Relative basicities of free base porphyrins; understanding the role of macrocyclic distortion

Porphyrins have been the center of numerous investigations in different areas of chemistry, geochemistry, and the life sciences. In nature the conformation of the porphyrin macrocycle varies, depending on the function of its apoenzyme. It is believed that the conformation of the porphyrin ring is necessary for the enzyme to achieve its function and modify its reactivity. It is important to understand how the conformation of the porphyrin ring will influence its properties. ^ In synthetic porphyrins particular conformations and ring deformations can be achieved by peripheral substitution, metallation, core substitution, and core protonation among other alterations of the macrocycle. The macrocyclic distortions will affect the ring current, the ability of pyrroles to intramolecularly hydrogen bond and the relative basicity of each of the porphyrins. To understand these effects different theoretical models are used. The ground state structure of each of 19 free base porphyrins is determined using molecular mechanics (MM+) and semiempirical methods (PM3). The energetics of deformation of the macrocyclic core is calculated by carrying out single point energy calculations for the conformation achieved by each synthetic compound. Enthalpies of solution and enthalpies of protonation of 10 porphyrins with varying degrees of macrocyclic deformation and varying electron withdrawing groups in the periphery are determined using solution calorimetry. Using Hess's Law, the relative basicity of each of the different free base porphyrins is calculated. NMR results are described, including the determination of free energies of activation of ring tautomerization and hydrogen bonding for several compounds. It was found that in the absence of electronic effects, the greater macrocyclic deformation, the greater the basicity of the porphyrins. This basicity is attenuated by the presence of electron withdrawing groups and ability to of the macrocycle to intramolecularly hydrogen bond. ^

Relative basicities of free base porphyrins : understanding the role of macrocyclic distortion

Porphyrins have been the center of numerous investigations in different areas of chemistry, geochemistry, and the life sciences. In nature the conformation of the porphyrin macrocycle varies, depending on the function of its apoenzyme. It is believed that the conformation of the porphyrin ring is necessary for the enzyme to achieve its function and modify its reactivity. It is important to understand how the conformation of the porphyrin ring will influence its properties. In synthetic porphyrins particular conformations and ring deformations can be achieved by peripheral substitution, metallation, core substitution, and core protonation among other alterations of the macrocycle. The macrocyclic distortions will affect the ring current, the ability of pyrroles to intramolecularly hydrogen bond and the relative basicity of each of the porphyrins. To understand these effects different theoretical models are used. The ground state structure of each of 19 free base porphyrins is determined using molecular mechanics (MM+) and semiempirical methods (PM3). The energetics of deformation of the macrocyclic core is calculated by carrying out single point energy calculations for the conformation achieved by each synthetic compound. Enthalpies of solution and enthalpies of protonation of 10 porphyrins with varying degrees of macrocyclic deformation and varying electron withdrawing groups in the periphery are determined using solution calorimetry. Using Hess's Law, the relative basicity of each of the different free base porphyrins is calculated. NMR results are described, including the determination of free energies of activation of ring tautomerization and hydrogen bonding for several compounds. It was found that in the absence of electronic effects, the greater macrocyclic deformation, the greater the basicity of the porphyrins. This basicity is attenuated by the presence of electron withdrawing groups and ability to of the macrocycle to intramolecularly hydrogen bond.

Organic matter dynamics in the Florida coastal Everglades: A molecular marker and isotopic approach

