The Kelvin measurement is a sensitive and label-free method based on work function measurements. Work function, the minimum energy required to extract an electron from a metallic material, can be shifted by ionic charges and dipoles present on the surface. The scanning Kelvin nanoprobe (SKN), a probe-based microscopic imaging device, was used in the detection of work function changes induced by surface-immobilized oligonucleotide / DNA microarrays. The scanning Kelvin nanoprobe was able to study DNA microarrays smaller than 100 µm in size, produced with solution concentrations lower than 10 µmol/L. The limit of detection was estimated to be 15 ng DNA. Better than ± 10% relative variation was achieved for replicate spots. It was observed that higher surface densities of immobilized DNA molecules produced greater work function changes than lower surface densities. Surface saturation with increasing solution concentrations was observed as well. Also, longer strands of DNA produced greater work function changes than shorter strands. Statistical analysis of the results confirmed that non-complementary DNA strands could be differentiated from complementary strands by the Kelvin measurement. Single base mismatches on the complementary DNA strands were also detected by the Kelvin measurement. Different substrate materials were tested in the search for reliable and inexpensive sample slides with satisfactory DNA immobilization efficiency. Materials such as silicon wafers, gold-coated glass slides, gold-coated stainless steel slides, and gold compact discs (CD) were tested. A surface property comparison of gold-coated glass slides and compact discs was made by atomic force microscopy (AFM), and revealed very different microscopic features. The effect of cleaning on gold-coated glass slides was examined by time-of-flight secondary ion mass spectrometry (TOF-SIMS). Technical improvements were made to the SKN equipment progressively. Several revisions to the tip holder design have been employed for better electromagnetic shielding, enhanced robustness and easier tip change. An older signal generator was replaced with a professional PC audio card to provide more stable signal and more convenient on-screen fine tuning, also at a reduced cost. The Labview-based controlling program has also been improved through multiple iterations.

Preliminary work towards the development of novel biosensing interfaces for EMPAS (ElectroMagnetic Piezoelectric Acoustic Sensor) is presented in this manuscript. This method involves the use of unprecedented thiosulfonate-based linkers to construct robust and durable SAMs (Self-Assembling Monolayer) onto piezoelectric quartz crystals, which can chemoselectively immobilize thiol-containing biomolecules under aqueous conditions in a single, straightforward, reliable and coupling-free manner. Initial efforts are devoted to the construction of SAMs and the subsequent immobilization of thiol-containing biomolecules, and then characterization by CAMs (Contact Angle Measurement) and ARXPS (Angle-Resolved X-ray Photoelectron Spectroscopy). This method is then implemented into the construction of biosensing interfaces dedicated to the detection of avidin. With the incorporation of OEG (Oligo(Ethylene Glycol)) backbone and diluent in the method, 14-fold difference in signal response of EMPAS was observed between biotinylated and unfunctionalized SAMs.

Preliminary work towards the development of novel biosensing interfaces for EMPAS (ElectroMagnetic Piezoelectric Acoustic Sensor) is presented in this manuscript. This method involves the use of unprecedented thiosulfonate-based linkers to construct robust and durable SAMs (Self-Assembling Monolayer) onto piezoelectric quartz crystals, which can chemoselectively immobilize thiol-containing biomolecules under aqueous conditions in a single, straightforward, reliable and coupling-free manner. Initial efforts are devoted to the construction of SAMs and the subsequent immobilization of thiol-containing biomolecules, and then characterization by CAMs (Contact Angle Measurement) and ARXPS (Angle-Resolved X-ray Photoelectron Spectroscopy). This method is then implemented into the construction of biosensing interfaces dedicated to the detection of avidin. With the incorporation of OEG (Oligo(Ethylene Glycol)) backbone and diluent in the method, 14-fold difference in signal response of EMPAS was observed between biotinylated and unfunctionalized SAMs.

