Improving the Interpretation of Small Molecule Diffusion Coefficients

Quantitative at-line monitoring of enzymatic hydrolysis using benchtop diffusion nuclear magnetic resonance spectroscopy

Benchtop diffusion nuclear magnetic resonance (NMR) spectroscopy was used to perform quantitative monitoring of enzymatic hydrolysis. The study aimed to test the feasibility of the technology to characterize enzymatic hydrolysis processes in real time. Diffusion ordered spectroscopy (DOSY) was used to measure the signal intensity and apparent self-diffusion constant of solubilized protein in hydrolysate. The NMR technique was tested on an enzymatic hydrolysis reaction of red cod, a lean white fish, by the endopeptidase alcalase at 50°C. Hydrolysate samples were manually transferred from the reaction vessel to the NMR equipment. Measurement time was approximately 3 min per time point. The signal intensity from the DOSY experiment was used to measure protein concentration and the apparent self-diffusion constant was converted into an average molecular weight and an estimated degree of hydrolysis. These values were plotted as a function of time and both the rate of solubilization and the rate of protein breakdown could be calculated. In addition to being rapid and noninvasive, DOSY using benchtop NMR spectroscopy has an advantage compared with other enzymatic hydrolysis characterization methods as it gives a direct measure of average protein size; many functional properties of proteins are strongly influenced by protein size. Therefore, a method to give protein concentration and average size in real time will allow operators to more tightly control production from enzymatic hydrolysis. Although only one type of material was tested, it is anticipated that the method should be applicable to a broad variety of enzymatic hydrolysis feedstocks.

Engineering Tunable, Low Latency Spatial Computation with Dual Input Quorum Sensing Promoters

Quorum sensing signals have evolved for population-level signaling in bacterial communities and are versatile tools for engineering cell-cell signaling in synthetic biology projects. Here, we characterize the spatial diffusion of a palette of quorum sensing signals and find that their diffusion in agar can be predicted from their molecular weight with a simple power law. We also engineer novel dual- and multi-input promoters that respond to quorum-sensing diffusive signals for use in engineered genetic systems. We engineer a promoter scaffold that can be adapted for activation and repression by multiple diffusers simultaneously. Lastly, we combine the knowledge on diffusion dynamics with the novel genetic components to build a new generation of spatial, stripe-forming systems with a simplified design, improved robustness, tuneability, and response time.

Mechanistic study of pyrazole synthesis via oxidation-induced N-N coupling of diazatitanacycles

Metal-mediated inner-sphere N-N coupling is an uncommon route to N-N bond formation. Herein, we report a mechanistic study of pyrazole formation via oxidation-induced N-N coupling of diazatitanacycles. In TEMPO oxidation reactions, the first of two oxidations is rate limiting and TEMPO coordination to Ti is critical for reactivity. In oxidations with Fc+ salts, coordinating counteranions such (eg. Cl-) aid an "inner-sphere-like" oxidation.

Metal-cation-induced shifts in thiolate redox and reduced sulfur speciation

Sulfur-containing anions (e.g. thiolates, polysulfides) readily exchange in solution, making control over their solution speciation and distribution challenging. Here, we demonstrate that different redox-inactive alkali, alkaline earth, and transition metals (Li+, Na+, K+, Mg2+, Ca2+, Zn2+, and Cd2+) shift the equilibria of sulfur catenation or sulfur reduction/oxidation between thiolate, polysulfanide, and polysulfide anions in acetonitrile solution. The thermodynamic factors that govern these equilibria are examined by identification of intermediate metal thiolate and metal polysulfide species using a combination of NMR spectroscopy, electronic absorption spectroscopy, and mass spectrometry. Electrochemical measurements demonstrate that the metal cation of the electrolyte modulates both sulfur reduction and thiolate oxidation potentials. DFT calculations suggest that the changes in equilibria are driven by stronger covalent interactions between polysulfide anions and more highly charged cations.

Supramolecular complexation of C60 with branched polyethylene

Fullerene C60 is a ubiquitous material for application in organic electronics and nanotechnology, due to its desirable optoelectronic properties including good molecular orbital alignment with electron-rich donor materials, as well as high and isotropic charge carrier mobility. However, C60 possesses two limitations that hinder its integration into large-scale devices: (1) poor solubility in common organic solvents leading to expensive device processing, and (2) poor optical absorbance in the visible portion of the spectrum. Covalent functionalization has long been the standard for introducing structural tunability into molecular design, but non-covalent interactions have emerged as an alternative strategy to tailor C60-based materials, offering a versatile and tuneable alternative to novel functional materials and applications. In this work, we report a straightforward non-covalent functionalization of C60 with a branched polyethylene (BPE), which occurs spontaneously in dilute chloroform solution under ambient conditions. A detailed characterization strategy, based on UV-vis spectroscopy and size-exclusion chromatography was performed to verify and investigate the structure of the C60+BPE complex. Among others, our work reveals that the supramolecular complex has an order of magnitude higher molecular weight than its C60 and BPE constituents and points towards oxidation as the driving force behind complexation. The C60+BPE complex also possesses significantly broadened optical absorbance compared to unfunctionalized C60, extending further into the visible portion of the spectrum. This non-covalent approach presents an inexpensive route to address the shortcomings of C60 for electronic applications, situating the C60+BPE complex as a promising candidate for further investigation in organic electronic devices.

