1.3 Å Crystal Structure of E. coli Peptidyl-Prolyl Isomerase B with Uniform Substitution of Valine by (2S,3S)-4-Fluorovaline Reveals Structure Conservation and Multiple Staggered Rotamers of CH2F Groups

(2S,3S)-4-Fluorovaline (FVal) is an analogue of valine, where a single CH3 group is substituted by a CH2F group. In the absence of valine, E. coli valyl-tRNA synthetase uses FVal as a substitute, enabling the production of proteins uniformly labeled with FVal. Here, we describe the production and analysis of E. coli peptidyl-prolyl isomerase B where all 16 valine residues have been replaced by FVal synthesized with a 13C-labeled CH2F group. Although the melting temperature is lower by about 11 °C relative to the wild-type protein, the three-dimensional protein structure is almost completely conserved, as shown by X-ray crystallography. The CH2F groups invariably populate staggered rotamers. Most CH2F groups populate two different rotamers. The increased space requirement of fluorine versus hydrogen does not prohibit rotamers that position fluorine next to a backbone carbonyl carbon. 19F NMR spectra show a signal dispersion over 25 ppm. The most high-field shifted 19F resonances correlate with large 3JHF coupling constants, confirming the impact of the γ-gauche effect on the signal dispersion. The present work is the second experimental verification of the effect and extends its validity to fluorovaline. The abundance of valine in proteins and structural conservation with FVal renders this valine analogue attractive for probing proteins by 19F NMR spectroscopy.

Synthesis and screening of a library of Lewisx deoxyfluoro-analogues reveals differential recognition by glycan-binding partners

Glycan-mediated interactions play a crucial role in biology and medicine, influencing signalling, immune responses, and disease pathogenesis. However, the use of glycans in biosensing and diagnostics is limited by cross-reactivity, as certain glycan motifs can be recognised by multiple biologically distinct protein receptors. To address this specificity challenge, we report the enzymatic synthesis of a 150-member library of site-specifically fluorinated Lewisx analogues ('glycofluoroforms') using naturally occurring enzymes and fluorinated monosaccharides. Subsequent incorporation of a subset of these glycans into nanoparticles or a microarray revealed a striking spectrum of distinct binding intensities across different proteins that recognise Lewisx. Notably, we show that for two proteins with unique binding sites for Lewisx, glycofluoroforms exhibited enhanced binding to one protein, whilst reduced binding to the other, with selectivity governed by fluorination patterns. We finally showcase the potential diagnostic utility of this approach in glycofluoroform-mediated bacterial toxin detection by lateral flow.

Nonpeptidic Irreversible Inhibitors of SARS-CoV-2 Main Protease with Potent Antiviral Activity

SARS-CoV-2 infections pose a high risk for vulnerable patients. In this study, we designed benzoic acid halopyridyl esters bearing a variety of substituents as irreversible inhibitors of the main viral protease (Mpro). Altogether, 55 benzoyl chloro/bromo-pyridyl esters were synthesized, with broad variation of the substitution pattern on the benzoyl moiety. A workflow was employed for multiparametric optimization, including Mpro inhibition assays of SARS-CoV-2 and related pathogenic coronaviruses, the duration of enzyme inhibition, the compounds' stability versus glutathione, cytotoxicity, and antiviral activity. Several compounds showed IC50 values in the low nanomolar range, kinact/Ki values of >100,000 M-1 s-1 and high antiviral activity. High-resolution X-ray cocrystal structures indicated an important role of ortho-fluorobenzoyl substitution, forming a water network that stabilizes the inhibitor-bound enzyme. The most potent antiviral compound was the p-ethoxy-o-fluorobenzoyl chloropyridyl ester (PSB-21110, 29b, MW 296 g/mol; EC50 2.68 nM), which may serve as a lead structure for broad-spectrum anticoronaviral therapeutics.

