Search

Changes in the structural dynamics of double stranded (ds)DNA upon ligand binding have been linked to the mechanism of allostery without conformational change, but direct experimental evidence remains elusive. To address this, a combination of steady state infrared (IR) absorption spectroscopy and ultrafast temperature jump IR absorption measurements has been used to quantify the extent of fast (∼100 ns) fluctuations in (ds)DNA·Hoechst 33258 complexes at a range of temperatures. Exploiting the direct link between vibrational band intensities and base stacking shows that the absolute magnitude of the change in absorbance caused by fast structural fluctuations following the temperature jump is only weakly dependent on the starting temperature of the sample. The observed fast dynamics are some two orders of magnitude faster than strand separation and associated with all points along the 10-base pair duplex d(GCATATATCC). Binding the Hoechst 33258 ligand causes a small but consistent reduction in the extent of these fast fluctuations of base pairs located outside of the ligand binding region. These observations point to a ligand-induced reduction in the flexibility of the dsDNA near the binding site, consistent with an estimated allosteric propagation length of 15 Å, about 5 base pairs, which agrees well with both molecular simulation and coarse-grained statistical mechanics models of allostery leading to cooperative ligand binding.

Malonoyl peroxide [6] is an effective reagent for the syn- or anti-oxyamination of alkenes. Reaction of [6] and an alkene in the presence of O-tert-butyl-N-tosylcarbamate (R3 = CO2tBu) leads to the anti-oxyaminated product in up to 99% yield. Use of O-methyl-N-tosyl carbamate (R3 = CO2Me) as the nitrogen nucleophile followed by treatment of the product with trifluoroacetic acid leads to the syn-oxyaminated product in up to 77% yield. Mechanisms consistent with the observed selectivities are proposed.

Transmetalation is a key method for the construction of element-element bonds. Here, we disclose the reactivity of [NiII(Ar)(I)(diphosphine)] compounds with arylgold(I) transmetalating agents, which is directly relevant to cross-coupling catalysis. Both aryl-for-iodide and unexpected aryl-for-aryl transmetalation are witnessed. Despite the strong driving force expected for Au-I bond formation, aryl scrambling can occur during transmetalation and may complicate the outcomes of attempted catalytic cross-coupling reactions.

An operationally simple E → Z isomerization of activated dienes, based on the β-ionyl motif intrinsic to retinal, is reported using inexpensive (−)-riboflavin (vitamin B2) under irradiation at 402 nm. Selective energy transfer from photoexcited (−)-riboflavin to the starting E-isomer enables geometrical isomerization. Since the analogous process with the Z-isomer is inefficient, microscopic reversibility is circumvented, thereby enabling a directional isomerization to generate the contra-thermodynamic product (up to 99% yield, up to 99:1 Z/E). Prudent choice of photocatalyst enables chemoselective isomerization to be achieved in both inter- and intramolecular systems. The principles established from this study, together with a molecular editing approach, have facilitated the development of a regioselective isomerization of a truncated triene based on the retinal scaffold.

A series of new Mg(ii) amides featuring a bulky β-diketiminate backstop ligand, has been synthesised. These complexes are demonstrated to be excellent sources of nucleophilic amides that can participate in rapid C-F activation of several fluoroarenes at room temperature or using microwave assistance, leading to the installment of synthetically important C-N bonds via nucleophilic substitution.

The processability and optoelectronic properties of organic semiconductors can be tuned and manipulated via chemical design. The substitution of the popular alkyl side chains by oligoethers has recently been successful for applications such as bioelectronic sensors and photocatalytic hydrogen evolution. Beyond the differences in polarity, the carbon–oxygen bond in oligoethers is likely to render the system softer and more prone to dynamical disorder that can be detrimental to charge transport for example. In this context, we use neutron spectroscopy as a master method of probe, in addition to characterisation techniques such as X-ray diffraction, differential scanning calorimetry and polarized optical microscopy to study the effect of the substitution of n-hexyl (Hex) chains by triethylene glycol (TEG) chains on the structural dynamics of two organic semiconducting materials: a phenylene–bithiophene–phenylene (PTTP) small molecule and a fluorene-co-dibenzothiophene (FS) polymer. Counterintuitively, inelastic neutron scattering (INS) reveals a general softening of the modes of PTTP and FS materials with Hex chains, pointing towards an increased dynamical disorder in the Hex-based systems. However, temperature-dependent X-ray and neutron diffraction as well as INS and differential scanning calorimetry evidence an extra reversible transition close to room temperature for PTTP with TEG chains. The observed extra structural transition, which is not accompanied by a change in birefringence, can also be observed by quasi-elastic neutron scattering (QENS). A fastening of the TEG chains dynamics is observed in the case of PTTP and not FS. We therefore assign this transition to the melt of the TEG chains. Overall the TEG chains are promoting dynamical order at room temperature, but if crystallising, may introduce an extra reversible structural transition above room temperature leading to thermal instabilities. Ultimately, a deeper understanding of chain polarity and structural dynamics can help guide new materials design and navigate the intricate balance between electronic charge transport and aqueous swelling that is being sought for a number of emerging organic electronic and bioelectronic applications.

International audience; Ionic liquids (ILs) are promising electrolytes for electrochemical applications due to their remarkable stability and high charge density. Molecular dynamics simulations are essential for a better understanding of the complex phenomena occurring at the electrode–IL interface. In this work, we have studied the interface between graphene and 1-ethyl-3-methyl-imidazolium tetrafluoroborate IL by density functional theory-based molecular dynamics (DFT-MD) simulations at variable surface charge densities. We have disassembled the electrical double layer potential drop into two main components: one involving atomic charges and the other dipoles. The former component arises due to the reorganization of ionic liquid and the latter due to the electronic polarization of the surface. It is related to concepts hotly debated in the literature, such as the Thomas–Fermi screening length, effective surface charge plane, and quantum capacitance.

