Syntheses of Cross-Linking Agents, Molecular Modeling of Oligonucleotides and Polypeptide-Ion Complexes

Each section of this thesis will be subdivided into three parts encompassing all of the research in which I have been involved during the past three years. These will be referred to under the headings "Syntheses:' "Molecular Modeling," and "Cross-linking Efficiencies." Each of these subdivisions may have divisions within them when necessary in order to fully detail the research.

Mapping and molecular modeling of S-adenosyl-L-methionine binding sites in N-methyltransferase domains of the multifunctional polypeptide cyclosporin synthetase

We employed a highly specific photoaffinity labeling procedure, using 14C-labeled S-adenosyl-L-methionine (AdoMet) to define the chemical structure of the AdoMet binding centers on cyclosporin synthetase (CySyn). Tryptic digestion of CySyn photolabeled with either [methyl-14C]AdoMet or [carboxyl-14C]AdoMet yielded the sequence H2N-Asn-Asp-Gly-Leu-Glu-Ser-Tyr-Val-Gly-Ile-Glu-Pro-Ser-Arg-COOH (residues 10644-10657), situated within the N-methyltransferase domain of module 8 of CySyn. Radiosequencing detected Glu10654 and Pro10655 as the major sites of derivatization. [carboxyl-14C]AdoMet in addition labeled Tyr10650. Chymotryptic digestion generated the radiolabeled peptide H2N-Ile-Gly-Leu-Glu-Pro-Ser-Gln-Ser-Ala-Val-Gln-Phe-COOH, corresponding to amino acids 2125-2136 of the N-methyltransferase domain of module 2. The radiolabeled amino acids were identified as Glu2128 and Pro2129, which are equivalent in position and function to the modified residues identified with tryptic digestions in module 8. Homology modeling of the N-methyltransferase domains indicates that these regions conserve the consensus topology of the AdoMet binding fold and consensus cofactor interactions seen in structurally characterized AdoMet-dependent methyltransferases. The modified sequence regions correspond to the motif II consensus sequence element, which is involved in directly complexing the adenine and ribose components of AdoMet. We conclude that the AdoMet binding to nonribosomal peptide synthetase N-methyltransferase domains obeys the consensus cofactor interactions seen among most structurally characterized low molecular weight AdoMet-dependent methyltransferases.

The influence of geometry and wall character of pores on the permeation of ions and water through desalination membranes

The transport of water and ions across mimicked nanotube membranes with pseudo atoms is studied using molecular dynamics simulations under equilibrium conditions and hydrostatic pressure. Different pore surface properties are constructed by assigning partial charges on the sites of specified atoms to explore the influence of charges and polarity. The energetics of water and ion transports through the nanopores was calculated to evaluate their filterability to water. The simulation results show that the free energy barriers to water and ion conductions much depend on the charges at the pore entrance and the dipole within the pore. The membranes with hydrophobic pores and negatively charged entrances would be very efficient in the water transport and ion rejection. The charges and dipoles of the pore wall and the aligned dipoles of water molecules in the pore can create a significant force on ions.

Improved extraction of heavy metal ions using membrane technology

Investigates tha application of polymer membranes in industrial wastewater treatment. Several novel membrane systems have been developed. The new systems overcome the problems of low extractant capacity and slow rate of extraction of the traditional membrane system. These new systems offer significant scope for the treatment of industrial wastewater containing heavy metal ions.

Using polyatomic primary ions to probe an amino acid and a nucleic base in water ice

In this study on pure water ice, we show that protonated water species [H₂O]_nH⁺ are more prevalent than (H₂O)_n⁺ ions after bombardment by Au+ monoatomic and Au₃⁺ and C₆₀⁺ polyatomic projectiles. This data also reveals significant differences in water cluster yields under bombardment by these three projectiles. The amino acid alanine and the nucleic base adenine in solution have been studied and have been shown to have an effect on the water cluster ion yields observed using an Au₃⁺ ion beam.

Wool powders used as sorbents to remove Co2+ ions from aqueous solution

The Co2+ sorption of two wool powders was investigated using its radioisotope 57Co (T1/2=271.8 days and γ=122.1 and 136.5 keV) as a tracer. The effects of the type of buffer, the pH value, the contact time and the initial concentration of Co2+ on the sorption behaviour of wool powders were studied. The Co2+ releasing ability of wool powders and the re-use of wool powders to sorb Co2+ were also examined. The optimum sorption of Co2+ by the powders occurred at pH 8 in phosphate buffer and pH 10 in ammonium sulphate buffer. Fourier-transform infrared spectroscopy (FTIR) was used to study the changes in chemical structure of the wool after exposure to both buffer solutions. Compared to the untreated wool fibre, the fine wool powders showed rapid sorption rates and high sorption capacities for Co2+. Co2+ ions were recovered after exposing the Co2+ loaded wool to HCl (0.1 M) and buffer at pH 3 (glycine/sodium chloride). After releasing Co2+ ions from wool powders, the efficiency of wool powders re-used to sorb Co2+ was 80% of that of the fresh wool powders. It is concluded from this study that wool powder can be used as an efficient sorbent to remove and release Co2+ from solution.

