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A method was developed for rapid qualitative determination of lignocellulose in the tobacco cell wall by utilizing 2D heteronuclear single quantum coherence NMR spectra (2D HSQC NMR). Traditional methods for analyzing the structure of lignocellulose involve many steps of separation and extraction, which is labor-intensive. In this work, the whole cell wall was milled and dissolved in deuterium solvent. The solvent dimethylsulfoxide (DMSO-d6) containing hexamethylphosphoramide (HMPA-d18) enhanced swelling of the sample and gave high-resolution spectra. The tobacco samples are ball milled at different ball milling times, and the state of the particles is observed through an electron microscope, and then the probability of the particles being less than 5 µm is counted. Through the comparison of the abundance and integration of the peak signals in the spectra under different transmittances, it was determined that when the milling time was 6 h, the quality of the NMR spectra was the best. The optimum conditions of characterizing tobacco structure were DMSO-d6/HMPA-d18 solution and 6 h milling time. Under these conditions, complete representation of the structure of lignocellulose and simplified process could be achieved.

Antimicrobial function of Ag nanoparticles (NPs) has a strong correlation with the released Ag+ cations that are produced by oxidation of Ag NPs in a solution state under ambient condition. Therefore, in order to develop anti-infective materials for biomedical applications, one needs to include Ag NPs inside biocompatible materials, which can allow slow release of Ag+ cations. Hydrogels of natural polymers could be an ideal choice for the purpose because (a) the physicochemical properties of hydrogels resemble with biological tissue, and (b) the inclusion of Ag NPs inside hydrogels prevents the direct release of Ag NPs, while allowing the release of Ag+ cations out of the hydrogels. In this regard, we present a simple strategy for producing Ag NPs-containing hydrogel based on natural alginate polymers. The chemical modification of alginate, blending with Ag NPs, gelation by photo-crosslinking process have been discussed in connection with antimicrobial reaction on model bacterium.

The development of a high-flux beamline for X-ray footprinting at NSLS-II is presented., Hydroxyl-radical mediated synchrotron X-ray footprinting (XF) is a powerful solution-state technique in structural biology for the study of macromolecular structure and dynamics of proteins and nucleic acids, with several synchrotron resources available to serve the XF community worldwide. The XFP (Biological X-ray Footprinting) beamline at the NSLS-II was constructed on a three-pole wiggler source at 17-BM to serve as the premier beamline for performing this technique, providing an unparalleled combination of high flux density broadband beam, flexibility in beam morphology, and sample handling capabilities specifically designed for XF experiments. The details of beamline design, beam measurements, and science commissioning results for a standard protein using the two distinct XFP endstations are presented here. XFP took first light in 2016 and is now available for general user operations through peer-reviewed proposals. Currently, beam sizes from 450 µm × 120 µm to 2.7 mm × 2.7 mm (FWHM) are available, with a flux of 1.6 × 1016 photons s−1 (measured at 325 mA ring current) in a broadband (∼5–16 keV) beam. This flux is expected to rise to 2.5 × 1016 photons s−1 at the full NSLS-II design current of 500 mA, providing an incident power density of >500 W mm−2 at full focus.

Nucleic acids do not fold into a single conformation, and dynamic ensembles are needed to describe their propensities to cycle between different conformations when performing cellular functions. We review recent advances in solution-state nuclear magnetic resonance (NMR) methods and their integration with computational techniques that are improving the ability to probe the dynamic ensembles of DNA and RNA. These include computational approaches for predicting chemical shifts from structure and generating conformational libraries from sequence, measurements of exact nuclear Overhauser effects, development of new probes to study chemical exchange using relaxation dispersion, faster and more sensitive real-time NMR techniques, and new NMR approaches to tackle large nucleic acid assemblies. We discuss how these advances are leading to new mechanistic insights into gene expression and regulation.

