Crystalline alignment of metal ions templated by β-chitin ester

The highly crystalline β-chitin from diatom Thalassiosira weissflogii was esterified via intercalation with succinic anhydride followed by simple heating, maintaining the original crystalline order. Due to the introduced free carboxyl groups, the chitin ester crystal showed ion exchange ability for metal cations in aq. solution. Heavy metal cations such as Pb²⁺ bound to the β-chitin succinate gave characteristic X-ray diffraction patterns, indicating regular alignment of metal ions. Such materials represent a new type of organometallic architecture, possibly leading to novel functionalities.     

Pairwise alignment of chromatograms using an extended Fisher–Rao metric

A conceptually new approach for aligning chromatograms is introduced and applied to examples of metabolite identification in human blood plasma by liquid chromatography–mass spectrometry (LC–MS). A square-root representation of the chromatogram's derivative coupled with an extended Fisher–Rao metric enables the computation of relative differences between chromatograms. Minimization of these differences using a common dynamic programming algorithm brings the chromatograms into alignment. Application to a complex sample, National Institute of Standards and Technology (NIST) Standard Reference Material 1950, Metabolites in Human Plasma, analyzed by two different LC–MS methods having significantly different ranges of elution time is described.     

Lyotropic liquid crystalline phases from helical β-peptides as alignment media

Lyotropic liquid crystalline (LLC) phases from helical β-peptides are proposed as novel water-based alignment media. In contrast to α-peptides, β-peptides form LLCs at very short chain lengths and at concentrations as low as 1 percent. Spectra obtained in these LLC phases are artefact-free and lead to RDCs of the desired size. First indications towards enantiodiscrimination are provided.     

Effect of the twisted alignment on the liquid crystal wave‐front corrector

The effect of twisted alignment on the phase modulation of a liquid crystal wave‐front corrector was investigated. First, the effect of twisted alignment is discussed in terms of the modulation principle of the liquid crystal molecule. Only partial incident light can be modulated because of the effect of the twisted alignment. Other unmodulated light will affect the correction accuracy and the resolution of the image. The blazed grating method is proposed to solve this problem. Adaptive correction was performed without the blazed grating method and the correction results are poor. A similar adaptive correction experiment was performed with the blazed grating method and a better correction result is obtained. The residual averaged wave‐front errors are PV = 0.101λ and RMS = 0.015λ and a resolvable image is obtained.     

Liquid crystal alignment on isotropic submicro‐textured surfaces of homeotropic‐planar states

The equilibrium configuration of liquid crystal molecules in contact with a periodicly patterned substrate has been theoretically analysed considering the variation of the order parameter at the interface, and a first order transition was predicted for a critical periodicity, or induced by temperature or an electric field. In this work, we experimentally investigated the equilibrium configuration of the director for a submicron patterned substrate, alternating homeotropic and random planar regions in the substrate. Experimentally, it was possible to access a starting point, theoretically close to the first order transition, however no transition was observed either on varying the temperature or on applying an electric field. The possible reasons for the non‐observation of the phase transition are discussed.     

Rehybridization and π-orbital alignment: the key to the existence of spheroidal carbon clusters

The rehybridization and bonding in large carbon spheroids (C_n) has been analyzed with POAV/3D HMO theory; larger clusters are shown to be favored, and the (lower) critical value of n for stable clusters is discussed. In the generic series of truncated icosahedral spheroids of I_h symmetry, C₂₄₀ is found to be significantly more stable than its lower homologue C₆₀.     

Non‐monotonic temperature dependence of the alignment of a nematic mixture on a ferroelectric substrate

Polarization optic techniques have been applied to study specific features of the anisotropic interaction between a dye‐doped eutectic mixture of nematic liquid crystals p‐methoxybenzylidene‐p‐n‐butylaniline and p‐ethoxybenzylidene‐p‐n‐butylaniline and a polar surface of a ferroelectric triglycine sulphate crystal over the temperature range including the substrate Curie point T _c. It has been found that the temperature‐induced structural changes in the nematic layer in the vicinity of T _c are related to the changes in the orientational part of the tensor order parameter Q_ik . The temperature dependence of the director angle θ¯, averaged over the nematic layer, has been obtained from the effective dichroism values of solute absorption. The experimental data were interpreted using the model, in which the anisotropic part of the surface energy has two terms with orthogonal easy axes.     

