The raspberry model for protein-like particles: Ellipsoids and confinement in cylindrical pores

The study of protein mass transport via atomistic simulation requires time and length scales beyond the computational capabilities of modern computer systems. The raspberry model for colloidal particles in combination with the mesoscopic hydrodynamic method of lattice Boltzmann facilitates coarse-grained simulations that are on the order of microseconds and hundreds of nanometers for the study of diffusive transport of protein-like colloid particles. The raspberry model reproduces linearity in resistance to motion versus particle size and correct enhanced drag within cylindrical pores at off-center coordinates for spherical particles. Owing to the high aspect ratio of many proteins, ellipsoidal raspberry colloid particles were constructed and reproduced the geometric resistance factors of Perrin and of Happel and Brenner in the laboratory-frame and in the moving body-frame. Accurate body-frame rotations during diffusive motion have been captured for the first time using projections of displacements. The spatial discretization of the fluid leads to a renormalization of the hydrodynamic radius, however, the data describes a self-consistent hydrodynamic frame within this renormalized system.     

Simulations of ferrite-dielectric-wire composite negative index materials

We perform extensive finite difference time domain simulations of ferrite based negative index of refraction composites. A wire grid is employed to provide negative permittivity. The ferrite and wire grid interact to provide both negative and positive index of refraction transmission peaks in the vicinity of the ferrite resonance. Notwithstanding the extreme anisotropy in the index of refraction of the composite, negative refraction is seen at the composite air interface allowing the construction of a focusing concave lens with a magnetically tunable focal length.     

Nonvolatile memory elements based on the intercalation of organic molecules inside carbon nanotubes

We propose a novel class of nonvolatile memory elements based on the modification of the transport properties of a conducting carbon nanotube by the presence of an encapsulated molecule. The guest molecule has two stable orientational positions relative to the nanotube that correspond to conducting and nonconducting states. The mechanism, governed by a local gating effect of the molecule on the electronic properties of the nanotube host, is studied using density functional theory. The mechanisms of reversible reading and writing of information are illustrated with a F4TCNQ molecule encapsulated inside a metallic carbon nanotube. Our results suggest that this new type of nonvolatile memory element is robust, fatigue-free, and can operate at room temperature.     

CORSICA: correction of structured noise in fMRI by automatic identification of ICA components

When applied to functional magnetic resonance imaging (fMRI) data, spatial independent component analysis (sICA), a data-driven technique that addresses the blind source separation problem, seems able to extract components specifically related to physiological noise and brain movements. These components should be removed from the data to achieve structured noise reduction and improve any subsequent detection and analysis of signal fluctuations related to neural activity. We propose a new automatic method called CORSICA (CORrection of Structured noise using spatial Independent Component Analysis) to identify the components related to physiological noise, using prior information on the spatial localization of the main physiological fluctuations in fMRI data. As opposed to existing spectral priors, which may be subject to aliasing effects for long-TR data sets (typically acquired with TR >1 s), such spatial priors can be applied to fMRI data, regardless of the TR of the acquisitions. By comparing the proposed automatic selection to a manual selection performed visually by a human operator, we first show that CORSICA is able to identify the noise-related components for long-TR data with a high sensitivity and a specificity of 1. On short-TR data sets, we validate that the proposed method of noise reduction allows a substantial improvement of the signal-to-noise ratio evaluated at the cardiac and respiratory frequencies, even in the gray matter, while preserving the main fluctuations related to neural activity.     

An Enantioselective Inverse‐Electron‐Demand Imino Diels–Alder Reaction

The imino Diels–Alder reaction is an efficient method for the synthesis of aza‐heterocycles. While different stereo‐ and enantioselective inverse‐electron‐demand imino Diels–Alder (IEDIDA) reactions have been reported before, IEDIDA reactions including electron‐deficient dienes are unprecedented. The first enantioselective IEDIDA reaction between electron‐poor chromone dienes and cyclic imines, catalyzed by zinc/binol complexes is described. The novel reaction provides a facile entry to a natural product inspired collection of ring‐fused quinolizines including a potent modulator of mitosis.     

Naphthocrown‐Strapped Calix[4]pyrroles: Formation of Self‐Assembled Structures by Ion‐Pair Recognition

A new approach to the construction of self‐assembled structures is reported that is based on ion‐pair recognition. Towards this end, the calix[4]pyrrole naphthocrown‐4 hybrid structures 2 and 3 were prepared. These multitopic receptors contain recognition sites for both anions and cations. On the basis of solution‐phase ¹H NMR spectroscopic analysis and solid‐state single‐crystal X‐ray diffraction structural studies, it was established that receptors 2 and 3 are able to bind specific ion pairs with high selectivity via different binding modes. In the case of CsF and CsCl, the ion‐pair complexes formed from receptors 2 and 3 were found to self‐assemble to produce either linear supramolecular polymeric crystalline solids or nanotube‐like cyclic hexamers depending on the specific choice of ion pairs and crystallization solvents. Proton NMR studies provided evidence for solution‐phase self‐association in organic media.     

