Conventional strain energy in dimethyl-substituted cyclobutane and the gem-dimethyl effect

The gem-dimethyl effect is the acceleration of cyclization by substituents in the chain and is often used in organic synthesis as a ring-closing effect. Calculations on cyclobutane, methylcyclobutane, and 1,1-dimethylcyclobutane are performed. 1,1-Dimethylcyclobutane is a four-membered carbon ring with gem-dimethyl substituents. Optimum equilibrium geometries, harmonic vibrational frequencies, and corresponding electronic energies are computed for all pertinent molecular systems using SCF theory, density functional theory (DFT), and second-order perturbation theory (MP2) with two triple-zeta quality basis sets, 6-311G(d,p) and 6-311G+(2df,2pd). Additional single-point calculations are performed using the optimized MP2/6-311G+(2df,2pd) geometries and coupled-cluster theory including single and double excitations and noniterative, linear triple excitations (CCSD(T)). Calculations indicate that 1,1-dimethylcyclobutane is more than 8 kcal mol-1 less strained than cyclobutane, that is, there is at least some thermodynamic component to the gem-dimethyl effect.     

Low-loss silica-on-silicon waveguides

Waveguiding structures are one of the fundamental components of integrated photonic circuitry. Devices with low loss and a linear response across a wide wavelength range are especially desirable. In the present Letter, we have successfully developed and characterized low-loss silica waveguides integrated on a silicon substrate with a novel suspended cylinder geometry. The unique design creates a device that is effectively air clad, resulting in a large refractive index contrast for improved optical field confinement. The measured loss is constant from 658 to 1550 nm, and it is independent of the polarization of the input light and the input power.     

Introducing structural flexibility into porphyrin-DNA zipper arrays

A more flexible nucleotide building block for the synthesis of new DNA based porphyrin-zipper arrays is described. Changing the rigid acetylene linker between the porphyrin substituent and the 2'-deoxyuridine to a more flexible propargyl amide containing linkage leads in part to an increased duplex stability. The CD spectra reveal different electronic interactions between the porphyrins depending on the type of linker used. Molecular modelling suggests large variation of the relative orientation of the porphyrins within the major groove of the DNA. The porphyrins can be metallated post-synthetically with different metals as shown with zinc, cobalt and copper. The spectroscopic features do not alter drastically upon metallation apart from the CD spectra, and the stability of the metal complex is highly dependent on the nature of the metal. As shown by CD spectroscopy, the zinc porphyrin is rapidly demetallated at high temperatures. Globular structure determination using SAXS indicates that a molecular assembly comprised of a two to four helical bundle dominates in solution at higher concentrations (≥50 μM) which is not observed by spectroscopy at lower concentrations (≤1 μM).     

Biomimetic mineralisation of polymeric scaffolds using a combined soaking and Kitano approach

Chitosan hydrogels are of considerable interest in synthetic biomimetic mineralisation strategies due to their favourable characteristics such as the presentation of a large surface area for crystal nucleation within a structured yet responsive scaffold. Chitosan hydrogels were prepared and subsequently calcium carbonate mineralisation was initiated using a method which combines alternate soaking of the films with precursor solutions followed by treatment with Kitano solution. This combined approach allows for increased extent of mineralisation, inducement of mineralisation uniformly throughout the hydrogel rather than only at the peripheral surface and ready scalability and shape manipulation. The base synthetic system is readily modified through the introduction of additives that manipulate the nucleation and growth of the calcium carbonate. Addition of poly(acrylic acid) inhibits nucleation and induces tangential crystal growth along the internal and external interfaces of the hydrogel. The resulting composite is comprised of stacked overlapping plates of calcium carbonate intercalated with carbohydrate. The method is applicable in combination with a variety of hydrogels including macroporous chitosan, chitosan-alginate bilayers and pure alginate hydrogels. The composite materials were analysed by SEM, XRD, microRaman spectroscopy and mechanical strength testing.     

Some new analysis results for a class of interface problems

Interface problems modeled by differential equations have many applications in mathematical biology, fluid mechanics, material sciences, and many other areas. Typically, interface problems are characterized by discontinuities in the coefficients and/or the Dirac delta function singularities in the source term. Because of these irregularities, solutions to the differential equations are not smooth or discontinuous. In this paper, some new results on the jump conditions of the solution across the interface are derived using the distribution theory and the theory of weak solutions. Some theoretical results on the boundary singularity in which the singular delta function is at the boundary are obtained. Finally, the proof of the convergency of the immersed boundary (IB) method is presented. The IB method is shown to be first‐order convergent in L ^∞ norm. Copyright © 2013 John Wiley & Sons, Ltd.     

