Resonance Raman spectroscopy and DFT calculations of the protonation of 4-(2-pyridylazo)-N,N-dimethylaniline in solution and adsorbed on oxide surfaces

The protonation of 4-(2-pyridylazo)-N,N-dimethylaniline (PYAD) in aqueous solution and its adsorption on oxide surfaces has been studied by resonance Raman (RR) spectroscopy. The gas phase structures of neutral, protonated and diprotonated forms of PYAD were modelled by SCF-DFT calculations at the B3-LYP/DZ level, enabling determination of the simulated vibrational spectra of these species, together with vibrational assignments, and providing confirmation that protonation occurs initially at the pyridyl nitrogen atom. Electronic absorption spectra were interpreted using time-dependent DFT calculations. Adsorption of PYAD on SiO₂ or Al₂O₃ surfaces is mainly via the neutral species, hydrogen bonded to surface OH groups, although a small proportion of adsorbed molecules are protonated. By contrast, adsorption on SiO₂–Al₂O₃ results in complete protonation, indicating the presence of Brønsted acidic sites with pK_a values ? 4.5, whereas adsorption on H-mordenite results in diprotonation, indicating the presence of Brønsted acidic sites with pK_a values ? 2.     

Crystal structures of syndiotactic poly(p-methylstyrene) clathrates with two guest molecules having very similar shape and volume

In the present paper we report on the clathrate structures of syndiotactic poly(p-methylstyrene) (s-PPMS) containing chlorobenzene (cell constants: a = 23.5 Å, b = 12.0 Å, c = 7.9 Å and γ = 112.4°; space group: P2₁/a) and toluene (cell constants: a = 19.5 Å, b = 13.5 Å, c = 7.9 Å and γ = 90°; space group: P2₁). Despite the extreme similarity between the shape and volume of these two molecules, they give rise to completely different clathrate structures, the first belonging to α class, the second belonging to β class. Moreover the clathrate form containing chlorobenzene represent the first case in which a α class clathrate form of s-PPMS contains two guest molecules in each cavity while the crystal structure here proposed for the s-PPMS/toluene clathrate represents a new example of chiral crystalline phase in which the polymer helices assume all the same chirality in the lattice. These results underline the fact that the choice of a particular structural organization in the process of clathrates’ formation of s-PPMS is not easily referable only to steric effects but seems to be dependant even on the chemical structure of the guest molecules. A comparison with syndiotactic polystyrene is also done.     

Study on the difference in adsorption thermodynamics for water on swelling and non-swelling clays with implications for prevention and treatment of pneumoconiosis

Excessive inhalation of mineral dust can cause irreversible damage such as diffuse fibrosis of lung tissue. Water-based dust reduction technology can effectively control the dust concentration. The study of the interaction of water-clay mineral dust is helpful to the prevention and treatment of pneumoconiosis by water-based dust removal technology. To better understand the underlying adsorption mechanisms of water molecules on clay mineral dust, the detailed adsorption thermodynamics analysis is necessary. In this paper, we research the thermodynamics of adsorption of water molecules on swelling clay of montmorillonite and non-swelling clay of illite. First, the adsorption isotherms of water molecules on montmorillonite and illite at 293–313 K were measured by gravimetric method. Then, the key thermodynamic variables, including entropy change (ΔS), surface potential (Ω), isosteric heat of adsorption (Q_st) and variation of Gibbs free energy (ΔG), were analyzed. Results illustrate that the adsorption amount for water molecules on illite is one order of magnitude smaller than that on montmorillonite, suggesting that swelling clay plays a dominant role in water molecules adsorption process. For water molecules adsorption on montmorillonite, the contribution of secondary adsorption to total adsorption (a₂/a) is always less than 30%. For water molecules adsorption on illite, the contribution of primary adsorption to total adsorption (a₁/a) is greater than a₂/a at the low pressure region, while a₂/a can exceed 60% at the high pressure region. The difference in the uptakes of water molecules adsorption on non-swelling and swelling clays is mainly resulted from the difference in primary adsorption on two clays. The Henry’s constant (K_AA) for montmorillonite is in the range of 21.37–75.08 mmol/g/kPa, which is evidently larger than the K_AA values of 0.34–0.98 mmol/g/kPa for illite. Compared with non-swelling clay, the adsorption spontaneity degree for water molecules on swelling clay is higher, and the interaction of swelling clay-water molecules is stronger. Meanwhile, the movement of adsorbed water molecules in swelling clay is more confined than that in non-swelling clay. These findings can offer meaningful guidelines for the prevention and treatment of pneumoconiosis.     

