Improving the Interpretation of Small Molecule Diffusion Coefficients

Investigation of the Formation of Squalene Oligomers Exposed to Ultraviolet Light and Changes in the Exposed Squalene as a Potential Skin Model

UV-induced oligomerisation of squalene was undertaken to indicate the potential for squalene-containing biological systems to exhibit rheology changes. DOSY NMR enabled the determination of the molecular weight (MW) range using Stokes–Einstein Gierer–Wirtz Estimation (SEGWE Calculator, University of Manchester). This approach was validated by Atmospheric Solids Analysis Probe Time of Flight Mass Spectrometry (ASAP TOF MS). To demonstrate the principle, both benzoyl peroxide and AIBN were used, separately, to initiate rapid, radical oligomerisation. Subsequent experiments in the absence of initiators compared the influence of UV wavelength and time on the resulting oligomer formation. To further model a relevant biological implication of this potentially chaotic UV oligomerisation, both saturated and unsaturated free fatty acids were added to squalene and exposed to UV at 285 nm and 300 nm to determine if cross oligomerisation could be observed. This representation of sebum evidenced the formation of a distribution of higher MW oligomers. Internal viscosity was normalised using the DMSO solvent, but to confirm that changes in rheology did not affect diffusion, a final experiment where fresh squalene was added to our oligomer mixture, representative of sebum, showed that unchanged squalene possessed the anticipated monomeric diffusion coefficient and hence MW. This work suggests, at least qualitatively, that UV-induced squalene oligomerisation can occur over time and that this may have a role in the behaviour of squalene on the skin.

Monitoring Protein Global and Local Parameters in Unfolding and Binding Studies: The Extended Applicability of the Diffusion Coefficient─Molecular Size Empirical Relations

Protein unfolding and denaturation are main issues in biochemical and pharmaceutical research. Using a global parameter, the translational diffusion coefficient D, folded, unfolded, and intrinsically disordered proteins of a given molar mass M can be distinguished based on their distinct hydrodynamic properties. For broader applications, we provide generalized, PFG-NMR-based empirical D-M relations validated at different temperatures and ready to use with the corresponding corrections in different media. We demonstrate that these relations enable a more accurate molecular mass determination and show fewer potential errors than those of the common methods based on small-molecular diffusion standards. We monitor unfolding of three model proteins using 8 M urea and dimethyl sulfoxide (DMSO)-water mixtures as denaturing agents, highlighting the effect of disulfide bonds. Denaturation in 8 M urea is pH-dependent; in addition, for proteins with highly stable disulfide bonds, a reducing agent (TCEP) is required to achieve complete unfolding. Regarding the effect of local parameters, we show that at low DMSO concentrations─common conditions in pharmaceutical binding studies─the PFG-NMR-derived global parameters are not significantly affected. Still, the atomic environments can change, and the bound solvent molecule can inhibit the binding of a partner molecule. Using proteins with natural isotopic abundance, this effect can be proven by fast ¹H-¹⁵N 2D correlation spectra. Our results enable fast and easy estimation of protein molecular mass and the degree of folding in various media; moreover, the effect of the cosolvent on the atomic-level structure can be traced without the need of isotope labeling.

Pulse-field gradient nuclear magnetic resonance of protein translational diffusion from native to non-native states

Hydrodynamic radii (R_h -values) calculated from diffusion coefficients measured by pulse-field-gradient nuclear magnetic resonance are compared for folded and unfolded proteins. For native globular proteins, the R_h -values increase as a power of 0.35 with molecular size, close to the scaling factor of 0.33 predicted from polymer theory. Unfolded proteins were studied under four sets of conditions: in the absence of denaturants, in the presence of 6 M urea, in 95% dimethyl sulfoxide (DMSO), and in 40% hexafluoroisopropanol (HFIP). Scaling factors under all four unfolding conditions are similar (0.49-0.53) approaching the theoretical value of 0.60 for a fully unfolded random coil. Persistence lengths are also similar, except smaller in 95% DMSO, suggesting that the polypeptides are more disordered on a local scale with this solvent. Three of the proteins in our unfolded set have an asymmetric sequence-distribution of charged residues. While these proteins behave normally in water and 6 M urea, they give atypically low R_h -values in 40% HFIP and 95% DMSO suggesting they are forming electrostatic hairpins, favored by their asymmetric sequence charge distribution and the low dielectric constants of DMSO and HFIP. While diffusion-ordered NMR spectroscopy can separate small molecules, we show a number of factors combine to make protein-sized molecules much more difficult to resolve in mixtures. Finally, we look at the temperature dependence of apparent diffusion coefficients. Small molecules show a linear temperature response, while large proteins show abnormally large apparent diffusion coefficients at high temperatures due to convection, suggesting diffusion reference standards are only useful near 25°C.

Mechanistic analysis by NMR spectroscopy: A users guide

A 'principles and practice' tutorial-style review of the application of solution-phase NMR in the analysis of the mechanisms of homogeneous organic and organometallic reactions and processes. This review of 345 references summarises why solution-phase NMR spectroscopy is uniquely effective in such studies, allowing non-destructive, quantitative analysis of a wide range of nuclei common to organic and organometallic reactions, providing exquisite structural detail, and using instrumentation that is routinely available in most chemistry research facilities. The review is in two parts. The first comprises an introduction to general techniques and equipment, and guidelines for their selection and application. Topics include practical aspects of the reaction itself, reaction monitoring techniques, NMR data acquisition and processing, analysis of temporal concentration data, NMR titrations, DOSY, and the use of isotopes. The second part comprises a series of 15 Case Studies, each selected to illustrate specific techniques and approaches discussed in the first part, including in situ NMR (^1/2H, ^10/11B, ¹³C, ¹⁵N, ¹⁹F, ²⁹Si, ³¹P), kinetic and equilibrium isotope effects, isotope entrainment, isotope shifts, isotopes at natural abundance, scalar coupling, kinetic analysis (VTNA, RPKA, simulation, steady-state), stopped-flow NMR, flow NMR, rapid injection NMR, pure shift NMR, dynamic nuclear polarisation, ¹H/¹⁹F DOSY NMR, and in situ illumination NMR.

