Time-Domain TeraHertz Spectroscopy and Observational Probes of Prebiotic Interstellar Gas and Ice Chemistry

Understanding the origin of life on Earth has long fascinated the minds of the global community, and has been a driving factor in interdisciplinary research for centuries. Beyond the pioneering work of Darwin, perhaps the most widely known study in the last century is that of Miller and Urey, who examined the possibility of the formation of prebiotic chemical precursors on the primordial Earth [1]. More recent studies have shown that amino acids, the chemical building blocks of the biopolymers that comprise life as we know it on Earth, are present in meteoritic samples, and that the molecules extracted from the meteorites display isotopic signatures indicative of an extraterrestrial origin [2]. The most recent major discovery in this area has been the detection of glycine (NH₂CH₂COOH), the simplest amino acid, in pristine cometary samples returned by the NASA STARDUST mission [3]. Indeed, the open questions left by these discoveries, both in the public and scientific communities, hold such fascination that NASA has designated the understanding of our "Cosmic Origins" as a key mission priority.

Despite these exciting discoveries, our understanding of the chemical and physical pathways to the formation of prebiotic molecules is woefully incomplete. This is largely because we do not yet fully understand how the interplay between grain-surface and sub-surface ice reactions and the gas-phase affects astrophysical chemical evolution, and our knowledge of chemical inventories in these regions is incomplete. The research presented here aims to directly address both these issues, so that future work to understand the formation of prebiotic molecules has a solid foundation from which to work.

From an observational standpoint, a dedicated campaign to identify hydroxylamine (NH₂OH), potentially a direct precursor to glycine, in the gas-phase was undertaken. No trace of NH₂OH was found. These observations motivated a refinement of the chemical models of glycine formation, and have largely ruled out a gas-phase route to the synthesis of the simplest amino acid in the ISM. A molecular mystery in the case of the carrier of a series of transitions was resolved using observational data toward a large number of sources, confirming the identity of this important carbon-chemistry intermediate B11244 as l-C₃H⁺ and identifying it in at least two new environments. Finally, the doubly-nitrogenated molecule carbodiimide HNCNH was identified in the ISM for the first time through maser emission features in the centimeter-wavelength regime.

In the laboratory, a TeraHertz Time-Domain Spectrometer was constructed to obtain the experimental spectra necessary to search for solid-phase species in the ISM in the THz region of the spectrum. These investigations have shown a striking dependence on large-scale, long-range (i.e. lattice) structure of the ices on the spectra they present in the THz. A database of molecular spectra has been started, and both the simplest and most abundant ice species, which have already been identified, as well as a number of more complex species, have been studied. The exquisite sensitivity of the THz spectra to both the structure and thermal history of these ices may lead to better probes of complex chemical and dynamical evolution in interstellar environments.

How do we raise the profile of ponds?

This article arises from the 1998 Ponds Conference organised by Pond Action. A workshop entitled "How do we raise the profile of ponds?" was held on the first evening of the conference, taking the form of three syndicate groups each tackling one of the following three issues: How to get volunteers and the community involved with ponds; raising the profile of ponds within the government sector; and raising the profile of ponds with scientists. It is clear that, as scientists, our understanding of ponds is not great. However, some progress has been made in understanding the rare species that are likely to occur in them. A great deal more scientific research is required to understand the nature, diversity, distribution, formative processes and wise management options for ponds. However, perhaps of equal or even greater importance is the need for scientists and pond managers to understand the broader values that people across society hold about ponds.

The heat capacity of superfluid ^4He in the presence of a constant heat flux near Tλ

We present the first experimental evidence that the heat capacity of superfluid ⁴He, at temperatures very close to the lambda transition temperature, T_λ,is enhanced by a constant heat flux, Q. The heat capacity at constant Q, C_Q,is predicted to diverge at a temperature T_c(Q) < T_λ at which superflow becomes unstable. In agreement with previous measurements, we find that dissipation enters our cell at a temperature, T_DAS(Q),below the theoretical value, T_c(Q). Our measurements of C_Q were taken using the discrete pulse method at fourteen different heat flux values in the range 1µW/cm² ≤ Q≤ 4µW /cm². The excess heat capacity ∆C_Q we measure has the predicted scaling behavior as a function of T and Q:∆C_Q • t^α ∝ (Q/Q_c)², where Q_cT) ~ t^2ν is the critical heat current that results from the inversion of the equation for T_c(Q). We find that if the theoretical value of T_c( Q) is correct, then ∆C_Q is considerably larger than anticipated. On the other hand,if T_c(Q)≈ T_DAS(Q),then ∆C_Q is the same magnitude as the theoretically predicted enhancement.

