Fluorine as a hydrogen-bond acceptor: experimental evidence and computational calculations

Influence of MXene Composition on Triboelectricity of MXene-Alginate Nanocomposites

MXenes are highly versatile and conductive 2D materials that can significantly enhance the triboelectric properties of polymer nanocomposites. Despite the growing interest in the tunable chemistry of MXenes for energy applications, the effect of their chemical composition on triboelectric power generation has yet to be thoroughly studied. Here, we investigate the impact of the chemical composition of MXenes, specifically the Ti3CNTx carbonitride vs the most studied carbide, Ti3C2Tx, on their interactions with sodium alginate biopolymer and, ultimately, the performance of a triboelectric nanogenerator (TENG) device. Our results show that adding 2 wt % of Ti3CNTx to alginate produces a synergistic effect that generates a higher triboelectric output than the Ti3C2Tx system. Spectroscopic analyses suggest that a higher oxygen and fluorine content on the surface of Ti3CNTx enhances hydrogen bonding with the alginate matrix, thereby increasing the surface charge density of the alginate oxygen atoms. This was further supported by Kelvin probe force microscopy, which revealed a more negative surface potential on Ti3CNTx-alginate, facilitating high charge transfer between the TENG electrodes. The optimized Ti3CNTx-alginate nanogenerator delivered an output of 670 V, 15 μA, and 0.28 W/m2. Additionally, we demonstrate that plasma oxidation of the MXene surface further enhances triboelectric performance. Due to the diverse surface terminations of MXene, we show that Ti3CNTx-alginate can function as either tribopositive or tribonegative material, depending on the counter-contacting material. Our findings provide a deeper understanding of how MXene composition affects their interaction with biopolymers and resulting tunable triboelectrification behavior. This opens up new avenues for developing flexible and efficient MXene-based TENG devices.

Unravelling the mechanism of neurotensin recognition by neurotensin receptor 1

The conformational ensembles of G protein-coupled receptors (GPCRs) include inactive and active states. Spectroscopy techniques, including NMR, show that agonists, antagonists and other ligands shift the ensemble toward specific states depending on the pharmacological efficacy of the ligand. How receptors recognize ligands and the kinetic mechanism underlying this population shift is poorly understood. Here, we investigate the kinetic mechanism of neurotensin recognition by neurotensin receptor 1 (NTS1) using 19F-NMR, hydrogen-deuterium exchange mass spectrometry and stopped-flow fluorescence spectroscopy. Our results indicate slow-exchanging conformational heterogeneity on the extracellular surface of ligand-bound NTS1. Numerical analysis of the kinetic data of neurotensin binding to NTS1 shows that ligand recognition follows an induced-fit mechanism, in which conformational changes occur after neurotensin binding. This approach is applicable to other GPCRs to provide insight into the kinetic regulation of ligand recognition by GPCRs.

Design, synthesis and cytotoxic evaluation of novel bis-thiazole derivatives as preferential Pim1 kinase inhibitors with in vivo and in silico study

Bis-thiazole derivatives were synthesised conforming to the Pim1 pharmacophore model following Hantzsch condensation. Pim1 has a major role in regulating the G1/S phase which upon inhibition the cell cycle stops at its early stages. Derivatives 3b and 8b showed the best Pim1 IC₅₀ 0.32 and 0.24 µM, respectively relative to staurosporine IC₅₀ 0.36 µM. Further confirmation of 3b and 8b Pim1 inhibition was implemented by hindering the T47D cell cycle at G0/G1 and S phases where 3b showed 66.5% cells accumulation at G0/G1 phase while 8b demonstrated 26.5% cells accumulation at the S phase compared to 53.9% and 14.9% of a control group for both phases, respectively. Additional in vivo cytotoxic evaluation of 3b and 8b revealed strong antitumor activity with up-regulation of caspase-3 and down-regulation of VEGF and TNF α immune expression with concomitant elevation of malondialdehyde levels in case of 8b.

Aptamer-Protein Interactions: From Regulation to Biomolecular Detection

Serving as the basis of cell life, interactions between nucleic acids and proteins play essential roles in fundamental cellular processes. Aptamers are unique single-stranded oligonucleotides generated by in vitro evolution methods, possessing the ability to interact with proteins specifically. Altering the structure of aptamers will largely modulate their interactions with proteins and further affect related cellular behaviors. Recently, with the in-depth research of aptamer-protein interactions, the analytical assays based on their interactions have been widely developed and become a powerful tool for biomolecular detection. There are some insightful reviews on aptamers applied in protein detection, while few systematic discussions are from the perspective of regulating aptamer-protein interactions. Herein, we comprehensively introduce the methods for regulating aptamer-protein interactions and elaborate on the detection techniques for analyzing aptamer-protein interactions. Additionally, this review provides a broad summary of analytical assays based on the regulation of aptamer-protein interactions for detecting biomolecules. Finally, we present our perspectives regarding the opportunities and challenges of analytical assays for biological analysis, aiming to provide guidance for disease mechanism research and drug discovery.