The key criteria of the short-term hydrothermal scheduling (StHS) problem is to minimize the gross fuel cost for electricity production by scheduling the hydrothermal power generators considering the constraints related to power balance, the gross release of water, and storage limitations of the reservoir, and the operating limitations of the thermal generators and hydropower plants. For addressing the same problem, numerous algorithms were being used, and related studies exist in the literature, however, they possess limitations concerning the solution state and the number of iterations it takes to reach the solution state. Hence, this article proposes using an enhanced cuckoo search algorithm (CSA) called the rigid cuckoo search algorithm (RCSA), a modified version of the traditional CSA for solving the StHS problem. The proposed RCSA improves the solution state and decreases the iteration numbers related to the CSA with a modified Lévy flight. Here, the movement distances are divided into multiple possible steps, which has infinite diversity. The effectiveness of RCSA has been validated by considering the hydrothermal power system. The observed results reveal the superior performance of RCSA among all other compared algorithms that recently have been used for the StHS problem. It is also observed that the RCSA approach has achieved minimum gross costs than other techniques. Thus, the proposed RCSA proves to be a highly effective and convenient approach for addressing the StHS problems

International audience; Here we show that nonanuclear lanthanide complexes respresent a new class of solution state upconversion (UC) molecules. For a composition of one Tb per eight Yb the nonanuclear complexes display a very efficient UC phenomenon with Tb luminescence in the visible region upon 980 nm NIR excitation of Yb. An unprecedented value of 1.0 × 10−7 was obtained for the UC efficiency at only 2.86 W cm−2, demonstrating these new molecular complexes to be up to 26 times more efficient than the best current molecular systems, the UC being observed down to a concentration of 10 nM.

Supramolecular gels are usually stable in time as they are formed under thermodynamic equilibrium or at least in a deep well of a kinetically trapped state. However, artificial construction of kinetically controlled transient supramolecular gels is an interesting challenge. In these systems, usually a kinetically trapped transient aggregate is formed by active building blocks that leads to gelation; the gel then typically returns to the solution state. In this work, we show that such transient aggregation can occur by successive formation of two distinctly different kinetically controlled metastable states. Control over the first metastable state allows us to achieve significant control over the stability and properties of the second metastable state.

Quantifying phospholipid bilayer-small molecule interactions is vital to the development of new drug candidates and/or medicinal therapies. However, obtaining these data remains problematic. Herein, we detail a phospholipid nanodisc assay which enables the elucidation of these interactions using conventional solution state NMR spectroscopy techniques.

Oxidation of dicyanomethyl-substituted hexa-peri-hexabenzocoronenes (HBCs) furnished a tetracyanoethylene-bridged HBC dimer and trimer. The solid state structures of the oligomers were elucidated using single crystal X-ray diffraction analysis. In the solution state, these HBC oligomers exhibited conformational isomerism, depending on solvents and temperatures. Moreover, solid samples of the HBC dimer and trimer exhibited mechanochromism, showing near IR absorption upon grinding through generation of radical species. The formed radical was stable for 4 months, indicating the persistent nature of the radical species. These NIR mechanochromic behaviours of the HBC oligomers were originated from the reversible C–C bond dissociation and formation of a tetracyanoethylene linkage between the HBC units.

The investigation of conformational features of regions of amyloidogenic proteins are of great interest to deepen the structural changes and consequent self-aggregation mechanisms at the basis of many neurodegenerative diseases. Here we explore the effect of β-hairpin inducing motifs on regions of prion protein covering strands S1 and S2. In detail, we unveiled the structural and functional features of two model chimeric peptides in which natural sequences are covalently linked together by two dipeptides (L-Pro-Gly and D-Pro-Gly) that are known to differently enhance β-hairpin conformations but both containing N- and the C-terminal aromatic cap motifs to further improve interactions between natural strands. Spectroscopic investigations at solution state indicate that primary assemblies of the monomers of both constructs follow different aggregative mechanisms during the self-assembly: these distinctions, evidenced by CD and ThT emission spectroscopies, reflect into great morphological differences of nanostructures and suggest that rigid β-hairpin conformations greatly limit amyloid-like fibrillogenesis. Overall data confirm the important role exerted by the β-structure of regions S1 and S2 during the aggregation process and lead to speculate to its persistence even in unfolding conditions.

Membrane interactions of proteins play a role in essential cellular processes in both physiological and disease states. The structural flexibility of intrinsically disordered proteins (IDPs) allows for interactions with multiple partners, including membranes. However, determining conformational states of IDPs when interacting with membranes can be challenging. Here we describe the use of nuclear magnetic resonance (NMR), including dark-state exchange saturation transfer (DEST), to probe IDP-membrane interactions in order to determine whether there is an interaction, which residues participate, and the extent/nature of the interaction between the protein and the membrane. Using α-synuclein and tau as typical examples, we provide protocols for how the membrane interactions of IDPs can be probed, including details of how the samples should be prepared and guidelines on how to interpret the results.