Colloid-matrix assemblies in regenerative medicine

The development of tissue engineering scaffolds has focused on mimicking the natural biochemical and biophysical environment of the extracellular matrix (ECM). In this review, we describe a variety of strategies aimed at reproducing and also simplifying the ECM. Despite the progress that has been made, the degree of complexity that needs to be incorporated into these scaffolds is still not known. We begin by describing the ECM and its biological functions followed by outlining current efforts to engineer ECMs with both natural and synthetic polymers. We then focus on colloidal particles as potential artificial ECM components that could increase the complexity as modular building blocks. Drawing from examples from the literature we present the broad utility of colloids and describe how these applications could be useful in the development of ECM mimetic systems.     

Synchrotron radiation based operando characterization of battery materials

Synchrotron radiation based techniques are powerful tools for battery research and allow probing a wide range of length scales, with different depth sensitivities and spatial/temporal resolutions. Operando experiments enable characterization during functioning of the cell and are thus a precious tool to elucidate the reaction mechanisms taking place. In this perspective, the current state of the art for the most relevant techniques (scattering, spectroscopy, and imaging) is discussed together with the bottlenecks to address, either specific for application in the battery field or more generic. The former includes the improvement of cell designs, multi-modal characterization and development of protocols for automated or at least semi-automated data analysis to quickly process the huge amount of data resulting from operando experiments. Given the recent evolution in these areas, accelerated progress is expected in the years to come, which should in turn foster battery performance improvements.

Synchrotron radiation enables probing a wide range of length scales operando, hence being a powerful tool in battery research. Challenges ahead involve cell design (especially for multi-modal approaches) and protocols for automated data analysis.     

Resolving the Heat Generated from ZrO2 Atomic Layer Deposition Surface Reactions

In situ pyroelectric calorimetry and spectroscopic ellipsometry were used to investigate surface reactions in atomic layer deposition (ALD) of zirconium oxide (ZrO₂). Calibrated and time-resolved in situ ALD calorimetry provides new insights into the thermodynamics and kinetics of saturating surface reactions for tetrakis(dimethylamino)zirconium(IV) (TDMAZr) and water. The net ALD reaction heat ranged from 0.197 mJ cm⁻² at 76 °C to 0.155 mJ cm⁻² at 158 °C, corresponding to an average of 4.0 eV/Zr at all temperatures. A temperature dependence for reaction kinetics was not resolved over the range investigated. The temperature dependence of net reaction heat and distribution among metalorganic and oxygen source exposure is attributed to factors including growth rate, equilibrium surface hydroxylation, and the extent of the reaction. ZrO₂-forming surface reactions were investigated computationally using DFT methods to better understand the influence of surface hydration on reaction thermodynamics.     

Structure and Function of the α-Hydroxylation Bimodule of the Mupirocin Polyketide Synthase

Mupirocin is a clinically important antibiotic produced by a trans-AT Type I polyketide synthase (PKS) in Pseudomonas fluorescens. The major bioactive metabolite, pseudomonic acid A (PA−A), is assembled on a tetrasubstituted tetrahydropyran (THP) core incorporating a 6-hydroxy group proposed to be introduced by α-hydroxylation of the thioester of the acyl carrier protein (ACP) bound polyketide chain. Herein, we describe an in vitro approach combining purified enzyme components, chemical synthesis, isotopic labelling, mass spectrometry and NMR in conjunction with in vivo studies leading to the first characterisation of the α-hydroxylation bimodule of the mupirocin biosynthetic pathway. These studies reveal the precise timing of hydroxylation by MupA, substrate specificity and the ACP dependency of the enzyme components that comprise this α-hydroxylation bimodule. Furthermore, using purified enzyme, it is shown that the MmpA KS⁰ shows relaxed substrate specificity, suggesting precise spatiotemporal control of in trans MupA recruitment in the context of the PKS. Finally, the detection of multiple intermodular MupA/ACP interactions suggests these bimodules may integrate MupA into their assembly.