Multispectral and hyperspectral image analysis of elemental and micro-Raman maps of cross-sections from a 16th century painting

Spectroscopic imaging is well suited to the study of micro-samples from artworks, where the sample material is limited and the maximum amount of information needs to be obtained. In this study, a new approach to imaging elemental data from energy dispersive X-ray analysis maps was used in conjunction with micro-Raman spectroscopic imaging to characterise the paint layers within micro-samples. Cross-sections from the 16th century painting Portrait of a Youth were found to contain vermilion, lead-tin yellow type 1 and a blue-green pigment consistent with terre-verte. The mid-preparatory layer (imprimatura) contains a high proportion of elements and mineral inclusions that indicates a clay-type composition. The ground layer was identified as anhydrite with large gypsum inclusions. The pigments and composition of the preparatory layers are consistent with those used by Italian Renaissance artist Dosso Dossi.     

Isolation, structure, and antibacterial activity of philipimycin, a thiazolyl peptide discovered from Actinoplanes philippinensis MA7347

Bacterial resistance to antibiotics, particularly to multiple drug resistant antibiotics, is becoming cause for significant concern. The only really viable course of action is to discover new antibiotics with novel mode of actions. Thiazolyl peptides are a class of natural products that are architecturally complex potent antibiotics but generally suffer from poor solubility and pharmaceutical properties. To discover new thiazolyl peptides potentially with better desired properties, we designed a highly specific assay with a pair of thiazomycin sensitive and resistant strains of Staphylococcus aureus, which led to the discovery of philipimycin, a new thiazolyl peptide glycoside. It was isolated along with an acid-catalyzed degradation product by bioassay-guided fractionation. Structure of both compounds was elucidated by extensive application of 2D NMR, 1D TOCSY, and HRESIFT-MS/MS. Both compounds showed strong antibacterial activities against gram-positive bacteria including MRSA and exhibited MIC values ranging from 0.015 to 1 microg/mL. Philipimycin was significantly more potent than the degradation product. Both compounds showed selective inhibition of protein synthesis, indicating that they targeted the ribosome. Philipimycin was effective in vivo in a mouse model of S. aureus infection exhibiting an ED50 value of 8.4 mg/kg. The docking studies of philipimycin suggested that a part of the molecule interacts with the ribosome and another part with Pro23, Pro22, and Pro26 of L11 protein, which helped in explaining the differential of activities between the sensitive and resistant strains. The design and execution of the bioassay, the isolation, structure, in vitro and in vivo antibacterial activity, and docking studies of philipimycin and its degradation product are described.     

Charge transfers at metal/oxide interfaces: a DFT study of formation of K delta+ and Au delta- species on MgO/Ag(100) ultra-thin films from deposition of neutral atoms

Ultra-thin oxide films grown on a metal substrate and of thickness smaller than 1 nm may exhibit unusual properties with respect to thicker films or single crystal oxide surfaces. In a previous study [G. Pacchioni, L. Giordano and M. Baistrocchi, Phys. Rev. Lett., 2005, 94, 226104] we have suggested that a Au atom adsorbed on a MgO/Mo(100) thin film becomes negatively charged by direct electron tunneling from the Mo metal and that this is related to the low MgO/Mo(100) work function. Here we show, based on periodic DFT supercell calculations, that charge transfer can occur also in the opposite direction by adsorption of electropositive K atoms on MgO/Ag(100) films. We predict the occurrence of a charge transfer also for Au on MgO/Ag(100) films despite the fact that here the work function is 1 eV larger than in MgO/Mo(100). The formation of a layer of adsorbed negative (Au delta-/MgO/Ag) or positive (K delta+/MgO/Ag) adsorbates results in an increase or decrease, respectively, of the MgO/Ag(100) work function as predicted by the classical Gurney model for ionic adsorbates on metal surfaces.     

Small molecule conformational preferences derived from crystal structure data. A medicinal chemistry focused analysis

Based on torsion angle distributions of frequently occurring substructures, conformation preferences of druglike molecules are presented, accompanied by a review of the relevant literature. First, the relevance of the Cambridge Structural Database (CSD) for drug design is demonstrated by comparing substructures present in compounds entering clinical trials with those found in the CSD and protein-bound ligands in the Protein Data Bank (PDB). Next, we briefly highlight preferred conformations of elementary acyclic systems, followed by a discussion of sulfonamide conformations. Due to their central role in medicinal chemistry, we discuss properties of aryl ring substituents in depth, including biaryl systems and systems of two aryl rings connected by two acyclic bonds. For a subset of torsion motifs, we also compare torsion angle histograms derived from CSD structures with those derived from ligands in the PDB. Furthermore, selected properties of some six- and seven-membered ring systems are discussed. The article closes with a section on attractive sulfur-oxygen contacts.     

