Studies on the substrate specificity of Escherichia coli galactokinase

In vitro glycorandomization (IVG) technology is dependent upon the ability to rapidly synthesize sugar phosphates. Compared with chemical synthesis, enzymatic (kinase) routes to sugar phosphates would be attractive for this application. This work focuses upon the development of a high-throughput colorimetric galactokinase (GalK) assay and its application toward probing the substrate specificity and kinetic parameters of Escherichia coli GalK. The demonstrated dinitrosalicylic assay should also be generally applicable to a variety of sugar-processing enzymes. [reaction: see text]     

Convenient syntheses of fluorous aryl iodides and hypervalent iodine compounds: ArI(L)n reagents that are recoverable by simple liquid/liquid biphase workups,and applications in oxidations of hydroquinones

Iodinations of the ortho, meta, and para fluorous arenes (R(f8)CH(2)CH(2)CH(2))(2)C(6)H(4) (R(f8)=(CF(2))(7)CF(3)) with I(2)/H(5)IO(6) in AcOH/H(2)SO(4)/H(2)O give 3,4-(R(f8)CH(2)CH(2)CH(2))(2)C(6)H(3)I (5) and the analogous 2,4- (6) and 2,5- (7) isomers, respectively. Spectroscopic yields are >90 %, but 5 and 7 must be separated by chromatography from by-products (yields isolated: 70 %, 97 %, 61 %). Reaction of 1,3,5-(R(f8)CH(2)CH(2)CH(2))(3)C(6)H(3) with PhI(OAc)(2)/I(2) gives 2,4,6-(R(f8)CH(2)CH(2)CH(2))(3)C(6)H(2)I (8) on multigram scales in 97 % yield. The CF(3)C(6)F(11)/toluene partition coefficients of 5-8 (24 degrees C: 69.5:30.5 (5), 74.7:25.3 (6), 73.9:26.1 (7), 98.0:2.0 (8)) are lower than those of the precursors, but CF(3)C(6)F(11)/MeOH gives higher values (97.0:3.0 (5), 98.6:1.4 (6), 98.0:2.0 (7), >99.3:<0.3 (8)). Reactions of 5-8 with excess NaBO(3) in AcOH yield the corresponding ArI(OAc)(2) species 9-12 (9, 85 % as a 90:10 9/5 mixture; 10, 97 %; 11, 95 %; 12, 93 % as a 95:5 12/8 mixture). These rapidly oxidize 1,4-hydroquinones in MeOH. Subsequent additions of CF(3)C(6)F(11) give liquid biphase systems. Solvent removal from the CF(3)C(6)F(11) phases gives 5-8 in >99-98 % yields, and solvent removal from the MeOH phases gives the quinone products, normally in >99-95 % yields. The recovered compounds 5-8 are easily reoxidized to 9-12 and used again.     

Real-space analysis of the exchange-correlation energy

The exchange-correlation energy of a many-electron system may be written as the electrostatic interaction between the electron density at position r and the density of the exchange-correlation hole at position r + u. If we average the hole over the entire system, we find that the energy is uniquely decomposed into contributions from various electronic separations u. We may also decompose the hole into contributions from parallel and antiparallel spins. We give several exact conditions which this system-averaged, spindecomposed exchange-correlation hole satisfies. Local spin density (LSD ) and generalized gradient approximations (GGAS ), are more appropriate for u → 0 than for large u and more trustworthy for antiparallel spins than for parallel spins. We illustrate how good LSD is as u = 0 with explicit examples, but also note that, contrary to expectation, LSD is not exact for u=0, except in certain limiting cases. We show that the dramatic failure of the second-order gradient expansion for large u can be cured by a real-space cutoff procedure which generates a nonempirical GGA, the Pw91 functional. We conclude with some thoughts about the search for greater accuracy in the next 30 years of density functional theory. © 1995 John Wiley & Sons, Inc.     

