Parametrization of an empirical correction term to density functional theory for an accurate description of pi-stacking interactions in nucleic acids

We present an accurate parametrization of density functional theory augmented with an empirical correction term to describe properly pi-stacking interactions in nucleic acids. The approach is based on the popular Perdew-Burke-Ernzerhof (PBE), Becke-Perdew (BP), and hybrid Becke-Lee-Yang-Parr (B3LYP) density functionals augmented by a classical London C(6)R(-6) dispersion term. The novelty of our implementation lies in the accurate tuning of the empirical parameters, included in the [formula: see text] damping function, to reproduce high-level post Hartree-Fock calculations. In particular, we present sets of parameters and the needed code to correct the PBE, BP, and B3LYP results from the Turbomole and ADF packages in connection with basis sets of double and triple zeta quality. The developed approach is validated by comparison with the JSCH-2005 benchmark and with best quality stacking energies reported in the literature for the stacking of H-bonded nucleic acids base pairs.     

Structure of SDS micelles with propylene carbonate as cosolvent: a PGSE-NMR and SAXS study

The effect of propylene carbonate on SDS micelles was investigated by means of pulsed gradient spin-echo (PGSE) NMR, small-angle X-ray scattering (SAXS), conductivity and ion-selective electrode (ISE) measurements. The knowledge of the cosolvent partition between continuous phase and micelles (obtained by means of PGSE-NMR) allowed the identification of relevant dilution paths. Along these paths the system is composed of identical micelles that become more and more diluted. The extrapolation of measured self-diffusion coefficient to infinite dilution (where direct and hydrodynamic interactions are negligible) permits the determination of hydrodynamic size of the micelles. Moreover, the micelle ionization degree (measured by means of ISE) combined with PGSE-NMR and conductivity data furnishes an estimate of the aggregation number without any assumptions on micellar shape. On the other hand, troublesome hydrodynamic interactions are irrelevant to SAXS, and scattering data collected at fixed composition can be analyzed according to a reasonable model by exploiting the insight on the propylene carbonate partition gained through PGSE-NMR. By means of these approaches, we have found that propylene carbonate acts mainly as cosurfactant for the SDS micelles, decreasing their size and aggregation number by increasing the mean headgroup area of SDS.     

High yield selective acylation of polyamines: proton as protecting group

An advance in the selective acylation of polyamines having identical or similar amine functions is reported. While nucleophilicity differences between the various amine functions are slight, the corresponding conjugate acids exhibit pKa values over a significant range. We have used proton as polyamine protecting group: the monoamine resulting from single deprotonation of a polyammonium compound has allowed for high yields of selective acylation.     

Creating functional artificial proteins

Much is now known about how protein folding occurs, through the sequence analysis of proteins of known folding geometry and the sequence/structural analysis of proteins and their mutants. This has allowed not only the modification of natural proteins but also the construction of de novo polypeptides with predictable folding patterns. Structure/function analysis of natural proteins is used to construct derived versions that retain a degree of biological activity. The constructed versions made of either natural or artificial sequences contain critical residues for activity such as receptor binding. In some cases, the functionality is introduced by incorporating binding sites for other elements, such as organic cofactors or transition metals, into the protein scaffold. While these modified proteins can mimic the function of natural proteins, they can also be constructed to have novel activities. Recently engineered photoactive proteins are good examples of such systems in which a light-induced electron transfer can be established in normally light-insensitive proteins. The present review covers some aspects of protein design that have been used to investigate protein receptor binding, cofactor binding and biological electron transfer.     

Comprehensive gas chromatography coupled to mass spectrometry for the separation of pesticides in a very complex matrix

The present research is focused on the development of a comprehensive two-dimensional gas chromatography–rapid scanning quadrupole mass spectrometric (GC x GC-qMS) methodology for the analysis of trace-amount pesticides contained in a complex real-world sample. Reliable peak assignment was carried out by using a recently developed, dedicated pesticide MS library (for comprehensive GC analysis), characterized by a twin-filter search procedure, the first based on a minimum degree of spectral similarity and the second on the interactive use of linear retention indices (LRI). The library was constructed by subjecting mixtures of commonly used pesticides to GC x GC-qMS analysis and then deriving their pure mass spectra and LRI values. In order to verify the effectiveness of the approach, a pesticide-contaminated red grapefruit extract was analysed. The certainty of peak assignment was attained by exploiting both the enhanced separation power of dual-oven GC x GC and the highly effective search procedure.     

The use of vetiver for remediation of heavy metal soil contamination

The use of Vetiveria zizanioides (vetiver) was studied to evaluate its efficiency for the remediation of soils contaminated by heavy metals. Vetiver plants were tested for Cr, Cu, Pb and Zn. Phytoextraction and bioremediation experiments were carried out by irrigating the vetiver plants and the dry plants with solutions containing suitable amounts of Cr, Cu, Pd and Zn. The concentrations of the heavy metals were determined in both experiments in shoot and root parts of vetiver plants using inductively coupled plasma atomic emission spectroscopy after a mineralization step. Phytoextraction experiments showed a poor efficiency of vetiver for Cr and Cu uptake (both less than 0.1% in shoots and roots after 30 days), but a quite high capability of Pb and Zn uptake (0.4% in shoots and 1% in roots for Pb and 1% both in shoots and in roots for Zn, after 30 days). For these reasons the vetiver plant can be considered a quite good “hyperaccumulator” only for Pb and Zn. As for bioremediation experiments, the vetiver plant showed heavy metal uptake values significantly lower than those obtained with other biological substrates. Figure Vetiver plant     