Conformational Preferences of the Non-Canonical Amino Acids (2S,4S)-5-Fluoroleucine, (2S,4R)-5-Fluoroleucine, and 5,5'-Difluoroleucine in a Protein

Proteins produced with leucine analogues, where CH2F groups substitute specific methyl groups, can readily be probed by 19F NMR spectroscopy. As CF and CH groups are similar in hydrophobicity and size, fluorinated leucines are expected to cause minimal structural perturbation, but the impact of fluorine on the rotational freedom of CH2F groups is unclear. We present high-resolution crystal structures of Escherichia coli peptidyl-prolyl cis-trans isomerase B (PpiB) prepared with uniform high-level substitution of leucine by (2S,4S)-5-fluoroleucine, (2S,4R)-5-fluoroleucine, or 5,5'-difluoroleucine. Apart from the fluorinated leucine residues, the structures show complete structural conservation of the protein backbone and the amino acid side chains except for a single isoleucine side chain located next to a fluorine atom in the hydrophobic core of the protein. The carbon skeletons of the fluorinated leucine side chains are also mostly conserved. The CH2F groups show a strong preference for staggered rotamers and often appear locked into single rotamers. Substitution of leucine CH3 groups for CH2F groups is thus readily tolerated in the three-dimensional (3D) structure of a protein, and the rotation of CH2F groups can be halted at cryogenic temperatures.

Synthesis and Monoamine Oxidase Inhibitory Activity of Halogenated Flavones

Small molecule neurotransmitters containing amines are metabolized by monoamine oxidase (MAO) in the nervous system. Monoamine oxidase inhibitors are a valuable class of drugs prescribed for the management of neurological disorders, including depression. A series of halogenated flavonoids similar to the dietary flavonoid acacetin were designed as selective MAO-B inhibitors. MAO-A and -B inhibition of 36 halogenated flavones were tested. The halogens (fluorine and chlorine) were placed at positions 5 and 7 on ring A of the flavone scaffold. All compounds were selective MAO-B inhibitors with micro- and nanomolar IC50 values. Compounds 9f, 10a-c, 11a-c, 11g,h, and 11l displayed inhibitory activity toward MAO-B with IC50 values between 16 to 74 nM. We conclude that halogenated flavonoids are promising molecules in pursuit of developing new agents for neurological disorders.

Molecular dynamics and NMR reveal the coexistence of H-bond-assisted and through-space JFH coupling in fluorinated amino alcohols

The JFH coupling constants in fluorinated amino alcohols were investigated through experimental and theoretical approaches. The experimental JFH couplings were only reproduced theoretically when explicit solvation through molecular dynamics (MD) simulations was conducted in DMSO as the solvent. The combination of MD conformation sampling and DFT NMR spin-spin coupling calculations for these compounds reveals the simultaneous presence of through-space (TS) and hydrogen bond (H-bond) assisted JFH coupling between fluorine and hydrogen of the NH group. Furthermore, MD simulations indicate that the hydrogen in the amino group participates in both an intermolecular bifurcated H-bond with DMSO and in transmitting the observed JFH coupling. The contribution of TS to the JFH coupling is due to the spatial proximity of the fluorine and the NH group, aided by a combination of the non-bonding transmission pathway and the hydrogen bonding pathway. The experimental JFH coupling observed for the molecules studied should be represented as 4TS/1hJFH coupling.

Electrostatic Contribution to 19F Chemical Shifts in Fluorotryptophans in Proteins

DFT calculations indicate that the 19F chemical shifts of aromatic rings containing single fluorine substituents are sensitive to the electric fields and electric field gradients at the position of the fluorine atom. The present work explores whether long-range structure restraints can be gained from changes in 19F chemical shifts following mutations of charged to uncharged residues. 19F chemical shifts of fluorotryptophan residues were measured in two different proteins, GB1 and the NT* domain, following mutations of single asparagine residues to aspartic acid. Four different versions of fluorotryptophan were investigated, including 4-, 5-, 6-, and 7-fluorotryptophan, which were simultaneously installed by cell-free protein synthesis using 4-, 5-, 6-, and 7-fluoroindole as precursors for the tryptophan synthase present in the S30 extract. For comparison, the 1H chemical shifts of the corresponding nonfluorinated protein mutants produced with 13C-labeled tryptophan were also measured. The results show that the 19F chemical shifts respond more sensitively to the charge mutations than the 1H chemical shifts in the nonfluorinated references, but the chemical shift changes were much smaller than predicted by DFT calculations of fluoroindoles in the electric field of a partial charge in vacuum, indicating comprehensive dielectric shielding by water and protein. No straightforward correlation with the location of the charge mutation could be established.