Protocol for localized macrophage stimulation with small-molecule TLR agonist via fluidic force microscopy

Here, we present a protocol to deliver nanoliter volumes of Toll-like receptor (TLR) agonist onto a culture of nuclear factor κB (NF-κB) reporter macrophages using fluidic force microscopy and a micron-scale probe. We describe steps for quantifying the dose of agonist by modeling their diffusion with experimental inputs. We then detail procedures for quantifying and categorizing macrophage responses to individual and varied doses and combining agonist concentration and macrophage response to analyze the NF-κB response to localized TLR stimulation. For complete details on the use and execution of this protocol, please refer to Mulder et al. (2024).1.

Direct Electrochemical Synthesis of Metal-Organic Frameworks: Cu3 (BTC)2 and Cu(TCPP) on Copper Thin films and Copper-Based Microstructures

Cu thin films and Cu2 O microstructures were partially converted to the Metal-Organic Frameworks (MOFs) Cu3 (BTC)2 or Cu(TCPP) using an electrochemical process with a higher control and at milder conditions compared to the traditional solvothermal MOF synthesis. Initially, either a Cu thin film was sputtered, or different kinds of Cu or Cu2 O microstructures were electrochemically deposited onto a conductive ITO glass substrate. Then, these Cu thin films or Cu-based microstructures were subsequently coated with a thin layer of either Cu3 (BTC)2 or Cu(TCPP) by controlled anodic dissolution of the Cu-based substrate at room temperature and in the presence of the desired organic linker molecules: 1,3,5-benzenetricarboxylic acid (BTC) or photoactive 4,4',4'',4'''-(Porphine-5,10,15,20-tetrayl) tetrakis(benzoic acid) (TCPP) in the electrolyte. An increase in size of the Cu micro cubes with exposed planes [100] of 38,7 % for the Cu2 O@Cu3 (BTC)2 and a 68,9 % increase for the Cu2 O@Cu(TCPP) was roughly estimated. Finally, XRD, Raman spectroscopy and UV-vis absorption spectroscopy were used to characterize the initial Cu films or Cu-based microstructures, and the obtained core-shell Cu2 O@Cu(BTC) and Cu2 O@Cu(TCPP) microstructures.

Hierarchical Self-Assembly of Curved Aromatics: From Donor-Acceptor Porphyrins to Triply Periodic Minimal Surfaces

A saddle-shaped π-extended zinc porphyrin containing a peripheral pyridyl ligand undergoes quantitative self-assembly into a cyclic trimer. The trimer has a prismatic structure with negatively curved side walls, which promote the formation of supramolecular organic frameworks stabilized by dispersion interactions. The first framework type, UWr-1, has the npo topology, with a hexagonal structure analogous to the Schwartz H triply periodic minimal surface. Co-crystallization of the trimer with either C60 and C70 produces the isomorphous cubic UWr-2 and UWr-3 phases, characterized by the ctn network topology and a structural relationship to the Fischer-Koch minimal surface S. All three phases contain complex labyrinths of solvent-filled channels, corresponding to very large probe-accessible volumes (68 % to 76 %). The UWr-2 network could be partly desolvated while retaining its long range dimensional order, indicating remarkable strength of the dispersion interactions in the crystal. A theoretical analysis of noncovalent interactions shows the role of geometrical matching between the negatively curved porphyrin units and positively curved fullerenes.

Diffusive dynamics of a model protein chain in solution

A Markov state model is a powerful tool that can be used to track the evolution of populations of configurations in an atomistic representation of a protein. For a coarse-grained linear chain model with discontinuous interactions, the transition rates among states that appear in the Markov model when the monomer dynamics is diffusive can be determined by computing the relative entropy of states and their mean first passage times, quantities that are unchanged by the specification of the energies of the relevant states. In this paper, we verify the folding dynamics described by a diffusive linear chain model of the crambin protein in three distinct solvent systems, each differing in complexity: a hard-sphere solvent, a solvent undergoing multi-particle collision dynamics, and an implicit solvent model. The predicted transition rates among configurations agree quantitatively with those observed in explicit molecular dynamics simulations for all three solvent models. These results suggest that the local monomer-monomer interactions provide sufficient friction for the monomer dynamics to be diffusive on timescales relevant to changes in conformation. Factors such as structural ordering and dynamic hydrodynamic effects appear to have minimal influence on transition rates within the studied solvent densities.

Comparison of the Interaction and Structure of Lignin in Pure Systems and in Asphalt Media by Molecular Dynamics Simulations

Lignin is a class of organic aromatic polymers contributing to the rigidity and strength of plants and has been proposed as a modifier to improve asphalt performance on road pavement. However, contradicting experimental results on the lignin miscibility in asphalt were found from different studies, and lignin has been found to self-assemble in different solutions. Thus, investigating the interaction and microstructure of lignin in asphalt media in molecular detail is necessary. Molecular dynamics (MD) simulations using both the LAMMPS program with the OPLS-aa force field and the NAMD program with the CHARMM force field have been conducted on pure lignin (including lignin monomer, dimer, and polymer with 17 and 31 units) and their mixtures with model asphalt molecules at different temperatures. Consistent results were observed from both programs and force fields in terms of density, hydrogen bonds, diffusion coefficient, radius of gyration, and radial distribution function. Glass transition was observed in the pure lignin systems based on density and diffusion coefficient calculations at different temperatures. Lignin can form intramolecular hydrogen bonds and intermolecular hydrogen bonds with other lignin and 1,7-dimethylnapthalene in the asphalt mixture, which has dependence on temperature and lignin chain length. Correlating the lignin size and chain length using the power-law relationship showed that lignin polymers in pure systems are in quasi-relaxed structures at different temperatures; lignin molecules stay in quasi-relaxed structures in asphalt mixtures at high temperatures but in collapsed structures at low temperatures. Implementing lignin monomer, dimer, and polymer into the model asphalt mixture can improve its density. Although lignin in different chain lengths aggregates in asphalt, lignin can modify the packing between different components in asphalt media at different temperatures. The work suggests that temperature can significantly influence the miscibility of lignin polymer in asphalt and that lignin can function as both a modifier and a resin in asphalt.