Development of Metalloenzyme Dioxygen Reduction Cathodes

The prime thrust of this dissertation is to advance the development of fuel cell dioxygen reduction cathodes that employ some variant of multicopper oxidase enzymes as the catalyst. The low earth-abundance of platinum metal and its correspondingly high market cost has prompted a general search amongst chemists and materials scientists for reasonable alternatives to this metal for facilitating catalytic dioxygen reduction chemistry. The multicopper oxidases (MCOs), which constitute a class of enzyme that naturally catalyze the reaction O₂ + 4H⁺ + 4e^- → 2H₂O, provide a promising set of biochemical contenders for fuel cell cathode catalysts. In MCOs, a substrate reduces a copper atom at the type 1 site, where charge is then transferred to a trinuclear copper cluster consisting of a mononuclear type 2 or “normal copper” site and a binuclear type 3 copper site. Following the reduction of all four copper atoms in the enzyme, dioxygen is then reduced to water in two two-electron steps, upon binding to the trinuclear copper cluster. We identified an MCO, a laccase from the hyperthermophilic bacterium Thermus thermophilus strain HB27, as a promising candidate for cathodic fuel cell catalysis. This protein demonstrates resilience at high temperatures, exhibiting no denaturing transition at temperatures high as 95°C, conditions relevant to typical polymer electrolyte fuel cell operation.

In Chapter I of this thesis, we discuss initial efforts to physically characterize the enzyme when operating as a heterogeneous cathode catalyst. Following this, in Chapter II we then outline the development of a model capable of describing the observed electrochemical behavior of this enzyme when operating on porous carbon electrodes. Developing a rigorous mathematical framework with which to describe this system had the potential to improve our understanding of MCO electrokinetics, while also providing a level of predictive power that might guide any future efforts to fabricate MCO cathodes with optimized electrochemical performance. In Chapter III we detail efforts to reduce electrode overpotentials through site-directed mutagenesis of the inner and outer-sphere ligands of the Cu sites in laccase, using electrochemical methods and electronic spectroscopy to try and understand the resultant behavior of our mutant constructs. Finally, in Chapter IV, we examine future work concerning the fabrication of enhanced MCO cathodes, exploring the possibility of new cathode materials and advanced enzyme deposition techniques.

Binding Studies of Neuronal Nicotinic Acetylcholine Receptors Expressing Unnatural Amino Acids

Nicotinic acetylcholine receptors are pentameric ligand-gated ion channels mediating fast synaptic transmission throughout the peripheral and central nervous systems. They have been implicated in various processes related to cognitive functions, learning and memory, arousal, reward, motor control and analgesia. Therefore, these receptors present alluring potential therapeutic targets for the treatment of pain, epilepsy, Alzheimer’s disease, Parkinson’s disease, Tourette’s syndrome, schizophrenia, anxiety, depression and nicotine addiction. The work detailed in this thesis focuses on binding studies of neuronal nicotinic receptors and aims to further our knowledge of subtype specific functional and structural information.

Chapter 1 is an introductory chapter describing the structure and function of nicotinic acetylcholine receptors as well as the methodologies used for the dissertation work described herein. There are several different subtypes of nicotinic acetylcholine receptors known to date and the subtle variations in their structure and function present a challenging area of study. The work presented in this thesis deals specifically with the α4β2 subtype of nicotinic acetylcholine receptor. This subtype assembles into 2 closely related stoichiometries, termed throughout this thesis as A3B2 and A2B3 after their respective subunit composition. Chapter 2 describes binding studies of select nicotinic agonists on A3B2 and A2B3 receptors determined by whole-cell recording. Three key binding interactions, a cation-π and two hydrogen bonds, were probed for four nicotinic agonists, acetylcholine, nicotine, smoking cessation drug varenicline (Chantix®) and the related natural product cytisine.

