Catalytic asymmetric addition of thiols to silyl glyoxylates for synthesis of multi-hetero-atom substituted carbon stereocenters

A chiral Lewis acid-catalyzed enantioselective addition of thiols to silyl glyoxylates was developed. The reaction proceeds well with a broad range of thiols and acylsilanes, affording the target tertiary chiral α-silyl–α-sulfydryl alcohols with multi-hetero-atom carbon stereocenters in excellent yields (up to 99%) and enantioselectivities (up to 98% ee). A series of control experiments were conducted to elucidate the reaction mechanism.

Enantioselective addition of thiols to silyl glyoxylates for construction of a multi-hetero-atom substituted carbon stereocenter was described.     

Kinetic effects of molecular clustering and solvation by extended networks in zeolite acid catalysis

Reactions catalyzed within porous inorganic and organic materials and at electrochemical interfaces commonly occur at high coverage and in condensed media, causing turnover rates to depend strongly on interfacial structure and composition, collectively referred to as “solvent effects”. Transition state theory treatments define how solvation phenomena enter kinetic rate expressions, and identify two distinct types of solvent effects that originate from molecular clustering and from the solvation of such clusters by extended solvent networks. We review examples from the recent literature that investigate reactions within microporous zeolite catalysts to illustrate these concepts, and provide a critical appraisal of open questions in the field where future research can aid in developing new chemistry and catalyst design principles.

“Solvent effects” at interfaces in heterogeneous catalysts are described by transition state theory treatments that identify kinetic regimes associated with molecular clustering and the solvation of such clusters by extended molecular networks.     

Recent advances in heterogeneous catalysis for the nonoxidative conversion of methane

The direct conversion of methane to high-value chemicals is an attractive process that efficiently uses abundant natural/shale gas to provide an energy supply. The direct conversion of methane to high-value chemicals is an attractive process that efficiently uses abundant natural/shale gas to provide an energy supply. Among all the routes used for methane transformation, nonoxidative conversion of methane is noteworthy owing to its highly economic selectivity to bulk chemicals such as aromatics and olefins. Innovations in catalysts for selective C–H activation and controllable C–C coupling thus play a key role in this process and have been intensively investigated in recent years. In this review, we briefly summarize the recent advances in conventional metal/zeolite catalysts in the nonoxidative coupling of methane to aromatics, as well as the newly emerging single-atom based catalysts for the conversion of methane to olefins. The emphasis is primarily the experimental findings and the theoretical understanding of the active sites and reaction mechanisms. We also present our perspectives on the design of catalysts for C–H activation and C–C coupling of methane, to shed some light on improving the potential industrial applications of the nonoxidative conversion of methane into chemicals.

The direct conversion of methane to high-value chemicals is an attractive process that efficiently uses abundant natural/shale gas to provide an energy supply.     

Leveraging autocatalytic reactions for chemical domain image classification

Autocatalysis is fundamental to many biological processes, and kinetic models of autocatalytic reactions have mathematical forms similar to activation functions used in artificial neural networks. Inspired by these similarities, we use an autocatalytic reaction, the copper-catalyzed azide–alkyne cycloaddition, to perform digital image recognition tasks. Images are encoded in the concentration of a catalyst across an array of liquid samples, and the classification is performed with a sequence of automated fluid transfers. The outputs of the operations are monitored using UV-vis spectroscopy. The growing interest in molecular information storage suggests that methods for computing in chemistry will become increasingly important for querying and manipulating molecular memory.

Kinetic models of autocatalytic reactions have mathematical forms similar to activation functions used in artificial neural networks. Inspired by these similarities, we use a copper-catalyzed reaction to perform digital image recognition tasks.     

Effects of applied voltage on water at a gold electrode interface from ab initio molecular dynamics

Electrode–water interfaces under voltage bias demonstrate anomalous electrostatic and structural properties that are influential in their catalytic and technological applications. Mean-field and empirical models of the electrical double layer (EDL) that forms in response to an applied potential do not capture the heterogeneity that polarizable, liquid-phase water molecules engender. To illustrate the inhomogeneous nature of the electrochemical interface, Born–Oppenheimer ab initio molecular dynamics calculations of electrified Au(111) slabs interfaced with liquid water were performed using a combined explicit–implicit solvent approach. The excess charges localized on the model electrode were held constant and the electrode potentials were computed at frequent simulation times. The electrode potential in each trajectory fluctuated with changes in the atomic structure, and the trajectory-averaged potentials converged and yielded a physically reasonable differential capacitance for the system. The effects of the average applied voltages, both positive and negative, on the structural, hydrogen bonding, dynamical, and vibrational properties of water were characterized and compared to literature where applicable. Controlled-potential simulations of the interfacial solvent dynamics provide a framework for further investigation of more complex or reactive species in the EDL and broadly for understanding electrochemical interfaces in situ.