Intricate 3D architecture of a DNA mimic of GFP

Numerous studies have shown how RNA molecules can adopt elaborate three-dimensional (3D) architectures1-3. By contrast, whether DNA can self-assemble into complex 3D folds capable of sophisticated biochemistry, independent of protein or RNA partners, has remained mysterious. Lettuce is an in vitro-evolved DNA molecule that binds and activates4 conditional fluorophores derived from GFP. To extend previous structural studies5,6 of fluorogenic RNAs, GFP and other fluorescent proteins7 to DNA, we characterize Lettuce-fluorophore complexes by X-ray crystallography and cryogenic electron microscopy. The results reveal that the 53-nucleotide DNA adopts a four-way junction (4WJ) fold. Instead of the canonical L-shaped or H-shaped structures commonly seen8 in 4WJ RNAs, the four stems of Lettuce form two coaxial stacks that pack co-linearly to form a central G-quadruplex in which the fluorophore binds. This fold is stabilized by stacking, extensive nucleobase hydrogen bonding-including through unusual diagonally stacked bases that bridge successive tiers of the main coaxial stacks of the DNA-and coordination of monovalent and divalent cations. Overall, the structure is more compact than many RNAs of comparable size. Lettuce demonstrates how DNA can form elaborate 3D structures without using RNA-like tertiary interactions and suggests that new principles of nucleic acid organization will be forthcoming from the analysis of complex DNAs.

Assessing the applicability of 19F labeled tryptophan residues to quantify protein dynamics

Nuclear magnetic resonance (NMR) spectroscopy is uniquely suited to study the dynamics of biomolecules in solution. Most NMR studies exploit the spins of proton, carbon and nitrogen isotopes, as these atoms are highly abundant in proteins and nucleic acids. As an alternative and complementary approach, fluorine atoms can be introduced into biomolecules at specific sites of interest. These labels can then be used as sensitive probes for biomolecular structure, dynamics or interactions. Here, we address if the replacement of tryptophan with 5-fluorotryptophan residues has an effect on the overall dynamics of proteins and if the introduced fluorine probe is able to accurately report on global exchange processes. For the four different model proteins (KIX, Dcp1, Dcp2 and DcpS) that we examined, we established that ¹⁵N CPMG relaxation dispersion or EXSY profiles are not affected by the 5-fluorotryptophan, indicating that this replacement of a proton with a fluorine has no effect on the protein motions. However, we found that the motions that the 5-fluorotryptophan reports on can be significantly faster than the backbone motions. This implies that care needs to be taken when interpreting fluorine relaxation data in terms of global protein motions. In summary, our results underscore the great potential of fluorine NMR methods, but also highlight potential pitfalls that need to be considered.

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.

Fluorination-Induced Charge Trapping and Operational Instability in Conjugated-Polymer Field-Effect Transistors

Fluorination of a conjugated polymer backbone is an effective strategy to control the microstructure and electronic structure of a conjugated polymer. Although fluorination has been widely reported to increase charge carrier mobility, its effect on the operational stability of electronic devices has not been extensively investigated. Here, the effect of fluorination of a conjugated polymer backbone on charge trapping and the operational stability of organic field-effect transistors is investigated. The results show that the device based on a fluorinated conjugated polymer exhibits relatively poor operational stability despite its greater charge carrier mobility compared with that in the device based on its nonfluorinated polymer counterpart. Experimental results reveal that the low stability originates from the greater degree of shallow trapping of charge carriers within the fluorinated polymer thin film and that the shallow trapping is closely related to the presence of minority charge carriers. A mechanism of charge trapping is proposed.

Discovery of Novel Acetylcholinesterase Inhibitors by Virtual Screening, In Vitro Screening, and Molecular Dynamics Simulations

Alzheimer's disease is the most common neurodegenerative disease and currently poses a significant socioeconomic problem. This study describes the uses of computer-aided drug discovery techniques to identify novel inhibitors of acetylcholinesterase, a target for Alzheimer's disease. High-throughput virtual screening was employed to predict potential inhibitors of acetylcholinesterase. Validation of enrichment was performed with the DUD-E data set, showing that an ensemble of binding pocket conformations is critical when a diverse set of ligands are being screened. A total of 720 compounds were submitted for in vitro screening, which led to 25 hits being identified with IC₅₀ values of less than 50 μM. The majority of these hits belonged to two scaffolds: 1-ethyl-3-methoxy-3-methylpyrrolidine and 1H-pyrrolo[3,2-c]pyridin-6-amine both of which are noted to be promising compounds for further optimization. As various possible binding poses were suggested from molecular docking, molecular dynamics simulations were employed to validate the poses. In the case of the most active compounds identified, a critical, stable water bridge formed deep within the binding pocket was identified potentially explaining in part the lack of activity for subsets of compounds that are not able to form this water bridge.

