Fluoromethylketone-Fragment Conjugates Designed as Covalent Modifiers of EcDsbA are Atypical Substrates.

Disulfide bond protein A (DsbA) is an oxidoreductase enzyme that catalyzes the formation of disulfide bonds in Gram-negative bacteria. In Escherichia coli, DsbA (EcDsbA) is essential for bacterial virulence, thus inhibitors have the potential to act as antivirulence agents. A fragment-based screen was conducted against EcDsbA and herein we describe the development of a series of compounds based on a phenylthiophene hit identified from the screen. A novel thiol reactive and "clickable" ethynylfluoromethylketone was designed for reaction with azide-functionalized fragments to enable rapid and versatile attachment to a range of fragments. The resulting fluoromethylketone conjugates showed selectivity for reaction with the active site thiol of EcDsbA, however unexpectedly, turnover of the covalent adduct was observed. A mechanism for this turnover was investigated and proposed which may have wider ramifications for covalent reactions with dithiol-disulfide oxidoreducatases.

Effects of Ionic Liquids on the Nucleofugality of Bromide.

The nucleofugality of bromide was measured in solvent mixtures containing ionic liquids. The solvolysis rate constants of the bromides of well-defined electrofuges were determined in mixtures containing different proportions of 1-butyl-3-methylimidazolium bis(trifluoromethanesulfonyl)imide in ethanol. Temperature-dependent kinetic studies allowed an explanation of the observed solvent effects in different mixtures in terms of interactions in solution. Using the solvolysis data, the nucleofugality of bromide in these systems was determined. Likewise, nucleofugality data for bromide were determined in mixtures containing high proportions of seven further ionic liquids. These data allowed quantification of the effects of both varying the amount of ionic liquid and the nature of ionic liquid components on the nucleofugality of bromide. Importantly, ionic liquid mixtures were shown to affect the nucleofugality in a manner similar to chloride, providing a method for predicting the effects of ionic liquids on other electrofuges. Further, the ionic liquids were shown to move the transition state earlier along the reaction coordinate, meaning that there is less charge development in the transition state.

Thermal Stability of Protic Ionic Liquids.

While protic ionic liquids (ILs) have found great success as solvents for a broad range of applications, little is known about their degradation when exposed to temperatures above ambient for extended periods of time. Here, we report the thermal stability of six protic ILs, namely, ethylammonium nitrate, ethylammonium formate, ethylammonium acetate, ethanolammonium nitrate, ethanolammonium formate, and ethanolammonium acetate. The effect of heating each ionic liquid to 60 °C for 1 h or 1 week (sealed or open to the atmosphere) was evaluated by considering the changes to water content, pH, mass, thermal phase transitions, and molecular structure after each treatment. Heating each of the six ILs when sealed led to measurable shifts in their water content and 10 wt % pH, but there was no significant change in their mass, thermal phase transitions according to differential scanning calorimetry (DSC), or molecular structure using proton nuclear magnetic resonance (1H NMR) spectra, indicating that the samples were largely unchanged. The samples that were heated open to the atmosphere also displayed no significant changes after 1 h but displayed significant changes after 1 week.

The effects of ionic liquids on the ethanolysis of a chloroacenaphthene. Evaluation of the effectiveness of nucleofugality data to predict reaction outcome.

The reaction of a chlorobenzene in mixtures containing ethanol and eight different ionic liquids was investigated in order to understand the effects of varying proportions and constituent ions of an ionic liquid on the rate constant of the process. The results were found to be generally consistent with previously studied reactions of the same type, with small proportions of an ionic liquid resulting in a rate constant increase compared to ethanol and large proportions causing a rate constant decrease. Temperature dependent kinetic studies were used to interpret the changes in reaction outcome, particularly noting an entropic cost on moving to high proportions of ionic liquid, consistent with organisation of solvent around the transition state. While attempts to use empirical solvent parameters to correlate outcome with the ionic liquid used were unsuccessful, use of recently acquired nucleofugality data for chloride and estimations for the electrofuge allowed for excellent prediction of the effects of ionic liquids, with rate constants quantitatively predicted in systems containing both different proportions of ionic liquid (mean absolute error (MAE) log(k1) = 0.11) and different ionic liquids (MAE log(k1) = 0.33). Importantly, this demonstrates the ready application of these quantitative reactivity parameters.