Self-Healing Composite Coating Fabricated with a Cystamine Cross-Linked Cellulose Nanocrystal-Stabilized Pickering Emulsion

A gelled Pickering emulsion system was fabricated by first stabilizing linseed oil droplets in water with dialdehyde cellulose nanocrystals (DACNCs) and then cross-linking with cystamine. Cross-linking of the DACNCs was shown to occur by a reaction between the amine groups on cystamine and the aldehyde groups on the CNCs, causing gelation of the nanocellulose suspension. Fourier transform infrared spectroscopy and X-ray photoelectron spectroscopy were used to characterize the cystamine-cross-linked CNCs (cysCNCs), demonstrating their presence. Transmission electron microscopy images evidenced that cross-linking between cysCNCs took place. This cross-linking was utilized in a linseed oil-in-water Pickering emulsion system, creating a novel gelled Pickering emulsion system. The rheological properties of both DACNC suspensions and nanocellulose-stabilized Pickering emulsions were monitored during the cross-linking reaction. Dynamic light scattering and confocal laser scanning microscopy (CLSM) of the Pickering emulsion before gelling imaged CNC-stabilized oil droplets along with isolated CNC rods and CNC clusters, which had not been adsorbed to the oil droplet surfaces. Atomic force microscopy imaging of the air-dried gelled Pickering emulsion also demonstrated the presence of free CNCs alongside the oil droplets and the cross-linked CNC network directly at the oil-water interface on the oil droplet surfaces. Finally, these gelled Pickering emulsions were mixed with poly(vinyl alcohol) solutions and fabricated into self-healing composite coating systems. These self-healing composite coatings were then scratched and viewed under both an optical microscope and a scanning electron microscope before and after self-healing. The linseed oil was demonstrated to leak into the scratches, healing the gap automatically and giving a practical approach for a variety of potential applications.

Boron diamide derivatives containing N-N and N-P molecular fragments

The cationic and neutral boron-diamide precursors are employed to target the inclusion of N2 and N-P molecular fragments. The species (HCN(Dipp))2BNH25, and (H2CN(Dipp))2BNH26 were prepared. While efforts to oxidize with [NO]+ gave mixtures of products, reactions with N2H4 gave the salts [(HCN(Dipp))2B(NHNH3)][O3SCF3] 7 [(H2CN(Dipp))2B(NHNH3)][O3SCF3] 8. Excess N2H4 gave the neutral species (HCN(Dipp))2B(NHNH2) 9 and (H2CN(Dipp))2B(NHNH2) 10, respectively. The species (H2CN(Dipp))2B(N3) 11 was prepared for comparative purposes. Turning to related NP species, compound 6 was converted to (HCN(Dipp))2B(NHPCl2) 12, while (HCN(Dipp))2BNK(SiMe3) 14 was used to give (HCN(Dipp))2BN(SiMe3)PCl215. Replacement of one of the chlorides gave (HCN(Dipp))2BN(SiMe3)PCl(OSO2CF3) 16 which converts to [(HCN(Dipp))2BNPCl]217. Similarly heating 15 afforded 17. The insights for the synthesis of further boron-N2 and boron-NP derivatives are discussed.

Are "Carbon Dots" Always Carbon Dots? Evidence for their Supramolecular Nature from Structural and Dynamic Studies in Solution and in the Pure Solid

A model for the morphology (size, shape, and crystallinity) of carbon dots (CDs) in the solid state consistent with the observed photoluminescence in solution is proposed herein. Overwhelming evidence has been collected that links the data coming from solid-state analysis (high-resolution transmission electron microscopy (HRTEM), atomic force microscopy (AFM), and matrix-assisted laser desorption/ionization (MALDI) mass spectrometry (MS)) to that of solution (pulsed-field gradient (PFG)-NMR spectroscopy, time-resolved fluorescence anisotropy (TRFA), and steady-state/time-resolved fluorescence), allowing the establishment of an overall structural model for CDs. According to this model, the so-called carbon dots, observed under HRTEM imaging, are in fact supramolecular organized structures dynamically assembled from small to medium-sized molecular species when the solvent is removed to give the solid form. In this way, the imaged nanoparticles (TEM/AFM) are not covalently bound entities formed during the synthetic process, but instead supramolecular entities formed by noncovalent interactions. These particles, if at all present in solution, have the form of loose associations of relatively small molecules. This study was conducted on CDs obtained from the hydrothermal carbonization (HTC) of a biomass waste (olive wet pomace).