A novel vertical alignment technology for nematic liquid crystals based on electrostatic self‐assembled method

A novel vertical alignment film for nematic liquid crystals is reported based on electrostatic self‐assembly of alkyl sulfonic salts in aqueous solution. A series of self‐assembled films with different alkyl chain lengths were prepared and used as alignment films. It was revealed that only when the number of carbon atoms in the alkyl chain approaches 11 or larger, could the self‐assembled film induce vertical alignment of liquid crystals. We also found that the homeotropic alignment of liquid crystals was related to the surface roughness of self‐assembled films. In addition, this vertical alignment film showed good electro‐optical characteristics and excellent thermal stability.     

The photodissociation of physisorbed alkyl nitrites.: Λ-doublet population and alignment of desorbed NO

The photolysis of thin layers of tert- and iso-butyl nitrite, physisorbed on a transparent insulating MgF₂ surface, has been investigated. (1+1′)-Resonance-enhanced multiphoton ionization (REMPI) spectroscopy was used to characterize the desorbed NO. For high-J rotational levels, a preference for the Π(A″) Λ-doublet and a small degree of alignment is observed. The axis of alignment is found to be parallel to the plane of polarization of the photolysis laser and perpendicular to the surface normal, indicating a cartwheeling mode of desorption. The photofragment yield (PHOFRY) spectrum of iso-butyl nitrite is also reported.     

Assessment of solvent effects: do weak alignment media affect the structure of the solute?

Alignment media used for measuring residual dipolar couplings, such as solutions of filamentous phages, phospholipid mixtures, polyacrylamide gels and various lyotropic liquid crystalline systems were investigated with respect to solvent effects on molecular structure. Structural parameters of the small rigid model compound 13C-acetonitrile were calculated from dipolar couplings and variations from expectation values were used for assessment of solvent effects. Only minor solvent effects were observed for most of the media employed and the measured structural data are in good agreement with microwave data and theoretical predictions.     

Versatile multilevel soft lithography method with micrometer alignment using all-flexible rubber stamps and moiré fringe technique

Soft lithography has gathered wide interest for the fabrication of unconventional micrometer and nanometer-sized structures and devices. Nevertheless, accurate alignment is essential to achieve multilevel soft lithography. Because of the soft nature of the stamp materials, such as soft polydimethylsiloxane, they are susceptible to mechanical distortions, which lower the registration accuracy. To reduce the distortions we backed the stamp with a polymer foil and minimized the overall forces applied to the stamp. We furthermore employed an alignment method using additive type moiré fringe technique that is easy to implement and does not require extensive processing steps. The alignment results show less than 1 μm misalignment when the stamp is brought again onto a previously structured rigid template. When performing two consecutive lithography steps by transfer printing of thin gold films, we were able to obtain average registration accuracy of 1.3 μm over an area of 400 mm(2). This method is versatile and can be used for several soft lithography techniques. Better results can be obtained with smaller moiré gratings and the use of harder materials.     

Field asymmetric waveform ion mobility spectrometry studies of proteins: Dipole alignment in ion mobility spectrometry?

Approaches to separation and characterization of ions based on their mobilities in gases date back to the 1960s. Conventional ion mobility spectrometry (IMS) measures the absolute mobility, and field asymmetric waveform IMS (FAIMS) exploits the difference between mobilities at high and low electric fields. However, in all previous IMS and FAIMS experiments ions experienced an essentially free rotation; thus the separation was based on the orientationally averaged cross-sections Omega(avg) between ions and buffer gas molecules. Virtually all large ions are permanent electric dipoles that will be oriented by a sufficiently strong electric field. Under typical FAIMS conditions this will occur for dipole moments >400 D, found for many macroions including most proteins above approximately 30 kDa. Mobilities of aligned dipoles depend on directional cross-sections Omega(dir) (rather than Omega(avg)), which should have a major effect on FAIMS separation parameters. Here we report the FAIMS behavior of electrospray-ionization-generated ions for 10 proteins up to approximately 70 kDa. Those above 29 kDa exhibit a strong increase of mobility at high field, which is consistent with predicted ion dipole alignment. This effect expands the useful FAIMS separation power by an order of magnitude, allowing separation of up to approximately 10(2) distinct protein conformers and potentially revealing information about Omega(dir) and ion dipole moment that is of utility for structural characterization. Possible approaches to extending dipole alignment to smaller ions are discussed.     

