Terahertz time domain spectroscopy of amino acids and sugars

A time-domain spectrometer for use in the terahertz (THz) spectral range was designed and constructed. Due to there being few existing methods of generating and detecting THz radiation, the spectrometer is expected to have vast applications to solid, liquid, and gas phase samples. In particular, knowledge of complex organic chemistry and chemical abundances in the interstellar medium (ISM) can be obtained when compared to astronomical data. The THz spectral region is of particular interest due to reduced line density when compared to the millimeter wave spectrum, the existence of high resolution observatories, and potentially strong transitions resulting from the lowest-lying vibrational modes of large molecules.

The heart of the THz time-domain spectrometer (THz-TDS) is the ultrafast laser. Due to the femtosecond duration of ultrafast laser pulses and an energy-time uncertainty relationship, the pulses typically have a several-THz bandwidth. By various means of optical rectification, the optical pulse carrier envelope shape, i.e. intensity-time profile, can be transferred to the phase of the resulting THz pulse. As a consequence, optical pump-THz probe spectroscopy is readily achieved, as was demonstrated in studies of dye-sensitized TiO₂, as discussed in chapter 4. Detection of the terahertz radiation is commonly based on electro-optic sampling and provides full phase information. This allows for accurate determination of both the real and imaginary index of refraction, the so-called optical constants, without additional analysis. A suite of amino acids and sugars, all of which have been found in meteorites, were studied in crystalline form embedded in a polyethylene matrix. As the temperature was varied between 10 and 310 K, various strong vibrational modes were found to shift in spectral intensity and frequency. Such modes can be attributed to intramolecular, intermolecular, or phonon modes, or to some combination of the three.

Structural and mechanistic study of monoalkyl diazenes. Synthesis, characterization, and reactivity of 1,6-didehydro[10]annulene

Methodology for the preparation of allenes from propargylic hydrazine precursors under mild conditions is described. Oxidation of the propargylic hydrazines, which can be readily prepared from propargylic alcohols, with either of two azo oxidants, diethyl azodicarboxylate (DEAD) or 4-methyl 1,2-triazoline-3,5-dione (MTAD), effects conversion to the allenes, presumably via sigmatropic rearrangement of a monoalkyl diazene intermediate. This rearrangement is demonstrated to proceed with essentially complete stereospecificity. The application of this methodology to the preparation of other allenes, including two that are notable for their reactivity and thermal instability, is also described.

The structural and mechanistic study of a monoalkyl diazene intermediate in the oxidative transformation of propargylic hydrazines to allenes is described. The use of long-range heteronuclear NMR coupling constants for assigning monoalkyl diazene stereochemistry (E vs Z) is also discussed. Evidence is presented that all known monoalkyl diazenes are the E isomers, and the erroneous assignment of stereochemistry in the previous report of the preparation of (Z)-phenyldiazene is discussed.

The synthesis, characterization, and reactivity of 1,6-didehydro[10]annulene are described. This molecule has been recognized as an interesting synthetic target for over 40 years and represents the intersection of two sets of extensively studied molecules: nonbenzenoid aromatic compounds and molecules containing sterically compressed π-systems.The formation of 1,5-dehydronaphthalene from 1 ,6-didehydro[10]annulene is believed to be the prototype for cycloaromatizations that produce 1,4-dehydroaromatic species with the radical centers disposed anti about the newly formed single bond. The aromaticity of this annulene and the facility of its cycloaromatization are also analyzed.

Model systems for the study of drug hypersensitivity

I. It was not possible to produce anti-tetracycline antibody in laboratory animals by any of the methods tried. Tetracycline protein conjugates were prepared and characterized. It was shown that previous reports of the detection of anti-tetracycline antibody by in vitro-methods were in error. Tetracycline precipitates non-specifically with serum proteins. The anaphylactic reaction reported was the result of misinterpretation, since the observations were inconsistent with the known mechanism of anaphylaxis and the supposed antibody would not sensitize guinea pig skin. The hemagglutination reaction was not reproducible and was extremely sensitive to minute amounts of microbial contamination. Both free tetracyclines and the conjugates were found to be poor antigens.

II. Anti-aspiryl antibodies were produced in rabbits using 3 protein carriers. The method of inhibition of precipitation was used to determine the specificity of the antibody produced. ε-Aminocaproate was found to be the most effective inhibitor of the haptens tested, indicating that the combining hapten of the protein is ε-aspiryl-lysyl. Free aspirin and salicylates were poor inhibitors and did not combine with the antibody to a significant extent. The ortho group was found to participate in the binding to antibody. The average binding constants were measured.

Normal rabbit serum was acetylated by aspirin under in vitro conditions, which are similar to physiological conditions. The extent of acetylation was determined by immunochemical tests. The acetylated serum proteins were shown to be potent antigens in rabbits. It was also shown that aspiryl proteins were partially acetylated. The relation of these results to human aspirin intolerance is discussed.

III. Aspirin did not induce contact sensitivity in guinea pigs when they were immunized by techniques that induce sensitivity with other reactive compounds. The acetylation mechanism is not relevant to this type of hypersensitivity, since sensitivity is not produced by potent acetylating agents like acetyl chloride and acetic anhydride. Aspiryl chloride, a totally artificial system, is a good sensitizer. Its specificity was examined.

