Solvent viscosity dependence of the folding rate of a small protein: distributed computing study

By using distributed computing techniques and a supercluster of more than 20,000 processors we simulated folding of a 20-residue Trp Cage miniprotein in atomistic detail with implicit GB/SA solvent at a variety of solvent viscosities (gamma). This allowed us to analyze the dependence of folding rates on viscosity. In particular, we focused on the low-viscosity regime (values below the viscosity of water). In accordance with Kramers' theory, we observe approximately linear dependence of the folding rate on 1/gamma for values from 1-10(-1)x that of water viscosity. However, for the regime between 10(-4)-10(-1)x that of water viscosity we observe power-law dependence of the form k approximately gamma(-1/5). These results suggest that estimating folding rates from molecular simulations run at low viscosity under the assumption of linear dependence of rate on inverse viscosity may lead to erroneous results.     

Interplay between the structural and magnetic probes in the elucidation of the structure of a novel 2D layered [V4O4(OH)2(O2CC6H4CO2)4]·DMF

The title compound has been synthesized under solvothermal conditions by reacting vanadium(V) oxytriisopropoxide with terephthalic acid in N,N-dimethylformamide. A combination of synchrotron powder diffraction, infrared spectroscopy, scanning and transmission electron microscopy, and thermal and chemical analysis elucidated the chemical, structural and microstructural features of a new 2D layered inorganic-organic framework. Due to the low-crystallinity of the final material, its crystal structure has been solved from synchrotron X-ray powder diffraction data using a direct space global optimization technique and subsequent constraint Rietveld refinement. [V(4)O(4)(OH)(2)(O(2)CC(6)H(4)CO(2))(4)]·DMF crystallizes in the monoclinic system (space group P2/m (No. 10)); cell parameters: a = 20.923(4) ?, b = 5.963(4) ?, c = 20.425(1) ?, β = 123.70(6)°, V = 2120.1(9) ?(3), Z = 2. The overall structure can be described as an array of parallel 2D layers running along [-101] direction, consisting of two types of vanadium oxidation states and coordination polyhedra: face-shared trigonal prisms (V(4+)) and distorted corner-shared square pyramids (V(5+)). Both configurations form independent parallel chains oriented along the 2-fold symmetry crystallographic b-axis mutually interlinked with terephthalate ligands in a monodentate mode perpendicular to it. The morphology of the compound exhibits long nanofibers, with the growth direction along the layered [-101] axis. The magnetic susceptibility measurements show that the magnetic properties of [V(4)O(4)(OH)(2)(O(2)CC(6)H(4)CO(2))(4)]·DMF can be described by a linear antiferromagnetic chain model, with the isotropic exchange interaction of J = -75 K between the nearest V(4+) neighbours of S = 1/2.     

Insight into the extractability of metals from soils using an implementation of the linear adsorption isotherm model

This paper deals with an often overlooked artifact in sequential and single extraction of metals from soils, viz. the volume to mass (V/m) ratio as a potential source for inadequate extraction yields. We offer a theoretical framework to get a grip on this intricate parameter and came up with a model based on a linear adsorption isotherm to derive the correct maximal metal extractability for a certain extractant. We verified the model experimentally using 0.1 mol l⁻¹ nitric acid for extraction of seven metals (Cr, Co, Cu, Cd, Pb, Ni and Zn) from an urban soil sample, and concluded that commonly used V/m ratios in the range of 10-40 ml g⁻¹ may give as much as 50% too low extraction yields. Thus, a strong caveat is in place as to be very critical what V/m ratios to use and preferably apply the model derived to obtain the correct maximal extractability using a variable V/m ratio method.     

