Stabilization of Large Adsorbates by Rotational Entropy: A Time‐Resolved Variable‐Temperature STM Study

Investigating the dynamics in an adlayer of the oligopyridine derivative 2‐phenyl‐4,6‐bis(6‐(pyridine‐2‐yl)‐4‐(pyridine‐4‐yl)pyridine‐2‐yl)pyrimidine (2,4′‐BTP) on Ag(111) by fast scanning tunneling microscopy (video‐STM), we found that rotating 2,4′‐BTP adsorbates coexist in a two‐dimensional (2D) liquid phase (β‐phase) in a dynamic equilibrium with static adsorbate molecules. Furthermore, exchange between an ordered phase (α‐phase) and β‐phase leads to fluctuations of the domain boundary on a time scale of seconds. Quantitative evaluation of the temperature‐dependent equilibrium between rotating and static adsorbates, evaluated from a large number of STM images, gains insight into energetic and entropic stabilization and underlines that the rotating adsorbate molecules are stabilized by an entropy contribution, which is compatible with that derived by using statistical mechanics. The general validity of the concept of entropic stabilization of rotating admolecules, favoring rotation already at room temperature, is tested for other typical small, mid‐size and large adsorbates.     

Characterisation of humic substances using atmospheric pressure chemical ionisation and electrospray ionisation mass spectrometry combined with size-exclusion chromatography

Humic substances were analysed by atmospheric pressure chemical ionisation (APCI) and electrospray ionisation (ESI) mass spectrometry in positive and negative modes. Using APCI the average m/z range of humic substances was reduced 5-fold compared to ESI. High-resolution time-of-flight mass spectrometry revealed the formation of multiply charged molecules in the ESI mode. Moreover, it was possible to obtain daughter ion mass spectra of humic substances by nanospray tandem mass spectrometry. The size-exclusion chromatography elution profile of humic substances was highly influenced by the pH of the analyte solution. By contrast, the pH had no significant influence on the observed mass spectra of humic substances.     

Viability of Biopolymers for Enhanced Oil Recovery

Xanthan gum and scleroglucan are assessed as environmentally friendly enhanced oil recovery (EOR) agents. Viscometric and interfacial tension measurements show that the polysaccharides exhibit favorable viscosifying performance, robust shear tolerance, electrolyte tolerance, and moderate interactions with surfactants. Non-ionic surfactants and anionic surfactants bind to xanthan gum and transform the backbone conformation from a strong helix to a more flexible structure, reducing the viscosifying efficacy of xanthan. In contrast, non-ionic surfactants and anionic surfactants bind to scleroglucan and increase the viscosifying efficacy by non-electrostatic interactions or imparted electrostatic effects. The two polysaccharides are technically viable as viscosifying agents in typical EOR injection fluid formulations.     

Electronic states of 1,4-bis(phenylethynyl)benzene: A synchrotron radiation linear dichroism investigation

The electronic transitions of 1,4-bis(phenylethynyl)benzene (BPEB) were investigated by UV synchrotron radiation linear dichroism (SRLD) spectroscopy in the range 25,000-58,000 cm⁻¹ (400-170 nm) on molecular samples aligned in stretched polyethylene. The investigation was supported by variable temperature spectroscopy and by quantum chemical calculations in the LCOAO and TD-DFT models. The molecular alignment of BPEB in stretched polyethylene was found to be remarkably efficient, leading to an orientation factor equal to 0.95 for the long molecular axis. The observed band shape depended strongly on the degree of stretching and on temperature. The combined experimental and theoretical evidence leads to the characterization of several previously unobserved transitions and supports the assumption that BPEB adopts a nearly planar conformation in stretched polyethylene.     

Combining weak affinity chromatography, NMR spectroscopy and molecular simulations in carbohydrate-lysozyme interaction studies

By examining the interactions between the protein hen egg-white lysozyme (HEWL) and commercially available and chemically synthesized carbohydrate ligands using a combination of weak affinity chromatography (WAC), NMR spectroscopy and molecular simulations, we report on new affinity data as well as a detailed binding model for the HEWL protein. The equilibrium dissociation constants of the ligands were obtained by WAC but also by NMR spectroscopy, which agreed well. The structures of two HEWL-disaccharide complexes in solution were deduced by NMR spectroscopy using (1)H saturation transfer difference (STD) effects and transferred (1)H,(1)H-NOESY experiments, relaxation-matrix calculations, molecular docking and molecular dynamics simulations. In solution the two disaccharides β-d-Galp-(1→4)-β-D-GlcpNAc-OMe and β-D-GlcpNAc-(1→4)-β-D-GlcpNAc-OMe bind to the B and C sites of HEWL in a syn-conformation at the glycosidic linkage between the two sugar residues. Intermolecular hydrogen bonding and CH/π-interactions form the basis of the protein-ligand complexes in a way characteristic of carbohydrate-protein interactions. Molecular dynamics simulations with explicit water molecules of both the apo-form of the protein and a ligand-protein complex showed structural change compared to a crystal structure of the protein. The flexibility of HEWL as indicated by a residue-based root-mean-square deviation analysis indicated similarities overall, with some residue specific differences, inter alia, for Arg61 that is situated prior to a flexible loop. The Arg61 flexibility was notably larger in the ligand-complexed form of HEWL. N,N'-Diacetylchitobiose has previously been observed to bind to HEWL at the B and C sites in water solution based on (1)H NMR chemical shift changes in the protein whereas the disaccharide binds at either the B and C sites or the C and D sites in different crystal complexes. The present study thus highlights that protein-ligand complexes may vary notably between the solution and solid states, underscoring the importance of targeting the pertinent binding site(s) for inhibition of protein activity and the advantages of combining different techniques in a screening process.     

