Investigating Alanine–Silica Interaction by Means of First‐Principles Molecular‐Dynamics Simulations

In our attempts to achieve a detailed understanding of protein–silica interactions at an atomic level we have, as a first step, simulated a small system consisting of one alanine in different protonation states, and a hydroxylated silica surface, using a first‐principles molecular‐dynamics technique. The simulations are carried out in vacuo as well as in the presence of water molecules. In the case of a negatively charged surface and an alanine cation, an indirect proton transfer from the alanine carboxylic group to the surface takes place. The transfer involves several water molecules revealing an alanine in its zwitterionic state interacting with the neutral surface through indirect hydrogen bonds mediated by water molecules. During the simulation of the zwitterionic state the ammonium group eventually establishes a direct ? N? H???O? Si interaction, suggesting that the surface–amino group interaction is stronger than the interaction between the surface and the carboxylic group. In vacuum simulations, the amino group exhibits clearly stronger interactions with the surface than the carboxylic group.     

Nonenzymic polycyclization of analogues of oxidosqualene with a preformed C-ring

Some nonenzymic epoxide-initiated polyolefin cyclization are reported. The presented molecules are partially constrained analogues of (3S)-oxidosqualene, the natural substrate to many important cyclase enzymes. These model compounds feature a preformed C-ring with built-in stereochemical information. The experimental results allow for an instructive comparison with the enzymic processes, particularly those of the cyclases in steroid biosynthesis (i.e. lanosterol synthase).     

Solvent effects on the rate of the keto-enol interconversion of 2-nitrocyclohexanone

The rates of tautomerization of 2-nitrocyclohexanone (2-NCH) have been measured spectrophotometrically at 25.0 +/- 0.1 degrees C in several organic aprotic solvents and their binary mixtures. In cyclohexane the reaction is effectively catalyzed by bases and inhibited by acids while the so-called "spontaneous reaction" appears essentially due to autocatalysis. Apparent second order rate constants (k(app)(B)) for the reaction catalyzed by triethylamine (TEA) and pyridine (Pyr) have been obtained. From the experimental k(app)(B) values rate constants for the enolization (k(1)(B)) and ketonization (k(-1)(B)) reactions have been calculated. A Kamlet-Taft type linear solvation energy relationship (LSER) adequately accounts for the observed solvent effects. Activation parameters for both reactions show that solvent effects are mainly entropic in origin and that there is a shift of the transition state from a ketone-like to an enol-like structure on passing from less to more polar solvents.     

A modular approach to catalyst hydrophobicity for an asymmetric aldol reaction in a biphasic aqueous environment

Catalyst 5, an ion pair consisting of a hydrophilic cation and a lipophilic anion, fulfils the solubility requirements needed to couple efficiency (enantioselectivities and anti-diastereoselectivities up to > or = 99%) and catalyst recyclability in asymmetric aldol reactions under aqueous biphasic conditions.     

Thioflavin T hydroxylation at basic pH and its effect on amyloid fibril detection

The fluorescent dye thioflavin T (ThT) is commonly used for in situ amyloid fibril detection. In this work, we focused on the spectroscopic properties and chemical stability of ThT in aqueous solution as a function of pH, temperature, and dye concentration. A reversible hydroxylation process occurs in alkaline solutions, which was characterized using a combination of UV-vis absorption spectroscopy, proton NMR, and density functional theory (DFT). On the basis of these studies, we propose a chemical structure for the hydroxylated form. Finally, by means of fluorescence spectroscopy, ThT hydroxylation effects on in situ amyloid detection have been investigated, providing new insights on the efficiency of the ThT assay for quantitative fibril evaluation at basic pH.     

