Impact of Multiple Hydrogen Bonds with Fluoride on Catalysis: Insight from NMR Spectroscopy

Urea-Based [2]Rotaxanes as Effective Phase-Transfer Organocatalysts: Hydrogen-Bonding Cooperative Activation Enabled by the Mechanical Bond

We finely designed a set of [2]rotaxanes with urea threads and tested them as hydrogen-bonding phase-transfer catalysts in two different nucleophilic substitutions requiring the activation of the reactant fluoride anion. The [2]rotaxane bearing a fluorinated macrocycle and a fluorine-containing urea thread displayed significantly enhanced catalytic activity in comparison with the combination of both noninterlocked components. This fact highlights the notably beneficial role of the mechanical bond, cooperatively activating the processes through hydrogen-bonding interactions.

Quaternary ammonium fluorides and difluorosilicates as nucleophilic fluorination reagents

TBAT (tetrabutylammonium difluorotriphenylsilicate) is an excellent homogeneous nucleophilic fluorination reagent, but a high excess of the reagent was reported to be essential. We hence optimized the reaction conditions and compared its nucleophilic fluorination reactivity with that of other common commercial nucleophilic fluorination reagents, such as anhydrous TBAF and TASF (tris(dimethylamino)sulfonium difluorotrimethylsilicate). As the substrates, we employed a standard set of primary and secondary octyl substrates under identical conditions. To eliminate the possibility of hydrogen fluoride elimination in the above reagents, we prepared four quaternary ammonium fluorides lacking β-elimination possibility in the hydrocarbon chain, transformed them to the corresponding difluorotriphenylsilicates, and compared their reactivity with that of the commercial reagents. Furthermore, attempts to isolate analogous tetrabutylammonium difluoromethyldiphenylsilicate or difluorodimethylphenylsilicate failed, as was confirmed by comparison of the published experimental data with computed 19F NMR spectra. Finally, we studied the transition states of decomposition of various tetramethylammonium methylphenyldifluorosilicates by DFT methods and found that their relative energies increase with an increasing number of phenyl groups. The formation of difluorosilicates is a nearly barrierless process.

Anion-assisted supramolecular polymerization of luminescent organic π-conjugated chromophores in a moderately polar solvent: tunable nanostructures and their corresponding effects on electronic properties

Supramolecular polymers of π-conjugated organic chromophores have emerged as promising candidates in organic electronics because of their dynamic and highly ordered molecular organization. Herein, we demonstrate the formation of luminescent, highly conducting supramolecular polymers of a functionalized naphthalimide π-chromophore-based organic semiconductor in a moderately polar organic solvent (tetrahydrofuran) by overcoming solute-solvent H-bonding via assistance from fluoride anions. The polymerization is exclusively guided by the synergistic effects of cascade H-bonding (F-⋯H-N- of primary amines, followed by -CO⋯H-N- of amides), π-π stacking and hydrophobic interactions. An increasing molar equivalent of anions leads to a morphology transition from 1D nanowires to 2D nanosheets via nanotubes and nanorings, but above a particular threshold of the same anion, depolymerization-mediated disruption of long-range order and formation of non-luminescent spherical particles was observed. Such significant impacts of anions in supramolecular polymerization-depolymerization were utilized in modulating the electronic properties of this naphthalimide-based organic semiconductor.

An NMR portrait of functional and dysfunctional allosteric cooperativity in cAMP-dependent protein kinase A

