<p> We studied the interactions of glyoxylic acid, pyruvic acid and oxalic acid with ammonium and corresponding sodium salts in aqueous solutions simulating a dark and radical free atmospheric aqueous aerosol condition. Cleavage of a carbon-carbon bond in pyruvic acid and glyoxylic acid leading to the decarboxylation was observed in the presence of ammo&not;nium salts but was not observed from oxalic acid. At the beginning of the reaction, the decarboxylation appeared to proceeding slower compare to the later stage of reaction. The empirical rate constants for decarboxylation in the reaction solutions were estimated using a 'quasi-steady state' model: (i) glyoxylic acid and ammonium sulfate was 3.3 (&plusmn; 0.7)&times;10^-8 M^-1 s^-1; (ii) glyoxylic acid and ammonium nitrate was 1.4 (&plusmn; 0.3)&times;10^-8 M^-1 s^-1; (ii) glyoxylic acid and ammonium chloride was 1.9 (&plusmn; 0.2)&times;10^-8 M^-1 s^-1; and (iii) pyruvic acid and ammonium sulfate was 15.8 (&plusmn; 0.4)&times;10^-8 M^-1 s^-1. Negligible CO₂ was observed in the experiments with the corresponding sodium salts indicating the ammonium ion or ammonia is facilitating the carbon-carbon bond cleavage leading to carboxyl fragmentation of the &agr;-oxo carboxylic acids. It was observed that pyruvic acid undergoes decarboxylation at least four times faster than that of glyoxylic acid under similar reaction conditions. This indicates that the structure of the acid plays an important role in the decarboxylation. In the case of pyruvic acid, the reaction is likely faster because of the inhibited hydration of the carbonyl moiety due to the inductive effect of the adjacent methyl group. A tentative set of reaction mechanisms is proposed involving nucleophilic attack by ammonia on the carbonyl carbon leading to fragmentation of the carbon-carbon bond between the carbonyl and carboxyl carbons. Similar carbon-carbon bond cleavage is anticipated for &agr;-dicarbonyl compounds, which are structurally similar to the &agr;-oxo carboxylic acids. In the absence of photolysis and under limited availability of OH radicals, the decay of pyruvic acid can be dominated by the reaction with ammonium sulfate and can be an order of magnitude higher than the loss via reaction with the OH radical. Under similar conditions the reactions with ammonium salts are likely be a major sink for &agr;-oxo carboxylic acids in the atmospheric aqueous phase.</p>

<p> Radical chemistry has attracted a large amount of research interest over the last few decades and radical reactions have recently been recognized as powerful tools for organic synthesis. The synthetic applications of radicals have been demonstrated in many fields, including in the synthesis of complex natural products. Radical reactions have a number of inherent synthetic advantages over their ionic counterparts. For example, they typically proceed at fast reaction rates under mild and neutral conditions in a broad spectrum of solvents and show significantly greater functional group tolerance. Furthermore, radical processes have the capability of performing in a cascade fashion, allowing for the rapid construction of complex molecular structures with multiple stereogenic centers. To further enhance the synthetic applications of radical reactions, current efforts are devoted toward the development of effective approaches for the regioselective control of their reactivity as well as stereoselectivity, especially enantioselectivity, a challenging issue that is intrinsically challenged by the "free" nature of radical chemistry. </p><p> This research has identified a fundamentally new approach to radical reactions based on the concept of metalloradical catalysis (MRC) for controlling the stereoselectivity of both C- and N-centered radical reactions. Cobalt(II) porphyrins [Co(Por)], are stable metalloradicals, and have been shown to enable the activation of diazo reagents and azides to cleanly generate C- and N-centered radicals, respectively, with N₂ as the only byproduct in a controlled and catalytic manner. In addition to the radical nature of [Co(Por)], the low bond dissociation energy of Co-C/Co-N bonds plays a key role in the successful turnover of the Co(II)-based catalytic carbene and nitrene transfers. Through the support of porphyrin ligands with tunable electronic, steric, and chiral environments, this general concept of Co(II)-based metalloradical catalysis (Co-MRC) has been successfully applied to the development of various radical processes that enable stereoselective carbene and nitrene transfers. </p>

Thesis (Ph.D.)--Indiana University, Dept. of Chemistry, 2009. / Title from PDF t.p. (viewed on Jul 20, 2010). Source: Dissertation Abstracts International, Volume: 70-12, Section: B, page: 7527. Adviser: Bogdan Dragnea.

Thesis (Ph. D.)--Indiana University, Dept. of Chemistry, 2006. / "Title from dissertation home page (viewed July 16, 2007)." Source: Dissertation Abstracts International, Volume: 67-10, Section: B, page: 5718. Adviser: David E. Clemmer.

Thesis (Ph. D.)--University of Illinois at Urbana-Champaign, 2006. / Source: Dissertation Abstracts International, Volume: 67-11, Section: B, page: 6424. Adviser: Ralph G. Nuzzo. Includes bibliographical references. Available on microfilm from Pro Quest Information and Learning.

