Global QSAR models of skin sensitisers for regulatory purposes

Background

The new European Regulation on chemical safety, REACH, (Registration, Evaluation, Authorisation and Restriction of CHemical substances), is in the process of being implemented. Many chemicals used in industry require additional testing to comply with the REACH regulations. At the same time EU member states are attempting to reduce the number of animals used in experiments under the 3 Rs policy, (refining, reducing, and replacing the use of animals in laboratory procedures). Computational techniques such as QSAR have the potential to offer an alternative for generating REACH data. The FP6 project CAESAR was aimed at developing QSAR models for 5 key toxicological endpoints of which skin sensitisation was one.

Results

This paper reports the development of two global QSAR models using two different computational approaches, which contribute to the hybrid model freely available online.

Conclusions

The QSAR models for assessing skin sensitisation have been developed and tested under stringent quality criteria to fulfil the principles laid down by the OECD. The final models, accessible from CAESAR website, offer a robust and reliable method of assessing skin sensitisation for regulatory use.

     

Redox Multifunctionality in a Series of PtII Dithiolene Complexes of a Tetrathiafulvalene‐Based Diphosphine Ligand

The redox‐active and chelating diphosphine, 3,4‐dimethyl‐3′,4′‐bis(diphenylphosphino)‐tetrathiafulvalene, denoted as P2 , is engaged in a series of platinum complexes, [(P2)Pt(dithiolene)], with different dithiolate ligands, such as 1,2‐benzenedithiolate (bdt), 1,3‐dithiole‐2‐thione‐4,5‐dithiolate (dmit), and 5,6‐dihydro‐1,4‐dithiin‐2,3‐dithiolate (dddt). The complexes are structurally characterized by X‐ray diffraction, together with a model compound derived from bis(diphenylphosphino)ethane, namely, [(dppe)Pt(dddt)] . Four successive reversible electron‐transfer processes are found for the [(P2)Pt(dddt)] complex, associated with the two covalently linked but electronically uncoupled electrophores, that is, the TTF core and the platinum dithiolene moiety. The assignments of the different redox processes to either one or the other electrophore is made thanks to the electrochemical properties of the model compound [(dppe)Pt(dddt)] lacking the TTF redox core, and with the help of theoretical calculations (DFT) to understand the nature and energy of the frontier orbitals of the [(P2)Pt(dithiolene)] complexes in their different oxidation states. The first oxidation of the highly electron‐rich [(P2)Pt(dddt)] complex can be unambiguously assigned to the redox process affecting the Pt(dddt) moiety rather than the TTF core, a rare example in the coordination chemistry of tetrathiafulvalenes acting as ligands.     

A neutral zwitterionic molecular solid

We report on the acid ethylenedithiotetrathiafulvaleneamidoglycine (EDT-TTF-CO-NH-CH(2)-CO(2)H; 1; EDT-TTF=ethylenedithiotetrathiafulvalene) and the 1:1 adduct [(EDT-TTF)(·+)-CO-NH-CH(2)-(CO(2))(-)][(EDT-TTF)-CO-NH-CH(2)-(CO(2)H)]·CH(3)OH (2), a new type of hydrogen-bonded, 1:1 acid/zwitterion hybrid embrace of redox peptidics into a two-dimensional architecture, an example of a system deliberately fashioned so that oxidation of π-conjugated cores toward the radical-cation form would interfere with the activity of the appended ionizable residues in the presence of a templating base during crystal growth. First-principles calculations demonstrate that, notwithstanding preconceived ideas, a metallic state is more stable than the hole-localized alternatives for a neat 1:1 neutral acid/zwitterion hybrid. The inhomogeneous Coulomb field associated with proton-shared, interstacks O-H···O hydrogen bonds between the ionizable residues distributed on both sides of the two-dimensional π-conjugated framework leads, however, to a weak hole localization responsible for the activated but high conductivity of 1 S cm(-1). This situation is reminiscent of the role of the environment on electron transfer in tetraheme cytochrome c, in which the protonation state of a heme propionate becomes paramount, or ion-gated transport phenomena in biology. These observations open rather intriguing opportunities for the construction of electronic systems at the interface of chemistry and biology.     

