Ionic Covalent Organic Framework as a Dual Functional Sensor for Temperature and Humidity

Visual sensing of humidity and temperature by solids plays an important role in the everyday life and in industrial processes. Due to their hydrophobic nature, most covalent organic framework (COF) sensors often exhibit poor optical response when exposed to moisture. To overcome this challenge, the optical response is set out to improve, to moisture by incorporating H-bonding ionic functionalities into the COF network. A highly sensitive COF, consisting of guanidinium and diformylpyridine linkers (TG-DFP), capable of detecting changes in temperature and moisture content is fabricated. The hydrophilic nature of the framework enables enhanced water uptake, allowing the trapped water molecules to form a large number of hydrogen bonds. Despite the presence of non-emissive building blocks, the H-bonds restrict internal bond rotation within the COF, leading to reversible fluorescence and solid-state optical hydrochromism in response to relative humidity and temperature.

Water/Vapor Assisted Fabrication of Large-Area Superprotonic Conductive Covalent Organic Framework Membranes

Fabrication of large-area ionic covalent organic framework membranes (iCOMs) remains a grand challenge. Herein, the authors report the liquid water and water vapor-assisted fabrication of large-area superprotonic conductive iCOMs. A mixed monomer solution containing 1,3,5-triformylphloroglucinol (TFP) in 1,4-dioxane and p-diaminobenzenesulfonic acid (DABA) in water is first polymerized to obtain a pristine membrane which subsequently underwent crystallization process in mixed vapors containing water vapor. During the polymerization stage, water played a role of a diluting agent, weakening the Coulombic repulsion between sulfonic acid groups. During the crystallization stage, water vapor played a role of a structure-directing agent to facilitate the formation of highly crystalline, large-area iCOMs. The resulting membranes achieved a proton conductivity value of 0.76 S cm-1 at 90 °C under 100% relative humidity, which is among the highest ever reported. Using liquid water and water vapor as versatile additives open a novel avenue to the fabrication of large-area membranes from covalent organic frameworks and other kinds of crystalline organic framework materials.

Light-driven self-assembly of spiropyran-functionalized covalent organic framework

Controlling the number of molecular switches and their relative positioning within porous materials is critical to their functionality and properties. The proximity of many molecular switches to one another can hinder or completely suppress their response. Herein, a synthetic strategy involving mixed linkers is used to control the distribution of spiropyran-functionalized linkers in a covalent organic framework (COF). The COF contains a spiropyran in each pore which exhibits excellent reversible photoswitching behavior to its merocyanine form in the solid state in response to UV/Vis light. The spiro-COF possesses an urchin-shaped morphology and exhibits a morphological transition to 2D nanosheets and vesicles in solution upon UV light irradiation. The merocyanine-equipped COFs are extremely stable and possess a more ordered structure with enhanced photoluminescence. This approach to modulating structural isomerization in the solid state is used to develop inkless printing media, while the photomediated polarity change is used for water harvesting applications.

Fluorescent Molecular Rotors Based on Hinged Anthracene Carboxyimides

Temperature and viscosity are essential parameters in medicine, environmental science, smart materials, and biology. However, few fluorescent sensor publications mention the direct relationship between temperature and viscosity. Three anthracene carboxyimide-based fluorescent molecular rotors, 1DiAC∙Cl, 2DiAC∙Cl, and 9DiAC∙Cl, were designed and synthesized. Their photophysical properties were studied in various solvents, such as N, N-dimethylacetamide, N, N-dimethylformamide, 1-propanol, ethanol, dimethyl sulfoxide, methanol, and water. Solvent polarizability resulted in a solvatochromism effect for all three rotors and their absorption and emission spectra were analyzed via the Lippert-Mataga equation and multilinear analysis using Kamlet-Taft and Catalán parameters. The rotors exhibited red-shifted absorption and emission bands in solution on account of differences in their torsion angle. The three rotors demonstrated strong fluorescence in a high-viscosity environment due to restricted intramolecular rotation. Investigations carried out under varying ratios of water to glycerol were explored to probe the viscosity-based changes in their optical properties. A good linear correlation between the logarithms of fluorescence intensity and solution viscosity for two rotors, namely 2DiAC∙Cl and 9DiAC∙Cl, was observed as the percentage of glycerol increased. Excellent exponential regression between the viscosity-related temperature and emission intensity was observed for all three investigated rotors.

Three-state fluorescence hydrochromism of a fluorophore-spacer-receptor system with variations in relative humidity

The uptake of atmospheric moisture by hygroscopic materials can have marked effects on a material's physical and chemical properties. This is true of materials that go on to incorporate waters of hydration in their molecular structural lattice, forming stable hydrates with fluctuations in relative humidity (RH). Nevertheless, RH remains relatively uncontrolled for a variable that can fluctuate widely depending on geographical climate, weather fluctuations, and building HVAC system stability. Herein, we report a processable 1,8-napthalimide-based fluorophore-spacer-receptor system that unexpectedly exhibited reversible three-state fluorescence hydrochromism with changes in RH due to RH-induced solid state molecular rearrangement. Care should be taken to evaluate the impact of variations in RH when characterising the solid state emission properties of charged fluorescent materials.

Assembling covalent organic framework membranes via phase switching for ultrafast molecular transport

Fabrication of covalent organic framework (COF) membranes for molecular transport has excited highly pragmatic interest as a low energy and cost-effective route for molecular separations. However, currently, most COF membranes are assembled via a one-step procedure in liquid phase(s) by concurrent polymerization and crystallization, which are often accompanied by a loosely packed and less ordered structure. Herein, we propose a two-step procedure via a phase switching strategy, which decouples the polymerization process and the crystallization process to assemble compact and highly crystalline COF membranes. In the pre-assembly step, the mixed monomer solution is casted into a pristine membrane in the liquid phase, along with the completion of polymerization process. In the assembly step, the pristine membrane is transformed into a COF membrane in the vapour phase of solvent and catalyst, along with the completion of crystallization process. Owing to the compact and highly crystalline structure, the resultant COF membranes exhibit an unprecedented permeance (water ≈ 403 L m^-2 bar^-1 h^-1 and acetonitrile ≈ 519 L m^-2 bar^-1 h^-1). Our two-step procedure via phase switching strategy can open up a new avenue to the fabrication of advanced organic crystalline microporous membranes.