Herein, the efficient serotonin (5-HT) sensing studies have been conducted using the (ZnO NRs)1−x(CNs)x nanocomposites (NCs) having appropriate structural and electrochemical properties. Initially, the different compositions of ZnO nanorods (NRs), with varying content of carbon nanostructures (CNs=MWCNTs and RGO), are prepared using simple in-situ wet chemical method and thereafter these NCs have been characterized for physico-chemical properties in correlation to the 5-HT sensing activity. XRD Rietveld refinement studies reveal the hexagonal Wurtzite ZnO NRs oriented in (101) direction with space group ‘P63mc’ and both orientation as well as phase of ZnO NRs are also retained in the NCs due to the small content of CNs. The interconnectivity between the ZnO NRs with CNs through different functional moieties is also studied using FTIR analysis; while phases of the constituents are confirmed through Raman analysis. FESEM images of the bare/NCs show hexagonal shaped rods with higher aspect ratio (4.87) to that of others. BET analysis and EIS measurements reveal the higher surface area (97.895 m2/g), lower charge transfer resistance (16.2 kΩ) for the ZCNT 0.1 NCs to that of other NCs or bare material. Thereafter, the prepared NCs are deposited on the screen printed carbon electrode (SPCE) using chitosan as cross-linked agent for 5-HT sensing studies; conducted through cyclic voltammetry (CV) and square wave voltammetry (SWV) measurements. Among the various composites, ZCNT0.1 NCs based electrodes exhibit higher sensing activity towards 5-HT in accordance to its higher surface area, lower particle size and lower charge transfer resistance. SWV measurements provide a wide linear response range (7.5–300 μM); lower limit of detection (0.66 μM), excellent limit of quantification (2.19 μM) and good reproducibility to ZCNT 0.1 NCs as compared to others for 5-HT sensing studies.

The liquid-liquid transition in supercooled liquid water, predicted to occur around 220 K, is controversial due to the difficulty of studying it caused by competition from ice crystallization (the so-called "no man's land"). In aqueous solutions, it has been predicted to give rise to phase separation on a nanometer scale between a solute-rich high-density phase and a water-rich low-density phase. Here we report direct experimental evidence for the formation of a nanosegregated phase in eutectic aqueous solutions of LiCl and LiSCN where the presence of crystalline water can be experimentally excluded. Femtosecond infrared and Raman spectroscopies are used to determine the temperature-dependent structuring of water, the solvation of the SCN- anion, and the size of the phase segregated domains.

The Community Bureau of Reference (BCR) four-step sequential extraction has been adapted for fractionation of potentially toxic elements (PTE) in simulant airborne particulate matter (APM) samples presented on 47 mm filter dynamics measurement system (FDMS) filters as used in routine air quality monitoring. Simulants were prepared from an urban soil reference material and from BCR CRM 701, which is certified for analytes extractable by the BCR procedure. Analysis was performed by inductively coupled plasma mass spectrometry using an Agilent 7700x instrument. Fractionation patterns similar to the full-scale protocol were obtained when test portions as small as 0.0625 g were extracted in 2–3 mL of reagents. However, changing the extraction vessel used was found to affect the outcome. This highlights the operational nature of sequential extraction procedures and the need carefully to evaluate the effects of procedural modifications. When the method developed was applied to blank FDMS filters, large amounts of Zn were detected, especially in step 3, the oxidisable fraction, and step 4, the residual fraction. Despite this, following blank-correction, fractionation patterns similar to certified values were obtained for BCR CRM 701, with overall recoveries (∑(steps 1–4)) of 84.2-113%. Given the increased awareness of public health risks associated with poor air quality, a sequential extraction procedure specifically designed for use with APM samples collected during routine air quality represents a valuable tool for use in source apportionment and to improve understanding of human exposure to PTE through inhalation.

In this work, we describe the development of a computational screening approach for tripeptide-dipeptide co-assembly. Studies are carried out both in water and in oil–water mixtures, to evaluate possible candidates that give rise to hydrogels or more stable emulsions, respectively, through nanofibre formation. The results give rise to design rules for the identification of promising systems for numerous types of soft materials. The possibility of achieving innovative functional materials through the co-assembly of tripeptides and dipeptides is studied. In particular, coarse-grained simulations allowed for the extraction of some promising dipeptides that, together with H-aspartyl-phenylalanyl-phenylalanine-OH (DFF), are able to act as hydrogelators or emulsifiers with superior characteristics relative to DFF on its own.

Reduction of nitrobenzene by excess organic electron donor, 12, affords diphenylhydrazine in a reaction where azobenzene oxide and azobenzene are likely intermediates. No cleavage of the N-N σ-bond is seen under photoactivation conditions, whereas traces are seen under thermal activation. Hydrazone derivatives were prepared to explore the cleavage of N-N σ-bonds; the results show that a low-lying LUMO assists the transition state for accepting an electron, and the stabilisation that the potential fragments from N-N bond cleavage afford to the fragments is important in determining whether cleavage is observed.