Whereas solution state NMR provided a wealth of information on the dynamics landscape of soluble proteins, only few studies have investigated membrane protein dynamics in a detergent-free lipid environment. Recent developments of smaller nanodiscs and other lipid-scaffolding polymers, such as styrene maleic acid (SMA), however, open new and promising avenues to explore the function-dynamics relationship of membrane proteins as well as between membrane proteins and their surrounding lipid environment. Favorably sized lipid-bilayer nanodiscs, established membrane protein reconstitution protocols and sophisticated solution NMR relaxation methods probing dynamics over a wide range of timescales will eventually reveal unprecedented lipid-membrane protein interdependencies that allow us to explain things we have not been able to explain so far. In particular, methyl group dynamics resulting from CEST, CPMG, ZZ exchange, and RDC experiments are expected to provide new and surprising insights due to their proximity to lipids, their applicability in large 100+ kDa assemblies and their simple labeling due to the availability of commercial precursors. This review summarizes the recent developments of membrane protein dynamics with a special focus on membrane protein dynamics in lipid-bilayer nanodiscs. Opportunities and challenges of backbone, side chain and RDC dynamics applied to membrane proteins are discussed. Solution-state NMR and lipid nanodiscs bear great potential to change our molecular understanding of lipid-membrane protein interactions.

Photomechanically responsive materials are promising candidates for future smart actuator applications. The photo-responsive behaviors originate from the photoisomerization of photochromic molecules. A typical photochromic compound, azobenzene, has been studied extensively in the solution state and has played a crucial role in the photomechanical behaviors of materials such as polymers and gels, via chemical bridging with their matrix. In contrast to polymers and gels, the photomechanical attributes of molecular crystals have not progressed to the same degree, due to their rigidity and fragility. However, the past decade has witnessed an increasing number of reports of the photomechanical motion of molecular crystals, including azobenzene crystals. This paper reviews the current state-of-the-art of mechanically responsive azobenzene crystals, including the history, crystal design strategy, and future promising applications.

We report herein on five new Fe(II) complexes of general formula [Fe(L)2(NCCH3)2](BF4)2•xCH3CN (L = substituted 2-pyridylimine-based ligands). The influence of proximally located electron withdrawing groups (e.g., NO2, CN, CF3, Cl, Br) bound to coordinated pyridylimine ligands has been studied for the effect on spin crossover in their Fe(II) complexes. Variable-temperature UV-visible spectroscopic studies performed on complexes with more strongly electronegative ligand substituents revealed spin crossover (SCO) in the solution, and thermodynamic parameters associated with the spin crossover were estimated.

A series of NMR supersequences are presented for the time-efficient structure characterisation of small molecules in the solution state. These triplet sequences provide HMBC, HSQC, and one homonuclear correlation experiment of choice according to the NMR by Ordered Acquisition using 1 H detection principle. The experiments are demonstrated to be compatible with non-uniform sampling schemes and may be acquired and processed under full automation.

Expanded polyglutamine (polyQ) tracts in protein, which are known to induce their aggregation, are associated with numerous neurodegenerative diseases. Longer polyQ tracts correlate with faster protein aggregation kinetics and a decreased age of onset for polyQ disease symptoms. Here, we use UV resonance Raman spectroscopy, circular dichroism spectroscopy, and metadynamics simulations to investigate the solution-state structures of the D(2)Q(15)K(2) (Q15) and D(2)Q(20)K(2) (Q20) peptides. Using metadynamics, we explore the conformational energy landscapes of Q15 and Q20 and investigate the relative energies and activation barriers between these low-energy structures. We compare the solution-state structures of D(2)Q(10)K(2) (Q10), Q15, and Q20 to determine the dependence of polyQ structure on the Q tract length. We show that these peptides can adopt two distinct monomeric conformations: an aggregation-resistant PPII-like conformation and an aggregation-prone β-strand-like conformation. We find that longer polyQ peptides have an increased preference for the aggregation-prone β-strand-like conformation. This preference may play an important role in the increased aggregation rate of longer polyQ peptides that are thought to lead to decreased neurodegenerative disease age of onset for polyQ disease patients.