Are perioperative outcomes in cancer-related ventral incisional hernia repair worse than in the general population? An Abdominal Core Health Quality Collaborative (ACHQC) database study

PURPOSE

Patients with a history of cancer-related abdominal surgery undergoing incisional hernia repair (IHR) are highly heterogenous and increasingly prevalent. We explored whether cancer surgery should be considered an independent risk factor for worse IHR perioperative outcomes.

METHODS

Patients undergoing IHR between 2018 and 2020 were identified within the Abdominal Core Health Quality Collaborative (ACHQC). Regression models were used to assess associations between cancer operation history and 30 d surgical site occurrences-exclusive of infection (SSO-EIs), surgical site infections (SSIs), reoperations, time to recurrence, and quality of life (QoL) scores. Cancer cohort subgroup analysis was performed for operative approach and mesh location.

RESULTS

8019 patients who underwent IHR were identified in the ACHQC, 1321 of which had a history of cancer operation. Cancer cohort patients were more likely to be older, males with a higher ASA status and lower BMI, and have longer and wider hernias (p < 0.001). After adjusting for confounding, the cancer cohort was less likely to experience SSO-EIs (OR 0.74, 95% CI 0.59-0.94 p = 0.0092) and showed lower odds of SSIs, reoperations, and recurrence (SSI OR 0.7, 95% CI 0.47-1.05, p = 0.0542; reoperation OR 0.66, 95% CI 0.37-1.17, p = 0.1002; recurrence OR 0.8, 95% CI 0.63-1.02, p = 0.08). There was no difference in postoperative QoL scores between cohorts. There were also no differences in perioperative or QoL outcomes within the cancer cohort based on operative approach or mesh location.

CONCLUSION

These data show no evidence that history of cancer operation predisposes patients to worse incisional hernia repair perioperative or quality of life outcomes.

Luteolin alleviates non-alcoholic fatty liver disease in rats via restoration of intestinal mucosal barrier damage and microbiota imbalance involving in gut-liver axis

Nonalcoholic fatty liver disease (NAFLD) is demonstrated to be closely related to the disorder of gut microbiota and the intestinal mucosal barrier. Luteolin is a natural flavonoid with various activities. We aimed to investigate whether Luteolin can alleviate NAFLD and its possible mechanism involving the gut-liver axis. A rat NAFLD model was established by feeding a high-fat diet (HFD), and Luteolin was administered intragastrically. The effects of Luteolin on liver biochemical parameters, intestinal histopathology and integrity, gut microbiota, lipopolysaccharides (LPS), inflammatory cytokines, and the Toll-like receptor 4 (TLR4) signaling pathway were evaluated. We found that Luteolin restored the expression of the tight junction proteins in the intestine and ameliorated the increase permeability of the intestinal mucosa to Fluorescein isothiocyanate-dextran (FD4) caused by a high-fat diet, thus enhancing the function of the intestinal barrier. In addition, Luteolin inhibited the TLR4 signaling pathway in the liver, thereby reducing the secretion of pro-inflammatory factors and alleviating NAFLD. 16S rRNA gene sequencing revealed that Luteolin intervention significantly altered the composition of the gut microbiota in NAFLD rats and increased the richness of gut microbiota. Luteolin alleviates NAFLD in rats via restoration and repair of the damaged intestinal mucosal barrier and microbiota imbalance.

Unexpected three-state hydrochromism of a donor-acceptor self-complex with fluctuations in relative humidity

Water in our environment is ever present, particularly in our atmosphere, from which it may be adsorbed by materials hygroscopically. At the molecular level, the binding of water molecules to various materials is driven by weak interactions but can have profound effects on physical properties, including the donor-acceptor interactions in charge transfer (CT) salts. Herein we present the unexpected three-state hydrochromatic switching of a bipyridinium-based donor-acceptor self-complex with changes in relative humidity (RH) and subsequent stable hydrate formation. RH is typically an overlooked variable that can vary greatly. These findings suggest that care should be taken to consider fluctuations in RH when characterizing the solid state optical band gap and CT absorption bands for organic donor-acceptor CT salt complexes.

The Unusual Photochromic and Hydrochromic Switching Behavior of Cellulose-Embedded 1,8-Naphthalimide-Viologen Derivatives in the Solid-State

Stimuli-responsive chromic materials such as photochromics, hydrochromics, thermochromics, and electrochromics have a long history of capturing the attention of scientists due to their potential industrial applications and novelty in popular culture. However, hybrid chromic materials that combine two or more stimuli-triggered color changing properties are not so well known. Herein, we report a design strategy that has led to a series of emissive 1,8-naphthalimide-viologen dyads which exhibit unusual dual photochromic and hydrochromic switching behavior in the solid-state when embedded in a cellulose matrix. This behavior manifests as reversible solid state fluorescence hydrochromism upon changes in atmospheric relative humidity (RH), and reversible solid state photochromism upon generation of a cellulose-stabilized viologen radical cation. In this design strategy, the bipyridinium unit serves as both a water-sensitive receptor for the hydrochromic fluorophore-receptor system, and a photochromic group, capable of eliciting its own visible colorimetric response, generating a fluorescence quenching radical cation with prolonged exposure to ultraviolet (UV) light. These dyes can be inkjet-printed onto cellulose paper or drop-cast as cellulose powder-based films and can be unidirectionally cycled between three different states which can be characteristically visualized under UV light or visible light. The material's photochromism, hydrochromism, and underlying mechanism of action was investigated using computational analysis, dynamic vapor sorption/desorption isotherms, electron paramagnetic resonance spectroscopy, and variable humidity UV-Vis adsorption and fluorescence spectroscopies.

Surgical management of infected abdominal wall mesh: an analysis using the American Hernia Society Quality Collaborative

INTRODUCTION

Several management strategies exist for the treatment of infected abdominal mesh. Using the American Hernia Society Quality Collaborative, we examined management patterns and 30-day outcomes of infected mesh removal with concomitant incisional hernia repair.

METHODS

All patients undergoing incisional hernia repair with removal of infected mesh were identified. A complete repair (CR) was defined as fascial closure with mesh; a partial repair (PR) was defined as fascial closure without mesh or no fascial closure with mesh. A two-tailed p value less than or equal to 0.05 was considered statistically significant.

