

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemical Engineering, 2013. / Cataloged from PDF version of thesis. / Includes bibliographical references (p. 102-107). / The control of crystallization steps is essential in the production of many materials in the pharmaceutical, materials, and chemical industries. Additionally, due to increasing costs of research and development, reductions in manufacturing costs by moving from batch to continuous manufacturing are necessary to sustain profitability of the pharmaceutical industry. Two different projects were researched to progress towards this goal. The first was the demonstration of a continuous manufacturing platform. The second goal was the development of new crystallization techniques. Two continuous crystallization processes were developed as part of a demonstration unit for continuous manufacturing of Aliskiren hemifumarate. The first process was an anti-solvent crystallization of an intermediate. The second process was a continuous reactive crystallization developed for the final product. The processes were able to crystallize the two compounds with both high yield (>90%) and purity (>99%). Population balance modeling was performed and experimental data were fit to the model to obtain kinetic parameters for crystal growth and nucleation for both systems. The models were used to optimize crystal purity and yield of the products. In addition, this thesis describes two separate projects involving spherical agglomerates. In the first study, acetaminophen was shown to crystallize significantly faster in the presence of spherical agglomerates of lactose than single crystal lactose. An epitaxy study and molecular dynamics simulations showed that the (141̄)/(001) pairing of faces showed coincident lattice matching and favorable energy interaction. Maximizing the number of substrate faces available for interaction increases the chance for a lattice match between the substrate and the crystallizing material which can be useful for controlling and increasing nucleation kinetics. Finally, water-in-oil emulsions were used to make composite spherical agglomerates with two components: a heterosurface, and a target compound that does not typically crystallize as spherical agglomerates on its own. The generated composite agglomerates were relatively monodisperse and were characterized using optical microscopy, scanning electron microscopy, x-ray powder diffraction, and differential scanning calorimetry. This technique could potentially be applied to other hydrophilic compounds, in particular water-soluble pharmaceuticals compounds, in order to change crystal morphology to spherical agglomerates in order to simplify downstream processing. / by Justin Quon. / Ph.D.

Thesis (Sc. D.)--Massachusetts Institute of Technology, Dept. of Chemical Engineering, 1996. / Includes bibliographical references (v. 2, leaves 303-319). / by Shakti Kumar Goel. / Sc.D.

Thesis (M.S.)--Massachusetts Institute of Technology, Dept. of Chemical Engineering, 1983. / MICROFICHE COPY AVAILABLE IN ARCHIVES AND SCIENCE. / Bibliography: leaves 130-135. / by Manoj Mangesh Nadkarni. / M.S.

Thesis: Ph. D., Massachusetts Institute of Technology, Department of Chemical Engineering, 2015. / Cataloged from PDF version of thesis. / Includes bibliographical references (pages 127-136). / Point of care testing is expanding the healthcare field towards personalized and early-detection medicine. Microfluidic platforms present an opportunity for low cost, portable diagnostic sensors through manipulation of small volumes of fluids on isolated, compact devices. One of the challenges of microfluidic sensors is the biological sample pretreatment steps that are manually performed prior to on-chip loading and sensing. This issue is especially prominent for human blood, which contains about a billion cells in one milliliter total volume. These blood cells can rupture, clog devices, block optical readouts, and foul electrodes. At the same time, the liquid portion of human blood, plasma, is rich in a variety of disease indicators, many of which have not yet been identified, and thus is an essential part in the diagnostic field. This thesis focuses on the design of a small, around 1 cm long, microfluidic device that separates out blood plasma from undiluted human blood. This design does not require any external field or equipment, beyond a loading syringe and collection tubing. The separation results show 10-100 times improvement in plasma purity over the literature values for passive separation designs. This separation system was then combined with a colorimetric malaria sensor that produced a visually detectable colored result with a 7.5 nM limit of detection in whole blood. This thesis details the design of a low power point of care diagnostic process that is capable of blood processing and detection, and which eliminates the need for any external laboratory-scale equipment. Advantages and challenges of other low power, microfluidic sensor constructs are also discussed. / by Tatyana A. Shatova. / Ph. D.