Results from the binding studies presented in Chapter 2 show that the major difference in binding of these four agonists to A3B2 and A2B3 receptors lies in one of the two hydrogen bond interactions where the agonist acts as the hydrogen bond acceptor and the backbone NH of a conserved leucine residue in the receptor acts as the hydrogen bond donor. Chapter 3 focuses on studying the effect of modulating the hydrogen bond acceptor ability of nicotine and epibatidine on A3B2 receptor function determined by whole-cell recording. Finally, Chapter 4 describes single-channel recording studies of varenicline binding to A2B3 and A3B2 receptors.

Strategies for the Stereoselective Synthesis of Carbon Quaternary Centers via Transition Metal-Catalyzed Alkylation of Enolate Compounds

Notwithstanding advances in modern chemical methods, the selective installation of sterically encumbered carbon stereocenters, in particular all-carbon quaternary centers, remains an unsolved problem in organic chemistry. The prevalence of all-carbon quaternary centers in biologically active natural products and pharmaceutical compounds provides a strong impetus to address current limitations in the state of the art of their generation. This thesis presents four related projects, all of which share in the goal of constructing highly-congested carbon centers in a stereoselective manner, and in the use of transition-metal catalyzed alkylation as a means to address that goal.

The first research described is an extension of allylic alkylation methodology previously developed in the Stoltz group to small, strained rings. This research constitutes the first transition metal-catalyzed enantioselective α-alkylation of cyclobutanones. Under Pd-catalysis, this chemistry affords all–carbon α-quaternary cyclobutanones in good to excellent yields and enantioselectivities.

Next is described our development of a (trimethylsilyl)ethyl β-ketoester class of enolate precursors, and their application in palladium–catalyzed asymmetric allylic alkylation to yield a variety of α-quaternary ketones and lactams. Independent coupling partner synthesis engenders enhanced allyl substrate scope relative to allyl β-ketoester substrates; highly functionalized α-quaternary ketones generated by the union of our fluoride-triggered β-ketoesters and sensitive allylic alkylation coupling partners serve to demonstrate the utility of this method for complex fragment coupling.

Lastly, our development of an Ir-catalyzed asymmetric allylic alkylation of cyclic β-ketoesters to afford highly congested, vicinal stereocenters comprised of tertiary and all-carbon quaternary centers with outstanding regio-, diastereo-, and enantiocontrol is detailed. Implementation of a subsequent Pd-catalyzed alkylation affords dialkylated products with pinpoint stereochemical control of both chiral centers. The chemistry is then extended to include acyclic β-ketoesters and similar levels of selective and functional group tolerance are observed. Critical to the successful development of this method was the employment of iridium catalysis in concert with N-aryl-phosphoramidite ligands.

Investigation of Fundamental Processes Governing Secondary Organic Aerosol Formation in Laboratory Chambers

Our understanding of the processes and mechanisms by which secondary organic aerosol (SOA) is formed is derived from laboratory chamber studies. In the atmosphere, SOA formation is primarily driven by progressive photooxidation of SOA precursors, coupled with their gas-particle partitioning. In the chamber environment, SOA-forming vapors undergo multiple chemical and physical processes that involve production and removal via gas-phase reactions; partitioning onto suspended particles vs. particles deposited on the chamber wall; and direct deposition on the chamber wall. The main focus of this dissertation is to characterize the interactions of organic vapors with suspended particles and the chamber wall and explore how these intertwined processes in laboratory chambers govern SOA formation and evolution.

A Functional Group Oxidation Model (FGOM) that represents SOA formation and evolution in terms of the competition between functionalization and fragmentation, the extent of oxygen atom addition, and the change of volatility, is developed. The FGOM contains a set of parameters that are to be determined by fitting of the model to laboratory chamber data. The sensitivity of the model prediction to variation of the adjustable parameters allows one to assess the relative importance of various pathways involved in SOA formation.