The use of DOSY experiments to determine the solution structures of coinage metal pyrazolates: The case of {[3,5-(CF3 )2 Pz]Ag}3

A series of DOSY experiments have been carried out to determine the solution stoichiometry of silver(I) 3,5-bis (trifluoromethyl)pyrazolate species. This compound exists as a trimer in the solid state (n = 3) but in solutions of chlorinated solvents, the DOSY data suggest the presence of a mixture of solvent stabilized monomer (n = 1) and dimer (n = 2) in equilibrium. Different approximations have been used including the Stokes-Einstein and the Stokes-Einstein-Gierer-Wirtz equations. Some methodological problems are discussed.

High drug-loaded microspheres enabled by controlled in-droplet precipitation promote functional recovery after spinal cord injury

Drug delivery systems with high content of drug can minimize excipients administration, reduce side effects, improve therapeutic efficacy and/or promote patient compliance. However, engineering such systems is extremely challenging, as their loading capacity is inherently limited by the compatibility between drug molecules and carrier materials. To mitigate the drug-carrier compatibility limitation towards therapeutics encapsulation, we developed a sequential solidification strategy. In this strategy, the precisely controlled diffusion of solvents from droplets ensures the fast in-droplet precipitation of drug molecules prior to the solidification of polymer materials. After polymer solidification, a mass of drug nanoparticles is embedded in the polymer matrix, forming a nano-in-micro structured microsphere. All the obtained microspheres exhibit long-term storage stability, controlled release of drug molecules, and most importantly, high mass fraction of therapeutics (21.8–63.1 wt%). Benefiting from their high drug loading degree, the nano-in-micro structured acetalated dextran microspheres deliver a high dose of methylprednisolone (400 μg) within the limited administration volume (10 μL) by one single intrathecal injection. The amount of acetalated dextran used was 1/433 of that of low drug-loaded microspheres. Moreover, the controlled release of methylprednisolone from high drug-loaded microspheres contributes to improved therapeutic efficacy and reduced side effects than low drug-loaded microspheres and free drug in spinal cord injury therapy.

High drug loading improves therapeutic efficacy and reduces side effects in drug delivery. Here, the authors use controlled diffusion of solvents to precipitate drug nanoparticles in polymer particles while the polymer is solidifying and demonstrate the particles for drug delivery in a spinal cord injury model.

Atomistic Simulations of Dopamine Diffusion Dynamics on a Pristine Graphene Surface

Carbon microelectrodes enable in vivo detection of neurotransmitters, and new electrodes aim to optimize the carbon surface. However, atomistic detail on the diffusion and orientation of neurotransmitters near these surfaces is lacking. Here, we employ molecular dynamics simulations to investigate the surface diffusion of dopamine (DA), its oxidation product dopamine-o-quinone (DOQ), and their protonated forms on the pristine basal plane of flat graphene. We find that all DA species rapidly adsorb to the surface and remain adsorbed, even without a holding potential or graphene surface defects. We also find that the diffusivities of the adsorbed and the fully solvated DA are similar and that the protonated species diffuse more slowly on the surface than their corresponding neutral forms, while the oxidized species diffuse more rapidly. Structurally, we find that the underlying graphene lattice has little influence over the molecular adsorbate's lateral position, and the vertical placement of the amine group on dopamine is highly dependent upon its charge. Finally, we find that solvation has a large effect on surface diffusivities. These first results from molecular dynamics simulations of dopamine at the aqueous-graphene interface show that dopamine diffuses rapidly on the surface, even without an applied potential, and provide a basis for future simulations of neurotransmitter structure and dynamics on advanced carbon materials electrodes.

27 Al NMR diffusometry of Al13 Keggin nanoclusters

Although nanometer-sized aluminum hydroxide clusters (i.e., ϵ-Al₁₃ , [Al₁₃ O₄ (OH)₂₄ (H₂ O)₁₂ ]⁷⁺ ) command a central role in aluminum ion speciation and transformations between minerals, measurement of their translational diffusion is often limited to indirect methods. Here, ²⁷ Al pulsed field gradient stimulated echo nuclear magnetic resonance (PFGSTE NMR) spectroscopy has been applied to the AlO₄ core of the ϵ-Al₁₃ cluster with complementary theoretical simulations of the diffusion coefficient and corresponding hydrodynamic radii from a boundary element-based calculation. The tetrahedral AlO₄ center of the ϵ-Al₁₃ cluster is symmetric and exhibits only weak quadrupolar coupling, which results in favorable T₁ and T₂ ²⁷ Al NMR relaxation coefficients for ²⁷ Al PFGSTE NMR studies. Stokes-Einstein relationship was used to relate the ²⁷ Al diffusion coefficient of the ϵ-Al₁₃ cluster to the hydrodynamic radius for comparison with theoretical simulations, dynamic light scattering from literature, and previously published ¹ H PFGSTE NMR studies of chelated Keggin clusters. This first-of-its-kind observation proves that ²⁷ Al PFGSTE NMR diffusometry can probe symmetric Al environments in polynuclear clusters of greater molecular weight than previously considered.