Homology model directed alignment selection for comparative molecular field analysis: Application to photosystem II inhibitors

The use of a computational docking protocol in conjunction with a protein homology model to derive molecular alignments for Comparative Molecular Field Analysis (CoMFA) was examined. In particular, the DOCK program and a model of the herbicidal target site, photosystem II (PSII), was used to derive alignments for two PSII inhibitor training sets, a set of benzo- and napthoquinones and a set of butenanilides. The protein design software in the QUANTA molecular modeling package was used to develop a homology model of spinach PSII based on the reported amino acid sequence and the X-ray crystal structure of the purple bacterium reaction center. The model is very similar to other reported PSII protein homology models. DOCK was then used to derive alignments for CoMFA modeling by docking the inhibitors in the PSII binding pocket. The molecular alignments produced from docking yielded highly predictive CoMFA models. As a comparison, the more traditional atom-atom alignments of the same two training sets failed to produce predictive CoMFA models. The general utilities of this application for homology model refinement and as an alternative scoring method are discussed.     

Semi-automated alignment and quantification of peaks using parallel factor analysis for comprehensive two-dimensional liquid chromatography–diode array detector data sets

Parallel factor analysis was used to quantify the relative concentrations of peaks within four-way comprehensive two dimensional liquid chromatography–diode array detector data sets. Since parallel factor analysis requires that the retention times of peaks between each injection are reproducible, a semi-automated alignment method was developed that utilizes the spectra of the compounds to independently align the peaks without the need for a reference injection. Peak alignment is achieved by shifting the optimized chromatographic component profiles from a three-way parallel factor analysis model applied to each injection. To ensure accurate shifting, components are matched up based on their spectral signature and the position of the peak in both chromatographic dimensions. The degree of shift, for each peak, is determined by calculating the distance between the median data point of the respective dimension (in either the second or first chromatographic dimension) and the maximum data point of the peak furthest from the median. All peaks that were matched to this peak are then aligned to this common retention data point. Target analyte recoveries for four simulated data sets were within 2% of 100% recovery in all cases. Two different experimental data sets were also evaluated. Precision of quantification of two spectrally similar and partially coeluting peaks present in urine was as good as or better than 4%. Good results were also obtained for a challenging analysis of phenytoin in waste water effluent, where the results of the semi-automated alignment method agreed with the reference LC–LC MS/MS method within the precision of the methods.     

3D-QSAR using `Multiconformer' alignment: The use of HASL in the analysis of 5-HT1A thienopyrimidinone ligands†

The observed 5-HT_1A and ₁-adrenergic receptor (₁-AR) receptor binding properties of a series of 23 thienopyrimidinones were used to develop HASL 3D-QSAR models. A single, low energy conformer of the most active analogue in the series, which was consistent with NMR structural studies, was chosen as a template molecule. Alignments of all the molecules to the template were provided by an Amber/MM2 superposition force field. In this manner, each molecule was represented by five separate low energy conformers which were subsequently used in the generation of HASL 3D-QSAR models. Models derived from multiple conformers were found to exhibit enhanced predictivity compared to models based on single, low energy conformers. In addition, the use of contour imaging of HASL multi-conformer model interactions was found to lead to a more consistent interpretation of those molecular features most significant for 5-HT_1A receptor binding.     

Langmuir–Blodgett films of stearic acid deposited on substrates at different orientations relative to compression direction: alignment layer for nematic liquid crystal

The Langmuir monolayer at an air–water interface shows remarkably different surface pressure (π)–area (A) isotherm, when measured with the surface normal of a Wilhelmy plate parallel or perpendicular to the direction of compression of the monolayer. Such difference arises due to difference in stress exerted by the monolayer on the plate in different direction. In this article, we report the effect of changing the direction of substrate normal with respect to the compression of the monolayer during Langmuir–Blodgett (LB) film deposition on the morphology of the films. The morphology of the LB film of stearic acid is studied using an atomic force microscope. The morphology of the LB films is found to be different due to difference in the stress in different directions. The role of such surface morphology on the alignment of a nematic liquid crystal (LC) in LC cells is studied. The granular texture of LB films of stearic acid supports the homogeneous alignment of the LC whereas the uniform texture supports the homeotropic alignment of the LC.