Ab initio molecular dynamics of an aqueous electrode interface reveal the electrostatic, structural, and dynamic effects of quantifiable voltage biases on water.     

Mechanism and origins of selectivity in the enantioselective oxa-Pictet–Spengler reaction: a cooperative catalytic complex from a hydrogen bond donor and chiral phosphoric acid

Enantioselective additions to oxocarbenium ions are high-value synthetic transformations but have proven challenging to achieve. In particular, the oxa-Pictet–Spengler reaction has only recently been rendered enantioselective. We report experimental and computational studies on the mechanism of this unusual transformation. Herein we reveal that this reaction is hypothesized to proceed through a self-assembled ternary hydrogen bonding complex involving the substrate, chiral phosphate ion, and a urea hydrogen-bond donor. The computed transition state reveals C2-symmetric grooves in the chiral phosphate that are occupied by the urea and substrate. Occupation of one of these grooves by the urea co-catalyst tunes the available reactive volume and enhances the stereoselectivity of the chiral phosphate catalyst.

A new model for the cooperative catalytic oxa-Pictet–Spengler reaction is disclosed. Supporting spectroscopic, kinetic, and computational quantum mechanics studies permit the rationalization of the reaction''s observed enantioselectivity.     

Counterintuitive solvation effect of ionic-liquid/DMSO solvents on acidic C–H dissociation and insight into respective solvation

How would acidic bond dissociation be affected by adding a small quantity of a weakly polar ionic liquid IL (the “apparent” or “measured” dielectric constant ε of the IL is around 10–15) into a strongly polar molecular solvent (e.g., ε of DMSO: 46.5), or vice versa? The answer is blurred, because no previous investigation was reported in this regard. Toward this, we, taking various IL/DMSO mixtures as representatives, have thoroughly investigated the effects of the respective solvent in ionic–molecular binary systems on self-dissociation of C–H acid phenylmalononitrile PhCH(CN)₂via pK_a determination. As disclosed, in this category of binary media, (1) no linear correspondence exists between pK_a and molar fractions of the respective solvent components; (2) only ∼1–2 mol% of weakly polar ILs in strongly polar DMSO make C–H bonds even more dissociative than in neat DMSO; (3) a small fraction of DMSO in ILs (<10 mol%) can dramatically ease acidic C–H-dissociation; and (4) while the DMSO fraction further increases, its acidifying effect becomes much attenuated. These findings, though maybe counterintuitive, have been rationalized on the basis of the precise pK_a measurement of this work in relation to the respective roles of each solvent component in solvation.

The dependence of PhCH(CN)₂ pK_a on the molar fraction of ionic liquids in ionic–molecular binary mixtures showed a nonlinear three-fragment plot, which was rationalized for the first time by the respective roles of each solvent component for solvation.     

Site-to-site peptide transport on a molecular platform using a small-molecule robotic arm

Peptides attached to a cysteine hydrazide ‘transporter module’ are transported selectively in either direction between two chemically similar sites on a molecular platform, enabled by the discovery of new operating methods for a molecular transporter that functions through ratcheting. Substrate repositioning is achieved using a small-molecule robotic arm controlled by a protonation-mediated rotary switch and attachment/release dynamic covalent chemistry. A polar solvent mixtures were found to favour Z to E isomerization of the doubly-protonated switch, transporting cargo in one direction (arbitrarily defined as ‘forward’) in up to 85% yield, while polar solvent mixtures were unexpectedly found to favour E to Z isomerization enabling transport in the reverse (‘backward’) direction in >98% yield. Transport of the substrates proceeded in a matter of hours (compared to 6 days even for simple cargoes with the original system) without the peptides at any time dissociating from the machine nor exchanging with others in the bulk. Under the new operating conditions, key intermediates of the switch are sufficiently stabilized within the macrocycle formed between switch, arm, substrate and platform that they can be identified and structurally characterized by ¹H NMR. The size of the peptide cargo has no significant effect on the rate or efficiency of transport in either direction. The new operating conditions allow detailed physical organic chemistry of the ratcheted transport mechanism to be uncovered, improve efficiency, and enable the transport of more complex cargoes than was previously possible.