Nanoparticle tracking analysis and statistical mixture distribution analysis to quantify nanoparticle-vesicle binding

Nanoparticle tracking analysis (NTA) is a single particle tracking technique that in principle provides a more direct measure of particle size distribution compared to dynamic light scattering (DLS). Here, we demonstrate how statistical mixture distribution analysis can be used in combination with NTA to quantitatively characterize the amount and extent of particle binding in a mixture of nanomaterials. The combined approach is used to study the binding of gold nanoparticles to two types of phospholipid vesicles, those containing and lacking the model ion channel peptide gramicidin A. This model system serves as both a proof of concept for the method and a demonstration of the utility of the approach in studying nano-bio interactions. Two diffusional models (Stokes-Einstein and Kirkwood-Riseman) were compared in the determination of particle size, extent of binding, and nanoparticle:vesicle binding ratios for each vesicle type. The combination of NTA and statistical mixture distributions is shown to be a useful method for quantitative assessment of the extent of binding between particles and determination of binding ratios.

Fast and Accurate Diffusion NMR Acquisition in Continuous Flow

FlowNMR spectroscopy has become a popular and powerful technique for online reaction monitoring. DOSY NMR is an established technique for obtaining information about diffusion rates and molecular size on static...

Use of heterometallic alkali metal–magnesium aryloxides in ring-opening polymerization of cyclic esters

The alkali metal–magnesium aryloxides of the general formula [Mg2M′2(OAr)6(THF)x] (for M′ = Li, Na, K, and x = 0, 2, 4) were used to investigate the cooperativity effect of different metal sites on the ring-opening polymerization of l-lactide.

A Direct NMR Method To Measure Self-Diffusion Coefficients in Liquids by Monitoring Diffusing Molecules through One-Dimensional Imaging

Diffusion processes can be followed directly by recording one-dimensional images of a selected slice at variable intervals after selective inversion of the magnetization. The resulting diffusion coefficients of H₂ O and DMSO are consistent with earlier studies at different temperatures, obtained by monitoring the attenuation of NMR signals as a function of the gradient amplitude in gradient echo sequences.

Synthetic spatial patterning in bacteria: advances based on novel diffusible signals

Engineering multicellular patterning may help in the understanding of some fundamental laws of pattern formation and thus may contribute to the field of developmental biology. Furthermore, advanced spatial control over gene expression may revolutionize fields such as medicine, through organoid or tissue engineering. To date, foundational advances in spatial synthetic biology have often been made in prokaryotes, using artificial gene circuits. In this review, engineered patterns are classified into four levels of increasing complexity, ranging from spatial systems with no diffusible signals to systems with complex multi‐diffusor interactions. This classification highlights how the field was held back by a lack of diffusible components. Consequently, we provide a summary of both previously characterized and some new potential candidate small‐molecule signals that can regulate gene expression in Escherichia coli. These diffusive signals will help synthetic biologists to successfully engineer increasingly intricate, robust and tuneable spatial structures.

Lipid-microparticles for pulmonary delivery of active pharmaceutical ingredients: Impact of lipid crystallization on spray-drying processability

Spray-drying is an extensively used technology for engineering inhalable particles. Important technical hurdles are however experienced when lipid-based excipients (LBEs) are spray-dried. Stickiness, extensive wall deposition, or simply inability to yield a solid product have been associated to the low melting points of LBEs. In this work, solutions containing polyglycerol esters of behenic acid (PGFA-behenates), or other high melting point LBEs, were spray-dried to produce ibuprofen (IBU)-loaded inhalable lipid-microparticles. Prior to spray-drying, rational boundaries for the outlet temperature of the process were defined using LBE-IBU phase diagrams. Despite spray-drying the solutions at outlet temperatures below the boundaries, process performance and yield among LBEs were entirely different. Lipid crystallization into polymorphs or multi-phases negatively impacted the yield (10-47%), associated to liquid fractions unable to recrystallize at the surrounding gas temperature in the spray-dryer. The highest yields (76-82%), ascribed to PGFA-behenates, resulted from monophasic crystallization and absence of polymorphism. Lipid-microparticles, composed of a PGFA-behenate, were characterized by a volume mean diameter of 6.586 µm, tap density of 0.389 g/cm³ and corrugated surface. Application as carrier-free dry powder for inhalation resulted in high emitted fraction (90.9%), median mass aerodynamic diameter of 3.568 µm, fine particle fraction of 45.6% and modified release in simulated lung fluid.

Structural Elucidation, Aggregation, and Dynamic Behaviour of N,N,N,N ‐Copper(I) Schiff Base Complexes in Solid and in Solution: A Combined NMR, X‐ray Spectroscopic and Crystallographic Investigation

A series of Cu(I) complexes of bidentate or tetradentate Schiff base ligands bearing either 1‐H‐imidazole or pyridine moieties were synthesized. The complexes were studied by a combination of NMR and X‐ray spectroscopic techniques. The differences between the imidazole‐ and pyridine‐based ligands were examined by ¹H, ¹³C and ¹⁵N NMR spectroscopy. The magnitude of the ¹⁵N_imine coordination shifts was found to be strongly affected by the nature of the heterocycle in the complexes. These trends showed good correlation with the obtained Cu−N_imine bond lengths from single‐crystal X‐ray diffraction measurements. Variable‐temperature NMR experiments, in combination with diffusion ordered spectroscopy (DOSY) revealed that one of the complexes underwent a temperature‐dependent interconversion between a monomer, a dimer and a higher aggregate. The complexes bearing tetradentate imidazole ligands were further studied using Cu K‐edge XAS and VtC XES, where DFT‐assisted assignment of spectral features suggested that these complexes may form polynuclear oligomers in solid state. Additionally, the Cu(II) analogue of one of the complexes was incorporated into a metal‐organic framework (MOF) as a way to obtain discrete, mononuclear complexes in the solid state.