Expanded Pyridiniums: Bis‐cyclization of Branched Pyridiniums into Their Fused Polycyclic and Positively Charged Derivatives—Assessing the Impact of Pericondensation on Structural,Electrochemical, Electronic,and Photophysical Features

This study evaluates the impact of the extension of the π‐conjugated system of pyridiniums on their various properties. The molecular scaffold of aryl‐substituted expanded pyridiniums (referred to as branched species) can be photochemically bis‐cyclized into the corresponding fused polycyclic derivatives (referred to as pericondensed species). The representative 1,2,4,6‐tetraphenylpyridinium ( 1^H ) and 1,2,3,5,6‐pentaphenyl‐4‐(p‐tolyl)pyridinium ( 2^Me ) tetra‐ and hexa‐branched pyridiniums are herein compared with their corresponding pericondensed derivatives, the fully fused 9‐phenylbenzo[1,2]quinolizino[3,4,5,6‐def]phenanthridinium ( 1^H f ) and the hitherto unknown hemifused 9‐methyl‐1,2,3‐triphenylbenzo[h]phenanthro[9,10,1‐def]isoquinolinium ( 2^Me f ). Combined solid‐state X‐ray crystallography and solution NMR experiments showed that stacking interactions are barely efficient when the pericondensed pyridiniums are not appropriately substituted. The electrochemical study revealed that the first reduction process of all the expanded pyridiniums occurs at around ?1 V vs. SCE, which indicates that the lowest unoccupied molecular orbital (LUMO) remains essentially localized on the pyridinium core regardless of pericondensation. In contrast, the electronic and photophysical properties are significantly affected on going from branched to pericondensed pyridiniums. Typically, the number of absorption bands increases with extended activity towards the visible region (down to ca. 450 nm in MeCN), whereas emission quantum yields are increased by three orders of magnitude (at ca. 0.25 on average). A relationship is established between the observed differential impact of the pericondensation and the importance of the localized LUMO on the properties considered: predominant for the first reduction process compared with secondary for the optical and photophysical properties.     

Evaluation of the LTQ-Orbitrap mass spectrometer for the analysis of polymerase chain reaction products

We have investigated the potential and robustness of the off‐line coupling of polymerase chain reaction (PCR) with electrospray ionization mass spectrometry (ESI‐MS), for further applications in the screening of single‐nucleotide polymorphisms (SNPs). This was based on recently reported data demonstrating that anion‐exchange solid‐phase extraction was the most efficient technique for efficiently desalting PCR products, with a recovery of ～70%. Results showed that this purification approach efficiently removes almost all the chemicals commonly added to PCR buffers. ESI‐MS analysis of a model 114‐bp PCR product performed on the LTQ‐Orbitrap instrument demonstrated that detection limits in the nM range along with an average mass measurement uncertainty of 9.15 ± 7.11 ppm can be routinely obtained using an external calibration. The PCR/ESI‐MS platform was able to detect just a few copies of a targeted oligonucleotide. However, it was shown that if two PCR products are present in a mixture in a ratio higher than 10 to 1, the lower abundance one might not be reproducibly detected. Applications to SNPs demonstrated that an LTQ‐Orbitrap with a resolution of 30 000 (at m/z 400) easily identified a single (A ? G) switch, i.e. a 16 Da difference, in binary mixtures of ～ 35 kDa PCR products. Complementary experiments also showed that the combination of endonucleases and ESI‐MS could be used to confirm base composition and sequence, and thus to screen for unknown polymorphisms in specific sequences. For example, a single (T ? A) switch (9 Da mass difference) was successfully identified in a 114‐bp PCR product. Copyright © 2010 John Wiley & Sons, Ltd.     