Diffusion Measurements To Understand Dynamics and Structuring in Solutions Involving a Homologous Series of Ionic Liquids.

The self-diffusion coefficients of each of the components in mixtures containing pyridine and each of the homologous series 1-alkyl-3-methylimidazolium bis(trifluoromethanesulfonyl)imides in acetonitrile were determined using NMR diffusometry (i. e., Pulsed Gradient Spin Echo). The nature of solvation was found to change significantly with the proportion of salt in the mixtures. Increased diffusion coefficients (when corrected for viscosity) for the molecular components were observed with increasing proportion of ionic liquid and with increasing alkyl chain length on the cation. Comparison of the molecular solvents suggests increased interactions in solution of the pyridine with other components of the mixture, consistent with the proposed interactions shown previously to drive changes in reaction kinetics. Discontinuities were seen in the diffusion data for each species in solution across different ionic liquids between the hexyl and octyl derivatives, suggesting a change in the structuring in solution as the alkyl chain on the cation changes and demonstrating the importance of such when considering homologous series.

The Core Difference between a Mesoionic and a Normal N-Heterocyclic Carbene.

The properties of the abnormal N-heterocyclic carbene (NHC) 1,4-dimesityl-3-methyl-1,2,3-triazolin-5-ylidene were comprehensively compared to those of the related normal carbene 1,3-dimesitylimidazolin-2-ylidene using a range of steric and electronic probe techniques (% V bur, steric maps, Tolman electronic parameter, alane, Huynh electronic parameter, selone, and pK a values). The two NHCs were determined to be sterically equivalent (isostructural), while the triazolin-5-ylidene was found to be a stronger σ-electron donor and a much weaker π-electron acceptor. These results were used to demonstrate that the electronic properties of these NHCs could affect the stereochemical outcome of an NHC-catalyzed reaction.

Improving the Accuracy of Quantum Mechanics/Molecular Mechanics (QM/MM) Models with Polarized Fragment Charges.

This paper introduces an economical approach for improving the accuracy and convergence of quantum mechanics/molecular mechanics (QM/MM) models. The approach is tested on a series of neutral and charged amino acids embedded in a 160-water cluster, where their intramolecular proton transfer energies (neutral amino acid → zwitterionic amino acid) were previously obtained at the ωB97X-D/6-31G(d) level of theory. When the charges on the MM atoms were replaced with those obtained at the same QM level of theory used to treat the QM atoms, this significantly improved the accuracy and convergence of the QM/MM models. In particular, the QM/MM model converged to within 1.4 kcal mol-1 of directly calculated DFT energies for smaller (by as many as 20 waters) QM regions. The use of atomic charges obtained from the natural population analysis yielded the most significant improvement, while other charge schemes such as Mulliken, electrostatic potential, or CM5 led to poorer outcomes. It is further demonstrated that the QM atomic charges can be accurately estimated in a highly efficient manner using an iterative fragmentation approach based on the moving-domain QM/MM method. Similar observations were made when the approach was used to predict the barrier of an SN2 reaction. Thus, the use of QM-quality atomic charges on MM atoms represents a simple and easy-to-implement strategy for improving the accuracy of QM/MM models.

Tofacitinib Appears Well Tolerated and Effective for the Treatment of Patients with Refractory Crohn's Disease.