Simulation of synergistic effect at coadsorption of two organic substances on electrode

Based of numerical calculations, it is shown that for two organic substances with similar dependences of adsorption on the electrode potential, the overall surface coverage is well described by the ordinary Frumkin isotherm with a certain effective attraction constant a _eff. A correlation between the a _eff value and the constants of intermolecular interaction in the adsorption layer was revealed for co-adsorbing molecules 1 and 2, namely, a ₁₁, a ₂₂, and a ₁₂.     

Author index

Electromotive-force measurements on cells without liquid junction have been used to determine the pK_a values of 7 mono-, 6 di-, and 2 tricarboxylic acids in formamide at 9 temperatures from 5 to 45°C. From the pK_a values, the thermodynamic quantities ΔG⁰, ΔH⁰, and ΔS⁰ for the acids have been calculated in formamide at 25°C.     

On the microstructure and symmetry of apparently hexagonal BaAl2O4

The P6₃ (a=2a_p, b=2b_p, c=c_p) crystal structure reported for BaAl₂O₄ at room temperature has been carefully re-investigated by a combined transmission electron microscopy and neutron powder diffraction study. It is shown that the poor fit of this P6₃ (a=2a_p, b=2b_p, c=c_p) structure model for BaAl₂O₄ to neutron powder diffraction data is primarily due to the failure to take into account coherent scattering between different domains related by enantiomorphic twinning of the P6₃22 parent sub-structure. Fast Fourier transformation of [0 0 1] lattice images from small localized real space regions (∼10 nm in diameter) are used to show that the P6₃ (a=2a_p, b=2b_p, c=c_p) crystal structure reported for BaAl₂O₄ is not correct on the local scale. The correct local symmetry of the very small nano-domains is most likely orthorhombic or monoclinic.     

IrSr2TbCu2O8, a high-pressure metamagnetic cuprate: Structure, microstructure and properties

The synthesis, structure and microstructure of the IrSr₂TbCu₂O₈ cuprate showing metamagnetic properties are described. The sample was prepared at high temperatures and pressures up to 9.2 GPa. The structure is tetragonal, showing a 1212 type structure, that derives from the classical YBaCuO superconductor structure, replacing the tetracoordinated square planar copper [Cu-O₄] in the “chains” by octahedral [Ir-O₆] groups that form a perovskite-like layer in the basal plane of the unit cell. A “simple” cell, ∼a_p×a_p×3a_p, where a_p is the basic perovskite unit cell parameter (a_p∼3.8 Å), is supported by X-ray powder diffraction (XRD) and a so-called “diagonal” one, ∼√2a_p×√2a_p×3a_p, by SAED; a microdomain texture of latter cell and a series of very interesting extended defects have been observed by HREM. Magnetic susceptibility measurements show a magnetic transition, T_N∼6 K, with negative Weiss temperature, that indicates antiferromagnetic interactions among the Tb moments. The magnetic structure has been determined by neutron diffraction. A detailed magnetic study has revealed a metamagnetic behavior, something not previously observed in this type of cuprates. Specific heat and resistivity measurements have also been performed to characterize the transition.     

Structural analysis of several W(VI) and Mo(VI) complex perovskites prepared by the polymeric precursors method

We describe in this work the synthesis by the Pechini method of five Mo(VI)- and W(VI)-containing complex perovskites and their structural characterisation by HREM and XRD. The compounds studied, Ba(B_2/3′B_1/3″)O₃ (B′=In and Y; B″=W and Mo) and Sr(In_2/3W_1/3)O₃, were obtained after firing the precursor powders for 8 h at 1200°C. Thermal analysis showed that the formation mechanism of the five perovskites is similar and implies the formation of barium carbonate and barium tungstates or molybdates of different stoichiometries as intermediate phases. Interesting enough, these similar mechanisms yield to materials of a quite different structure. Indeed, Ba(In_2/3Mo_1/3)O₃ and Sr(In_2/3W_1/3)O₃ were found to be disordered perovskites (unit cells: a_p×a_p×a_p and , respectively); on the other hand, two phases coexist in the sample Ba(In_2/3W_1/3)O₃ at the synthesis conditions: an ordered predominant phase (unit cell: 2a_p×2a_p×2a_p) and, as a minor phase, a disordered perovskite (unit cell: a_p×a_p×a_p). Finally, the two yttrium-containing compounds were found to be ordered perovskites (2a_p×2a_p×2a_p).     