Comprehensive multidimensional study of the self-assembly properties of a three residue substituted β3 oligoamide

Substituted β3 oligoamides form a unique self-assembling system where each monomer folds into a helix containing approximately three β3 amino acids per turn, yielding a geometrically well-defined cylindrical building block that, when N-acylated, is able to self-assemble head-to-tail into nanorods that can reach several 100 μm length. It was shown in previous works that self-assembly can be achieved with a three residue long oligoamide as well that lacks any intramolecular H-bonds, yet it crystallizes in a helix-like conformation. The self-assembly properties of these small oligoamides are however elusive, suggesting a more complex system than the self-assembly of the H-bond stabilized helical monomers. Here we focus on the self-assembly behaviour of a three residue oligoamide, Ac-β3[LIA] where the letters denote the side chain of the analogous α amino acid. Ac-β3[LIA] can yield highly inhomogeneous suspensions in water with a broad range of large fibrous structures that seem to be very stable, yet occasionally fibre growth is only observed upon heating. The small size of the monomer suggests a highly dynamic equilibrium yet all previous attempts failed to clearly identify low molecular weight species. Therefore a special methodology was employed in this study to characterize the suspensions at different size ranges: SANS that is optimal to measure the small oligomers and cross sectional diameter of the assemblies, DLS that is sensitive to the large populations and therefore the length of the superstructures, and NMR that is sensitive to monomeric and small oligomeric form, in conjunction with IR spectroscopy to probe the folding and AFM to image the morphology of the assemblies. Temperature ramping was used to perturb the system to probe the dynamicity of the self-assembly. It was found that the anomalous self-assembly behaviour of Ac-β3[LIA] is caused by its two stable conformations, a helix-building “horseshoe” fold and a linear conformer. The latter is exclusively found in monomeric form in solution whereas the horseshoe fold is stable in solid phase and in fibrous assemblies. Small oligomers were absent. Thus the self-assembly of Ac-β3[LIA] is arrested by the activation energy need of the conformation change; fibre growth might be triggered by conditions that allow increased conformational freedom of the monomers. This observation may be used to develop strategies for controlled switchable self-assembly.

Pincer-Supported Gallium Complexes for the Catalytic Hydroboration of Aldehydes, Ketones and Carbon Dioxide

Gallium hydrides stabilised by primary and secondary amines are scarce due to their propensity to eliminate dihydrogen. Consequently, their reactivity has received limited attention. The synthesis of two novel gallium hydride complexes HGa(THF)[ON(H)O] and H₂Ga[μ²‐ON(H)O]Ga[ON(H)O] ([ON(H)O]²⁻=N,N‐bis(3,5‐di‐tert‐butyl‐2‐phenoxy)amine) is described and their reactivity towards aldehydes and ketones is explored. These reactions afford alkoxide‐bridged dimers through 1,2‐hydrogallation reactions. The gallium hydrides can be regenerated through Ga−O/B−H metathesis from the reaction of such dimers with pinacol borane (HBpin) or 9‐borabicyclo[3.3.1]nonane (9‐BBN). These observations allowed us to target the catalytic reduction of carbonyl substrates (aldehydes, ketones and carbon dioxide) with low catalyst loadings at room temperature.

A diffusion cell adapted to nuclear imaging instruments for the measurement of molecular release and pharmacokinetics across membranes

Diffusion cells are routinely used in pharmacology to measure the permeation of pharmaceutical compounds and contaminants across membranes (biological or synthetic). They can also be used to study drug release from excipients. The device is made of a donor (DC) and an acceptor (AC) compartment, separated by a membrane. Usually, permeation of molecules across membranes is measured by sampling from the AC at different time points. However, this process disturbs the equilibrium of the cell. Furthermore, analytical techniques used in association with diffusion cells sometimes lack either accuracy, sensitivity, or both. This work reports on the development of nuclear imaging - compatible diffusion cells. The cell is made of a polymer transparent to high-energy photons typically detected in positron emission tomography (PET). It was tested in a finite-dose set-up experiment with a pre-clinical PET system. Porous cellulose membranes (3.5, 25 and 300 kDa), a common excipient in pharmacology, as well as for dialysis membranes, were used as test membranes. The radioisotope ⁸⁹Zr chelated with deferoxamine B (DFO; 0.65 kDa), was used as an imaging probe (7-10 MBq; 0.2-0.3 nMol ⁸⁹Zr-DFO). In medicine, DFO is also commonly used for iron removal treatments and pharmacological formulations often require the association of this molecule with cellulose. Permeation profiles were obtained by measuring the radioactivity in the DC and AC for up to 2 weeks. The kinetic profiles were used to extract lag time, influx, and diffusion coefficients of DFO across porous cellulose membranes. A sensitivity threshold of 0.005 MBq, or 3.4 fmol of ⁸⁹Zr-DFO, was revealed. The lag time to permeation (τ) measured in the AC compartment, was found to be 1.33, 0.5, and 0.19 h with 3.5, 25, and 300 kDa membranes, respectively. Diffusion coefficients of 3.65 × 10^-6, 8.33 × 10^-6, and 4.74 × 10^-5 cm² h^-1 where revealed, with maximal pseudo steady-state influx values (J_pss) of 6.55 × 10^-6, 1.76 × 10^-5, and 1.29 × 10^-5 nmol cm^-2 h^-1. This study confirms the potential of the technology for monitoring molecular diffusion and release processes at low concentrations, high sensitivities, in real time and in a visual manner.