The cAMP-dependent protein kinase A (PKA) is the archetypical eukaryotic kinase. The catalytic subunit (PKA-C) structure is highly conserved among the AGC-kinase family. PKA-C is a bilobal enzyme with a dynamic N-lobe, harbouring the Adenosine-5'-triphosphate (ATP) binding site and a more rigid helical C-lobe. The substrate-binding groove resides at the interface of the two lobes. A distinct feature of PKA-C is the positive binding cooperativity between nucleotide and substrate. Several PKA-C mutations lead to the development of adenocarcinomas, myxomas, and other rare forms of liver tumours. Nuclear magnetic resonance (NMR) spectroscopy shows that these mutations disrupt the allosteric communication between the two lobes, causing a drastic decrease in binding cooperativity. The loss of cooperativity correlates with changes in substrate fidelity and reduced kinase affinity for the endogenous protein kinase inhibitor (PKI). The similarity between PKI and the inhibitory sequence of the kinase regulatory subunits suggests that the overall mechanism of regulation of the kinase may be disrupted. We surmise that a reduced or obliterated cooperativity may constitute a common trait for both orthosteric and allosteric mutations of PKA-C that may lead to dysregulation and disease.

Molecular Understanding and Practical In Silico Catalyst Design in Computational Organocatalysis and Phase Transfer Catalysis-Challenges and Opportunities

Through the lens of organocatalysis and phase transfer catalysis, we will examine the key components to calculate or predict catalysis-performance metrics, such as turnover frequency and measurement of stereoselectivity, via computational chemistry. The state-of-the-art tools available to calculate potential energy and, consequently, free energy, together with their caveats, will be discussed via examples from the literature. Through various examples from organocatalysis and phase transfer catalysis, we will highlight the challenges related to the mechanism, transition state theory, and solvation involved in translating calculated barriers to the turnover frequency or a metric of stereoselectivity. Examples in the literature that validated their theoretical models will be showcased. Lastly, the relevance and opportunity afforded by machine learning will be discussed.

Synthesis of Trifluoromethylated Monoterpene Amino Alcohols

For the first time, monoterpene trifluoromethylated β-hydroxy-benzyl-O-oximes were synthesized in 81–95% yields by nucleophilic addition of the Ruppert–Prakash reagent (TMSCF3) to the corresponding β-keto-benzyl-O-oximes based on (+)-nopinone, (−)-verbanone and (+)-camphoroquinone. Trifluoromethylation has been determined to entirely proceed chemo- and stereoselective at the C=O rather than C=N bond. Trifluoromethylated benzyl-O-oximes were reduced to the corresponding α-trifluoromethyl-β-amino alcohols in 82–88% yields. The structure and configuration of the compounds obtained have been established.

Insight into Substrate Recognition by Urea-Based Helical Foldamer Catalysts Using a DFT Global Optimization Approach

Peptides and foldamers have recently gained increasing attention as chiral catalysts to achieve challenging (asymmetric) transformations. We previously reported that short helically folded aliphatic oligoureas in combination with achiral Brønsted bases are effective H-bonding catalysts for C-C bond-forming reactions─i.e., the conjugate addition of 1,3-dicarbonyl pronucleophiles to nitroalkenes─with high reactivity and selectivity and at remarkably low chiral catalyst/substrate molar ratios. This theoretical investigation at the density functional theory level of theory, aims to both analyze how the substrates of the reaction interact with the foldamer catalyst and rationalize a chain-length dependence effect on the catalytic properties. We confirm that the first two ureas are the only H-bond donors available to interact with external molecules. Moreover, each urea site interacts with one of the two reactants allowing a short distance between the two reacting carbons, thus facilitating the conjugated addition. Additionally, it was observed that the molecular recognition and catalyst-substrate interactions are mainly governed by electrostatic interactions but not orbital interactions (see from NBO if this is finally true). On these grounds, an electrostatic potential (ESP) analysis showed an important internal charge separation in the catalyst, the positive ESP region being concentrated around the first two ureas, with its area extending as the number of residues increases.

