Bayesian Self-Optimization for Telescoped Continuous Flow Synthesis.

The optimization of multistep chemical syntheses is critical for the rapid development of new pharmaceuticals. However, concatenating individually optimized reactions can lead to inefficient multistep syntheses, owing to chemical interdependencies between the steps. Herein, we develop an automated continuous flow platform for the simultaneous optimization of telescoped reactions. Our approach is applied to a Heck cyclization-deprotection reaction sequence, used in the synthesis of a precursor for 1-methyltetrahydroisoquinoline C5 functionalization. A simple method for multipoint sampling with a single online HPLC instrument was designed, enabling accurate quantification of each reaction, and an in-depth understanding of the reaction pathways. Notably, integration of Bayesian optimization techniques identified an 81 % overall yield in just 14 h, and revealed a favorable competing pathway for formation of the desired product.

Multi-objective optimisation of polymerase chain reaction continuous flow systems.

A surrogate-enabled multi-objective optimisation methodology for a continuous flow Polymerase Chain Reaction (CFPCR) systems is presented, which enables the effect of the applied PCR protocol and the channel width in the extension zone on four practical objectives of interest, to be explored. High fidelity, conjugate heat transfer (CHT) simulations are combined with Machine Learning to create accurate surrogate models of DNA amplification efficiency, total residence time, total substrate volume and pressure drop throughout the design space for a practical CFPCR device with sigmoid-shape microfluidic channels. A series of single objective optimisations are carried out which demonstrate that DNA concentration, pressure drop, total residence time and total substrate volume within a single unitcell can be improved by up to [Formula: see text]5.7%, [Formula: see text]80.5%, [Formula: see text]17.8% and [Formula: see text]43.2% respectively, for the practical cases considered. The methodology is then extended to a multi-objective problem, where a scientifically-rigorous procedure is needed to allow designers to strike appropriate compromises between the competing objectives. A series of multi-objective optimisation results are presented in the form of a Pareto surface, which show for example how manufacturing and operating cost reductions from device miniaturisation and reduced power consumption can be achieved with minimal impact on DNA amplification efficiency. DNA amplification has been found to be strongly related to the residence time in the extension zone, but not related to the residence times in denaturation and annealing zones.

Towards sub-millisecond cryo-EM grid preparation.

Sample preparation is still a significant problem for many single particle cryo-EM workflows and our understanding and developments in the area lag behind that of image processing and microscope design. Over the last few years there has been growing evidence that many of the problems which occur during sample preparation are during the time the sample resides within the thin film created during the conventional blotting process. In parallel, faster grid preparation approaches have been developed for time-resolved cryo-EM experiments allowing for non-equilibrium intermediates to be captured on the ms timescale. Therefore, an important question is how fast can we prepare suitable grids for imaging by cryo-EM and how much does this mitigate the problems observed in sample preparation? Here we use a novel approach which has been developed for time-resolved studies to produce grids on an estimated sub-1 ms timescale. While the method comes with its own challenges, a 3.8 Å reconstruction of apoferritin prepared with the ultrafast method shows that good resolutions can be achieved. Although several orders of magnitude faster than conventional approaches we show using a ribosome sample, that interactions with the air-water interface cannot be avoided with preferred orientations still present. Therefore, the work shows that faster reactions can be captured but poses the question whether speed is the answer to problems with sample preparation.

Microfluidic In Vitro Platform for (Nano)Safety and (Nano)Drug Efficiency Screening.