Low-energy electron interaction with 2-(trifluoromethyl)acrylic acid, a potential component for EUVL resist material

Motivated by the current introduction of extreme ultraviolet lithography (EUVL) into chip manufacturing processes, and thus the transition to electron-induced chemistry within the respective resist materials, we have studied low energy electron-induced fragmentation of 2-(trifluoromethyl)acrylic acid (TFMAA). This compound is chosen as a potential resist component, whereby fluorination enhances the EUV adsorption and may at the same time promote electron-induced dissociation. Dissociative ionization and dissociative electron attachment are studied, and to aid the interpretation of the observed fragmentation channels, the respective threshold values are calculated at the DFT and coupled cluster level of theory. Not surprisingly, we find significantly more extensive fragmentation in DI than in DEA and in fact, the only significant DEA fragmentation channel is the cleavage of HF from the parent molecule upon electron attachment. Rearrangement and new bond formation are substantial in DI and are, in fact, similar to DEA, mainly associated with HF formation. The observed fragmentation reactions are discussed in relation to the underlying reactions and potential implications for the suitability of TFMAA as a component of EUVL resist materials.

Structure-Activity Relationship Studies of the Aryl Acetamide Triazolopyridazines against Cryptosporidium Reveals Remarkable Role of Fluorine

Our previous work identified compound 1 (SLU-2633) as a potent lead compound toward the identification of a novel treatment for cryptosporidiosis, caused by the parasite Cryptosporidium (EC50 = 0.17 μM). While this compound is potent and orally efficacious, the mechanism of action and biological target(s) of this series are currently unknown. In this study, we synthesized 70 compounds to develop phenotypic structure-activity relationships around the aryl "tail" group. In this process, we found that 2-substituted compounds are inactive, confirmed that electron withdrawing groups are preferred over electron donating groups, and that fluorine plays a remarkable role in the potency of these compounds. The most potent compound resulting from this work is SLU-10482 (52, EC50 = 0.07 μΜ), which was found to be orally efficacious with an ED90 < 5 mg/kg BID in a Cryptosporidium-infection mouse model, superior to SLU-2633.

Synthesis of Chiral Tricyclic Pyrone Molecules via Palladium(0)-Catalyzed Displacement Reactions of Chiral Tricyclic Pyrone Acetate With Azide or Amine

Tricyclic pyrone (TP) molecules have shown protection of MC65 neuroblastoma cells death induced by amyloid-β proteins through SβC gene, a decrease of amyloid-β peptide levels, and improvement of motor functions and memory in Alzheimer's disease mouse and rat models. Mechanistic studies suggest TP molecules modulate N-methyl-D-aspartate receptor. A short synthesis of chiral TP analogs was sought using a Pd(0)-catalyzed displacement of TP allylic acetate intermediate with sodium azide or substituted benzylamines. A three-step sequence of reactions by the treatment of 2-{(5aS,7S)-3-methyl-1-oxo-1,5a,6,7,8,9-hexahydropyrano[4,3-b]chromen-7-yl}allyl acetate (9) with (Ph3P)4Pd and sodium azide, followed by reduction with Zn-NH4OCHO and coupling with 3-fluoro-4-hydroxybenzaldehyde and NaCNBH3 was found to give TP coupling molecule, (5aS,7S)-7-(1-(3-fluoro-4-hydroxybenzylamino)prop-2-en-2-yl)-3-methyl-6,7,8,9-tetrahydropyrano[4,3-b]chromen-1(5aH)-one (2), in a good yield. An alternative shorter pathway - a two-step sequence of reactions - by the displacement of 9 by 4-(t-butyldimethylsilyloxy)-3-fluoro-benzylamine with a catalytic amount of (Ph3P)4Pd in THF followed by removal of the silyl ether protecting group gave 2, albeit in a lower chemical yield. The described syntheses should provide general procedures for the synthesis of a library of TP molecules for the discovery of anti-Alzheimer drugs.

Facile one-step synthesis of a versatile nitrogen-doped hydrochar from olive oil production waste, "alperujo", for removing pharmaceuticals from wastewater

In line with the principles of zero waste and recycling, alperujo (AL) was used in this study to produce a value-added product: hydrochar (HC) with high adsorption capacity. An optimization of the hydrothermal carbonization (HTC) conditions, such as temperature, residence time, and water/solid ratio, was carried out to maximize the adsorption capacity. Eight HCs were obtained, and an in-depth comparative characterization, as well as adsorption tests of two pharmaceuticals with very different physicochemical properties (fluoxetine (FLX) and cefazolin (CFZ)), were performed. This first step allowed for elucidation of the best candidates to carry out nitrogen grafting on their surface, resulting in the HC obtained at a higher water/solid ratio and temperature, and longer residence time: 3-220ºC-2.5 h with a maximum uptake of 4.6 and 0.4 mg/g for FLX and CFZ, respectively. After that, a facile one-step, one-pot synthesis of nitrogen-doped hydrochars (N-HC) was developed to prepare a versatile bio-adsorbent with enhanced adsorption capacity. Two N-HCs were prepared using urea (U-HC) and polyethyleneimine (PEI-HC) and were intensively characterized to shed light on the adsorption mechanism. In both cases, amide groups were formed, which favored the adsorption process. PEI-HC acquired an outstanding maximum adsorption capacity of 983.84 mg/g for CFZ, and 29.31 mg/g for FLX, and the process was well described by the Freundlich isotherm and pseudo-second-order kinetic model. A co-adsorption test was performed using PEI-HC for both pharmaceuticals, finding that the adsorption process occurs in different active sites because there was no interference between the pollutants. This fact corroborates the versatility of the new bio-adsorbent synthesized.