IV. Protein conjugates were prepared with p-aminosalicylic acid and various carriers using azo, carbodiimide and mixed anhydride coupling. These antigens were injected into rabbits and guinea pigs and no anti-hapten IgG or IgM response was obtained. Delayed hypersensitivity was produced in guinea pigs by immunization with the conjugates, and its specificity was determined. Guinea pigs were not sensitized by either injections or topical application of p-amino-salicylic acid or p-aminosalicylate.

Entrainment of fine sediments by turbulent flows

A study was made of the means by which turbulent flows entrain sediment grains from alluvial stream beds. Entrainment was considered to include both the initiation of sediment motion and the suspension of grains by the flow. Observations of grain motion induced by turbulent flows led to the formulation of an entrainment hypothesis. It was based on the concept of turbulent eddies disrupting the viscous sublayer and impinging directly onto the grain surface. It is suggested that entrainment results from the interaction between fluid elements within an eddy and the sediment grains.

A pulsating jet was used to simulate the flow conditions in a turbulent boundary layer. Evidence is presented to establish the validity of this representation. Experiments were made to determine the dependence of jet strength, defined below, upon sediment and fluid properties. For a given sediment and fluid, and fixed jet geometry there were two critical values of jet strength: one at which grains started to roll across the bed, and one at which grains were projected up from the bed. The jet strength K, is a function of the pulse frequency, ω, and the pulse amplitude, A, defined by

K = Aω^-s

Where s is the slope of a plot of log A against log ω. Pulse amplitude is equal to the volume of fluid ejected at each pulse divided by the cross sectional area of the jet tube.

Dimensional analysis was used to determine the parameters by which the data from the experiments could be correlated. Based on this, a method was devised for computing the pulse amplitude and frequency necessary either to move or project grains from the bed for any specified fluid and sediment combination.

Experiments made in a laboratory flume with a turbulent flow over a sediment bed are described. Dye injection was used to show the presence, in a turbulent boundary layer, of two important aspects of the pulsating jet model and the impinging eddy hypothesis. These were the intermittent nature of the sublayer and the presence of velocities with vertical components adjacent to the sediment bed.

A discussion of flow conditions, and the resultant grain motion, that occurred over sediment beds of different form is given. The observed effects of the sediment and fluid interaction are explained, in each case, in terms of the entrainment hypothesis.

The study does not suggest that the proposed entrainment mechanism is the only one by which grains can be entrained. However, in the writer’s opinion, the evidence presented strongly suggests that the impingement of turbulent eddies onto a sediment bed plays a dominant role in the process.

I. The structure and properties of closed circular duplex DNA. II. Chemically interacting systems at equilibrium in a buoyant density gradient

I. The binding of the intercalating dye ethidium bromide to closed circular SV 40 DNA causes an unwinding of the duplex structure and a simultaneous and quantitatively equivalent unwinding of the superhelices. The buoyant densities and sedimentation velocities of both intact (I) and singly nicked (II) SV 40 DNAs were measured as a function of free dye concentration. The buoyant density data were used to determine the binding isotherms over a dye concentration range extending from 0 to 600 µg/m1 in 5.8 M CsCl. At high dye concentrations all of the binding sites in II, but not in I, are saturated. At free dye concentrations less than 5.4 µg/ml, I has a greater affinity for dye than II. At a critical amount of dye bound I and II have equal affinities, and at higher dye concentration I has a lower affinity than II. The number of superhelical turns, τ, present in I is calculated at each dye concentration using Fuller and Waring's (1964) estimate of the angle of duplex unwinding per intercalation. The results reveal that SV 40 DNA I contains about -13 superhelical turns in concentrated salt solutions.

The free energy of superhelix formation is calculated as a function of τ from a consideration of the effect of the superhelical turns upon the binding isotherm of ethidium bromide to SV 40 DNA I. The value of the free energy is about 100 kcal/mole DNA in the native molecule. The free energy estimates are used to calculate the pitch and radius of the superhelix as a function of the number of superhelical turns. The pitch and radius of the native I superhelix are 430 Å and 135 Å, respectively.

A buoyant density method for the isolation and detection of closed circular DNA is described. The method is based upon the reduced binding of the intercalating dye, ethidium bromide, by closed circular DNA. In an application of this method it is found that HeLa cells contain in addition to closed circular mitochondrial DNA of mean length 4.81 microns, a heterogeneous group of smaller DNA molecules which vary in size from 0.2 to 3.5 microns and a paucidisperse group of multiples of the mitochondrial length.

II. The general theory is presented for the sedimentation equilibrium of a macromolecule in a concentrated binary solvent in the presence of an additional reacting small molecule. Equations are derived for the calculation of the buoyant density of the complex and for the determination of the binding isotherm of the reagent to the macrospecies. The standard buoyant density, a thermodynamic function, is defined and the density gradients which characterize the four component system are derived. The theory is applied to the specific cases of the binding of ethidium bromide to SV 40 DNA and of the binding of mercury and silver to DNA.