Comprehensive Characterisation of the Ketoprofen-β-Cyclodextrin Inclusion Complex Using X-ray Techniques and NMR Spectroscopy

Racemic ketoprofen (KP) and β-cyclodextrin (β-CD) powder samples from co-precipitation (1), evaporation (2), and heating-under-reflux (3) were analysed using X-ray techniques and nuclear magnetic resonance (NMR) spectroscopy. On the basis of NMR studies carried out in an aqueous solution, it was found that in the samples obtained by methods 1 and 2, there were large excesses of β-CD in relation to KP, 10 and 75 times, respectively, while the sample obtained by method 3 contained equimolar amounts of β-CD and KP. NMR results indicated that KP/β-CD inclusion complexes were formed and the estimated binding constants were approximately 2400 M^-1, showing that KP is quite strongly associated with β-CD. On the other hand, the X-ray single-crystal technique in the solid state revealed that the (S)-KP/β-CD inclusion complex with a stoichiometry of 2:2 was obtained as a result of heating-under-reflux, for which the crystal and molecular structure were examined. Among the methods used for the preparation of the KP/β-CD complex, only method 3 is suitable.

Mechanistic Model for the Prediction of Small-Molecule Vitreal Clearance Combining Diffusion-Limited and Permeability-Limited Clearance

The discovery of new small-molecule drugs for intravitreal administration would benefit from simple models to predict vitreal clearance (CL). The current models available have limitations in their applicability to small-molecule drugs and translatability to humans. We developed a mechanistic model combining the diffusion rate of the molecule in the vitreous and permeability across posterior segment tissues and applied it to 30 small molecules with observed CL available mostly from literature. We used Caco-2 permeability as a surrogate for ocular tissue permeability. The model predicted rabbit vitreal CL well, with 80% of the predictions being within a 2-fold range of the observed CL. For an accurate prediction, it was crucial to consider the anterior diffusion CL from the vitreous to the aqueous and a limiting diffusion CL for the whole eye. We observed no major differences in model accuracy when using literature permeability values from retinal pigment epithelial cell models. Importantly, by adopting the specific dimensions of the human eye, the model was able to accurately predict vitreal CL of four compounds for which human vitreal CL data are available. In summary, this mechanistic model enables a simple, accurate, and translatable estimation of small-molecule vitreal CL.

The Whole Is Bigger than the Sum of Its Parts: Drug Transport in the Context of Two Membranes with Active Efflux

Cell envelope plays a dual role in the life of bacteria by simultaneously protecting it from a hostile environment and facilitating access to beneficial molecules. At the heart of this ability lie the restrictive properties of the cellular membrane augmented by efflux transporters, which preclude intracellular penetration of most molecules except with the help of specialized uptake mediators. Recently, kinetic properties of the cell envelope came into focus driven on one hand by the urgent need in new antibiotics and, on the other hand, by experimental and theoretical advances in studies of transmembrane transport. A notable result from these studies is the development of a kinetic formalism that integrates the Michaelis-Menten behavior of individual transporters with transmembrane diffusion and offers a quantitative basis for the analysis of intracellular penetration of bioactive compounds. This review surveys key experimental and computational approaches to the investigation of transport by individual translocators and in whole cells, summarizes key findings from these studies and outlines implications for antibiotic discovery. Special emphasis is placed on Gram-negative bacteria, whose envelope contains two separate membranes. This feature sets these organisms apart from Gram-positive bacteria and eukaryotic cells by providing them with full benefits of the synergy between slow transmembrane diffusion and active efflux.

Tripodal, Squaramide-Based Ion Pair Receptor for Effective Extraction of Sulfate Salt

Combining three features-the high affinity of squaramides toward anions, cooperation in ion pair binding and preorganization of the binding domains in the tripodal platform-led to the effective receptor 2. The lack of at least one of these key elements in the structures of reference receptors 3 and 4 caused a lower affinity towards ion pairs. Receptor 2 was found to form an intramolecular network in wet chloroform, which changed into inorganic-organic associates after contact with ions and allowed salts to be extracted from an aqueous to an organic phase. The disparity in the binding mode of 2 with sulfates and with other monovalent anions led to the selective extraction of extremely hydrated sulfate anions in the presence of more lipophilic salts, thus overcoming the Hofmeister series.

Phenylpyridyl-Fused Boroles: A Unique Coordination Mode and Weak B-N Coordination-Induced Dual Fluorescence

Using 4-phenylpyridine or 2-phenylpyridine in place of biphenyl, two electron-poor phenylpyridyl-fused boroles, [TipPBB1]4 and TipPBB2 were prepared. [TipPBB1]4 adopts a unique coordination mode and forms a tetramer with a cavity in both the solid state and solution. The boron center of TipPBB2 is 4-coordinate in the solid state but the system dissociates in solution, leading to 3-coordinate borole species. Compared to its borafluorene analogues, the electron-accepting ability of TipPBB2 is largely enhanced by the pyridyl group. TipPBB2 exhibits dual fluorescence in solution due to an equilibrium between free TipPBB2 and a weak intermolecular coordination adduct with a second molecule. This equilibrium was further investigated by low-temperature NMR spectroscopy and photophysical studies. Theoretical studies indicate that the highest occupied molecular orbital (HOMO) of TipPBB2 localizes at the Tip group, in contrast to its borafluorene derivatives, wherein the HOMOs are localized on the borafluorene cores.

