Mechanism of the Asymmetric Autocatalytic Soai Reaction Studied by Density Functional Theory

The mechanism of the Soai reaction has been thoroughly investigated at the M05‐2X/6‐31G(d) level of theory, by considering ten energetically distinct paths. The study indicates the fully enantioselective catalytic cycle of the homochiral dimers to be the dominant mechanism. Two other catalytic cycles are shown to both be important for correct understanding of the Soai reaction. These are the catalytic cycle of the heterochiral dimer and the non‐enantioselective catalytic cycle of the homochiral dimers. The former has been proved to be not really competitive with the principal cycle, as required for the Soai reaction to manifest chiral amplification, whereas the latter, which is only slightly competitive with the principal one, nicely explains the experimental enantioselectivity observed in the reaction of 2‐methylpyrimidine‐5‐carbaldehyde. The study has also evidenced the inadequacy of the B3LYP functional for mechanistic investigations of the Soai reaction.     

Structural Analysis of a Helical Peptide Unfolding Pathway

The analysis of the folding mechanism in peptides adopting well‐defined secondary structure is fundamental to understand protein folding. Herein, we describe the thermal unfolding of a 15‐mer vascular endothelial growth factor mimicking α‐helical peptide (QK_L10A) through the combination of spectroscopic and computational analyses. In particular, on the basis of the temperature dependencies of QK_L10A H_α chemical shifts we show that the first phase of the thermal helix unfolding, ending at around 320 K, involves mainly the terminal regions. A second phase of the transition, ending at around 333 K, comprises the central helical region of the peptide. The determination of high‐resolution QK_L10A conformational preferences in water at 313 K allowed us to identify, at atomic resolution, one intermediate of the folding–unfolding pathway. Molecular dynamics simulations corroborate experimental observations detecting a stable central helical turn, which represents the most probable site for the helix nucleation in the folding direction. The data presented herein allows us to draw a folding–unfolding picture for the small peptide QK_L10A compatible with the nucleation–propagation model. This study, besides contributing to the basic field of peptide helix folding, is useful to gain an insight into the design of stable helical peptides, which could find applications as molecular scaffolds to target protein–protein interactions.     

Fluorescent and Electrochemical Sensing of Polyphosphate Nucleotides by Ferrocene Functionalised with Two ZnII(TACN)(pyrene) Complexes

The [Fc? bis{Zn^II(TACN)(Py)}] complex, comprising two Zn^II(TACN) ligands (Fc=ferrocene; Py=pyrene; TACN=1,4,7‐triazacyclononane) bearing fluorescent pyrene chromophores linked by an electrochemically active ferrocene molecule has been synthesised in high yield through a multistep procedure. In the absence of the polyphosphate guest molecules, very weak excimer emission was observed, indicating that the two pyrene‐bearing Zn^II(TACN) units are arranged in a trans‐like configuration with respect to the ferrocene bridging unit. Binding of a variety of polyphosphate anionic guests (PPi and nucleotides di‐ and triphosphate) promotes the interaction between pyrene units and results in an enhancement in excimer emission. Investigations of phosphate binding by ³¹P NMR spectroscopy, fluorescence and electrochemical techniques confirmed a 1:1 stoichiometry for the binding of PPi and nucleotide polyphosphate anions to the bis(Zn^II(TACN)) moiety of [Fc? bis{Zn^II(TACN)(Py)}] and indicated that binding induces a trans to cis configuration rearrangement of the bis(Zn^II(TACN)) complexes that is responsible for the enhancement of the pyrene excimer emission. Pyrophosphate was concluded to have the strongest affinity to [Fc? bis{Zn^II(TACN)(Py)}] among the anions tested based on a six‐fold fluorescence enhancement and 0.1 V negative shift in the potential of the ferrocene/ferrocenium couple. The binding constant for a variety of polyphosphate anions was determined from the change in the intensity of pyrene excimer emission with polyphosphate concentration, measured at 475 nm in CH₃CN/Tris‐HCl (1:9) buffer solution (10.0 mM , pH 7.4). These measurements confirmed that pyrophosphate binds more strongly (K_b=(4.45±0.41)×10⁶ M ^?1) than the other nucleotide di‐ and triphosphates (K_b=1–50×10⁵ M ^?1) tested.     