Cooperative CO2 adsorption mechanism in a perfluorinated CeIV-based metal organic framework

Adsorbents able to uptake large amounts of gases within a narrow range of pressure, i.e., phase-change adsorbents, are emerging as highly interesting systems to achieve excellent gas separation performances with little energy input for regeneration. A recently discovered phase-change metal-organic framework (MOF) adsorbent is F4_MIL-140A(Ce), based on Ce^IV and tetrafluoroterephthalate. This MOF displays a non-hysteretic step-shaped CO₂ adsorption isotherm, reaching saturation in conditions of temperature and pressure compatible with real life application in post-combustion carbon capture, biogas upgrading and acetylene purification. Such peculiar behaviour is responsible for the exceptional CO₂/N₂ selectivity and reverse CO₂/C₂H₂ selectivity of F4_MIL-140A(Ce). Here, we combine data obtained from a wide pool of characterisation techniques - namely gas sorption analysis, in situ infrared spectroscopy, in situ powder X-ray diffraction, in situ X-ray absorption spectroscopy, multinuclear solid state nuclear magnetic resonance spectroscopy and adsorption microcalorimetry - with periodic density functional theory simulations to provide evidence for the existence of a unique cooperative CO₂ adsorption mechanism in F4_MIL-140A(Ce). Such mechanism involves the concerted rotation of perfluorinated aromatic rings when a threshold partial pressure of CO₂ is reached, opening the gate towards an adsorption site where CO₂ interacts with both open metal sites and the fluorine atoms of the linker.

Synergistic effect of intra- and intermolecular hydrogen bond in 2-haloethanols probed by infrared

Fluorine is often considered the only halogen to effectively engage in hydrogen bonds, while the other halogens, particularly iodine, are not electronegative enough to participate as hydrogen bond acceptors in electrostatic interactions. 2-Fluoroethanol and 2-iodoethanol have been studied herein to test this assumption, since a highly stable gauche conformation can experience the intramolecular hydrogen bond. However, the infrared O  H stretching frequency indicates that the hydroxyl group in 2-fluoroethanol is not engaged in intramolecular hydrogen bond, while the corresponding vibration mode for 2-iodoethanol suggests that not only the O  H is engaged in such interaction, but also that intramolecular hydrogen bond may drive the conformational equilibrium in this molecule. Theoretical calculations support the covalent nature of this interaction, and provide evidence that intermolecular hydrogen bond with a water molecule, and probably with the polar solvents tested experimentally, occurs with the hydroxyl rather than with the iodine substituent, as conventionally, in order to keep the intramolecular hydrogen bond effective.

i-Motif folding intermediates with zero-nucleotide loops are trapped by 2'-fluoroarabinocytidine via F···H and O···H hydrogen bonds

G-quadruplex and i-motif nucleic acid structures are believed to fold through kinetic partitioning mechanisms. Such mechanisms explain the structural heterogeneity of G-quadruplex metastable intermediates which have been extensively reported. On the other hand, i-motif folding is regarded as predictable, and research on alternative i-motif folds is limited. While TC₅ normally folds into a stable tetrameric i-motif in solution, we report that 2'-deoxy-2'-fluoroarabinocytidine (araF-C) substitutions can prompt TC₅ to form an off-pathway and kinetically-trapped dimeric i-motif, thereby expanding the scope of i-motif folding landscapes. This i-motif is formed by two strands, associated head-to-head, and featuring zero-nucleotide loops which have not been previously observed. Through spectroscopic and computational analyses, we also establish that the dimeric i-motif is stabilized by fluorine and non-fluorine hydrogen bonds, thereby explaining the superlative stability of araF-C modified i-motifs. Comparative experimental findings suggest that the strength of these interactions depends on the flexible sugar pucker adopted by the araF-C residue. Overall, the findings reported here provide a new role for i-motifs in nanotechnology and also pose the question of whether unprecedented i-motif folds may exist in vivo.

Exploring the Chemical Space of Proluciferins as Probe Substrates for Human Cytochrome P450 Enzymes

We report the synthesis of 21 new proluciferin compounds that bear a small aliphatic ether group connected to the 6' hydroxy function of firefly luciferin and either contain an acid or methyl ester function at the dihydrothiazole ring. Each of these compounds was found to be a substrate for some members of the human CYP1 and CYP3 families; a total of 92 new enzyme-substrate pairs were identified. In a screen of the whole human P450 complement (CYPome) with three selected proluciferin acid substrates, another 13 enzyme-substrate pairs were detected, which involve enzymes belonging to the CYP2, CYP4, CYP7, CYP21, and CYP27 families. All in all, we identified new probe substrates for members of seven out of 18 human CYP families.

Effects of fluorine bonding and nonbonding interactions on 19F chemical shifts

19F-NMR signals are sensitive to local electrostatic fields and are useful in probing protein structures and dynamics. Here, we used chemically identical ortho-F nuclei in N-phenyl γ-lactams to investigate the relationship between 19F NMR chemical shifts and local environments. By varying the structures at the C5- and C7-substituents, we demonstrated that 19F shifts and Hammett coefficients in Hammett plots follow typical relationships in bonding interactions, while manifesting reverse correlations in nonbonding contacts. Quantum mechanics calculations revealed that one of the ortho-F nuclei engages in n → π* orbital delocalization between F lone pair electrons (n) and a C[double bond, length as m-dash]O/Ar[double bond, length as m-dash]N antibonding orbital (π*), and the other ortho-F nucleus exhibits n ↔ σ orbital polarization between the n electrons and the C-H σ bonding orbital. As 19F NMR spectroscopy find increasing use in molecular sensors and biological sciences, our findings are valuable for designing sensitive probes, elucidating molecular structures, and quantifying analytes.

