Computational studies of the x-ray scattering properties of laser aligned stilbene

The enhancement of the x-ray scattering signal from partially aligned molecular samples is investigated. The alignment properties of the studied molecular system are modeled based on the method of laser alignment. With the advances in the area of laser alignment of molecules, the application of this sample manipulation technique promises a great potential for x-ray scattering measurements. Preferential alignment of molecules in an otherwise amorphous sample leads to constructive interference and thus increases the scattering intensity. This enhances the structural information encoded in the scattering images and enables improved resolution in studies of reaction dynamics, as in this work is shown for the example of the photo-isomerization of stilbene. We demonstrate that the scattering signal is strongly influenced by the alignment axis. Even the most basic one-dimensional alignment offers significant improvement compared to the structural information provided by a randomly oriented sample. Although the signal is sensitive to the uncertainty in the alignment angle, it offers encouraging results even at realistic alignment uncertainties.     

Physical interpretation of residual dipolar couplings in neutral aligned media

A novel method is described for rapidly calculating alignment tensors from hydrodynamic shape, required for the prediction of residual dipolar couplings in neutral aligned media. Simulations of alignment were used to show that for steric restriction at a planar surface, the alignment process is dependent on linear hydrodynamic length. However, as discussed, previous methods are not in agreement with this observation. Therefore, the method presented here is the first to provide simple, accurate predictions of the alignment tensor for neutral and dilute media, while being consistent with simulations of alignment. It provides predictions in a fraction of the time of a simulation approach, while aiding physical intuition by providing a direct link between shape and alignment. Not only is this physically gratifying, but it also permits residual dipolar couplings to be applied in demanding situations where simulations of alignment are not desirable, such as in studies of molecular dynamics.     

Simultaneous formation behaviour of surface structures and molecular alignment by patterned photopolymerisation

ABSTRACT

Highly functional soft materials with fine control of molecular alignment are of great interest for the applications in various fields. However, the current method of molecular alignment still has some challenges. Recently, we have developed a new alignment process based on a concept of scanning wave photopolymerisation (SWaP). When a sample is irradiated with spatially selected light, a polymerisation occurs only in an irradiated region, leading to a molecular motion between the irradiated and unirradiated regions. Such molecular motion generates the alignment of liquid crystal molecules. Moreover, a surface relief structure is formed in the polymer film by the molecular motion. In this study, we simultaneously formed the surface structure and molecular alignment by the patterned photopolymerisation. We compared the degree of molecular alignment with the shape of the created surface structure, and revealed that the degree of molecular alignment was maximized at the boundary of irradiated and unirradiated regions. This method enables one to form both molecular alignment patterning and surface structuring in a single step.     

Time-dependent alignment of molecules trapped in octahedral crystal fields

The hindered rotational states of molecules confined in crystal fields of octahedral symmetry, and their time-dependent alignment obtained by pulsed nonresonant laser fields, are studied computationally. The control over the molecular axis direction is discussed based on the evolution of the rotational wave packet generated in the cubic crystal-field potential. The alignment degree obtained in a cooperative case, where the alignment field is applied in a favorable crystal-field direction, or in a competitive direction, where the crystal field has a saddle point, is presented. The investigation is divided into two time regimes where the pulse duration is either ultrashort, leading to nonadiabatic dynamics, or long with respect to period of molecular libration, which leads to synchronous alignment due to nearly adiabatic following. The results are contrasted to existing gas phase studies. In particular, the irregularity of the crystal-field energies leads to persistent interference patterns in the alignment signals. The use of nonadiabatic alignment for interrogation of crystal-field energetics and the use of adiabatic alignment for directional control of molecular dynamics in solids are proposed as practical applications.     

Alignment of polymer network-stabilized ferroelectric liquid crystal using a magnetic field

Polymer network-stabilized ferroelectric liquid crystals with homogeneous alignment have been produced in cells without a surface alignment layer. In this technique, a crosslinkable monomer is mixed into a ferroelectric liquid crystal and polymerized in a magnetic field to form a polymer network that will stabilize the alignment of the ferroelectric liquid crystal. The concentration of the monomer is an important factor in achieving alignment of the ferroelectric liquid crystal. Both the morphology of the final composite layer and the molecular alignment of the host FLC are affected by the curing temperature at which the UV curing of the sample is started.     

