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.

Effect of rapid thermal annealing and hydrogen plasma treatment on the microstructure and light-emission of silicon-rich oxide film

Silicon-rich silicon oxide (SRSO) films are prepared by plasma-enhanced chemical vapor deposition method at the substrate temperature of 200degreesC. The effect of rapid thermal annealing and hydrogen plasma treatment on tire microstructure and light-emission of SRSO films are investigated in detail using micro-Raman spectroscopy, Fourier transform infrared (FTIR) spectroscopy and photoluminescence (PL) spectra. It is found that the phase-separation degree of the films decreases with increasing annealing temperature from 300 to 600degreesC, while it increases with increasing annealing temperature from 600 to 900degreesC. The light-emission of the films are enhanced with increasing annealing temperature up to 500degreesC, while it is rapidly reduced when the annealing temperature exceeds 600degreesC. The peak position of the PL spectrum blueshifts by annealing at the temperature of 300degreesC, then it red-shifts with further raising annealing temperature. The following hydrogen plasma treatment results in a disproportionate increase of the PL intensity and a blueshift or redshift of the peak positions, depending on the pristine annealing temperature. It is thought that the size of amorphous silicon clusters, surface structure of the clusters and the distribution of hydrogen in the films can be changed during the annealing procedure. The results indicate that not only cluster size but also surface state of the clusters plays an important role in the determination of electronic structure of the amorphous silicon cluster and recombination process of light-generated carriers.

Hydrate dissociation conditions for gas mixtures containing carbon dioxide, hydrogen, hydrogen sulfide, nitrogen, and hydrocarbons using SAFT

A new method, a molecular thermodynamic model based on statistical mechanics, is employed to predict the hydrate dissociation conditions for binary gas mixtures with carbon dioxide, hydrogen, hydrogen sulfide, nitrogen, and hydrocarbons in the presence of aqueous solutions. The statistical associating fluid theory (SAFT) equation of state is employed to characterize the vapor and liquid phases and the statistical model of van der Waals and Platteeuw for the hydrate phase. The predictions of the proposed model were found to be in satisfactory to excellent agreement with the experimental data.

STUDY ON C2H62+ DOUBLY CHARGED IONS - EVIDENCE FOR THE EXISTENCE OF C2H62+ IN GAS-PHASE

Collision-Induced Dissociation (CID) or Collision Activation (CA) of ion involves high kinetic energy colliding with neutral gas molecules. In part of the ions, the translational energy is converted into excitation energy, Which may lead to subsequent ion decomposition. CID has developed into an important technique for elucidating the

Investigation into the potential of using micro gas turbines in plug-in hybrid electric vehicles

The transport sector is considered to be one of the most dependent sectors on fossil fuels. Meeting ecological, social and economic demands throughout the sector has got increasingly important in recent times. A passenger vehicle with a more environmentally friendly propulsion system is the hybrid electric vehicle. Combining an internal combustion engine and an electric motor offers the potential to reduce carbon dioxide emissions. The overall objective of this research is to provide an appraisal of the use of a micro gas turbine as the range extender in a plug-in hybrid electric vehicle. In this application, the gas turbine can always operate at its most efficient operating point as its only requirement is to recharge the battery. For this reason, it is highly suitable for this purpose. Gas turbines offer many benefits over traditional internal combustion engines which are traditionally used in this application. They offer a high power-to-weight ratio, multi-fuel capability and relatively low emission levels due to continuous combustion.

First Detection of Gas-phase Methanol in a Protoplanetary Disk

The first detection of gas-phase methanol in a protoplanetary disk (TW Hya) is presented. In addition to being one of the largest molecules detected in disks to date, methanol is also the first disk organic molecule with an unambiguous ice chemistry origin. The stacked methanol emission, as observed with the Atacama Large Millimeter/submillimeter Array, is spectrally resolved and detected across six velocity channels (>3σ), reaching a peak signal-to-noise of 5.5σ, with the kinematic pattern expected for TW Hya. Using an appropriate disk model, a fractional abundance of 3 x 10^-12 – 4 x 10^-11 (with respect to H₂) reproduces the stacked line profile and channel maps, with the favored abundance dependent upon the assumed vertical location (midplane versus molecular layer). The peak emission is offset from the source position, suggesting that the methanol emission has a ring-like morphology: the analysis here suggests it peaks at ≈30 au, reaching a column density ≈3–6 x 10¹² cm⁻². In the case of TW Hya, the larger (up to millimeter-sized) grains, residing in the inner 50 au, may thus host the bulk of the disk ice reservoir. The successful detection of cold gas-phase methanol in a protoplanetary disk implies that the products of ice chemistry can be explored in disks, opening a window into studying complex organic chemistry during planetary system formation.