Peptides are transported in either direction between chemically similar sites on a molecular platform, substrate repositioning is achieved using a cysteine hydrazide transporter module and a small-molecule robotic arm controlled by a rotary switch.     

Exploring the self-assembly of dumbbell-shaped polyoxometalate hybrids,from molecular building units to nanostructured soft materials

The formation of hierarchical nanostructures using preformed dumbbell-like species made of covalent organic–inorganic polyoxometalate (POM)-based hybrids is herein described. In this system, the presence of charged subunits (POM, metal linkers, and counter ions) in the complex molecular architecture can drive their aggregation, which results from a competition between the solvation energy of the discrete species and intermolecular electrostatic interactions. We show that the nature of the POM and the charge of the metal linker are key parameters for the hierarchical nanoorganization. The experimental findings were corroborated with a computational investigation combining DFT and molecular dynamics simulation methods, which outlines the importance of solvation of the counter ion and POM/counter ion association in the aggregation process. The dumbbell-like species can also form gels, in the presence of a poorer solvent, displaying similar nanoorganization of the aggregates. We show that starting from the designed molecular building units whose internal charges can be controlled by redox trigger we can achieve their implementation into soft nanostructured materials through the control of their supramolecular organization.

The formation of hierarchical nanostructures using supramolecular dumbbell-like species made of organic–inorganic polyoxometalate-based hybrids is investigated by combination of SAXS and computational methods.     

Single electron transfer events and dynamical heterogeneity in the small protein azurin from Pseudomonas aeruginosa

Monitoring the fluorescence of single-dye-labeled azurin molecules, we observed the reaction of azurin with hexacyanoferrate under controlled redox potential yielding data on the timing of individual (forward and backward) electron transfer (ET) events. Change-point analysis of the time traces demonstrates significant fluctuations of ET rates and of mid-point potential E₀. These fluctuations are a signature of dynamical heterogeneity, here observed on a 14 kDa protein, the smallest to date. By correlating changes in forward and backward reaction rates we found that 6% of the observed change events could be explained by a change in midpoint potential, while for 25% a change of the donor–acceptor coupling could explain the data. The remaining 69% are driven by variations in complex association constants or structural changes that cause forward and back ET rates to vary independently. Thus, the observed spread in individual ET rates could be related in a unique way to variations in molecular parameters. The relevance for the understanding of metabolic processes is briefly discussed.

Observing electron transfer events in individual azurin molecules, we relate the spread in transfer rates in a unique way to variations in molecular parameters.     

Peptide-based inhibitors of protein–protein interactions: biophysical,structural and cellular consequences of introducing a constraint

Protein–protein interactions (PPIs) are implicated in the majority of cellular processes by enabling and regulating the function of individual proteins. Thus, PPIs represent high-value, but challenging targets for therapeutic intervention. The development of constrained peptides represents an emerging strategy to generate peptide-based PPI inhibitors, typically mediated by α-helices. The approach can confer significant benefits including enhanced affinity, stability and cellular penetration and is ingrained in the premise that pre-organization simultaneously pays the entropic cost of binding, prevents a peptide from adopting a protease compliant β-strand conformation and shields the hydrophilic amides from the hydrophobic membrane. This conceptual blueprint for the empirical design of peptide-based PPI inhibitors is an exciting and potentially lucrative way to effect successful PPI inhibitor drug-discovery. However, a plethora of more subtle effects may arise from the introduction of a constraint that include changes to binding dynamics, the mode of recognition and molecular properties. In this review, we summarise the influence of inserting constraints on biophysical, conformational, structural and cellular behaviour across a range of constraining chemistries and targets, to highlight the tremendous success that has been achieved with constrained peptides alongside emerging design opportunities and challenges.

This review summarizes the influence of inserting constraints on biophysical, conformational, structural and cellular behaviour for peptides targeting α-helix mediated protein–protein interactions.     

