Absolute structure of the chiral pyrrolidine derivative (2S)‐methyl (Z)‐5‐(2‐tert‐butoxy‐1‐cyano‐2‐oxoethylidene)pyrrolidine‐2‐carboxylate,a compound with low resonant scattering

The enantiopure monopyrrolidine derivative (2S)‐methyl (Z)‐5‐(2‐tert‐butoxy‐1‐cyano‐2‐oxoethylidene)pyrrolidine‐2‐carboxylate, C₁₃H₁₈N₂O₄, ( 1 ), represents a potential ligand and an attractive intermediate for the synthesis of chiral metal complexes. At the molecular level, the compound features an intramolecular N—H…O hydrogen bond; neighbouring molecules interact via N—H…N contacts to form chains along [100]. Due to its elemental composition, resonant scattering of the target compound is entirely insignificant for diffraction experiments with Mo Kα and small even for Cu Kα radiation. A preliminary study with the harder radiation type confirmed the chiral space group and the suitability of the single crystal chosen; as expected, the results concerning the absolute structure remained completely inconclusive. A second data collection with the longer wavelength gave satisfactory quality indicators for the correct handedness of the molecule, albeit with high standard uncertainties. The absolute configuration has been assessed independently: CD spectra for both enantiomers of the target molecule were calculated and the spectrum for the S‐configured stereoisomer was in agreement with the experiment. The Cotton effect of ( 1 ) may be ascribed to π–π* transitions from HOMO to LUMO and from HOMO to LUMO+1. As both independent techniques agree with respect to the handedness of the target molecule, the absolute structure may be assigned with a high degree of confidence.     

Application of structure‐based focusing to the estrogen receptor

We present the Cerius² Structure‐Based Focusing (SBF) application. This application was applied to the estrogen receptor. A series of three‐dimensional queries were generated for the binding site of the receptor. The queries consist of combinations of hydrogen bond donors and acceptors, and lipophilic features for the binding site along with excluded volume regions occupied by the receptor atoms. A database of 31 ligands with known relative binding affinities for the estrogen receptor was used to examine the selectivity of the queries. The objective of the study was to determine if queries generated by the Cerius² SBF method could differentiate between the more and less active ligands of the training set. Results are promising, with the generated queries showing greater selectivity toward the more active ligands. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 993–1003, 2001     

Revisiting the absolute chirality and polymorphism of (–)‐Istanbulin A

The terpenoid (?)‐Istanbulin A is a natural product isolated from Senecio filaginoides DC, one of the 270 species of Senecio (Asteraceae) which occurs in Argentina. The structure and absolute configuration of this compound [9a‐hydroxy‐3,4a,5‐trimethyl‐4a,6,7,8a,9,9a‐hexahydro‐4H,5H‐naphtho[2,3‐b]‐furan‐2,8‐dione or (4S,5R,8R,10S)‐1‐oxo‐8β‐hydroxy‐10βH‐eremophil‐7(11)‐en‐12,8β‐olide, C₁₅H₂₀O₄] were determined by single‐crystal X‐ray diffraction studies. It proved to be a sesquiterpene lactone showing an eremophilanolide skeleton whose chirality is described as 4S,5R,8R,10S. Structural results were also in agreement with the one‐ and two‐dimensional (1D and 2D) NMR and HR–ESI–MS data, and other complementary spectroscopic information. In addition, (?)‐Istanbulin A is a polymorph of the previously reported form of (?)‐Istanbulin A, form I; thus, the title compound is denoted form II or polymorph II. Structural data and a literature search allowed the chirality of Istanbulin A to be revisited. The antimicrobial and antifungal activities of (?)‐Istanbulin A, form II, were evaluated in order to establish a reference for future comparisons and applications related to specific crystal forms of Istanbulins.     