Investigations into the determinations of hydride-forming elements

Analytical methods for the determination of trace amounts of germanium, tin and arsenic were established using hydride generation coupled with direct current plasma atomic emission spectrometry. A continuous gas flowing batch system for the hydride generation was investigated and was applied to the determination of germanium(Ge), tin(Sn), antimony(Sb) and lead(Pb) (Preliminary results suggest that it is also applicable to arsenic)As) ). With this system, the reproducibility of signals was improved and the determination was speeded up, compared with the conventional batch type hydride generation system. Each determination was complete within one minute. Interferences from a number of transition metal ions, especially from Pd(II), Pt(IV), Ni(II), Cu(II), Co(II), and Fe(II, III), have proven to be very serious under normal conditions, in the determination of germanium, tin, and arsenic. These interference effects were eliminated or significantly reduced in the presence of L-cystine or L-cysteine. Thus, a 10-1000 fold excess of Ni(II), Cu(II), Co(II), Fe(II), Pt(IV), Pd(II), etc. can be tolerated without interference, In the presence of L-cystine or L-cysteine, compared with absence of interference reducing agent. The methods for the determination of Ge, Sn, and As were examined by the analyses of standard reference materials. Interference effects from the sample matrix, for example, in transition metal-rich samples, copper, iron and steel, were eliminated by L-cystine (for As and Sn) and by LI cysteine (for Ge). The analysis of a number of standard reference materials gave excellent results of As and Sn contents in agreement with the certified values, showing there was no systematic interference. The detection limits for both germanium and tin were 20 pg ml- I . Preliminary studies were carried out for the determination of antimony and lead. Antimony was found to react with NaBH4, remaInIng from the previous determinations, giving an analytical signal. A reversed injection manner, i.e., injection of the NaBH4 solution prior to the analyte solution was used to avoid uncertainty caused by residual NaBH4 present and to ensure that an excess of NaB H4 was available. A solution of 0.4% L-cysteine was found to reduce the interference from selected transition metal ions, Co(II), Cu(II), Ni(II) and Pt(IV). Hydrochloric acid - hydrogen peroxide, nitric acid - ammonium persulphate, and potassium dichromate malic acid reaction systems for lead hydride generation were compared. The potassium dichromate - malic acid reaction medium proved to be the best with respect to reproducibility and minimal interference. Cu(II), Ni(II), and Fe(II) caused strong interference In lead determinations, which was not reduced by L-cysteine or Lcystine. Sodium citrate, ascorbic acid, dithizone, thiosemicarbazide and penicillamine reduced interferences to some extent. Further interference reduction studies were carried out uSIng a number of amino acids, glycine, alanine, valine, leucine and histidine, as possible interference reducing agents in the determination of germanium. From glycine, alanine, valine to leucine, the interference reduction effect in germanium determinations decreased. Histidine II was found to be very promising In the reduction of interference. In fact, histidine proved more efficient than L-cystine and L-cysteine In the reduction of interference from Ni(II) in the determination of germanium. Signal enhancement by easily ionized elements (EIEs), usually regarded as an interference effect in analysis by DCP-AES, was studied and successfully applied to advantage in improving the sensitivity and detection limit in the determination of As, Ge, Sn, Sb, and Pb. The effect of alkali and alkaline-earth elements on the determination of the above five hydride forming elements was studied. With the appropriate EIE, a signal enhancement of 40-115% was achieved. Linear calibration and good reproducibility were also obtained in the presence of EIEs. III

Investigations into the determination of polycyclic aromatic hydrocarbons (PAHs) and polychlorinated biphenyls (PCBs) by capillary gas chromatography