The focus of this review is to provide an overview of the field of organocatalysed photoredox chemistry relevant to synthetic medicinal chemistry. Photoredox transformations have been shown to enable key transformations that are important to the pharmaceutical industry. This type of chemistry has also demonstrated a high degree of sustainability, especially when organic dyes can be employed in place of often toxic and environmentally damaging transition metals. The sections are arranged according to the general class of the presented reactions and the value of these methods to medicinal chemistry is considered. An overview of the general characteristics of the photocatalysts as well as some electrochemical data is presented. In addition, the general reaction mechanisms for organocatalysed photoredox transformations are discussed and some individual mechanistic considerations are highlighted in the text when appropriate.

Ligand metathesis of Pd(II) complexes is mechanistically essential for cross-coupling. We present a study of halide→OH anion metathesis of (Ar)Pd(II) complexes using vinylBPin as a bifunctional chemical probe with Pd(II)-dependent cross-coupling pathways. We identify the variables that profoundly impact this event and allow control to be leveraged. This then allows control of cross-coupling pathways via promotion or inhibition of organoboron transmetalation, leading to either Suzuki-Miyaura or Mizoroki-Heck products. We show how this transmetalation switch can be used to synthetic gain in a cascade cross-coupling/Diels-Alder reaction, delivering borylated or non-borylated carbocycles, including steroid-like scaffolds.

Spatially offset Raman spectroscopy (SORS) provides chemical analysis at depth even when obscuring barriers such as plastic or tissue are present. As the collection probe is moved further away from the point of laser excitation, scattered photons from deeper layers begin to dominate the acquired spectra, thus giving rise to through barrier detection. Here, we demonstrate the potential of conventional Raman (CR) and SORS for through barrier detection using handheld spectrometers. We report the collection of Raman signals from an ethanol solution through plastic at thicknesses of up to 21 mm using SORS in combination with multivariate analysis. SORS is compared to CR, where we also demonstrate impressive through barrier detection of ethanol at depths up to 9 mm. We also highlight the advantage of applying multivariate analysis for through barrier detection using CR or SORS, particularly when peaks with similar spectral features are present in both the barrier and analyte spectra. In addition, to the best of our knowledge, this is the first report of the assessment of the maximum level of through barrier detection using handheld CR and SORS instruments with a backscattering geometry.

Designing molecular disorder Melanins are a group of natural pigments that are the primary factor affecting skin color. Lampel et al. examined a family of melanin-inspired materials based on tripeptides containing tyrosine as precursors for polymeric pigments. They found that the supramolecular organization of the tripeptide assembly is the most important factor for the enzymatic oxidation, with the position of the tyrosine residue playing a dominant role. Thus, simply juggling the order of the peptides allowed tuning of the optical and electrical properties of the resulting polymers. Science , this issue p. 1064

Nanozymes are metal nanoparticles with catalytic properties that can be used to oxidise peroxidase substrates giving a colorimetric response which can be detected using UV-vis, and recently, Raman spectroscopy. Due to their ease of synthesis and increased stability, nanozymes are being increasing investigated to replace conventional enzymes for the detection of biomolecules. Here we exploit the catalytic activity of iron oxide (Fe2O3) nanoparticles combined with the substrate 2,2-Azinobis(3-ethyl-benzothiazoline-6-sulfonic acid) (ABTS) in a decolourisation assay for the detection of antioxidants. Fe2O3 nanoparticles were used to catalyse the oxidation of ABTS to its green radical cation which, upon the addition of an antioxidant, resulted in a decolourisation due to the reduction of the radical cation caused by the hydrogen donating antioxidant. The assay was applied for the detection of multiple antioxidants (glutathione, chlorogenic acid and ascorbic acid), and was followed by monitoring the resonance Raman scattering from the ABTS solution using a portable Raman system with 785 nm laser excitation. This novel assay has the potential to be optimised to detect antioxidant activity in body fluid with low limits of detection with point of use monitoring.

The fluorescent dye 8-hydroxypyrene-1,3,6-trisulfonate (pyranine) combines high photostability with ratiometric pH detection in the physiological range, making it a prime candidate for optical sensors in biomedical applications, such as pH-based chronic wound monitoring. However, pyranine's high water solubility and the difficulty of covalent attachment pose severe limitations in terms of leaching from sensor matrices. Herein, pyranine-modified nanophase-separated amphiphilic polymer conetworks (APCNs) are reported as fluorescent ratiometric pH sensors. The thin, freestanding APCN membranes composed of one hydrophilic and one hydrophobic polymer provide an optically transparent, flexible, and stable ideal matrix that enables contact between dye and aqueous environment. An active ester-based conjugation approach results in a highly homogeneous and stable pyranine modification of the APCN's hydrophilic phase. This concept effectively solves the leaching challenge for pyranine without compromising its functionality, which is demonstrated by ratiometric pH detection in the range of pH 5-9.

Fourier transform-infrared spectroscopy (FT-IR) represents an attractive molecular diagnostic modality for translation to the clinic, where comprehensive chemical profiling of biological samples may revolutionize a myriad of pathways in clinical settings. Principally, FT-IR provides a rapid, cost-effective platform to obtain a molecular fingerprint of clinical samples based on vibrational transitions of chemical bonds upon interaction with infrared light. To date, considerable research activities have demonstrated competitive to superior performance of FT-IR strategies in comparison to conventional techniques, with particular promise for earlier, accessible disease diagnostics, thereby improving patient outcomes. However, amidst the changing healthcare landscape in times of aging populations and increased prevalence of cancer and chronic disease, routine adoption of FT-IR within clinical laboratories has remained elusive. Hence, this perspective shall outline the significant clinical potential of FT-IR diagnostics and subsequently address current barriers to translation from the perspective of all stakeholders, in the context of biofluid, histopathology, cytology, microbiology, and biomarker discovery frameworks. Thereafter, future perspectives of FT-IR for healthcare will be discussed, with consideration of recent technological advances that may facilitate future clinical translation.