Mechanistic investigation of vibrational fine structure in e‐H2 scattering using local complex potential‐based time dependent wave packet approach

The structural features of vibrational excitation cross‐sections in resonant e‐H₂ scattering have been investigated using a time dependent wave packet approach and a local complex potential to describe the ²Σ H anion. An analysis of the partial contributions to the vibrational excitation cross‐sections reveals that all features of the excitation profile result from simple interference between bound vibrational levels of H₂ and H. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2008     

1,7‐Dideaza‐2′‐deoxy‐6‐nitronebularine: a pyrrolo[2,3‐b]pyridine nucleoside with an intramolecular hydrogen bond stabilizing the syn conformation

The title compound [systematic name: 1‐(2‐deoxy‐β‐D‐erythro‐pentofuranosyl)‐4‐nitro‐1H‐pyrrolo[2,3‐b]pyridine], C₁₂H₁₃N₃O₅, forms an intramolecular hydrogen bond between the pyridine N atom as acceptor and the 5′‐hydroxy group of the sugar residue as donor. Consequently, the N‐glycosylic bond exhibits a syn conformation, with a χ torsion angle of 61.6 (2)°, and the pentofuranosyl residue adopts a C2′‐endo envelope conformation (²E, S‐type), with P = 162.1 (1)° and τ_m = 36.2 (1)°. The orientation of the exocyclic C4′—C5′ bond is +sc (gauche, gauche), with a torsion angle γ = 49.1 (2)°. The title nucleoside forms an ordered and stacked three‐dimensional network. The pyrrole ring of one layer faces the pyridine ring of an adjacent layer. Additionally, intermolecular O—H...O and C—H...O hydrogen bonds stabilize the crystal structure.     

Direct observation of scattering contributions in X-ray attenuation measurements, and evidence for Rayleigh scattering from copper samples rather than thermal-diffuse or Bragg–Laue scattering

High-precision attenuation measurements can now lead to a direct assessment of scattering models in the X-ray regime. This is true not just at high energies but even when scattering cross-sections typically lie below 0.1% of the photoelectric absorption cross-section. This allows model-independent results to be obtained in these attenuation experiments for the first time.     

Fluorinated benzoxazines and the structure‐property relationship of resulting polybenzoxazines

Three fluorinated benzoxazines ( 14–16 ), which cannot be synthesized by the traditional one‐step approaches, were synthesized by a three‐step procedure using fluorinated aromatic diamines ( 2–4 ) as starting materials. The structures of the monomers were confirmed by ¹H NMR, IR, and high‐resolution mass spectra. The low dielectric thermosets, P( 14–16 ), were prepared by ring‐opening of ( 14–16 ). IR analysis was utilized to monitor the ring‐opening reaction of ( 14–16 ) and to propose the structures of P( 14–16 ). The thermal and dielectric properties of P( 14–16 ) were studied and compared with a nonfluorinated polybenzoxazine P( 13 ), which is derived form the ring‐opening of 2,2‐bis(4‐aminophenoxy)phenyl)propane ( 1 ). Besides, the structure–property relationship of the P( 13–16 ) is discussed. According to T_g measurement, the ortho‐positioned CF₃ substituents impart greater steric hindrance for ring‐opening of benzoxazines than CF₃ substituents of hexafluoropropane. Incorporating a biphenol F‐based benzoxazine, ( F‐a ), into fluorinated benzoxazines ( 15–16 ) can dilute the effect of ortho‐positioned CF₃ substituents on steric hindrance, leading to a higher crosslinking density and consequently a higher Tg. © 2008 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 46: 4970–4983, 2008     

Probing the use of small‐angle light scattering for characterizing structure of titanium dioxide/low‐density polyethylene nanocomposites

Small‐angle light scattering (SALS) measurements were used to study the structure of titanium dioxide (TiO₂)/low‐density polyethylene (LDPE) nanocomposites. The results showed that the scattering from LDPE crystalline structures and the scattering from TiO₂ nanoparticles can be resolved and separated. It is shown that the independent effects of crystallization conditions and the presence of nanoparticle aggregates on the spherulitic structure of the LDPE matrix can be determined by analyzing the scattering patterns using the methods proposed. From the SALS results, we conclude that the nanoparticle surface chemistry affects both nucleation of spherulites and their structure particularly under rapid cooling conditions. © 2006 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 44: 1084–1095, 2006     