The fluorescent aptamer Squash extensively repurposes the adenine riboswitch fold

Squash is an RNA aptamer that strongly activates the fluorescence of small-molecule analogs of the fluorophore of green fluorescent protein (GFP). Unlike other fluorogenic aptamers, isolated de novo from random-sequence RNA, Squash was evolved from the bacterial adenine riboswitch to leverage its optimized in vivo folding and stability. We now report the 2.7-Å resolution cocrystal structure of fluorophore-bound Squash, revealing that while the overall fold of the riboswitch is preserved, the architecture of the ligand-binding core is dramatically transformed. Unlike previously characterized aptamers that activate GFP-derived fluorophores, Squash does not harbor a G-quadruplex, sandwiching its fluorophore between a base triple and a noncanonical base quadruple in a largely apolar pocket. The expanded structural core of Squash allows it to recognize unnatural fluorophores that are larger than the simple purine ligand of the parental adenine riboswitch, and suggests that stable RNA scaffolds can tolerate larger variation than has hitherto been appreciated.

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 (dH,F ∼2.0 Å, ∠∼138°), and a through-space interaction is observed by NMR spectroscopy with couplings (1h JNH,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.

Single Isomer Heterometallic {CrIII6MII2} Rings Templated by Tetramethylammonium

A family of heterometallic rings [Me₄N]₂[Cr^III₆M^II₂F₈(O₂C^tBu)₁₆] is reported using tetramethylammonium hydroxide pentahydrate as the source of a template, where M = Zn, Mn, Ni, and Co. The metal cores are octagons with metal-metal edges bridged by one fluoride and two carboxylate ligands. The divalent metal ions are found ordered at positions 1 and 5 in the octagon. The tetramethylammonium cations are above and below the metal plane of the ring in the crystal structure. Magnetic studies show antiferromagnetic coupling between the paramagnetic metal ions present, leading to paramagnetic ground states in each case. ¹H NMR spectroscopy confirms that the structure of the {Cr^III₆Co^II₂} ring exists in solution, and electron paramagnetic resonance spectroscopy confirms the magnetic structure of the other three rings.

Tuning Proton Exchange and Transport in Protic Ionic Liquid Solution through Anion Chemistry

Herein, we demonstrate that the potential difference of proton reduction and hydrogen gas oxidation of protic ionic liquids is closely related to the proton exchange rate in the electrolyte. Through a careful design of anion chemistry, the proton exchange rate can be boosted by several orders of magnitude, reaching 200 kHz at 100 °C. It is found that the enhanced proton exchange rate can effectively decrease the potential loss at the electrode, most likely through alleviating the H⁺ concentration gradient incurred by electrochemical reactions at the electrode surfaces. This research therefore highlights the strategy of using anions of medium-strength acids, such as H₂PO₄^-, for protic ionic liquids with enhanced proton exchange capability.

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.

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.

A C^N Cycloplatinated(II) Fluoride Complex: Photophysical Studies and Csp3-F Bond Formation

This work reports the synthesis and characterization of a new C^N-based cycloplatinated(II) fluoride complex, [Pt(ppy)(PPh₃)F] (2; ppy = 2-phenylpyridinate), involving a Pt-F bond. The new complex is highly luminescent in the green area with a high quantum yield of 94.6% at 77 K. A comparison study of the heavier halogen derivatives reveals a descending emission quantum yield order of F > Cl > Br > I. Time-dependent density functional theory calculations ascribe the decreased emission efficiency to the decreasing trend of an intraligand (IL) transition from F to I, which accounts for the major radiative pathway. In addition, 2 is capable of the fluorinating alkyl halides, leading to C_sp³-F bond formation at room temperature.

