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The history and development of 4'-fluoro-nucleosides is discussed in this review. This is a class of nucleosides which have their origin in the discovery of the rare fluorine containing natural product nucleocidin. Nucleocidin contains a fluorine atom located at the 4'-position of its ribose ring. From its early isolation as an unexpected natural product, to its total synthesis and bioactivity assessment, nucleocidin has played a role in inspiring the exploration of 4'-fluoro-nucleosides as a privileged motif for nucleoside-based therapeutics.

Synthetic routes following a sequential MacMillan organocatalytic asymmetric a-fluorination protocol for aldehydes and then reductive amination, has allowed ready access to bioactive b-fluoroamines. The approach is demonstrated with a short synthesis of (S)-3-fluoro-g-aminobutyric acid (3F-GABA) and was extended to b-fluoroamine stereoisomers of cinacalcet, tecalcet, fendilines and NPS R-467, all allosteric modulators of the calcium receptor (CaR). Stereoisomers of the fluorinated calcimimetic analogues were then assayed in a CaR receptor assay and a comparison of b-fluoroamine matched pair stereoisomers revealed a binding mode preference to the receptor as deduced from conformations which will be favoured as a consequence of the electrostatic gauche effect.

Authors thank the Chinese Scholarship Council for funding a Studentship (No. 202008060063) at the University of St. Andrews, U.K. C-2 fluorinated and methylated stereoisomers of the fragrance citronellol 1 and its oxalate esters were prepared from (R)-pulegone 11 and explored as agonists of the human olfactory receptor OR1A1 and assayed also against site-specific mutants. There were clear isomer preferences and C-2 difluorination as in 18 led to the most active compound suggesting an important hydrogen bond donor role for citronellol 1. C-2 methylation and the corresponding oxalate ester analogues were less active. Publisher PDF

We thank the EPSRC for a studentship (TJP) through the CRITICAT Doctoral Training Centre. FAPESP is also gratefully acknowledged for a studentship (BAP, #2021/09716-5) and a Young Researcher Award (RAC, #2018/03910-1). Concise and general synthesis protocols are reported to generate all-syn mono-, di- and tri-alkylated cyclohexanes where a single fluorine is located on the remaining carbons of the ring. The alkyl groups are positioned to lie equatorially and to have triaxial C–F bonds imparting polarity to these ring systems. Intermolecular electrostatic interactions in the solid-state structure of the trialkylated systems are explored and the resultant supramolecular order opens up prospects for design in soft materials. Publisher PDF

Funding: Authors are grateful to the Chinese Scholarship Council for studentship (Z. F. and C. Y.) support and also the Scientific Research Project of Hubei Education Department (Q20211402) and the open project of Hubei Provincial Key Laboratory of Green Materials for Light Industry (202107B06) for financial support. Stimulated by a suggestion of the late Professor Jack D. Dunitz, that perdeuterated Janus face cycloalkanes may be more polar than their unlabelled forms, the deuterated isotopologue of all cis-1,2,3,4,5,6-hexafluorocyclohexane ([2H6]- 1a ) and all cis-1,2,3,4-tetrafluorocyclopentane ([2H6]- 3a ) were prepared. Computation at the B3LYP−D3 level indicated that [2H6]- 1a is not more polar than its protio form 1, however perdeuterated cyclopentane [2H6]- 3a may indeed be more polar than 3 , although the magnitude is predicted to be small. None-the-less retention time analysis on a reverse phase GC/MS column of an add-mix of 3 and [2H6]- 3a gave some indication that the per-deuterated isotopologue 3a was detected marginally before the unlabelled compound consistent with increased polarity associated with perdeuteration. Publisher PDF

Funding: Authors thank the EPSRC, Leverhulme Trust and the EU Horizon 2020 Sinfonia consortia for financial support. The Chinese Scholarship Council is acknowledged for studentship support (Y.C.). The gene cluster in Streptomyces calvus associated with the biosynthesis of the fluoro- and sulfamyl-metabolite nucleocidin was interrogated by systematic gene knockouts. Out of the 26 gene deletions most did not affect fluorometabolite production, nine abolished sulfamylation but not fluorination, and three precluded fluorination, having no effect on sulfamylation. In addition to nucI, nucG, nucJ, nucK, nucL, nucN, nucO, nucQ and nucP we identified two genes (nucW, nucA), belonging to a phosphoadenosine phosphosulfate (PAPS) gene cluster, as required for sulfamyl assembly. Three genes (orf(-3), orf2 and orf3) were found to be essential for fluorination, although the activities of their protein products are unknown. These genes as well as nucK, nucN, nucO and nucPNP, whose knockouts produced results differing from those described in a recent report, were also deleted in Streptomyces virens - with confirmatory outcomes. This genetic profile should inform biochemistry aimed at uncovering the enzymology behind nucleocidin biosynthesis. Publisher PDF

