Monte Carlo simulations of the hydrophobic effect in aqueous electrolyte solutions

The hydrophobic interaction between two methane molecules in salt-free and high salt-containing aqueous solutions and the structure in such solutions have been investigated using an atomistic model solved by Monte Carlo simulations. Monovalent salt representing NaCl and divalent salt with the same nonelectrostatic properties as the monovalent salt have been used to examine the influence of the valence of the salt species. In salt-free solution the effective interaction between the two methane molecules displayed a global minimum at close contact of the two methane molecules and a solvent-separated secondary minimum. In 3 and 5 M monovalent salt solution the potential of mean force became slightly more attractive, and in a 3 M divalent salt solution the attraction became considerably stronger. The structure of the aqueous solutions was determined by radial distribution functions and angular probability functions. The distortion of the native water structure increased with ion valence. The increase of the hydrophobic attraction was associated with (i) a breakdown of the tetrahedral structure formed by neighboring water molecules and of the hydrogen bonds between them and (i) the concomitant increase of the solution density.     

Rapid isolation of plutonium in environmental solid samples using sequential injection anion exchange chromatography followed by detection with inductively coupled plasma mass spectrometry

This paper reports an automated analytical method for rapid determination of plutonium isotopes (²³⁹Pu and ²⁴⁰Pu) in environmental solid extracts. Anion exchange chromatographic columns were incorporated in a sequential injection (SI) system to undertake the automated separation of plutonium from matrix and interfering elements. The analytical results most distinctly demonstrated that the crosslinkage of the anion exchanger is a key parameter controlling the separation efficiency. AG 1-×4 type resin was selected as the most suitable sorbent material for analyte separation. Investigation of column size effect upon the separation efficiency revealed that small-sized (2 mL) columns sufficed to handle up to 50 g of environmental soil samples. Under the optimum conditions, chemical yields of plutonium exceeded 90% and the decontamination factors for uranium, thorium and lead ranged from 10³ to 10⁴. The determination of plutonium isotopes in three standard/certified reference materials (IAEA-375 soil, IAEA-135 sediment and NIST-4359 seaweed) and two reference samples (Irish Sea sediment and Danish soil) revealed a good agreement with reference/certified values. The SI column-separation method is straightforward and less labor intensive as compared with batch-wise anion exchange chromatographic procedures. Besides, the automated method features low consumption of ion-exchanger and reagents for column washing and elution, with the consequent decrease in the generation of acidic waste, thus bearing green chemical credentials.     

High-resolution,imaging TOF-SIMS: novel applications in medical research

The use of high-resolution, imaging TOF-SIMS is described and examples are made to demonstrate the application of the method in medical research. Cytochemistry by TOF-SIMS is shown by localization of diacylglycerol (DG) in cryostat sections of hyaline cartilage and by localization of corticosterone in cryostat sections of the adrenal gland cortex. Quantitative measurements and comparison of groups is shown by comparing the lipid content of adipose tissue from two mouse strains, transgenic mouse expressing the FOXC2 gene and wild-type controls. Finally, biopsies made for histopathological diagnosis of infantile reversible cytochrome c oxidase deficiency myopathy were analyzed in order to define the chemical content of areas showing a pathological structure in the light microscope. The use of high-resolution, imaging TOF-SIMS in medical research allows analysis of intact tissue and probe-free localization of specific target molecules in cells and tissues. The TOF-SIMS analysis is not dependent on penetration of reagents into the sample and also independent of probe reactivity such as cross-reactivity or background staining. The TOF-SIMS method can be made quantitative and allows for analysis of specific target molecules in defined tissue compartments.     

Reductive Dephthalimidation: A Mild and Efficient Method for The N-Phthaumido Deprotection During Ougosaccharide Synthesis

Abstract

Synthesis of biologically active oligosaccharides, haptens and their protein conjugates is a major area of interest because of their role in antigen-antibody interaction and receptor effects¹. A number of these molecules contain α-or β-linked 2-acetamido-2-deoxy-D-glucosamine (GlcNAc) moieties. Most commonly, during the oligosaccharide synthesis, introduction of the β-glycosidically linked GlcNAc residue is achieved by either the oxazoline² or the phthalimido method³. Of these, the latter is preferred because 2-N-phthalimido protected glycosamine units having a halogen or a thioalkyl group at C-1 have consistently proved to be more efficient donors than are the oxazolines. However, time and again, subsequent conversion of the N-phthalimido to amine by hydrazinolysis has proved inadequate. This has often resulted in a poor overall yield after an otherwise efficient synthesis. Recently it was shown that the phthalimido function could be removed under mild conditions from a number of amino acids⁴. We now report that this technique can be efficiently used for the deprotection of the phthalimido function in suitably protected carbohydrate compounds (2,3 and 5).     

