Pressure-Induced Amidine Formation via Side-Chain Polymerization in a Charge-Transfer Cocrystal

Compression of small molecules can induce solid-state reactions that are difficult or impossible under conventional, solution-phase conditions. Of particular interest is the topochemical-like reaction of arenes to produce polymeric nanomaterials. However, high reaction onset pressures and poor selectivity remain significant challenges. Herein, the incorporation of electron-withdrawing and -donating groups into π-stacked arenes is proposed as a strategy to reduce reaction barriers to cycloaddition and onset pressures. Nevertheless, competing side-chain reactions between functional groups represent alternative viable pathways. For the case of a diaminobenzene:tetracyanobenzene cocrystal, amidine formation between amine and cyano groups occurs prior to cycloaddition with an onset pressure near 9 GPa, as determined using vibrational spectroscopy, X-ray diffraction, and first-principles calculations. This work demonstrates that reduced-barrier cycloaddition reactions are theoretically possible via strategic functionalization; however, the incorporation of pendant groups may enable alternative reaction pathways. Controlled reactions between pendant groups represent an additional strategy for producing unique polymeric nanomaterials.

A simple topology-based model for predicting the activation barriers of reactive processes at 0 K

This work reveals an underlying correlation between the topology and energetic features of matter configurations/rearrangements by exploiting two topological concepts, namely, structural stability and persistency, leading thus to a model capable of predicting activation energies at 0 K. This finding provides some answers to the difficulties of applying Thom's functions for extracting energetic information of rate processes, which has been a limitation for exact, biological, and technological sciences. A linear relationship between the experimental barriers of 17 chemical reactions and both concepts was found by studying these systems' topography along the intrinsic reaction coordinate. Such a procedure led to the model , which accurately predicts the activation energy in reacting systems involving organic and organometallic compounds under different conditions, e.g., the gas-phase, solvent media, and temperature. This function was further recalibrated to enhance its predicting capabilities, generating the equation for this procedure, characterized by a squared Pearson correlation coefficient (r² = 0.9774) 1.1 times higher. Surprisingly, no improvement was observed.

Hydrogen-Bond-Assisted Diels–Alder Kinetics or Self-Healing in Reversible Polymer Networks? A Combined Experimental and Theoretical Study

Diels–Alder (DA) cycloadditions in reversible polymer networks are important for designing sustainable materials with self-healing properties. In this study, the DA kinetics of hydroxyl-substituted bis- and tetrafunctional furans with bis- and tris-functional maleimides, both containing ether-functionalized spacers, is investigated by modelling two equilibria representing the endo and exo cycloadduct formation. Concretely, the potential catalysis of the DA reaction through hydrogen bonding between hydroxyl of the furans and carbonyl of the maleimides or ether of the spacers is experimentally and theoretically scrutinized. Initial reaction rates and forward DA rate constants are determined by microcalorimetry at 20 °C for a model series of reversible networks, extended with (i) a hydroxyl-free network and hydroxyl-free linear or branched systems, and (ii) polypropylene glycol additives, increasing the hydroxyl concentration. A computational density-functional theory study is carried out on the endo and exo cycloadditions of furan and maleimide derivatives, representative for the experimental ones, in the absence and presence of ethylene glycol as additive. Additionally, an ester-substituted furan was investigated as a hydroxyl-free system for comparison. Experiment and theory indicate that the catalytic effect of H-bonding is absent or very limited. While increased concentration of H-bonding could in theory catalyze the DA reaction, the experimental results rule out this supposition.

Click Chemistry Hydrogels for Extrusion Bioprinting: Progress, Challenges, and Opportunities