Microfluidic technology is a valuable tool for realizing more in vitro models capturing cellular and organ level responses for rapid and animal-free risk assessment of new chemicals and drugs. Microfluidic cell-based devices allow high-throughput screening and flexible automation while lowering costs and reagent consumption due to their miniaturization. There is a growing need for faster and animal-free approaches for drug development and safety assessment of chemicals (Registration, Evaluation, Authorisation and Restriction of Chemical Substances, REACH). The work presented describes a microfluidic platform for in vivo-like in vitro cell cultivation. It is equipped with a wafer-based silicon chip including integrated electrodes and a microcavity. A proof-of-concept using different relevant cell models shows its suitability for label-free assessment of cytotoxic effects. A miniaturized microscope within each module monitors cell morphology and proliferation. Electrodes integrated in the microfluidic channels allow the noninvasive monitoring of barrier integrity followed by a label-free assessment of cytotoxic effects. Each microfluidic cell cultivation module can be operated individually or be interconnected in a flexible way. The interconnection of the different modules aims at simulation of the whole-body exposure and response and can contribute to the replacement of animal testing in risk assessment studies in compliance with the 3Rs to replace, reduce, and refine animal experiments.

On-Demand Electrochemical Synthesis of Tetrakisacetonitrile Copper(I) Triflate and Its Application in the Aerobic Oxidation of Alcohols.

An on-demand electrochemical synthesis of copper(I) triflate under both batch and continuous flow conditions has been developed. A major benefit of the electrochemical methodology is that the only byproduct of the reaction is hydrogen gas, which obviates the need for workup and purification, and water is not incorporated into the product. Upon completion of the electrochemical synthesis, solutions are directly transferred or dispensed into reaction mixtures for the catalytic oxidation of benzyl alcohol with no requirement for workup or purification.

Predicting Solvent-Dependent Nucleophilicity Parameter with a Causal Structure Property Relationship.

Solvent-dependent reactivity is a key aspect of synthetic science, which controls reaction selectivity. The contemporary focus on new, sustainable solvents highlights a need for reactivity predictions in different solvents. Herein, we report the excellent machine learning prediction of the nucleophilicity parameter N in the four most-common solvents for nucleophiles in the Mayr's reactivity parameter database (R2 = 0.93 and 81.6% of predictions within ±2.0 of the experimental values with Extra Trees algorithm). A Causal Structure Property Relationship (CSPR) approach was utilized, with focus on the physicochemical relationships between the descriptors and the predicted parameters, and on rational improvements of the prediction models. The nucleophiles were represented with a series of electronic and steric descriptors and the solvents were represented with principal component analysis (PCA) descriptors based on the ACS Solvent Tool. The models indicated that steric factors do not contribute significantly, because of bias in the experimental database. The most important descriptors are solvent-dependent HOMO energy and Hirshfeld charge of the nucleophilic atom. Replacing DFT descriptors with Parameterization Method 6 (PM6) descriptors for the nucleophiles led to an 8.7-fold decrease in computational time, and an ∼10% decrease in the percentage of predictions within ±2.0 and ±1.0 of the experimental values.

Confinement generates single-crystal aragonite rods at room temperature.

The topic of calcite and aragonite polymorphism attracts enormous interest from fields including biomineralization and paleogeochemistry. While aragonite is only slightly less thermodynamically stable than calcite under ambient conditions, it typically only forms as a minor product in additive-free solutions at room temperature. However, aragonite is an abundant biomineral, and certain organisms can selectively generate calcite and aragonite. This fascinating behavior has been the focus of decades of research, where this has been driven by a search for specific organic macromolecules that can generate these polymorphs. However, despite these efforts, we still have a poor understanding of how organisms achieve such selectivity. In this work, we consider an alternative possibility and explore whether the confined volumes in which all biomineralization occurs could also influence polymorph. Calcium carbonate was precipitated within the cylindrical pores of track-etched membranes, where these enabled us to systematically investigate the relationship between the membrane pore diameter and polymorph formation. Aragonite was obtained in increasing quantities as the pore size was reduced, such that oriented single crystals of aragonite were the sole product from additive-free solutions in 25-nm pores and significant quantities of aragonite formed in pores as large as 200 nm in the presence of low concentrations of magnesium and sulfate ions. This effect can be attributed to the effect of the pore size on the ion distribution, which becomes of increasing importance in small pores. These intriguing results suggest that organisms may exploit confinement effects to gain control over crystal polymorph.