Alignment of polymer network-stabilized ferroelectric liquid crystal using a magnetic field

Polymer network-stabilized ferroelectric liquid crystals with homogeneous alignment have been produced in cells without a surface alignment layer. In this technique, a crosslinkable monomer is mixed into a ferroelectric liquid crystal and polymerized in a magnetic field to form a polymer network that will stabilize the alignment of the ferroelectric liquid crystal. The concentration of the monomer is an important factor in achieving alignment of the ferroelectric liquid crystal. Both the morphology of the final composite layer and the molecular alignment of the host FLC are affected by the curing temperature at which the UV curing of the sample is started.     

Photopolymerization induced orientation transition in a nematic liquid crystal cell

We report the observation of a liquid crystal tilt transition from homeotropic to planar orientation induced by photopolymerization of the alignment layer in the absence of liquid crystal. The alignment agent is a unique, polymerizable lecithin (DC₂₃PC), which induces homeotropic alignment before UV exposure. After non-polarized UV exposure, a tilted orientation is obtained. Moreover, further buffing of the UV treated substrate yields a homogeneous alignment. We believe that the conformation change in the lecithin array caused by solid state polymerization is primarily responsible for the transition. These results help to explain the mechanism of liquid crystal alignment and will lead to several potential applications.     

Technique for generating three-dimensional alignments of multiple ligands from one-dimensional alignments

We describe and demonstrate a method for the simultaneous, fully flexible alignment of multiple molecules with a common biological activity. The key aspect of the algorithm is that the alignment problem is first solved in a lower dimensional space, in this case using the one-dimensional representations of the molecules. The three-dimensional alignment is then guided by constraints derived from the one-dimensional alignment. We demonstrate using 10 hERG channel blockers, with a total of 72 rotatable bonds, that the one-dimensional alignment is able to effectively isolate key conserved pharmacophoric features and that these conserved features can effectively guide the three-dimensional alignment. Further using 10 estrogen receptor agonists and 5 estrogen receptor antagonists with publicly available cocrystal structures we show that the method is able to produce superpositions comparable to those derived from crystal structures. Finally, we demonstrate, using examples from peptidic CXCR3 agonists, that the method is able to generate reasonable binding hypotheses.     

The PRALINE online server: optimising progressive multiple alignment on the web

We introduce the online server for PRALINE (http://ibium.cs.vu.nl/programs/pralinewww/), an iterative versatile progressive multiple sequence alignment (MSA) tool. PRALINE provides various MSA optimisation strategies including weighted global and local profile pre-processing, secondary structure-guided alignment and a reliability measure for aligned individual residue positions. The latter can also be used to optimise the alignment when the profile pre-processing strategies are iterated. In addition, we have modelled the server output to enable comprehensive visualisation of the generated alignment and easy figure generation for publications. The alignment is represented in five default colour schemes based on: residue type, position conservation, position reliability, residue hydrophobicity and secondary structure; depending on the options set. We have also implemented a custom colour scheme that allows the user to select which colour will represent one or more amino acids in the alignment. The grouping of sequences, on which the alignment is based, can also be visualised as a dendrogram. The PRALINE algorithm is designed to work more as a toolkit for MSA rather than a one step process.     

ALIGN_MTX—An optimal pairwise textual sequence alignment program,adapted for using in sequence-structure alignment

The presented program ALIGN_MTX makes alignment of two textual sequences with an opportunity to use any several characters for the designation of sequence elements and arbitrary user substitution matrices. It can be used not only for the alignment of amino acid and nucleotide sequences but also for sequence-structure alignment used in threading, amino acid sequence alignment, using preliminary known PSSM matrix, and in other cases when alignment of biological or non-biological textual sequences is required. This distinguishes it from the majority of similar alignment programs that make, as a rule, alignment only of amino acid or nucleotide sequences represented as a sequence of single alphabetic characters. ALIGN_MTX is presented as downloadable zip archive at http://www.imbbp.org/software/ALIGN_MTX/ and available for free use.As application of using the program, the results of comparison of different types of substitution matrix for alignment quality in distantly related protein pair sets were presented. Threading matrix SORDIS, based on side-chain orientation in relation to hydrophobic core centers with evolutionary change-based substitution matrix BLOSUM and using multiple sequence alignment information position-specific score matrices (PSSM) were taken for test alignment accuracy. The best performance shows PSSM matrix, but in the reduced set with lower sequence similarity threading matrix SORDIS shows the same performance and it was shown that combined potential with SORDIS and PSSM can improve alignment quality in evolutionary distantly related protein pairs.     