Analytical method for the determination of mycotoxins in indoor/outdoor airborne particulate matter by HPLC-MS-MS

An effective analytical method for the screening of mycotoxins, in indoor/outdoor airborne particulate matter, was developed and method performance data are presented. Mycotoxins are natural compounds produced, in particular conditions, as secondary metabolites by filamentous fungi and moulds, and, after their production, they can be transported far from their source. To simulate real samples, an urban dust (reference material 1649a) free from mycotoxins was used as matrix and spiked by the most common mycotoxins, chosen on the basis of studies carried out previously in other real matrices: deoxynivalenol, aflatoxin B1, ochratoxin A, T-2 toxin, zearalenone and sterigmatocystin. The analytical method was optimised and structured in four successive steps: (1) accelerated solvent extraction of the (spiked) analytes from matrix, (2) solid-phase purification (SPE) of the previous extract, (3) pre-concentration of the eluates from SPE and (4) analysis of the concentrated eluates by high performance liquid chromatography tandem mass spectrometry in multiple reaction monitoring mode. After a proper sampling campaign, the method was applied to real indoor and outdoor particulate matter samples, where the clean-up step showed to be very effective and fundamental to avoid misleading analytical results.     

Insights into Functional‐Group‐Tolerant Polymerization Catalysis with Phosphine–Sulfonamide Palladium(II) Complexes

Two series of cationic palladium(II) methyl complexes {[(2‐MeOC₆H₄)₂PC₆H₄SO₂NHC₆H₃(2,6‐R¹,R²)]PdMe}₂[A]₂ ( ^X 1⁺‐A : R¹=R²=H: ^H 1⁺‐A ; R¹=R²=CH(CH₃)₂: ^DIPP 1⁺‐A ; R¹=H, R²=CF₃: ^CF3 1⁺‐A ; A =BF₄ or SbF₆) and neutral palladium(II) methyl complexes {[(2‐MeOC₆H₄)₂PC₆H₄SO₂NC₆H₃(2,6‐R¹,R²)]PdMe(L)} ( ^X 1‐acetone : L=acetone; ^X 1‐dmso : L=dimethyl sulfoxide; ^X 1‐pyr : L=pyridine) chelated by a phosphine–sulfonamide were synthesized and fully characterized. Stoichiometric insertion of methyl acrylate (MA) into all complexes revealed that a 2,1 regiochemistry dominates in the first insertion of MA. Subsequently, for the cationic complexes ^X 1⁺‐A , β‐H elimination from the 2,1‐insertion product ^X 2⁺‐A_MA‐2,1 is overwhelmingly favored over a second MA insertion to yield two major products ^X 4⁺‐A_MA‐1,2 and ^X 5⁺‐A_MA . By contrast, for the weakly coordinated neutral complexes ^X 1‐acetone and ^X 1‐dmso , a second MA insertion of the 2,1‐insertion product ^X 2_MA‐2,1 is faster than β‐H elimination and gives ^X 3_MA as major products. For the strongly coordinated neutral complexes ^X 1‐pyr , no second MA insertion and no β‐H elimination (except for ^DIPP 2‐pyr_MA‐2,1 ) were observed for the 2,1‐insertion product ^X 2‐pyr_MA‐2,1 . The cationic complexes ^X 1⁺‐A exhibited high catalytic activities for ethylene dimerization, affording butenes (C₄) with a high selectivity of up to 97.7 % (1‐butene: 99.3 %). Differences in activities and selectivities suggest that the phosphine–sulfonamide ligands remain coordinated to the metal center in a bidentate fashion in the catalytically active species. By comparison, the neutral complexes ^X 1‐acetone , ^X 1‐dmso , and ^X 1‐pyr showed very low activity towards ethylene to give traces of oligomers. DFT analyses taking into account the two possible coordination modes (O or N) of the sulfonamide ligand for the cationic system ^CF3 1⁺ suggested that the experimentally observed high activity in ethylene dimerization is the result of a facile first ethylene insertion into the O‐coordinated PdMe isomer and a subsequent favored β‐H elimination from the N‐coordinated isomer formed by isomerization of the insertion product. Steric hindrance by the N‐aryl substituent in the neutral systems ^CF3 1 and ^H 1 appears to contribute significantly to a higher barrier of insertion, which accounts for the experimentally observed low activity towards ethylene oligomerization.     

Resolving the Differences Between the 1.9 Å and 1.95 Å Crystal Structures of Photosystem II: A Single Proton Relocation Defines Two Tautomeric Forms of the Water‐Oxidizing Complex

Great progress has been made in characterizing the water‐oxidizing complex (WOC) in photosystem II (PSII) with the publication of a 1.9 Å resolution X‐ray diffraction (XRD) and recently a 1.95 Å X‐ray free‐electron laser (XFEL) structure. However, these achievements are under threat because of perceived conflicts with other experimental data. For the earlier 1.9 Å structure, lack of agreement with extended X‐ray absorption fine structure (EXAFS) data led to the notion that the WOC suffered from X‐ray photoreduction. In the recent 1.95 Å structure, Mn photoreduction is not an issue, but poor agreement with computational models which adopt the ‘high’ oxidation state paradigm, has again resulted in criticism of the structure on the basis of contamination with lower S states of the WOC. Here we use DFT modeling to show that the distinct WOC geometries in the 1.9 and 1.95 Å structures can be straightforwardly accounted for when the Mn oxidation states are consistent with the ‘low’ oxidation state paradigm. Remarkably, our calculations show that the two structures are tautomers, related by a single proton relocation.