Polar substituent effects in the bicyclo[1.1.1]pentane ring system: acidities of 3-substituted bicyclo[1.1.1]pentane-1-carboxylic acids

Experimental gas-phase acidities are reported for a series of 3-substituted (X) bicyclo [1.1.1]pent-1-yl carboxylic acids (1, Y = COOH). A comparison with available calculated data (MP2/6-311++G**// B3LYP/6-311+G**) reveals good agreement. The relative substituent effects are shown to be adequately described by a much lower level of theory (B3LYP/6-31+G*). Various correlations are presented which clearly point to polar field effects as being the origin of the relative acidities.     

On the chemistry of flavin-dependent oxygen activation III. synthesis of 1.10a-dihydroflavin and its 10.10-aring opened derivative as model chromophores for enzyme-bound intermediates

Model chromophores of 1.10-dihydroflavin and its 10.10a-ring opened derivative have been isolated. By comparison with enzymatic intermediates, reaction mechanisms of flavin-dependent oxygenase and luciferase are discussed in terms of chemical structure.     

NO Chemisorption on Pt(111), Rh/Pt(111), and Pd/Pt(111)

The chemisorption of NO on clean Pt(111), Rh/Pt(111) alloy, and Pd/Pt(111) alloy surfaces has been studied by first principles density functional theory (DFT) computations. It was found that the surface compositions of the surface alloys have very different effects on the adsorption of NO on Rh/Pt(111) versus that on Pd/Pt(111). This is due to the different bond strength between the two metals in each alloy system. A complex d-band center weighting model developed by authors in a previous study for SO2 adsorption is demonstrated to be necessary for quantifying NO adsorption on Pd/Pt(111). A strong linear relationship between the weighted positions of the d states of the surfaces and the molecular NO adsorption energies shows the closer the weighted d-band center is shifted to the Fermi energy level, the stronger the adsorption of NO will be. The consequences of this study for the optimized design of three-way automotive catalysts, (TWC) are also discussed.     

Oxidation of methionine residues in aqueous solutions: free methionine and methionine in granulocyte colony-stimulating factor

The free energy barriers and a mechanism of the oxidation of the amino acid methionine in water and in granulocyte colony-stimulating factor (G-CSF) are analyzed via combined quantum mechanical and molecular mechanical (QM/MM) methods, constrained molecular dynamics, and committor probability calculations. The computed free energy barrier of free methionine amino acid is very close to the measured value (14.7 +/- 1.2 versus 15.5 +/- 0.02 kcal/mol). The reaction coordinate was found to be the difference between the O-O bond of H2O2 and the S-O bond, where the S is the sulfur atom of the methionine residue. It was confirmed by computing the committor probability distribution and the distribution of constrained forces that this coordinate is not coupled to the activation of other degrees of freedom. The computed free energies of the oxidation of methionine residues in G-CSF indicate that the protein environment has insignificant effects on the reaction barriers of oxidation. This result further validates our proposal that the access of solvent to methionine sites, as measured by the two-shell water coordination number, governs the kinetics of the oxidation reaction of methionine groups in a protein molecule. We also found that the number of hydrogen bonds between the distal oxygen of H2O2 and the water molecules near the methionine increases along the reaction coordinate as oxidation progresses, indicating that the charge separation developed during the oxidation by H2O2 is stabilized by specific interactions with water molecules, such as hydrogen bonding.     

Diastereofacial selectivity in some 4‐substituted (X) 2‐adamantyl derivatives: electronic versus steric effects

π‐Facial selectivity data for the reduction and methylation of some 4^ax‐substituted (X) 2‐adamantanones ( 3 , Y = O) as well as the nucleophilic trapping of secondary and tertiary 4^ax‐substituted (X)‐2‐adamantyl cations ( 4 ; R = H and CH₃, respectively) and the 4‐methylene‐2‐adamantyl radical ( 8 ) are presented. The pronounced anti‐face selectivities observed for ( 3 , Y = O and 4 , R = CH₃) emphasize the importance of the steric factor as expected for systems with a strong steric bias. However, the dominant syn‐face capture of 4 (R = H) was completely unexpected and highlights a subtle interplay between steric and electronic effects. Finally, the very high anti‐face stereoselectivity for the trapping of ( 8 ) with the trimethylstannyl anion (Me₃Sn^?) is rationalized in terms of an electrostatic effect overwhelming the steric factor. Copyright © 2007 John Wiley & Sons, Ltd.     

Direct capillary electrophoretic detection of carbohydrate-deficient transferrin in neat serum

Transferrin, an iron transport protein found in serum and cerebrospinal fluid, is known to be microheterogeneous with respect to its carbohydrate and sialic acid content. The forms of transferrin deficient in sialic acid and/or carbohydrate, termed carbohydrate-deficient transferrin (CDT), have been of clinical interest for almost two decades as a result of the initial finding that elevated CDT concentrations are associated with chronic, excessive alcohol abuse. We demonstrate the utility of capillary electrophoresis for examining the CDT sialoform profile via the direct electrophoresis of serum. The need for negligible preelectrophoresis sample preparation and absence of postelectrophoresis processing dramatically decreases analysis time compared to slab gel-based separations. Using a fluorocarbon-coated capillary containing a hydroxyethyl cellulose/borate buffer, the high resolution separation of serum components is effected in less than 30 min. Under these conditions, the beta region proteins (including transferrin) are well resolved from the alpha-2 and gamma zone proteins in a window where the individual transferrin sialoforms can be detected. The usefulness of this method is demonstrated with the electrophoresis of serum from subjects known to be either non-alcoholic and alcoholic.     

A general set of order parameters for molecular crystals

Crystallization is fundamental to many aspects of physics and chemistry in addition to being of technological relevance, for example, in the chemical, food, and pharmaceutical industries. However, the design of crystalline materials and crystallization processes is often challenging due to the many variables that can influence the process. As a part of an effort to gain a molecular-level understanding of the way molecules aggregate and organize themselves into crystal structures, in this work we present a new method to construct order parameters suitable for the study of crystallization and polymorph transformations in molecular systems. Our order parameters can be systematically defined for complex systems using information that can be obtained from simple molecular dynamics simulations of the crystals. We show how to construct the order parameters for the study of three different systems: the formation of α-glycine crystals in solution, the crystallization of benzene from the melt, and the polymorph transformation of terephthalic acid. Finally, we suggest how these order parameters could be used to study order-disorder transitions in molecular systems.     

Correlation of observed and model vibrational frequencies for aqueous organic acids: UV resonance Raman spectra and molecular orbital calculations of benzoic, salicylic, and phthalic acids

The aromatic carboxylic acids benzoic, salicylic and phthalic acid were used to study the interaction of soluble organics compounds with metal cations. To accomplish this, we have developed methods for studying the carboxylic acids using UV resonance Raman (UVRR) combined with molecular orbital density functional theory calculations. The pH values of the acid solutions were based on the pK(a)'s for the different acids to examine the neutral and charged species. Deprotonation of the organic acids was detectable down to 10(-4)M using UVRR (two orders of magnitude lower than previous vibrational spectroscopy studies). Limitations to decreasing the concentration lower using the current UVRR facilities are discussed. Two methods were used to calculate the optimized geometry and frequencies of the acids: explicit and continuum solvation. The frequencies from the experimental spectra were then compared to the theoretical results obtained from the two methods.