Protein-fragment complex structures derived by NMR molecular replacement

Recently we have established an NMR molecular replacement method, which is capable of solving the structure of the interaction site of protein-ligand complexes in a fully automated manner. While the method was successfully applied for ligands with strong and weak binding affinities, including small molecules and peptides, its applicability on ligand fragments remains to be shown. Structures of fragment-protein complexes are more challenging for the method since fragments contain only few protons. Here we show a successful application of the NMR molecular replacement method in solving structures of complexes between three derivatives of a ligand fragment and the protein receptor PIN1. We anticipate that this approach will find a broad application in fragment-based lead discovery.

Review of Mutarotase in ‘Metabolic Subculture’ and Analytical Biochemistry: Prelude to 19F NMR Studies of its Substrate Specificity and Mechanism

This is the first paper in a sequential pair devoted to the enzyme mutarotase (aldose 1-epimerase; EC 5.1.3.3). Here, the broader context of the physiological role of mutarotase, among those enzymes considered to be part of ‘metabolic structure’, is reviewed. We also summarise the current knowledge about the molecular mechanism and substrate specificity of the enzyme, which is considered in the context of the binding of fluorinated glucose analogues to the enzyme’s active site. This was done as a prelude to our experimental studies of the anomerisation of fluorinated sugars by mutarotase that are described in the following paper.

Anomerisation of Fluorinated Sugars by Mutarotase Studied Using 19F NMR Two-Dimensional Exchange Spectroscopy

Five 19F-substituted glucose analogues were used to probe the activity and mechanism of the enzyme mutarotase by using magnetisation-exchange NMR spectroscopy. The sugars (2-fluoro-2-deoxy-d-glucose, FDG2; 3-fluoro-3-deoxy-d-glucose, FDG3; 4-fluoro-4-deoxy-d-glucose, FDG4; 2,3-difluoro-2,3-dideoxy-d-glucose, FDG23; and 2,2,3,3-tetrafluoro-2,3-dideoxy-d-glucose (2,3-dideoxy-2,2,3,3-tetrafluoro-d-erythro-hexopyranose), FDG2233) showed separate 19F NMR spectroscopic resonances from their respective α- and β-anomers, thus allowing two-dimensional exchange spectroscopy measurements of the anomeric interconversion at equilibrium, on the time scale of a few seconds. Mutarotase catalysed the rapid exchange between the anomers of FDG4, but not the other four sugars. This finding, combined with previous work identifying the mechanism of the anomerisation by mutarotase, suggests that the rotation around the C1–C2 bond of the pyranose ring is the rate-limiting reaction step. In addition to d-glucose itself, it was shown that all other fluorinated sugars inhibited the FDG4 anomerisation, with the tetrafluorinated FDG2233 being the most potent inhibitor. Inhibition of mutarotase by F-sugars paves the way for the development of novel fluorinated compounds that are able to affect the activity of this enzyme invitro and invivo.

Progressive Hydrophobicity of Fluorobenzenes

The potentials of mean force for the dimers of fluorobenzenes sample both π-stacked and T-shaped structures for partially fluorinated benzenes, namely, 1,4-difluorobenzene, 1,3,5-trifluorobenzene, and 1,2,4,5-tetrafluorobenzene, and sample only the T-shaped structures for benzene and hexafluorobenzene. While the free energy for the dimerization in water is very weakly dependent on the number of fluorine atoms, the formation of π-stacked structures is entropy-driven and the T-shaped structures appear due to an enthalpic minimum. Interestingly, the solvation behavior suggests that the accumulation of water around the contact and solvent-separated pairs decreases with the increase in the number of fluorine atoms, which signifies progressive hydrophobicity of fluorobenzenes.