Factors involved in the determination of PAHs (16 priority PAHs as an example) and PCBs (10 PCB congeners, representing 10 isomeric groups) by capillary gas chromatography coupled with mass spectrometry (GC/MS, for PAHs) and electron capture detection (GC/ECD , for PCBs) were studied, with emphasis on the effect of solvent. Having various volatilities and different polarities, solvent studied included dichloromethane, acetonitrile, hexan e, cyclohexane, isooctane, octane, nonane, dodecane, benzene, toluene, p-xylene, o-xylene, and mesitylene. Temperatures of the capillary column, the injection port, the GC/MS interface, the flow rates of carrier gas and make-up gas, and the injection volume were optimized by one factor at a time method or simplex optimization method. Under the optimized conditions, both peak height and peak area of 16 PAHs, especially the late-eluting PAHs, were significantly enhanced (1 to 500 times) by using relatively higher boiling point solvents such as p-xylene and nonane, compared with commonly used solvents like benzene and isooctane. With the improved sensitivity, detection limits of between 4.4 pg for naphthalene and 30.8 pg for benzo[g,h,i]perylene were obtained when p-xylene was used as an injection solvent. Effect of solvent on peak shape and peak intensity were found to be greatly dependent on temperature parameters, especially the initial temperature of the capillary column. The relationship between initial temperature and shape of peaks from 16 PAHs and 10 PCBs were studied and compared when toluene, p-xylene, isooctane, and nonane were used as injection solvents. If a too low initial temperature was used, fronting or split of peaks was observed. On the other hand, peak tailing occurred at a too high initial column temperature. The optimum initial temperature, at which both peak fronting and tailing were avoided and symmetrical peaks were obtained, depended on both solvents and the stationary phase of the column used. On a methyl silicone column, the alkane solvents provided wider optimum ranges of initial temperature than aromatic solvents did, for achieving well-shaped symmetrical GC peaks. On a 5% diphenyl: 1% vinyl: 94% dimethyl polysiloxane column, when the aromatic solvents were used, the optimum initial temperature ranges for solutes to form symmetrical peaks were improved to a similar degree as those when the alkanes were used as injection solvents. A mechanism, based on the properties of and possible interactions among the analyte, the injection solvent, and the stationary phase of the capillary column, was proposed to explain these observations. The effect of initial temperature on peak height and peak area of the 16 PAHs and the 10 PCBs was also studied. The optimum initial temperature was found to be dependent on the physical properties of the solvent used and the amount of the solvent injected. Generally, from the boiling point of the solvent to 10 0C above its boiling point was an optimum range of initial temperature at which cthe highest peak height and peak area were obtained.

Gas-phase rate coefficients for the reactions of nitrate radicals with (Z)-pent-2-ene, (E)-pent-2-ene, (Z)-hex-2-ene, (E)-hex-2-ene, (Z)-hex-3-ene, (E)-hex-3-ene and (E)-3-methylpent-2-ene at room temperature

Rate coefficients for reactions of nitrate radicals (NO3) with (Z)-pent-2-ene, (E)-pent-2-ene, (Z)-hex-2-ene, (E)-hex-2-ene, (Z)-hex-3-ene, (E)-hex-3-ene and (E)-3-methylpent-2-ene were determined to be (6.55 +/- 0.78) x 10(-13) cm(3) molecule(-1) s(-1), (3.78 +/- 0.45) x 10(-13) cm(3) molecule(-1) s(-1), (5.30 +/- 0.73) x 10(-13) cm(3) molecule(-1) s(-1), (3.83 +/- 0.47) x 10(-13) cm(3) molecule(-1) s(-1), (4.37 +/- 0.49) x 10(-13) cm(3) molecule(-1) s(-1), (3.61 +/- 0.40) x 10(-13) cm(3) molecule(-1) s(-1) and (8.9 +/- 1.5) x 10(-12) cm(3) molecule(-1) s(-1), respectively. We performed kinetic experiments at room temperature and atmospheric pressure using a relative-rate technique with GC-FID analysis. The experimental results demonstrate a surprisingly large cis-trans (Z-E) effect, particularly in the case of the pent-2-enes, where the ratio of rate coefficients is ca. 1.7. Rate coefficients are discussed in terms of electronic and steric influences, and our results give some insight into the effects of chain length and position of the double bond on the reaction of NO3 with unsaturated hydrocarbons. Atmospheric lifetimes were calculated with respect to important oxidants in the troposphere for the alkenes studied, and NO3-initiated oxidation is found to be the dominant degradation route for (Z)-pent-2-ene, (Z)-hex-3-ene and (E)-3-methylpent-2-ene.

An investigation into the influence of zinc precursor on the microstructural, photoluminescence, and gas-sensing properties of ZnO nanoparticles

Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)

iCONVERT: an integrated device for the UV-assisted determination of H2S via mid-infrared gas sensors

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)

Modeling the Histidine–Phenylalanine Interaction: The NH···π Hydrogen Bond of Imidazole·Benzene

