Locked vs. unlocked nucleic acids (LNA vs. UNA): contrasting structures work towards common therapeutic goals

Oligonucleotide chemistry has been developed greatly over the past three decades, with many advances in increasing nuclease resistance, enhancing duplex stability and assisting with cellular uptake. Locked nucleic acid (LNA) is a structurally rigid modification that increases the binding affinity of a modified-oligonucleotide. In contrast, unlocked nucleic acid (UNA) is a highly flexible modification, which can be used to modulate duplex characteristics. In this tutorial review, we will compare the synthetic routes to both of these modifications, contrast the structural features, examine the hybridization properties of LNA and UNA modified duplexes, and discuss how they have been applied within biotechnology and drug research. LNA has found widespread use in antisense oligonucleotide technology, where it can stabilize interactions with target RNA and protect from cellular nucleases. The newly emerging field of siRNAs has made use of LNA and, recently, also UNA. These modifications are able to increase double-stranded RNA stability in serum and decrease off-target effects seen with conventional siRNAs. LNA and UNA are also emerging as versatile modifications for aptamers. Their application to known aptamer structures has opened up the possibility of future selection of LNA-modified aptamers. Each of these oligonucleotide technologies has the potential to become a new type of therapy to treat a wide variety of diseases, and LNA and UNA will no doubt play a part in future developments of therapeutic and diagnostic oligonucleotides.     

Adsorption of sophorolipid biosurfactants on their own and mixed with sodium dodecyl benzene sulfonate, at the air/water interface

The adsorption of the lactonic (LS) and acidic (AS) forms of sophorolipid and their mixtures with the anionic surfactant sodium dodecyl benzene sulfonate (LAS) has been measured at the air/water interface by neutron reflectivity, NR. The AS and LS sophorolipids adsorb with Langmuir-like adsorption isotherms. The more hydrophobic LS is more surface active than the AS, with a lower critical micellar concentration, CMC, and stronger surface adsorption, with an area/molecule ～70 ?(2) compared with 85 ?(2) for the AS. The acidic sophorolipid shows a maximum in its adsorption at the CMC which appears to be associated with a mixture of different isomeric forms. The binary LS/AS and LS/LAS mixtures show a strong surface partitioning in favor of the more surface active and hydrophobic LS component but are nevertheless consistent with ideal mixing at the interface. In contrast, the surface composition of the AS/LAS mixture is much closer to the solution composition, but the surface mixing is nonideal and can be accounted for by regular solution theory, RST. In the AS/LS/LAS ternary mixtures, the surface adsorption is dominated by the sophorolipid, and especially the LS component, in a way that is not consistent with the observations for the binary mixtures. The extreme partitioning in favor of the sophorolipid for the LAS/LS/AS (1:2) mixtures is attributed to a reduction in the packing constraints at the surface due to the AS component. Measurements of the surface structure reveal a compact monolayer for LS and a narrow solvent region for LS, LS/AS, and LS/LAS mixtures, consistent with the more hydrophobic nature of the LS component. The results highlight the importance of the relative packing constraints on the adsorption of multicomponent mixtures, and the impact of the lactonic form of the sophorolipid on the adsorption of the sophorolipid/LAS mixtures.     

Electron excitation of the Schumann-Runge continuum, longest band, and second band electronic states in O2

We report measurements of differential and integral cross sections for electron excitation of the Schumann-Runge continuum, longest band, and second band electronic states in molecular oxygen. The energy range of the present study is 15-200 eV, with the angular range of the differential cross section (DCS) measurements from 2 to 130°. A generalized oscillator strength analysis is then employed in order to derive integral cross sections (ICSs) from the corresponding DCSs, and these ICSs are compared with relevant energy and oscillator strength scaled Born cross section (BEf-scaling [Y.-K. Kim, J. Chem. Phys. 126, 064305 (2007)]) results determined as a part of this investigation. Interestingly, while the present Schumann-Runge continuum and second band ICSs were in reasonable agreement with the respective BEf-scaling results, agreement for the longest band was poor below 100 eV with a possible reason for this apparently anomalous behavior being canvassed here. Finally, where possible all present data are compared with the results from earlier measurements and calculations with the level of agreement found being very good in some cases and marginal in others.     

Effects of peripheral and axial substitutions on electronic transitions of tin naphthalocyanines

Tin naphthalocyanine molecules display strong absorption in the infrared region (IR), making them ideal as components of organic photodiodes and solar cells. We use density functional theory and time-dependent density functional theory (TD-DFT) at the B3LYP level to study the influence of axial and peripheral ligands on the absorption wavelength of tin naphthalocyanines. We find that TD-DFT is successful at reproducing the experimental absorption spectra of free base naphthalocyanine and tin naphthalocyanine molecules and can be used as a reliable tool to predict absorption spectra of substituted naphthalocyanines. Functional groups attached axially to tin (-F, -Cl, -Br, -I) and peripherally to the inner ring (-F, -Cl, -Br, -Ph, -OH, -COCH(3), -O(CH(2))(3)CH(3)) of the tin naphthalocyanine molecule tune the excitation wavelength in the near-infrared region between 770 and 940 nm. While substituents to the outer naphthalocyanine ring (-Cl, -Br) affect the intensity of the absorption peaks in the NIR region, they do not influence their absorption wavelength. Asymmetric substitution of naphthalocyanine pendant arms can be employed to decrease intensity of the absorption peaks in the visible region with respect to the intensity of the peaks in the NIR.     