Exchange-modified DOSY experiments. the use of chiral solvating agents and lanthanide shift reagents as matrices

(S)-BINOL and Eu(fod)₃ were tried as matrices to improve DOSY performance and D^t and MW prediction power on small organic molecules.

Solid-state versus solution investigation of a luminescent chiral BINOL-derived bisphosphate single-molecule magnet

The enantiopure coordination polymer [Dy(hfac)₃((S/R)-L)]_n ([(S/R)-1]n) involving a BINOL-derived bisphosphate ligand (S/R)-L is investigated both in solution and solid-state.

Astrocytes Control Sensory Acuity via Tonic Inhibition in the Thalamus

Sensory discrimination is essential for survival. However, how sensory information is finely controlled in the brain is not well defined. Here, we show that astrocytes control tactile acuity via tonic inhibition in the thalamus. Mechanistically, diamine oxidase (DAO) and the subsequent aldehyde dehydrogenase 1a1 (Aldh1a1) convert putrescine into GABA, which is released via Best1. The GABA from astrocytes inhibits synaptically evoked firing at the lemniscal synapses to fine-tune the dynamic range of the stimulation-response relationship, the precision of spike timing, and tactile discrimination. Our findings reveal a novel role of astrocytes in the control of sensory acuity through tonic GABA release.

2-Methyl-β-cyclodextrin grafted ammonium chitosan: synergistic effects of cyclodextrin host and polymer backbone in the interaction with amphiphilic prednisolone phosphate salt as revealed by NMR spectroscopy

Reduced molecular weight chitosan was quaternized with 2-chloro-N,N-diethylethylamine to obtain a water soluble derivative (N⁺-rCh). Methylated-β-cyclodextrin (MCD), with 0.5 molar substitution, was covalently linked to N⁺-rCh through 1,6-hexamethylene diisocyanate spacer to give the derivatized ammonium chitosan N⁺-rCh-MCD. To shed light on the role of the cyclodextrin pendant in guiding binding interactions with amphiphilic active ingredients, corticosteroid prednisolone phosphate salt (PN) was considered. The deep inclusion of PN into cyclodextrin in PN/MCD model system was pointed out by analysis of ¹H NMR complexation shifts, 1D ROESY spectra, and diffusion measurements (DOSY). By using proton selective relaxation rates measurements as investigation tool, the superior affinity of N⁺-rCh-MCD towards PN was demonstrated in comparison with parent ammonium chitosan N⁺-rCh.

In Vitro-In Silico Modeling Approach to Rationally Designed Simple and Versatile Drug Delivery Systems

Rational design and development of a nanosystem usually relies on empirical approaches as well as a fair degree of serendipity. Understanding how nanosystems behave at the molecular level is of great importance for potential biomedical applications. In this work, we describe a nanosystem composed of two natural compounds, vitamin E and sphingomyelin, prepared by spontaneous emulsification (vitamin E-sphingomyelin nanosystems (VSNs)). Extensive characterization revealed suitable physicochemical properties, very high biocompatibility in vitro and in vivo, and colloidal stability during storage and in biological media, all relevant properties for clinical translation. We have additionally pursued a computational approach to gain an improved understanding of the assembling, structure, dynamics, and drug-loading capacity of VSNs, using both small molecules and biomolecules (resveratrol, curcumin, gemcitabine, and two peptides). The spontaneous formation of compartmentalized VSNs starting from completely disassembled molecules, observed here for the first time, was accurately assessed from the computational molecular dynamics trajectories. We describe here a synergistic in silico/in vitro approach showing the predictive power of computational simulations for VSNs' structural characterization and description of internal interaction mechanisms responsible for the association of bioactive molecules, representing a paradigm shift in the rational design of nanotechnologies as drug delivery systems for advanced personalized medicine.

Modeling Thrombin Generation in Plasma under Diffusion and Flow

We investigate the capacity of published numerical models of thrombin generation to reproduce experimentally observed threshold behavior under conditions in which diffusion and/or flow are important. Computational fluid dynamics simulations incorporating species diffusion, fluid flow, and biochemical reactions are compared with published data for thrombin generation in vitro in 1) quiescent plasma exposed to patches of tissue factor and 2) plasma perfused through a capillary coated with tissue factor. Clot time is correctly predicted in individual cases, and some models qualitatively replicate thrombin generation thresholds across a series of tissue factor patch sizes or wall shear rates. Numerical results suggest that there is not a genuine patch size threshold in quiescent plasma-clotting always occurs given enough time-whereas the shear rate threshold observed under flow is a genuine physical limit imposed by flow-mediated washout of active coagulation factors. Despite the encouraging qualitative results obtained with some models, no single model robustly reproduces all experiments, demonstrating that greater understanding of the underlying reaction network, and particularly of surface reactions, is required. In this direction, additional simulations provide evidence that 1) a surface-localized enzyme, speculatively identified as meizothrombin, is significantly active toward the fluorescent thrombin substrate used in the experiments or, less likely, 2) thrombin is irreversibly inhibited at a faster-than-expected rate, possibly explained by a stimulatory effect of plasma heparin on antithrombin. These results highlight the power of simulation to provide novel mechanistic insights that augment experimental studies and build our understanding of complex biophysicochemical processes. Further validation work is critical to unleashing the full potential of coagulation models as tools for drug development and personalized medicine.