The emergence of 3D bioprinting has allowed a variety of hydrogel-based "bioinks" to be printed in the presence of cells to create precisely defined cell-loaded 3D scaffolds in a single step for advancing tissue engineering and/or regenerative medicine. While existing bioinks based primarily on ionic cross-linking, photo-cross-linking, or thermogelation have significantly advanced the field, they offer technical limitations in terms of the mechanics, degradation rates, and the cell viabilities achievable with the printed scaffolds, particularly in terms of aiming to match the wide range of mechanics and cellular microenvironments. Click chemistry offers an appealing solution to this challenge given that proper selection of the chemistry can enable precise tuning of both the gelation rate and the degradation rate, both key to successful tissue regeneration; simultaneously, the often bio-orthogonal nature of click chemistry is beneficial to maintain high cell viabilities within the scaffolds. However, to date, relatively few examples of 3D-printed click chemistry hydrogels have been reported, mostly due to the technical challenges of controlling mixing during the printing process to generate high-fidelity prints without clogging the printer. This review aims to showcase existing cross-linking modalities, characterize the advantages and disadvantages of different click chemistries reported, highlight current examples of click chemistry hydrogel bioinks, and discuss the design of mixing strategies to enable effective 3D extrusion bioprinting of click hydrogels.

Designing Hydrogels for 3D Cell Culture Using Dynamic Covalent Crosslinking

Designing simple biomaterials to replicate the biochemical and mechanical properties of tissues is an ongoing challenge in tissue engineering. For several decades, new biomaterials have been engineered using cytocompatible chemical reactions and spontaneous ligations via click chemistries to generate scaffolds and water swollen polymer networks, known as hydrogels, with tunable properties. However, most of these materials are static in nature, providing only macroscopic tunability of the scaffold mechanics, and do not reflect the dynamic environment of natural extracellular microenvironment. For more complex applications such as organoids or co-culture systems, there remain opportunities to investigate cells that locally remodel and change the physicochemical properties within the matrices. In this review, advanced biomaterials where dynamic covalent chemistry is used to produce stable 3D cell culture models and high-resolution constructs for both in vitro and in vivo applications, are discussed. The implications of dynamic covalent chemistry on viscoelastic properties of in vitro models are summarized, case studies in 3D cell culture are critically analyzed, and opportunities to further improve the performance of biomaterials for 3D tissue engineering are discussed.

The mechanism of conversion of substituted glycals to chiral acenes via Diels-Alder reaction: a computational study

Synthesis of linearly fused aromatic systems using a glycal-based diene with an aryne is a long-standing topic of interest in glycal chemistry. We have examined the mechanistic pathways for the transformation of substituted glycals to chiral fused aromatic cores via Diels-Alder (DA) reaction using the SMDACN-M06-2X/6-31G(d) level of theory. The DA reactions of E (1a) and Z (1a') forms of C-2 alkenyl glycal and an aryl glycal (1b) as a diene were examined with a benzyne intermediate generated as a dienophile. The computational results reveal that 1a and 1b can only be transformed into the fused aromatic cores by the base-catalyzed reaction because a [1,5] sigmatropic hydrogen shift is not feasible. The activation free energy barrier for the base-catalyzed proton abstraction process is 4.2 kcal mol-1 and there is almost no barrier for stereoisomeric 1a DA-complexes. The activation free energy barrier values for stereoisomeric 1b DA-complexes for the base-catalyzed proton abstraction process are 10.8 and 12.4 kcal mol-1. The appropriate orientation of glycal-ring-oxygen and hydrogen at the 5th position of Z (1a') forms of C-2 alkenyl glycal facilitates the [1,5] sigmatropic hydrogen shift; however, the base-catalyzed reaction is energetically more favored than the former case. The rate-determining step for 1a and 1a' is the ring-opening step (18.2 and 19.5 kcal mol-1 for the S-stereoisomer), whereas the DA adduct formation step is the rate-determining step for 1b (16.1 kcal mol-1 for the S-stereoisomer). The structural analysis reveals the formation of the preferred S-stereoisomer over the R-stereoisomer with the respective dienes.

Tailored Bioorthogonal and Bioconjugate Chemistry: A Source of Inspiration for Developing Kinetic Target-Guided Synthesis Strategies

Kinetic target-guided synthesis (KTGS) is a promising tool for the discovery of biologically active compounds. It relies on the identification of potent ligands that are covalently assembled by the biological targets themselves from a pool of reagents. Significant effort is devoted to developing new KTGS strategies; however, only a handful of biocompatible reactions are available, which may be insufficient to meet the specificities (stability, dynamics, active site topology, etc.) of a wide range of biological targets with therapeutic potential. This Topical Review proposes a retrospective analysis of existing KTGS ligation tools, in terms of their kinetics and analogy with other biocompatible reactions, and provides new clues to expand the KTGS toolkit. By way of examples, a nonexhaustive selection of such chemical ligation tools belonging to different classes of reactions as promising candidate reactions for KTGS are suggested.