A critical aspect of the environmental chamber is the presence of the wall, which can induce deposition of SOA-forming vapors and promote heterogeneous reactions. An experimental protocol and model framework are first developed to constrain the vapor-wall interactions. By optimal fitting the model predictions to the observed wall-induced decay profiles of 25 oxidized organic compounds, the dominant parameter governing the extent of wall deposition of a compound is identified, i.e., wall accommodation coefficient. By correlating this parameter with the molecular properties of a compound via its volatility, the wall-induced deposition rate of an organic compound can be predicted based on its carbon and oxygen numbers in the molecule.

Heterogeneous transformation of δ-hydroxycarbonyl, a major first-generation product from long-chain alkane photochemistry, is observed on the surface of particles and walls. The uniqueness of this reaction scheme is the production of substituted dihydrofuran, which is highly reactive towards ozone, OH, and NO3, thereby opening a reaction pathway that is not usually accessible to alkanes. A spectrum of highly-oxygenated products with carboxylic acid, ester, and ether functional groups is produced from the substituted dihydrofuran chemistry, thereby affecting the average oxidation state of the alkane-derived SOA.

The vapor wall loss correction is applied to several chamber-derived SOA systems generated from both anthropogenic and biogenic sources. Experimental and modeling approaches are employed to constrain the partitioning behavior of SOA-forming vapors onto suspended particles vs. chamber walls. It is demonstrated that deposition of SOA-forming vapors to the chamber wall during photooxidation experiments can lead to substantial and systematic underestimation of SOA. Therefore, it is likely that a lack of proper accounting for vapor wall losses that suppress chamber-derived SOA yields contribute substantially to the underprediction of ambient SOA concentrations in atmospheric models.

On Ultrafast Time-Domain TeraHertz Spectroscopy in the Condensed Phase: Linear Spectroscopic Measurements of Hydrogen-Bond Dynamics of Astrochemical Ice Analogs and Nonlinear TeraHertz Kerr Effect Measurements of Vibrational Quantum Beats

Much of the chemistry that affects life on planet Earth occurs in the condensed phase. The TeraHertz (THz) or far-infrared (far-IR) region of the electromagnetic spectrum (from 0.1 THz to 10 THz, 3 cm^-1 to 300 cm^-1, or 3000 μm to 30 μm) has been shown to provide unique possibilities in the study of condensed-phase processes. The goal of this work is to expand the possibilities available in the THz region and undertake new investigations of fundamental interest to chemistry. Since we are fundamentally interested in condensed-phase processes, this thesis focuses on two areas where THz spectroscopy can provide new understanding: astrochemistry and solvation science. To advance these fields, we had to develop new instrumentation that would enable the experiments necessary to answer new questions in either astrochemistry or solvation science. We first developed a new experimental setup capable of studying astrochemical ice analogs in both the TeraHertz (THz), or far-Infrared (far-IR), region (0.3 - 7.5 THz; 10 - 250 cm^-1) and the mid-IR (400 - 4000 cm^-1). The importance of astrochemical ices lies in their key role in the formation of complex organic molecules, such as amino acids and sugars in space. Thus, the instruments are capable of performing variety of spectroscopic studies that can provide especially relevant laboratory data to support astronomical observations from telescopes such as the Herschel Space Telescope, the Stratospheric Observatory for Infrared Astronomy (SOFIA), and the Atacama Large Millimeter Array (ALMA). The experimental apparatus uses a THz time-domain spectrometer, with a 1750/875 nm plasma source and a GaP detector crystal, to cover the bandwidth mentioned above with ~10 GHz (~0.3 cm^-1) resolution.

Using the above instrumentation, experimental spectra of astrochemical ice analogs of water and carbon dioxide in pure, mixed, and layered ices were collected at different temperatures under high vacuum conditions with the goal of investigating the structure of the ice. We tentatively observe a new feature in both amorphous solid water and crystalline water at 33 cm^-1 (1 THz). In addition, our studies of mixed and layered ices show how it is possible to identify the location of carbon dioxide as it segregates within the ice by observing its effect on the THz spectrum of water ice. The THz spectra of mixed and layered ices are further analyzed by fitting their spectra features to those of pure amorphous solid water and crystalline water ice to quantify the effects of temperature changes on structure. From the results of this work, it appears that THz spectroscopy is potentially well suited to study thermal transformations within the ice.