Stirring rate affects thermodynamics and unfolding kinetics in isothermal titration calorimetry

Isothermal titration calorimetry (ITC) directly provides thermodynamic parameters depicting the energetics of intermolecular interactions in solution. During ITC experiments, a titration syringe with a paddle is continuously rotating to promote a homogeneous mixing. Here, we clarified that the shape of the paddles (flat, corkscrew and small-pitched corkscrew) and the stirring rates influence on the thermodynamic parameters of protein-ligand interaction. Stirring with the flat paddle at lower and higher rate both yielded a lower exothermic heat due to different reasons. The complete reaction with no incompetent fractions was achieved only when the stirring was performed at 500 or 750 rpm using the small-pitched corkscrew paddle. The evaluation of the protein solution after 1,500 rpm stirring indicated that proteins in the soluble fraction decreased to 94% of the initial amount, among which 6% was at an unfolded state. In addition, a significant increase of micron aggregates was confirmed. Furthermore, a new approach for the determination of the unfolding kinetics based on the time dependence of the total reaction heat was developed. This study demonstrates that a proper stirring rate and paddle shape are essential for the reliable estimation of thermodynamic parameters in ITC experiments.

Chemical Signaling in the Turbulent Ocean—Hide and Seek at the Kolmogorov Scale

Chemical cues and signals mediate resource acquisition, mate finding, and the assessment of predation risk in marine plankton. Here, we use the chemical properties of the first identified chemical cues from zooplankton together with in situ measurements of turbulent dissipation rates to calculate the effect of turbulence on the distribution of cues behind swimmers as well as steady state background concentrations in surrounding water. We further show that common zooplankton (copepods) appears to optimize mate finding by aggregating at the surface in calm conditions when turbulence do not prevent trail following. This near surface environment is characterized by anisotropic turbulence and we show, using direct numerical simulations, that chemical cues distribute more in the horizontal plane than vertically in these conditions. Zooplankton may consequently benefit from adopting specific search strategies near the surface as well as in strong stratification where similar flow fields develop. Steady state concentrations, where exudation is balanced by degradation develops in a time scale of ~5 h. We conclude that the trails behind millimeter-sized copepods can be detected in naturally occurring turbulence below the wind mixed surface layer or in the absence of strong wind. The trails, however, shorten dramatically at high turbulent dissipation rates, above ~10−3 cm2 s−3 (10−7 W kg−1)

When organophosphorus ruthenium complexes covalently bind to ruthenium nanoparticles to form nanoscale hybrid materials

A hybrid material made of mononuclear organophosphorus polypyridyl ruthenium complexes covalently bonded to ruthenium nanoparticles has been synthesized via a one-pot organometallic procedure and finely characterized. These results open new avenues to access unique hybrid transition metal nanomaterials.

The interpretation of small molecule diffusion coefficients: Quantitative use of diffusion-ordered NMR spectroscopy

Measuring accurate molecular self-diffusion coefficients, D, by nuclear magnetic resonance (NMR) techniques has become routine as hardware, software and experimental methodologies have all improved. However, the quantitative interpretation of such data remains difficult, particularly for small molecules. This review article first provides a description of, and explanation for, the failure of the Stokes-Einstein equation to accurately predict small molecule diffusion coefficients, before moving on to three broadly complementary methods for their quantitative interpretation. Two are based on power laws, but differ in the nature of the reference molecules used. The third addresses the uncertainties in the Stokes-Einstein equation directly. For all three methods, a wide range of examples are used to show the range of chemistry to which diffusion NMR can be applied, and how best to implement the different methods to obtain quantitative information from the chemical systems studied.

Hyperthermia can alter tumor physiology and improve chemo- and radio-therapy efficacy

Hyperthermia has demonstrated clinical success in improving the efficacy of both chemo- and radio-therapy in solid tumors. Pre-clinical and clinical research studies have demonstrated that targeted hyperthermia can increase tumor blood flow and increase the perfused fraction of the tumor in a temperature and time dependent manner. Changes in tumor blood circulation can produce significant physiological changes including enhanced vascular permeability, increased oxygenation, decreased interstitial fluid pressure, and reestablishment of normal physiological pH conditions. These alterations in tumor physiology can positively impact both small molecule and nanomedicine chemotherapy accumulation and distribution within the tumor, as well as the fraction of the tumor susceptible to radiation therapy. Hyperthermia can trigger drug release from thermosensitive formulations and further improve the accumulation, distribution, and efficacy of chemotherapy.

Hyperbranched polymers with step-growth chemistries from transfer-dominated branching radical telomerisation (TBRT) of divinyl monomers

The commercially relevant synthesis of novel materials with step-growth backbones has been achieved by applying conventional chemistries to the radical telomerisation of divinyl monomers leading to high molecular weight branched polymers.