A sialic acid-binding lectin (SRC) was created from the C-terminal domain of an R-type N-acetyl lactosamine-binding lectin (EW29Ch) by natural evolution-mimicry. Here, we clarified its sialic acid-binding mechanism using NMR spectroscopy. The NMR analysis showed differences between conformations of the 6'-sialyllactose-bound SRC in the solution state and that in the crystal state, and differences between the internal motion of the loop region in subdomain γ in SRC and that of the corresponding region in EW29Ch. The NMR analysis thus provided useful information to explain the manner of binding to 6'-sialyllactose in solution, which the previous X-ray crystal structure analysis lacked.

Reactions in solvothermal or microwave-assisted conditions between a hexanuclear rare-earth entity ([Ln6] with Ln = Eu-Dy) and m-halogeno-benzoic acids lead to three series of isostructural complexes with respective chemical formulas [Ln6(μ3-OH)2(H2O)2(NO3)2(3-cb)14]·4CH3CN, [Ln6(μ3-OH)2(H2O)2(NO3)2(3-bb)14]·6CH3CN, and [Ln6(μ3-OH)2(H2O)2(NO3)2(3-ib)14]·6CH3CN, where 3-cb-, 3-bb-, and 3-ib- represent 3-chloro-, 3-bromo-, and 3-iodo-benzoate, respectively. These three series of compounds are almost isostructural. Their luminescent properties, in the solid and solution states, have been studied in detail and compared. This study shows that hexanuclear complexes own strong intermetallic energy transfers. This makes these complexes good candidates for thermometric probes in solid state or in solution state.

The sol-gel method is an attractive synthetic approach in the design of advanced catalytic formulations that are based on metal and metal oxide with high degree of structural and compositional homogeneity. Nowadays, though it originated with the hydrolysis and condensation of metal alkoxides, sol-gel chemistry gathers plenty of fascinating strategies to prepare materials from solution state precursors. Low temperature chemistry, reproducibility, and high surface to volume ratios of obtained products are features that add merit to this technology. The development of different and fascinating procedure was fostered by the availability of new molecular precursors, chelating agents and templates, with the great advantage of tailoring the physico-chemical properties of the materials through the manipulation of the synthesis conditions. The aim of this review is to present an overview of the “traditional” sol-gel synthesis of tailored and multifunctional inorganic materials and their application in the main domain of heterogeneous catalysis. One of the main achievements is to stress the versatility of sol-gel preparation by highlighting its advantage over other preparation methods through some specific examples of the synthesis of catalysts.

Conformational dynamics of GPCRs are central to their function but are difficult to explore at the atomic scale. Solution-state NMR has provided the major contribution in that area of study during the past decade, despite nonoptimized labeling schemes due to the use of insect cells and, to a lesser extent, yeast as the main expression hosts. Indeed, the most efficient isotope-labeling scheme ever to address energy landscape issues for large proteins or protein complexes relies on the use of 13CH3 probes immersed in a perdeuterated dipolar environment, which is essentially out of reach of eukaryotic expression systems. In contrast, although its contribution has been underestimated because of technical issues, Escherichia coli is by far the best-adapted host for such labeling. As it is now tightly controlled, we show in this review that bacterial expression can provide an NMR spectral resolution never achieved in the GPCR field.

Ionic liquid solutions of cellulose or dopes can be spun into Lyocell-type textile fibers by dry-jet wet spinning. An extruded dope is drawn over an air gap into water, where the water hydrates the ionic liquid and cellulose is regenerated. Spinnability studies have concentrated on the deformation and failure modes in the air gap and thus the rheology of the unhydrated spinning dope. Herein, a breach in the bath, another failure mode, is discussed. Dopes are prepared from the good spinning solvents NMMO·H2O and [DBNH]OAc and the poor spinning solvents [emim]OAc and [TMGH]OAc. The diffusion constants for water diffusing inwards and for ionic liquid diffusing outwards the emerging filament are measured offline. The resiliences and strengths of cellulose–ionic liquid solutions with different hydration stoichiometries are measured by means of rheometry. By calculating the diffusion dynamics, the resilience distribution of the forming filament is simulated. Gel strength distribution accounts for the tendency of [emim]OAc dopes to undergo a telescope-type breach, whereas the gelatinous solution state of [TMGH]OAc dopes accounts for their poor spinnability.