Rare tetranuclear mixed-valent [Mn(II)2Mn(IV)2] clusters as building blocks for extended networks

We report the synthesis of a series of mixed valence Mn(II/IV) tetranuclear clusters [Mn(II)(2)Mn(IV)(2)O(2)(heed)(2)(EtOH)(6)Br(2)]Br(2) (), [Mn(II)(2)Mn(IV)(2)O(2)(heed)(2)(H(2)O)(2)Cl(4)].2EtOH.H(2)O (.2EtOH.H(2)O), [Mn(II)(2)Mn(IV)(2)O(2)(heed)(2)(heedH(2))(2)](ClO(4))(4) (), [Mn(II)(2)Mn(IV)(2)O(2)(heed)(2)(MeCN)(2)(H(2)O)(2)(bpy)(2)](ClO(4))(4) () and [Mn(II)(2)Mn(IV)(2)O(2)(heed)(2)(bpy)(2)Br(4)].2MeOH (.2MeOH). Clusters are constructed from the tripodal ligand N,N-bis(2-hydroxyethyl)ethylene diamine (heedH(2)) and represent rare examples of tetranuclear Mn clusters possessing the linear trans zig-zag topology, being the first Mn(II/IV) mixed-valent clusters of this type. The molecular clusters can then be used as building blocks in tandem with the (linear) linker dicyanamide ([N(CN)(2)](-), dca(-)) for the formation of a novel extended network {[Mn(II)(2)Mn(IV)(2)O(2)(heed)(2)(H(2)O)(2)(MeOH)(2)(dca)(2)]Br(2)}(n) (), which exhibits a rare form of the 2D herring bone topology.     

Solvation in pure liquids: what can be learned from the use of pairs of indicators?

The solvation of six solvatochromic probes in a large number of solvents (33-68) was examined at 25 degrees C. The probes employed were the following: 2,6-diphenyl-4-(2,4,6-triphenylpyridinium-1-yl) phenolate (RB); 4-[(E)2-(1-methylpyridinium-4-yl)ethenyl] phenolate, MePM; 1-methylquinolinium-8-olate, QB; 2-bromo-4-[(E)-2-(1-methylpyridinium-4-yl)ethenyl] phenolate, MePMBr, 2,6-dichloro-4-(2,4,6-triphenyl pyridinium-1-yl) phenolate (WB); and 2,6-dibromo-4-[(E)-2-(1-methylpyridinium-4-yl)ethenyl] phenolate, MePMBr(2), respectively. Of these, MePMBr is a novel compound. They can be grouped in three pairs, each with similar pK(a) in water but with different molecular properties, for example, lipophilicity and dipole moment. These pairs are formed by RB and MePM; QB and MePMBr; WB and MePMBr(2), respectively. Theoretical calculations were carried out in order to calculate their physicochemical properties including bond lengths, dihedral angles, dipole moments, and wavelength of absorption of the intramolecular charge-transfer band in four solvents, water, methanol, acetone, and DMSO, respectively. The data calculated were in excellent agreement with available experimental data, for example, bond length and dihedral angles. This gives credence to the use of the calculated properties in explaining the solvatochromic behaviors observed. The dependence of an empirical solvent polarity scale E(T)(probe) in kcal/mol on the physicochemical properties of the solvent (acidity, basicity, and dipolarity/polarizability) and those of the probes (pK(a), and dipole moment) was analyzed by using known multiparameter solvation equations. For each pair of probes, values of E(T)(probe) (for example, E(T)(MePM) versus E(T)(RB)) were found to be linearly correlated with correlation coefficients, r, between 0.9548 and 0.9860. For the mercyanine series, the values of E(T)(probe) also correlated linearly, with (r) of 0.9772 (MePMBr versus MePM) and 0.9919 (MePMBr(2) versus MePM). The response of each pair of probes (of similar pK(a)) to solvent acidity is the same, provided that solute-solvent hydrogen-bonding is not seriously affected by steric crowding (as in case of RB). We show, for the first time, that the response to solvent dipolarity/polarizability is linearly correlated to the dipole moment of the probes. The successive introduction of bromine atoms in MePM (to give MePMBr, then MePMBr(2)) leads to the following linear decrease: pK(a) in water, length of the phenolate oxygen-carbon bond, length of the central ethylenic bond, susceptibility to solvent acidity, and susceptibility to solvent dipolarity/polarizability. Thus studying the solvation of probes whose molecular structures are varied systematically produces a wealth of information on the effect of solute structure on its solvation. The results of solvation of the present probes were employed in order to test the goodness of fit of two independent sets of solvent solvatochromic parameters.