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemical Engineering, 2005. / Includes bibliographical references. / Programmed self-assembly using non-covalent DNA-DNA interactions is a promising technique for the creation of next-generation functional devices for electronic, optical, and magnetic applications. This thesis develops the ability to tailor surfaces for the DNA-driven assembly of molecular, nano-, and micron-sized objects. Specifically, DNA hybridization was employed to direct the regiospecific assembly of DNA molecules onto substrates and in the targeted assembly of supraparticulate structures from nanoparticles and microparticles that express DNA molecules on their surfaces. These studies provide fundamental information needed for deploying a programmable process for the 'bottom-up' assembly of smaller species into large aggregates. DNA-based assembly spans areas of molecular biology and nanotechnology. In the former area, DNA microarrays have become a standard tool for gene expression analysis. In spite of the large number of studies that employ DNA microarrays, fundamental aspects of DNA hybridization on these platforms have been largely unexplored. In this thesis, the effects of immobilized probe density on DNA hybridization were examined by employing a mixed silane chemistry to systematically control the density of immobilized probe DNA strands (0.2 x 10¹³ probes/cm² to 5.2 x 10¹³ probes/cm²) on glass surfaces. The surface density of the immobilized species was found to significantly affect the hybridization yields; the equilibrium dsDNA amounts being highest on surfaces with ss-DNA probe densities corresponding to average inter- strand distances of 18 [Angstroms]. The strong effects of surface probe density on hybridization performance indicate that it can be a useful parameter for improving the signal-to-noise ratios for assays performed on microarrays. / (cont.) A target in nanotechnology is the generation of larger functional units from smaller nanoscale objects. Using a mixed silane chemistry, the DNA-directed assembly of gold nanoparticles was investigated on surfaces with different probe densities. Gold nanoparticles could be assembled at a dense coverage of [approx.] 28% corresponding to a density of [approx.] 1070 particles/[mu]m². As with DNA-DNA hybridization, particle coverage was reduced at high probe densities due to strong steric and electrostatic hindrances. Non-specific adsorption-crucial for the creation of defect-free assembled devices-was three orders of magnitude lower than the specific adsorption of nanoparticles demonstrating the effectiveness of the surface chemistry in blocking extraneous particle-substrate interactions. The effect of probe density on the thermodynamics of nanoparticle adsorption was found to be fundamentally different than that on the thermodynamics of molecular DNA adsorption due to the multivalent nature of nanoparticle attachment. Asymmetric building blocks can substantially broaden the creation of novel self- assembled devices because of their morphological and/or chemical asymmetry. In this thesis, DNA-based recognition was employed to achieve orthogonal self-assembly on asymmetric microspheres. Dual-functional microspheres with two different DNA sequences were made by a shadow deposition of gold onto silica microspheres in conjunction with DNA immobilization procedures using thiol and silane chemistries. The prepared microspheres were used as templates for the selective orthogonal assembly of fluorophore-tagged target oligonucleotides and for the regiospecific assembly of nanoparticles of two different sizes. / (cont.) The selective attachment of nanoparticles and DNA molecules onto different specified regions of the building block was achieved solely by the sequence complementarity of the various components. Extending the shadow deposition technique a step further, tri-functional particles were formed by the shadow deposition of gold and aluminum. After functionalizing the silica and gold surfaces with two different DNA sequences and passivating the aluminum surface with stearic acid, an orthogonal assembly of DNA molecules was successfully performed within specified regions on these tri- functional particles. The flexibility for specifying the regio-selective attachment of DNA molecules and nanoparticles onto these building block objects will be important for the modular creation of a variety of novel self-assembled devices. In order to expand the assembly to other asymmetric structures and to understand the effect of shape on DNA-mediated attachment, microrods were selectively assembled via DNA- DNA interactions on complementary surfaces. Because of the weak nature of the DNA-DNA interactions, a large contact area between the building block and substrate-as made possible by the microrod geometry-was essential in ensuring robust assembly. Further, dual-functional microrods were prepared by a shadow deposition of gold and could be assembled on flat surfaces in an orientation-specific manner highlighting another advantage of DNA-directed assembly beyond regiospecificity. / (cont.) In essence, employing DNA as the linker molecule and a robust chemistry for DNA attachment, asymmetric multi-functional particles were assembled into novel configurations, which would be difficult to realize using symmetrical building blocks. This programmable self-assembly approach exploits the multiplicity and specificity of DNA-DNA interactions and provides a powerful strategy for the generation of novel l-D, 2-D, and 3-D functional devices. / by Manish G. Bajaj. / Ph.D.