Benchmarking and validating algorithms that estimate p<Emphasis Type="Italic">K</Emphasis><Subscript>a</Subscript> values of drugs based on their molecular structures

The REGDIA regression diagnostics algorithm in S-Plus is introduced in order to examine the accuracy of pK _a predictions made with four updated programs: PALLAS, MARVIN, ACD/pKa and SPARC. This report reviews the current status of computational tools for predicting the pK _a values of organic drug-like compounds. Outlier predicted pK _a values correspond to molecules that are poorly characterized by the pK _a prediction program concerned. The statistical detection of outliers can fail because of masking and swamping effects. The Williams graph was selected to give the most reliable detection of outliers. Six statistical characteristics (F _exp, R ², , MEP, AIC, and s(e) in pK _a units) of the results obtained when four selected pK _a prediction algorithms were applied to three datasets were examined. The highest values of F _exp, R ², , the lowest values of MEP and s(e), and the most negative AIC were found using the ACD/pK _a algorithm for pK _a prediction, so this algorithm achieves the best predictive power and the most accurate results. The proposed accuracy test performed by the REGDIA program can also be applied to test the accuracy of other predicted values, such as log P, log D, aqueous solubility or certain physicochemical properties of drug molecules.     

Reversible and irreversible adsorption of particles on homogeneous surfaces

The kinetics of localized reversible and irreversible adsorption of interacting particles on homogeneous surfaces was analysed. Asymptotic analytical equations were derived for the surface blocking parameter B(0), and for adsorption kinetics and adsorption isotherms in the limit of low and high surface concentrations. It was found that the geometrical blocking effect was much more pronounced than the Langmuir model predicts, especially for high surface concentrations and low ionic strengths of suspensions.The new adsorption isotherm formulated indicates that for a large adsorption constant, K_a, the equilibrium surface concentration becomes proportional to K^−1/3_a, whereas in the Langmuir model this quantity is approached as K⁻¹_a (for K_a ≫I). In the case of irreversible adsorption the theoretical predictions were experimentally tested by applying the direct microscope observation method. Monodisperse suspensions of negatively charged latex particles were used in these experiments with silanized mica sheets as the adsorbing surface. Our theoretical predictions were quantitatively confirmed, indicating that the Langmuir model is not appropriate for describing localized adsorption of particles on homogeneous surfaces.     

Humidity sensors composed of grafted copolymers

Sulphonated polystyrene branch was grafted on the surface of a tetrafluoroethylene (PTFE) film. The impedance of the surface of the grafted film decreases as the humidity increases. Li, Na and K salts of PTFE—sytrenesulphonate film were also prepared. The impedance of the alkali salts is one order of magnitude higher than that of the acid form. An equivalent circuit of parallel resistance R_p and capacitance C_p was assumed for these films. R_p depends on the amount of water adsorbed in the grafted layer irrespective of the species of cations. C_p is independent of the humidity. The activation energy of R_p decreases as the humidity increases. It is not the alkali ions but the proton from the adsorbed water that predominantly contributes to the charge transport.     