Application of photosensitive polyimides as alignment layer to optical switching devices of a nematic liquid crystal

We have explored the change in alignment of a nematic liquid crystal, 4'-pentyl-4-cyanobiphenyl (5CB) with three types of photosensitive polyimide as the alignment layer by photoirradiation at 366 nm. The photosensitive polyimide alignment layer induced a reversible change in alignment of 5CB. It was observed that the 5CB molecules became aligned from homogeneous alignment to homeotropic on photoirradiation with a d.c. electric field as a bias, and reversed to the homogeneous state when photoirradiation was ceased. This result indicates that optical switching could be repeated by on and off switching of the excitation light at 366 nm. The optical switching of the nematic liquid crystal might be mainly due to a photophysical change in the polyimide surface which is affected by the chemical structures of the polyimides at the temperature at which 5CB exhibits a nematic phase. The optical switching of nematic liquid crystals with photosensitive polyimides as the alignment layer is a novel driving method for nematic liquid crystals.     

Application of photosensitive polyimides as alignment layer to optical switching devices of a nematic liquid crystal

We have explored the change in alignment of a nematic liquid crystal, 4'-pentyl-4-cyanobiphenyl (5CB) with three types of photosensitive polyimide as the alignment layer by photoirradiation at 366 nm. The photosensitive polyimide alignment layer induced a reversible change in alignment of 5CB. It was observed that the 5CB molecules became aligned from homogeneous alignment to homeotropic on photoirradiation with a d.c. electric field as a bias, and reversed to the homogeneous state when photoirradiation was ceased. This result indicates that optical switching could be repeated by on and off switching of the excitation light at 366 nm. The optical switching of the nematic liquid crystal might be mainly due to a photophysical change in the polyimide surface which is affected by the chemical structures of the polyimides at the temperature at which 5CB exhibits a nematic phase. The optical switching of nematic liquid crystals with photosensitive polyimides as the alignment layer is a novel driving method for nematic liquid crystals.     

Parameter selection for peak alignment in chromatographic sample profiling: objective quality indicators and use of control samples

In chromatographic profiling applications, peak alignment is often essential as most chromatographic systems exhibit small peak shifts over time. When using currently available alignment algorithms, there are several parameters that determine the outcome of the alignment process. Selecting the optimum set of parameters, however, is not straightforward, and the quality of an alignment result is at least partly determined by subjective decisions. Here, we demonstrate a new strategy to objectively determine the quality of an alignment result. This strategy makes use of a set of control samples that are analysed both spiked and non-spiked. With this set, not only the system and the method can be checked but also the quality of the peak alignment can be evaluated. The developed strategy was tested on a representative metabolomics data set using three software packages, namely Markerlynx™, MZmine and MetAlign. The results indicate that the method was able to assess and define the quality of an alignment process without any subjective interference of the analyst, making the method a valuable contribution to the data handling process of chromatography-based metabolomics data.     

Detecting conserved secondary structures in RNA molecules using constrained structural alignment

Constrained sequence alignment has been studied extensively in the past. Different forms of constraints have been investigated, where a constraint can be a subsequence, a regular expression, or a probability matrix of symbols and positions. However, constrained structural alignment has been investigated to a much lesser extent. In this paper, we present an efficient method for constrained structural alignment and apply the method to detecting conserved secondary structures, or structural motifs, in a set of RNA molecules. The proposed method combines both sequence and structural information of RNAs to find an optimal local alignment between two RNA secondary structures, one of which is a query and the other is a subject structure in the given set. The method allows a biologist to annotate conserved regions, or constraints, in the query RNA structure and incorporates these regions into the alignment process to obtain biologically more meaningful alignment scores. A statistical measure is developed to assess the significance of the scores. Experimental results based on detecting internal ribosome entry sites in the RNA molecules of hepatitis C virus and Trypanosoma brucei demonstrate the effectiveness of the proposed method and its superiority over existing techniques.     