Measuring Liquid-into-Liquid Diffusion Coefficients by Dissolving Microdroplet Electroanalysis

Diffusion is a fundamental process in various domains, such as pollution control, drug delivery, and isotope separation. Accurately measuring the diffusion coefficients (D) of one liquid into another often encounters challenges stemming from intermolecular interactions, precise observations at the liquid interface, convection, etc. Here, we present an innovative electrochemical methodology for determining the diffusion coefficient of a liquid into another liquid. The method involves precisely tracking the lifetime of a nonaqueous droplet. An organic droplet is placed on an ultramicroelectrode surrounded by an aqueous solution of potassium hexacyanoferrate(II/III). The droplet initially blocks the reduction or oxidation of the redox species. As the droplet dissolves, giving access to the conductive microelectrode surface, a continuously increasing current is observed in voltammetry and the amperometric i-t response. The electrochemical response thus directly reports on the flux of redox species on the electrode surface, allowing us to precisely determine the lifetime of the droplet. D values are directly determined through a combination of electrochemical analysis and the principles of droplet dissolution. We demonstrate the quantification of 1,2-dichloroethane and nitrobenzene into water, yielding diffusion coefficients of (11.3 ± 1.2) × 10-6 cm2/s and (5.2 ± 1.1) × 10-6 cm2/s, respectively. This work establishes a reliable electrochemical approach for quantifying diffusion coefficients based on droplet lifetime analysis.

Molecular Recognition of Tyrosine-Containing Polypeptides with Pseudopeptidic Cages Unraveled by Fluorescence and NMR Spectroscopies

The molecular recognition of Tyr-containing peptide copolymers with pseudopeptidic cages has been studied using a combination of fluorescence and NMR spectroscopies. Fluorescence titrations rendered a reasonable estimation of the affinities, despite the presence of dynamic quenching masking the unambiguous detection of the supramolecular complexes. Regarding NMR, the effect of polypeptide (PP) binding on relaxation and diffusion parameters of the cages is much more reliable than the corresponding chemical shift perturbations. To that, purification of the commercial PPs is mandatory to obtain biopolymers with lower polydispersity. Thus, the relaxation/diffusion-filtered 1H spectra of the cages in the absence vs presence of the PPs represent a suitable setup for the fast detection of the noncovalent interactions. Additional key intermolecular NOE cross-peaks supported by molecular models allow the proposal of a structure of the supramolecular species, stabilized by the Tyr encapsulation within the cage cavity and additional attractive polar interactions between the side chains of cage and PP, thus defining a binding epitope with a potential for implementing sequence selectivity. Accordingly, the cages bearing positive/negative residues prefer to bind the peptides having complementary negative/positive side chains close to the target Tyr, suggesting an electrostatic contribution to the interaction. Overall, our results show that both techniques represent a powerful and complementary combination for studying cage-to-PP molecular recognition processes.

Synthesis of 177Lu-Labeled, Somatostatin-2 Receptor-Targeted Metalla-Assemblies: Challenges in the Design of Supramolecular Radiotherapeutics

Self-assembled supramolecular coordination complexes (SCCs) hold promise for biomedical applications in cancer therapy, although their potential in the field of nuclear medicine is still substantially unexplored. Therefore, in this study an exo-functionalized cationic [Pd2L2]4+ metallacycle (L = 3,5-bis(3-ethynylpyridine)phenyl), targeted to the somatostatin-2 receptor (sst2R) and featuring the DOTA chelator (1,4,7,10-tetraazacyclododecane-1,4,7,10-tetraacetic acid) in order to bind the β-- and γ-emitter lutetium-177, was synthesized by self-assembly following ligand synthesis via standard solid-phase peptide synthesis (SPPS). This metallacycle was then characterized by reverse-phase high-performance liquid chromatography (RP-HPLC), electrospray ionization mass spectrometry (ESI-MS), and 1H and 1H-DOSY NMR (DOSY = diffusion-ordered spectroscopy). A procedure for the radiolabeling of the metallacycle with 177Lu was also optimized. The resulting [nat/177Lu]Lu-DOTA-metallacycle, termed [nat/177Lu]Lu-Cy, was evaluated concerning its stability and in vitro properties. The compound was more lipophilic compared to the reference [177Lu]Lu-DOTA-TATE (logPOct/H2O = -0.85 ± 0.10 versus -3.67 ± 0.04, respectively). While [natLu]Lu-Cy revealed low stability in a DMEM/F12 GlutaMax medium, it demonstrated good stability in other aqueous media as well as in DMSO. A high sst2R binding affinity (expressed as IC50) was determined in CHOsst2 cells (Chinese hamster ovary cells that were stably transfected with human sst2R). Moreover, the metallacycle exhibited high human serum albumin binding, as assessed by high-performance affinity chromatography (HPAC), and moderate stability in human serum compared to [177Lu]Lu-DOTA-TATE (TATE = (Tyr3)-octreotate). In order to improve stability, a heteroleptic approach was used to develop a less sterically hindered cage-like SCC that is potentially endowed with host-guest chemistry capability, which has been preliminarily characterized by RP-HPLC and ESI-MS. Overall, our initial results encourage future studies on sst2R-directed SCCs and have led to new insights into the chemistry of ss2R-directed SCCs for radiopharmaceutical applications.

Tracking nitrite's deviation from Stokes-Einstein predictions with pulsed field gradient 15N NMR spectroscopy

Predicting the behavior of oxyanions in radioactive waste stored at the Department of Energy legacy nuclear sites requires the development of novel analytical methods. This work demonstrates 15N pulsed field gradient nuclear magnetic resonance spectroscopy to quantify the diffusivity of nitrite. Experimental results, supported by molecular dynamics simulations, indicate that the diffusivity of free hydrated nitrite exceeds that of free hydrated sodium despite the greater hydrodynamic radius of nitrite. Investigations are underway to understand how the compositional and dynamical heterogeneities of the ion networks at high concentrations affect rheological and transport properties.