Evolution of the AgCdO Contact Material Surface Microstructure with the Number of Arcs

This paper describes a study of the evolution of the AgCdO contact material surface microstructure as a function of the number of electrical arcs imposed on the switching surface. Five power switching devices were tested under different conditions. They were subjected to, respectively, 1, 2, 3, 10, and 100 electrical arcs under the same operating conditions: supply current of 400 A, circuit voltage of 28 V direct current (DC), and resistive load. For the analysis, a binocular microscope and a scanning electron microscope with an energy-dispersive x-ray spectrometer were used.     

Using Stochastic Differential Equation for Verification of Noise in Analog/RF Circuits

Today’s analog/RF design and verification face significant challenges due to circuit complexity, process variations and short market windows. In particular, the influence of technology parameters on circuits, and the issues related to noise modeling and verification still remain a priority for many applications. Noise could be due to unwanted interaction between the circuit elements or it could be inherited from the circuit elements. In addition, manufacturing disparity influence the characteristic behavior of the manufactured circuits. In this paper, we propose a methodology for modeling and verification of analog/RF designs in the presence of noise and process variations. Our approach is based on modeling the designs using stochastic differential equations (SDE) that will allow us to incorporate the statistical nature of noise. We also integrate the device variation due to 0.18μ m fabrication process in an SDE based simulation framework for monitoring properties of interest in order to quickly detect errors. Our approach is illustrated on nonlinear Tunnel-Diode and a Colpitts oscillator circuits.     

High-efficiency hydrophilic interaction chromatography by coupling 25 cm × 4.6 mm ID × 5 μm silica columns and operation at 80 °C

Recently, hydrophilic interaction chromatography (HILIC) has emerged as a valuable orthogonal tool to reversed-phase liquid chromatography (RP-LC) as it allows for resolution of highly polar ionisable compounds. The relationships between separation efficiency, column length and speed of analysis for 4.6 mm ID × 5 μm silica particle columns in HILIC are demonstrated using kinetic plots. The kinetic plots constructed for conventional pressure systems operating at 350 bar and at 30 °C and 80 °C are confirmed using experimental data for different column lengths. Efficiencies of more than 130,000 theoretical plates could be achieved by connecting up to six columns of 25 cm. As expected, a significant gain in analysis speed without loss of efficiency could be obtained by operating at 80 °C compared to 30 °C. The advantages of using long columns in HILIC in combination with elevated column temperature for the pharmaceutical industry are illustrated using test mixtures comprised of commercially available ionisable compounds (including some containing functional groups with potential genotoxic typical structural alerts) as well as real polar ionisable pharmaceuticals.     

LocalSolver 1.x: a black-box local-search solver for 0-1 programming

This paper introduces LocalSolver 1.x, a black-box local-search solver for general 0-1 programming. This software allows OR practitioners to focus on the modeling of the problem using a simple formalism, and then to defer its actual resolution to a solver based on efficient and reliable local-search techniques. Started in 2007, the goal of the LocalSolver project is to offer a model-and-run approach to combinatorial optimization problems which are out of reach of existing black-box tree-search solvers (integer or constraint programming). Having outlined the modeling formalism and the main technical features behind LocalSolver, its effectiveness is demonstrated through an extensive computational study. The version 1.1 of LocalSolver can be freely downloaded at and used for educational, research, or commercial purposes.     

Geometric Inference for Probability Measures

Data often comes in the form of a point cloud sampled from an unknown compact subset of Euclidean space. The general goal of geometric inference is then to recover geometric and topological features (e.g., Betti numbers, normals) of this subset from the approximating point cloud data. It appears that the study of distance functions allows one to address many of these questions successfully. However, one of the main limitations of this framework is that it does not cope well with outliers or with background noise. In this paper, we show how to extend the framework of distance functions to overcome this problem. Replacing compact subsets by measures, we introduce a notion of distance function to a probability distribution in ℝ ^d . These functions share many properties with classical distance functions, which make them suitable for inference purposes. In particular, by considering appropriate level sets of these distance functions, we show that it is possible to reconstruct offsets of sampled shapes with topological guarantees even in the presence of outliers. Moreover, in settings where empirical measures are considered, these functions can be easily evaluated, making them of particular practical interest.