Everglades National Park (ENP) is about to undergo the world's largest wetland restoration with the aim of improving the quality, timing and distribution of water flow. The changes in water flow are hypothesized to alter the nutrient fluxes and organic matter (OM) dynamics within ENP, especially in the estuarine areas. This study used a multi-proxy approach of molecular markers and stable δ 13C isotope measurements, to determine the present day OM dynamics in ENP. ^ OM dynamics in wetland soils/sediments have proved to be difficult to understand using traditional geochemical approaches. These are often inadequate to describe the multitude of OM sources (e.g. higher land plant, emergent vegetation, submerged vegetation) to the soils/sediments and the complex diagenetic processes that can alter the OM characteristics. A multi-proxy approach, however, that incorporates both molecular level and bulk parameter information is ideal to comprehend complex OM dynamics in aquatic environments. Therefore, biomass-specific molecular markers or proxies can be useful in tracing the sources and processing of OM. This approach was used to examine the OM dynamics in the two major drainage basins, Shark River Slough and Taylor River Slough, of ENP. Freshwater to marine transects were sampled in both systems for soils/sediments and suspended particulate organic matter (SPOM) to be characterized through bulk OM analyses, lipid biomarker determinations (e.g. sterols, fatty acids, hydrocarbons and triterpenoids) and compound-specific stable carbon isotope (δ 13C) determinations. ^ One key accomplishment of the research was the assessment of a molecular marker proxy (Paq) to distinguish between emergent/higher plant vegetation from submerged vegetation within ENP. This proxy proved to be quite useful at tracing OM inputs to the soils/sediments of ENP. A second key accomplishment was the development of a 3-way model using vegetation specific molecular markers. This novel, descriptive model was successfully applied to the estuarine areas of Taylor and Shark River sloughs, providing clear evidence of mixing of freshwater, estuarine and marine derived OM in these areas. In addition, diagenetic transformations of OM in these estuaries were found to be quite different between Taylor and Shark Rivers, and are likely a result of OM quality and hydrological differences. ^

The thermodynamics and statistical mechanics of protein folding

The physics of self-organization and complexity is manifested on a variety of biological scales, from large ecosystems to the molecular level. Protein molecules exhibit characteristics of complex systems in terms of their structure, dynamics, and function. Proteins have the extraordinary ability to fold to a specific functional three-dimensional shape, starting from a random coil, in a biologically relevant time. How they accomplish this is one of the secrets of life. In this work, theoretical research into understanding this remarkable behavior is discussed. Thermodynamic and statistical mechanical tools are used in order to investigate the protein folding dynamics and stability. Theoretical analyses of the results from computer simulation of the dynamics of a four-helix bundle show that the excluded volume entropic effects are very important in protein dynamics and crucial for protein stability. The dramatic effects of changing the size of sidechains imply that a strategic placement of amino acid residues with a particular size may be an important consideration in protein engineering. Another investigation deals with modeling protein structural transitions as a phase transition. Using finite size scaling theory, the nature of unfolding transition of a four-helix bundle protein was investigated and critical exponents for the transition were calculated for various hydrophobic strengths in the core. It is found that the order of the transition changes from first to higher order as the strength of the hydrophobic interaction in the core region is significantly increased. Finally, a detailed kinetic and thermodynamic analysis was carried out in a model two-helix bundle. The connection between the structural free-energy landscape and folding kinetics was quantified. I show how simple protein engineering, by changing the hydropathy of a small number of amino acids, can enhance protein folding by significantly changing the free energy landscape so that kinetic traps are removed. The results have general applicability in protein engineering as well as understanding the underlying physical mechanisms of protein folding. ^

Theoretical study of chloroperoxidase catalyzed chlorination of beta-cyclopentanedione and role of water in the chlorination mechanism