Size Determination of Organic Cages by Diffusion NMR Spectroscopy

Reliable structure elucidation of covalent organic cage compounds remains challenging as routine analysis might leave ambiguities. Diffusion-ordered NMR spectroscopy (DOSY) allows insight into the molecular size and mass of the species present in solution, but a systematic evaluation of the diffusion behavior for cage assemblies is rarely considered. Here we report the synthesis of four series of covalent organic cages based on tribenzotriquinacenes and diboronic acids with varying geometry and exohedral substituents. We provide a guideline for the consistent measurement of diffusion coefficients from 1 H-DOSY NMR spectroscopy, which was utilized to study the diffusion behavior for the whole set of cages and selected examples from the literature. For structurally similar cages, a linear correlation between the solvodynamic volume and the molecular mass allows precise size determination. For more complex systems, multiple parameters, such as window size or rigid exohedral functionalization. further modulate cage diffusion in solution.

Prediction of the Time to Reach Equilibrium for Improved Estimation of the Unbound Fraction of Compounds in Equilibrium Dialysis Using kinetic Modeling

Equilibrium dialysis (ED) is widely used in pharmacokinetics to determine the fraction of unbound (fu) compounds in plasma; however, the kinetics of drugs in the ED system with respect to their permeation across semi-permeable membranes has not been systemically studied. Here, the kinetics of the ED system, including the binding of drugs to plasma proteins, non-specific binding, and permeation across the membrane, was described to enable verification of the equilibrium, prediction of the time to reach equilibrium, and estimations of fu with data obtained during pre-equilibrium. Using data obtained during pre-equilibrium, the time to reach 90% equilibrium (t90%) and fu were estimated with reasonable accuracy. Notably, fu could be estimated reasonably well using one-time-point data for the calculation. Furthermore, the current modeling approach allowed concurrent estimations of fu and the decomposition rate of compounds that were metabolically unstable in the plasma. Reasonable metabolic rate constants were determined for cefadroxil and diltiazem, demonstrating the practicality of this method for determining kinetics related to fu characterization. Because the determination of fu of compounds with 'unfavorable' physicochemical properties is known to be experimentally challenging, the current method may be useful in determining the fu of compounds in vitro.

Schlenk-Type Equilibria of Grignard-Analogous Arylberyllium Complexes: Steric Effects

The presence of complex Schlenk equilibria is a central property of synthetically invaluable Grignard reagents substantially affecting their reactivity and selectivity in chemical transformations. In this work, the steric effects of aryl substituents on the Schlenk-type equilibria of their lighter congeners, arylberyllium bromides, are systematically studied. Combination of diarylberyllium complexes Ar2 Be(OEt2 ) (1Ar, Ar=Tip, Tcpp; Tip=2,4,6-iPr3 C6 H3 , Tcpp=2,4,6-Cyp3 C6 H3 , Cyp=c-C5 H9 ), containing sterically demanding aryl groups, and BeBr2 (OEt2 )2 (2) affords the Grignard-analogous arylberyllium bromides ArBeBr(OEt2 ) (3Ar, Ar=Tip, Tcpp). In contrast, Mes2 Be(OEt2 ) (1Mes, Mes=2,4,6-Me3 C6 H3 ) and 2 exist in a temperature-dependent equilibrium with MesBeBr(OEt2 ) (3Mes) and free OEt2 . Ph2 Be(OEt2 ) (1Ph) reacts with 2 to afford dimeric [PhBeBr(OEt2 )]2 ([3Ph]2 ). Moreover, the influence of replacing the OEt2 donor by an N-heterocyclic carbene, IPr2 Me2 (IPr2 Me2 =C(iPrNCMe)2 ), on the redistribution reactions was investigated. The solution- and solid-state structures of the diarylberyllium and arylberyllium bromide complexes were comprehensively characterized using multinuclear (1 H, 9 Be, 13 C) NMR spectroscopic methods and single-crystal X-ray diffraction, while DFT calculations were employed to support the experimental findings.

Pathway complexity in fibre assembly: from liquid crystals to hyper-helical gelmorphs

Pathway complexity results in unique materials from the same components according to the assembly conditions. Here a chiral acyl-semicarbazide gelator forms three different gels of contrasting fibre morphology (termed 'gelmorphs') as well as lyotropic liquid crystalline droplets depending on the assembly pathway. The gels have morphologies that are either hyperhelical (HH-Gel), tape-fibre (TF-Gel) or thin fibril derived from the liquid crystalline phase (LC-Gels) and exhibit very different rheological properties. The gelator exists as three slowly interconverting conformers in solution. All three gels are comprised of an unsymmetrical, intramolecular hydrogen bonded conformer. The kinetics show that formation of the remarkable HH-Gel is cooperative and is postulated to involve association of the growing fibril with a non-gelling conformer. This single molecule dynamic conformational library shows how very different materials with different morphology and hence very contrasting materials properties can arise from pathway complexity as a result of emergent interactions during the assembly process.

