Ab initio molecular dynamics simulations of the liquid/vapor interface of sulfuric acid solutions

Ab initio molecular dynamics simulations of the liquid-vapor interface are presented for thin slabs of 72 water molecules containing a single molecule of sulfuric acid. Trajectories in the 306-330 K range are calculated for two functionals with double- and triple-ζ quality basis sets. Comparisons are made between BLYP and HCTH/120 results for the slab simulations and for bulk simulations of one H(2)SO(4) in a periodic box with 63 waters. Good agreement is found with the available experimental data and the results of other relevant AIMD studies with respect to ionization of the acid, size of the coordination shells, partitioning of the ions with the hydronium exhibiting a surface preference and the anions in the interior, and the orientational distributions for the hydronium ions and for the surface/subsurface water molecules. The major differences in the performance of the two functionals are attributable to the greater basicity of the anion oxygen atoms with the HCTH functional and the more structured aqueous solution with BLYP. The enhanced basicity results in larger aqueous coordination shells for the anion oxygens. The structuring of the BLYP aqueous solution is observed in the corrugation of the water density profile, the higher first peak in g(OO)(r), and a smaller water self-diffusion constant. This structuring with the BLYP functional yields anion hydrogen bonds that endure longer and where the dissociated ions more rapidly and directly segregate in the slab. The simulations indicate that aqueous surfaces containing ionizable diprotic acids can be modeled with rather modest sized systems and be informative.     

Dynamic supercoiling bifurcations of growing elastic filaments

Certain bacteria form filamentous colonies when the cells fail to separate after dividing. In Bacillus subtilis, Bacillus thermus, and Cyanobacteria, the filaments can wrap into complex supercoiled structures as the cells grow. The structures may be solenoids or plectonemes, with or without branches in the latter case. Any microscopic theory of these morphological instabilities must address the nature of pattern selection in the presence of growth, for growth renders the problem nonautonomous and the bifurcations dynamic. To gain insight into these phenomena, we formulate a general theory for growing elastic filaments with bending and twisting resistance in a viscous medium, and study an illustrative model problem: a growing filament with preferred twist, closed into a loop. Growth depletes the twist, inducing a twist strain. The closure of the loop prevents the filament from unwinding back to the preferred twist; instead, twist relaxation is accomplished by the formation of supercoils. Growth also produces viscous stresses on the filament which even in the absence of twist produce buckling instabilities. Our linear stability analysis and numerical studies reveal two dynamic regimes. For small intrinsic twist the instability is akin to Euler buckling, leading to solenoidal structures, while for large twist it is like the classic writhing of a twisted filament, producing plectonemic windings. This model may apply to situations in which supercoils form only, or more readily, when axial rotation of filaments is blocked. Applications to specific biological systems are proposed.     

Synthesis and characterization of some vanadyl complexes with flavonoid derivatives as potential insulin-mimetic agents

Two new complexes with formula VOL₂·nH₂O ((1) L: 4′,5,7-trihydroxyflavone-7-rhamnoglucoside (naringin), n = 8; (2) L: 3′,4′,7-tris[O-(2-hydroxyethyl)]rutin (troxerutin), n = 0) were synthesised and characterised. The IR and UV–Vis spectral data indicate that these flavones act as bidentate chelating ligands and generate VO(II) complexes with a square-pyramidal stereochemistry. The thermal analysis (TG, DTA) elucidated the composition and also the number and nature of the water molecules. The thermal behavior indicates also a strong interaction between oxovanadium (IV) and these oxygen donor ligands.     

Autoionization at the surface of neat water: is the top layer pH neutral, basic, or acidic?

Autoionization of water which gives rise to its pH is one of the key properties of aqueous systems. Surfaces of water and aqueous electrolyte solutions are traditionally viewed as devoid of inorganic ions; however, recent molecular simulations and spectroscopic experiments show the presence of certain ions including hydronium in the topmost layer. This raises the question of what is the pH (defined using proton concentration in the topmost layer) of the surface of neat water. Microscopic simulations and measurements with atomistic resolution show that the water surface is acidic due to a strong propensity of hydronium (but not of hydroxide) for the surface. In contrast, macroscopic experiments, such as zeta potential and titration measurements, indicate a negatively charged water surface interpreted in terms of preferential adsorption of OH(-). Here we review recent simulations and experiments characterizing autoionization at the surface of liquid water and ice crystals in an attempt to present and discuss in detail, if not fully resolve, this controversy.     

Sulfonamide carbazole receptors for anion recognition

Carbazole-based receptors functionalized with two sulfonamide groups have been synthesized and their properties as anion receptors have been evaluated. The receptor with bis(trifluoromethyl)aniline groups has shown a very high affinity for halide ions, especially remarkable as only two hydrogen bonds are formed in the complexes. (1)H NMR and fluorescence titrations have been carried out and binding constants up to 7.9 × 10(6) M(-1) have been reached. X-ray structures have been obtained and a modelling study has shown the possible reasons for the large affinity of these compounds for halide anions.     