BACKGROUND: Active Crohn's disease increases the risk of strictures, fistulas, and abscesses. Less than 30% of patients with Crohn's disease achieve endoscopic remission on any therapy. Tofacitinib may be a therapeutic option for patients with refractory Crohn's disease. AIMS: We aimed to evaluate the safety and effectiveness of off-label tofacitinib for refractory Crohn's disease. METHODS: We retrospectively assessed adverse events and clinical/endoscopic response after therapy. RESULTS: Forty-four patients were included in the safety analysis and 35 were included in the clinical and/or endoscopic assessments. The mean age was 41.8 years and the mean disease duration was 17.4 years. All patients had prior biologic exposure. Adverse events were reported in 52.3% of patients; 13.6% had ≥ 1 serious adverse event after a median 54.6 weeks of treatment. Seventy percent achieved clinical response after a mean 29.4 (SD 15.1) weeks, and 33.3% achieved clinical remission after a mean 33.4 (SD 17.6) weeks of therapy. Endoscopic improvement occurred in 25.0%, endoscopic remission in 12.5%, and endoscopic healing in 4.2% of patients after a mean 52.0 (SD 15.0) weeks of therapy. The mean Simple Endoscopic Score in Crohn's disease significantly improved from 23.1 ± 3.7 to 18.0 ± 13.7 after treatment (P = .02). CONCLUSIONS: In the short term, tofacitinib appears well tolerated. The most common adverse event was minor infection. One serious infection and one colorectal cancer occurred. While half of patients reported adverse events, this likely reflects the severe refractory disease in this population and no new safety events were observed. Tofacitinib achieved clinical and endoscopic improvement in some patients with refractory Crohn's disease. Further research is needed to understand the long-term safety and efficacy of tofacitinib in Crohn's disease.

Safety and Efficacy of Tofacitinib in Combination With Biologic Therapy for Refractory Crohn's Disease.

BACKGROUND: The majority of patients with Crohn's disease (CD) will not achieve endoscopic remission on current therapy. Addition of tofacitinib to biologics may improve remission rates. METHODS: We retrospectively assessed safety and clinical and endoscopic effectiveness of off-label tofacitinib and biologics for CD. RESULTS: We identified 19 patients treated with tofacitinib and a biologic for refractory CD between 2017 and 2019. Tofacitinib was added for luminal disease on colonoscopy (n = 13), luminal disease on capsule (n = 3), and pyoderma gangrenosum (n = 3). The mean age was 41.2 years (28-62), mean disease was duration 16.9 years (6-36), and prior exposure to biologics was a median of 4 (1-6). Mean treatment duration was 9.6 months (SD, 3.3). Adverse events (AEs) were reported in 36.8% of patients, most commonly minor infection or CD flare, and no patients had a serious AE; 80.0% (n = 8) achieved clinical response, and 60.0% (n = 6) achieved clinical remission based on Harvey-Bradshaw Index. Endoscopic improvement occurred in 54.5% (n = 6), endoscopic remission in 18.2% (n = 2), and endoscopic healing in 18.2% (n = 2) of patients. Mean Simple Endoscopic Score in CD significantly improved from 13.6 ±â€…5.2 to 6.5 ±â€…4.0 after treatment (P < .01). CONCLUSIONS: In patients treated with tofacitinib in combination with a biologic, no new safety signals were observed. Combination tofacitinib and a biologic was effective in achieving clinical and endoscopic improvement in some patients with severe, refractory CD, although a larger sample size is needed to further assess the efficacy and long-term safety of this treatment strategy.

Effects of Ionic Liquids on the Nucleofugality of Chloride.

The nucleofugality of chloride has been measured in solvent mixtures containing ionic liquids for the first time, allowing reactivity in these solvents to be put in context with molecular solvents. Using well-described electrofuges, solvolysis rate constants were determined in mixtures containing different proportions of ethanol and the ionic liquid 1-butyl-3-methylimidazolium bis(trifluoromethanesulfonyl)imide; the different solvent effects observed as the mixture changed could be explained using interactions of the ionic liquid with species along the reaction coordinate, determined using temperature dependent kinetic studies. The solvolysis data allowed determination of the nucleofugality of chloride in these mixtures, which varied with the proportion of salt in the reaction mixture, demonstrating quantitatively the importance of the amount of ionic liquid in the reaction mixture in determining reaction outcome. Nucleofugality data for chloride were determined in seven further ionic liquids, with the reactivity shown to vary over more than an order of magnitude. This outcome illustrates that the components of the ionic liquid are critical in determining reaction outcome. Overall, this work quantitatively extends the understanding of solvent effects in ionic liquids and demonstrates the potential for such information to be used to rationally select an ionic liquid to control reaction outcome.

The effect of anion architecture on the lubrication chemistry of phosphonium orthoborate ionic liquids.