Iron(II)-Catalyzed Activation of Si-N and Si-O Bonds Using Hydroboranes

We report the activation and functionalization of Si-N bonds with pinacol borane catalyzed by a three-coordinate iron(II) β-diketiminate complex. The reactions proceed via the mild activation of silazanes to yield useful hydrosilanes and aminoboranes. The reaction is studied by kinetic analysis, along with a detailed investigation of decomposition pathways using catecholborane as an analogue of the pinacol borane used in catalysis. We have extended the methodology to develop a polycarbosilazane depolymerization strategy, which generates hydrosilane quantitatively along with complete conversion to the Bpin-protected diamine. The analogous Si-O bond cleavage can also be achieved with heating, using silyl ether starting materials to generate hydrosilane and alkoxyborane products. Depolymerization of poly(silyl ether)s using our strategy successfully converts the polymer to 90% Bpin-protected alcohols.

Evaluation of nuclear magnetic resonance spectroscopy for characterisation and quantitation of water-soluble polymers in river water

Water-soluble polymers (WSPs) are commonly used in industrial, commercial, agricultural and pharmaceutical products and their molecular weights and concentrations vary considerably. Methods commonly used in the analysis of WSPs are often for pure products or formulations with only a few other high MW constituents. These methods, like size exclusion chromatography (SEC) or Gel Permeation Chromatography coupled with Mass Spectrometry (MS) can be frustrated by the impact of the necessary separation steps prior to identification and the limitations of MS when identifying and quantifying polymers. To that end, the employment of a Nuclear Magnetic Resonance (NMR) method to identify, characterize and quantify WSPs in the real-world is reported for the first time. Samples were taken from fourteen UK inland river sites, concentrated via air-drying, freeze-drying or vacuum-drying and analyzed using 1D 1H NMR and 2D 1H Diffusion Ordered Spectroscopy (DOSY) NMR analysis. Seven of the river sites showed the presence of polyethylene glycol (PEG) with a range of molecular weights, evidencing the application of these techniques in analysis of WSPs. Soil percolation models evidenced the proof of principle that these techniques can also be used for the detection of polyacrylamide (PAM) and polyacrylic acid (PAA). This work should better enable the evaluation of the biological impact of WSPs on aquatic organisms in future studies.

Gas Permeation through Mechanically Resistant Self-Standing Membranes of a Neat Amorphous Organic Cage

The synthesis and characterization of a novel film-forming organic cage and of its smaller analogue are here described. While the small cage produced single crystals suitable for X-ray diffraction studies, the large one was isolated as a dense film. Due to its remarkable film-forming properties, this latter cage could be solution processed into transparent thin-layer films and mechanically stable dense self-standing membranes of controllable thickness. Thanks to these peculiar features, the membranes were also successfully tested for gas permeation, reporting a behavior similar to that found with stiff glassy polymers such as polymers of intrinsic microporosity or polyimides. Given the growing interest in the development of molecular-based membranes, for example for separation technologies and functional coatings, the properties of this organic cage were investigated by thorough analysis of their structural, thermal, mechanical and gas transport properties, and by detailed atomistic simulations.

Raman Diffusion-Ordered Spectroscopy

The Stokes-Einstein relation, which relates the diffusion coefficient of a molecule to its hydrodynamic radius, is commonly used to determine molecular sizes in chemical analysis methods. Here, we combine the size sensitivity of such diffusion-based methods with the structure sensitivity of Raman spectroscopy by performing Raman diffusion-ordered spectroscopy (Raman-DOSY). The core of the Raman-DOSY setup is a flow cell with a Y-shaped channel containing two inlets: one for the sample solution and one for the pure solvent. The two liquids are injected at the same flow rate, giving rise to two parallel laminar flows in the channel. After the flow stops, the solute molecules diffuse from the solution-filled half of the channel into the solvent-filled half at a rate determined by their hydrodynamic radius. The arrival of the solute molecules in the solvent-filled half of the channel is recorded in a spectrally resolved manner by Raman microspectroscopy. From the time series of Raman spectra, a two-dimensional Raman-DOSY spectrum is obtained, which has the Raman frequency on one axis and the diffusion coefficient (or equivalently, hydrodynamic radius) on the other. In this way, Raman-DOSY spectrally resolves overlapping Raman peaks arising from molecules of different sizes. We demonstrate Raman-DOSY on samples containing up to three compounds and derive the diffusion coefficients of small molecules, proteins, and supramolecules (micelles), illustrating the versatility of Raman-DOSY. Raman-DOSY is label-free and does not require deuterated solvents and can thus be applied to samples and matrices that might be difficult to investigate with other diffusion-based spectroscopy methods.

Nickel Complexes of Allyl and Vinyldiphenylphosphine

Monodentate phosphine-ligated nickel compounds, e.g., [Ni(PPh3)4] are relevant as active catalysts across a broad range of reactions. This report expands upon the coordination chemistry of this family, offering the reactivity of allyl- and vinyl-substituted diphenylphosphine (PPh2R) with [Ni(COD)2] (COD = 1,5-cyclooctadiene). These reactions provide three-coordinate dinickelacycles that are intermolecularly tethered through adjacent {Ni}-olefin interactions. The ring conformation of such cycles has been studied in the solid-state and using theoretical calculations. Here, a difference in reaction outcome is linked to the presence of an allyl vs vinyl group, where the former is observed to undergo rearrangement, bringing about challenges in clean product isolation.