Hydrated Metal Ion Salts of the Weakly Coordinating Fluoroanions PF6-, TiF62-, B12F122-, Ga(C2F5)4-, B(3,5-C6H3(CF3)2)4-, and Al(OC(CF3)3)4-. In Search of the Weakest HOH···F Hydrogen Bonds

FTIR spectra of microcrystalline samples of 11 metal ion salt hydrates of a variety of weakly coordinating fluoroanions are reported. The compounds studied were Li(H₂O)₄(Al(OC(CF₃)₃)₄), Li(H₂O)(B(3,5-C₆H₃(CF₃)₂)₄), Li(H₂O)_n(Ga(C₂F₅)₄), Li(H₂O)(PF₆), Li₂(H₂O)₂(TiF₆), Li₂(H₂O)₄(B₁₂F₁₂), Na(H₂O)(PF₆), Na₂(H₂O)₂(B₁₂F₁₂), K₂(H₂O)₂(B₁₂F₁₂), Rb₂(H₂O)₂(B₁₂F₁₂), Cs₂(H₂O)(B₁₂F₁₂), and their partially or completely deuterated isotopologs and isotopomers. The O-D···F hydrogen bonds in Li(HOD)(H₂O)₃(Al(OC(CF₃)₃)₄) (ν(OD) = 2706 cm^-1), Li(HOD)(B(3,5-C₆H₃(CF₃)₂)₄) (ν(OD) = 2705 cm^-1), and Li(HOD)(H₂O)_n(Ga(C₂F₅)₄) (ν(OD) = 2697 cm^-1) rival HOD absorbed in polyvinylidene difluoride (ν(OD) = 2696 cm^-1) and HOD···FCH₃ in a frozen Ar matrix (ν(OD) = 2685 cm^-1) for the weakest hydrogen bonds between a water molecule and an F atom in any compound. As weak as they are, minor differences in O-H···F hydrogen bonds in the same fluoroanion salt can be distinguished spectroscopically. Uncoupled HOD molecules in asymmetric F···HOD···F' hydrogen bonding environments in Rb⁺, Cs⁺, Mg²⁺, and Co²⁺ hydrates of B₁₂F₁₂^2- gave rise to two observable ν(OD) bands even though the two R(O···F) distances differ by only 0.010(4) Å (Mg²⁺), 0.033(2) Å (Co²⁺), 0.074(4) Å (Rb⁺), and 0.106(6) Å (Cs⁺). A plot of ν(OD) for hydrates with a single uncoupled HOD molecule per metal ion (e.g., Li(HOD)(H₂O)₃(Al(OC(CF₃)₃)₄)) vs R(O···F) distance from single-crystal X-ray or neutron diffraction structures was prepared. The ν(OD) values range from 2305 to 2706 cm^-1 and the R(O···F) distances range from 2.58 to 3.17 Å. The plot consists of 53 {ν(OD), R(O···F)} data points, 23 of which are new and have ν(OD) > 2600 cm^-1, in contrast to a 1994 ν(OD) vs R(O···F) plot with 28 data points, none of which had ν(OD) > 2600 cm^-1. There is a clear and significant difference between the new ν(OD) vs R(O···F) plot and a literature ν(OD) vs R(O···O) plot for hydrates containing O-D···O hydrogen bonds. For a given ν(OD) stretching frequency, the exponential regression curves show that R(O···F) is typically 0.1-0.2 Å shorter than R(O···O), in harmony with the lower basicity and smaller size of F atoms vs O atoms.

Substrate-Based Allosteric Regulation of a Homodimeric Enzyme

Many enzymes operate through half-of-the sites reactivity wherein a single protomer is catalytically engaged at one time. In the case of the homodimeric enzyme, fluoroacetate dehalogenase, substrate binding triggers closing of a regulatory cap domain in the empty protomer, preventing substrate access to the remaining active site. However, the empty protomer serves a critical role by acquiring more disorder upon substrate binding, thereby entropically favoring the forward reaction. Empty protomer dynamics are also allosterically coupled to the bound protomer, driving conformational exchange at the active site and progress along the reaction coordinate. Here, we show that at high concentrations, a second substrate binds along the substrate-access channel of the occupied protomer, thereby dampening interprotomer dynamics and inhibiting catalysis. While a mutation (K152I) abrogates second site binding and removes inhibitory effects, it also precipitously lowers the maximum catalytic rate, implying a role for the allosteric pocket at low substrate concentrations, where only a single substrate engages the enzyme at one time. We show that this outer pocket first desolvates the substrate, whereupon it is deposited in the active site. Substrate binding to the active site then triggers the empty outer pocket to serve as an interprotomer allosteric conduit, enabling enhanced dynamics and sampling of activation states needed for catalysis. These allosteric networks and the ensuing changes resulting from second substrate binding are delineated using rigidity-based allosteric transmission theory and validated by nuclear magnetic resonance and functional studies. The results illustrate the role of dynamics along allosteric networks in facilitating function.