Supramolecular chemistry under mechanochemical conditions: a small molecule template generated and integrated into a molecular-to-supramolecular and back-to-molecular cascade reaction

We describe the integration of a small-molecule hydrogen-bond-donor template into a cascade reaction that is comprised of a combination of molecular and supramolecular events. The cascade is performed mechanochemically and in the presence of μL amounts of water. The small-molecule template is generated (molecular) using water-assisted vortex grinding and is then used to assemble an alkene (supramolecular) to undergo an intermolecular [2 + 2] photodimerization reaction (molecular). The chemical cascade results in a cyclobutane photoproduct that we show serves as a building block of a hydrogen-bonded network with a topology that conforms to T-silica. Remarkably, the molecular–supramolecular–molecular chemical cascade occurs stepwise and entirely regioselectively within the continuous mechanochemical conditions employed.

Mechanochemistry is applied to molecular and supramolecular chemistry to support a template-directed photochemical reaction.     

Pot and time economies in the total synthesis of Corey lactone

The Corey lactone is a highly versatile intermediate for the synthesis of a variety of prostaglandin hormones that natively control a multitude of important physiological processes. Starting from commercially available compounds, we herein disclose a time-economical, one-pot enantioselective preparation of the Corey lactone by virtue of a new diphenylprolinol silyl ether-mediated domino Michael/Michael reaction to afford the substituted cyclopentanone core in a formal (3 + 2) cycloadditive fashion. More broadly, this work advances the on-demand, gram-scale synthesis of high-value targets involving chemically orthogonal transformations, whereby distinct reactions of acids, bases, organometalics, reductants and oxidants can be carried out in a single reaction vessel in a sequential fashion.

The Corey lactone was synthesized by one-pot within 152 minutes from comercially available compounds using organocatalyst.     

Selective catalytic transformation of lignin with guaiacol as the only liquid product

Guaiacol is an important feedstock for producing various high-value chemicals. However, the current production route of guaiacol relies heavily on fossil resources. Using lignin as a cheap and renewable feedstock to selectively produce guaiacol has great potential, but it is a challenge because of its heterogeneity and inert reactivity. Herein, we discovered that La(OTf)₃ could catalyze the transformation of lignin with guaiacol as the only liquid product. In the reaction, La(OTf)₃ catalyzed the hydrolysis of lignin ether linkages to form alkyl-syringol and alkyl-guaiacol, which further underwent decarbonization and demethoxylation to produce guaiacol with a yield of up to 25.5 wt%, and the remaining residue was solid. In the scale-up experiment, the isolated yield of guaiacol reached up to 21.2 wt%. To our knowledge, this is the first work to produce pure guaiacol selectively from lignin. The bio-guaiacol may be considered as a platform to promote lignin utilization.

La(OTf)₃ can catalyze the transformation of lignin efficiently with guaiacol as the only liquid product, and guaiacol produced can be isolated easily in a scaled up experiment.     

Folding and fluorescence enhancement with strong odd–even effect for a series of merocyanine dye oligomers

A series of merocyanine (MC) oligomers with a varying number of chromophores from two to six has been synthesized via a peptide synthesis strategy. Solvent-dependent UV/vis spectroscopic studies reveal folding processes for the MC oligomers driven by strong dipole–dipole interactions resulting in well-defined π-stacks with antiparallel orientation of the dyes. Whilst even-numbered tetramer 4 and hexamer 6 only show partial folding into dimeric units, odd-numbered trimer 3 and pentamer 5 fold into π-stacks of three and five MC units upon decreasing solvent polarity. In-depth 2D NMR studies provided insight into the supramolecular structure. For trimer 3, an NMR structure could be generated revealing the presence of a well-defined triple π-stack in the folded state. Concomitant with folding, the fluorescence quantum yield is increased for all MC oligomers in comparison to the single chromophore. Based on radiative and non-radiative decay rates, this fluorescence enhancement can be attributed to the rigidification of the chromophores within the π-stacks that affords a pronounced decrease of the non-radiative decay rates. Theoretical investigations for the double and triple dye stacks based on time-dependent density functional theory (TD-DFT) calculations indicate for trimer 3 a pronounced mixing of Frenkel and charge transfer (CT) states. This leads to significant deviations from the predictions obtained by the molecular exciton theory which only accounts for the Coulomb interaction between the transition dipole moments of the chromophores.