Distribution of florfenicol and norfloxacin in ice during water freezing process: Dual effects by fluorine substituents

Distribution in ice is regarded as one of important transport modes for pollutants in seasonal freeze-up waters in cold regions. However, the distribution characteristics and mechanisms of fluorinated antibiotics as emerging contaminants during the water freezing process remain unclear. Here, florfenicol and norfloxacin were selected as model fluorinated antibiotics to investigate their ice-water distribution. Effects of antibiotic molecular structure on the distribution were explored through comparative studies with their non-fluorinated structural analogs. Results showed that phase changes during the ice growth process redistributed the antibiotics, with antibiotic concentrations in water 3.0-6.4 times higher than those in ice. The solute-rich boundary layer with a concentration gradient was presented at the ice-water interface and controlled by constitutional supercooling during the freezing process. The ice-water distribution coefficient (K_IW) values of antibiotics increased by 34.8%-38.0% with a doubling of the cooling area. The solute distribution coefficient (K_bs) values of antibiotics at -20 °C were 65.6%-70.3% higher than at -10 °C. The K_IW and K_bs values of all antibiotics were negatively correlated with their water solubilities. The fluorine substituents influenced the binding energies between antibiotics and ice, resulting in a 1.1-fold increase in the binding energy of norfloxacin on the ice surface relative to its structural analog pipemidic acid. The results provide a new insight into the transport behaviors of fluorinated pharmaceuticals in ice-water systems.

Phospha-Michael Addition on α-Fluorinated Acrylates: A Straightforward Access to Polyfunctionalized Fine Chemicals

α-Fluorinated acrylates could act as Michael acceptors and become a platform toward the synthesis of relevant complex molecules. Very few conjugate additions have been developed in the literature with these specific substrates, and herein, we reported the first phospha-Michael addition (PMA) on α-trifluoromethylacrylates and α-fluoromethylacrylates. The reaction proved to be highly tolerant and gave original products containing contiguous C-P and C-CFY₂ (Y = F or H) bonds in good to excellent yields and diastereoselectivities.

Ligands with polyfluorophenyl moieties promote a local structural rearrangement in the Spinach2 and Broccoli aptamers that increases ligand affinities

The interaction of nucleic acids with their molecular targets often involves structural reorganization that may traverse a complex folding landscape. With the more recent recognition that many RNAs, both coding and noncoding, may regulate cellular activities by interacting with target molecules, it becomes increasingly important to understand how nucleic acids interact with their targets and how drugs might be developed that can influence critical folding transitions. We have extensively investigated the interaction of the Spinach2 and Broccoli aptamers with a library of small molecule ligands modified by various extensions from the imido nitrogen of DFHBI [(Z)-5-(3,5-difluoro-4-hydroxybenzylidene)-2,3-dimethyl-3,5-dihydro-4H-imidazol-4-one] that reach out from the Spinach2 ligand binding pocket. Studies of the interaction of these compounds with the aptamers revealed that polyfluorophenyl-modified ligands initiate a slow change in aptamer affinity that takes an extended time (half-life of ∼40 min) to achieve. The change in affinity appears to involve an initial disruption of the entrance to the ligand binding pocket followed by a gradual transition to a more defined structure for which the most likely driving force is an interaction of the gateway adenine with a nearby 2'OH group. These results suggest that polyfluorophenyl modifications might increase the ability of small molecule drugs to disrupt local structure and promote RNA remodeling.

Effect of gem-Difluorination on the Key Physicochemical Properties Relevant to Medicinal Chemistry: The Case of Functionalized Cycloalkanes

Physico-chemical properties important to drug discovery (pK_a , LogP, and aqueous solubility), as well as metabolic stability, were studied for a series of functionalized gem-difluorinated cycloalkanes and compared to those of non-fluorinated and acyclic counterparts to evaluate the impact of the fluorination. It was found that the influence of the CF₂ moiety on the acidity/basicity of the corresponding carboxylic acids and amines was defined by inductive the effect of the fluorine atoms and was nearly the same for acyclic and cyclic aliphatic compounds. Lipophilicity and aqueous solubility followed more complex trends and were affected by the position of the fluorine atoms, ring size, and even the nature of the functional group present; also, significant differences were found for the acyclic and cyclic series. Also, gem-difluorination either did not affect or slightly improved the metabolic stability of the corresponding model derivatives. The presented results can be used as a guide for rational drug design employing fluorine and establish the first chapter in a catalog of the key in vitro properties of fluorinated cycloalkanes.

Halogen bonding organocatalysis enhanced through intramolecular hydrogen bonds

Recent results indicate a halogen bond donor is strengthened through direct interaction with a hydrogen bond to the electron-rich belt of the halogen. Here, this Hydrogen Bond enhanced Halogen Bond (HBeXB) plays a clear role in a catalyst. Our HBeXB catalyst improves product conversion in a halide abstraction reaction over a traditional halogen bonding derivative.

Energetic and Geometric Characteristics of Substituents, Part 3: The Case of NO2 and NH2 Groups in Their Mono-Substituted Derivatives of Six-Membered Heterocycles

Substituted heterocyclic arenes play important roles in biochemistry, catalysis, and in the design of functional materials. Exemplary six-membered heteroaromatic molecules, that differ from benzene by inclusion of one heteroatom, are pyridine, phosphorine, arsabenzene, and borabenzene. This theoretical study concerns the influence of the heteroatom present in these molecules on the properties of substituents of two types: electron-donating (ED) NH2 group and electron-accepting (EA) NO2 group, attached at the 2-, 3-, or 4-position. The effect is evaluated by the energy of interaction (Erel) between the substituent and the substituted system and electronic properties of the substituents described by the charge of the substituent active region (cSAR) index. In addition, several geometric descriptors of the substituent and heteroaromatic ring, as well as changes in the aromaticity, are considered. The latter are assessed using the Electron Density of Delocalized Bonds (EDDBs) property of delocalized π electrons. The obtained results show that the electronegativity (EN) of the heteroatom has a profound effect on the EA/ED properties of the substituents. This effect is also reflected in the geometry of studied molecules. The Erel parameter indicates that the relative stability of the molecules is highly related to the electronic interactions between the substituent and the heteroarene. This especially applies to the enhancement or weakening of π-resonance due to the EN of the heteroatom. Additionally, in the 2-heteroarene derivatives, specific through-space ortho interactions contribute to the heteroatom effects.