Imaging Saturation Transfer Difference (STD) NMR: Affinity and Specificity of Protein-Ligand Interactions from a Single NMR Sample

We have combined saturation transfer difference NMR (STD NMR) with chemical shift imaging (CSI) and controlled concentration gradients of small molecule ligands to develop imaging STD NMR, a new tool for the assessment of protein-ligand interactions. Our methodology allows the determination of protein-ligand dissociation constants (K_D) and assessment of the binding specificity in a single NMR tube, avoiding time-consuming titrations. We demonstrate the formation of suitable and reproducible concentration gradients of ligand along the vertical axis of the tube, against homogeneous protein concentration, and present a CSI pulse sequence for the acquisition of STD NMR experiments at different positions along the sample tube. Compared to the conventional methodology in which the [ligand]/[protein] ratio is increased manually, we can perform STD NMR experiments at a greater number of ratios and construct binding epitopes in a fraction (∼20%) of the experimental time. Second, imaging STD NMR also allows us to screen for non-specific binders, by monitoring any variation of the binding epitope map at increasing [ligand]/[protein] ratios. Hence, the proposed method does carry the potential to speed up and smooth out the drug discovery process.

Synthesis and isolation of a triplet bismuthinidene with a quenched magnetic response

Large Spin-Orbit Coupling (SOC) is an intrinsic property of the heavy-elements that directly affects the electronic structures of the compounds. Herein we report the synthesis and characterization of a mono-coordinate bismuthinidene featuring a rigid and bulky ligand. All magnetic measurements (SQUID, NMR) point to a diamagnetic compound. However, multiconfigurational quantum chemical calculations predict the ground state of the compound to be dominated (76%) by a spin-triplet. The apparent diamagnetism is explained by an extremely large SOC induced positive zero-field-splitting of more than 4500 cm^-1 that leaves the M_S = 0 magnetic sublevel thermally isolated in the electronic ground state.

Empirically validated theoretical analysis of visual-spatial perception under change of nervous system arousal

Introduction

Visual-spatial perception is a process for extracting the spatial relationship between objects in the environment. The changes in visual-spatial perception due to factors such as the activity of the sympathetic nervous system (hyperactivation) or parasympathetic nervous system (hypoactivation) can affect the internal representation of the external visual-spatial world. We formulated a quantitative model of the modulation of visual-perceptual space under action by hyperactivation or hypoactivation-inducing neuromodulating agents. We showed a Hill equation based relationship between neuromodulator agent concentration and alteration of visual-spatial perception utilizing the metric tensor to quantify the visual space.

Methods

We computed the dynamics of the psilocybin (hyperactivation-inducing agent) and chlorpromazine (hypoactivation-inducing agent) in brain tissue. Then, we validated our quantitative model by analyzing the findings of different independent behavioral studies where subjects were assessed for alterations in visual-spatial perception under the action of psilocybin and under chlorpromazine. To validate the neuronal correlates, we simulated the effect of the neuromodulating agent on the computational model of the grid-cell network, and also performed diffusion MRI-based tractography to find the neural tracts between the cortical areas involved: V2 and the entorhinal cortex.

Results

We applied our computational model to an experiment (where perceptual alterations were measured under psilocybin) and found that for n (Hill-coefficient) = 14.8 and k = 1.39, the theoretical prediction followed experimental observations very well (χ2 test robustly satisfied, p > 0.99). We predicted the outcome of another psilocybin-based experiment using these values (n = 14.8 and k = 1.39), whereby our prediction and experimental outcomes were well corroborated. Furthermore, we found that also under hypoactivation (chlorpromazine), the modulation of the visual-spatial perception follows our model. Moreover, we found neural tracts between the area V2 and entorhinal cortex, thus providing a possible brain network responsible for encoding visual-spatial perception. Thence, we simulated the altered grid-cell network activity, which was also found to follow the Hill equation.

Conclusion

We developed a computational model of visuospatial perceptual alterations under altered neural sympathetic/parasympathetic tone. We validated our model using analysis of behavioral studies, neuroimaging assessment, and neurocomputational evaluation. Our quantitative approach may be probed as a potential behavioral screening and monitoring methodology in neuropsychology to analyze perceptual misjudgment and mishaps by highly stressed workers.

Diffusion and molecular partitioning in hierarchically complex virus-like particles

Viruses are diverse infectious agents found in virtually every type of natural environment. Due to the range of conditions in which viruses have evolved, they exhibit a wide range of structure and function which has been exploited for biotechnology. The self-assembly process of virus-like particles (VLPs), derived from structural virus components, allows for the assembly of a hierarchy of materials. Because VLPs are robust in both their assembly and the final product, functionality can be incorporated through design of their building blocks or chemical modification after their synthesis and assembly. In particular, encapsulation of active enzymes inside VLP results in macromolecular concentration approximating that of cells, introducing excluded volume effects on encapsulated cargo which are not present in traditional experiments done on dilute proteins. This work reviews the hierarchical assembly of VLPs, experiments investigating diffusion in VLP systems, and methods for partitioning of chemical species in VLPs as functional biomaterials.

Infrared Diffusion-Ordered Spectroscopy Reveals Molecular Size and Structure

Inspired by ideas from NMR, we have developed Infrared Diffusion-Ordered Spectroscopy (IR-DOSY), which simultaneously characterizes molecular structure and size. We rely on the fact that the diffusion coefficient of a molecule is determined by its size through the Stokes-Einstein relation, and achieve sensitivity to the diffusion coefficient by creating a concentration gradient and tracking its equilibration in an IR-frequency resolved manner. Analogous to NMR-DOSY, a two-dimensional IR-DOSY spectrum has IR frequency along one axis and diffusion coefficient (or equivalently, size) along the other, so the chemical structure and the size of a compound are characterized simultaneously. In an IR-DOSY spectrum of a mixture, molecules with different sizes are nicely separated into distinct sets of IR peaks. Extending this idea to higher dimensions, we also perform 3D-IR-DOSY, in which we combine the conformation sensitivity of femtosecond multi-dimensional IR spectroscopy with size sensitivity.