CF2H, a Functional Group-Dependent Hydrogen-Bond Donor: Is It a More or Less Lipophilic Bioisostere of OH, SH, and CH3?

The effects of the CF₂H moiety on H-bond (HB) acidity and lipophilicity of various compounds, when attached directly to an aromatic ring or to other functions like alkyls, ethers/thioethers, or electron-withdrawing groups, are discussed. It was found that the CF₂H group acts as a HB donor with a strong dependence on the attached functional group ( A = 0.035-0.165). Regarding lipophilicity, the CF₂H group may act as a more lipophilic bioisostere of OH but as a similar or less lipophilic bioisostere of SH and CH₃, respectively, when attached to Ar or alkyl. In addition, the lipophilicity of ethers, sulfoxides, and sulfones is dramatically increased upon CH₃/CF₂H exchange at the α position. Interestingly, this exchange significantly affects not only the polarity and the volume of the solutes but also their HB-accepting ability, the main factors influencing log  P_oct. Accordingly, this study may be helpful in the rational design of drugs containing this moiety.

Halogens in Protein-Ligand Binding Mechanism: A Structural Perspective

Halogen atoms have been at the center of many rational medicinal chemistry applications in drug design. While fluorine and chlorine atoms are often added to enhance physicochemical properties, bromine and iodine elements are generally inserted to improve selectivity. Favorable halogen interactions such as halogen bond have been thoroughly studied through quantum mechanics and statistical analyses. Although most of the studies focus on halogen interaction through its σ-hole, hydrogen bonding also has a significant impact. Here, we present an analysis describing the interacting environment of halogen atoms in protein-ligand context. With consideration of structural redundancy in the PDB, tendencies toward specific molecular interactions consideration have been refined and implications for rational drug design with halogens further discussed. Finally, we highlight the moderate occurrence of halogen bonding and present the other roles of halogen in protein-ligand complexes, completing the medicinal chemistry guide to rational halogen interactions.

A ribose modification of Spinach aptamer accelerates lead(ii) cation association in vitro

Spinach aptamer fluorescence requires formation of a tripartite complex composed of folded RNA, a GFP-like fluorophore, and selective cation coordination. 2'F pyrimidine modified Spinach has retained fluorescence, increased chemical stability, and accelerated cation association via increased G-quadruplex dynamics, thereby reducing readout time and enhancing Spinach utility for aqueous Pb²⁺ detection.

Spy vs. spy: selecting the best reporter for 19F NMR competition experiments

Systematic characterization of a series of fluorinated VHL ligands, varying binding affinity and position of the trifluoromethyl group, qualifies a spy molecule for competitive 19F NMR screening and reveals guiding principles to develop highly sensitive assays with low material consumption.

Is the Fluorine in Molecules Dispersive? Is Molecular Electrostatic Potential a Valid Property to Explore Fluorine-Centered Non-Covalent Interactions?

Can two sites of positive electrostatic potential localized on the outer surfaces of two halogen atoms (and especially fluorine) in different molecular domains attract each other to form a non-covalent engagement? The answer, perhaps counterintuitive, is yes as shown here using the electronic structures and binding energies of the interactions for a series of 22 binary complexes formed between identical or different atomic domains in similar or related halogen-substituted molecules containing fluorine. These were obtained using various computational approaches, including density functional and ab initio first-principles theories with M06-2X, RHF, MP2 and CCSD(T). The physical chemistry of non-covalent bonding interactions in these complexes was explored using both Quantum Theory of Atoms in Molecules and Symmetry Adapted Perturbation Theories. The surface reactivity of the 17 monomers was examined using the Molecular Electrostatic Surface Potential approach. We have demonstrated inter alia that the dispersion term, the significance of which is not always appreciated, which emerges either from an energy decomposition analysis, or from a correlated calculation, plays a structure-determining role, although other contributions arising from electrostatic, exchange-repulsion and polarization effects are also important. The 0.0010 a.u. isodensity envelope, often used for mapping the electrostatic potential is found to provide incorrect information about the complete nature of the surface reactive sites on some of the isolated monomers, and can lead to a misinterpretation of the results obtained.