Oxidation of Styrene in a Silent Discharge Plasma

A silent discharge plasma reactor has been developed to study the oxidation of styrene vapor in argon/oxygen mixtures. A number of analytical techniques were employed to determine the destruction efficiency and to characterize the intermediate products. The destruction efficiency was measured as a function of initial styrene concentration, temperature, and energy density of the plasma. The formation of solid products was observed in most experiments. At low temperature (100°C), the solid deposit was polymeric in nature, while at high temperature (300°C) the solid appeared to be amorphous carbon. A combination of high temperature and high energy density resulted in high destruction efficiency and minimal production of solid films. The destruction efficiency vs. energy density is shown to be more complex than a simple model predicting exponential behavior. Several reasons for the discrepancy are suggested. The e-folding energy density for the destruction of styrene is compared to literature values for other organic compounds, measured using similar types of plasma reactors.     

Ion Association in Lanthanide Chloride Solutions

A better understanding of the solution chemistry of the lanthanide (Ln) salts in water would have wide ranging implications in materials processing, waste management, element tracing, medicine and many more fields. This is particularly true for minerals processing, given governmental concerns about lanthanide security of supply and the drive to identify environmentally sustainable processing routes. Despite much effort, even in simple systems, the mechanisms and thermodynamics of Ln^III association with small anions remain unclear. In the present study, molecular dynamics (MD), using a newly developed force field, provide new insights into LnCl₃(aq) solutions. The force field accurately reproduces the structure and dynamics of Nd³⁺, Gd³⁺ and Er³⁺ in water when compared to calculations using density functional theory (DFT). Adaptive-bias MD simulations show that the mechanisms for ion pairing change from dissociative to associative exchange depending upon cation size. Thermodynamics of association reveal that whereas ion pairing is favourable, the equilibrium distribution of species at low concentration is dominated by weakly bound solvent-shared and solvent-separated ion pairs, rather than contact ion pairs, reconciling a number of contrasting observations of Ln^III–Cl association in the literature. In addition, we show that the thermodynamic stabilities of a range of inner sphere and outer sphere coordination complexes are comparable and that the kinetics of anion binding to cations may control solution speciation distributions beyond ion pairs. The techniques adopted in this work provide a framework with which to investigate more complex solution chemistries of cations in water.     

Alloxazines and isoalloxazines. Mass spectrometric analysis of riboflavin and related compounds

The positive ion electron-impact mass spectra of a series of alloxazines, iso-alloxazines and some derivatives have been examined. The compounds employed were lumichrome (7,8-dimethylalloxazine), 1,3-dimethyllumichrome, lumiflavin (7,8,10-trimethyl-iso-alloxazine), 3-methyllumiflavin, riboflavin [7,8-dimethyl-10-(D-1′-ribityl)-iso-alloxazine], riboflavin tetraacetate, 3-methylriboflavin tetraacetate and riboflavin tetrapropionate. By using exact mass measurements, metastable ion defocusing and the mass/composition shifts occurring with derivatives, it has been possible to arrive at detailed interpretations of the mass spectra of all compounds. With lumichrome and lumiflavin, fragmentation commences by elimination of HNCO from the pyrimidine ring. With riboflavin and its derivatives the ribityl chain cleaves off first, followed by decomposition of the iso-alloxazine ring. Application of these methods and findings to the structural analysis of chemically interesting modified flavins is predicted to be rewarding.     

Chloromethylsilane functionalised dendrimers: synthesis and reactivity

Tetraallylsilane was functionalised using (chloromethyl)dimethylsilane to give the first generation chloromethyl terminated dendrimer 1. The resulting dendrimer was successfully reacted with K[CpM(CO)₂] (Cp=η⁵-C₅H₅; M=Fe, Ru) to give Si[(CH₂)₃SiMe₂CH₂MCp(CO)₂]₄ functionalised dendrimers in satisfactory yield. Reaction of dendrimer 1 with NaI in acetone gave the -SiMe₂CH₂I functionalised dendrimer, while reactions of 1 with K[CpM(CO)₃] (M=Mo, W, Re), Li[C₅Me₄H], Na[C₅Me₄H], the cobaloxime nucleophile or tert-BuLi were not successful.     