Dynamic Crystallization Pathways of Polymorphic Pharmaceuticals Revealed in Segmented Flow with Inline Powder X-ray Diffraction.

Understanding the transitions between polymorphs is essential in the development of strategies for manufacturing and maximizing the efficiency of pharmaceuticals. However, this can be extremely challenging: crystallization can be influenced by subtle changes in environment, such as temperature and mixing intensity or even imperfections in the crystallizer walls. Here, we highlight the importance of in situ measurements in understanding crystallization mechanisms, where a segmented flow crystallizer was used to study the crystallization of the pharmaceuticals urea: barbituric acid (UBA) and carbamazepine (CBZ). The reactor provides highly reproducible reaction conditions, while in situ synchrotron powder X-ray diffraction (PXRD) enables us to monitor the evolution of this system. UBA has two polymorphs of almost equivalent free-energy and so is typically obtained as a polymorphic mixture. In situ PXRD analysis uncovered a progression of polymorphs from UBA III to the thermodynamic polymorph UBA I, where different positions along the length of the tubular flow crystallizer correspond to different reaction times. Addition of UBA I seed crystals modified this pathway such that only UBA I was observed throughout, while transformation from UBA III into UBA I still occurred in the presence of UBA III seeds. Information regarding the mixing-dependent kinetics of the CBZ form II to III transformation was also uncovered in a series of seeded and unseeded flow crystallization runs, despite atypical habit expression. These results illustrate the importance of coupling controlled reaction environments with in situ XRD to study the phase relationships in polymorphic materials.

Reaction Rate Governs the Viscoelasticity and Nanostructure of Folded Protein Hydrogels.

Hydrogels constructed from folded protein domains are of increasing interest as resilient and responsive biomaterials, but their optimization for applications requires time-consuming and costly molecular design. Here, we explore a complementary approach to control their properties by examining the influence of crosslinking rate on the structure and viscoelastic response of a model hydrogel constructed from photochemically crosslinked bovine serum albumin (BSA). Gelation is observed to follow a heterogeneous nucleation pathway in which BSA monomers crosslink into compact nuclei that grow into fractal percolated networks. Both the viscoelastic response probed by shear rheology and the nanostructure probed by small-angle X-ray scattering (SAXS) are shown to depend on the photochemical crosslinking reaction rate, with increased reaction rates corresponding to higher viscoelastic moduli, lower fractal dimension, and higher fractal cluster size. Reaction rate-dependent changes are shown to be consistent with a transition between diffusion- and rate-limited assembly, and the corresponding changes to viscoelastic response are proposed to arise from the presence of nonfractal depletion regions, as confirmed by SAXS. This controllable nanostructure and viscoelasticity constitute a potential route for the precise control of hydrogel properties, without the need for molecular modification.

Inducing protein aggregation by extensional flow.

Relative to other extrinsic factors, the effects of hydrodynamic flow fields on protein stability and conformation remain poorly understood. Flow-induced protein remodeling and/or aggregation is observed both in Nature and during the large-scale industrial manufacture of proteins. Despite its ubiquity, the relationships between the type and magnitude of hydrodynamic flow, a protein's structure and stability, and the resultant aggregation propensity are unclear. Here, we assess the effects of a defined and quantified flow field dominated by extensional flow on the aggregation of BSA, ß2-microglobulin (ß2m), granulocyte colony stimulating factor (G-CSF), and three monoclonal antibodies (mAbs). We show that the device induces protein aggregation after exposure to an extensional flow field for 0.36-1.8 ms, at concentrations as low as 0.5 mg mL-1 In addition, we reveal that the extent of aggregation depends on the applied strain rate and the concentration, structural scaffold, and sequence of the protein. Finally we demonstrate the in situ labeling of a buried cysteine residue in BSA during extensional stress. Together, these data indicate that an extensional flow readily unfolds thermodynamically and kinetically stable proteins, exposing previously sequestered sequences whose aggregation propensity determines the probability and extent of aggregation.