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemical Engineering, 2010. / Cataloged from student submitted PDF version of thesis. / Includes bibliographical references (p. 231-246). / Although the field of microbial metabolic engineering has traditionally been dominated by rational and knowledge-driven approaches, recent advances in genetic engineering have led to the emergence of a new methodology based on phenotypic diversification and screening. Unlike "classical strain improvement," which requires the use of general mutagens to introduce nonspecific chromosomal substitutions, these novel combinatorial methods enable sampling of a wider range of phenotypic space and, additionally, offer the important feature of genetic traceability. As an example, the use of transposon mutagenesis allows for the random integration of a genetic cassette within the chromosome for the generation of gene knockout libraries. More recently, the mutagenesis of cellular transcriptional components (global transcription machinery engineering, gTME) has enabled a complete reprogramming of the transcriptome, a useful feature for eliciting a broad array of phenotypes. Despite these advances in library generation, however, the application of these combinatorial approaches has surprisingly been limited to the engineering of only a handful of cellular properties. Thus, there remains a pressing need for a full evaluation of these techniques and, more specifically, an objective comparison of their relative strengths and weaknesses when applied towards strain improvement endeavors. We decided to explore these specific issues using the metabolic engineering framework of L-tyrosine overproduction in Escherichia coli. Although this particular strain optimization problem merely represents a "model system" for these studies, such endeavors do have important industrial implications, as L-tyrosine serves both as a dietary supplement and a valuable precursor for a myriad of polymers, adhesives and coatings, pharmaceuticals, biocosmetics, and flavonoid products. To establish the early foundations for a combinatorial approach, we began with the construction of a "parental" or starting strain for the generation of these genetic libraries. This was achieved by utilizing several common rational engineering strategies to both deregulate and increase the flux through the aromatic amino acid biosynthetic pathway. The resulting strains, P1 and P2, exhibited L-tyrosine production levels of 358 mg/l and 418 mg/l, respectively, thus establishing an already high base line for this study. In a parallel investigation, we also worked on developing a simple high-throughput screen for Ltyrosine production in E. coli, another prerequisite for the use of these combinatorial approaches. This was accomplished through the heterologous expression of a bacterial tyrosinase which provided a visual link between L-tyrosine production and the synthesis of the colored pigment, melanin. When implemented on a solid agar format, this assay allowed for the identification and isolation of high L-tyrosine producers from combinatorial libraries of more than 106 mutants. Having established the basis for a combinatorial study, these strains and tools were subsequently applied for the generation and screening of three separate libraries - a random knockout library constructed through transposon integration and two plasmid-encoded gTME libraries based on the mutagenesis of the a subunit and the s70 sigma factor of RNA polymerase (rpoA and rpoD, respectively). Several strains were isolated, with some gTME mutants exhibiting impressive titers of up to ~900 mg/l L-tyrosine, a 114% increase over the parental. Upon further examination, however, we discovered that phenotypic transferability was somewhat hampered in these strains due to an unusual requirement for both the plasmidencoded rpoA/rpoD and a mutated chromosomal background to achieve the desired phenotype. Furthermore, the biochemical mechanisms triggered by these factors appeared to be nonspecific, as several plasmid-background combinations were found to lead to the same cellular behaviors. To elucidate the biochemical underpinnings for these phenomena, we decided to conduct a full characterization of three isolated gTME strains through both microarray analysis and whole genome sequencing. Interestingly, whole genome sequencing revealed the presence of a separate unique mutation within each strain in two biochemically-related loci (hisH, purF). Although microarray experiments generally yield intractable results, we were also fortunate to find patterns of expression linking this phenotype to two different cellular responses -- the acid stress resistance pathway and the stringent response. Indeed, the overexpression of two transcriptional regulators for these pathways (evgA, relA) was able to supplant the need for the mutant rpoA or rpoD plasmids, thus validating the contributions of these specific mechanisms towards determining cellular phenotype. The successful identification of these critical genetic factors led us to the construction of a novel, genetically-defined strain (rpoA14R) exhibiting a titer of 902 mg/l L-tyrosine and a yield of 0.18 g L-tyrosine/g glucose in 50 ml cultures. To put these numbers into perspective, this yield on glucose is more than 150% greater than a classically-improved strain (DPD4195) currently used for the industrial production of L-tyrosine and, when excluding biomass-related glucose utilization, represents 85% of the maximum theoretical yield. As an added feature, further engineering of this strain has established its capacity to produce the flavonoid precursor naringenin at competitive levels, thus providing a route for the synthesis of other important Ltyrosine derivatives. During this study, we have successfully applied a combinatorial engineering approach for both eliciting a complex phenotype and identifying novel biochemical and genetic avenues by which to engineer future strains. As such, these combinatorial techniques have certainly proven to be valuable tools within the metabolic engineer's ever-expanding arsenal. / by Christine Nicole S. Santos. / Ph.D.

Thesis (M.S.) Massachusetts Institute of Technology. Dept. of Chemical Engineering, 1950. / Bibliography: leaves 126-132. / by John H. Rees. / M.S.