Chiral ligand-modified polyoxometalates (POMs), (Bu4N)4[ﾎｳ-SiTi2W10O36(ﾎｼ-OH)2(ﾎｼ-BINOLate)], were successfully synthesized by the introduction of (R)- or (S)-BINOL into the dititanium-substituted tungstosilicate POM in an org. medium and characterized by x-ray crystallog., spectroscopy, and elemental analyses. These BINOL-modified POMs were stable in the soln. state and showed catalytic activity for asym. oxidn. of thioanisole. [on SciFinder(R)]

Minimally invasive intervention strategies after myocardial infarction use state-of-the-art catheter systems that are able to combine mapping of the infarcted area with precise, local injection of drugs. To this end, catheter delivery of drugs that are not immediately pumped out of the heart is still challenging, and requires a carrier matrix that in the solution state can be injected through a long catheter, and instantaneously gelates at the site of injection. To address this unmet need, a pH-switchable supramolecular hydrogel is developed. The supramolecular hydrogel is switched into a liquid at pH > 8.5, with a viscosity low enough to enable passage through a 1-m long catheter while rapidly forming a hydrogel in contact with tissue. The hydrogel has self-healing properties taking care of adjustment to the injection site. Growth factors are delivered from the hydrogel thereby clearly showing a reduction of infarct scar in a pig myocardial infarction model.

Although several computational modelling studies have investigated the conformational behaviour of inherently disordered protein (IDP) amylin, discrepancies in identifying its preferred solution conformations still exist between various forcefields and sampling methods used. Human islet amyloid polypeptide has long been a subject of research, both experimentally and theoretically, as the aggregation of this protein is believed to be the lead cause of type-II diabetes. In this work, we present a systematic forcefield assessment using one of the most advanced non-biased sampling techniques, Replica Exchange with Solute Tempering (REST2), by comparing the secondary structure preferences of monomeric amylin in solution. This study also aims to determine the ability of common forcefields to sample a transition of the protein from a helical membrane bound conformation into the disordered solution state of amylin. Our results demonstrated that the CHARMM22* forcefield showed the best ability to sample multiple conformational states inherent for amylin. It is revealed that REST2 yielded results qualitatively consistent with experiments and in quantitative agreement with other sampling methods, however far more computationally efficiently and without any bias. Therefore, combining an unbiased sampling technique such as REST2 with a vigorous forcefield testing could be suggested as an important step in developing an efficient and robust strategy for simulating IDPs.

Herein, we present the synthesis of ten structurally related ‘frustrated’ amphiphiles, from which were obtained eleven single crystal X-ray structures, allowing observation of the hydrogen bonding modes present in the solid state. We previously reported the synthesis of a novel amphiphilic salt which contains both hydrogen bond donating (HBD) and hydrogen bond accepting (HBA) functionalities. This amphiphilic salt was shown to self-associate in the solution state, aided by the formation of hydrogen bonds. The exact nature of the hydrogen bonding modes involved in this self-association process remains unclear due to the combination of HBD and HBA groups present in the amphiphile structure. This results in a ‘frustrated’ system with access to a variety of possible hydrogen bonding modes.

The favored (R(S)*,M*) diastereoisomer of 2-aryl-pyridine 1 in the solution state results from intramolecular dipole-dipole interactions. In the crystalline state, intermolecular interactions dominate, and the conformation switches reversibly to (R(S)*,P*). Only racemic 1 exhibits this switching property: enantiomerically pure 1 exists as the (R(S)*,M*) diastereoisomer in both the solution and crystalline state.

An isophthalate-bearing DOTA monoamide derivative has been synthesised and used to prepare a family of lanthanide complexes. Luminescence and NMR studies in solution show that the predominant form of the complexes in solution is a mono-capped square antiprism about the lanthanide centre, in which a solvent molecule occupies the ninth coordination site. The crystal structure of the terbium complex is presented and is in close agreement with the solution state data.