A series of merocyanine (MC) oligomers with a varying number of chromophores from two to six has been synthesized via a peptide synthesis strategy.     

Total synthesis of dimeric Securinega alkaloids (−)-flueggenines D and I

We describe the total synthesis of (−)-flueggenines D and I. This features the first total synthesis of dimeric Securinega alkaloids with a C(α)–C(δ′) connectivity between two monomeric units. The key dimerization was enabled by a sequence that involves Stille reaction and conjugate reduction. The high chemofidelity of the Stille reaction enabled us to assemble two structurally complex fragments that could not be connected by other methods. Stereochemical flexibility and controllability at the δ′-junction of the dimeric intermediate render our synthetic strategy broadly applicable to the synthesis of other high-order Securinega alkaloids.

The first total synthesis of dimeric securinega alkaloids (−)-flueggenines D and I was completed by a dimerization strategy that involves Stille reaction and stereoselective conjugate reduction.     

Carbon nanodots revised: the thermal citric acid/urea reaction

Luminescent compounds obtained from the thermal reaction of citric acid and urea have been studied and utilized in different applications in the past few years. The identified reaction products range from carbon nitrides over graphitic carbon to distinct molecular fluorophores. On the other hand, the solid, non-fluorescent reaction product produced at higher temperatures has been found to be a valuable precursor for the CO₂-laser-assisted carbonization reaction in carbon laser-patterning. This work addresses the question of structural identification of both, the fluorescent and non-fluorescent reaction products obtained in the thermal reaction of citric acid and urea. The reaction products produced during autoclave–microwave reactions in the melt were thoroughly investigated as a function of the reaction temperature and the reaction products were subsequently separated by a series of solvent extractions and column chromatography. The evolution of a green molecular fluorophore, namely HPPT, was confirmed and a full characterization study on its structure and photophysical properties was conducted. The additional blue fluorescence is attributed to oligomeric ureas, which was confirmed by complementary optical and structural characterization. These two components form strong hydrogen-bond networks which eventually react to form solid, semi-crystalline particles with a size of ∼7 nm and an elemental composition of 46% C, 22% N, and 29% O. The structural features and properties of all three main components were investigated in a comprehensive characterization study.

Products of the thermal reaction of citric acid and urea have been identified as a complex mixture of fluorophores and particles.     

Single point activation of pyridines enables reductive hydroxymethylation

The single point activation of pyridines, using an electron-deficient benzyl group, facilitates the ruthenium-catalysed dearomative functionalisation of a range of electronically diverse pyridine derivatives. This transformation delivers hydroxymethylated piperidines in good yields, allowing rapid access to medicinally relevant small heterocycles. A noteworthy feature of this work is that paraformaldehyde acts as both a hydride donor and an electrophile in the reaction, enabling the use of cheap and readily available feedstock chemicals. Removal of the activating group can be achieved readily, furnishing the free NH compound in only 2 steps. The synthetic utility of the method was illustrated with a synthesis of (±)-Paroxetine.

Pyridines can be activated at a single point with a new benzyl group, followed by dearomative functionalisation at C3 using formaldehyde.     

Broadband fluorescence reveals mechanistic differences in excited-state proton transfer to protic and aprotic solvents

Excited-state proton transfer (ESPT) to solvent is often explained according to the two-step Eigen–Weller model including a contact ion pair (CIP*) as an intermediate, but general applicability of the model has not been thoroughly examined. Furthermore, examples of the spectral identification of CIP* are scarce. Here, we report on a detailed investigation of ESPT to protic (H₂O, D₂O, MeOH and EtOH) and aprotic (DMSO) solvents utilizing a broadband fluorescence technique with sub-200 fs time resolution. The time-resolved spectra are decomposed into contributions from the protonated and deprotonated species and a clear signature of CIP* is identified in DMSO and MeOH. Interestingly, the CIP* intermediate is not observable in aqueous environment although the dynamics in all solvents are multi-exponential. Global analysis based on the Eigen–Weller model is satisfactory in all solvents, but the marked mechanistic differences between aqueous and organic solvents cast doubt on the physical validity of the rate constants obtained.

Time-resolved broadband fluorescence facilitates direct observation of reaction intermediates in excited-state proton transfer to solvent in protic and aprotic solvents.