High-speed peak matching algorithm for retention time alignment of gas chromatographic data for chemometric analysis

A rapid retention time alignment algorithm was developed as a preprocessing utility to be used prior to chemometric analysis of large datasets of diesel fuel profiles obtained using gas chromatography (GC). Retention time variation from chromatogram-to-chromatogram has been a significant impediment against the use of chemometric techniques in the analysis of chromatographic data due to the inability of current chemometric techniques to correctly model information that shifts from variable to variable within a dataset. The alignment algorithm developed is shown to increase the efficacy of pattern recognition methods applied to diesel fuel chromatograms by retaining chemical selectivity while reducing chromatogram-to-chromatogram retention time variations and to do so on a time scale that makes analysis of large sets of chromatographic data practical. Two sets of diesel fuel gas chromatograms were studied using the novel alignment algorithm followed by principal component analysis (PCA). In the first study, retention times for corresponding chromatographic peaks in 60 chromatograms varied by as much as 300 ms between chromatograms before alignment. In the second study of 42 chromatograms, the retention time shifting exhibited was on the order of 10 s between corresponding chromatographic peaks, and required a coarse retention time correction prior to alignment with the algorithm. In both cases, an increase in retention time precision afforded by the algorithm was clearly visible in plots of overlaid chromatograms before and then after applying the retention time alignment algorithm. Using the alignment algorithm, the standard deviation for corresponding peak retention times following alignment was 17 ms throughout a given chromatogram, corresponding to a relative standard deviation of 0.003% at an average retention time of 8 min. This level of retention time precision is a 5-fold improvement over the retention time precision initially provided by a state-of-the-art GC instrument equipped with electronic pressure control and was critical to the performance of the chemometric analysis. This increase in retention time precision does not come at the expense of chemical selectivity, since the PCA results suggest that essentially all of the chemical selectivity is preserved. Cluster resolution between dissimilar groups of diesel fuel chromatograms in a two-dimensional scores space generated with PCA is shown to substantially increase after alignment. The alignment method is robust against missing or extra peaks relative to a target chromatogram used in the alignment, and operates at high speed, requiring roughly 1 s of computation time per GC chromatogram.     

In situ self-assembled homeotropic alignment layer for fast-switching liquid crystal devices

We propose a novel method for homeotropic alignment of liquid crystals (LCs) utilising in situ self-assembly of a low concentration of 4-(4-heptylphenyl)benzoic acids that form hydrogen bond with the indium tin oxide (ITO) substrates. Stable homeotropic alignment in the LC device is achieved with a simple mixing process of benzoic acid derivative in LC media, and it yields electro-optical performance similar to that achieved with the conventional alignment method using polyimides. It is experimentally confirmed that an ultrathin self-assembled molecular layer of 4-(4-heptylphenyl)benzoic acid formed by hydrogen bonding on ITO substrate makes it possible to attain a reliable homeotropic alignment of LCs. Furthermore, this simple approach provides a cost-effective and stable LC alignment layer with fast response time and thermal stability.     

Orientation Control of Molecularly Functionalized Surfaces Applied to the Simultaneous Alignment and Sorting of Carbon Nanotubes

Self‐assembly has been relied upon for molecular alignment in many advanced technological applications. However, although effective, it is inherently limited in its capability for optimization. Despite the potential benefits, the seemingly fundamental strategy of external orientation control has yet to be realized. Herein we demonstrate an approach that allows control of the orientation of small molecules covalently bound to a surface. The method exploits an alignment relay technique, passing alignment information through a liquid‐crystal medium to small molecules to control surface functionalization events. The method is technically simple and can be carried out on a bench top without the need for specialized equipment. Moreover, we demonstrate the utility of the resulting surfaces to address two long‐standing problems in nanoscience: the sorting and alignment of single‐walled carbon nanotubes. This new method enabled significant alignment of the nanotubes as well as length and diameter sorting.     

Unidirectional Alignment of Surface-Grafted ZnO Nanorods in Micrometer-Thick Cells Using Low-Molecular-Weight Liquid Crystals

Inorganic nanomaterials such as nanotubes and nanorods have attracted great attention due to their anisotropic properties. Although the alignment control of inorganic nanomaterials is key to the development of functional devices utilizing their fascinating properties, there is still difficulty in achieving uniform alignment over a large area with a micrometer thickness. To overcome this problem, we focused on liquid crystals (LCs) to promote the alignment of anisotropic nanomaterials, taking advantage of the cooperative motion of LCs. We present the uniform, one-dimensional alignment of ZnO nanorods along the direction of LCs in micrometer-thick cells by grafting nematic LC polymers from the nanorod surfaces to provide miscibility with the host LCs. Polarized optical microscopy and polarized UV–visible absorption spectroscopy revealed the unidirectional alignment of nematic LC polymer-grafted ZnO nanorods parallel to the nematic host LCs.