Experimental and Theoretical Investigation of Droplet Evaporation on Heated Hydrophilic and Hydrophobic Surfaces.

The evaporation characteristics of sessile droplets on heated hydrophobic and hydrophilic surfaces are investigated. Results are reported for the evaporation of water droplet volumes covering a range of shapes dominated by surface tension or gravity and over a range of temperatures between 40 and 60 °C. The weight evolution and total time of evaporation is measured using a novel self-contained heating stage on a high resolution analytical balance, which has advantages over visualization measurement techniques as it allows free choice of the initial droplet size and surface and the ability to record the droplet evaporation right through to the final stages of droplet life. Evaporation is modeled through a combination of a constant contact area and a constant contact angle model with the switch from the former to the latter occurring when the contact angle falls below its predetermined receding value. Theoretical results compare well with the experimental results for the hydrophobic substrate. However, a significant deviation is observed for the hydrophilic substrate due to the combined effects of the droplet surface cooling due to evaporation and buoyancy effects that are not included in the model. The proposed method of using the stick-slip model offers a convenient means of modeling droplet evaporation by mimicking the drying modes based on initial measurements of the static and receding contact angles.

A Hybridised Optimisation of an Automated Photochemical Continuous Flow Reactor.

A new hybridized algorithm that combines process optimisation with response surface mapping was developed and applied in an automated continuous flow reaction. Moreover, a photochemical cascade CSTR was developed and characterised by chemical actinometry, showing photon flux density of ten times greater than previously reported in batch. The success of the algorithm was then evaluated in the aerobic oxidation of sp³ C-H bonds using benzophenone as photosensitizer in the newly developed photo reactor.

Using extensional flow to reveal diverse aggregation landscapes for three IgG1 molecules.

Monoclonal antibodies (mAbs) currently dominate the biopharmaceutical sector due to their potency and efficacy against a range of disease targets. These proteinaceous therapeutics are, however, susceptible to unfolding, mis-folding, and aggregation by environmental perturbations. Aggregation thus poses an enormous challenge to biopharmaceutical development, production, formulation, and storage. Hydrodynamic forces have also been linked to aggregation, but the ability of different flow fields (e.g., shear and extensional flow) to trigger aggregation has remained unclear. To address this question, we previously developed a device that allows the degree of extensional flow to be controlled. Using this device we demonstrated that mAbs are particularly sensitive to the force exerted as a result of this flow-field. Here, to investigate the utility of this device to bio-process/biopharmaceutical development, we quantify the effects of the flow field and protein concentration on the aggregation of three mAbs. We show that the response surface of mAbs is distinct from that of bovine serum albumin (BSA) and also that mAbs of similar sequence display diverse sensitivity to hydrodynamic flow. Finally, we show that flow-induced aggregation of each mAb is ameliorated by different buffers, opening up the possibility of using the device as a formulation tool. Perturbation of the native state by extensional flow may thus allow identification of aggregation-resistant mAb candidates, their bio-process parameters and formulation to be optimized earlier in the drug-discovery pipeline using sub-milligram quantities of material.

Highly Productive Oxidative Biocatalysis in Continuous Flow by Enhancing the Aqueous Equilibrium Solubility of Oxygen.

We report a simple, mild, and synthetically clean approach to accelerate the rate of enzymatic oxidation reactions by a factor of up to 100 when compared to conventional batch gas/liquid systems. Biocatalytic decomposition of H2 O2 is used to produce a soluble source of O2 directly in reaction media, thereby enabling the concentration of aqueous O2 to be increased beyond equilibrium solubility under safe and practical conditions. To best exploit this method, a novel flow reactor was developed to maximize productivity (g product L-1 h-1 ). This scalable benchtop method provides a distinct advantage over conventional bio-oxidation in that no pressurized gas or specialist equipment is employed. The method is general across different oxidase enzymes and compatible with a variety of functional groups. These results culminate in record space-time yields for bio-oxidation.

Rapid Mapping of Protein Interactions Using Tag-Transfer Photocrosslinkers.