Phosphonium ionic liquids with orthoborate anions have been studied in terms of their interfacial film formation, both physisorbed and sacrificial from chemical breakdown, in sheared contacts of varying harshness. The halogen-free anion architecture was varied through (i) the heteronuclear ring size, (ii) the hybridisation of the constituent atoms, and (iii) the addition of aryl functionalities. Time of Flight-Secondary Ion Mass Spectrometry analysis revealed the extent of sacrificial tribofilm formation allowing the relative stability of the ionic liquids under tribological conditions to be determined and their breakdown mechanisms to be compared to simple thermal decomposition. Overall, ionic liquids outperformed reference oils as lubricants; in some cases, sacrificial films were formed (with anion breakdown a necessary precursor to phosphonium cation decomposition) while in other cases, a protective, self-assembly lubricant layer or hybrid film was formed. The salicylate-based anion was the most chemically stable and decomposed only slightly even under the harshest conditions. It was further found that surface topography influenced the degree of breakdown through enhanced material transport and replenishment. This work thus unveils the relationship between ionic liquid composition and structure, and the ensuing inter- and intra-molecular interactions and chemical stability, and demonstrates the intrinsic tuneability of an ionic liquid lubrication technology.

On the Accuracy of QM/MM Models: A Systematic Study of Intramolecular Proton Transfer Reactions of Amino Acids in Water.

This work presents a systematic assessment of QM/QM' and QM/MM models with respect to direct QM calculations for the tautomerization (neutral to zwitterion) reactions of amino acids (glycine, alanine, valine, aspartate, and neutral and protonated histidine) solvated in a 160 water cluster. The effect of varying QM region size and choice of embedding potentials, including fixed-charge and polarizable molecular mechanics force fields (TIP3P and EFP) and various semiempirical QM methods (PM7, GFN2-xTB, DFTBA, DFTB3, HF-3c, and PBEh-3c), on the accuracy of the models was examined. A surprising finding was that molecular mechanics force fields outperformed many of the semiempirical methods. Generally, the errors in the QM/QM' and QM/MM models converge slowly with respect to the QM region size, requiring 50 or more waters to be included in the QM region before the error in the model falls below 1 kcal mol-1 of its pure QM result. Different QM region selection schemes were also compared, and it was found that selection based on Natural Population Analysis (NPA) atomic charges significantly reduced the error in the QM/QM' and QM/MM models particularly if a low-quality embedding potential was used. It is envisaged that these results will be useful for the development of future hybrid QM models.

Rapid relaxation NMR measurements to predict rate coefficients in ionic liquid mixtures. An examination of reaction outcome changes in a homologous series of ionic liquids.

A series of ionic liquids based on the 1-alkyl-3-methylimidazolium cations were examined as components of the solvent mixture for a bimolecular substitution process. The effects on both the rate coefficient of the process and the NMR spin-spin relaxation of the solvent components of changing either the alkyl chain length or the amount of ionic liquid in the reaction mixture were determined. At a constant mole fraction, a shorter alkyl chain length resulted in a greater rate coefficient enhancement and a longer relaxation time, with the opposite effects for a longer alkyl chain length. For a given ionic liquid, increasing the proportion of salt in the reaction mixture resulted in a greater rate coefficient and a shorter relaxation time. The microscopic origins of the rate coefficient enhancement were determined and a step change found in the activation parameters on increasing the alkyl chain length from hexyl to octyl, suggesting notable structuring in solution. Across a range of ionic liquids and solvent compositions, the relaxation time from NMR measurements was shown to relate to the reaction rate coefficient. The approach of using fast and simple NMR relaxation measurements to predict reaction outcomes was exemplified using a morpholinium-based ionic liquid.

Machine learning approaches to understand and predict rate constants for organic processes in mixtures containing ionic liquids.