Platinum-Catalyzed Hydrofluorination of Alkynes: Hydrogen Bonding to Indolylphosphine Ligands to Provide Fluoride Reactivity

The reaction of the Pt complexes cis-[Pt(CH3 )2 {R2 P(Ind)}2 ] (Ind=2-(3-methyl)indolyl, R=Ph (1 a), 4-FC6 H4 (1 b), 4-CF3 C6 H4 (1 c)) with HF afforded the fluorido complexes trans-[Pt(F(HF)2 )(CH3 ){R2 P(Ind)}2 ] 2 a-c, which can be converted into trans-[Pt(F)(CH3 ){R2 P(Ind)}2 ] (3 a-c) by treatment with CsF. Addition of 3-hexyne to 2 a-c gave alkyne complexes trans-[Pt(C,C-η2 -C2 H5 C≡CC2 H5 )(CH3 ){R2 P(Ind)}2 {F(HF)2 }] (4 a-c) at which a fluoride is stabilised as polyfluoride in the coordination sphere by hydrogen bonding to the indolyl-substituted phosphine ligands. Subsequent heating of a solution of 4 a in the presence of PVPHF led to fluoroalkene formation. Selective catalytic hydrofluorination of alkynes to yield (Z)-fluoroalkenes were developed. The ability of hydrogen bonding to polyfluoride favours the fluorination step as demonstrated by studies with complexes bearing no indolyl groups at the phosphine ligands.

The pKBHX Hydrogen-Bond Basicity Scale: From Molecules to Anions

The pK_BHX (logarithm of complexation constant K of 4-fluorophenol with bases) hydrogen-bond basicity scale of neutral hydrogen-bond acceptors (HBAs) is extended to anionic HBAs. The scale is constructed for 26 anions through (i) the infrared measurement of K on NBu₄⁺X^- ion pairs in CCl₄, (ii) the estimation of K from linear free energy relationships between measured K values and literature K values for various phenols in polar solvents, and (iii) the computation of K at the density functional theory level in CCl₄. The scale extends on a 9.4 pK unit range from fluoride to tetraphenylborate. Considering a number of anions as organic functions substituted with unipolar substituents, their pK_BHX values can be related to the Hammett-Taft substituent constants σ. Unipolar substituents (O^- and S^-) obey the same pK_BHX versus σ relationships as dipolar ionic (N^-N⁺R₃) and dipolar (OH, CF₃, NR₂, or OR) ones for the nitrile, carbonyl, nitroso, nitro, sulfonyl, and phosphoryl functions. Like dipolar substituents, unipolar substituents at carbon and nitrogen operate by field-inductive and resonance effects, whereas substituents at sulfur and phosphorus operate only by the field-inductive effect.

Hydrogen Bonding Phase-Transfer Catalysis with Alkali Metal Fluorides and Beyond

Phase-transfer catalysis (PTC) is one of the most powerful catalytic manifolds for asymmetric synthesis. Chiral cationic or anionic PTC strategies have enabled a variety of transformations, yet studies on the use of insoluble inorganic salts as nucleophiles for the synthesis of enantioenriched molecules have remained elusive. A long-standing challenge is the development of methods for asymmetric carbon-fluorine bond formation from readily available and cost-effective alkali metal fluorides. In this Perspective, we describe how H-bond donors can provide a solution through fluoride binding. We use examples, primarily from our own research, to discuss how hydrogen bonding interactions impact fluoride reactivity and the role of H-bond donors as phase-transfer catalysts to bring solid-phase alkali metal fluorides in solution. These studies led to hydrogen bonding phase-transfer catalysis (HB-PTC), a new concept in PTC, originally crafted for alkali metal fluorides but offering opportunities beyond enantioselective fluorination. Looking ahead, the unlimited options that one can consider to diversify the H-bond donor, the inorganic salt, and the electrophile, herald a new era in phase-transfer catalysis. Whether abundant inorganic salts of lattice energy significantly higher than those studied to date could be considered as nucleophiles, e.g., CaF₂, remains an open question, with solutions that may be found through synergistic PTC catalysis or beyond PTC.