Intramolecular N-H⋅⋅⋅F Hydrogen Bonding Interaction in a Series of 4-Anilino-5-Fluoroquinazolines: Experimental and Theoretical Characterization of Electronic and Conformational Effects

The 4-anilino-6,7-ethylenedioxy-5-fluoroquinazoline scaffold is presented as a novel model system for the characterization of the weak NH⋅⋅⋅F hydrogen bonding (HB) interaction. In this scaffold, the aniline NH proton is forced into close proximity with the nearby fluorine (d_H,F ∼2.0 Å, ∠∼138°), and a through-space interaction is observed by NMR spectroscopy with couplings (^1h J_NH,F ) of 19±1 Hz. A combination of experimental (NMR spectroscopy and X-ray crystallography) and theoretical methods (DFT calculations) were used for the characterization of this weak interaction. In particular, the effects of conformational rigidity and steric compression on coupling were investigated. This scaffold was used for the direct comparison of fluoride with methoxy as HB acceptors, and the susceptibility of the NH⋅⋅⋅F interaction to changes in electron distribution and resonance was probed by preparing a series of molecules with different electron-donating or -withdrawing groups in the positions para to the NH and F. The results support the idea that fluorine can act as a weak HB acceptor, and the HB strength can be modulated through additive and linear electronic substituent effects.

Pushing the Limits of the Hydrogen Bond Enhanced Halogen Bond —The Case of the C–H Hydrogen Bond

C–H hydrogen bonds have remarkable impacts on various chemical systems. Here we consider the influence of C–H hydrogen bonds to iodine atoms. Positioning a methyl group between two iodine halogen bond donors of the receptor engendered intramolecular C–H hydrogen bonding (HBing) to the electron-rich belt of both halogen bond donors. When coupled with control molecules, the role of the C–H hydrogen bond was evaluated. Gas-phase density functional theory studies indicated that methyl C–H hydrogen bonds help bias a bidentate binding conformation. Interaction energy analysis suggested that the charged C–H donors augment the halogen bond interaction—producing a >10 kcal mol⁻¹ enhancement over a control lacking the C–H⋯I–C interaction. X-ray crystallographic analysis demonstrated C–H hydrogen bonds and bidentate conformations with triflate and iodide anions, yet the steric bulk of the central functional group seems to impact the expected trends in halogen bond distance. In solution, anion titration data indicated elevated performance from the receptors that utilize C–H Hydrogen Bond enhanced Halogen Bonds (HBeXBs). Collectively, the results suggest that even modest hydrogen bonds between C–H donors and iodine acceptors can influence molecular structure and improve receptor performance.

C–H hydrogen bonds to iodine halogen bond donors are shown to improve halogen bonding and molecular preorganization.

Energetic and Geometric Characteristics of the Substituents: Part 2: The Case of NO2, Cl, and NH2 Groups in Their Mono-Substituted Derivatives of Simple Nitrogen Heterocycles

Variously substituted N-heterocyclic compounds are widespread across bio- and medicinal chemistry. The work aims to computationally evaluate the influence of the type of N-heterocyclic compound and the substitution position on the properties of three model substituents: NO2, Cl, and NH2. For this reason, the energetic descriptor of global substituent effect (Erel), geometry of substituents, and electronic descriptors (cSAR, pEDA, sEDA) are considered, and interdependences between these characteristics are discussed. Furthermore, the existence of an endocyclic N atom may induce proximity effects specific for a given substituent. Therefore, various quantum chemistry methods are used to assess them: the quantum theory of atoms in molecules (QTAIM), analysis of non-covalent interactions using reduced density gradient (RDG) function, and electrostatic potential maps (ESP). The study shows that the energetic effect associated with the substitution is highly dependent on the number and position of N atoms in the heterocyclic ring. Moreover, this effect due to interaction with more than one endo N atom (e.g., in pyrimidines) can be assessed with reasonable accuracy by adding the effects calculated for interactions with one endo N atom in substituted pyridines. Finally, all possible cases of proximity interactions for the NO2, Cl, and NH2 groups are thoroughly discussed.

Evidence of C-F···H-C Attractive Interaction: Enforced Coplanarity of a Tetrafluorophenylene-Ethynylene-Linked Porphyrin Dimer

The formation of C-F···H-C "hydrogen bonds" has been a controversial subject because, in principle, fluorine is hardly an acceptor for less acidic protons contrasting to the C-F···H-O and C-F···H-N hydrogen bonds. Nevertheless, the interaction is emerging as a powerful implement for confining the torsional rotation in the design of fully coplanar π-conjugated polymers. Heretofore, no evidence of the C-F···H-C interaction has been observed in solutions. We herein disclose comprehensive evidence that the C-F···H-C interaction produces an attractive force. A ¹⁹F-¹H heteronuclear Overhauser effect experiment elucidated the close proximity of the F and H atoms in the doubly edge-facing C-F···H-C interactions of a meso-tetrafluorophenylene-ethynylene-conjugated porphyrin dimer (1). Extensive electronic and photophysical property investigations confirmed that all the aromatic units were torsionally restricted by the C-F···H-C interactions. Moreover, the enforced coplanarity invoked a markedly high π-staking propensity. Thus, we have firmly established the formation of a C-F···H-C interaction that produces a hydrogen-bond-like attractive force in solution.