NH···π hydrogen bonds occur frequently between the amino acid side groups in proteins and peptides. Data-mining studies of protein crystals find that ~80% of the T-shaped histidine···aromatic contacts are CH···π, and only ~20% are NH···π interactions. We investigated the infrared (IR) and ultraviolet (UV) spectra of the supersonic-jet-cooled imidazole·benzene (Im·Bz) complex as a model for the NH···π interaction between histidine and phenylalanine. Ground- and excited-state dispersion-corrected density functional calculations and correlated methods (SCS-MP2 and SCS-CC2) predict that Im·Bz has a Cs-symmetric T-shaped minimum-energy structure with an NH···π hydrogen bond to the Bz ring; the NH bond is tilted 12° away from the Bz C₆ axis. IR depletion spectra support the T-shaped geometry: The NH stretch vibrational fundamental is red shifted by −73 cm⁻¹ relative to that of bare imidazole at 3518 cm⁻¹, indicating a moderately strong NH···π interaction. While the Sₒ(A1g) → S₁(B₂u) origin of benzene at 38 086 cm⁻¹ is forbidden in the gas phase, Im·Bz exhibits a moderately intense Sₒ → S₁ origin, which appears via the D₆h → Cs symmetry lowering of Bz by its interaction with imidazole. The NH···π ground-state hydrogen bond is strong, De=22.7 kJ/mol (1899 cm⁻¹). The combination of gas-phase UV and IR spectra confirms the theoretical predictions that the optimum Im·Bz geometry is T shaped and NH···π hydrogen bonded. We find no experimental evidence for a CH···π hydrogen-bonded ground-state isomer of Im·Bz. The optimum NH···π geometry of the Im·Bz complex is very different from the majority of the histidine·aromatic contact geometries found in protein database analyses, implying that the CH···π contacts observed in these searches do not arise from favorable binding interactions but merely from protein side-chain folding and crystal-packing constraints. The UV and IR spectra of the imidazole·(benzene)₂ cluster are observed via fragmentation into the Im·Bz+ mass channel. The spectra of Im·Bz and Im·Bz₂ are cleanly separable by IR hole burning. The UV spectrum of Im·Bz₂ exhibits two 000 bands corresponding to the Sₒ → S₁ excitations of the two inequivalent benzenes, which are symmetrically shifted by −86/+88 cm⁻¹ relative to the 000 band of benzene.

Methane and hydrogen sulfide in porewater of sediment cores from the upwelling area off Namibia

Porewater concentrations of sulfate, methane, and other relevant constituents were determined on four sediment cores from the high productivity upwelling area off Namibia which were recovered from the continental slope at water depths of 1300 and 2000 m. At all four stations a distinct sulfate-methane transition zone was observed several meters below the seafloor in which both sulfate and methane are consumed. Nutrient porewater concentration profiles do not show gradient slope changes at the depths of the transition zones. Flux calculations carried out on the basis of the determined porewater profiles revealed that anaerobic methane oxidation accounts for 100% of deep sulfate reduction within the sulfate-methane transition zone and consumes the total net diffusive sulfate flux. A significant contribution of organic carbon oxidation to the reduction of sulfate at these depths could, therefore, be excluded. We state that porewater profiles of sulfate with constant gradients above the transition zones are indicative for anaerobic methane oxidation controlling sulfate reduction.

Depth profiles of dissolved sulfide and sulfate in the pore water of hydrocarbon seep sediments offshore Pakistan

The interaction between fluid seepage, bottom water redox, and chemosynthetic communities was studied at cold seeps across one of the world's largest oxygen minimum zones (OMZ) located at the Makran convergent continental margin. Push cores were obtained from seeps within and below the core-OMZ with a remotely operated vehicle. Extracted sediment pore water was analyzed for sulfide and sulfate concentrations. Depending on oxygen availability in the bottom water, seeps were either colonized by microbial mats or by mats and macrofauna. The latter, including ampharetid polychaetes and vesicomyid clams, occurred in distinct benthic habitats, which were arranged in a concentric fashion around gas orifices. At most sites colonized by microbial mats, hydrogen sulfide was exported into the bottom water. Where macrofauna was widely abundant, hydrogen sulfide was retained within the sediment. Numerical modeling of pore water profiles was performed in order to assess rates of fluid advection and bioirrigation. While the magnitude of upward fluid flow decreased from 11 cm yr**-1 to <1 cm yr**-1 and the sulfate/methane transition (SMT) deepened with increasing distance from the central gas orifice, the fluxes of sulfate into the SMT did not significantly differ (6.6-9.3 mol m**-2 yr**-1). Depth-integrated rates of bioirrigation increased from 120 cm yr**-1 in the central habitat, characterized by microbial mats and sparse macrofauna, to 297 cm yr**-1 in the habitat of large and few small vesicomyid clams. These results reveal that chemosynthetic macrofauna inhabiting the outer seep habitats below the core-OMZ efficiently bioirrigate and thus transport sulfate down into the upper 10 to 15 cm of the sediment. In this way the animals deal with the lower upward flux of methane in outer habitats by stimulating rates of anaerobic oxidation of methane (AOM) with sulfate high enough to provide hydrogen sulfide for chemosynthesis. Through bioirrigation, macrofauna engineer their geochemical environment and fuel upward sulfide flux via AOM. Furthermore, due to the introduction of oxygenated bottom water into the sediment via bioirrigation, the depth of the sulfide sink gradually deepens towards outer habitats. We therefore suggest that - in addition to the oxygen levels in the water column, which determine whether macrofaunal communities can develop or not - it is the depth of the SMT and thus of sulfide production that determines which chemosynthetic communities are able to exploit the sulfide at depth. We hypothesize that large vesicomyid clams, by efficiently expanding the sulfate zone down into the sediment, could cut off smaller or less mobile organisms, as e.g. small clams and sulfur bacteria, from the sulfide source.