Structure-enantioselectivity effects in 3,4-dihydropyrimido[2,1-b]benzothiazole-based isothioureas as enantioselective acylation catalysts

The catalytic activity and enantioselectivity in the kinetic resolution of (±)-1-naphthylethanol with a range of structurally related 3,4-dihydropyrimido[2,1-b]benzothiazole-based catalysts is examined. Of the isothiourea catalysts screened, (2S,3R)-2-phenyl-3-isopropyl substitution proved optimal, giving good levels of selectivity in the kinetic resolution of a number of secondary alcohols (S values up to >100 at ~50% conversion). Low catalyst loadings (0.10-0.25 mol%) of the optimal isothiourea can be used to generate enantiopure alcohols (>99% ee) in good yields.     

Organic base effects in NHC promoted O- to C-carboxyl transfer; chemoselectivity profiles, mechanistic studies and domino catalysis

The O- to C-carboxyl transfer of oxazolyl carbonates promoted by triazolinylidenes, generated in situ with NEt(3), shows a markedly different rate and chemoselectivity profile to the same reaction promoted by triazolinylidenes generated using KHMDS. The mechanism of these pathways has been probed through extensive crossover studies to understand this process. The use of NEt(3) as a base allows domino multi-step reaction sequences to be developed, although chiral NHCs only generate modest levels of asymmetric induction (<15% ee) in these domino reaction processes.     

A two-stage stochastic program for scheduling and allocating cross-trained workers

A two-stage stochastic program is developed for scheduling and allocating cross-trained workers in a multi-department service environment with random demands. The first stage corresponds to scheduling days-off over a time horizon such as a week or month. The second stage is the recourse action that deals with allocating available workers at the beginning of a day to accommodate realized demands. After the general two-stage model is formulated, a special case is introduced for computational testing. The testing helps quantify the value of cross-training as a function of problem characteristics. Results show that cross-training can be more valuable than perfect information, especially when demand uncertainty is high.     

Ruthenium nanoparticles in ionic liquids: structural and stability effects of polar solutes

Ionic liquids are a stabilizing medium for the in situ synthesis of ruthenium nanoparticles. Herein we show that the addition of molecular polar solutes to the ionic liquid, even in low concentrations, eliminates the role of the ionic liquid 3D structure in controlling the size of ruthenium nanoparticles, and can induce their aggregation. We have performed the synthesis of ruthenium nanoparticles by decomposition of [Ru(COD)(COT)] in 1-butyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide, [C(1)C(4)Im][NTf(2)], under H(2) in the presence of varying amounts of water or 1-octylamine. For water added during the synthesis of metallic nanoparticles, a decrease of the solubility in the ionic liquid was observed, showed by nanoparticles located at the interface between aqueous and ionic phases. When 1-octylamine is present during the synthesis, stable nanoparticles of a constant size are obtained. When 1-octylamine is added after the synthesis, aggregation of the ruthenium nanoparticles is observed. In order to explain these phenomena, we have explored the molecular interactions between the different species using (13)C-NMR and DOSY (Diffusional Order Spectroscopy) experiments, mixing calorimetry, surface tension measurements and molecular simulations. We conclude that the behaviour of the ruthenium nanoparticles in [C(1)C(4)Im][NTf(2)] in the presence of 1-octylamine depends on the interaction between the ligand and the nanoparticles in terms of the energetics but also of the structural arrangement of the amine at the nanoparticle's surface.     

Adsorption energetics of CO on supported Pd nanoparticles as a function of particle size by single crystal microcalorimetry

The heat of adsorption and sticking probability of CO on well-defined Pd nanoparticles were measured as a function of particle size using single crystal adsorption microcalorimetry. Pd particles of different average sizes ranging from 120 to 4900 atoms per particle (or from 1.8 to 8 nm) and Pd(111) were used that were supported on a model in situ grown Fe(3)O(4)/Pt(111) oxide film. To precisely quantify the adsorption energies, the reflectivities of the investigated model surfaces were measured as a function of the thickness of the Fe(3)O(4) oxide layer and the amount of deposited Pd. A substantial decrease of the binding energy of CO was found with decreasing particle size. Initial heat of adsorption obtained on the virtually adsorbate-free surface was observed to be reduced by about 20-40 kJ mol(-1) on the smallest 1.8 nm sized Pd particles as compared to the larger Pd clusters and the extended Pd(111) single crystal surface. This effect is discussed in terms of the size-dependent properties of the Pd nanoparticles. The CO adsorption kinetics indicates a strong enhancement of the adsorbate flux onto the metal particles due to a capture zone effect, which involves trapping of adsorbates on the support and diffusion to metal clusters. The CO adsorption rate was found to be enhanced by a factor of ～8 for the smallest 1.8 nm sized particles and by ～1.4 for the particles of 7-8 nm size.     

The proton relaxation of CH3OD in the presence of Co(II) ions,as studied by spin-echo techniques

By measurement of the proton relaxation times T ₁ and T ₂ of CH₃OD containing Co⁺⁺ ions in dilute solution and the dependence of the observed decay time (T ₂ ^?) on t _ep the separation between pulses in a Carr-Purcell sequence the coordination number is shown to be six. Since this result has previously been obtained by an independent method, the use of the dependence of T ₂ ^? on t _ep to determine coordination numbers is justified for solutions of paramagnetic ions. The validity of analytical expressions derived previously has been checked by numerical methods, and the analytical expression is shown to be valid even in the presence of H ₀ and H ₁ inhomogeneity and inaccurate pulses of finite duration, provided that the Meiboom-Gill method is used. In an Appendix insight derived from the results of the numerical solutions is used to give a brief derivation of the dependence of T ₂ ^? on H ₀, exchange rate and t _ep.