Imaging chirality with surface second harmonic generation microscopy

Chirality is a fundamental construct in nature which arises from an antisymmetric arrangement of atoms, molecules, or larger structures, resulting in the formation of nonsuperimposable mirror images. Bulk chiral effects can easily be measured using circular dichroism (CD) or optical rotary dispersion (ORD). However, the imaging of chirality originating from molecular surface films cannot be obtained with these linear optical methods. By using chiral second harmonic generation (C-SHG), with its inherent surface sensitivity and ability to discriminate between the symmetry of surface adsorbed species in combination with a counter-propagating optical geometry, we have developed the first nonlinear chiral microscope. In the study presented here, the intrinsic chirality of R- and S-(+)-1,1'-bi-2-naphthol (RBN, SBN) has been used to image a patterned planar supported lipid bilayer (PSLB) of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine (POPC) using C-SHG. Spatial resolution of the patterned PSLB is visible when either RBN or SBN is intercalated into the membrane. No image is observed when a racemic mixture of RBN and SBN is present. The C-SHG images are compared with those obtained from fluorescence microscopy to verify the C-SHG imaging technique. The results presented here demonstrate that C-SHG possesses the requisite surface selectivity and sensitivity to detect interfacial chirality and provides a direct route for the visualization of chirality originating from molecular surface films.     

Studies on the subcellular localization of the porphycene CPO

This study was designed to provide more detailed information on the subcellular sites of binding of the porphycene, termed 9-capronyloxytetrakis (methoxyethyl) porphycene (CPO), with a fluorescence resonance energy transfer (FRET) technique. The proximity of CPO to two fluorescent probes was determined: nonyl acridine orange (NAO), a dye with specific affinity for the mitochondrial lipid cardiolipin, and dihexa-oxacarbocyanine iodide (DiOC6), an agent that labels the endoplasmic reticulum (ER). FRET spectra indicated energy transfer between DiOC6 and CPO but no significant transfer between NAO and CPO. These results confirm data obtained by fluorescence microscopy, suggesting a similar pattern of subcellular localization by CPO and DiOC6 but not by CPO and NAO. However, when cells containing CPO were irradiated and then loaded with NAO, FRET between the two fluorophores was observed. Hence, a relocalization of CPO can occur during irradiation. These data provide an explanation for recent studies on CPO-catalyzed photodamage to both ER and mitochondrial Bcl-2.     

Molecular view of water dynamics near model peptides

Incoherent quasi-elastic neutron scattering (QENS) has been used to measure the dynamics of water molecules in solutions of a model protein backbone, N-acetyl-glycine-methylamide (NAGMA), as a function of concentration, for comparison with results for water dynamics in aqueous solutions of the N-acetyl-leucine-methylamide (NALMA) hydrophobic peptide at comparable concentrations. From the analysis of the elastic incoherent structure factor, we find significant fractions of elastic intensity at high and low concentrations for both solutes, which corresponds to a greater population of protons with rotational time scales outside the experimental resolution (>13 ps). The higher-concentration solutions show a component of the elastic fraction that we propose is due to water motions that are strongly coupled to the solute motions, while for low-concentration solutions an additional component is activated due to dynamic coupling between inner and outer hydration layers. An important difference between the solute types at the highest concentration studied is found from stretched exponential fits to their experimental intermediate scattering functions, showing more pronounced anomalous diffusion signatures for NALMA, including a smaller stretched exponent beta and a longer structural relaxation time tau than those found for NAGMA. The more normal water diffusion exhibited near the hydrophilic NAGMA provides experimental support for an explanation of the origin of the anomalous diffusion behavior of NALMA as arising from frustrated interactions between water molecules when a chemical interface is formed upon addition of a hydrophobic side chain, inducing spatial heterogeneity in the hydration dynamics in the two types of regions of the NALMA peptide. We place our QENS measurements on model biological solutes in the context of other spectroscopic techniques and provide both confirming as well as complementary dynamic information that attempts to give a unifying molecular view of hydration dynamics signatures near peptides and proteins.