RESULTS

A total of 282 patients were identified: 136 patients in CR group and 146 patients in PR group. Patients had similar comorbidities but differed in wound class (class IV: 55% CR vs 83% SR, p < 0.001) and incidence of associated concomitant colorectal procedures (5% CR vs 18% SR, p = 0.015). Sublay placement was used primarily in CR (94%) compared to PR (52% inlay, 48% sublay). When comparing CR to PR, length of stay (median 6, p = 0.69), complications (40% vs 44%, p = 0.44), surgical site infections (16% vs 21%, p = 0.27), surgical site occurrence (30% vs 35%, p = 0.45), and readmission within 30 days (9% vs. 13%) were not statistically different.

CONCLUSIONS

Analysis of data from a multicenter hernia registry comparing CR and PR during infected mesh removal and concurrent incisional hernia repair has not identified higher rates of short-term complications between groups in the presence of infection.

Adsorption isotherms and kinetic studies for the removal of toxic reactive dyestuffs from contaminated water using a viologen-based covalent polymer

A polyviologen-based adsorbent was prepared via polymerization of a viologen-dialdehyde with a hydroxyl-substituted aryl-dihydrazide in acidified water.

Viologen–cucurbituril host/guest chemistry – redox control of dimerization versus inclusion

Two calix[4]arene systems, C23⁴⁺ and C24⁴⁺ – where 2 corresponds to the number of viologen units and 3–4 corresponds to the number of carbon atoms connecting the viologen units to the macrocyclic core – have been synthesized and led to the formation of [3]pseudorotaxanes when combined with either CB[7] or CB[8]. The [3]pseudorotaxanes spontaneously dissociate upon reduction of the bipyridinium units as the result of intramolecular dimerization of the two face-to-face viologen radical cations. CB[7] and CB[8]-based [2]pseudorotaxanes containing monomeric viologen guest model compounds, MC3²⁺ and MC⁴⁺, do not undergo decomplexation and dimerization following electrochemical reduction of their bipyridinium units.

Two calix[4]arenes with two viologen units separated by 3 or 4 carbon atoms from the macrocyclic core were synthesized and led to the formation of [3]pseudorotaxanes when combined with CB[7] or CB[8].

Multivariate one-sided testing in matched observational studies as an adversarial game

We present a multivariate one-sided sensitivity analysis for matched observational studies, appropriate when the researcher has specified that a given causal mechanism should manifest itself in effects on multiple outcome variables in a known direction. The test statistic can be thought of as the solution to an adversarial game, where the researcher determines the best linear combination of test statistics to combat nature’s presentation of the worst-case pattern of hidden bias. The corresponding optimization problem is convex, and can be solved efficiently even for reasonably sized observational studies. Asymptotically, the test statistic converges to a chi-bar-squared distribution under the null, a common distribution in order-restricted statistical inference. The test attains the largest possible design sensitivity over a class of coherent test statistics, and facilitates one-sided sensitivity analyses for individual outcome variables while maintaining familywise error control through its incorporation into closed testing procedures.

Rapid and Efficient Removal of Perfluorooctanoic Acid from Water with Fluorine-Rich Calixarene-Based Porous Polymers

On account of its nonbiodegradable nature and persistence in the environment, perfluorooctanoic acid (PFOA) accumulates in water resources and poses serious environmental issues in many parts of the world. Here, we present the development of two fluorine-rich calix[4]arene-based porous polymers, FCX4-P and FCX4-BP, and demonstrate their utility for the efficient removal of PFOA from water. These materials featured Brunauer-Emmett-Teller (BET) surface areas of up to 450 m² g^-1, which is slightly lower than their nonfluorinated counterparts (up to 596 m² g^-1). FCX4-P removes PFOA at environmentally relevant concentrations with a high rate constant of 3.80 g mg^-1 h^-1 and reached an exceptional maximum PFOA uptake capacity of 188.7 mg g^-1. In addition, it could be regenerated by simple methanol wash and reused without a significant decrease in performance.

Prediction of chlorine and fluorine crystal structures at high pressure using symmetry driven structure search with geometric constraints

The high-pressure properties of fluorine and chlorine are not yet well understood because both are highly reactive and volatile elements, which have made conducting diamond anvil cell and x-ray diffraction experiments a challenge. Here, we use ab initio methods to search for stable crystal structures of both elements at megabar pressures. We demonstrate how symmetry and geometric constraints can be combined to efficiently generate crystal structures that are composed of diatomic molecules. Our algorithm extends the symmetry driven structure search method [R. Domingos et al., Phys. Rev. B 98, 174107 (2018)] by adding constraints for the bond length and the number of atoms in a molecule while still maintaining generality. As a method of validation, we have tested our approach for dense hydrogen and reproduced the known molecular structures of Cmca-12 and Cmca-4. We apply our algorithm to study chlorine and fluorine in the pressure range of 10 GPa-4000 GPa while considering crystal structures with up to 40 atoms per unit cell. We predict chlorine to follow the same series of phase transformations as elemental iodine from Cmca to Immm to Fm3¯m, but at substantially higher pressures. We predict fluorine to transition from a C2/c to Cmca structure at 70 GPa, to a novel orthorhombic and metallic structure with P4₂/mmc symmetry at 2500 GPa, and finally to its cubic analog form with Pm3¯n symmetry at 3000 GPa.

Covalent Organic Framework Nanosheets as Reactive Fillers To Fabricate Free-Standing Polyamide Membranes for Efficient Desalination

Mixed matrix membranes (MMMs) have been increasingly utilized in membrane processes. Covalent organic frameworks (COFs) hold great promise as emergent nanofillers to fabricate high-performance MMMs; however, only few studies about COF materials in MMMs have been reported where COFs are all used as nonreactive fillers. Herein, we propose using -NH₂-functionalized COF nanosheets as reactive fillers (rCON) to fabricate MMMs. rCON altered the morphology and chemistry of MMMs by controlling the diffusion rate of piperazine through hydrogen bonding prior to the interfacial polymerization process and inducing the creation of ridges in the MMMs with subsequent increase in surface area (∼24%). rCON was chemically cross-linked to the trimesoyl chloride through amide bonding, subsequently elevating the hydrophilicity (∼35%) and fouling resistance of MMMs. The presence of -NH₂ groups elevated the rCON-PA compatibility, ensuring the high rCON loading of 5 wt % in the MMMs without sacrificing salt rejection. Accordingly, the PA-rCON MMMs exhibited a flux of 46.5 L m^-2 h^-1 bar^-1, which is 6.8 times higher than that of the pristine PA membrane, with a high rejection rate of 93.5% for Na₂SO₄.

