Reactions of the peroxo intermediate of soluble methane monooxygenase hydroxylase with ethers

Soluble methane monooxygenase (sMMO) isolated from Methylococcus capsulatus (Bath) utilizes a carboxylate-bridged diiron center and dioxygen to catalyze the conversion of methane to methanol. Previous studies revealed that a di(mu-oxo)diiron(IV) intermediate termed Q is responsible for the catalytic activity with hydrocarbons. In addition, the peroxodiiron(III) intermediate (H(peroxo)) that precedes Q formation in the catalytic cycle has been demonstrated to react with propylene, but its reactivity has not been extensively investigated. Given the burgeoning interest in the existence of multiple oxidants in metalloenzymes, a more exhaustive study of the reactivity of H(peroxo) was undertaken. The kinetics of single turnover reactions of the two intermediates with ethyl vinyl ether and diethyl ether were monitored by single- and double-mixing stopped-flow optical spectroscopy. For both substrates, the rate constants for reaction with H(peroxo) are greater than those for Q. An analytical model for explaining the transient kinetics is described and used successfully to fit the observed data. Activation parameters were determined through temperature-dependent studies, and the kinetic isotope effects for the reactions with diethyl ether were measured. The rate constants indicate that H(peroxo) is a more electrophilic oxidant than Q. We propose that H(peroxo) reacts via two-electron transfer mechanisms, and that Q reacts by single-electron transfer steps.     

I.M. Kolthoff,P.J. Elving and F.H. Stross (Editors), Treatise on analytical chemistry. Part III. Analytical chemistry in industry : Vol. 2, Wiley-Interscience,New York, 1971, xxiv+597 pp., price £ 12.00

The titration of some substituted azoles in non-aqueous solution has been studied and their relative basic strengths determined. Differentiating titration of mixtures of substituted imidazoles is only possible when one of the imidazoles is substituted with a powerful electronegative substituent, e.g. a nitro group. Azolium halides may be titrated with perchloric acid in anhydrous acetic acid after addition of mercury(II) acetate, or dissolved in acetic anhydride without addition of mercury(II) acetate; dissolved in methanol, they may be titrated as acids with tetrabutylammonium hydroxide in benzene/methanol. The acidic and basic properties of some substituted pyrazol-5-ones have been compared.     

Stericaliy Congested Molecules: 2,2′-[(Biaryldiyl)bis(oxy)]bis[1,3,2-oxazaphospholidines]