Exposing Small-Molecule Nanoentities by a Nuclear Magnetic Resonance Relaxation Assay

Small molecules can self-assemble in aqueous solution into a wide range of nanoentity types and sizes (dimers, n-mers, micelles, colloids, etc.), each having their own unique properties. This has important consequences in the context of drug discovery including issues related to nonspecific binding, off-target effects, and false positives and negatives. Here, we demonstrate the use of the spin-spin relaxation Carr-Purcell-Meiboom-Gill NMR experiment, which is sensitive to molecular tumbling rates and can expose larger aggregate species that have slower rotational correlations. The strategy easily distinguishes lone-tumbling molecules versus nanoentities of various sizes. The technique is highly sensitive to chemical exchange between single-molecule and aggregate states and can therefore be used as a reporter when direct measurement of aggregates is not possible by NMR. Interestingly, we found differences in solution behavior for compounds within structurally related series, demonstrating structure-nanoentity relationships. This practical experiment is a valuable tool to support drug discovery efforts.

Extraction of Reliable Molecular Information from Diffusion NMR Spectroscopy: Hydrodynamic Volume or Molecular Mass?

Measuring accurate translational self-diffusion coefficients (D_t ) by NMR techniques with modern spectrometers has become rather routine. In contrast, the derivation of reliable molecular information therefrom still remains a nontrivial task. In this paper, two established approaches to estimating molecular size in terms of hydrodynamic volume (V_H ) or molecular weight (M) are compared. Ad hoc designed experiments allowed the critical aspects of their application to be explored by translating relatively complex theoretical principles into practical take-home messages. For instance, comparing the D_t values of three isosteric Cp₂ MCl₂ complexes (Cp=cyclopentadienyl, M=Ti, Zr, Hf), having significantly different molecular mass, provided an empirical demonstration that V_H is the critical molecular property affecting D_t . This central concept served to clarify the assumptions behind the derivation of D_t =ƒ(M) power laws from the Stokes-Einstein equation. Some pitfalls in establishing log (D_t ) versus log (M) linear correlations for a set of species have been highlighted by further investigations of selected examples. The effectiveness of the Stokes-Einstein equation itself in describing the aggregation or polymerization of differently shaped species has been explored by comparing, for example, a ball-shaped silsesquioxane cage with its cigar-like dimeric form, or styrene with polystyrene macromolecules.

The Ensemble of Conformations of Antifreeze Glycoproteins (AFGP8): A Study Using Nuclear Magnetic Resonance Spectroscopy

The primary sequence of antifreeze glycoproteins (AFGPs) is highly degenerate, consisting of multiple repeats of the same tripeptide, Ala–Ala–Thr*, in which Thr* is a glycosylated threonine with the disaccharide beta-d-galactosyl-(1,3)-alpha-N-acetyl-d-galactosamine. AFGPs seem to function as intrinsically disordered proteins, presenting challenges in determining their native structure. In this work, a different approach was used to elucidate the three-dimensional structure of AFGP8 from the Arctic cod Boreogadussaida and the Antarctic notothenioid Trematomusborchgrevinki. Dimethyl sulfoxide (DMSO), a non-native solvent, was used to make AFGP8 less dynamic in solution. Interestingly, DMSO induced a non-native structure, which could be determined via nuclear magnetic resonance (NMR) spectroscopy. The overall three-dimensional structures of the two AFGP8s from two different natural sources were different from a random coil ensemble, but their “compactness” was very similar, as deduced from NMR measurements. In addition to their similar compactness, the conserved motifs, Ala–Thr*–Pro–Ala and Ala–Thr*–Ala–Ala, present in both AFGP8s, seemed to have very similar three-dimensional structures, leading to a refined definition of local structural motifs. These local structural motifs allowed AFGPs to be considered functioning as effectors, making a transition from disordered to ordered upon binding to the ice surface. In addition, AFGPs could act as dynamic linkers, whereby a short segment folds into a structural motif, while the rest of the AFGPs could still be disordered, thus simultaneously interacting with bulk water molecules and the ice surface, preventing ice crystal growth.

Using Fractionation and Diffusion Ordered Spectroscopy to Study Lignin Molecular Weight

Recent reports demonstrate that applications of the biopolymer lignin can be helped by the use of a fraction of the lignin which has an optimal molecular weight range. Unfortunately, the current methods used to determine lignin's molecular weight are inconsistent or not widely accessible. Here, an approach that relies on 2D DOSY NMR analysis is described that provides a measure of lignin's molecular weight. Consistent results were obtained using this well-established NMR technique across a range of lignins.

Nuclear magnetic resonance spectroscopic study of the inclusion complex of (R)-tedizolid with HDAS-β-CD, β-CD, and γ-cyclodextrin in aqueous solution

NMR spectroscopy is used to investigate the host-guest complexation of (R)-tedizolid, such as tedizolid with the hydroxymethyl substituent at the C5 position of the oxazolidinone ring ((R)-TED) or tedizolid with 5-methyl dihydrogen phosphate ((R)-TED-PO₄) with heptakis-(2,3-diacetyl-6-sulfo)-β-cyclodextrin (HDAS-β-CD), β-CD and γ-CD, in particular to obtain information about the mode and strength of the guest complexation into the hydrophobic cavity of the host. The complex stoichiometries of 1:1 (host:guest) and 1:2 were detected in millimolar concentrations for HDAS-β-CD and γ-CD with TED-PO₄ complexes, respectively. In the meantime, the mixed of complexes with stoichiometries of 1:1 and 2:1 were found for β-CD with both TED and TED-PO₄, however the 1:1 complex had a significant advantage.The binding mode was proposed. The estimated binding constants K_a of the complexes of TED or TED-PO₄ with CDs differ significantly in the order HDAS-β-CD<<β-CD<<γ-CD.