The potential of Raman spectroscopy for characterisation of the fatty acid unsaturation of salmon

Raman spectroscopy has been evaluated for characterisation of the degree of fatty acid unsaturation (iodine value) of salmon (Salmo salar). The Norwegian Quality Cuts from 50 salmon samples were obtained, and the samples provided an iodine value range of 147.8-170.0 g I₂/100 g fat, reflecting a normal variation of farmed salmon. Raman measurements were performed both on different spots of the intact salmon muscle, on ground salmon samples as well as on oil extracts, and partial least squares regression (PLSR) was utilised for calibration. The oil spectra provided better iodine value predictions than the other data sets, and a correlation coefficient of 0.87 with a root mean square error of cross-validation of 2.5 g I₂/100 g fat was achieved using only one PLSR component. The ground samples provided comparable results, but at least two PLSR components were needed. Higher prediction errors were obtained from Raman spectra of intact salmon muscle, and this may partly be explained by sampling uncertainties in the relation between Raman measurements and reference analysis. All PLSR models obtained were based on chemically sound regression coefficients, and thus information regarding fatty acid unsaturation is readily available from Raman spectra even in systems with high contents of protein and water. The accuracy, the robustness and the low complexity of the PLSR models obtained suggest Raman spectroscopy as a promising method for rapid in-process control of the degree of unsaturation in salmon samples.     

Locked nucleic acid (LNA) recognition of RNA: NMR solution structures of LNA:RNA hybrids

Locked nucleic acids (LNAs) containing one or more 2'-O,4'-C-methylene-linked bicyclic ribonucleoside monomers possess a number of the prerequisites of an effective antisense oligonucleotide, e.g. unprecedented helical thermostability when hybridized with cognate RNA and DNA. To acquire a detailed understanding of the structural features of LNA giving rise to its remarkable properties, we have conducted structural studies by use of NMR spectroscopy and now report high-resolution structures of two LNA:RNA hybrids, the LNA strands being d(5'-CTGAT(L)ATGC-3') and d(5'-CT(L)GAT(L)AT(L)GC-3'), respectively, T(L) denoting a modified LNA monomer with a thymine base, along with the unmodified DNA:RNA hybrid. In the structures, the LNA nucleotides are positioned as to partake in base stacking and Watson-Crick base pairing, and with the inclusion of LNA nucleotides, we observe a progressive change in duplex geometry toward an A-like duplex structure. As such, with the inclusion of three LNA nucleotides, the hybrid adopts an almost canonical A-type duplex geometry, and thus it appears that the number of modifications has reached a saturation level with respect to structural changes, and that further incorporations would furnish only minute changes in the duplex structure. We attempt to rationalize the conformational steering induced by the LNA nucleotides by suggesting that the change in electronic density at the brim of the minor groove, introduced by the LNA modification, is causing an alteration of the pseudorotational profile of the 3'-flanking nucleotide, thus shifting this sugar equilibrium toward N-type conformation.     

Synthesis and PET oxidative cyclization of silyl enol ethers: build-up of quasi-steroidal carbocycles

PET oxidative cyclization of silyl enol ethers carrying suitable side chains with olefinic double bonds results in the stereoselective formation of carbocycles. Two model compounds for investigating the influence of silyl enol ether ring size are synthesized. Furthermore the synthesis of a quasi-steroidal carbocycle with an unnatural configuration is presented.     

SPE HG-AAS method for the determination of inorganic arsenic in rice—results from method validation studies and a survey on rice products

The present paper describes the development, validation and application of a method for inorganic arsenic (iAs) determination in rice samples. The separation of iAs from organoarsenic compounds was done by off-line solid-phase extraction (SPE) followed by hydride generation atomic absorption spectrometry (HG-AAS) detection. This approach was earlier developed for seafood samples (Rasmussen et al., Anal Bioanal Chem 403:2825–2834, 2012) and has in the present work been tailored for rice products and further optimised for a higher sample throughput and a lower detection limit. Water bath heating (90 °C, 60 min) of samples with dilute HNO₃ and H₂O₂ solubilised and oxidised all iAs to arsenate (As^V). Loading of buffered sample extracts (pH 6?±?1) followed by selective elution of arsenate from a strong anion exchange SPE cartridge enabled the selective iAs quantification by HG-AAS, measuring total arsenic (As) in the SPE eluate. The in-house validation gave mean recoveries of 101–106 % for spiked rice samples and in two reference samples. The limit of detection was 0.02 mg kg^?1, and repeatability and intra-laboratory reproducibility were less than 6 and 9 %, respectively. The SPE HG-AAS method produced similar results compared to parallel high-performance liquid chromatography coupled to inductively coupled plasma mass spectrometry (ICP-MS) analysis. The SPE separation step was tested collaboratively, where the laboratories (N?=?10) used either HG-AAS or ICP-MS for iAs determination in a wholemeal rice powder. The trial gave satisfactory results (HorRat value of 1.6) and did not reveal significant difference (t test, p?>?0.05) between HG-AAS and ICP-MS quantification. The iAs concentration in 36 rice samples purchased on the Danish retail market varied (0.03–0.60 mg kg^?1), with the highest concentration found in a red rice sample.