Accurate Diels-Alder Energies and Endo Selectivity in Ionic Liquids Using the OPLS-VSIL Force Field

Our recently developed optimized potentials for liquid simulations-virtual site ionic liquid (OPLS-VSIL) force field has been shown to provide accurate bulk phase properties and local ion-ion interactions for a wide variety of imidazolium-based ionic liquids. The force field features a virtual site that offloads negative charge to inside the plane of the ring with careful attention given to hydrogen bonding interactions. In this study, the Diels-Alder reaction between cyclopentadiene and methyl acrylate was computationally investigated in the ionic liquid 1-butyl-3-methylimidazolium hexafluorophosphate, [BMIM][PF₆], as a basis for the validation of the OPLS-VSIL to properly reproduce a reaction medium environment. Mixed ab initio quantum mechanics and molecular mechanics (QM/MM) calculations coupled to free energy perturbation and Monte Carlo sampling (FEP/MC) that utilized M06-2X/6-31G(d) and OPLS-VSIL gave activation free energy barriers of 14.9 and 16.0 kcal/mol for the endo-cis and exo-cis Diels-Alder reaction pathways, respectively (exptl. ΔH^‡ of 14.6 kcal/mol). The endo selectivity trend was correctly predicted with a calculated 73% endo preference. The rate and selectivity enhancements present in the endo conformation were found to arise from preferential hydrogen bonding with the exposed C4 ring hydrogen on the BMIM cation. Weaker electronic stabilization of the exo transition state was predicted. For comparison, our earlier ±0.8 charge-scaled OPLS-2009IL force field also yielded a ΔG^‡ of 14.9 kcal/mol for the favorable endo reaction pathway but did not adequately capture the highly organized solvent interactions present between the cation and Diels-Alder transition state.

Maleimide-based metal-free ligation with dienes: a comparative study

Maleimide-based Diels–Alder strategies for bioconjugation are compared in terms of dienes accessibility and stability, reactions rates, as well as products isolation and stability.

A new healable polymer material based on ultrafast Diels–Alder ‘click’ chemistry using triazolinedione and fluorescent anthracyl derivatives: a mechanistic approach

Development of a new healable polymer based on ultrafast Diels–Alder ‘click’ chemistry using fluorescent anthracyl and TAD derivatives. The ultrafast mechanistic approach is rationalized via Density Functional Theory (DFT) study.

Preparation and Characterization of a Small Library of Thermally-Labile End-Caps for Variable-Temperature Triggering of Self-Immolative Polymers

The reaction between furans and maleimides has increasingly become a method of interest as its reversibility makes it a useful tool for applications ranging from self-healing materials, to self-immolative polymers, to hydrogels for cell culture and for the preparation of bone repair. However, most of these applications have relied on simple monosubstituted furans and simple maleimides and have not extensively evaluated the potential thermal variability inherent in the process that is achievable through simple substrate modification. A small library of cycloadducts suitable for the above applications was prepared, and the temperature dependence of the retro-Diels-Alder processes was determined through in situ ¹H NMR analyses complemented by computational calculations. The practical range of the reported systems ranges from 40 to >110 °C. The cycloreversion reactions are more complex than would be expected based on simple trends expected based on frontier molecular orbital analyses of the materials.

Calculating Free Energy Changes in Continuum Solvation Models

We recently showed for a large data set of pKas and reduction potentials that free energies calculated directly within the SMD continuum model compares very well with corresponding thermodynamic cycle calculations in both aqueous and organic solvents [ Phys. Chem. Chem. Phys. 2015 , 17 , 2859 ]. In this paper, we significantly expand the scope of our study to examine the suitability of this approach for calculating general solution phase kinetics and thermodynamics, in conjunction with several commonly used solvation models (SMD-M062X, SMD-HF, CPCM-UAKS, and CPCM-UAHF) for a broad range of systems. This includes cluster-continuum schemes for pKa calculations as well as various neutral, radical, and ionic reactions such as enolization, cycloaddition, hydrogen and chlorine atom transfer, and SN2 and E2 reactions. On the basis of this benchmarking study, we conclude that the accuracies of both approaches are generally very similar-the mean errors for Gibbs free energy changes of neutral and ionic reactions are approximately 5 and 25 kJ mol(-1), respectively. In systems where there are significant structural changes due to solvation, as is the case for certain ionic transition states and amino acids, the direct approach generally afford free energy changes that are in better agreement with experiment.