The original suggestion that a through-space mechanism was operative in the seven-bond J(P, P) coupling constant of 30.3 Hz observed for 3.3′-bis(1,1-dimethylethyl)-2,2′-[3,3′,5,5′-tetrakis(1,1-dimethylethyl)-1,1′-biphenyl-2,2′-diyl]bis(oxy)}bis[1,3,2-oxazaphospholidine] ( 1a )) was investigated. In the solid-state CP-MAS ³¹PNMR spectrum of 1a , two nonequivalent P -atoms were observed; sufficient resolution could not be obtained to determine whether P, P coupling was present. The preparation and spectral data of the N-methyl analogue 1b and of the acyclic N-isopropyl analogue 6 (Scheme 1) provided evidence that a) the essentially exclusive formation (R*, R*,S*)- 1a in the reaction of the disodium biphenyldiolate 3a with the phosphorochloridite 4a is the result of significant differences in the free energy of activation (ΔG*) for the formation of the various diastereoisomers due to the steric congestion within the molecule and that b) the magnitude of the observed P,P coupling is dependent upon the degree of conformational freedom within the molecule. In the ³¹P-NMR spectrum of the P-sulfide 7 , which was prepared by the reaction of la with sulfur, 2s resonances were observed that strongly suggested that the lone electrons pair on P are involved in the mechanism for the transmission of coupling data. The (4S,5R) -12 and (4R, 5S) -12 of la were prepared in a three-step reaction sequence starting from the corresponding enantiomerically pure norephredine 8 (Scheme 2). Both (4S, 5R)- and (4R, 5S) -12 were obtained as a diastereoisomer mixture that differ by the configuration of the axis of chirality, i.e., (R*R*,R*)- and (R*,S*,R*) -12 were obtained. The major diastereoisomer was obtained upon recrystallization, and the atropisomers were observed to equilibrate in solution by monitoring the H? C(5) resonance in the ¹H-NMR with time (ΔG° = 0.4 kcal/mol; Fig. 2). The process observed corresponds to the restricted rotation about the central single bond of the biphenyl system. The isolation of an atropisomer with only a single ortho substituent on each aryl ring is quite rare. In the ¹³C-NMR spectrum of both (R*,R*,R*)- and (R*,S*,R*) -12 , C(5) is two-bond-coupled to the oxazaphospholidine P-atom (²J(C(5),P((2)) = 8.5 Hz) that is further virtually coupled to the P-atom of the other oxazaphospholidine ring (7J(P(2),P(2′)) = 30 Hz; ⁹J(C(5),P(2′)) = 0 Hz; δ(P(2)) = δ(P(2′)) = 136 ppm. In the ³¹P-NMR spectrum of (R*,R*,S*) -12 , which was prepared from the racemic chloridite (mixture of three diastereoisomers was obtained), a ⁷J(P(2),P(2′) of 36 Hz was observed. These observations provide strong evidence that seven-bond P,P coupling occurs in all three diastereoisomers of 12 . The observed P,P coupling is both independent of the configuration of the chiral axis and the configuration of the asymmetric P-centers. This independence of P,P coupling upon the configuration on P implies also the independence of the observed coupling upon the orientation of the lone-pair of electrons on P provided that the conformations of the diastereoisomers are similar in solution. The X-ray crystal structure of the complex formed from 1a and dichloro(cycloocta-1,5-diene)platinum(II) was obtained and the solid-state structure discussed. The major diastereoisomer of (4S,5R) -12 was used as a chiral ligand in asymmetric hydrosilylation and hydrogenation reactions (Scheme 3).     

Systems-based design of bi-ligand inhibitors of oxidoreductases: filling the chemical proteomic toolbox

Genomics-driven growth in the number of enzymes of unknown function has created a need for better strategies to characterize them. Since enzyme inhibitors have traditionally served this purpose, we present here an efficient systems-based inhibitor design strategy, enabled by bioinformatic and NMR structural developments. First, we parse the oxidoreductase gene family into structural subfamilies termed pharmacofamilies, which share pharmacophore features in their cofactor binding sites. Then we identify a ligand for this site and use NMR-based binding site mapping (NMR SOLVE) to determine where to extend a combinatorial library, such that diversity elements are directed into the adjacent substrate site. The cofactor mimic is reused in the library in a manner that parallels the reuse of cofactor domains in the oxidoreductase gene family. A library designed in this manner yielded specific inhibitors for multiple oxidoreductases.     

An automated method for the analysis of stable isotope labeling data in proteomics

An algorithm is presented for the generation of a reliable peptide component peak table from liquid chromatography-mass spectrometry (LC-MS) and subsequent quantitative analysis of stable isotope coded peptide samples. The method uses chemical noise filtering, charge state fitting, and deisotoping toward improved analysis of complex peptide samples. Overlapping peptide signals in mass spectra were deconvoluted by correlation with modeled peptide isotopic peak profiles. Isotopic peak profiles for peptides were generated in silico from a protein database producing reference model distributions. Doublets of heavy and light labeled peak clusters were identified and compared to provide differential quantification of pairs of stable isotope coded peptides. Algorithms were evaluated using peptides from digests of a single protein and a seven-protein mixture that had been differentially coded with stable isotope labeling agents and mixed in known ratios. The experimental results correlated well with known mixing ratios.     