Angle‐dependent light scattering by highly uniform colloidal rod‐shaped microparticles: Experiment and simulation

While extensive theoretical work has been devoted to analyzing scattering behavior for nonspherical particles, few experimental studies of the light‐scattering properties of such particles are available, largely because of the difficulty of synthesizing such particles with uniform geometries. Here we report the synthesis of highly uniform, volume‐equivalent rod‐shaped colloidal particles prepared from their commercial spherical counterparts, on which we performed light scattering experiments as a function of scattering angle for micro rods with varying aspect ratio and volume. These results were compared to values calculated using the T‐Matrix method. Good agreement with theoretical predictions was found for the experimentally measured scattering cross sections and the angular dependence of the scattering intensity. An increase in the forward scattering intensity is observed and predicted for particles with larger aspect ratios relative to their volume equivalent spheres, with only minor differences observed at both mid‐range and backscattering angles. Furthermore, the light scattering results for the rod‐shaped particles did not show the scattering fringes seen in scattering by the spheres, indicating that as three‐dimensional symmetry is broken, the associated Lorenz–Mie resonances are strongly attenuated. This observation also was predicted by theory. © 2016 Wiley Periodicals, Inc. J. Polym. Sci., Part B: Polym. Phys. 2016 , 54, 1889–1895     

Resonant soft x‐ray scattering and reflectivity study of the phase‐separated structure of thin poly(styrene‐b‐methyl methacrylate) films

Combined soft X‐ray scattering and reflectometry techniques promise analysis of polymer thin film domain structure and composition without resorting to chemical modification or isotopic labeling. This work explores the capabilities of these techniques in polymer films of poly(styrene‐b‐methyl methacrylate) (P(S‐b‐MMA)). The results demonstrate that the techniques give detailed information on the domain structure of thin films using well‐known modeling procedures. Discrepancies were noted between the X‐ray optical parameters that are needed to best fit the reflectivity data to the model and the expected parameters. The sources of these discrepancies are discussed in terms of instrument configuration parameters, sample attributes, and, particularly, anisotropy of the chromophore parameters. The results show that fitting the soft X‐ray reflectivity data is much more sensitive to these X‐ray optical parameters than the soft X‐ray scattering data. Nevertheless, fits to both types of data yield quantitative measures of the polymer film's lamellar morphology that are consistent with each other and with literature values. © 2012 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys, 2013     

Theoretical insight into the disordered structure of (Z)‐2‐[(E)‐(4‐methoxybenzylidene)hydrazinylidene]‐1,2‐diphenylethanone: the role of noncovalent interactions

A global glide disorder has been discovered during an X‐ray investigation of the crystal structure of (Z)‐2‐[(E)‐(4‐methoxybenzylidene)hydrazinylidene]‐1,2‐diphenylethanone ( MHDE , C₂₂H₁₈N₂O₂) at room temperature. In another crystal, however, such disorder disappears (still at room temperature). Even though the disorder may be partly due to the poor quality of the harvested crystal, the structure can shed light on the nature of disorder. With the help of quantum chemical calculations, it is found that the global disorder seems to be connected with the need for stabilization of the somewhat rigid but mobile and unstable molecular structure. The most relevant feature driving the packing of the disordered structure concerns the slight perturbations (such as glide) of two or more disorder components (fractional occupancies) distributed throughout the crystal.     