Classical and non-classical melatonin receptor agonist-directed micellization of bipyridinium-based supramolecular amphiphiles in water

The addition of molecular recognition units into structures of amphiphiles is a means by which soft matter capable of undergoing template-directed micellization can be obtained. These supramolecular amphiphiles can bind with molecular templates using non-covalent bonding interactions, forming host-guest complexes that hold the amphiphiles together as they undergo micellization. In most cases, such templates are synthesized and designed for a specific molecular recognition motif. It is not clear, however, to what extent these types of amphiphile systems are responsive to members of a biologically derived class of molecular targets, for example, melatonin receptor agonists and their numerous isosteres. Herein, we describe the template-directed micellization and arrangement at the air-water interface of a bipyridinium-based gemini surfactant, driven by the influence of donor-acceptor CT interactions with a series of bioactive classical and non-classical melatonin isosteres. Under the conditions of templation by either 5-methoxytryptophol, N-acetylserotonin, N-acetyltryptamine, or the pharmaceutical agent agomelatine, favorable Gibbs free energies of micellization were observed with decreases in CMC by up to 70%, and concomitant increases of 28% in surface pressure, and decreases of 20% in contact angle versus untemplated solutions. Solid state thermochromic transition temperatures for inkjet-printed patterns of the templated amphiphile solutions were inversely correlated with trends observed for their respective CMCs, and exhibited no correlation to their binding constants. These findings contend for the generalizable use of melatonin receptor agonists as targets and/or templates for chemical systems, which rely on π-stacking donor-acceptor CT interactions in water to facilitate the actions of binding, sequestration, or template-directed self-assembly.

Is there an advantage to laparoscopy over open repair of primary umbilical hernias in obese patients? An analysis of the Americas Hernia Society Quality Collaborative (AHSQC)

PURPOSE

The most common techniques used to repair umbilical hernias are open and laparoscopic. As the obesity epidemic in the United States is growing, it is essential to understand how this morbidity affects umbilical hernia repairs. This study compares laparoscopic versus open umbilical hernia repairs in obese patients.

METHODS

All patients with body mass index (BMI) ≥ 30 kg/m² who underwent elective, open or laparoscopic repair of a primary umbilical hernia with mesh were identified from the Americas Hernia Society Quality Collaborative (AHSQC). A retrospective review of the prospectively collected data was conducted. Outcomes of interest included surgical site infections (SSI), surgical site occurrences requiring procedural intervention (SSOPI), hernia-related quality-of-life survey (HerQles), and long-term recurrence. A logistic regression model was used to generate propensity scores.

RESULTS

Of 1507 patients who met the inclusion criteria, 322 were laparoscopic, and 1185 were open cases. The laparoscopic group had higher mean BMI (37 ± 6 vs. 35 ± 5 kg/m² , P < 0.001 ) and mean hernia width (3 cm ± 1 vs. 2 cm ± 2, P < 0.001). Using a propensity score model, we controlled for several clinically relevant covariates. Propensity score adjustment showed no differences in the 30-day HerQles score (OR 0.93, 95% CI 0.58-1.49), SSI (OR 1.57, 95% CI 0.52-4.77), SSOPI (OR 2.85, 95% CI 0.84-9.62) or hernia recurrence (hazard ratio 0.86, 95% CI 0.50-1.49).

CONCLUSION

In obese patients with primary umbilical hernias, there is likely no benefit to laparoscopy over open umbilical hernia repair with mesh with regard to wound morbidity. Although, the long-term recurrence also showed no difference between these two approaches, overall follow up was lacking.

Intraperitonealversusretromuscular mesh placement for open incisional hernias: an analysis of the Americas Hernia Society Quality Collaborative

Background

Incisional hernia repair with mesh improves long-term outcomes, but the ideal mesh position remains unclear. This study compared intraperitoneal versus retromuscular or preperitoneal sublay (RPS) mesh positions for open incisional hernia repairs.

Methods

All patients who had elective open incisional hernia repairs were identified retrospectively in the Americas Hernia Society Quality Collaborative database. The primary outcome was the rate of 30-day surgical-site infection (SSI). Other outcomes of interest included 30-day surgical-site occurrences requiring procedural intervention (SSOPI), hernia-related quality-of-life survey (HerQLes) scores and long-term recurrence. A logistic model was used to generate propensity scores for mesh position using several clinically relevant co-variables. Regression models adjusting for propensity score and baseline characteristics were developed to assess the effect of mesh placement.

Results

A total of 4211 patients were included in the study population: 587 had intraperitoneal mesh and 3624 had RPS mesh. Analysis with propensity score adjustment provided no evidence for differences in SSOPI (odds ratio (OR) 0·79, 95 per cent c.i. 0·49 to 1·26) and SSI (OR 0·91, 0·50 to 1·67) rates or HerQLes scores at 30 days (OR 1·20, 0·79 to 1·82), or recurrence rates (hazard ratio 1·28, 0·90 to 1·82).

Conclusion

Mesh position had no effect on short- or long-term outcomes, including SSOPI and SSI rates, HerQLes scores and long-term recurrence rates.

Disorder-Order Transitions in Conformational Selection of a Peptide by Ebola Virus Nucleoprotein

This study presents parallel-tempering lattice Monte Carlo simulations based on the side-chain-only (SICHO) model for calculating the conformational landscape of a 28-residue intrinsically disordered peptide extracted from the Ebola virus protein VP35. The central issue is the applicability of the SICHO potential energy function and in general coarse-grained (CG) representations of intermediate resolution for modeling large-scale conformational heterogeneity that includes both folded and unstructured peptide states. Crystallographic data shows that the peptide folds in a 4₁₀-helix-turn-3₁₀-helix topology upon complex formation with the Ebola virus nucleoprotein, whereas in isolation, the peptide transitions to a disordered conformational ensemble as observed in circular dichroism experiments. The simulation reveals a potential of mean force that displays conformational diversity along the helix-forming reaction coordinate consistent with disorder-order transitions, yet unexpectedly the bound topology is poorly sampled, and a population shift to an unstructured state incurs a significant free-energy penalty. Applying an elastic network interpolation model suggests a hybrid binding mechanism through conformational selection of the 4₁₀-helix followed by an induced fit of the 3₁₀-helix. A comparison of the CG model with previously reported all-atom CHARMM-based simulations highlights a lattice-based approach that is computationally fast and with the correct parameterization yields good resolution to modeling conformational plasticity.