Unraveling the Crystal Structure of Lanthanide–Murexide Complexes: Use of an Ancient Complexometry Indicator as a Near‐Infrared‐Emitting Single‐Ion Magnet

Herein, we provide some structural evidence of the complexation color‐change of murexide solutions in presence of lanthanide, which has been used for decades in complexometric studies. For Ln=Sm to Lu and Y, the compounds crystallize as monomeric [Ln(Murex)₃] ? 11 H₂O with an N3O6 tricapped square‐antiprism environment, which are stable up to 250 °C. Single‐ion magnet (SIM) behavior is then observed on the Yb^III derivative in an original nine‐coordinated environment. In‐field slow relaxation (Δ=(15.6±1) K; τ₀=2.73×10^?6 s) is observed with a very narrow distribution of the relaxation time (α_max=0.09). Magnetic and photophysical properties can be correlated. On one hand the analysis of NIR emission spectrum permits to have access to crystal field parameters and to compare them with those extracted from dc measurements. On the other hand, magnetic measurements permit to identify the nature of the M _J states involved in the ²F_5/2→²F_7/2 luminescence spectrum. The gap between the low‐lying states is in agreement with the energy barrier obtained from magnetic slow‐relaxation measurement.     

Two‐Photon‐Induced Fluorescence in New π‐Expanded Diketopyrrolopyrroles

Structurally unique π‐expanded diketopyrrolopyrroles (EDPP) were designed and synthesized. Strategic placement of a fluorene scaffold at the periphery of a diketopyrrolopyrrole through tandem Friedel–Crafts‐dehydration reactions resulted in dyes with supreme solubility. The structure of the dyes was confirmed by X‐ray crystallography verifying a nearly flattened arrangement of the ten fused rings. Despite the extended ring system, the dye still preserved good solubility and was further functionalized by using Pd‐catalyzed coupling reactions, such as the Buchwald–Hartwig amination. Photophysical studies of these new functional dyes revealed that they possess enhanced properties when compared with expanded DPPs in terms of two‐photon absorption cross‐section. It is further demonstrated that in addition to the initial diacetals, the final electrophilic cyclization step can also be applied to diketones. By placing two amine groups at peripheral positions of the resulting dyes, values of two‐photon absorption cross‐section on the level of 2000 GM around 1000 nm were achieved, which in combination with high fluorescence quantum yield (Φ_fl), generated a two‐photon brightness of approximately 1600 GM. These characteristics in combination with strong red emission (665 nm) make these new π‐expanded diketopyrrolopyrroles of major promise as two‐photon dyes for bioimaging applications. Finally, the corresponding N‐alkylated DPPs displayed a solid‐state fluorescence.     

Molecular dynamics simulation study of xyloglucan adsorption on cellulose surfaces: effects of surface hydrophobicity and side-chain variation

The effect of surface hydrophobicity and side-chain variation on xyloglucan adsorption onto cellulose microfibrils (CMF) is investigated via molecular dynamics simulations. A molecular model of CMF with (100), (010), (1–10), (110) and (200) crystal faces was built. We considered xylogluco-oligosaccharides (XGO) with three repeating units, namely (XXXG)_3, (XXLG)₃, and (XXFG)₃ (where each (1,4)-β-d-glucosyl residue in the backbone is given a one-letter code according to its substituents: G = β-d-Glc; X = α-d-Xyl-(1,6)-β-d-Glc; L = β-d-Gal-(1,2)-α-d-Xyl-(1,6)-β-d-Glc; F = α-l-Fuc-(1,2)-β-d-Gal-(1,2)-α-d-Xyl-(1,6)-β-d-Glc). Our work shows that (XXXG)₃ binds more favorably to the CMF (100) and (200) hydrophobic surfaces than to the (110), (010) and (1–10) hydrophilic surfaces. The origin of this behavior is attributed to the topography of hydrophobic CMF surface, which stabilizes (XXXG)₃ in flat conformation. In contrast, on the rough hydrophilic CMF surface (XXXG)₃ adopts a less favorable random-coil conformation to facilitate more hydrogen bonds with the surface. Extending the xyloglucan side chains from (XXXG)₃ to (XXLG)₃ hinders their stacking on the CMF hydrophobic surface. For (XXFG)₃, the interaction with the hydrophobic surface is as strong as (XXXG)₃. All three XGOs have similar binding to the hydrophilic surface. Steered molecular dynamics simulation was performed on an adhesive model where (XXXG)₃ was sandwiched between two CMF hydrophobic surfaces. Our analysis suggests that this sandwich structure might help provide mechanical strength for plant cell walls. Our study relates to a recently revised model of primary cell walls in which extensibility is largely determined by xyloglucan located in limited regions of tight contact between CMFs.