Thermodynamic characterization of 3-[(3-cholamidopropyl)-dimethylammonium]-1-propanesulfonate (CHAPS) micellization using isothermal titration calorimetry: temperature, salt, and pH dependence

A systematic investigation of the micellization process of a biocompatible zwitterionic surfactant 3-[(3-cholamidopropyl)-dimethylammonium]-1-propanesulfonate (CHAPS) has been carried out by isothermal titration calorimetry (ITC) at temperatures between 278.15 K and 328.15 K in water, aqueous NaCl (0.1, 0.5, and 1 M), and buffer solutions (pH = 3.0, 6.8, and 7.8). The effect of different cations and anions on the micellization of CHAPS surfactant has been also examined in LiCl, CsCl, NaBr, and NaI solutions at 308.15 K. It turned out that the critical micelle concentration, cmc, is only slightly shifted toward lower values in salt solutions, whereas in buffer media it remains similar to its value in water. From the results obtained, it could be assumed that CHAPS behaves as a weakly charged cationic surfactant in salt solutions and as a nonionic surfactant in water and buffer medium. Conventional surfactants alike, CHAPS micellization is endothermic at low and exothermic at high temperatures, but the estimated enthalpy of micellization, ΔHM0, is considerably lower in comparison with that obtained for ionic surfactants in water and NaCl solutions. The standard Gibbs free energy, ΔGM0, and entropy, ΔSM0, of micellization were estimated by fitting the model equation based on the mass action model to the experimental data. The aggregation numbers of CHAPS surfactant around cmc, obtained by the fitting procedure also, are considerably low (nagg ≈ 5 ± 1). Furthermore, some predictions about the hydration of the micelle interior based on the correlation between heat capacity change, Δcp,M0, and changes in solvent-accessible surface upon micelle formation were made. CHAPS molecules are believed to stay in contact with water upon aggregation, which is somehow similar to the micellization process of short alkyl chain cationic surfactants.     

Influence of chain length and degree of branching of alcohol + chlorobenzene mixtures on determination and modelling of V by CEOS and CEOS/G mixing rules

The densities of binary mixtures of (1-propanol, or 1-butanol, or 2-butanol, or 1-pentanol + chlorobenzene) have been measured at temperatures 288.15, 293.15, 298.15, 303.15, 308.15 and 313.15 K and atmospheric pressure while for the system (2-methyl-2-propanol + chlorobenzene) measurements were performed at the same pressure and temperatures 303.15, 308.15, 313.15, 318.15 and 323.15 K. All measurements were performed by means of an Anton Paar DMA 5000 digital vibrating-tube densimeter. Excess molar volumes V^E were determined and fitted by the Redlich–Kister equation. It was observed that in all cases, V^E increase with rising of temperature. The values of limiting excess partial molar volumes have been calculated, as well. The obtained results have been analysed in terms of specific molecular interactions present in these mixtures taking into consideration effect of the chain length of alcohols, degree of branching in the chain, relative position of the alkyl and OH group in an alcohol and the effect of temperature on them. In addition, the correlation of V^E binary data was performed with the Peng–Robinson–Stryjek–Vera cubic equation of state (PRSV CEOS) coupled with the van der Waals (vdW1) and CEOS/G^E mixing rule introduced by Twu, Coon, Bluck and Tilton (TCBT). Also, the possibility of cross prediction between V^E and VLE by means of the NRTL parameters of G^E model available in literature and those incorporated in the TCBT model was tested.     

Combination of three analytical techniques for speciation of Al in environmental samples

An analytical scheme is proposed which combines three speciation techniques for determination of particular Al species in soil extracts and percolating waters. A cation-exchange fast protein liquid chromatography — inductively coupled plasma atomic emission spectrometry (FPLC-ICP-AES) procedure, a microcolumn chelating ion-exchange chromatography- atomic absorption spectrometry (MCC-ETAAS) technique and the 8-hydroxyquinoline spectrophotometric method (8HQ-spectrophotometry) were employed. The FPLC-ICP-AES procedure offers determination of Al³⁺ (retention time 4.5 min) and Al(OH)²⁺ species (retention time 4.0 min) which are separated from Al(OH)⁺ ₂ (retention time 1.5min). AlF²⁺ coelutes with Al(OH)²⁺ species, while Al(SO₄)⁺, AlF⁺ ₂ and negatively charged Al organic complexes coelute with Al(OH)⁺ ₂ species. The MCC-ETAAS technique enables determination of the sum of positively charged monomeric aqua- and hydroxy-Al species plus sulphate- and fluoro-Al complexes. Employing the 8HQ-spectrophotometry the sum of positively charged monomeric aqua- and hydroxy-Al species plus sulphato- and most of the labile organic Al species are determined. The sensitivities of these selected techniques were adequate for speciation of Al in the samples analyzed. On the basis of the specific selectivity of a particular technique various groups of Al species may be determined. Thus, the comparison of analytical data from complementary procedures provides more comprehensive information on Al species present in soil extracts and percolating waters.     