Augmented polyhydrazone formation in water by template-assisted polymerization using dual-purpose supramolecular templates

Template-assisted polymerization using donor–acceptor supramolecular templates results in higher M_w and M_n values, decreased critical hydrogelation concentrations, and increased gel recovery velocity following shear-induced breakdown.

Remarkably efficient removal of toxic bromate from drinking water with a porphyrin-viologen covalent organic framework

The presence of carcinogenic bromate (BrO₃⁻) in drinking water became a global concern and efforts towards its removal mainly focused on addressing the source. Herein, we rationally designed a porphyrin-based covalent organic framework (PV-COF) with a cationic surface to provide electrostatic interactions and a porphyrin core to induce hydrogen bonding interactions for the efficient removal of BrO₃⁻ from water. Through H-bonding and electrostatic interactions, PV-COF exhibited an exceptional bromate removal efficiency (maximum adsorption capacity, Q_max: 203.8 mg g⁻¹) with the fastest uptake rate (k_ads) of 191.45 g mg⁻¹ min⁻¹. The bromate concentration was reduced to far below the allowed concentration in drinking water (10 ppb) within 20 minutes. We studied the relationship between bromate adsorption and COF surface modification by metalation of the porphyrinic core or neutralization of the viologen linkers by chemical reduction. The bromate adsorption mechanism was studied by EDAX mapping and molecular simulations, and it was found that ion exchange and hydrogen bonding formation drive the adsorption. Importantly, PV-COF could be easily recycled several times without compromising its adsorption efficiency.

A cationic COF removes carcinogenic bromate with a remarkable rate constant of 191.45 g mg⁻¹ min⁻¹.

Experimental evaluation of single-domain antibodies predicted by molecular dynamics simulations to have elevated thermal stability

Recently Bekker et al. [Bekker G-J et al. Protein Sci. 2019;28:429-438.] described a computational strategy of applying molecular-dynamics simulations to estimate the relative stabilities of single-domain antibodies, and utilized their method to design changes with the aim of increasing the stability of a single-domain antibody with a known crystal structure. The structure from which they generated potentially stabilizing mutations is an anti-cholera toxin single domain antibody selected from a naïve library which has relatively low thermal stability, reflected by a melting point of 48°C. Their work was purely theoretical, so to examine their predictions, we prepared the parental and predicted stabilizing mutant single domain antibodies and examined their thermal stability, ability to refold and affinity. We found that the mutation that improved stability the most (~7°C) was one which changed an amino acid in CDR1 from an asparagine to an aspartic acid. This change unfortunately was also accompanied by a reduction in affinity. Thus, while their modeling did appear to successfully predict stabilizing mutations, introducing mutations in the binding regions is problematic. Of further interest, the mutations selected via their high temperature simulations, did improve refolding, suggesting that they were successful in stabilizing the structure at high temperatures and thereby decrease aggregation. Our result should permit them to reassess and refine their model and may one day lead to a usefulin silico approach to protein stabilization.

Sequence Tolerance of a Single-Domain Antibody with a High Thermal Stability: Comparison of Computational and Experimental Fitness Profiles

The sequence fitness of a llama single-domain antibody with an unusually high thermal stability is explored by a combined computational and experimental study. Starting with the X-ray crystallographic structure, RosettaBackrub simulations were applied to model sequence-structure tolerance profiles and identify key substitution sites. From the model calculations, an experimental site-directed mutagenesis was used to produce a panel of mutants, and their melting temperatures were determined by thermal denaturation. The results reveal a sequence fitness of an excess stability of approximately 12 °C, a value taken from a decrease in the melting temperature of an electrostatic charge-reversal substitution in the CRD3 without a deleterious effect on the binding affinity to the antigen. The tolerance for the disruption of antigen recognition without loss in the thermal stability was demonstrated by the introduction of a proline in place of a tyrosine in the CDR2, producing a mutant that eliminated binding. To further assist the sequence design and the selection of engineered single-domain antibodies, an assessment of different computational strategies is provided of their accuracy in the detection of substitution "hot spots" in the sequence tolerance landscape.

Design Strategies and Redox-Dependent Applications of Insoluble Viologen-Based Covalent Organic Polymers

Dicationic quaternary salts of 4,4'-bipyridine, also referred to as the viologen family, are well-known for their interesting redox chemistry, whereby they can be reversibly reduced into radical cationic and neutral moieties. Because of this ability to switch between different redox states, viologens have frequently been incorporated into covalent organic polymers (COPs) as molecular switches to construct stimuli-responsive materials. Although many viologen-based COPs have been reported, hyper-conjugated insoluble COPs started to emerge fairly recently and have not been comprehensively reviewed. In this review, we investigate the design strategies employed in the synthesis of insoluble viologen-based COPs, which can be broadly classified as those with viologen in the backbone and those with viologen as pendant groups. Chemical reactions used in the synthesis of each category, including Sonogashira-Hagihara cross-coupling, Menshutkin and Zincke reactions, are highlighted. Diverse applications of these COPs are discussed with particular reference to the redox state of viologen in each material. Uses of these materials for gas adsorption, organic and inorganic pollutant removal, catalysis, sensing and film fabrication are explored.

Correction: Covalent organic nanosheets for bioimaging

Correction for ‘Covalent organic nanosheets for bioimaging’ by Gobinda Das et al., Chem. Sci., 2018, DOI: ; 10.1039/c8sc02842g.