Adaptation of a fast Fourier transform-based docking algorithm for protein design

Designing proteins with novel protein/protein binding properties can be achieved by combining the tools that have been developed independently for protein docking and protein design. We describe here the sequence-independent generation of protein dimer orientations by protein docking for use as scaffolds in protein sequence design algorithms. To dock monomers into sequence-independent dimer conformations, we use a reduced representation in which the side chains are approximated by spheres with atomic radii derived from known C2 symmetry-related homodimers. The interfaces of C2-related homodimers are usually more hydrophobic and protein core-like than the interfaces of heterodimers; we parameterize the radii for docking against this feature to capture and recreate the spatial characteristics of a hydrophobic interface. A fast Fourier transform-based geometric recognition algorithm is used for docking the reduced representation protein models. The resulting docking algorithm successfully predicted the wild-type homodimer orientations in 65 out of 121 dimer test cases. The success rate increases to approximately 70% for the subset of molecules with large surface area burial in the interface relative to their chain length. Forty-five of the predictions exhibited less than 1 A C(alpha) RMSD compared to the native X-ray structures. The reduced protein representation therefore appears to be a reasonable approximation and can be used to position protein backbones in plausible orientations for homodimer design.     

Two-particle dynamics on an electrode in ac electric fields

The relative motion between pairs of negatively charged latex particles 9.7 microm in diameter and deposited on an electrode was measured by optical microscopy and image analysis. At an rms field of approximately 30 V cm(-1), the two particles moved toward each other at frequencies below 500 Hz, but they separated at 1000 Hz. In the cases of aggregation, there are several interesting characteristics. First, when the center-to-center separation of a pair was initially 6 particle radii or more apart, a transient 'incubation' period of tens of seconds was observed before the particles began to move toward each other. Second, the two particles never came into contact, rather at long times the pair maintained a stationary gap between them equal to approximately one-half the particle radius. This stationary gap between particles was also observed for the aggregation of clusters of three or more particles. Finally, the rate of approach for a pair of particles decreased as the frequency increased. Larger fields are required to move particles together in ac compared to dc fields; at 30 Hz the ac field must be 130 times greater than the dc field to achieve the same rate of approach. Taking advantage of the qualitative and quantitative differences of the cooperative motion of particles in dc vs. ac fields, one should be able to re-position particles by alternating between these two modes. We demonstrated that the same pair of particles can be brought together at low frequency (100 or 200 Hz) and then separated at high frequency (1000 Hz).     

Synthesis of an Azasteroid Using an Acyl Iminium Ion-Initiated Tandem Cyclization

An acyl iminium ion-initiated tandem cyclization gave an unexpected dienone product, a seco-azasteroid (2). The factors governing the formation of 2 were investigated in an attempt to optimize its formation. The reaction was applied to a more elaborate system, resulting in the synthesis of the full steroid skeleton of 13-azaandrosta-1,4-diene-3,17-dione (3), which contains the unusual substitution of a chlorine atom for the axial 19-methyl.     

Estimating probabilities of correct identification from results of mass spectral library searches

This work presents a method for using mass spectral match factors reported by library search systems to obtain certain probabilistic indicators of correct identification. The overall probability that a retrieval is correct is formally separated into two independent terms. One of these is the probability that a retrieval is correct assuming that the correct match is contained in the library. This can be computed directly from test results. The other term represents the probability that the spectrum of the unknown compound is actually in the library. While the absolute value of this term cannot be computed, a relative value based solely on search results can be derived. This value may, if desired, be used to refine an initial estimate of the overall probability. Parameters used in this calculation are based on changes in test results caused by the logical removal of the test compounds from the library. These methods were parameterized from results of searching the MST/EPA/NIH Mass Spectral Database with 12,592 good quality replicate spectra and a simple mass spectral comparison function. The methodology should be equal1 applicable to other libraries and search systems.     

Modeling of the adsorption behavior and the chromatographic band profiles of enantiomers : Behavior of methyl mandelate on immobilized cellulose

The adsorption isotherms of (−)- and (+)-methyl mandelate from a hexane-isopropanol (90:10) solution were measured on a chromatographic column packed with 4-methylcellulose tribenzoate coated on silica. These isotherms are accounted for by a bi-Langmuir isotherm model, the two Langmuir terms having widely different initial slopes and saturation capacities, but each term having the same saturation capacity for the two enantiomers. The competitive isotherms were also measured. They are in excellent agreement with the prediction of a competitive bi-Langmuir model based on the single-component isotherms. The individual band profiles are in agreement with the profiles calculated from these isotherms. Thus, a simplified competitive isotherm can be used to model a separation on a chiral stationary phase the recognition mechanism of which is not well identified and the adsorption behavior of which is certainly not ideal.