A gas chromatography/mass spectrometry method for the determination of sildenafil,vardenafil and tadalafil and their metabolites in human urine

Sildenafil (SDF), vardenafil (VDF) and tadalafil (TDF) are phosphodiesterase type 5 enzyme inhibitors (PDE5Is), used in the treatment of erectile disorders and to improve breathing efficiency in pulmonary hypertension. The increasing incidence of their use among young athletes has drawn the attention of the anti‐doping authorities to the possible abuse of PDE5Is by athletes due to their pharmacological activities. This paper describes a method for the determination in urine of PDE5Is and their metabolites by gas chromatography/mass spectrometry (GC/MS) after liquid/liquid extraction of the analytes from urine and derivatisation to obtain trimethylsilyl derivatives. The metabolic profile was studied on real samples collected from subjects taking PDE5Is (Viagra®, Levitra® or Cialis®); the main urinary metabolites were identified and their MS fragmentation characterized. The sample pre‐treatment and GC/MS conditions for the detection of the metabolites have been optimised. A method for their preliminary screening and subsequent confirmation is described that takes into account the general requirements of a routine doping analysis to be used for the screening of large numbers of samples. The main metabolites identified can be included in a general purpose screening method and all the metabolites in a more specific confirmation method. The method developed has been applied for the screening of PDE5Is in 5000 urine samples. Based on the obtained results, the proposed method appears to be of practical use in analytical and forensic toxicology, including doping analysis. Copyright © 2010 John Wiley & Sons, Ltd.     

Quantitation of a de‐fluorinated analogue of Casopitant Mesylate by normal‐phase liquid chromatography/mass spectrometry

The introduction of Quality by Design (QbD) in Drug Development has resulted in a greater emphasis on chemical process understanding, in particular on the origin and fate of impurities. Therefore, the identification and quantitation of low level impurities in new Active Pharmaceutical Ingredients (APIs) play a crucial role in project progression and this has created a greater need for sensitive and selective analytical methodology. Consequently, scientists are constantly challenged to look for new applications of traditional analytical techniques. In this context a normal‐phase liquid chromatography/electrospray ionization mass spectrometry (LC/ESI‐MS) method was developed to determine the amount of a de‐fluorinated analogue impurity in Casopitant Mesylate, a new API under development in GlaxoSmithKline, Verona. Normal‐phase LC provided the selectivity needed between our target analyte and Casopitant, while a single quadrupole mass spectrometer was used to ensure the sensitivity needed to detect the impurity at <0.05%w/w. Standard solutions and samples were prepared in heptane/ethanol (50:50, v/v) containing 1% of 2 M NH₃ in ethanol; the mobile phase consisted of heptane/ethanol (95:5, v/v) with isocratic elution (flow rate: 1.0 mL/min, total run time: 23 min). To allow the formation of ions in solutions under normal‐phase (apolar) conditions, a post‐column infusion of a solution of 0.1% v/v of formic acid in methanol was applied (flow rate: 200 µL/min). The analysis was carried out in positive ion mode, monitoring the impurity by single ion monitoring (SIM). The method was fully validated and its applicability was demonstrated by the analysis of real‐life samples. This work is an example of the need for selective and accurate methodology during the development of a new chemical entity in order to develop an appropriate control strategy for impurities to ultimately ensure patient safety. Copyright © 2010 John Wiley & Sons, Ltd.     

Halo-carbonyl complexes of palladium,platinum and gold

In this review we summarize some recent literature data concerning synthetic procedures, properties, structure, reactivity and applications of halo-carbonyl complexes of palladium, platinum and gold, taking into consideration that the organometallic chemistry of these metals, with a particular attention to the halo-carbonyls, has been reviewed 20 years ago [F. Calderazzo, J. Organomet. Chem. 400 (1990) 303]. A brief overview of the early studies is provided.     