Spectroscopic, single crystal XRD structure, DFT and molecular dynamics investigation of 1-(3-chloro-4-fluorophenyl)-3-[3-(trifluoromethyl)phenyl]thiourea

The title compound 1-(3-chloro-4-fluorophenyl)-3-[3-(trifluoromethyl) phenyl]thiourea (ANF-2) was synthesized and structurally characterized by single crystal XRD.

The Mosaic of Rottlerin

The first total synthesis of rottlerin is described. The methodology allows the development of potential novel protein kinase C δ (PKCδ) analogues for better treatment of various diseases. Kamalachalcone A and dimeric rottlerin were synthesized in a very practical and economical way using FeCl3 as a catalyst.

New insights into the cross-linking and degradation mechanism of Diels–Alder hydrogels

Degradation of Diels–Alder hydrogels occurs by retro-Diels–Alder reaction followed by OH⁻-catalyzed ring-opening hydrolysis of maleimide groups to unreactive maleamic acid derivatives.

A computationally designed titanium-mediated amination of allylic alcohols for the synthesis of secondary allylamines

A direct amination on allylic alcohols under mild conditions was enlightened by computational investigations and implemented in secondary allylamines synthesis.

Quantitative structure-activation barrier relationship modeling for Diels-Alder ligations utilizing quantum chemical structural descriptors

Background

In the present study, we show the correlation of quantum chemical structural descriptors with the activation barriers of the Diels-Alder ligations. A set of 72 non-catalysed Diels-Alder reactions were subjected to quantitative structure-activation barrier relationship (QSABR) under the framework of theoretical quantum chemical descriptors calculated solely from the structures of diene and dienophile reactants. Experimental activation barrier data were obtained from literature. Descriptors were computed using Hartree-Fock theory using 6-31G(d) basis set as implemented in Gaussian 09 software.

Results

Variable selection and model development were carried out by stepwise multiple linear regression methodology. Predictive performance of the quantitative structure-activation barrier relationship (QSABR) model was assessed by training and test set concept and by calculating leave-one-out cross-validated Q² and predictive R² values. The QSABR model can explain and predict 86.5% and 80% of the variances, respectively, in the activation energy barrier training data. Alternatively, a neural network model based on back propagation of errors was developed to assess the nonlinearity of the sought correlations between theoretical descriptors and experimental reaction barriers.

Conclusions

A reasonable predictability for the activation barrier of the test set reactions was obtained, which enabled an exploration and interpretation of the significant variables responsible for Diels-Alder interaction between dienes and dienophiles. Thus, studies in the direction of QSABR modelling that provide efficient and fast prediction of activation barriers of the Diels-Alder reactions turn out to be a meaningful alternative to transition state theory based computation.

Stepwise Diels-Alder: more than just an oddity? A computational mechanistic study

We have employed hybrid DFT and SCS-MP2 calculations at the SMD-PCM-6-311++G(2d,2p)//6-31+G(d) level to investigate the relationship between three possible channels for forming a Diels-Alder adduct from a highly nucleophilic diene and moderately to highly electrophilic dienophiles. We discuss geometries optimized using the B3LYP and M06-2X functionals with the 6-31+(d) basis set. The transition states and intermediates are characterized on the basis of geometric and electronic properties, and we also address the possibility of predicting detectability of a zwitterionic intermediate based on its relative stability. Our results show that a conventional Diels-Alder transition state conformation yields intermediates in all four investigated cases, but that these are too short-lived to be detected experimentally for the less activated reactants. The stepwise trans pathway, beginning with a conjugate addition-like transition state, becomes increasingly competitive with more activated reactants and is indeed favored for the most electrophilic dienophiles. Addition of a trans diene leads to a dead-end as the trans intermediates have insurmountable rotation barriers that prohibit formation of the second bond, unless another, heterocyclic intermediate is formed. We also show that introduction of a hydrogen bond donating catalyst favors a stepwise pathway even for less activated dienophiles.