To advance the study of liquids with THz spectroscopy, we developed a new ultrafast nonlinear THz spectroscopic technique: heterodyne-detected, ultrafast THz Kerr effect (TKE) spectroscopy. We implemented a heterodyne-detection scheme into a TKE spectrometer that uses a stilbazoiumbased THz emitter, 4-N,N-dimethylamino-4-N-methyl-stilbazolium 2,4,6-trimethylbenzenesulfonate (DSTMS), and high numerical aperture optics which generates THz electric field in excess of 300 kV/cm, in the sample. This allows us to report the first measurement of quantum beats at terahertz (THz) frequencies that result from vibrational coherences initiated by the nonlinear, dipolar interaction of a broadband, high-energy, (sub)picosecond THz pulse with the sample. Our instrument improves on both the frequency coverage, and sensitivity previously reported; it also ensures a backgroundless measurement of the THz Kerr effect in pure liquids. For liquid diiodomethane, we observe a quantum beat at 3.66 THz (122 cm^-1), in exact agreement with the fundamental transition frequency of the υ4 vibration of the molecule. This result provides new insight into dipolar vs. Raman selection rules at terahertz frequencies.

To conclude we discuss future directions for the nonlinear THz spectroscopy in the Blake lab. We report the first results from an experiment using a plasma-based THz source for nonlinear spectroscopy that has the potential to enable nonlinear THz spectra with a sub-100 fs temporal resolution, and how the optics involved in the plasma mechanism can enable THz pulse shaping. Finally, we discuss how a single-shot THz detection scheme could improve the acquisition of THz data and how such a scheme could be implemented in the Blake lab. The instruments developed herein will hopefully remain a part of the groups core competencies and serve as building blocks for the next generation of THz instrumentation that pushes the frontiers of both chemistry and the scientific enterprise as a whole.

Nonvolatile holograms in LiNbO3 : Fe : Cu by use of the bleaching effect

We report our observation of a bleaching effect under an ultraviolet exposure in LiNbO3:Fe:Cu crystals. Two three-step recording-transferring-fixing schemes are proposed to record nonvolatile photorefractive holograms in such crystals. In the schemes two red laser beams and an ultraviolet illumination are used selectively to write the charge grating in the shallow-level Fe centers, to develop the charge grating in the deep-level Cu centers by transferring the charge grating in the Fe centers, and to fix only the charge grating in the Cu centers for unerasable read-out. Experimental results, verifications, and an optimal recording scheme are given. A comparison of the lithium niobate crystals of the same double-doping system of Fe:Mn, Ce:Mn, Ce:Cu, and Fe:Cu is outlined. (C) 2002 Optical Society of America.

Experimental research on the development of Ceratium hirundinella O.F.Muller [Translation from: Z.Bot. 14, 337-371, 1922]

The most important aim of this study lay in filling in the great gap in our knowledge of the processes of germination in the Ceratium cyst and the early developmental stages in the standing stock of Ceratium hirundinella. contained rich cysts, we now succeeded extraordinarily well in pursuing the consistent development of Ceratium from the cyst to the completed cell. A series of experiments were carried out on the cysts and the juvenile stages of Ceratium, which showed very interesting results. The author presents in a general descriptive part the normal processes of germination in Ceratium cysts and the development of the juvenile stages in order to show in an experimental part the changes in form of C. hirundinella under the influence of temperature, light and varying salinities.

Could the library be dismantled/role of unique holdings in modern times

I have been asked by administration, how much of our collection could go into storage. They optimistically hoping for a room or two for faculty/staff offices, as some buildings need renovation or need to be closed due to safety issues. Clearly, much of the population believes that all/most library materials are available on-line – free. I will present the results of our survey’s of material held and available on-line and space “freed” thanks to archiving. How little space is freed.