Hydrogen bond interactions at the TiO2 surface: Their contribution to the pH dependent photo-catalytic degradation of p-nitrophenol

We have obtained pK_a values of p-nitrophenol–TiO₂ by measuring the adsorption equilibrium constants of p-nitrophenol (PNP) on the TiO₂ surface at different pH values. These values have been obtained from Langmuir isotherms and from a plot of 1/rate vs. 1/[PNP]_o obtained during TiO₂ catalyzed solar light photo-degradation of PNP. Two limit equilibrium constants are readily obtained depending on the solution pH: at pH 5 at which the TiO₂ surface is mainly positively charged and at pH 8 when it is negatively charged. With these and other adsorption equilibrium constants and the PNP pK_a value in solution, thermodynamic cycles are established in order to obtain the PNP pK_a when it is adsorbed on positively charged, neutral and negatively charged TiO₂ surfaces. From these pK_a values useful information on the PNP–TiO₂ interaction is readily obtained. For instance, the PNP nitro group interacts with the TiO₂ surface via a hydrogen bond, arising from the complex of water molecules with the Ti⁴⁺ ions on its surface. The weaker the hydrogen bond donor, the stronger the oxygen nitro group basicity. Therefore, pK_a changes on the phenolic hydroxyl group result from these interactions. Linear free energy correlations, maximum PNP adsorption capacity values (Q_L) and FTIR ATR, spectrum support this proposal. A k_obs vs. pH degradation profile of p-nitrophenol is also provided.     

Acid dissociation constants of uridine-5′-diphosphate compounds determined by phosphorus nuclear magnetic resonance spectroscopy and internal pH referencing

The acid dissociation constant (pK_a) of small, biological molecules is an important physical property used for investigating enzyme mechanisms and inhibitor design. For phosphorus-containing molecules, the ³¹P nuclear magnetic resonance (NMR) chemical shift is sensitive to the local chemical environment, particularly to changes in the electronic state of the molecule. Taking advantage of this property, we present a ³¹P NMR approach that uses inorganic phosphate buffer as an internal pH reference to determine the pK_a values of the imide and second diphosphate of uridine-5′-diphosphate compounds, including the first reported values for UDP-GlcNAc and UDP-S-GlcNAc. New methods for using inorganic phosphate buffer as an internal pH reference, involving mathematical correction factors and careful control of the chemical shift reference sample, are illustrated. A comparison of the newly determined imide and diphosphate pK_a values of UDP, UDP-GlcNAc, and UDP-S-GlcNAc with other nucleotide phosphate and thio-analogs reveals the significance of the monosaccharide and sulfur position on the pK_a values.     

The adsorption of RNAse A,BSA and cytochrome c at the graphite powder|liquid interface using in parallel the adsorption isotherm plot and linear sweep voltammetry on graphite paste electrode

The adsorption of RNAse A, BSA and cytochrome c on graphite powder has been investigated using in parallel the adsorption isotherm plot and linear sweep voltammetry on a graphite paste electrode (g.p.e.). The principle of the latter depends on the determination by electrochemical oxidation of tyrosyl or tryptophan residues having access to the interface. Adsorption isotherms exhibit bimodal adsorption features with a cooperative phenomenon leading to the formation of a close-packed two dimensional surface phase. Protein molecules are adsorbed in a monolayer when the pH is different from the isoelectric point. This layer is built up by the entanglement of a double network:

• •A network of molecules irreversibly adsorbed side-on, where hydrophobic residues move from the core to the surface. The tertiary structure is likely altered. The new dimensions of these adsorbed molecules have been determined (surface area per molecule, thickness).
• •A network of molecules adsorbed end-on, lying between the irreversibly adsorbed molecules.

     

Orthorhombic superstructures within the rare earth strontium-doped cobaltate perovskites: Ln1−xSrxCoO3−δ (Ln=Y, Dy-Yb; 0.750?x?0.875)

A combination of electron, synchrotron X-ray and neutron powder diffraction reveals a new orthorhombic structure type within the Sr-doped rare earth perovskite cobaltates Ln_1−xSr_xCoO_3−δ (Ln=Y³⁺, Dy³⁺, Ho³⁺, Er³⁺, Tm³⁺and Yb³⁺). Electron diffraction shows a C-centred cell based on a 2√2a_p×4a_p×4√2a_p superstructure of the basic perovskite unit. Not all of these very weak satellite reflections are evident in the synchrotron X-ray and neutron powder diffraction data and the average structure of each member of this series could only be refined based on Cmma symmetry and a 2√2a_p×4a_p×2√2a_p cell. The nature of structural and magnetic ordering in these phases relies on both oxygen vacancy and cation distribution. A small range of solid solution exists where this orthorhombic structure type is observed, centred roughly around the compositions Ln_0.2Sr_0.8CoO_3−δ. In the case of Yb³⁺ the pure orthorhombic phase was only observed for 0.850?x?0.875. Tetragonal (I4/mmm; 2a_p×2a_p×4a_p) superstructures were observed for compositions having higher or lower Sr-doping levels, or for compounds with rare earth ions larger than Dy³⁺. These orthorhombic phases show mixed valence (3+/4+) cobalt oxidation states between 3.2+ and 3.3+. DC magnetic susceptibility measurements show an additional magnetic transition for these orthorhombic phases compared to the associated tetragonal compounds with critical temperatures > 330 K.     