Asymmetric Azidation under Hydrogen Bonding Phase-Transfer Catalysis: A Combined Experimental and Computational Study

Asymmetric catalytic azidation has increased in importance to access enantioenriched nitrogen containing molecules, but methods that employ inexpensive sodium azide remain scarce. This encouraged us to undertake a detailed study on the application of hydrogen bonding phase-transfer catalysis (HB-PTC) to enantioselective azidation with sodium azide. So far, this phase-transfer manifold has been applied exclusively to insoluble metal alkali fluorides for carbon–fluorine bond formation. Herein, we disclose the asymmetric ring opening of meso aziridinium electrophiles derived from β-chloroamines with sodium azide in the presence of a chiral bisurea catalyst. The structure of novel hydrogen bonded azide complexes was analyzed computationally, in the solid state by X-ray diffraction, and in solution phase by ¹H and ¹⁴N/¹⁵N NMR spectroscopy. With N-isopropylated BINAM-derived bisurea, end-on binding of azide in a tripodal fashion to all three NH bonds is energetically favorable, an arrangement reminiscent of the corresponding dynamically more rigid trifurcated hydrogen-bonded fluoride complex. Computational analysis informs that the most stable transition state leading to the major enantiomer displays attack from the hydrogen-bonded end of the azide anion. All three H-bonds are retained in the transition state; however, as seen in asymmetric HB-PTC fluorination, the H-bond between the nucleophile and the monodentate urea lengthens most noticeably along the reaction coordinate. Kinetic studies corroborate with the turnover rate limiting event resulting in a chiral ion pair containing an aziridinium cation and a catalyst-bound azide anion, along with catalyst inhibition incurred by accumulation of NaCl. This study demonstrates that HB-PTC can serve as an activation mode for inorganic salts other than metal alkali fluorides for applications in asymmetric synthesis.

H-Bonded Counterion-Directed Enantioselective Au(I) Catalysis

A new strategy for enantioselective transition-metal catalysis is presented, wherein a H-bond donor placed on the ligand of a cationic complex allows precise positioning of the chiral counteranion responsible for asymmetric induction. The successful implementation of this paradigm is demonstrated in 5-exo-dig and 6-endo-dig cyclizations of 1,6-enynes, combining an achiral phosphinourea Au(I) chloride complex with a BINOL-derived phosphoramidate Ag(I) salt and thus allowing the first general use of chiral anions in Au(I)-catalyzed reactions of challenging alkyne substrates. Experiments with modified complexes and anions, ¹H NMR titrations, kinetic data, and studies of solvent and nonlinear effects substantiate the key H-bonding interaction at the heart of the catalytic system. This conceptually novel approach, which lies at the intersection of metal catalysis, H-bond organocatalysis, and asymmetric counterion-directed catalysis, provides a blueprint for the development of supramolecularly assembled chiral ligands for metal complexes.

Multigram synthesis of N-alkyl bis-ureas for asymmetric hydrogen bonding phase-transfer catalysis

Fluorine is a key element present in ~35% of agrochemicals and 25% of marketed pharmaceutical drugs. The availability of reliable synthetic protocols to prepare catalysts that allow the efficient incorporation of fluorine in organic molecules is therefore essential for broad applicability. Herein, we report a protocol for the multigram synthesis of two representative enantiopure N-alkyl bis-urea organocatalysts derived from (S)-(-)-1,1'-binaphthyl-2,2'-diamine ((S)-BINAM). These tridentate hydrogen bond donors are highly effective phase-transfer catalysts for solubilizing safe and inexpensive metal alkali fluorides (KF and CsF) in organic solvents for enantioselective nucleophilic fluorinations. The first catalyst, characterized by N-isopropyl substitution, was obtained by using a two-step sequence consisting of reductive amination followed by urea coupling from commercially available starting materials (14 g, 48% yield and 5-d total synthesis time). The second catalyst, featuring N-ethyl alkylation and meta-terphenyl substituents, was accessed via a novel, scalable, convergent route that concluded with the coupling between N-ethylated (S)-BINAM and a preformed isocyanate (52 g and 52% overall yield). On this scale, the synthesis requires ~10 d. This can be reduced to 5 d by performing some steps in parallel. Compared to the previous synthetic route, this protocol avoids the final chromatographic purification and produces the desired catalysts in very high purity and improved yield.