Chloroperoxidase (CPO) is a potential biocatalyst for use in asymmetric synthesis. The mechanisms of CPO catalysis are therefore of interest. The halogenation reaction, one of several chemical reactions that CPO catalyzes, is not fully understood and is the subject of this dissertation. The mechanism by which CPO catalyzes halogenation is disputed. It has been postulated that halogenation of substrates occurs at the active site. Alternatively, it has been proposed that hypochlorous acid, produced at the active site via oxidation of chloride, is released prior to reaction, so that halogenation occurs in solution. The free-solution mechanism is supported by the observation that halogenation of most substrates often occurs non-stereospecifically. On the other hand, the enzyme-bound mechanism is supported by the observation that some large substrates undergo halogenation stereospecifically. The major purpose of this research is to compare chlorination of the substrate β-cyclopentanedione in the two environments. One study was of the reaction with limited hydration because such a level of hydration is typical of the active site. For this work, a purely quantum mechanical approach was used. To model the aqueous environment, the limited hydration environment approach is not appropriate. Instead, reaction precursor conformations were obtained from a solvated molecular dynamics simulation, and reaction of potentially reactive molecular encounters was modeled with a hybrid quantum mechanical/molecular mechanical approach. Extensive work developing parameters for small molecules was pre-requisite for the molecular dynamics simulation. It is observed that a limited and optimized (active-site-like) hydration environment leads to a lower energetic barrier than the fully solvated model representative of the aqueous environment at room temperature, suggesting that the stable water network near the active site is likely to facilitate the chlorination mechanism. The influence of the solvent environment on the reaction barrier is critical. It is observed that stabilization of the catalytic water by other solvent molecules lowers the barrier for keto-enol tautomerization. Placement of water molecules is more important than the number of water molecules in such studies. The fully-solvated model demonstrates that reaction proceeds when the instantaneous dynamical water environment is close to optimal for stabilizing the transition state.

Using soil profiles of seeds and molecular markers as proxies for sawgrass and wet prairie slough vegetation in Shark Slough, Everglades National Park

We measured the abundance of Cladium jamaicense (Crantz) seeds and three biomarkers in freshwater marsh soils in Shark River Slough (SRS), Everglades National Park (ENP) to determine the degree to which these paleoecological proxies reflect spatial and temporal variation in vegetation. We found that C. jamaicense seeds and the biomarkers Paq, total lignin phenols (TLP) and kaurenes analyzed from surface soils were all significantly correlated with extant aboveground C. jamaicense biomass quantified along a vegetation gradient from a C. jamaicense to a wet prairie/slough (WPS) community. Our results also suggest that these individual proxies may reflect vegetation over different spatial scales: Paq and kaurenes correlated most strongly (R 2 = 0.88 and 0.99, respectively) with vegetation within 1 m of a soil sample, while seeds and TLP reflected vegetation 0–20 m upstream of soil samples. These differences in the spatial scale depicted by the different proxies may be complementary in understanding aspects of historic landscape patterning. Soil profiles of short (25 cm) cores showed that downcore variation in C. jamaicense seeds was highly correlated with two of the three biomarkers (Paq, R 2 = 0.84, p<0.005; TLP, R 2 = 0.97, p<0.0001), and all four of the proxies indicated a recent increase in C. jamaicense biomass at the site. Using a preliminary depth-to-age relationship based on matching charcoal peaks with available ENP fire records (1980-present) specific to our coring site, we found that peak-depths in C. jamaicense seed concentration appeared to correspond to recent minimum water levels (e.g., 1989 and 2001), and low seed abundance corresponded to high water levels (e.g., 1995), consistent with the known autecology of C. jamaicense. In summary, the combination of C. jamaicense seeds and biomarkers may be useful for paleoecological reconstruction of vegetation change and ultimately in guaging the success of ongoing efforts to restore historic hydrologic conditions in the South Florida Everglades.

Quantitative Analysis and Determination of Microcystin in water by Capillary Electrophoresis Mass Spectrometry

The presence of harmful algal blooms (HAB) is a growing concern in aquatic environments. Among HAB organisms, cyanobacteria are of special concern because they have been reported worldwide to cause environmental and human health problem through contamination of drinking water. Although several analytical approaches have been applied to monitoring cyanobacteria toxins, conventional methods are costly and time-consuming so that analyses take weeks for field sampling and subsequent lab analysis. Capillary electrophoresis (CE) becomes a particularly suitable analytical separation method that can couple very small samples and rapid separations to a wide range of selective and sensitive detection techniques. This paper demonstrates a method for rapid separation and identification of four microcystin variants commonly found in aquatic environments. CE coupled to UV and electrospray ionization time-of-flight mass spectrometry (ESI-TOF) procedures were developed. All four analytes were separated within 6 minutes. The ESI-TOF experiment provides accurate molecular information, which further identifies analytes.