Interactions modes and physical properties in transition metal chalcogenolene-based molecular materials

Molecule-based materials are extremely versatile materials as they can be built from specifically designed building blocks with the desired size, shape, charge and electronic properties which determine their intermolecular interactions and, thus, their organization in the solid. The intermolecular interactions, therefore, in particular van der Waals interactions, π–π and π–d interactions, H-bonding, etc., play a crucial role in self-assembling these pre-designed molecular units and may provide a powerful way to afford layered mono- and multifunctional molecular materials with new or unknown physical properties. In this review the relationship between interaction modes and physical properties of organic/inorganic hybrids based on transition metal complexes with chalcogenolene ligands will be examined and an outlook will be proposed. With this goal, magnetic materials, highly conducting and metallic single-component materials containing dithiolene complex building blocks, multifunctional materials where the dithiolene complex is the magnetic or conducting component in addition to more complex systems involving other types of building block such as the metal oxalate complexes, will be discussed.     

Wavelet formulation of the polarizable continuum model

The first implementation of a wavelet discretization of the Integral Equation Formalism (IEF) for the Polarizable Continuum Model (PCM) is presented here. The method is based on the application of a general purpose wavelet solver on the cavity boundary to solve the integral equations of the IEF‐PCM problem. Wavelet methods provide attractive properties for the solution of the electrostatic problem at the cavity boundary: the system matrix is highly sparse and iterative solution schemes can be applied efficiently; the accuracy of the solver can be increased systematically and arbitrarily; for a given system, discretization error accuracy is achieved at a computational expense that scales linearly with the number of unknowns. The scaling of the computational time with the number of atoms N is formally quadratic but a N^1.5 scaling has been observed in practice. The current bottleneck is the evaluation of the potential integrals at the cavity boundary which scales linearly with the system size. To reduce this overhead, interpolation of the potential integrals on the cavity surface has been successfully used. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010     

A first‐order system least‐squares finite element method for the Poisson‐Boltzmann equation

The Poisson‐Boltzmann equation is an important tool in modeling solvent in biomolecular systems. In this article, we focus on numerical approximations to the electrostatic potential expressed in the regularized linear Poisson‐Boltzmann equation. We expose the flux directly through a first‐order system form of the equation. Using this formulation, we propose a system that yields a tractable least‐squares finite element formulation and establish theory to support this approach. The least‐squares finite element approximation naturally provides an a posteriori error estimator and we present numerical evidence in support of the method. The computational results highlight optimality in the case of adaptive mesh refinement for a variety of molecular configurations. In particular, we show promising performance for the Born ion, Fasciculin 1, methanol, and a dipole, which highlights robustness of our approach. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010     

One-pot preparation and uranyl adsorption properties of hierarchically porous zirconium titanium oxide beads using phase separation processes to vary macropore morphology

A simple and engineering friendly one-step process has been used to prepare zirconium titanium mixed oxide beads with porosity on multiple length scales. In this facile synthesis, the bead diameter and the macroporosity can be conveniently controlled through minor alterations in the synthesis conditions. The precursor solution consisted of poly(acrylonitrile) dissolved in dimethyl sulfoxide to which was added block copolymer Pluronic F127 and metal alkoxides. The millimeter-sized spheres were fabricated with differing macropore dimensions and morphology through dropwise addition of the precursor solution into a gelation bath consisting of water (H(2)O beads) or liquid nitrogen (LN(2) beads). The inorganic beads obtained after calcination (550 °C in air) had surface areas of 140 and 128 m(2) g(-1), respectively, and had varied pore architectures. The H(2)O-derived beads had much larger macropores (5.7 μm) and smaller mesopores (6.3 nm) compared with the LN(2)-derived beads (0.8 μm and 24 nm, respectively). Pluronic F127 was an important addition to the precursor solution, as it resulted in increased surface area, pore volume, and compressive yield point. From nonambient XRD analysis, it was concluded that the zirconium and titanium were homogeneously mixed within the oxide. The beads were analyzed for surface accessibility and adsorption rate by monitoring the uptake of uranyl species from solution. The macropore diameter and morphology greatly impacted surface accessibility. Beads with larger macropores reached adsorption equilibrium much faster than the beads with a more tortuous macropore network.