Soluble Methane Monooxygenase Component Interactions Monitored by 19F NMR

Soluble methane monooxygenase (sMMO) is a multicomponent metalloenzyme capable of catalyzing the fissure of the C-H bond of methane and the insertion of one atom of oxygen from O2 to yield methanol. Efficient multiple-turnover catalysis occurs only in the presence of all three sMMO protein components: hydroxylase (MMOH), reductase (MMOR), and regulatory protein (MMOB). The complex series of sMMO protein component interactions that regulate the formation and decay of sMMO reaction cycle intermediates is not fully understood. Here, the two tryptophan residues in MMOB and the single tryptophan residue in MMOR are converted to 5-fluorotryptophan (5FW) by expression in defined media containing 5-fluoroindole. In addition, the mechanistically significant N-terminal region of MMOB is 19F-labeled by reaction of the K15C variant with 3-bromo-1,1,1-trifluoroacetone (BTFA). The 5FW and BTFA modifications cause minimal structural perturbation, allowing detailed studies of the interactions with sMMOH using 19F NMR. Resonances from the 275 kDa complexes of sMMOH with 5FW-MMOB and BTFA-K15C-5FW-MMOB are readily detected at 5 μM labeled protein concentration. This approach shows directly that MMOR and MMOB competitively bind to sMMOH with similar KD values, independent of the oxidation state of the sMMOH diiron cluster. These findings suggest a new model for regulation in which the dynamic equilibration of MMOR and MMOB with sMMOH allows a transient formation of key reactive complexes that irreversibly pull the reaction cycle forward. The slow kinetics of exchange of the sMMOH:MMOB complex is proposed to prevent MMOR-mediated reductive quenching of the high-valent reaction cycle intermediate Q before it can react with methane.

Automated Glycan Assembly of 19 F-labeled Glycan Probes Enables High-Throughput NMR Studies of Protein-Glycan Interactions

Protein–glycan interactions mediate important biological processes, including pathogen host invasion and cellular communication. Herein, we showcase an expedite approach that integrates automated glycan assembly (AGA) of ¹⁹F‐labeled probes and high‐throughput NMR methods, enabling the study of protein–glycan interactions. Synthetic Lewis type 2 antigens were screened against seven glycan binding proteins (GBPs), including DC‐SIGN and BambL, respectively involved in HIV‐1 and lung infections in immunocompromised patients, confirming the preference for fucosylated glycans (Le^x, H type 2, Le^y). Previously unknown glycan–lectin weak interactions were detected, and thermodynamic data were obtained. Enzymatic reactions were monitored in real‐time, delivering kinetic parameters. These results demonstrate the utility of AGA combined with ¹⁹F NMR for the discovery and characterization of glycan–protein interactions, opening up new perspectives for ¹⁹F‐labeled complex glycans.

Hydrogen Bond Acceptor Propensity of Different Fluorine Atom Types: An Analysis of Experimentally and Computationally Derived Parameters

The propensity of organic fluorine acting as a weak hydrogen bond acceptor (HBA) in intermolecular and intramolecular interactions has been the subject of many experimental and theoretical studies often reaching different conclusions. Over the last few years, new and stronger evidences have emerged for the direct involvement of fluorine in weak hydrogen bond (HB) formation. However, not all the fluorine atom types can act as weak HBA. In this work, the differential HBA propensity of various types of fluorine atoms was analyzed with a particular emphasis for the different types of alkyl fluorides. This was carried out by evaluating ab initio computed parameters, experimental ¹⁹ F NMR chemical shifts and small molecule crystallographic structures (extracted from the CSD database). According to this analysis, shielded (with reference to the ¹⁹ F NMR chemical shift) alkyl mono-fluorinated motifs display the highest HBA propensity in agreement with solution studies. Although much weaker than other well-characterized HB complexes, the fragile HBs formed by these fluorinated motifs have important implications for the chemical-physical and structural properties of the molecules, chemical reactions, and protein-ligand recognition.

Solvent-Switched Oxidation Selectivities with O2 : Controlled Synthesis of α-Difluoro(thio)methylated Alcohols and Ketones

The solvent-switched hydroxylation and oxygenation of α-difluoro(thio)methylated carbanions with molecular oxygen under mild conditions are reported. This strategy tames the redox reactions of the in situ generated hydroperoxy difluoromethylsulfides, in which solvent-bonding can alter their reactivity and switch the oxidation selectivities. These controllable three-component reactions of gem-difluoroalkenes, thiols and molecular oxygen afford various useful α-difluoro(thio)methylated alcohols and ketones in high yields. Significantly, this protocol has been applied in the synthesis different bioactive molecules. Mechanism studies enable the detection of the hydroperoxy difluoromethylsulfide intermediates and exclude the thiol-based radical pathway.