Closing the gap between 19F and 18F chemistry

Positron emission tomography (PET) has become an invaluable tool for drug discovery and diagnosis. The positron-emitting radionuclide fluorine-18 is frequently used in PET radiopharmaceuticals due to its advantageous characteristics; hence, methods streamlining access to 18F-labelled radiotracers can make a direct impact in medicine. For many years, access to 18F-labelled radiotracers was limited by the paucity of methodologies available, and the poor diversity of precursors amenable to 18F-incorporation. During the last two decades, 18F-radiochemistry has progressed at a fast pace with the appearance of numerous methodologies for late-stage 18F-incorporation onto complex molecules from a range of readily available precursors including those that do not require pre-functionalisation. Key to these advances is the inclusion of new activation modes to facilitate 18F-incorporation. Specifically, new advances in late-stage 19F-fluorination under transition metal catalysis, photoredox catalysis, and organocatalysis combined with the availability of novel 18F-labelled fluorination reagents have enabled the invention of novel processes for 18F-incorporation onto complex (bio)molecules. This review describes these major breakthroughs with a focus on methodologies for C-18F bond formation. This reinvigorated interest in 18F-radiochemistry that we have witnessed in recent years has made a direct impact on 19F-chemistry with many laboratories refocusing their efforts on the development of methods using nucleophilic fluoride instead of fluorination reagents derived from molecular fluorine gas.

Electrical Detection of Molecular Transformations Associated with Chemical Reactions Using Graphene Devices

This study proposes a method to electrically detect chemical reactions that involve bond changes through reactions on graphene surfaces. To achieve a highly sensitive detection, we focused on the thiol-ene reaction that combines the maleimide and thiol groups. Graphene field-effect transistors (FETs) were used to detect the binding changes of the modified molecules. Graphene has high carrier mobility and is sensitive to changes in the electronic state of its surface. Graphene has been used as a sensor to detect low-concentration targets with high sensitivity. N-(9-Acridinyl)maleimide (NAM) was chosen as the modified molecule to immobilize maleimide on graphene through π-interaction, and methanethiol (MeSH) was set as the target thiol. The modification of NAM to graphene was first confirmed by attenuated total reflection Fourier transform infrared spectroscopy, and the modification density was 0.5 ± 0.1/nm² through cyclic voltammetry. Owing to a bond exchange, the transfer characteristics of the graphene FET shifted by 2 V to the negative direction after being exposed to MeSH at 10 parts per billion (ppb), equivalent to 0.2 ng, under ultraviolet irradiation. With 5000 ppb of acetic acid, it only shifted 0.7 V. With 1000 ppb of ethanol and 10,000 ppb of methanol, it shifted to the positive direction by 0.4 and 0.6 V, respectively. Because the nontarget molecule showed only a slight response, a thiol-ene chemical reaction was detected. The proposed method can detect the bond-change reaction using an ultralow concentration of MeSH, which indicates that at least 10 ppb (or 0.2 ng) of MeSH was detected by the graphene FET.

A quantum crystallographic approach to short hydrogen bonds

In this work we use high-resolution synchrotron X-ray diffraction for electron density mapping, in conjunction with ab initio modelling, to study short O-H⋯O and O+-H⋯O- hydrogen bonds whose behaviour is known to be tuneable by temperature. The short hydrogen bonds have donor-acceptor distances in the region of 2.45 Å and are formed in substituted urea and organic acid molecular complexes of N,N'-dimethylurea oxalic acid 2 : 1 (1), N,N-dimethylurea 2,4-dinitrobenzoate 1 : 1 (2) and N,N-dimethylurea 3,5-dinitrobenzoic acid 2 : 2 (3). From the combined analyses, these complexes are found to fall within the salt-cocrystal continuum and exhibit short hydrogen bonds that can be characterised as both strong and electrostatic (1, 3) or very strong with a significant covalent contribution (2). An additional charge assisted component is found to be important in distinguishing the relatively uncommon O-H⋯O pseudo-covalent interaction from a typical strong hydrogen bond. The electron density is found to be sensitive to the extent of static proton transfer, presenting it as a useful parameter in the study of the salt-cocrystal continuum. From complementary calculated hydrogen atom potentials, we attribute changes in proton position to the molecular environment. Calculated potentials also show zero barrier to proton migration, forming an 'energy slide' between the donor and acceptor atoms. The better fundamental understanding of the short hydrogen bond in the 'zone of fluctuation' presented in a salt-cocrystal continuum, enabled by studies like this, provide greater insight into their related properties and can have implications in the regulation of pharmaceutical materials.