The effects of environmental stress on the physiology of growth in rainbow trout, Salmo gairderi Richardson

There is little doubt that both mammalian and teleost growth hormones can accelerate growth and increase food conversion efficiency in all commonly-reared species of salmonid fish. In those vertebrates that have been closely studied (predominantly mammals), the pituitary hormone somatotropin (GH or growth hormone) is a prime determinant of somatic growth. The hormone stimulates protein biosynthesis and tissue growth, enhances lipid utilization and lipid release from the adipose tissues (a protein-sparing effect) and suppresses the peripheral utilization of glucose. The present study is a prerequisite for future work on growth hormone physiology in salmonids and should contribute to our understanding of the mechanisms of growth suppression in stressed fish. Plasma growth hormone (GH) levels were measured in rainbow trout using a radioimmunoassay developed against chinook salmon growth hormone.

The effects of stress on benthic algal communities

The effects of stress on both microalgal and macroalgal communities are considered. On one hand the contrasting approaches of studies of these two communities reflect intrinsic differences in plant size, longevity and ease of handling. On the other hand they reveal that biological monitoring of the potentially deleterious effects of man's activities has focused largely on freshwater environments in which macroalgae only occasionally dominate. Large conspicuous plants can be readily investigated as individuals, whereas it is virtually impossible to trace effects of stress on an individual cell of a vegetatively-reproducing microalga; a population approach is almost inevitably necessary. However, rapid turnover rates, a spectrum of ecological characteristics distributed between many taxa, and the potential for statistical analysis, have facilitated the use of microalgae in environmental impact studies. Failure to extend such investigations into marine systems rests as much on man's ability to ignore environmental deterioration until it affects his quality of life as on the visual dominance of seaweeds around our coasts. However, large gaps remain in our knowledge of both large and small algae; some reported community changes over time are suspect, and the causes of even blatant changes are not always apparent.

Metallothionein as an indicator of water quality: assessment of the bioavailability of cadmium, copper, mercury and zinc in aquatic animals at the cellular level

The study of metallothioneins (MTs) has greatly improved our understanding of body burdens, metal storage and detoxification in aquatic organisms subjected to contamination by the toxic heavy metals, Cd, Cu, Hg and Zn. These studies have shown that in certain organisms MT status can be used to assess impact of these metals at the cellular level and, whilst validation is currently limited to a few examples, this stress response may be linked to higher levels of organisation, thus indicating its potential for environmental quality assessment. Molluscs, such as Mytilus spp., and several commonly occurring teleost species, are the most promising of the indicator species tested. Natural variability of MT levels caused by the organism's size, condition, age, position in the sexual cycle, temperature and various stressors, can lead to difficulties in interpretation of field data as a definitive response-indicator of metal contamination unless a critical appraisal of these variables is available. From laboratory and field studies these data are almost complete for teleost fish. Whilst for molluscs much of this information is lacking, when suitable controls are utilised and MT measurements are combined with observations of metal partitioning, current studies indicate that they are nevertheless a powerful tool in the interpretation of impact, and may prove useful in water quality assessment.

Production of positive controls for calcivirus-specific PCR using recombinant baculiovirus technology

Recent advances in our knowledge of the genetic structure of human caliciviruses (HuCVs) and small round-structured viruses (SRSVs) have led to the development of polymerase chain reaction (PCR)-based molecular tests specific for these viruses. These methods have been developed to detect a number of human pathogenic viruses in environmental samples including water, sewage and shellfish. HuCVs and SRSVs are not culturable, and no animal model is currently available. Therefore there is no convenient method of preparing viruses for study or for reagent production. One problem facing those attempting to use PCR-based methods for the detection of HuCVs and SRSVs is the lack of a suitable positive control substrate. This is particularly important when screening complex samples in which the levels of inhibitors present may significantly interfere with amplificiation. Regions within the RNA polymerase regions of two genetically distinct human caliciviruses have been amplified and used to produce recombinant baculoviruses which express RNA corresponding to the calicivirus polymerase. This RNA is being investigated as a positive control substrate for PCR testing, using current diagnostic primer sets. Recombinant baculovirus technology will enable efficient and cost-effective production of large quantities of positive control RNA with a specific known genotype. We consider the development of these systems as essential for successful screening and monitoring applications.