p<Emphasis Type="Italic">K</Emphasis><Subscript>a</Subscript> measurements for the SAMPL6 prediction challenge for a set of kinase inhibitor-like fragments

Determining the net charge and protonation states populated by a small molecule in an environment of interest or the cost of altering those protonation states upon transfer to another environment is a prerequisite for predicting its physicochemical and pharmaceutical properties. The environment of interest can be aqueous, an organic solvent, a protein binding site, or a lipid bilayer. Predicting the protonation state of a small molecule is essential to predicting its interactions with biological macromolecules using computational models. Incorrectly modeling the dominant protonation state, shifts in dominant protonation state, or the population of significant mixtures of protonation states can lead to large modeling errors that degrade the accuracy of physical modeling. Low accuracy hinders the use of physical modeling approaches for molecular design. For small molecules, the acid dissociation constant (pK_a) is the primary quantity needed to determine the ionic states populated by a molecule in an aqueous solution at a given pH. As a part of SAMPL6 community challenge, we organized a blind pK_a prediction component to assess the accuracy with which contemporary pK_a prediction methods can predict this quantity, with the ultimate aim of assessing the expected impact on modeling errors this would induce. While a multitude of approaches for predicting pK_a values currently exist, predicting the pK_as of drug-like molecules can be difficult due to challenging properties such as multiple titratable sites, heterocycles, and tautomerization. For this challenge, we focused on set of 24 small molecules selected to resemble selective kinase inhibitors—an important class of therapeutics replete with titratable moieties. Using a Sirius T3 instrument that performs automated acid–base titrations, we used UV absorbance-based pK_a measurements to construct a high-quality experimental reference dataset of macroscopic pK_as for the evaluation of computational pK_a prediction methodologies that was utilized in the SAMPL6 pK_a challenge. For several compounds in which the microscopic protonation states associated with macroscopic pK_as were ambiguous, we performed follow-up NMR experiments to disambiguate the microstates involved in the transition. This dataset provides a useful standard benchmark dataset for the evaluation of pK_a prediction methodologies on kinase inhibitor-like compounds.     

H2分子在LaFeO3表面吸附的第一性原理研究

基于密度泛函理论的第一性原理方法,通过计算表面能确定LaFeO₃(010)表面为最稳定的吸附表面,研究了H₂分子在LaFeO₃(010)表面的吸附性质。LaFeO₃(010)表面存在LaO和FeO₂两种终止表面,但吸附主要发生在FeO₂终止表面,由于LaFeO₃(010)表面弛豫的影响,使得凹凸不平的表面层增加了表面原子与H原子的接触面积,表面晶胞的纵向体积增加约2.5%,有利于H原子向晶体内扩散。研究发现,H₂分子在LaFeO₃(010)表面主要存在3种化学吸附方式:第一种吸附发生在O-O桥位,2个H原子分别吸附在2个O原子上,形成2个-OH基,这是最佳吸附位置,此时H原子与表面O原子的作用主要是H1s与O2p轨道杂化作用的结果,H-O之间为典型的共价键。H₂分子的解离能垒为1.542 eV,说明表面需要一定的热条件,H₂分子才会发生解离吸附;第二种吸附发生在Fe-O桥位,1个H原子吸附在O原子上形成1个-OH基,另一个H原子吸附在Fe原子上形成金属键;第三种吸附发生在O顶位,2个H原子吸附在同一个O原子上,形成H₂O分子,此时H₂O分子与表面形成物理吸附,H₂O分子逃离表面后容易形成氧空位。此外,H₂分子在LaFeO₃(010)表面还可以发生物理吸附。