The discovery of the enhancement of Raman scattering by molecules adsorbed on nanostructured metal surfaces is a landmark in the history of spectroscopic and analytical techniques. Significant experimental and theoretical effort has been directed toward understanding the surface-enhanced Raman scattering (SERS) effect and demonstrating its potential in various types of ultrasensitive sensing applications in a wide variety of fields. In the 45 years since its discovery, SERS has blossomed into a rich area of research and technology, but additional efforts are still needed before it can be routinely used analytically and in commercial products. In this Review, prominent authors from around the world joined together to summarize the state of the art in understanding and using SERS and to predict what can be expected in the near future in terms of research, applications, and technological development. This Review is dedicated to SERS pioneer and our coauthor, the late Prof. Richard Van Duyne, whom we lost during the preparation of this article., Funding is acknowledged from the European Research Council (ERC Advanced Grant No. 787510-4DBIOSERS to L.M.L.-M., ERC Advanced Grant No. 789104-eNANO to F.J.G.A., ERC Starting Grant No. 259432-MULTIBIOPHOT to J.K., ERC Consolidator Grant No. 772108-DarkSERS); the Department of Education of the Basque Government (Grant No. IT1164-19 to J.A.); the Spanish MINECO (CTQ2017-88648-R to R.A.-P., MAT2016-77809-R to I.P.-S. and J.P.-J.); the EPSRC (EP/P034063/1 to S.B., EP/L027151/1 to J.B., EP/L014165/1 to D.G. and K.F.); IDUN-Danish National Research Foundation (DNRF122) and Villum Fonden (Grant No. 9301) to A.B.; the National Research Foundation of Korea (Grant No. 2019R1A2C3004375 to J.B.); the German Science Foundation, DFG (SFB 1278 Polytarget (Project B4) to V.D., Grant No. SCHL 594/13-1 to S.S., Germany’s Excellence Strategy (EXC 2089/1-390776260) to S.M.); the Federal Ministry of Education and Research, Germany (BMBF) (Grant InfectoGnostics 13GW0096F to D.C.-M. and J.P.); DARPA-16-35-INTERCEPT-FP-018 to L.F.; the UK BBSRC (Grant No. BB/L014823/1 to R.G.); the Department of Science and Technology (DST Nanomission Project SR/NM/NS-23/2016 to K.G.T.); the U.S. National Science Foundation (Grant No. CHE-1707859 to A.J.H., Center for Sustainable Nanotechnology CHE-1503408 (Centers for Chemical Innovation Program) to C.L.H., Center for Chemical Innovation Chemistry at the Space-Time Limit (CaSTL) CHE-1414466 to G.C.S. and R.P.V.D., Grant No. CHE-1807269 to K.A.W.); the Knut and Alice Wallenberg Foundation to M.K.; the Office of Naval Research (Grant No. N00014-18-1-2876 to N.A.K.); Royal Society of New Zealand Te Apa̅rangi to E.L.R. and B.A.; Singapore Ministry of Education, Tier 1 (RG11/18) to X.Y.L.; the Photoexcitonix Project in Hokkaido Univ., Japan, to K.M.; BioNano Health-Guard Research Center funded by the Ministry of Science and ICT (MSIT) of Korea as Global Frontier Project (Grant No. H-GUARD_2013M3A6B2078947) to J.-M.N.; NSFC of P. R. China (Grant No. 21705015 to Y.O., Grant No. 21633005 to B.R.); National Key R&D Program (2017YFA0206902) to C.X. This work was coordinated under the Maria de Maeztu Units of Excellence Program from the Spanish State Research Agency—Grant No. MDM-2017-0720.

Main group bimetallic complexes, while being increasingly used in stoichiometric deprotonation and metal–halogen exchange reactions, have not yet made a significant impact in catalytic applications. This paper explores the ability of alkali metal magnesiates to catalyse the intermolecular hydroamination of alkynes and alkenes using sytrene and diphenylacetylene as principle setting model substrates. By systematically studying the role of the alkali–metal and the formulation of the heterobimetallic precatalyst, this study establishes higher order potassium magnesiate [(PMDETA)2K2Mg(CH2SiMe3)4] (7) as a highly effective system capable of catalysing hydroamination of styrene and diphenylacetylene with several amines while operating at room temperature. This high reactivity contrasts with the complete lack of catalytic ability of neutral Mg(CH2SiMe3)2, even when harsher reaction conditions are employed (24 h, 80 °C). A pronounced alkali metal effect is also uncovered proving that the alkali metal (Li, Na, or K) is not a mere spectating counterion. Through stoichiometric reactions, and structural and spectroscopic (DOSY NMR) investigations we shed some light on the potential reaction pathway as well as the constitution of key intermediates. This work suggests that the enhanced catalytic activity of 7 can be rationalised in terms of the superior nucleophilic power of the formally dianionic magnesiate {Mg(NR2)4}2− generated in situ during the hydroamination process, along with the ability of potassium to engage in π-interactions with the unsaturated organic substrate, enhancing its susceptibility towards a nucleophilic attack by the amide anion.