Modulation of the H-Bond Basicity of Functional Groups by α-Fluorine-Containing Functions and its Implications for Lipophilicity and Bioisosterism

Modulation of the H-bond basicity (pK_HB) of various functional groups (FGs) by attaching fluorine functions and its impact on lipophilicity and bioisosterism considerations are described. In general, H/F replacement at the α-position to H-bond acceptors leads to a decrease of the pK_HB value, resulting, in many cases, in a dramatic increase in the compounds' lipophilicity (log P_o/w). In the case of α-CF₂H, we found that these properties may also be affected by intramolecular H-bonds between CF₂H and the FG. A computational study of ketone and sulfone series revealed that α-fluorination can significantly affect overall polarity, charge distribution, and conformational preference. The unique case of α-di- and trifluoromethyl ketones, which exist in octanol/water phases as ketone, hemiketal, and gem-diol forms, in equilibrium, prevents direct log P_o/w determination by conventional methods, and therefore, the specific log P_o/w values of these species were determined directly, for the first time, using Linclau's ¹⁹F NMR-based method.

The role of intermolecular interactions in stabilizing the structure of the nematic twist-bend phase

The understanding of the relationship between molecular structure and the formation of the nematic twist-bend phase is still at an early stage of development. This is mainly related to molecular geometry, while the correlation between the nematic twist-bend phase and the electronic structure is ambiguous. To explore the electronic effect on properties and stabilization of the nematic twist-bend phase we investigated 2′,3′-difluoro-4,4′′-dipentyl-p-terphenyl dimers (DTC5Cn). We used polarized fourier transform infrared spectroscopy, which can, at least in principle, provide information about the ordering in the twist-bend phase. All dimers show a significant drop in the average value of the transition dipole moment for parallel dipoles at the transition from the nematic to the twist-bend phase, and an increase for perpendicular dipoles, despite remaining unchanged for the monomer. Density functional theory calculations were used to determine the geometric and electronic properties of the hydrogen bonded complexes. We have provided experimental and theoretical evidence of stabilization of the nematic twist-bend phase by arrays of multiple hydrogen bonds (XF⋯HX, X–benzene ring).

Stabilization of the nematic twist-band phase by arrays of multiple nonspecific short-range intermolecular interactions.

Theoretical, Solid-State, and Solution Quantification of the Hydrogen Bond-Enhanced Halogen Bond

Proximal noncovalent forces are commonplace in natural systems and understanding the consequences of their juxtaposition is critical. This paper experimentally quantifies for the first time a Hydrogen Bond-Enhanced Halogen Bond (HBeXB) without the complexities of protein structure or preorganization. An HBeXB is a halogen bond that has been strengthened when the halogen donor simultaneously accepts a hydrogen bond. Our theoretical studies suggest that electron-rich halogen bond donors are strengthened most by an adjacent hydrogen bond. Furthermore, stronger hydrogen bond donors enhance the halogen bond the most. X-ray crystal structures of halide complexes (X^- =Br^- , I^- ) reveal that HBeXBs produce shorter halogen bonds than non-hydrogen bond analogues. ¹⁹ F NMR titrations with chloride highlight that the HBeXB analogue exhibits stronger binding. Together, these results form the foundation for future studies concerning hydrogen bonds and halogen bonds in close proximity.

Fluorinated Carbohydrates as Lectin Ligands: Simultaneous Screening of a Monosaccharide Library and Chemical Mapping by 19F NMR Spectroscopy

Molecular recognition of carbohydrates is a key step in essential biological processes. Carbohydrate receptors can distinguish monosaccharides even if they only differ in a single aspect of the orientation of the hydroxyl groups or harbor subtle chemical modifications. Hydroxyl-by-fluorine substitution has proven its merits for chemically mapping the importance of hydroxyl groups in carbohydrate-receptor interactions. 19F NMR spectroscopy could thus be adapted to allow contact mapping together with screening in compound mixtures. Using a library of fluorinated glucose (Glc), mannose (Man), and galactose (Gal) derived by systematically exchanging every hydroxyl group by a fluorine atom, we developed a strategy combining chemical mapping and 19F NMR T2 filtering-based screening. By testing this strategy on the proof-of-principle level with a library of 13 fluorinated monosaccharides to a set of three carbohydrate receptors of diverse origin, i.e. the human macrophage galactose-type lectin, a plant lectin, Pisum sativum agglutinin, and the bacterial Gal-/Glc-binding protein from Escherichia coli, it became possible to simultaneously define their monosaccharide selectivity and identify the essential hydroxyls for interaction.

Fluorine effect in nucleophilic fluorination at C4 of 1,6-anhydro-2,3-dideoxy-2,3-difluoro-β-D-hexopyranose

In this work, we have developed a simple synthetic approach using Et₃N·3HF as an alternative to the DAST reagent. We controlled the stereochemistry of the nucleophilic fluorination at C4 of 1,6-anhydro-2,3-dideoxy-2,3-difluoro-4-O-triflate-β-ᴅ-talopyranose using Et₃N·3HF or in situ generated Et₃N·1HF. The influence of the fluorine atom at C2 on reactivity at C4 could contribute to a new fluorine effect in nucleophilic substitution. Finally, with the continuous objective of synthesizing novel multi-vicinal fluorosugars, we prepared one difluorinated and one trifluorinated alditol analogue.