Conformational Selection of a Polyproline Peptide by Ebola Virus VP30

An adaptive temperature-based replica-exchange simulation of a peptide extracted from the Ebola virus nucleoprotein containing a polyproline sequence motif is reported. The simulation results of applying the CHARMM36m force field with a generalized Born solvent model is presented. Conformational heterogeneity is described by potentials of mean force (PMFs) for a set of reaction coordinates that define the topological fold space. Starting from an extended backbone conformation of the peptide observed in an X-ray crystallographic assembly with the Ebola virus protein VP30, the PMFs report a conformational landscape populated by chain excursions to collapsed states with limited transitions to either an extended fold or a canonical polyproline type II helix. Clustering of the conformations and applying an elastic network interpolation model yield a multistep pathway of conformational selection that minimizes the net transition-state cost from the population hub to the bound state. Related difference between the pathway endpoints taken from the PMFs reveal a significant free-energy penalty in reaching a population shift. To evaluate sequence fitness of the Ebola virus peptide in generating probability distributions, two human sequence variants are modeled and are found to produce profiles that show extensive deviations, thus suggesting either dissimilar binding mechanisms or the lack of recognition by VP30.

Covalent organic nanosheets for bioimaging

Non-toxic covalent organic nanosheet-based fluorescent nuclear stains.

Covalent organic nanosheets (CONs) have attracted much attention because of their excellent physical, chemical, electronic, and optical properties. Although covalent organic nanosheets have widely been used in many applications, there are only a few CONs that have been tested for bio-medical applications. Nanometer sized triazine-based nanosheets were obtained by exfoliating their bulk counterparts in water. The obtained nanosheets were dispersible and stable in water with enhanced photoluminescence properties compared to the bulk material. The nanosheets were biocompatible and non-toxic and showed ability to stain HeLa cell nuclei without additional assistance of an external targeting agent.

Melatonin-directed micellization: a case for tryptophan metabolites and their classical bioisosteres as templates for the self-assembly of bipyridinium-based supramolecular amphiphiles in water

The bulk solution properties of amphiphilic formulations are derivative of their self-assembly into higher ordered supramolecular assemblies known as micelles and of their ordering at the air-water interface. Exerting control over the surface-active properties of amphiphiles and their propensity to aggregate in pure water is most often fine-tuned by covalent modification of their molecular structure. Nevertheless structural constraints which limit the performance of amphiphiles do emerge when trying to develop more sophisticated systems which undergo for example, shape-defined controlled assembly and/or respond to external stimuli. In this regard, the template-modulated assembly of the so-called "supramolecular amphiphiles" continues to make progress ordering molecules that otherwise have very little to no driving force to aggregate in a prescribed manner in aqueous solutions. Herein we describe the template-modulated micellization and ordering at the air-water interface of bipyridinium-based supramolecular amphiphiles triggered by host-guest interactions with high specificity for the neurotransmitter melatonin over its biosynthetic synthon l-tryptophan and the thermodynamic parameters governing the template-modulated micellization process. When bound to the bipyridinium units of micellized surfactant molecules, melatonin effectively serves as "molecular glue" capable of lowering the CMC by 52% as compared to untemplated solutions. Analysis of this system suggests that a hallmark of donor-acceptor template-modulated micellization in water is a strong positively correlated temperature dependence of the CMC and the absence of a U-shaped CMC-temperature curve. Our findings make a case for the incorporation of l-tryptophan-based metabolites and their classical synthetic pharmaceutical bioisosteres as potential targets/components of donor-acceptor CT-based supramolecular amphiphile systems/materials operating in water.

Small Molecule Analogues of the parasitic worm product ES-62 interact with the TIR domain of MyD88 to inhibit pro-inflammatory signalling

ES-62 is a protein secreted by the parasitic worm Acanthocheilonema viteae that is anti-inflammatory by virtue of covalently attached phosphorylcholine. Previously we have reported that drug-like Small Molecule Analogues (SMAs) of its phosphorylcholine moiety can mimic ES-62 in protecting against disease development in certain mouse models of autoimmune and allergic conditions, due to them causing partial degradation of the TLR/IL-1R adaptor MyD88. We have now taken a molecular modelling approach to investigating the mechanism underlying this effect and this predicts that the SMAs interact directly with the MyD88 TIR domain. Further support for this is provided by assay of LPS-induced MyD88/NF-κB-driven secreted alkaline phosphatase (SEAP) reporter activity in commercially-available stably transfected (TLR4-MD2-NF-κB-SEAP) HEK293 cells, as SMA12b-mediated inhibition of such SEAP activity is blocked by its pre-incubation with recombinant MyD88-TIR domain. Direct binding of SMA12b to the TIR domain is also shown to inhibit homo-dimerization of the adaptor, an event that can explain the observed degradation of the adaptor and inhibition of subsequent downstream signalling. Thus, these new data identify initial events by which drug-like ES-62 SMAs, which we also demonstrate are able to inhibit cytokine production by human cells, homeostatically maintain "safe" levels of MyD88 signalling.

Rim-Differentiated C5-Symmetric Tiara-Pillar[5]arenes

The synthesis of “rim-differentiated” C₅-symmetric pillar[5]arenes, whose two rims are decorated with different chemical functionalities, has remained a challenging task. This is due to the inherent statistical nature of the cyclization of 1,4-disubstituted alkoxybenzenes with different substituents, which leads to four constitutional isomers with only 1/16th being rim-differentiated. Herein, we report a “preoriented” synthetic protocol based on FeCl₃-catalyzed cyclization of asymmetrically substituted 2,5-dialkoxybenzyl alcohols. This yields an unprecedented 55% selectivity of the C₅-symmetric tiara-like pillar[5]arene isomer among four constitutional isomers. Based on this new method, a series of functionalizable tiara-pillar[5]arene derivatives with C₅-symmetry was successfully synthesized, isolated, and fully characterized in the solid state.