The Kelvin measurement is a sensitive and label-free method based on work function measurements. Work function, the minimum energy required to extract an electron from a metallic material, can be shifted by ionic charges and dipoles present on the surface. The scanning Kelvin nanoprobe (SKN), a probe-based microscopic imaging device, was used in the detection of work function changes induced by surface-immobilized oligonucleotide / DNA microarrays. The scanning Kelvin nanoprobe was able to study DNA microarrays smaller than 100 µm in size, produced with solution concentrations lower than 10 µmol/L. The limit of detection was estimated to be 15 ng DNA. Better than ± 10% relative variation was achieved for replicate spots. It was observed that higher surface densities of immobilized DNA molecules produced greater work function changes than lower surface densities. Surface saturation with increasing solution concentrations was observed as well. Also, longer strands of DNA produced greater work function changes than shorter strands. Statistical analysis of the results confirmed that non-complementary DNA strands could be differentiated from complementary strands by the Kelvin measurement. Single base mismatches on the complementary DNA strands were also detected by the Kelvin measurement. Different substrate materials were tested in the search for reliable and inexpensive sample slides with satisfactory DNA immobilization efficiency. Materials such as silicon wafers, gold-coated glass slides, gold-coated stainless steel slides, and gold compact discs (CD) were tested. A surface property comparison of gold-coated glass slides and compact discs was made by atomic force microscopy (AFM), and revealed very different microscopic features. The effect of cleaning on gold-coated glass slides was examined by time-of-flight secondary ion mass spectrometry (TOF-SIMS). Technical improvements were made to the SKN equipment progressively. Several revisions to the tip holder design have been employed for better electromagnetic shielding, enhanced robustness and easier tip change. An older signal generator was replaced with a professional PC audio card to provide more stable signal and more convenient on-screen fine tuning, also at a reduced cost. The Labview-based controlling program has also been improved through multiple iterations.

Accurate measurements of the trace nitrogenous atmospheric species amines (NR3) and nitrous acid (HONO) are essential to understanding their chemistry and potential influence on new particle formation and oxidation capacity in the atmospheric boundary-layer, respectively. Ambient Ion Monitor – Ion Chromatography (AIM-IC) methods developed in this work have provided quantitative online observations of atmospheric amines in the gaseous and condensed phases with detection limits of pptv and ng m-3 at hourly time resolution. Size-resolved particle observations demonstrated maximum amine mass loadings in 320 – 560 nm particles, and an increase in importance relative to ammonium for the smallest particles measured (56 – 180 nm). In particular, the size-resolved samples analysed in this work indicate that bulk aerosol measurements may not be appropriate for modelling the atmospheric processes that govern the incorporation of amines and ammonia in to atmospheric particles. Measurements of HONO made during the two intensive field campaigns (NACHTT, CalNex) and a lab study provided a new perspective on the interactions of this trace compound with ground surfaces. Integrated atmospheric column measurements of HONO and NO2 during NACHTT provided clear evidence that the ground surface dominates HONO production and loss at night. Simultaneous measurements of the gas and particle phases made by the AIM-IC system during CalNex demonstrated the potential for reactive uptake of HONO on mineral dust/soil as a nocturnal sink. Similarly, the potential for nitrite salts to react with strong acids, displacing HONO during the day was suggested by this dataset. Lab study results showed that HONO is taken up irreversibly on carbonate salts and real soil extracts. Relative humidity-dependent reactive uptake coefficients were derived. Subsequent release of HONO by displacement reactions with HNO3 and HCl was also confirmed. Together, these field and lab studies have produced a new picture of HONO surface interactions by providing i) a more explicit description of a nocturnal sink of HONO that could act as a surface reservoir and ii) a new mechanism for daytime HONO formation that does not require NO2.

Accurate measurements of the trace nitrogenous atmospheric species amines (NR3) and nitrous acid (HONO) are essential to understanding their chemistry and potential influence on new particle formation and oxidation capacity in the atmospheric boundary-layer, respectively. Ambient Ion Monitor – Ion Chromatography (AIM-IC) methods developed in this work have provided quantitative online observations of atmospheric amines in the gaseous and condensed phases with detection limits of pptv and ng m-3 at hourly time resolution. Size-resolved particle observations demonstrated maximum amine mass loadings in 320 – 560 nm particles, and an increase in importance relative to ammonium for the smallest particles measured (56 – 180 nm). In particular, the size-resolved samples analysed in this work indicate that bulk aerosol measurements may not be appropriate for modelling the atmospheric processes that govern the incorporation of amines and ammonia in to atmospheric particles. Measurements of HONO made during the two intensive field campaigns (NACHTT, CalNex) and a lab study provided a new perspective on the interactions of this trace compound with ground surfaces. Integrated atmospheric column measurements of HONO and NO2 during NACHTT provided clear evidence that the ground surface dominates HONO production and loss at night. Simultaneous measurements of the gas and particle phases made by the AIM-IC system during CalNex demonstrated the potential for reactive uptake of HONO on mineral dust/soil as a nocturnal sink. Similarly, the potential for nitrite salts to react with strong acids, displacing HONO during the day was suggested by this dataset. Lab study results showed that HONO is taken up irreversibly on carbonate salts and real soil extracts. Relative humidity-dependent reactive uptake coefficients were derived. Subsequent release of HONO by displacement reactions with HNO3 and HCl was also confirmed. Together, these field and lab studies have produced a new picture of HONO surface interactions by providing i) a more explicit description of a nocturnal sink of HONO that could act as a surface reservoir and ii) a new mechanism for daytime HONO formation that does not require NO2.

