An incremental mean first passage analysis for a quasistatic model of polymer translocation through a nanopore

For the translocation of a polymer through a nanopore, a quasistatic assumption for the dynamics yields a tractable form for the entropic barrier. Although this is a much simplified model, interesting features such as robust scaling emerge from its application. To explore these details, we present a method of mapping the translocation process as an incremental mean first passage problem. In this approach, the quantity of interest is the average first time t(0) at which the polymer achieves a displacement of Δs in the translocation coordinate s. Constructing scenarios with different initial conditions and boundary conditions, analytic and exact numerical approaches are used to resolve the dynamics of translocation in detail and generate new insight into the nature of the entropic barrier.     

Size-exclusion chromatography of perfluorosulfonated ionomers

A size-exclusion chromatography (SEC) method in N,N-dimethylformamide containing 0.1 M LiNO₃ is shown to be suitable for the determination of molar mass distributions of three classes of perfluorosulfonated ionomers, including Nafion^®. Autoclaving sample preparation is optimized to prepare molecular solutions free of aggregates, and a solvent exchange method concentrates the autoclaved samples to enable the use of molar-mass-sensitive detection. Calibration curves obtained from light scattering and viscometry detection suggest minor variation in the specific refractive index increment across the molecular size distributions, which introduces inaccuracies in the calculation of local absolute molar masses and intrinsic viscosities. Conformation plots that combine apparent molar masses from light scattering detection with apparent intrinsic viscosities from viscometry detection partially compensate for the variations in refractive index increment. The conformation plots are consistent with compact polymer conformations, and they provide Mark–Houwink–Sakurada constants that can be used to calculate molar mass distributions without molar-mass-sensitive detection. Unperturbed dimensions and characteristic ratios calculated from viscosity–molar mass relationships indicate unusually free rotation of the perfluoroalkane backbones and may suggest limitations to applying two-parameter excluded volume theories for these ionomers.     

The IUPAC aqueous and non-aqueous experimental pKa data repositories of organic acids and bases

Accurate and well-curated experimental pKa data of organic acids and bases in both aqueous and non-aqueous media are invaluable in many areas of chemical research, including pharmaceutical, agrochemical, specialty chemical and property prediction research. In pharmaceutical research, pKa data are relevant in ligand design, protein binding, absorption, distribution, metabolism, elimination as well as solubility and dissolution rate. The pKa data compilations of the International Union of Pure and Applied Chemistry, originally in book form, have been carefully converted into computer-readable form, with value being added in the process, in the form of ionisation assignments and tautomer enumeration. These compilations offer a broad range of chemistry in both aqueous and non-aqueous media and the experimental conditions and original reference for all pKa determinations are supplied. The statistics for these compilations are presented and the utility of the computer-readable form of these compilations is examined in comparison to other pKa compilations. Finally, information is provided about how to access these databases.     

Formation of a Dimer of Trinuclear Helicates which Encapsulates an Array of Six Hydrogen‐Bonded Anions

The amine‐containing ligand L, composed of two bidentate pyridyl‐thiazole moieties linked by a 1,3‐diaminophenylene unit, reacts with copper(II) ions to form a dinuclear double helicate [Cu₂L₂]⁴⁺. Reaction of [Cu₂L₂]⁴⁺ with dihydrogen phosphate (0.5 equivalents) gives the unsaturated dinuclear double helicate [Cu₂L₂(OPO₃H₂)]³⁺. [Cu₂L₂(OPO₃H₂)]³⁺ further reacts with another 0.5 equivalents of dihydrogen phosphate to give a trinuclear circular helicate which then self‐assembles into a hexameric cluster [{Cu₃L₃(OPO₃H₂)₃}]²⁶⁺.     

Atomic-scale mechanistic features of oxide ion conduction in apatite-type germanates

Atomistic modelling studies of the apatite-type oxide ion conductor La9.33(GeO4)6O2 show that a key role of the O4 channel oxygen atoms appears to be as a reservoir for the creation of interstitial oxide ion defects, while the migration of these defects proceeds via the GeO4 tetrahedra.     