Analysing protein complexes by chemical crosslinking-mass spectrometry (XL-MS) is limited by the side-chain reactivities and sizes of available crosslinkers, their slow reaction rates, and difficulties in crosslink enrichment, especially for rare, transient or dynamic complexes. Here we describe two new XL reagents that incorporate a methanethiosulfonate (MTS) group to label a reactive cysteine introduced into the bait protein, and a residue-unbiased diazirine-based photoactivatable XL group to trap its interacting partner(s). Reductive removal of the bait transfers a thiol-containing fragment of the crosslinking reagent onto the target that can be alkylated and located by MS sequencing and exploited for enrichment, enabling the detection of low abundance crosslinks. Using these reagents and a bespoke UV LED irradiation platform, we show that maximum crosslinking yield is achieved within 10 seconds. The utility of this "tag and transfer" approach is demonstrated using a well-defined peptide/protein regulatory interaction (BID80-102 /MCL-1), and the dynamic interaction interface of a chaperone/substrate complex (Skp/OmpA).

Detection and quantification of new psychoactive substances (NPSs) within the evolved "legal high" product, NRG-2, using high performance liquid chromatography-amperometric detection (HPLC-AD).

The global increase in the production and abuse of cathinone-derived New Psychoactive Substances (NPSs) has developed the requirement for rapid, selective and sensitive protocols for their separation and detection. Electrochemical sensing of these compounds has been demonstrated to be an effective method for the in-field detection of these substances, either in their pure form or in the presence of common adulterants, however, the technique is limited in its ability to discriminate between structurally related cathinone-derivatives (for example: (±)-4'-methylmethcathinone (4-MMC, 2a) and (±)-4'-methyl-N-ethylmethcathinone (4-MEC, 2b) when they are both present in a mixture. In this paper we demonstrate, for the first time, the combination of HPLC-UV with amperometric detection (HPLC-AD) for the qualitative and quantitative analysis of 4-MMC and 4-MEC using either a commercially available impinging jet (LC-FC-A) or custom-made iCell channel (LC-FC-B) flow-cell system incorporating embedded graphite screen-printed macroelectrodes. The protocol offers a cost-effective, reproducible and reliable sensor platform for the simultaneous HPLC-UV and amperometric detection of the target analytes. The two systems have similar limits of detection, in terms of amperometric detection [LC-FC-A: 14.66 µg mL(-1) (2a) and 9.35 µg mL(-1) (2b); LC-FC-B: 57.92 µg mL(-1) (2a) and 26.91 µg mL(-1) (2b)], to the previously reported oxidative electrochemical protocol [39.8 µg mL(-1) (2a) and 84.2 µg mL(-1) (2b)], for two synthetic cathinones, prevalent on the recreational drugs market. Though not as sensitive as standard HPLC-UV detection, both flow cells show a good agreement, between the quantitative electroanalytical data, thereby making them suitable for the detection and quantification of 4-MMC and 4-MEC, either in their pure form or within complex mixtures. Additionally, the simultaneous HPLC-UV and amperometric detection protocol detailed herein shows a marked improvement and advantage over previously reported electroanalytical methods, which were either unable to selectively discriminate between structurally related synthetic cathinones (e.g. 4-MMC and 4-MEC) or utilised harmful and restrictive materials in their design.

Development and validation of a mouse model to investigate post surgical pain after laparotomy.