It is well-established that dynamics are central to protein function; their importance is implicitly acknowledged in the principles of the Monod, Wyman and Changeux model of binding cooperativity, which was originally proposed in 1965. Nowadays the concept of protein dynamics is formulated in terms of the energy landscape theory, which can be used to understand protein folding and conformational changes in proteins. Because protein dynamics are so important, a key to understanding protein function at the molecular level is to design experiments that allow their quantitative analysis. Nuclear magnetic resonance (NMR) spectroscopy is uniquely suited for this purpose because major advances in theory, hardware, and experimental methods have made it possible to characterize protein dynamics at an unprecedented level of detail. Unique features of NMR include the ability to quantify dynamics (i) under equilibrium conditions without external perturbations, (ii) using many probes simultaneously, and (iii) over large time intervals. Here we review NMR techniques for quantifying protein dynamics on fast (ps-ns), slow (μs-ms), and very slow (s-min) time scales. These techniques are discussed with reference to some major discoveries in protein science that have been made possible by NMR spectroscopy.

Complex overlapping multiplets due to scalar couplings (n)J(C-13, C-13) in fully C-13-enriched molecules can be simplified by polychromatic irradiation of selected spins. The signal intensities of the remaining non-irradiated signals are proportional to the concentrations, as shown in this work for the anomeric C-13 signals of the alpha- and beta-conformers of glucose. Homonuclear decoupling can therefore be useful for quantitative NMR studies. The resulting decoupled lineshapes show residual fine structures that have been investigated by means of numerical simulations. Simulations also show that homonuclear decoupling schemes remain effective despite inhomogeneous static fields that tend to hamper in cellulo and in vivo studies. Homonuclear decoupling schemes can be combined with dissolution DNP to obtain signal enhancements of more than four orders of magnitude. Polychromatic irradiation of selected spins does not cause significant losses of hyperpolarization of the remaining non-irradiated spins.

Dynamic nuclear polarization (DNP) has become a very important hyperpolarization method because it can dramatically increase the sensitivity of nuclear magnetic resonance (NMR) of various molecules. Liquid-state DNP based on Overhauser effect is capable of directly enhancing polarizations of all kinds of nuclei in the system. The combination of simultaneous Overhauser multi-nuclei enhancements with the multi-nuclei parallel acquisitions provides a variety of important applications in both MR spectroscopy (MRS) and image (MRI). Here we present two simple illustrative examples for simultaneously enhanced multi-nuclear spectra and images to demonstrate the principle and superiority. We have observed very large simultaneous DNP enhancements for different nuclei, such as 1H and 23Na, 1H and 31P, 19F and 31P, especially for the first time to report sodium ion enhancement in liquid. We have also obtained the simultaneous imaging of 19H and 31P at low field by solution-state DNP for the first time. This method can obtain considerably complementary structure-determination information of miscellaneous biomolecules from a single measurement. It can also be used in combination with the fast acquisition schemes and quantitative analysis with reduced scan time.

International audience; The paper concerns parallel methods for Extremal Optimization (EO) applied for processor load balancing for distributed programs. In these methods the EO approach is used which is parallelized and extended by a guided search of next solution state. EO detects the best strategy of tasks migration leading to a reduction in program execution time. We assume a parallel improvement of the EO algorithm with guided state changes which provides a parallel search for a solution based on two step stochastic selection during the solution improvement based on two fitness functions. The load balancing improvements based on EO aim at better convergence of the algorithm and better quality of program execution in terms of the execution time. The proposed load balancing algorithm is evaluated by experiments with simulated parallelized load balancing of distributed program graphs.

For the M intermediate (putative signaling state) of photoactive yellow protein, there are serious disagreements between the crystalline structure based on time-resolved Laue diffraction analysis and the solution-structure obtained from various spectroscopic studies. Here, to explore the origin of such disagreements, molecular dynamics (MD) simulation for the crystalline state is performed and the results are compared with those from MD simulation for the solution state reported previously.

We report a novel diagonal suppressed two-dimensional total correlation experiment in solution state and demonstrate its performance in 1H and 2H NMR. In DIagonal Suppressed spin echo TOtal Correlation SpectroscopY (DISTOCSY), diagonal peaks which occur around F1 = 0 in spin echo mode are removed by conversion to unobservable multiple quantum or longitudinal terms in each scan of a two scan procedure, on application of an appropriately phased 90� pulse at the time of the echo maximum. The limitation of this approach to short FID acquisition times is discussed, and an alternative two-scan version of DISTOCSY for high resolution situations is presented. � 2015 Elsevier B.V. All rights reserved.