Tracelessness Unmasked: A General Linker Nomenclature

Nowadays it is rare to find an issue of a major chemistry journal without at least one article on solid-phase synthesis. This is hardly surprising: the technique promises an end to arduous work-up procedures and the ability to facilitate the creation of vast libraries of compounds using combinatorial techniques. No longer is the technique only of interest to those involved in peptide synthesis: an enormous variety of product classes have now been prepared on and isolated from the solid phase. It is the "linker" which is the focus of this article. The linker's ultimate function is to release a product from the support into solution: it does this, without exception, with a chemical change to the product at the former linkage site. Some linkers, apparently, are "traceless". But what, in fact, is "tracelessness"? Twenty years ago, in a climate where cleavage of a linker resulted in formation of a polar carboxylic acid as the vestige of the support, the concept was attractive. Today the chemist is faced with a myriad of novel linkers which have the ability to release products bearing most major functionalities at the former linkage site and we will argue here that the term "traceless", although currently in widespread use, is meaningless. Instead, we propose a new categorization of linkers based on the functionality they release upon cleavage, and suggest a nomenclature to underpin this categorization. We anticipate that the article will also serve to highlight areas of linker technology in need of further research.     

Precision of Raman depolarization and optical attenuation measurements of sound tooth enamel

The demineralization of enamel that is associated with early caries formation affects the optical properties of the enamel. Polarized Raman spectroscopy and optical coherence tomography have been used to detect these changes and potentially offer a means to detect and monitor early caries development. The total optical attenuation coefficient as measured by optical coherence tomography and the polarization anisotropy of the Raman peak arising from the symmetric ν₁ vibration of at approximately 959 cm⁻¹ have been demonstrated as being sensitive markers of early caries. This ex vivo study on extracted human teeth demonstrates that these measurements can be made with reasonable precision with concomitantly good repeatability and reproducibility in sound enamel. Such reliability is crucial for these techniques to have a practical clinical value.     

Comparison of thermodynamic properties of coarse-grained and atomic-level simulation models.

Thermodynamic data are often used to calibrate or test amomic-level (AL) force fields for molecular dynamics (MD) simulations. In contrast, the majority of coarse-grained (CG) force fields do not rely extensively on thermodynamic quantities. Recently, a CG force field for lipids, hydrocarbons, ions, and water, in which approximately four non-hydrogen atoms are mapped onto one interaction site, has been proposed and applied to study various aspects of lipid systems. To date, no extensive investigation of its capability to describe salvation thermodynamics has been undertaken. In the present study, a detailed picture of vaporization, solvation, and phase-partitioning thermodynamics for liquid hydrocarbons and water was obtained at CG and AL resolutions, in order to compare the two types or models and evaluate their ability to describe thermodynamic properties in the temperature range between 263 and 343 K. Both CG and AL models capture the experimental dependence of the thermodynamic properties on the temperature, albeit a systematically weaker dependence is found for the CG model. Moreover, deviations are found for solvation thermodynamics and for the corresponding enthalpy-entropy compensation for the CG model. Particularly water/oil repulsion seems to be overestimated. However, the results suggest that the thermodynamic properties considered should be reproducible by a CG model provided it is reparametrized on the basis of these liquid-phase properties.     

Dual quartz crystal microbalance compensation using a submerged reference crystal. Effect of surface roughness and liquid properties

Absolute resonant frequency measurements were made on gold-coated AT-cut quartz crystals with one face in contact with a series of liquids. The effect of surface roughness and liquid properties (viscosity and density) was analyzed in terms of a “trapped liquid” model. In this model, liquid present in surface imperfections is viewed as rigidly coupled mass. In some of the literature this density-dependent, but not viscosity-dependent, term is viewed as being additive to the hydrodynamic shift seen for a smooth surface. Data obtained using 1 μm and 5 μm surface finish crystals are inconsistent with the predictions of the trapped liquid model. This suggests hydrodynamic coupling between liquid internal and external to the crevices. Despite the lack of a theoretical model for the liquid motion, it is possible to compensate for frequency variations resulting from changing liquid properties and for roughness effects by making direct measurements of the resonant frequency difference between two crystals exposed to the same solution. This novel procedure works to the extent that the two crystals have similar surface topographies. Compensation is excellent for 1 μm finish crystals and good for 5 μm finish crystals.     

Synthesis of Novel C/D Ring Modified Bile Acids

Bile acid receptors have been identified as important targets for the development of new therapeutics to treat various metabolic and inflammatory diseases. The synthesis of new bile acid analogues can help elucidate structure–activity relationships and define compounds that activate these receptors selectively. Towards this, access to large quantities of a chenodeoxycholic acid derivative bearing a C-12 methyl and a C-13 to C-14 double bond provided an interesting scaffold to investigate the chemical manipulation of the C/D ring junction in bile acids. The reactivity of this alkene substrate with various zinc carbenoid species showed that those generated using the Furukawa methodology achieved selective α-cyclopropanation, whereas those generated using the Shi methodology reacted in an unexpected manner giving rise to a rearranged skeleton whereby the C ring has undergone contraction to form a novel spiro–furan ring system. Further derivatization of the cyclopropanated steroid included O-7 oxidation and epimerization to afford new bile acid derivatives for biological evaluation.     