A Mechanistic Probe into 1,2-cis Glycoside Formation Catalyzed by Phenanthroline and Further Expansion of Scope

Phenanthroline, a rigid and planar compound with two fused pyridine rings, has been used as a powerful ligand for metals and a binding agent for DNA/RNA. We discovered that phenanthroline could be used as a nucleophilic catalyst to efficiently access high yielding and diastereoselective α-1,2-cis glycosides through the coupling of hydroxyl acceptors with α-glycosyl bromide donors. We have conducted an extensive investigation into the reaction mechanism, wherein the two glycosyl phenanthrolinium ion intermediates, a 4C1 chair-liked β-conformer and a B2,5 boat-like α-conformer, have been detected in a ratio of 2:1 (β:α) using variable temperature NMR experiments. Furthermore, NMR studies illustrate that a hydrogen bonding is formed between the second nitrogen atom of phenanthroline and the C1-anomeric hydrogen of sugar moiety to stabilize the phenanthrolinium ion intermediates. To obtain high α-1,2-cis stereoselectivity, a Curtin-Hammett scenario was proposed wherein interconversion of the 4C1 chair-like β-conformer and B2,5 boat-like α-conformer is more rapid than nucleophilic addition. Hydroxyl attack takes place from the α-face of the more reactive 4C1 β-phenanthrolinium intermediate to give an α-anomeric product. The utility of the phenanthroline catalysis is expanded to sterically hindered hydroxyl nucleophiles and chemoselective coupling of an alkyl hydroxyl group in the presence of a free C1-hemiacetal. In addition, the phenanthroline-based catalyst has a pronounced effect on site-selective couplings of triol motifs and orthogonally activates the anomeric bromide leaving group over the anomeric fluoride and sulfide counterparts.

Alkali Metal Fluorides in Fluorinated Alcohols: Fundamental Properties and Applications to Electrochemical Fluorination

Fundamental properties of alkali metal fluorides (MF, M = Cs, K) dissolved in 1,1,1,3,3,3-hexafluoroisopropanol (HFIP) or in 3,3,3-trifluoroethanol (TFE) are investigated, including solubility, conductivity, and viscosity. Solid-state structures of single crystals obtained from CsF/HFIP and CsF/TFE are described for the first time, giving insights into the multiple interactions between fluorinated alcohols and CsF. Applications in electrochemical fluorination reactions are successfully demonstrated.

Diversity-Oriented Synthesis of Aliphatic Fluorides via Reductive C(sp3 )-C(sp3 ) Cross-Coupling Fluoroalkylation

Monofluorinated alkyl compounds are of great importance in pharmaceuticals, agrochemicals and materials. Herein, we describe a direct nickel-catalyzed monofluoromethylation of unactivated alkyl halides using a low-cost industrial raw material, bromofluoromethane, by demonstrating a general and efficient reductive cross-coupling of two alkyl halides. Results with 1-bromo-1-fluoroalkane also demonstrate the viability of monofluoroalkylation, which further established the first example of reductive C(sp³ )-C(sp³ ) cross-coupling fluoroalkylation. These transformations demonstrate high efficiency, mild conditions, and excellent functional-group compatibility, especially for a range of pharmaceuticals and biologically active compounds. Mechanistic studies support a radical pathway. Kinetic studies reveal that the reaction is first-order dependent on catalyst and alkyl bromide whereas the generation of monofluoroalkyl radical is not involved in the rate-determining step. This strategy provides a general and efficient method for the synthesis of aliphatic fluorides.