The ability to tailor the constituent ions in ionic liquids (ILs) is highly advantageous as it provides access to solvents with a range of physicochemical properties. However, this benefit also leads to large compositional spaces that need to be explored to optimise systems, often involving time consuming experimental work. The use of machine learning methods is an effective way to gain insight based on existing data, to develop structure-property relationships and to allow the prediction of ionic liquid properties. Here we have applied machine learning models to experimentally determined rate constants of a representative organic process (the reaction of pyridine with benzyl bromide) in IL-acetonitrile mixtures. Multiple linear regression (MLREM) and artificial neural networks (BRANNLP) were both able to model the data well. The MLREM model was able to identify the structural features on the cations and anions that had the greatest effect on the rate constant. Secondly, predictive MLREM and BRANNLP models were developed from the full initial set of rate constant data. From these models, a large number of predictions (>9000) of rate constant were made for mixtures of different ionic liquids, at different proportions of ionic liquid and molecular solvent, at different temperatures. A selection of these predictions were tested experimentally, including through the preparation of novel ionic liquids, with overall good agreement between the predicted and experimental data. This study highlights the benefits of using machine learning methods on kinetic data in ionic liquid mixtures to enable the development of rigorous structure-property relationships across multiple variables simultaneously, and to predict properties of new ILs and experimental conditions.

Health Maintenance in Patients with Ulcerative Colitis.

Medical care for individuals with ulcerative colitis (UC) has become increasingly subspecialized, and this population presents unique challenges in the delivery of care. Most points of contact are with gastroenterology subspecialty clinics, and primary care providers have shown concern and unfamiliarity about managing these individuals. Gastroenterology subspecialists need to be comfortable discussing the unique preventive care needs of patients with UC, tailored to specific recommendations based on their demographics and current medication usage. This article reviews pertinent topics in preventive care for individuals with UC to provide a framework for gastroenterology subspecialists to be able to provide patient-centered care.

Controlling the outcome of SN2 reactions in ionic liquids: from rational data set design to predictive linear regression models.

Rate constants for a bimolecular nucleophilic substitution (SN2) process in a range of ionic liquids are correlated with calculated parameters associated with the charge localisation on the cation of the ionic liquid (including the molecular electrostatic potential). Simple linear regression models proved effective, though the interdependency of the descriptors needs to be taken into account when considering generality. A series of ionic liquids were then prepared and evaluated as solvents for the same process; this data set was rationally chosen to incorporate homologous series (to evaluate systematic variation) and functionalities not available in the original data set. These new data were used to evaluate and refine the original models, which were expanded to include simple artificial neural networks. Along with showing the importance of an appropriate data set and the perils of overfitting, the work demonstrates that such models can be used to reliably predict ionic liquid solvent effects on an organic process, within the limits of the data set.

The effect of bisimidazolium-based ionic liquids on a bimolecular substitution process. Are two head(group)s better than one?

A homologous series of biscationic ionic liquids based on two imidazolium centres, separated by alkyl chains of varying length, were examined as solvents for a bimolecular substitution reaction across a range of proportions of ionic liquid in the reaction mixture. Their effects on the rate constant of the process were compared to monocationic ionic liquids, with generally a greater rate constant increase observed. Importantly, it was observed that the magnitude of the effect was shown to vary with the length of the linking chain. To investigate the origins of these solvent effects, temperature dependent kinetic studies were performed to obtain activation parameters at high and low mole fractions of ionic liquid. The observed activation parameters showed the rate constant enhancement was due to interaction of the ionic liquid with the starting materials, consistent with previous results. Significantly, however, these data also showed that the balance of enthalpic and entropic effects varied dramatically with the length of the alkyl chain between the cationic centres.

Controlling the reactions of 1-bromogalactose acetate in methanol using ionic liquids as co-solvents.

The reactions of an acetobromogalactose in mixtures of methanol and one of seven different ionic liquids with varying constituent ions were studied. In general, small amounts of ionic liquid in the reaction mixture led to increases in the rate constant compared to methanol, whilst large amounts of ionic liquid led to decreases in the rate constant; this outcome differs significantly from previous reactions proceeding through this mechansim. Temperature dependent kinetic studies indicated that the dominant interaction driving these changes was between the ionic liquid and the transition state of the process. Through considering solvent parameters of ionic liquids, a relationship was found between the changes in the rate constant and both the hydrogen bond accepting ability and polarisability of the solvent, indicating that the interactions affecting reaction outcome are both specific and non-specific in nature; once more, these interactions were different to those observed in previous similar reactions. By changing the amount of ionic liquid in the reaction mixture, additional products not seen in the molecular solvent case were observed, the ratios of which are dependent on the anion of the ionic liquid and the proportion of ionic liquid in the reaction mixture. This demonstrates the importance of considering solvent effects on both the rate and product determining steps and the potential application of such changes is discussed.