Intramolecular hydrogen bond directed distribution of conformational populations in the derivatives of N′-benzylidenebenzohydrazide

The extensive NMR investigations reveal the presence of E-isomers in the derivative of N′-benzylidenebenzohydrazide. The different conformer populations are controlled by the strength of intramolecular hydrogen bonds.

Carbohydrate Transport by Group Translocation: The Bacterial Phosphoenolpyruvate: Sugar Phosphotransferase System

The Bacterial Phosphoenolpyruvate (PEP) : Sugar Phosphotransferase System (PTS) mediates the uptake and phosphorylation of carbohydrates, and controls the carbon- and nitrogen metabolism in response to the availability of sugars. PTS occur in eubacteria and in a few archaebacteria but not in animals and plants. All PTS comprise two cytoplasmic phosphotransferase proteins (EI and HPr) and a species-dependent, variable number of sugar-specific enzyme II complexes (IIA, IIB, IIC, IID). EI and HPr transfer phosphorylgroups from PEP to the IIA units. Cytoplasmic IIA and IIB units sequentially transfer phosphates to the sugar, which is transported by the IIC and IICIID integral membrane protein complexes. Phosphorylation by IIB and translocation by IIC(IID) are tightly coupled. The IIC(IID) sugar transporters of the PTS are in the focus of this review. There are four structurally different PTS transporter superfamilies (glucose, glucitol, ascorbate, mannose) . Crystal structures are available for transporters of two superfamilies: bcIIC^mal (MalT, 5IWS, 6BVG) and bcIIC^chb (ChbC, 3QNQ) of B. subtilis from the glucose family, and IIC^asc (UlaA, 4RP9, 5ZOV) of E. coli from the ascorbate superfamily . They are homodimers and each protomer has an independent transport pathway which functions by an elevator-type alternating-access mechanism. bcIIC^mal and bcIIC^chb have the same fold, IIC^asc has a completely different fold. Biochemical and biophysical data accumulated in the past with the transporters for mannitol (IICBA^mtl) and glucose (IICB^glc) are reviewed and discussed in the context of the bcIIC^mal crystal structures. The transporters of the mannose superfamily are dimers of protomers consisting of a IIC and a IID protein chain. The crystal structure is not known and the topology difficult to predict. Biochemical data indicate that the IICIID complex employs a different transport mechanism . Species specific IICIID serve as a gateway for the penetration of bacteriophage lambda DNA across, and insertion of class IIa bacteriocins into the inner membrane. PTS transporters are inserted into the membrane by SecYEG translocon and have specific lipid requirements. Immunoelectron- and fluorescence microscopy indicate a non-random distribution and supramolecular complexes of PTS proteins.

19F multiple-quantum coherence NMR spectroscopy for probing protein-ligand interactions

A new 19F NMR method is presented which can be used to detect weak protein binding of small molecules with up to mM affinity. The method capitalizes on the synthetic availability of unique SF5 containing compounds and the generation of five-quantum coherences (5QC). Given the high sensitivity of 5QC relaxation to exchange events (i.e. reversible protein binding) fragments which bind to the target with weak affinity can be identified. The utility of the method in early stage drug discovery programs is demonstrated with applications to two model proteins, the neurotoxic NGAL and the prominent tumor target β-catenin.

The NMR 'split peak effect' in cell suspensions: Historical perspective, explanation and applications

The physicochemical environment inside cells is distinctly different from that immediately outside. The selective exchange of ions, water and other molecules across the cell membrane, mediated by integral, membrane-embedded proteins is a hallmark of living systems. There are various methodologies available to measure the selectivity and rates (kinetics) of such exchange processes, including several that take advantage of the non-invasive nature of NMR spectroscopy. A number of solutes, including particular inorganic ions, show distinctive NMR behaviour, in which separate resonances arise from the intra- and extracellular solute populations, without the addition of shift reagents, differences in pH, or selective binding partners. This 'split peak effect/phenomenon', discovered in 1984, has become a valuable tool, used in many NMR studies of cellular behaviour and function. The explanation for the phenomenon, based on the differential hydrogen bonding of the reporter solutes to water, and the various ways in which this phenomenon has been used to investigate aspects of cellular biochemistry and physiology, are the topics of this review.