A mechanism from quantum chemical studies for methane formation in methanogenesis

The mechanism for methane formation in methyl-coenzyme M reductase (MCR) has been investigated using the B3LYP hybrid density functional method and chemical models consisting of 107 atoms. The experimental X-ray crystal structure of the enzyme in the inactive MCR(ox1)(-)(silent) state was used to set up the initial model structure. The calculations suggest a mechanism not previously proposed, in which the most remarkable feature is the formation of an essentially free methyl radical at the transition state. The reaction cycle suggested starts from a Michaelis complex with CoB and methyl-CoM coenzymes bound and with a squareplanar coordination of the Ni(I) center in the tetrapyrrole F(430) prosthetic group. In the rate-limiting step the methyl radical is released from methyl-CoM, induced by the attack of Ni(I) on the methyl-CoM thioether sulfur. In this step, the metal center is oxidized from Ni(I) to Ni(II). The resulting methyl radical is rapidly quenched by hydrogen-atom transfer from the CoB thiol group, yielding the methane molecule and the CoB radical. The estimated activation energy is around 20 kcal/mol, which includes a significant contribution from entropy due to the formation of the free methyl. The mechanism implies an inversion of configuration at the reactive carbon. The size of the inversion barrier is used to explain the fact that CF(3)-S-CoM is an inactive substrate. Heterodisulfide CoB-S-S-CoM formation is proposed in the final step in which nickel is reduced back to Ni(I). The suggested mechanism agrees well with experimental observations.     

Theoretical study of the mechanism of peptide ring formation in green fluorescent protein

Density functional calculations using hybrid functionals (B3LYP) have been performed to study the mechanism of peptide ring formation in green fluorescent protein (GFP). Several different chemical models were used ranging from a minimal model of the ring formation to a model including the full side chains of the groups involved in forming the peptide ring. The surrounding protein was described using a dielectric cavity model. The previously most accepted mechanism was found to lead to an endothermic cyclization of about 10 kcal/mol, independent of chemical model used. The formation of the required dihydro‐imidazolone intermediate was found to be even more endothermic with 16–18 kcal/mol. In contrast, another mechanism where the dehydration of residue 66 precedes cyclization was found to be exothermic by 1.9 kcal/mol and to go over an endothermic intermediate of only 6.7 kcal/mol. Correcting these results using the more accurate G2‐M scheme leads to an intermediate with an energy of only +3.7 kcal/mol and an overall exothermicity of 4.7 kcal/mol. Possible transition states involving proton transfer steps were also investigated. Comparisons are made to the similar and more well‐known deamination reaction of Asn‐Gly sequences in peptides, for which good agreement is obtained with experiments. The results are discussed with respect to available experiments. © 2001 John Wiley & Sons, Inc. Int J Quant Chem 81: 169–186, 2001     

Synthesis of imidazoles as novel emivirine and S‐DABO analogues

5‐Alkyl‐4‐benzyl‐1,3‐dihydroimidazol‐2‐ones ( 3a‐d ) and 5‐alkyl‐4‐benzyl‐1,3‐dihydroimidazole‐2‐thiones (7a‐d) were prepared via Dakin West reaction on DL‐phenylalanine with the appropriate aliphatic acid anhydrides followed by hydrolysis and reaction with potassium cyanate or potassium thiocyanate. Compounds 3a‐d were alkylated with ethoxymethyl chloride to give the alkylated imidazoles 5a‐d which were considered analogues of Emivirine with deletion of carbonyl group at the 4‐position. Alkylation of 7a‐d afforded the corresponding S‐alkylated derivatives 8a‐p which in a similar way were considered analogues of S‐DABO. However all the imidazole derivatives were devoid of activity against HIV.     

Determination of Fucose Concentration in a Lectin-Based Displacement Microfluidic Assay

We compare three different methods to quantify the monosaccharide fucose in solutions using the displacement of a large glycoprotein, lactoferrin. Two microfluidic analysis methods, namely fluorescence detection of (labeled) lactoferrin as it is displaced by unlabeled fucose and the displacement of (unlabeled) lactoferrin in SPR, provide fast responses and continuous data during the experiment, theoretically providing significant information regarding the interaction kinetics between the saccharide groups and binding sites. For comparison, we also performed a static displacement ELISA. The stationary binding site in all cases was immobilized S2-AAL, a monovalent polypeptide based on Aleuria aurantia lectin. Although all three assays showed a similar dynamic range, the microfluidic assays with fluorescent or SPR detection show an advantage in short analysis times. Furthermore, the microfluidic displacement assays provide a possibility to develop a one-step analytical platform.