Background: Postoperative pain following abdominal surgery is a significant obstacle to patient recovery, often necessitating high analgesic doses associated with adverse effects like cognitive impairment and cardiorespiratory depression. Reliable animal models are crucial for understanding the pathophysiology of post surgical pain and developing more effective pain-relieving strategies. Methods: We developed a mouse model to replicate peritoneal trauma induced by abdominal surgery. 30 C57BL/6 mice underwent laparotomy, with half undergoing standardised peritoneal abrasion and the rest serving as controls. Mouse recovery was assessed using two validated scoring systems of surgical recovery: Post surgery Severity Assessment (PSSA) and Mouse Grimace Score (MGS). Blood samples were taken for cytokine analysis. Adhesions were evaluated on day 6, and peritoneal tissue was examined for healing markers. Results: After laparotomy, all mice exhibited expected pain profiles. Mice with peritoneal abrasion had significantly higher PSSA (7.2 ± 1.2 vs 4.68 ± 0.82, p ≤ 0.001) and MGS scores (3.62 ± 0.74 vs 0.82 ± 0.40, p ≤ 0.05) with slower recovery. Serum inflammatory cytokine levels were significantly elevated in the abraded group, and adhesion formation was higher in this group. Immunohistochemical analysis showed significantly increased expression of α-SMA, CD31, CD68, and F4/80 in peritoneal tissue in the abraded group. Discussion: A mouse model involving laparotomy and standardised peritoneal abrasion replicates the expected pathophysiological changes following abdominal surgery. It will be a useful model for better understanding the mechanisms of post surgical pain and developing improved pain-relief strategies. It also has utility for the study of intra-abdominal adhesion formation. Key message: To understand the intricate relationship between peritoneal trauma-induced pain, cytokine response, and post-operative adhesion formation in mouse models for advancing therapeutic interventions and enhancing post-operative recovery outcomes.

A Coalescing Filter for Liquid-Liquid Separation and Multistage Extraction in Continuous-Flow Chemistry.

Presented here is the design and performance of a coalescing liquid-liquid filter, based on low-cost and readily available meltblown nonwoven substrates for separation of immiscible phases. The performance of the coalescer was determined across three broad classes of fluid mixtures: (i) immiscible organic/aqueous systems, (ii) a surfactant laden organic/aqueous system with modification of the type of emulsion and interfacial surface tension through the addition of sodium chloride, and (iii) a water-acetone/toluene system. The first two classes demonstrated good performance of the equipment in effecting separation, including the separation of a complex emulsion system for which a membrane separator, operating through transport of a preferentially wetting fluid through the membrane, failed entirely. The third system was used to demonstrate the performance of the separator within a multistage liquid-liquid counterflow extraction system. The performance, robust nature, and scalability of coalescing filters should mean that this approach is routinely considered for liquid-liquid separations and extractions within the fine chemical and pharmaceutical industry.

Activation of fluoride anion as nucleophile in water with data-guided surfactant selection.

A principal component surfactant_map was developed for 91 commonly accessible surfactants for use in surfactant-enabled organic reactions in water, an important approach for sustainable chemical processes. This map was built using 22 experimental and theoretical descriptors relevant to the physicochemical nature of these surfactant-enabled reactions, and advanced principal component analysis algorithms. It is comprised of all classes of surfactants, i.e. cationic, anionic, zwitterionic and neutral surfactants, including designer surfactants. The value of this surfactant_map was demonstrated in activating simple inorganic fluoride salts as effective nucleophiles in water, with the right surfactant. This led to the rapid development (screening 13-15 surfactants) of two fluorination reactions for ß-bromosulfides and sulfonyl chlorides in water. The latter was demonstrated in generating a sulfonyl fluoride with sufficient purity for direct use in labelling of chymotrypsin, under physiological conditions.

Determining Phase Separation Dynamics with an Automated Image Processing Algorithm.

The problems of extracting products efficiently from reaction workups are often overlooked. Issues such as emulsions and rag layer formation can cause long separation times and slow production, thus resulting in manufacturing inefficiencies. To better understand science within this area and to support process development, an image processing methodology has been developed that can automatically track the interface between liquid-liquid phases and provide a quantitative measure of the separation rate of two immiscible liquids. The algorithm is automated and has been successfully applied to 29 cases. Its robustness has been demonstrated with a variety of different liquid mixtures that exhibit a wide range of separation behavior-making such an algorithm suited to high-throughput experimentation. The information gathered from applying the algorithm shows how issues resulting from poor separations can be detected early in process development.