Exploring polar hydrophobicity in organized media for extracting oligopeptides: application to the extraction of opiorphin in human saliva

Supramolecular solvents (dubbed SUPRAS) are gaining momentum as extractants of compounds of interest from complex matrixes such as foodstuff and biological and environmental samples. However, their powerful extraction mechanism, based on multiligand ability for solute binding, fails when applied to very polar compounds, hindering their applicability to the extraction of highly polar metabolites. In this work, we introduce the synthesis, characterization, and application of a new kind of SUPRAS formed by heptafluorobutyric acid (HFBA). The polar hydrophobicity of this perfluorinated acid results in a SUPRAS, which coacervates at acidic pHs, that shows a great capability to extract amino acids and oligopeptides (recoveries in the range 81-105%) with nonpolar alkyl, cyclic or aromatic side chain substituents (with log D > -3.62). To further demonstrate the potential of this novel SUPRAS, an analytical methodology for the determination of opiorphin in real saliva samples was developed and fully validated. The HFBA-based SUPRAS was synthetized in situ from 950 µL of stabilized saliva, by the addition of 150 µL of HFBA and 400 µL of HCl 37% (v/v). The resulting SUPRAS was directly injected into a LC-MS/MS system for further quantification. Quantitative recoveries in the range of 87-110% were obtained with relative standard deviations below 20%. The HFBA-based SUPRAS is, therefore, capable of efficiently extracting opiorphin from saliva samples and shows a high potential for the determination of several amino acids and oligopeptides from biological samples.

Bi-functional hydrogen and coordination bonding surfactant: A novel and promising collector for improving the separation of calcium minerals

Mono-functional chelating collectors exhibit limited selectivity in the flotation of minerals. In particular, the selective separation of calcium minerals presents a significant challenge because mono-functional chelating collectors, such as fatty acid, indistinguishably adsorb onto mineral surfaces by coordinating with the same metal cation (Ca²⁺). Thus, there is an urgent need to develop new-mode-functional collectors to separate calcium minerals and a need to understand the underlying chemoselectivity. Given the difference of the hydrogen bonding ability of anions with fluorite, calcite and scheelite surfaces, the introduction of additional hydrogen bonding functional groups into collector molecules is a novel strategy to improve selectivity. In this study, a hydrogen and coordination bonding (bi-functional) collector, 2-cyano-N-ethylcarbamoyl acetamide (CEA) was developed, which could form coordination bonds with the Ca²⁺ ions (by carbonyl groups) and hydrogen bonds with the anions (by amino groups) on calcium mineral surfaces. The results of flotation tests showed that CEA can selectively separate fluorite and calcite from scheelite at pH 7. The promising selectivity of CEA lies in both the electrical properties and the anions' hydrogen bonding ability with the three calcium minerals. The negatively charged scheelite surfaces are not conducive to coordination bonding with CEA while the positively charged fluorite and calcite surfaces are. Besides, the hydrogen bonding ability of fluorite (F^-) and calcite (CO₃^2-) with carbamido in CEA is higher than that of scheelite (WO₄^2-), and this also plays an essential role. This coordination and hydrogen bonding based surfactant design protocol has a great potential in the development of tail-made collectors/depressants for the separation of other oxidized minerals.

Addressing the Structural Complexity of Fluorinated Glucose Analogues: Insight into Lipophilicities and Solvation Effects

In this work, we synthesized all mono-, di-, and trifluorinated glucopyranose analogues at positions C-2, C-3, C-4, and C-6. This systematic investigation allowed us to perform direct comparison of ¹⁹ F resonances of fluorinated glucose analogues and also to determine their lipophilicities. Compounds with a fluorine atom at C-6 are usually the most hydrophilic, whereas those with vicinal polyfluorinated motifs are the most lipophilic. Finally, the solvation energies of fluorinated glucose analogues were assessed for the first time by using density functional theory. This method allowed the log P prediction of fluoroglucose analogues, which was comparable to the C log P values obtained from various web-based programs.

Multicomponent Synthesis, Binding Mode, and Structure-Activity Relationship of Selective Histone Deacetylase 6 (HDAC6) Inhibitors with Bifurcated Capping Groups

Histone deacetylase 6 (HDAC6) is an emerging target for the treatment of cancer, neurodegenerative diseases, inflammation, and other diseases. Here, we present the multicomponent synthesis and structure-activity relationship of a series of tetrazole-based HDAC6 inhibitors. We discovered the hit compound NR-160 by investigating the inhibition of recombinant HDAC enzymes and protein acetylation. A cocrystal structure of HDAC6 complexed with NR-160 disclosed that the steric complementarity of the bifurcated capping group of NR-160 to the L1 and L2 loop pockets may be responsible for its HDAC6-selective inhibition. While NR-160 displayed only low cytotoxicity as a single agent against leukemia cell lines, it augmented the apoptosis induction of the proteasome inhibitor bortezomib in combination experiments significantly. Furthermore, a combinatorial high-throughput drug screen revealed significantly enhanced cytotoxicity when NR-160 was used in combination with epirubicin and daunorubicin. The synergistic effect in combination with bortezomib and anthracyclines highlights the potential of NR-160 in combination therapies.

Directing the Crystal Packing in Triphenylphosphine Gold(I) Thiolates by Ligand Fluorination

We explore herein the supramolecular interactions that control the crystalline packing in a series of fluorothiolate triphenylphosphine gold(I) compounds with the general formula [Au(SR_F)(Ph₃P)] in which Ph₃P = triphenylphosphine and SR_F = SC₆F₅, SC₆HF₄-4, SC₆F₄(CF₃)-4, SC₆H₃F₂-2,4, SC₆H₃F₂-3,4, SC₆H₃F₂-3,5, SC₆H₄(CF₃)-2, SC₆H₄F-2, SC₆H₄F-3, SC₆H₄F-4, SCF₃, and SCH₂CF₃. We use for this purpose (i) DFT electronic structure calculations and (ii) the quantum theory of atoms in molecules and the non-covalent interactions index methods of wave function analyses. Our combined experimental and computational approach yields a general understanding of the effects of ligand fluorination in the crystalline self-assembly of the examined systems, in particular, about the relative force of aurophilic contacts compared with other supramolecular interactions. We expect this information to be useful in the design of materials based on gold coordination compounds.