Crystal structure and structural disorder of poly‐(p‐phenylenebenzobisthiazole)

X‐ray structure analysis was carried out in order to clarify the crystal structure and structural disorder of poly‐(p‐phenylenebenzobisthiazole). Two molecular chains pass through an oblique unit cell with parameters a = 11.60 Å, b = 3.588 Å, γ = 92.0° and the plane group p2. The angle between the phenylene and benzobisthiazole rings was estimated as 20.5°. Poly‐(p‐phenylenebenzobisthiazole) includes the disorder with respect to the molecular height, because the first and third layer lines are diffuse streak. On the ac plane, the molecular heights are disordered by 1/2 because 102, 602, and 404 reflections can be observed. On the bc plane, the molecular heights are disordered by every 1/5 because the 015 reflection can be observed. © 2000 John Wiley & Sons, Inc. J Polym Sci B: Polym Phys 38: 376–382, 2000     

Electron Rutherford back‐scattering case study: oxidation and ion implantation of aluminium foil

Electron Rutherford back scattering (ERBS) is a new spectroscopy for determining the composition of surfaces. In this work the surface sensitivity of ERBS was investigated by changing the entrance and exit angle of the electron beam while keeping the scattering angle constant. It was found that in this way the surface sensitivity of the technique can be varied considerably. We use aluminium as a test case for ERBS, as it is well studied. The technique has been used to investigate the oxide film of aluminium foil as manufactured and the native oxide (Al₂O₃) film formed on a clean aluminium surface exposed to air. We have also used ERBS to investigate the presence of Xe, implanted during the sputter cleaning process, at a variety of depths within an aluminium matrix. Copyright © 2007 John Wiley & Sons, Ltd.     

SPOT‐Ligand: Fast and effective structure‐based virtual screening by binding homology search according to ligand and receptor similarity

Structure‐based virtual screening usually involves docking of a library of chemical compounds onto the functional pocket of the target receptor so as to discover novel classes of ligands. However, the overall success rate remains low and screening a large library is computationally intensive. An alternative to this “ab initio” approach is virtual screening by binding homology search. In this approach, potential ligands are predicted based on similar interaction pairs (similarity in receptors and ligands). SPOT‐Ligand is an approach that integrates ligand similarity by Tanimoto coefficient and receptor similarity by protein structure alignment program SPalign. The method was found to yield a consistent performance in DUD and DUD‐E docking benchmarks even if model structures were employed. It improves over docking methods (DOCK6 and AUTODOCK Vina) and has a performance comparable to or better than other binding‐homology methods (FINDsite and PoLi) with higher computational efficiency. The server is available at http://sparks-lab.org . © 2016 Wiley Periodicals, Inc.     

A procedure for the analysis of site‐specific and structure‐specific fucosylation in alpha‐1‐antitrypsin

A MS‐based methodology has been developed for analysis of core‐fucosylated versus antennary‐fucosylated glycosites in glycoproteins. This procedure is applied to the glycoprotein alpha‐1‐antitrypsin (A1AT), which contains both core‐ and antennary‐fucosylated glycosites. The workflow involves digestion of intact glycoproteins into glycopeptides, followed by double digestion with sialidase and galactosidase. The resulting glycopeptides with truncated glycans were separated using an off‐line HILIC (hydrophilic interaction liquid chromatography) separation where multiple fractions were collected at various time intervals. The glycopeptides in each fraction were treated with PNGase F and then divided into halves. One half of the sample was applied for peptide identification while the other half was processed for glycan analysis by derivatizing with a meladrazine reagent followed by MS analysis. This procedure provided site‐specific identification of glycosylation sites and the ability to distinguish core fucosylation and antennary fucosylation via a double digestion and a mass profile scan. Both core and antennary fucosylation are shown to be present on various glycosites in A1AT.     

Small‐angle X‐ray scattering and polymer melting: A model study

Small‐angle X‐ray scattering (SAXS) gives information on lamellar stacks in semicrystalline polymers. SAXS experiments have been used to follow the melting transition that occurs over a temperature range of 10 °C or more. One common feature is the increase in the average period by 50–100% during the melting process, a change that is often attributed to sequential melting of crystals in the lamellar stack. A quantitative treatment shows that the scattering experiment indicates only the original period, not the average period that increases throughout sequential melting. With this model, I discuss the relation between structural parameters of the melting structure and quantities derived from the SAXS intensity, the correlation function, and the interface distribution function. Uncertainties persist in our understanding of polymer melting. © 2001 John Wiley & Sons, Inc. J Polym Sci Part B: Polym Phys 39: 2454–2460, 2001