Thesis (Sc. D.)--Massachusetts Institute of Technology, Dept. of Chemical Engineering, February 2013. / "February 2013." Cataloged from PDF version of thesis. / Includes bibliographical references (p. 151-168). / The thermodynamics and mass transfer kinetics of adsorption and desporption at interfaces play vital roles in chemical analysis, separation processes, and many natural phenomena. In this work, computer simulations were used to design interfacial modifications to alter the physical processes of adsorption and desorption, using two different approaches to molecular design. In the first application, the finite-temperature string method was used to elucidate the mechanism of water's evaporation at its liquid/vapor interface, with the goal of designing a soluble additive that could impede evaporation there. These simulations used the SPC/E water model, and identified a minimum free energy path for this process in terms of 10 descriptive order parameters. The measured free energy change was 7.4 kcal/mol at 298 K, in reasonable agreement with the experimental value of 6.3 kcal/mol, and the mean first-passage time was 1375 ns for a single molecule, corresponding to an evaporation coefficient of 0.25. In the observed minimum free energy process, the water molecule diffuses to the surface, and tends to rotate so that its dipole and one 0-H bond are oriented outward as it crosses the Gibbs dividing surface. As the molecule moves further outwards through the interfacial region, a local solvation shell tends to protrudes from the interface. The water molecule loses donor and acceptor hydrogen bonds, and then, with its dipole nearly normal to the interface, stops donating its remaining donor hydrogen bond. After the final, accepted hydrogen bond is broken, the water molecule is free. An analysis of reactive trajectories showed that the relative orientation of nearby water molecules, and the number of accepted hydrogen bonds, were important variables in a kinetic description of the process. In the second application, we developed an in silico screening process to design organic ligands which, when chemically bound to a solid surface, would constitute an effective adsorption for a pharmaceutically relevant mixture of reaction products. This procedure employs automated molecular dynamics simulations to evaluate potential ligands, by measuring the difference in adsorption energy of two solutes which differed by one functional group. Then, a genetic algorithm was used to iteratively improve a population of ligands through selection and reproduction steps. This procedure identified chemical designs of the surface-bound ligands that were outside the set considered using chemical intuition. The ligand designs achieved selectivity by exploiting phenyl-phenyl stacking which was sterically hindered in the case of one solution component. The ligand designs had selectivity energies of 0.8 to 1.6 kcal/mol in single-ligand, solvent-free simulations, if entropic contributions to the relative selectivity are neglected. This molecular evolution technique presents a useful method for the directed exploration of chemical space or for molecular design. / by Nicholas J. Musolino. / Sc.D.

Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Chemical Engineering, 2002. / Includes bibliographical references. / This electronic version was submitted by the student author. The certified thesis is available in the Institute Archives and Special Collections. / Silicon microfabrication techniques and scale-up by replication have for decades fueled spectacular advances in the electronics industry. More recently, with the rise of microfluidics, microfabrication has enabled the development of microchemical systems for a variety of chemical and biological applications. This work focuses on the development of these systems for improved gas phase heterogeneous catalysis research. The catalyst development process often requires fundamental information such as reaction rate constants, activation energies, and reaction mechanisms to gauge and understand catalyst performance. To this end, we have examined the ability of microreactors with a variety of geometries to efficiently obtain accurate kinetic information. This work primarily focuses on microfabricated packed-bed reactors that utilize standard catalyst particles and briefly explores the use of membrane based reactors to obtain kinetic information. Initial studies with microfabricated packed-beds led to the development of a microfabricated silicon reactor that incorporates a novel cross-flow design with a short pass multiple flow-channel geometry to reduce the gradients that often confound kinetics in macroscale reactors. The cross-flow geometry minimizes pressure drop though the particle bed and incorporates a passive flow distribution system composed of an array of shallow flow channels. Combined experiments and modeling confirm the even distribution of flow across the wide catalyst bed with a pressure drop [approx.] 1600 times smaller than typical microfabricated packed-bed configurations. / (cont.) Coupled with the inherent heat and mass transfer advantages at the sub-millimeter length scale achievable through microfabrication, the cross-flow microreactor has been shown to operate in near-gradientless conditions and is an advantageous design for catalyst testing. The ability of microfabricated packed-beds to obtain accurate catalytic information has been demonstrated through experiments with phosgene generation over activated carbon, and CO oxidation and acetylene hydrogenation over a variety of noble metals on alumina. The advantages of using microreactors for catalyst testing is quantitatively highlighted throughout this work. / by Sameer K. Ajmera. / Ph.D.