Sub-ppt detection limits for copper ions with Gly-Gly-His modified electrodes

An electrochemical metal ion sensor has been developed with a detection limit of less than 0.2 ppt by the covalent attachment of the tripeptide Gly-Gly-His as a recognition element to a 3-mercaptopropionic acid modified gold electrode.

Fast colorimetric detection of copper ions using L-Cysteine functionalized gold nanoparticles

This communication reports an efficient visual detection method of Cu²⁺ by L-cysteine functionalized gold nanoparticles in aqueous solution. Upon exposure to Cu²⁺, the gold nanoparticle solution changed from red to blue, in response to surface plasmon absorption of dispersed and aggregated nanoparticles. This colorimetric sensor allows a rapid quantitative assay of Cu²⁺ down to the concentration range of 10⁻⁵ M. Recognition of Cu²⁺ and formation of the aggregates are proposed to occur via a 2 : 1 sandwich complex between L-cysteine and Cu²⁺.

Extraction of copper(II) ions from aqueous solutions with a methimazole-based ionic liquid

The recently synthesized ionic liquid (IL) 2-butylthiolonium bis(trifluoromethanesulfonyl)amide, [mimSBu][NTf2], has been used for the extraction of copper(II) from aqueous solution. The pH of the aqueous phase decreases upon addition of [mimSBu]+, which is attributed to partial release of the hydrogen attached to the N(3) nitrogen atom of the imidazolium ring. The presence of sparingly soluble water in [mimSBu][NTf2] also is required in solvent extraction studies to promote the incorporation of Cu(II) into the [mimSBu][NTf2] ionic liquid phase. The labile copper(II) system formed by interacting with both the water and the IL cation component has been characterized by cyclic voltammetry as well as UV−vis, Raman, and 1H, 13C, and 15N NMR spectroscopies. The extraction process does not require the addition of a complexing agent or pH control of the aqueous phase. [mimSBu][NTf2] can be recovered from the labile copper−water−IL interacting system by washing with a strong acid. High selectivity of copper(II) extraction is achieved relative to that of other divalent cobalt(II), iron(II), and nickel(II) transition-metal cations. The course of microextraction of Cu2+ from aqueous media into the [mimSBu][NTf2] IL phase was monitored in situ by cyclic voltammetry using a well-defined process in which specific interaction with copper is believed to switch from the ionic liquid cation component, [mimSBu], to the [NTf2] anion during the course of electrochemical reduction from Cu(II) to Cu(I). The microextraction−voltammetry technique provides a fast and convenient method to determine whether an IL is able to extract electroactive metal ions from an aqueous solution.

Contribution of fungi to primary biogenic aerosols in the atmosphere : active discharge of spores, carbohydrates, and inorganic ions by Asco- and Basidiomycota

Spores and related chemical compounds from actively spore-discharging Ascomycota (AAM) and actively spore-discharging Basidiomycota (ABM) are primary biogenic components of air particulate matter (characteristic size range 1–10 μm). Measurement results and budget calculations based on investigations in Amazonia (Balbina, Brazil, July 2001) indicate that the forcible discharge of fungal spores may account for a large proportion of coarse air particulate matter in tropical rainforest regions during the wet season. For the particle diameter range of 1–10 μm, the estimated proportions are ~25% during day-time, ~45% at night, and ~35% on average. For the sugar alcohol, mannitol, the budget calculations indicate that it is suitable for use as a molecular tracer for actively discharged basidiospores (ABS), and that the literature-derived emission ratio of about 5 pg per ABS may be taken as a representative average. ABM emissions may account for most of the atmospheric abundance of mannitol, and can explain the observed diurnal cycle (higher abundance at night). ABM emissions of hexose carbohydrates might also account for a significant proportion of glucose and fructose in air particulate matter, but the literature-derived ratios are not consistent with the observed diurnal cycle (lower abundance at night). AAM emissions appear to account for a large proportion of potassium in air particulate matter over tropical rainforest regions during the wet season, and they can also explain the observed diurnal cycle (higher abundance at night). The results of our investigations and budget calculations for tropical rainforest aerosols are consistent with measurements performed at other locations.

Based on the average abundance of mannitol in particulate matter, which is consistent with the above emission ratio and the observed abundance of ABS, we have also calculated a value of ~17 Tg yr−1 as a first estimate for the global average emission rate of ABS over land surfaces. Comparisons with estimated rates of emission and formation of other major types of organic aerosol (~47 Tg yr−1 of anthropogenic primary organic aerosol; 12–70 Tg yr−1 of secondary organic aerosol) indicate that emissions from actively spore-discharging fungi should be taken into account as a significant source of organic aerosol. Their effects might be particularly important in tropical regions, where both physicochemical processes in the atmosphere and biological activity at the Earth's surface are particularly intense, and where the abundance of fungal spores and related chemical compounds are typically higher than in extratropical regions.