Synthesis and Characterization of Partially Substituted at Lower Rim Phosphorus Containing Calix(4)arenes

The synthesis and characterization of several new phosphorus-containing partially lower rim substituted derivatives of 5,11,17,23-tetra(t-butyl) calix(4)arene (I) and 5,11,17,23-tetra(t-octyl)calix(4)arene (II), namely 5,11,17,23-tetra(t-butyl)-25,27-dihydroxy-26,28-bis(diphenylphosphinoyl-oxy) calix(4)arene (IV); 5,11,17,23-tetra(t-butyl)-25-hydroxy-26,27,28-tris(tetramethyldiamido-phosphinoyl-oxy) calix(4)arene (Vb); 5,11,17,23-tetra(t-butyl)-25,27-dihydroxy-26,28-bis(dimethyl-phosphinoyl-methoxy) calix(4)arene (VI); 5,11,17,23-tetra (t-octyl)-25,27-dihydroxy-26,28-bis(dimethyl-phosphinoyl-methoxy) calix(4)arene (VII) are reported. The structure of the synthesized calix(4)arene derivatives are identified and confirmed by elemental analysis, IR, ¹H, ¹³C, ³¹P{¹H} NMR spectroscopy and mass spectrometry as and X-ray crystallographic analysis of 5,11,17,23-tetra(t-butyl)-25,27-dihydroxy-26,28-bis(dimethyl-phosphinoyl-methoxy) calix(4)arene VI. According to the NMR spectra, all calix(4)arenes are in cone conformation.     

DOT2: Macromolecular docking with improved biophysical models

Computational docking is a useful tool for predicting macromolecular complexes, which are often difficult to determine experimentally. Here, we present the DOT2 software suite, an updated version of the DOT intermolecular docking program. DOT2 provides straightforward, automated construction of improved biophysical models based on molecular coordinates, offering checkpoints that guide the user to include critical features. DOT has been updated to run more quickly, allow flexibility in grid size and spacing, and generate an infinitive complete list of favorable candidate configurations. Output can be filtered by experimental data and rescored by the sum of electrostatic and atomic desolvation energies. We show that this rescoring method improves the ranking of correct complexes for a wide range of macromolecular interactions and demonstrate that biologically relevant models are essential for biologically relevant results. The flexibility and versatility of DOT2 accommodate realistic models of complex biological systems, improving the likelihood of a successful docking outcome. © 2013 Wiley Periodicals, Inc.     

Multiresidue LC–MS/MS analysis of cephalosporins and quinolones in milk following ultrasound‐assisted matrix solid‐phase dispersive extraction combined with the quick,easy, cheap,effective, rugged,and safe methodology

A sensitive and selective confirmatory method for milk‐residue analysis of ten quinolones and eight cephalosporins by LC‐MS/MS has been developed herein. For the chromatographic separation of target analytes, a Perfectsil ODS‐2 (250 × 4 mm, 5 μm) analytical column was used and gradient elution was applied, using a mobile phase of 0.1% w/w TFA in water and 0.1% w/w TFA in ACN. Ultrasound‐assisted matrix solid‐phase dispersion procedure was applied for the extraction and clean‐up procedure of antimicrobials agents from milk matrix using a mixture of Bond Elut Plexa sorbent and QuEChERS. The method was validated meeting the European Legislation determining selectivity, linearity response, trueness, precision (repeatability and between‐day reproducibility), decision limit, detection capability, and ruggedness following the Youden approach. Recoveries of all antibiotics ranged from 81.7 to 117.9%, while RSD values were lower than 13.7%. Limits of quantification for all examined compounds ranged from 2.4 to 15.0 μg/kg, substantially lower than the maximum residue limits established by the European Union (30–100 μg/kg).     

Comparative study of photodynamic properties of 13,15-N-cycloimide derivatives of chlorin p6

Comparative study of 13,15-[N-(2-hydroxyethyl)]cycloimide chlorin p6 (2), 13,15-(N-acetoxy)cycloimide chlorin p6 (3), 13,15-(N-hydroxy)cycloimide chlorin p6 methyl ester (4) and 13,15-(N-methoxy)cycloimide chlorin p6 methyl ester (5) together with the previously investigated 13,15-[N-(3-hydroxypropyl)]cycloimide chlorin p6 (1) was performed. The dependence of the key photodynamic properties of 1-5 on the introduced substituents was analyzed. The photoinduced cell-killing activity of 4 is 100- and 280-fold higher than that of chlorin p6 and Photogem, respectively, as estimated on A549 human lung adenocarcinoma cells. The activity is reduced eight times in the order 4 > 5 > 1 > 2 > 3. The intracellular accumulation of 1-5 occurs in cytoplasm in a monomeric form bound to the lipids of cellular membranes. This form of 1, 2, 3, 4 and 5 is characterized by the high quantum yield of singlet oxygen generation, which depends on the introduced substituents, 0.66, 0.59, 0.35, 0.51 and 0.73, respectively. The photostability is two-fold less for 1 and four-fold less for 2, 3 and 5 than for 4. The rates of cellular uptake and efflux of 1-5 vary widely, thus providing the way to optimize the pharmacological properties of the photosensitizer (PS) using the respective substituents. Modifying the substituents, 1-5 were targeted to different cellular organelles. The enhanced accumulation in the Golgi apparatus and mitochondria complemented with diffuse staining of intracellular membranous structures is a property of 1-4. Compound 5 accumulates selectively in the lipid droplets and stains weakly perinuclear structures. Temperature-sensitive mechanisms of transport are responsible for the 1-4 uptake. Diffusion can play a role in the internalization of 5 but not of 1-4. Endocytosis via caveolae, clathrin-dependent and adenosine triphosphate-dependent pathways are not noticeably involved in the 1-5 internalization. Independently from their intracellular localization 1, 4 and 5 are highly efficient near-IR PS, which induce predominantly an apoptotic type of cell death under conditions providing ca 50% level of phototoxicity and necrosis at the 100% level of phototoxicity.