Lysozyme is one of the most commonly used proteins for encapsulating gold nanoclusters, yielding Ly-AuNC complexes. While possible applications of Ly-AuNCs in environmental, biological and trace metal sensing in solution have been demonstrated, there is currently a poor understanding of the physical characteristics of the Ly-AuNC complex. In this study we have employed fully atomistic molecular dynamics simulations to gain an understanding of the formation of Au clusters within the protein. It was found that in order to form AuNCs in the simulations, an approach of targeted insertion of Au atoms at a critical surface residue was needed. Tyrosine is known to be crucial for the reduction of Au salts experimentally, and our simulations showed that Tyr20 is the key residue for the formation of an AuNC beneath the protein surface in the α-helical domain. It is hoped these observations will aid future improvements and modification of Ly-AuNCs via alterations of the alpha-helix domain or Tyr20.

This study establishes a new trans‐metal‐trapping (TMT) procedure based on a mixture of LiTMP (the base) and tris(trimethylsilylmethyl)gallium [Ga(CH2SiMe3)3, GaR3] (the trap) that, operating in a tandem manner, is effective for the regioselective deprotonation of sensitive diazines in hydrocarbon solution, as illustrated through reactions of pyrazine, pyridazine, and pyrimidine, as well as through the N‐S heterocycle benzothiazole. The metallo‐activated complexes of all of these compounds were isolated and structurally defined.

Aromatic peptide amphiphiles are known to self-assemble into nanostructures but the molecular level structure and the mechanism of formation of these nanostructures is not yet understood in detail. Molecular dynamic simulations using the CHARMM force field have been applied to a wide variety of peptide-based systems to obtain molecular level details of processes that are inaccessible with experimental techniques. However, this force field does not include parameters for the aromatic moieties which dictate the self-assembly of these systems. The standard CHARMM force field parameterization protocol uses hydrophilic interactions for the non-bonding parameters evaluation. However, to effectively reproduce the self-assembling behaviour of these molecules, the balance between the hydrophilic and hydrophobic nature of the molecule is essential. In this work, a modified parameterization protocol for the CHARMM force field for these aromatic moieties is presented. This protocol is applied for the specific case of the Fmoc moiety. The resulting set of parameters satisfies the conformational and interactions analysis and is able to reproduce experimental results such as the Fmoc-S-OMe water/octanol partition free energy and the self-assembly of Fmoc-S-OH and Fmoc-Y-OH into spherical micelles and fibres, respectively, while also providing detailed information on the mechanism of these processes. The effectiveness of the parameters for the Fmoc moiety validates the protocol as a robust approach to paramterise this class of compounds.

Hydrogen atom transfer-mediated intramolecular C-C coupling reactions between alkenes and nitriles, using PhSiH3 and catalytic Fe(acac)3 , are described. This introduces a new strategic bond disconnection for ring-closing reactions, forming ketones via imine intermediates. Of note is the scope of the reaction, including formation of sterically hindered ketones, spirocycles and fused cyclic systems.

In this work, we present a new method for predicting complex physicalchemical properties of organic molecules. The approach utilizes 3D convolutional neural network (ActivNet4) that uses solvent spatial distributions around solutes as input. These spatial distributions are obtained by a molecular theory called threedimensional reference interaction site model (3D-RISM). We have shown that the method allows one to achieve a good accuracy of prediction of bioconcentration factor (BCF) which is difficult to predict by direct application of methods of molecular theory or simulations. Our research demonstrates that combination of molecular theories with modern machine learning approaches can be effectively used for predicting properties that are otherwise inaccessible to purely theory-based models.

International audience; In-solution small-angle X-ray and neutron scattering (SAXS/SANS) have become popular methods to characterize the structure of membrane proteins, solubilized by either detergents or nanodiscs. SANS studies of protein-detergent complexes usually require deuterium-labeled proteins or detergents, which in turn often lead to problems in their expression or purification. Here, we report an approach whose novelty is the combined analysis of SAXS and SANS data from an unlabeled membrane protein complex in solution in two complementary ways. First, an explicit atomic analysis, including both protein and detergent molecules, using the program WAXSiS, which has been adapted to predict SANS data. Second, the use of MONSA which allows one to discriminate between detergent head- and tail-groups in an ab initio approach. Our approach is readily applicable to any detergent-solubilized protein and provides more detailed structural information on protein-detergent complexes from unlabeled samples than SAXS or SANS alone.

Ten isostructural single-crystal diffraction studies of mixed cation Ca/Sr salt forms of the salicylate anion are presented, namelycatena-poly[[diaquacalcium(II)/strontium(II)]-bis(μ2-2-hydroxybenzoato)], [Ca1–xSrx(C7H5O3)2(H2O)2]n, wherex= 0, 0.041, 0.083, 0.165, 0.306, 0.529, 0.632, 0.789, 0.835 and 1. The structure of an isostructural Sr/Ba species, namelycatena-poly[[diaquastrontium(II)/barium(II)]-bis(μ2-2-hydroxybenzoato)], [Sr0.729Ba0.271(C7H5O3)2(H2O)2], is also described. The Ca/Sr structures form a series where, with increasing Sr content, the unit cell expands in both the crystallographicaandcdirections (by 1.80 and 3.18%, respectively), but contracts slightly in thebdirection (−0.31%). The largest percentage structural expansion lies parallel to the direction of propagation of the one-dimensional coordination polymer that is the primary structural feature. This structural expansion is thus associated with increasedM—O distances. Aqueous solubility measurements show that solubility generally increases with increasing Sr content. Thus, tuning the composition of these mixed counter-ion salt forms leads to systematic structural changes and allows solubility to be tuned to values between those for the pure Ca and Sr species.