Parallel Tempering of Dark Matter from the Ebola Virus Proteome: Comparison of CHARMM36m and CHARMM22 Force Fields with Implicit Solvent

Intrinsically disordered proteins are characterized by their large manifold of thermally accessible conformations and their related statistical weights, making them an interesting target of simulation studies. To assess the development of a computational framework for modeling this distinct class of proteins, this work examines temperature-based replica-exchange simulations to generate a conformational ensemble of a 28-residue peptide from the Ebola virus protein VP35. Starting from a prefolded helix-β-turn-helix topology observed in a crystallographic assembly, the simulation strategy tested is the recently refined CHARMM36m force field combined with a generalized Born solvent model. A comparison of two replica-exchange methods is provided, where one is a traditional approach with a fixed set of temperatures and the other is an adaptive scheme in which the thermal windows are allowed to move in temperature space. The assessment is further extended to include a comparison with equivalent CHARMM22 simulation data sets. The analysis finds CHARMM36m to shift the minimum in the potential of mean force (PMF) to a lower fractional helicity compared with CHARMM22, while the latter showed greater conformational plasticity along the helix-forming reaction coordinate. Among the simulation models, only the adaptive tempering method with CHARMM36m found an ensemble of conformational heterogeneity consisting of transitions between α-helix-β-hairpin folds and unstructured states that produced a PMF of fractional fold propensity in qualitative agreement with circular dichroism experiments reporting a disordered peptide.

[3+3] Cyclocondensation of Disubstituted Biphenyl Dialdehydes: Access to Inherently Luminescent and Optically Active Hexa-substituted C3-Symmetric and Asymmetric Trianglimine Macrocycles

A general synthetic route to inherently luminescent and optically active 6-fold substituted C₃-symmetric and asymmetric biphenyl-based trianglimines has been developed. The synthesis of these hexa-substituted triangular macrocycles takes advantage of a convenient method for the synthesis of symmetrically and asymmetrically difunctionalized biphenyl dialdehydes through a convergent two-step aromatic nucleophilic substitution-one-pot Suzuki-coupling reaction protocol. A modular [3+3] diamine-dialdehyde cyclocondensation reaction between both the symmetrically and asymmetrically difunctionalized-4,4'-biphenyldialdehydes with enantiomerically pure (1R,2R)-1,2-diaminocyclohexane was employed to construct the hexa-substituted triangular macrocycles. B97-D/6-311G(2d,p) density functional theory determined structures and X-ray crystallographic analysis reveal that the six substituents appended to the biphenyl legs of the trianglimine macrocycles adopt an alternating conformation not unlike the 1,3,5-alternate conformation observed for calix[6]arenes. Reduction of the imine bonds using NaBH₄ afforded the corresponding 6-fold substituted trianglamine without the need to alkylate the amine nitrogen atoms which could hinder their later use as metal coordination sites and without having to introduce asymmetric carbons.

On the Helix Propensity in Generalized Born Solvent Descriptions of Modeling the Dark Proteome

Intrinsically disordered proteins that populate the so-called “Dark Proteome” offer challenging benchmarks of atomistic simulation methods to accurately model conformational transitions on a multidimensional energy landscape. This work explores the application of parallel tempering with implicit solvent models as a computational framework to capture the conformational ensemble of an intrinsically disordered peptide derived from the Ebola virus protein VP35. A recent X-ray crystallographic study reported a protein-peptide interface where the VP35 peptide underwent a folding transition from a disordered form to a helix-β-turn-helix topological fold upon molecular association with the Ebola protein NP. An assessment is provided of the accuracy of two generalized Born solvent models (GBMV2 and GBSW2) using the CHARMM force field and applied with temperature-based replica exchange dynamics to calculate the disorder propensity of the peptide and its probability density of states in a continuum solvent. A further comparison is presented of applying an explicit/implicit solvent hybrid replica exchange simulation of the peptide to determine the effect of modeling water interactions at the all-atom resolution.

Membrane insertion of fusion peptides from Ebola and Marburg viruses studied by replica-exchange molecular dynamics simulations

This work presents replica-exchange molecular dynamics simulations of inserting a 16-residue Ebola virus fusion peptide into a membrane bilayer. A computational approach is applied for modeling the peptide at the explicit all-atom level and the membrane-aqueous bilayer by a generalized Born continuum model with a smoothed switching function (GBSW). We provide an assessment of the model calculations in terms of three metrics: (1) the ability to reproduce the NMR structure of the peptide determined in the presence of SDS micelles and comparable structural data on other fusion peptides; (2) determination of the effects of the mutation Trp-8 to Ala and sequence discrimination of the homologous Marburg virus; and (3) calculation of potentials of mean force for estimating the partitioning free energy and their comparison to predictions from the Wimley-White interfacial hydrophobicity scale. We found the GBSW implicit membrane model to produce results of limited accuracy in conformational properties of the peptide when compared to the NMR structure, yet the model resolution is sufficient to determine the effect of sequence differentiation on peptide-membrane integration. © 2016 Wiley Periodicals, Inc.

Complex formation dynamics in a single-molecule electronic device

Single-molecule electronic devices offer unique opportunities to investigate the properties of individual molecules that are not accessible in conventional ensemble experiments. However, these investigations remain challenging because they require (i) highly precise device fabrication to incorporate single molecules and (ii) sufficient time resolution to be able to make fast molecular dynamic measurements. We demonstrate a graphene-molecule single-molecule junction that is capable of probing the thermodynamic and kinetic parameters of a host-guest complex. By covalently integrating a conjugated molecular wire with a pendent crown ether into graphene point contacts, we can transduce the physical [2]pseudorotaxane (de)formation processes between the electron-rich crown ether and a dicationic guest into real-time electrical signals. The conductance of the single-molecule junction reveals two-level fluctuations that are highly dependent on temperature and solvent environments, affording a nondestructive means of quantitatively determining the binding and rate constants, as well as the activation energies, for host-guest complexes. The thermodynamic processes reveal the host-guest binding to be enthalpy-driven and are consistent with conventional ¹H nuclear magnetic resonance titration experiments. This electronic device opens up a new route to developing single-molecule dynamics investigations with microsecond resolution for a broad range of chemical and biochemical applications.