Synthesis of trifluoromethyl cyclohexyl, cyclohexenyl and aryl compounds via stepwise Robinson annulation

The diketone 2-fluoro-2-(trifluoromethyl)-1-phenylhexane-1,5-dione 3 was synthesized by a Mukaiyama Michael type reaction from the corresponding tetrafluoroenol silyl ether prepared from pentafluoropropiophenone. This diketone was treated under basic conditions and was converted, depending on the stoichiometry of the base, into the surprisingly stable ketol 4-fluoro-4-(trifluoromethyl)-3-hydroxy-3-phenylcyclohexanone 4 as a single diastereomer (catalytic KOH) or to the biphenylol 6-(trifluoromethyl)biphenyl-3-ol (excess KOH, THF) 5. Solvolysis of the trifluoromethyl group (anionic activation) occurred using excess KOH in alcohol. The corresponding cyclohexenone derivative 7, the usual product of Robinson annulation, might be prepared in good yield via mesylation of the ketol. Thus various unprecedented fluorinated cyclohexane and aromatic derivatives were achieved in a few steps from the commercially available pentafluoropropiophenone.     

H2O‐Catalyzed Route to Early Lanthanide Tribromide THF and DME Solvates from Oxides

A convenient one‐pot synthetic protocol towards THF and DME solvates of lanthanum and other early lanthanide tribromides was developed using the water‐catalyzed reaction of lanthanide(III) oxides with highly reactive Me₃SiBr in situ formed from commercially available disilane Si₂Me₆ and Br₂. This practical route allows to obtain the target lanthanum tribromide solvates [LaBr₃(thf)₄] ( 1a ) and [LaBr₃(dme)₂]₂ ( 1b ) as well as analogous early lanthanide molecular tribromide solvates [NdBr₃(thf)₄] ( 2a ), [NdBr₃(dme)₂] ( 2b ), [SmBr₃(thf)₂] ( 3a ), and [SmBr₃(dme)₂] ( 3b ) difficult to prepare by other solution‐based procedures. The molecular structure of 1b· 2CH₂Cl₂ was determined by an XRD study.     

Formation of stable Meisenheimer adduct ion pairs in apolar solvents: implications for stereoselective reactions

[reaction: see text] A detailed study concerning the formation of Meisenheimer adducts in biphasic solvent systems is described. The process relies on utilizing a significantly lipophilic quaternary ammonium salt to transfer a nucleophile (e.g., hydroxide ion) between an aqueous and organic layer containing the electron-deficient aromatic substrate. Provided that the organic layer is sufficiently apolar, the resultant Meisenheimer adduct is considerably stable, likely the result of a strong ion-pairing interaction between the large polarizable anionic complex and the diffusively charged tetraalkylammonium cation. Using the diethylamide of 3,5-dinitrobenzoic acid as a model compound, the influence of ion-pairing reagents and solvents on adduct formation was investigated. Dramatically increased equilibrium formation of the Meisenheimer adduct is observed in the biphasic medium (e.g., benzene/2 M NaOH) relative to the same adduct generated in single-phase systems. Spectroscopic studies on this adduct are consistent with those conducted in single-phase polar or dipolar aprotic solvents. The methodology is extended to performing highly enantioselective biphasic kinetic resolutions of several racemic electron-deficient amides.     

Sequence-specific fragmentation of deprotonated peptides containing H or alkyl side chains

The [M - H]- ions of a variety of di- to pentapeptides containing H or alkyl side chains have been prepared by electrospray ionization and low-energy collision-induced dissociation (CID) of the deprotonated species carried out in the interface region between the atmospheric pressure source and the quadrupole mass analyzer. Using the nomenclature applied to the fragmentation of protonated peptides, deprotonated dipeptides fragment to give a2 ions (CO2 loss) and y1 ions, where the y1 ion has two fewer hydrogens than the y"1 ions formed from protonated peptides. Deprotonated tri- and tetrapeptides fragment to give primarily y1, c1, and "b2 ions, where the "b2 ion has two fewer hydrogens than the b2 ion observed for protonated peptides. More minor yields of y2, c2, and a2 ions also are observed. The a ion formed by loss of CO2 from the [M - H]- ion shows loss of the N-terminal residue for tripeptides and sequential loss of two amino acid residues from the N-terminus for tetrapeptides. The formation of c(n) ions and the sequential loss of N-terminus residues from the [M - H - CO2]- ion serves to sequence the peptide from the N-terminus, whereas the formation of y(n) ions serves to sequence the peptide from the C-terminus. It is concluded that low-energy CID of deprotonated peptides provides as much (or more) sequence information as does CID of protonated peptides, at least for those peptides containing H or alkyl side chains. Mechanistic aspects of the fragmentation reactions observed are discussed.     

Unimolecular reactions of [C5H10O]+ ˙ radical cations derived from4-penten-1-ol

The reactions of metastable [C₅H₁₀O]^{+ ˙} radical cations produced by ionization of 4-penten-1-ol are reported and discussed. These [C₅H₁₀O]^{+ ˙} species undergo mainly ethyl radical loss, with smaller contributions of methyl radical and water expulsion. ²H-Labelling studies reveal different specificities of hydrogen selection in these three fragmentations. The behaviour of these [C₅H₁₀O]^{+ ˙} ions is compared to those reported previously for isomeric radical cations containing linear alkenyl chains and a terminal hydroxyl group.