An NMR spectroscopic study has been conducted into the reactivity of alkali metal benzyls [M(CH2Ph)], (M = Li, Na, K) with lanthanide tris(amide) complexes [Ln(N″)3] (Ln = Y, Ce, Nd; N″ = N(SiMe3)2) and [Ce(TMP)3] (TMP = 2,2,6,6-tetramethylpiperidide). It was found that for [Ln(N″)3], benzyl adducts [M][Ln(N″)3(CH2Ph)] were initially formed, and the molecular structure for M = Li(TMEDA)2 and Ln = Nd was determined revealing a distorted tetrahedral [Nd(N″)3(CH2Ph)] anion. In all cases, these adduct complexes were unstable, intramolecularly deprotonating a methyl arm of a N″ ligand via benzyl basicity and eliminating toluene to prepare cyclometallated complexes of the form [M][Ln(N″)2{κ2-CH2Si(Me)2N(SiMe3)}]. In parallel studies, reactions of [Li(Ph)] with [Ln(N″)3] (Ln = Ce, Nd) afforded [Li(N″)], whilst for (Ln = Y) adduct formation was observed. [Ce(TMP)3] did not generate any characterisable bimetallic adducts. The reaction of [Li(Ph)] with [Li(TMP)] afforded the hexanuclear [{Li(TMP)}2{Li(μ-Ph)}]2, which features lithium in three different coordination environments.

Successful pathogen detection is crucial for public health as the threat of infectious disease is dramatically increasing globally due to bacteria developing resistance to many anti-microbial drugs. The increase in bacterial infections has led to urgent demands for simpler, faster and more reliable detection methods to be developed, so that the most appropriate therapy can be provided. Surface enhanced Raman scattering (SERS) is an analytical technique which has gained a great deal of interest for biosensing due to its sensitivity, selectivity and multiplexing capabilities. A new bionanosensor has been developed for the isolation and detection of multiple bacterial pathogens via magnetic separation and SERS. This novel assay format involves using lectin functionalised magnetic nanoparticles for capture and isolation of bacteria from the sample matrix followed by specifically detecting bacterial pathogens using SERS active nanoparticles functionalised with antibodies which are strain specific. Therefore, the sample is captured using a ‘magnetic plug’ and interrogated with a laser allowing simple and fast optical detection. Three bacterial pathogens – Escherichia coli, Salmonella typhimurium and methicillin-resistant Staphylococcus aureus – were successfully isolated and detected, with the lowest concentration for each of the strains detected at just 101 colony forming units per mL (CFU/mL). In addition to single pathogen detection, a mixture of all three bacterial strains were isolated and identified within the same sample matrix using SERS with the triplex detection also being confirmed using principal component analysis. Herein, we demonstrate that this multiplexed bionanosensor is capable of providing rapid and sensitive discrimination of bacterial pathogens both individually, and within a multiplex system, offering opportunities for future point of care devices and advancements in bio-medical applications.

The Friedel–Crafts reaction ( 1 ), named after its respective French and American pioneers, has long been used to attach alkyl groups to aromatic rings. This reaction is an electrophilic aromatic substitution. Electrophiles are electron-poor species, whereas nucleophiles are electron-rich species. Electron-rich aromatic molecules such as benzene can use their surplus of electrons to react with electron-poor, positively charged species, enabling benzene to exchange one of its hydrogen atoms for the electrophilic group to make a new, substituted benzene. Because “like species repel,” electron-rich species should not react with other electron-rich species, so benzene should never undergo direct nucleophilic alkylation. Nonetheless, on page [1168][1] of this issue, Wilson et al. ( 2 ) report the facile nucleophilic alkylation of benzene accomplished through highly reactive alkylcalcium nucleophiles. [1]: /lookup/doi/10.1126/science.aao5923

We report that gold-coated nanodisk arrays of nearly micron periodicity have high figure of merit (FOM) and sensitivity necessary for plasmonic refractometric sensing, with the added benefit of suitability for surface-enhanced Raman scattering (SERS), large scale microfabrication using standard photolithographic techniques and a simple instrumental setup. Gold nanodisk arrays were covered with a gold layer to excite the Bragg modes (BM) which are the propagative surface plasmons localized by the diffraction from the disk array. This generated surface-guided modes, localized as standing waves, leading to highly confined fields confirmed by a mapping of the SERS intensity and numerical simulations with 3D finite element method (3D FEM). The optimal gold-coated nanodisk arrays were applied for refractometric sensing in transmission spectroscopy with better performance than nanohole arrays and they were integrated to a 96-well plate reader for detection of IgY proteins in the nM range in PBS. The potential for sensing in biofluids was assessed with IgG detection in 1:1 diluted urine. The structure exhibits a high FOM of up to 46, exceeding the FOM of structures supporting surface plasmon polaritons (SPPs) and comparable to more complex nanostructures, demonstrating that sub-wavelength features are not necessary for high performance plasmonic sensing.

Artificial enzymes have become an increasingly interesting area of research due to their many advantages over natural protein enzymes which are expensive, difficult to isolate and unable to stand harsh environments. An important area of this research involves using metal nanoparticles as artificial enzymes, known as nanozymes, which exhibit peroxidase-like activity enabling them to catalyse the oxidation of substrates such as 3,3′,5,5′-tetramethylbenzidine (TMB) in the presence of hydrogen peroxide (H2O2), giving a colorimetric response. Here we exploit the catalytic activity of silver nanoparticles (Ag NPs) in a surface based silver-linked immunosorbent assay (SLISA) to detect human C-reactive protein (CRP), an inflammatory marker. Ag NPs were conjugated to antibodies with specific recognition for the corresponding target antigenic molecule, CRP, and the Ag NPs were used to catalyse the oxidation of TMB by H2O2. The resulting coloured oxidation product was detected using SERRS. We demonstrate that Ag NPs can replace the enzymes used in a conventional ELISA and a detection limit of 1.09 ng mL−1 of CRP can be achieved. It indicates the promise for SLISAs for biomarker detection and opens the way for further assays of this nature to be created. This novel assay has the potential to be optimised to detect lower levels of CRP and can be further extended for the sensitive and specific detection of other relevant biomarkers.