Nature of point defects on SiO2/Mo(112) thin films and their interaction with Au atoms

We have studied by means of periodic DFT calculations the structure and properties of point defects at the surface of ultrathin silica films epitaxially grown on Mo(112) and their interaction with adsorbed Au atoms. For comparison, the same defects have been generated on an unsupported silica film with the same structure. Four defects have been considered: nonbridging oxygen (NBO, [triple bond]Si-O(*)), Si dangling bond (E' center, [triple bond]Si(*)), oxygen vacancy (V(O), [triple bond]Si-Si[triple bond]), and peroxo group ([triple bond]Si-O-O-Si[triple bond]), but only the NBO and the V(O) centers are likely to form on the SiO(2)/Mo(112) films under normal experimental conditions. The [triple bond]Si-O(*) center captures one electron from Mo forming a silanolate group, [triple bond]Si-O(-), sign of a direct interaction with the metal substrate. Apart from the peroxo group, which is unreactive, the other defects bind strongly the Au atom forming stable surface complexes, but their behavior may differ from that of the same centers generated on an unsupported silica film. This is true in particular for the two most likely defects considered, the nonbridging oxygen, [triple bond]Si-O(*), and the oxygen vacancy, [triple bond]Si-Si[triple bond].     

MSE with mass defect filtering for in vitro and in vivo metabolite identification

Metabolite identification studies involve the detection and structural characterization of the biotransformation products of drug candidates. These experiments are necessary throughout the drug discovery and development process. The use of high-resolution chromatography and high-resolution mass spectrometry together with data processing using mass defect filtering is described for in vitro and in vivo metabolite identification studies. Data collection was done using UPLC coupled with an orthogonal hybrid quadrupole time-of-flight mass spectrometer. This experimental approach enabled the use of MS(E) data collection (where E represents collision energy) which has previously been shown to be a powerful approach for metabolite identification studies. Post-acquisition processing with a prototype mass defect filtering program was used to eliminate endogenous interferences in the study samples, greatly enhancing the discovery of metabolites. The ease of this approach is illustrated by results showing the detection and structural characterization of metabolites in plasma from a preclinical rat pharmacokinetic study.     

High-density targeting of a viral multifunctional nanoplatform to a pathogenic, biofilm-forming bacterium

Nanomedicine directed at diagnosis and treatment of infections can benefit from innovations that have substantially increased the variety of available multifunctional nanoplatforms. Here, we targeted a spherical, icosahedral viral nanoplatform to a pathogenic, biofilm-forming bacterium, Staphylococcus aureus. Density of binding mediated through specific protein-ligand interactions exceeded the density expected for a planar, hexagonally close-packed array. A multifunctionalized viral protein cage was used to load imaging agents (fluorophore and MRI contrast agent) onto cells. The fluorescence-imaging capability allowed for direct observation of penetration of the nanoplatform into an S. aureus biofilm. These results demonstrate that multifunctional nanoplatforms based on protein cage architectures have significant potential as tools for both diagnosis and targeted treatment of recalcitrant bacterial infections.     

Cluster and periodic DFT calculations of MgO/Pd(CO) and MgO/Pd(CO)(2) surface complexes

The bonding and vibrational properties of Pd(CO) and Pd(CO)(2) complexes formed at the (100) surface of MgO have been investigated using the gradient-corrected DFT approach and have been compared to the results of infrared and thermal desorption experiments performed on ultrathin MgO films. Two complementary approaches have been used for the calculation of the electronic properties: the embedded cluster method using localized atomic orbital basis sets and supercell periodic calculations using plane waves. The results show that the two methods provide very similar answers, provided that sufficiently large supercells are used. Various regular and defect adsorption sites for the Pd(CO) and Pd(CO)(2) have been considered: terraces, steps, neutral and charged oxygen vacancies (F and F(+) centers), and divacancies. From the comparison of the computed and experimental results, it is concluded that the most likely site where the Pd atoms are stabilized and where carbonyl complexes are formed are the F(+) centers, paramagnetic defects consisting of a single electron trapped in an anion vacancy.     

The PyPES library of high quality semi‐global potential energy surfaces

In this article, we present a Python‐based library of high quality semi‐global potential energy surfaces for 50 polyatomic molecules with up to six atoms. We anticipate that these surfaces will find widespread application in the testing of new potential energy surface construction algorithms and nuclear ro‐vibrational structure theories. To this end, we provide the ability to generate the energy derivatives required for Taylor series expansions to sixth order about any point on the potential energy surface in a range of common coordinate systems, including curvilinear internal, Cartesian, and normal mode coordinates. The PyPES package, along with FORTRAN, C, MATLAB and Mathematica wrappers, is available at http://sourceforge.net/projects/pypes-lib . © 2015 Wiley Periodicals, Inc.     

Elasticity of flexible and semiflexible polymers with extensible bonds in the Gibbs and Helmholtz ensembles

Stretching experiments on single molecules of arbitrary length opened the way for studying the statistical mechanics of small systems. In many cases in which the thermodynamic limit is not satisfied, different macroscopic boundary conditions, corresponding to different statistical mechanics ensembles, yield different force-displacement curves. We formulate analytical expressions and develop Monte Carlo simulations to quantitatively evaluate the difference between the Helmholtz and the Gibbs ensembles for a wide range of polymer models of biological relevance. We consider generalizations of the freely jointed chain and of the worm-like chain models with extensible bonds. In all cases we show that the convergence to the thermodynamic limit upon increasing contour length is described by a suitable power law and a specific scaling exponent, characteristic of each model.