Stability of isolated antibody-antigen complexes as a predictive tool for selecting toxin neutralizing antibodies

Ricin is an A-B ribosome inactivating protein (RIP) toxin composed of an A-chain subunit (RTA) that contains a catalytic N-glycosidase and a B-chain (RTB) lectin domain that binds cell surface glycans. Ricin exploits retrograde transport to enter into the Golgi and the endoplasmic reticulum, and then dislocates into the cytoplasm where it can reach its substrate, the rRNA. A subset of isolated antibodies (Abs) raised against the RTA subunit protect against ricin intoxication, and RTA-based vaccine immunogens have been shown to provide long-lasting protective immunity against the holotoxin. Anti-RTA Abs are unlikely to cross a membrane and reach the cytoplasm to inhibit the enzymatic activity of the A-chain. Moreover, there is not a strict correlation between the apparent binding affinity (K_a) of anti-RTA Abs and their ability to successfully neutralize ricin toxicity. Some anti-RTA antibodies are toxin-neutralizing, whereas others are not. We hypothesize that neutralizing anti-RTA Abs may interfere selectively with conformational change(s) or partial unfolding required for toxin internalization. To test this hypothesis, we measured the melting temperatures (T_m) of neutralizing single-domain Ab (sdAb)-antigen (Ag) complexes relative to the T_m of the free antigen (T_m-shift = T_m^complex – T_m^Ag), and observed increases in the T_m^complex of 9–20 degrees. In contrast, non-neutralizing sdAb-Ag complexes shifted the T_m^Complex by only 6–7 degrees. A strong linear correlation (r² = 0.992) was observed between the magnitude of the T_m-shift and the viability of living cells treated with the sdAb and ricin holotoxin. The T_m-shift of the sdAb-Ag complex provided a quantitative biophysical parameter that could be used to predict and rank-order the toxin-neutralizing activities of Abs. We determined the first structure of an sdAb-RTA1-33/44-198 complex, and examined other sdAb-RTA complexes. We found that neutralizing sdAb bound to regions involved in the early stages of unfolding. These Abs likely interfere with steps preceding or following endocytosis that require conformational changes. This method may have utility for the characterization or rapid screening of other Ab that act to prevent conformational changes or unfolding as part of their mechanism of action.

Kinetic, Mutational, and Structural Studies of the Venezuelan Equine Encephalitis Virus Nonstructural Protein 2 Cysteine Protease

The Venezuelan equine encephalitis virus (VEEV) nonstructural protein 2 (nsP2) cysteine protease (EC 3.4.22.-) is essential for viral replication and is involved in the cytopathic effects (CPE) of the virus. The VEEV nsP2 protease is a member of MEROPS Clan CN and characteristically contains a papain-like protease linked to an S-adenosyl-l-methionine-dependent RNA methyltransferase (SAM MTase) domain. The protease contains an alternative active site motif, (475)NVCWAK(480), which differs from papain's (CGS(25)CWAFS), and the enzyme lacks a transition state-stabilizing residue homologous to Gln-19 in papain. To understand the roles of conserved residues in catalysis, we determined the structure of the free enzyme and the first structure of an inhibitor-bound alphaviral protease. The peptide-like E64d inhibitor was found to bind beneath a β-hairpin at the interface of the SAM MTase and protease domains. His-546 adopted a conformation that differed from that found in the free enzyme; one or both of the conformers may assist in leaving group departure of either the amine or Cys thiolate during the catalytic cycle. Interestingly, E64c (200 μM), the carboxylic acid form of the E64d ester, did not inhibit the nsP2 protease. To identify key residues involved in substrate binding, a number of mutants were analyzed. Mutation of the motif residue, N475A, led to a 24-fold reduction in kcat/Km, and the conformation of this residue did not change after inhibition. N475 forms a hydrogen bond with R662 in the SAM MTase domain, and the R662A and R662K mutations both led to 16-fold decreases in kcat/Km. N475 forms the base of the P1 binding site and likely orients the substrate for nucleophilic attack or plays a role in product release. An Asn homologous to N475 is similarly found in coronaviral papain-like proteases (PLpro) of the Severe Acute Respiratory Syndrome (SARS) virus and Middle East Respiratory Syndrome (MERS) virus. Mutation of another motif residue, K480A, led to a 9-fold decrease in kcat and kcat/Km. K480 likely enhances the nucleophilicity of the Cys. Consistent with our substrate-bound models, the SAM MTase domain K706A mutation increased Km 4.5-fold to 500 μM. Within the β-hairpin, the N545A mutation slightly but not significantly increased kcat and Km. The structures and identified active site residues may facilitate the discovery of protease inhibitors with antiviral activity.

Comparison of Replica Exchange Simulations of a Kinetically Trapped Protein Conformational State and its Native Form

Recently an X-ray crystallographic structure of a single-domain antibody was reported with the protein chain trapped in a rare homodimeric form. One of the conformers appears to exhibit a misfolded region, and thus presumably the configurational stability is less favorable. To investigate whether simulation methods can detect any difference between the conformers and buttress the notion that one conformation is trapped on a pathway that incurs lower activation energy to unfold, adaptive temperature-based replica exchange simulations were applied to each chain to model conformational transitions. Simulation results found that the observed crystallographic difference between the two chains in the complementarity determining region CDR2 induces a stark distinction in conformational populations on the energy landscape. An appraisal of the energetic difference between the CDR2 conformations at 300 K revealed a localized order-disorder free-energy transition of roughly equivalent to two peptide hydrogen bonds in solution. It was also found that interconversion between the conformers is slower than the rate to unfold and that near an unfolding transition temperature one conformer retained a greater fraction of native-like contacts and energy over a longer time span before fully populating the denatured state, thus verifying the coexistence of a metastable conformation in the crystallographic assembly.

Assessment of Detection and Refinement Strategies for de novo Protein Structures Using Force Field and Statistical Potentials

De novo predictions of protein structures at high resolution are plagued by the problem of detecting the native conformation from false energy minima. In this work, we provide an assessment of various detection and refinement protocols on a small subset of the second-generation all-atom Rosetta decoy set (Tsai et al. Proteins 2003, 53, 76-87) using two potentials:  the all-atom CHARMM PARAM22 force field combined with generalized Born/surface-area (GB-SA) implicit solvation and the DFIRE-AA statistical potential. Detection schemes included DFIRE-AA conformational scoring and energy minimization followed by scoring with both GB-SA and DFIRE-AA potentials. Refinement methods included short-time (1-ps) molecular dynamics simulations, temperature-based replica exchange molecular dynamics, and a new computational unfold/refold procedure. Refinement methods include temperature-based replica exchange molecular dynamics and a new computational unfold/refold procedure. Our results indicate that simple detection with only minimization is the best protocol for finding the most nativelike structures in the decoy set. The refinement techniques that we tested are generally unsuccessful in improving detection; however, they provide marginal improvements to some of the decoy structures. Future directions in the development of refinement techniques are discussed in the context of the limitations of the protocols evaluated in this study.