A theoretical study of the possible use of electroosmotic flow to extend the read length of DNA sequencing by end-labeled free solution electrophoresis

End-labeled free solution electrophoresis (ELFSE) provides a means of separating DNA with free-solution CE, eliminating the need for gels and polymer solutions which increase the run time and can be difficult to load into a capillary. In free-solution electrophoresis, DNA is normally free-draining and all fragments reach the detector at the same time, whereas ELFSE uses an uncharged label molecule attached to each DNA fragment in order to render the electrophoretic mobility size-dependent. With ELFSE, however, the larger molecules are not separated enough (limiting the read length in the case of ssDNA sequencing) while the smaller ones are overseparated; the larger ones are too fast while the shorter ones are too slow, which is the opposite of traditional gel-based methods. In this article, we show how an EOF could be used to overcome these problems and extend the DNA sequencing read length of ELFSE. This counterflow would allow the larger, previously unresolved molecules more time to separate and thereby increase the read length. Through our theoretical investigation, we predict that an EOF mobility of approximately the same magnitude as that of unlabeled DNA would provide the best results for the regime where all molecules move in the same direction. Even better resolution would be possible for smaller values of EOF which allow different directions of migration; however, the migration times then would become too large. The flow would need to be well controlled since the gain in read length decreases as the magnitude of the counterflow increases; an EOF mobility double that of unlabeled DNA would no longer increase the read length, although ELFSE would still benefit from a reduction in migration time.     

A concise, convergent total synthesis of monocerin

A concise and convergent eight-step synthesis of the antifungal metabolite monocerin 1 is reported. The key step involves an allylsilane metathesis/aldehyde condensation sequence to establish the core 2,3,5-trisubstituted tetrahydrofuran. End-game approaches based around intramolecular Heck chemistry revealed an interesting example of formal 6-endo cyclisation, the origin of which was probed using model substrates. The synthesis was ultimately completed by a strategy involving stepwise oxidative cleavage of the C3-ethenyl substituent.     

Detrapping particles in gel electrophoresis: a numerical study of different pulsed field sequences

Large particles tend to get trapped in dead-ends more often than small particles when electrophoresed in random cross-linked gels. It is known that pulsed electric fields can be used to free particles from these traps, leading to an increase in velocity and improved size separation. Although numerical and theoretical models have been proposed for the mobility of smaller particles in the so-called Ogston sieving limit, the effect of pulsed fields on trapping has not been previously modeled. We present a numerical study of detrapping and we compare our results with those of To and Boyde (To, K.-Y., Boyde, T. R., Electrophoresis 1993, 14, 597). We use an exact numerical method to examine detrapping in various two-dimensional systems of obstacles. We also propose and investigate new ways to optimize the pulse sequence in order to separate particles of different sizes.     

In‐column preparation of a brush‐type chiral stationary phase using click chemistry and a silica monolith

Brush‐type chiral stationary phases (CSP) have been prepared both from a silica monolith and, separately, from 10 μm porous silica beads via a process of in‐column modification including attachment of the chiral selector via copper‐catalyzed azide–alkyne cycloaddition. Azide functionalities were first introduced on the pore surface of each type of support by reaction with 3‐(azidopropyl)trimethoxysilane, followed by immobilization of a proline‐derived chiral selector containing an alkyne moiety. This functionalization reaction was carried out in dimethylformamide (DMF) in the presence of catalytic amounts of copper (I) iodide. The separation performance of these triazole linked stationary phases was demonstrated in enantioseparations of four model analytes, which afforded separation factors as high as 11.4.     

Construction of approximate entropic forces for finitely extensible nonlinear elastic (FENE) polymers

When the stress applied to a Rouse-like polymer chain is large enough, one must use anharmonic entropic spring forces in order to keep the chain contour length from increasing to unphysical values. Although one can derive “exact” equations relating the spring extension to the entropic force produced by a finitely extensible non-linear elastic (FENE) random-walk polymer, such expressions are usually of little interest because their complexity would entail large evaluation times in numerical studies by computer. Moreover, these expressions can rarely be used directly in analytical studies. In this article, we describe a systematic method to construct analytically simple yet numerically accurate expressions to relate the entropic force to the extension of an entropic spring for a random-walk polymer chain in arbitrary dimension d ≥ 2. These expressions are modified Pade approximants which yield the correct asymptotic behaviours in both the small and large extension limits. It is shown that the well-known Warner empirical approximation is but a limiting case (for infinite dimensions).