Turning Enantiomeric Relationships into Diastereomeric Ones: Self-Resolving α-Ureidophosphonates and Their Organocatalytic Enantioselective Synthesis

Controlling chiral recognition and chiral information transfer has major implications in areas ranging from drug design and asymmetric catalysis to supra- and macromolecular chemistry. Especially intriguing are phenomena associated with chiral self-recognition. The design of systems that show self-induced recognition of enantiomers, i.e., involving homochiral versus heterochiral dimers, is particularly challenging. Here, we report the chiral self-recognition of α-ureidophosphonates and its application as both a powerful analytical tool for enantiomeric ratio determination by NMR and as a convenient way to increase their enantiomeric purity by simple achiral column chromatography or fractional precipitation. A combination of NMR, X-ray, and DFT studies indicates that the formation of homo- and heterochiral dimers involving self-complementary intermolecular hydrogen bonds is responsible for their self-resolving properties. It is also shown that these often unnoticed chiral recognition phenomena can facilitate the stereochemical analysis during the development of new asymmetric transformations. As a proof of concept, the enantioselective organocatalytic hydrophosphonylation of alkylidene ureas toward self-resolving α-ureidophosphonates is presented, which also led us to the discovery of the largest family of self-resolving compounds reported to date.

Mucus-inspired organogel as an efficient absorbent and retention agent for volatile organic compounds

Nasal mucus plays a key role in the sense of smell by absorbing and transporting chemicals to olfactory receptors. Inspired by the physical properties of mucus that enable it to transport molecules despite its high viscosity, we developed a polymeric organogel with similar viscosity and analyzed its general performance. Through qualitative and quantitative analysis, we confirmed that the matrix viscosity mainly affects the absorption and retention of volatile organic compounds (VOCs) and not their diffusion inside the matrix. Additionally, the vapor pressure of VOCs influences the absorption and retention efficiencies of the matrix. Finally, a detailed understanding of the properties of mucus along with the use of sol-gel transition enabled us to create an efficient VOC absorbent and retention agent.

Modelling drug diffusion through unstirred water layers allows real-time quantification of free/loaded drug fractions and release kinetics from colloidal-based formulations

The correlation between in vivo and in vitro data is yet not sufficiently optimized to allow a significant reduction and replacement of animal testing in pharmaceutical development. One of the main reasons for this lies in the poor mechanistic understanding and interpretation of the physical mechanisms enabling formulation rely on for deploying the drug. One mechanism that still lacks a proper interpretation is the kinetics of drug release from nanocarriers. In this work, we investigate two different types of classical enabling formulations - i) cyclodextrin solutions and ii) liposomal dispersions - by a combination of an experimental method (i.e. UV-Vis localized spectroscopy) and mathematical modelling/numerical data fitting. With this approach, we are able to discriminate precisely between the amount of drug bound to nanocarriers or freely dissolved at any time point; in addition, we can precisely estimate the binding and diffusivity constants of all chemical species (free drug/bound drug). The results obtained should serve as the first milestone for the further development of reliable in vitro/in silico models for the prediction of in vivo drug bioavailability when enabling formulations are used.

Quantitative Interpretation of Protein Diffusion Coefficients in Mixed Protiated-Deuteriated Aqueous Solvents

Diffusion-ordered nuclear magnetic resonance (NMR) spectroscopy is widely used for the analysis of mixtures, dispersing the signals of different species in a two-dimensional spectrum according to their diffusion coefficients. However, interpretation of these diffusion coefficients is typically purely qualitative, for example, to deduce which species are bigger or smaller. In studies of proteins in solution, important questions concern the molecular weight of the proteins, the presence or absence of aggregation, and the degree of folding. The Stokes–Einstein Gierer–Wirtz estimation (SEGWE) method has been previously developed to simplify the complex relationship between diffusion coefficient and molecular mass, allowing the prediction of a species’ diffusion coefficient in a pure solvent based on its molecular weight. Here, we show that SEGWE can be extended to successfully predict both peptide and protein diffusion coefficients in mixed protiated–deuteriated water samples and, hence, distinguish effectively between globular and disordered proteins.

Eccrine Sweat Molecular Model for Development of de novo Biosensors

In this paper, we present a validated, novel, in silico molecular dynamics (MD) model of eccrine sweat with approx. 35k atoms developed using Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) program. CHARMMS36m force field for constituent atoms and SPC/E water model are used to develop this model. The model outputs transport properties such as self-diffusivity computed using mean squared displacement and bulk viscosity computed via Green-Kubo correlations, which are compared with existing literature values and experimental studies and presented. This validated model is intended to serve as a tool to develop eccrine sweat based biosensors.

Cluster self-assembly and anion binding by metal complexes of non-innocent thiazolidinyl-thiolate ligands

Zn^II and Fe^II chloride complexes of a di(methylthiazolidinyl)pyridine ligand were deprotonated to form the corresponding thiolate complexes supported by redox-active iminopyridine moieties. The thiolate donor groups are nucleophilic and reactive toward oxidants, electrophiles, and protons, while the pendant thiazolidine rings are available for hydrogen bonding. Anion exchange with the weakly-coordinating triflate anion resulted in self-assembly of the iminopyridine complexes to form a trimeric [M₃S₃] cluster. Hydrogen bonding closely associates anions with this trimetallic core.

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.