Erratum to: Solution behavior of aqueous mixtures of low and high molecular weight hydrophobic amphiphiles

Mixtures of a hydrophobic triblock copolymer (L121, PEO₅PPO₆₈PEO₅) and a hydrophobic anionic surfactant (AOT, Sodium bis(2-ethylhexyl)sulfosuccinate), each alone forming turbid vesicular solutions in water, aggregate to produce a thermodynamically stable, transparent and isotropic solution. Mixed AOT/L121 aggregates could be confirmed by fluorescence, surface tension, differential scanning calorimetry (DSC) and isothermal titration calorimetry (ITC). In an isotropic region, where mixed aggregates are formed, there is a synergistic interaction between monomers of AOT and L121 in the mixture. In addition, Small Angle Neutron Scattering (SANS) experiments provided evidence that mixed aggregates have the shape of either spheres (with a certain polydispersity) or very short ellipsoids (axial ratio below 2), confirming a transition from giant multilamellar vesicles to small aggregates upon mixing the two hydrophobic amphiphiles. Upon dilution, the morphology changes to disk-like. From an examination of the results of all the methods the peculiar behavior of the mixed AOT/L121 system is explained.     

Topographical distance matrices for porous arrays

The topographical Wiener index is calculated for two-dimensional graphs describing porous arrays, including bee honeycomb. For tiling in the plane, we model hexagonal, triangular, and square arrays and compare with topological formulas for the Wiener index derived from the distance matrix. The normalized Wiener indices of C₄, T₁₃, and O(4), for hexagonal, triangular, and square arrays are 0.993, 0.995, and 0.985, respectively, indicating that the arrays have smaller bond lengths near the center of the array, since these contribute more to the Wiener index. The normalized Perron root (the first eigenvalue, λ ₁), calculated from distance/distance matrices describes an order parameter, f = l₁/n{\phi=\lambda_1/n} , where f = 1{\phi= 1} for a linear graph and n is the order of the matrix. This parameter correlates with the convexity of the tessellations. The distributions of the normalized distances for nearest neighbor coordinates are determined from the porous arrays. The distributions range from normal to skewed to multimodal depending on the array. These results introduce some new calculations for 2D graphs of porous arrays.     

Organomercury(II) and tellurium(II) compounds with the "pincer" ligand 2,6-[O(CH2CH2)2NCH2]2C6H3--stabilization of an unusual organotellurium(II) cationic species

The reaction of RH (1) with Hg(OAc)(2), in EtOH, gave the acetate RHgOAc (2) [R = 2,6-[O(CH(2)CH(2))(2)NCH(2)](2)C(6)H(3)]. The corresponding RHgCl (3) was obtained from 2 and LiCl. The reaction of 3 with TeCl(4) (1:1 molar ratio), in anhydrous 1,4-dioxane, resulted in the transfer of the organic ligand from mercury to tellurium and the isolation of the unexpected ionic compounds [RTe](2)[Hg(2)Cl(6)] (4) and [RH(3)][HgCl(4)] (5). The molecular structures of 1-4 and 5·H(2)O were established by single-crystal X-ray diffraction. The acetate 2 and the chloride 3 are monomeric in solid state. In both mercury and tellurium organometallic compounds the organic group acts as an (N,C,N) "pincer" ligand. This coordination pattern provided stability for the rare [RTe](+) cation. Weak cation-anion interactions [Te···Cl 3.869(3) ?] are present between [RTe](+) and the dinuclear anion [Hg(2)Cl(6)](2-) in the crystal of 4. Theoretical calculations with DFT methods were performed for models of 3 and 4. The results show that in the cation of 4 the coordination of the nitrogen atoms play an important role for the stabilization of the structure found in the crystal whereas in 3 the coordination of the nitrogen atoms to the metal centre stabilizes to a less extent the structure found in solid state.