The number of newly discovered Metal-Organic Frameworks is growing exponentially. Molecular simulation is becoming increasingly important to screen large databases of structures and identify potential candidates for challenging gas separations, but such efforts rely on the availability of accurate molecular models that can predict adsorption in a wide range of different MOFs. MOFs with co-ordinatively unsaturated sites (CUS) pose particular problems because standard force fields are unable to describe their specific interactions with certain adsorbates. In this paper, we demonstrate that our previous approach to describe adsorption in open metal sites, based on a combination of classical Monte Carlo simulations and quantum-mechanical Density Functional Theory calculations, is transferable to several Cu-containing MOFs. By fitting the parameters of our model to match adsorption energies of ethylene on HKUST-1 and transferring them to the Cu-paddlewheel units of other MOFs, we have obtained predictions in good agreement with experimental adsorption measurements. Where agreement is not as satisfactory, we show that this can be explained by limited accessibility or diffusion through the pore network. For one particular MOF, UMCM-150, we show that separate parameters need to be used for the Cu-trimer unit, for which the interaction energies with ethylene are much lower than in the Cu-paddlewheel. Overall, our approach demonstrates that the specific CUS interactions in MOFs can be parameterised separately from other interaction types, such as van der Waals, thus opening the way for the development of an accurate and fully transferable force field for this class of materials.

We demonstrate that using a pressure corrected three-dimensional reference interaction site model one can accurately predict salting-out (Setschenow's) constants for a wide range of organic compounds in aqueous solutions of NaCl. The approach, based on classical molecular force fields, offers an alternative to more heavily parametrized methods. Published by AIP Publishing.

Simple smectic A liquid crystal phases with different types of prescribed orientational distribution functions have been simulated and compared in order to study the possibility to distinguish between the Maier-Saupe type and cone-like orientational distributions using the popular method of Davidson et al. [J. Phys. II 5, 113 (1995)]. This method has been used to extract the orientational distribution functions from simulated diffraction patterns, and the results have been compared with actual distribution functions which have been prescribed during simulations. It has been shown that it is indeed possible to distinguish between these two qualitatively different types of orientational distribution already from the shape of the 2D diffraction pattern. Moreover, typical experimental diffraction patterns for “de Vries”-type smectic liquid crystals appear to be close to the ones which have been simulated using the prescribed Maier-Saupe orientational distribution function.

Despite progress, a fundamental understanding of the relationships between the molecular structure and self-assembly configuration of Fmoc-dipeptides is still in its infancy. In this work, we provide a combined experimental and computational approach that makes use of free energy equilibration of a number of related Fmoc-dipeptides to arrive at an atomistic model of Fmoc-threonine-phenylalanine-amide (Fmoc-TF-NH2) which forms twisted fibres. By using dynamic peptide libraries where closely related dipeptide sequences are dynamically exchanged to eventually favour the formation of the thermodynamically most stable configuration, the relative importance of C-terminus modifications (amide versus methyl ester) and contributions of aliphatic versus aromatic amino acids (phenylalanine F vs. leucine L) is determined (F > L and NH2 > OMe). The approach enables a comparative interpretation of spectroscopic data, which can then be used to aid the construction of the atomistic model of the most stable structure (Fmoc-TF-NH2). The comparison of the relative stabilities of the models using molecular dynamic simulations and the correlation with experimental data using dynamic peptide libraries and a range of spectroscopy methods (FTIR, CD, fluorescence) allow for the determination of the nanostructure with atomistic resolution. The final model obtained through this process is able to reproduce the experimentally observed formation of intertwining fibres for Fmoc-TF-NH2, providing information of the interactions involved in the hierarchical supramolecular self-assembly. The developed methodology and approach should be of general use for the characterization of supramolecular structures.

Three simple semiconducting acceptor–donor–acceptor (A–D–A) small molecules based on an electron-rich (3,4-ethylenedioxythiophene) EDOT central core have been synthesised (DIN-2TE, DRH-2TE, DECA-2TE) and characterised. Organic photovoltaic (OPV) devices incorporating these materials have been prepared and evaluated. The physical properties of the molecules were characterised by TGA, DSC, UV/vis spectroscopy and cyclic voltammetry. The optical HOMO–LUMO energy gaps of the molecules in the solid state were in the range 1.57–1.82 eV, and in solution 1.88–2.04 eV. Electrochemical HOMO–LUMO energy gaps determined by cyclic voltammetry were found to be in the range 1.97–2.31 eV. The addition of 1% 1,8-diiodooctane (DIO) to photoactive blends of the A–D–A molecules and PC71BM more than doubled the power conversion efficiency (PCE) in the case of DRH-2TE:PC71BM devices to 1.36%.