This thesis explored new methods for understanding the fate and transport of halogenated organic contaminants in the environment. A theoretical method of hazard assessment of chemical mixtures containing large numbers of components was developed and its application illustrated using polychlorinated alkanes, toxaphene, and halogenated dibenzo-para-dioxins and furans. Partitioning properties predicted by high-throughput quantitative structure property relationships were used to locate mixture constituents on plots displaying equilibrium phase distribution in various environmental compartments and the potential for bioaccumulation and long range transport. Potentially hazardous components were identified graphically for more detailed assessments. The applicability of XAD-resin based passive air samplers (XAD-PAS) for studying neutral polyfluoroalkyl substances (nPFAS) in the atmosphere was tested empirically. XAD-PASs have sufficiently high uptake capacity to yield temporally averaged nPFAS concentrations over period as long as a year. When applied as part of the Global Atmospheric Passive Sampling network, nPFAS were found to be truly global contaminants.

This thesis explored new methods for understanding the fate and transport of halogenated organic contaminants in the environment. A theoretical method of hazard assessment of chemical mixtures containing large numbers of components was developed and its application illustrated using polychlorinated alkanes, toxaphene, and halogenated dibenzo-para-dioxins and furans. Partitioning properties predicted by high-throughput quantitative structure property relationships were used to locate mixture constituents on plots displaying equilibrium phase distribution in various environmental compartments and the potential for bioaccumulation and long range transport. Potentially hazardous components were identified graphically for more detailed assessments. The applicability of XAD-resin based passive air samplers (XAD-PAS) for studying neutral polyfluoroalkyl substances (nPFAS) in the atmosphere was tested empirically. XAD-PASs have sufficiently high uptake capacity to yield temporally averaged nPFAS concentrations over period as long as a year. When applied as part of the Global Atmospheric Passive Sampling network, nPFAS were found to be truly global contaminants.

Mass spectrometry has become an important tool for analysis of protein complexes. This study utilizes electrospray ionization (ESI) coupled to a Fourier transform ion cyclotron resonance mass spectrometer (FTICR-MS) to analyze noncovalent complexes in the gas phase. Binding of cucurbit[7]uril (CB7) to intact bovine insulin and the B-chain of insulin was investigated. Competition experiments involving the B-chain and a mutant B-chain were performed to probe the solution-phase binding site. Electron capture dissociation (ECD) of CB7 complexed to intact insulin and to the B-chain, produced a series of peptidic fragments of insulin in complex with CB7. Analysis of these fragments allowed the determination of the apparent gas-phase binding site, which appears different than the proposed solution-phase binding-site. These studies thus suggest that CB7 migrates when the complex is transferred from solution to gas phase. The results of this study caution against using ECD-MS as a stand-alone structural probe of solutionphase binding.

The unique optical properties of quantum dots (QDs) have been widely used to develop bioassays based on Fluorescence Resonance Energy Transfer (FRET). The solid-phase assays using QDs as FRET donors have numerous practical advantages, including at least 10-fold enhancement in FRET efficiency, which is not immediately explained by theoretical predictions that model energy transfer processes of QDs in two-dimensional layers. Donor-acceptor separation distance, acceptor and donor concentrations were found to influence FRET efficiency in solid-phase assays. A novel immobilization strategy was implemented which made use of the high affinity of imidazole moieties to QD shells to build solid-phase QD bioassays. A 96-well polystyrene plate is presented as a platform suitable for rapid and convenient multiplexed detection. A typical microtiter plate reader was shown to be capable of discriminating different FRET pairs to picomol detection levels of target oligonucleotides. Furthermore, the QD-FRET bioassays provided for mismatch discrimination, and multiple cycles of regeneration were also demonstrated.