Thesis (Ph. D.)--University of Illinois at Urbana-Champaign, 2006. / Source: Dissertation Abstracts International, Volume: 67-11, Section: B, page: 6426. Advisers: Paul J.A. Kenis; Andrzej Wieckowski. Includes bibliographical references. Available on microfilm from Pro Quest Information and Learning.

<p> Cytochrome P450s (P450s) are a superfamily of enzymes that catalyze oxidation of unactivated hydrocarbons. However, the means by which P450s control (1) regioselectivity of their activity and (2) specificity in their molecular recognition remain largely elusive. Toward investigation of the role of dynamics in the regioselectivity of the archetypal cytochrome P450cam (P450cam), two-dimensional infrared spectroscopy has been applied with heme-bound carbon monoxide (CO) as an infrared probe of the active site. The data support a model for P450cam regioselectivity in which binding of different substrates to P450cam variably stabilizes the active site into two distinct states, each associated with different dynamics linked to different levels of regioselectivity. To investigate the role of conformational heterogeneity in P450cam substrate specificity, infrared spectoscopy was combined with the site-specific incorporation of nitrile probes at distinct P450cam microenvironments. This approach enabled differentiation of changes experienced at each of those environments when <i> d</i>-camphor and/or CO binds to the active site. Finally, the impact of conformational heterogeneity on the affinity of substrate molecular recognition by wild-type and mutant P450cam was evaluated using both CO and nitrile probes. This study suggests that the nature of the conformations populated in the unbound states influences the affinity for different substrates. Collectively, these studies provide new insight into the roles of conformational heterogeneity and dynamics in P450cam activity. Furthermore, these studies help to lay the foundation for efforts toward understanding the roles of conformational heterogeneity and dynamics in the function of human P450s, for which unraveling the mechanisms involved in Phase I metabolism is a topic of great pharmacological concern. </p><p>

<p> X-ray absorption spectromicroscopy combines microscopy and spectroscopy to provide rich information about the chemical organization of materials down to the nanoscale. But with richness also comes complexity: natural materials such as biological or environmental science specimens can be composed of complex spectroscopic mixtures of different materials. The challenge becomes how we could meaningfully simplify and interpret this information. Approaches such as principal component analysis and cluster analysis have been used in previous studies, but with some limitations that we will describe. This leads us to develop a new approach based on a development of non-negative matrix approximation (NNMA) analysis with both sparseness and spectra similarity regularizations. We apply this new technique to simulated spectromicroscopy datasets as well as a preliminary study of the large-scale biochemical organization of a human sperm cell. NNMA analysis is able to select major features of the sperm cell without the physically erroneous negative weightings or thicknesses in the calculated image which appeared in previous approaches.</p>

Thesis (Ph. D.)--University of Illinois at Urbana-Champaign, 2006. / Source: Dissertation Abstracts International, Volume: 68-02, Section: B, page: 0944. Adviser: Kenneth S. Suslick. Includes bibliographical references. Available on microfilm from Pro Quest Information and Learning.

The molecular mechanism of transmembrane signaling is unknown. Investigations have been hampered by the limits of current biophysical methods. Recently developed solid-state nuclear magnetic resonance (NMR) techniques provide a new approach for selective distance measurements probing structure and function of membrane proteins including ligand interactions. The environmental signal transduced by the serine receptor of bacterial chemotaxis is initiated by the attractant molecule serine. We initially demonstrated the feasibility of direct internuclear distance measurements between the 15N-amino labeled serine ligand and phenylalanine 13C-carbonyl labeled receptor. The two 4.0 ± 0.2 Å distances measured from the serine receptor to the ligand match the distances observed in the crystal structure of the ligand-binding domain fragment of the homologous aspartate receptor. Demonstration of the structural similarity between the aspartate receptor and serine receptor instigated further investigations into the mechanism of ligand specificity. To probe transmembrane signaling we developed a new constant time version of the rotational resonance solid-state NMR technique with improved reliability and efficiency. Combined with a site-directed strategy, this is a valuable and general tool for probing structure in large membrane proteins. A CO( i) to Cβ(i + 3) distance measurement along the periplasmic edge of the second membrane-spanning helix, provides a structural constraint for an unmapped region of the serine receptor. The 5.4 Å internuclear distance measured in the presence and in the absence of serine shows that any signaling mechanism must conserve the helical pitch of the second transmembrane domain. To test abundant and conflicting models of transmembrane signaling we measured an inter-helical distance across the dimer interface in the transmembrane region of the receptor. Computer modeling of this distance predicted sensitivity to proposed long-range ligand-induced conformational changes including piston, scissors, and rotational motions. Ile measured 5.0 Å distance provides a valuable structural constraint of tertiary structure. Both ligand-free and -bound signaling states of the receptor show the same inter-helical distance, suggesting that conformational changes are not propagated into the transmembrane domain. This approach provides a means for testing proposed mechanisms and mapping conformational changes involved in transmembrane signaling.