The search for new fluorescent molecules is vital to the advancement of molecular imaging and sensing for the benefit of medical and biological studies. One such class of new fluorescent molecule is fluorescent gold nanoclusters encapsulated in Human Serum Albumin (HSA-AuNC). In order to use this new fluorescent molecule as a sensor or fluorescent marker in biological imaging both in vitro and in vivo it is important to understand whether/how the proteins function is changed by the synthesis and presence of the gold nanoclusters inside the protein. Natural HSA acts as the main drug carrier in the blood stream, carrying a multitude of molecules in two major binding sites (Sudlow I and II). To test the effects of gold on the ability of HSA to act as a drug carrier we employed warfarin, an anticoagulant drug, as a fluorescent probe to detect changes between natural HSA and HSA-AuNCs. AuNCs are found to inhibit the take up of warfarin by HSA. Evidence for this is found from fluorescence spectral and lifetime measurements. Interestingly, the presence of warfarin bound to HSA also inhibits the formation of gold nanoclusters within protein. This research provides valuable insight into how protein function can change upon synthesis of AuNCs and how that will affect their use as a fluorescent probe.

Encapsulation of subsite analogues of the [FeFe]-hydrogenase enzymes in supramolecular structures has been shown to dramatically increase their catalytic ability, but the molecular basis for this enhancement remains unclear. We report the results of experiments employing infrared absorption, ultrafast infrared pump-probe, and 2D-IR spectroscopy to investigate the molecular environment of Fe2(pdt)(CO)6 (pdt: propanedithiolate) [1] encapsulated in the dispersed alkane phase of a heptane-dodecyltrimethylammonium bromide-water microemulsion. It is demonstrated that 1 is partitioned between two molecular environments, one that closely resembles bulk heptane solution and a second that features direct hydrogen-bonding interactions with water molecules that penetrate the surfactant shell. Our results demonstrate that the extent of water access to the normally water-insoluble subsite analogue 1 can be tuned with micelle size, while IR spectroscopy provides a straightforward tool that can be used to measure and fine-tune the chemical environment of catalyst species in self-assembled structures.

This article reviews the application of transient techniques in the elucidation of electron, proton and photon chemistry related to the catalytic subsite of [FeFe]-hydrogenase from the perspective of research in this area carried out at the UEA and Strathclyde laboratories. The detection of mixed valence states, bridging CO intermediates, paramagnetic hydrides and coordinatively unsaturated species has both informed an understanding of the biological catalysis and stimulated the search for stable analogues of key structural motifs likely involved in turnover states.

We describe a photonic waveguide where FRET is routed uni-directionally along a double-stranded DNA track. The efficiency of FRET is modulated by the supramolecular control of fluorophores along double-stranded DNA using fluorophore-tethered Pyrrole-Imidazole polyamides (PAs). We show that uni-directional FRET is enhanced by the complete assembly of each of the constituent parts, resulting in the selective routing of light along simple DNA duplexes as well as a three-way junction (3WJ).

Anodically bonded etched silicon microfluidic devices that allow infrared spectroscopic measurement of solutions are reported. These extend spatially well-resolved in situ infrared measurement to higher temperatures and pressures than previously reported, making them useful for effectively time-resolved measurement of realistic catalytic processes. A data processing technique necessary for the mitigation of interference fringes caused by multiple reflections of the probe beam is also described.

Water soluble positively charged 2-(dimethylamino) ethanethiol (DAET)-protected core-shell CdSe/ZnS quantum dots (QDs) were synthesized and incorporated within negatively charged Nafion polymer films. The water soluble QDs were characterized using UV-visible and fluorescence spectroscopies. Nafion/QDs composite films were deposited on glassy carbon electrodes and characterized using cyclic voltammetry. The electrochemiluminescence (ECL) using hydrogen peroxide as co-reactant was enhanced for Nafion/QDs composite films compared to films of the bare QDs. Significantly, no ECL was observed for Nafion/QDs composite films when peroxydisulfate was used as the co-reactant, suggesting that the permselective properties of the Nafion effectively exclude the co-reactant. The ECL quenching by glutathione depends linearly on its concentration when hydrogen peroxide is used as the co-reactant, opening up the possibility to use Nafion/QDs composite films for various electroanalytical applications.

The ability to accurately and sensitively measure the activity of specific enzymes is central to many aspects of modern chemistry and when combined with new nanoscience based approaches, offers significant opportunities for advancing other scientific disciplines. We review the development of surface enhanced resonance Raman scattering (SERRS) for the detection of enzymes, from the initial direct spectroscopy of enzymes, substrate/product and inhibitors adsorbed onto metallic colloids, to the current approach of measuring enzymatic activity by recording the SERRS spectra of a product which is only 'switched on' after enzyme activity. Developments focussed on improvements to modular masked SERRS substrates, which are unmasked by specific enzymes, are also reviewed. Finally, we set out the remaining grand challenges within the area of enzymatic analysis by SERRS which include single molecule detection, in vivo studies and increased multiplexing for screening of evolved enzyme libraries.

Diffusion of Ti through the TiO(2)(110) rutile surface plays a key role in the growth and reactivity of TiO(2). To understand the fundamental aspects of this important process, we present an analysis of the diffusion of Ti ad-species at the stoichiometric TiO(2)(110) surface using complementary computational methodologies of density functional theory corrected for on-site Coulomb interactions (DFT + U) and a charge equilibration (QEq) atomistic potential to identify minimum energy pathways. We find that diffusion of Ti from the surface to subsurface (and vice versa) follows an interstitialcy exchange mechanism, involving exchange of surface Ti with the 6-fold coordinated Ti below the bridging oxygen rows. Diffusion in the subsurface between layers also follows an interstitialcy mechanism. The diffusion of Ti is discussed in light of continued attempts to understand the re-oxidation of non-stoichiometric TiO(2)(110) surfaces.

Classical MD simulations for surfactant-bromide-water solutions containing several organosilicate precursors show that the presence or absence of molecular-scale periodicity in the pore walls of PMOs is dictated by the strength of the surfactant micelle-organosilica interaction and by the relative flexibility and orientation of the organic linker.