Funding: Authors thank the Chinese Scholarship Council and FAPESP for studentships (BAP, #2021/09716-5) a Young Researcher Award (RAC, #2018/03910-1) and FAEPEX for a fellowship (RAC, #2479/21). Theory and solution NMR indicate that all-syn 1,3,5-trifluorocyclohexane 5 adopts the expected tri-equatorial conformation, however in the solid state the more polar triaxial conformation is observed. This and the favoured conformations of substituted (Me, OMe, NH(CO)Me, NHBoc) derivatives of 5 are investigated to explore triaxial C–F preferences. Publisher PDF

Theory and solution NMR indicate that all

Due to the high variation in viral surface properties, a platform method for virus purification is still lacking. A potential alternative to the high-cost conventional methods is aqueous two-phase systems (ATPSs). However, optimizing virus purification in ATPS requires a large experimental design space, and the optimized systems are generally found to operate at high ATPS component concentrations. The high concentrations capitalize on hydrophobic and electrostatic interactions to obtain high viral particle yields. This study investigated using osmolytes as driving force enhancers to reduce the high concentration of ATPS components while maintaining high yields. The partitioning behavior of porcine parvovirus (PPV), a nonenveloped mammalian virus, and human immunodeficiency virus-like particle (HIV-VLP), a yeast-expressed enveloped VLP, were studied in a polyethylene glycol (PEG) 12 kDa-citrate system. The partitioning of the virus modalities was enhanced by osmoprotectants glycine and betaine, while trimethylamine N-oxide was ineffective for PPV. The increased partitioning to the PEG-rich phase pertained only to viruses, resulting in high virus purification. Recoveries were 100% for infectious PPV and 92% for the HIV-VLP, with high removal of the contaminant proteins and more than 60% DNA removal when glycine was added. The osmolyte-induced ATPS demonstrated a versatile method for virus purification, irrespective of the expression system.

Funding: We thank EPSRC (EP/R013799/1) for a grant (DB) and the University of St Andrews for a Studentship (XF). The isolation of three adenosine based metabolites 6–8 from Streptomyces calvus is reported. The metabolites are structurally related to the fluorine containing antibiotic nucleocidin 1 and two recently identified glycosylated fluoroadenosines 2 and 3, however in this case the three metabolites do not contain a fluorine, suggesting that the biosynthetic enzymes to the fluorometabolites also process their non-fluorinated counterparts. Publisher PDF

We thank EPSRC for a grant (EP/R013799/1) and for a Studentship (JC) through the CRITICAT Centre for Doctoral training (CDT). FAPESP is also gratefully acknowledged for a studentship (BAP, #2019/03855-3), and a Young Research Award (RAC, #2018/03910-1). CENAPAD-SP, CESUP and SDumont are acknowledged for computational clusters used in theory calculations. This study uses X-ray crystallography, theory and Langmuir isotherm analysis to explore the conformations and molecular packing of alkyl all-cis 2,3,4,5,6-pentafluorocyclohexyl motifs, which are prepared by direct aryl hydrogenations from alkyl- or vinyl- pentafluoroaryl benzenes. Favoured conformations retain the more polar triaxial C-F bond arrangement of the all-cis 2,3,4,5,6-pentafluorocyclohexyl ring systems with the alkyl substituent adopting an equatorial orientation, and accommodating strong supramolecular interactions between rings. Langmuir isotherm analysis on a water subphase of a long chain fatty acid and alcohol carrying terminal all-cis 2,3,4,5,6-pentafluorocyclohexyl rings do not show any indication of monolayer assembly relative to their cyclohexane analogues, instead the molecules appear to aggregate and form higher molecular assemblies prior to compression. The study indicates the power and potential of this ring system as a motif for ordering supramolecular assembly. Publisher PDF

We report the synthesis of all‐cis 1,2,4,5‐tetrakis (trifluoromethyl)‐ and all‐cis 1,2,3,4,5,6‐hexakis (trifluoromethyl)‐ cyclohexanes by direct hydrogenation of precursor tetrakis‐ or hexakis‐ (trifluoromethyl)benzenes. The resultant cyclohexanes have a stereochemistry such that all the CF3 groups are on the same face of the cyclohexyl ring. All‐cis 1,2,3,4,5,6‐hexakis(trifluoromethyl)cyclohexane is the most sterically demanding of the all‐cis hexakis substituted cyclohexanes prepared to date, with a barrier (ΔG) to ring inversion calculated at 27 kcal mol−1. The X‐ray structure of all‐cis 1,2,3,4,5,6‐hexakis(trifluoromethyl)cyclohexane displays a flattened chair conformation and the electrostatic profile of this compound reveals a large diffuse negative density on the fluorine face and a focused positive density on the hydrogen face. The electropositive hydrogen face can co‐ordinate chloride (K≈103) and to a lesser extent fluoride and iodide ions. Dehydrofluorination promoted decomposition occurs with fluoride ion acting as a base., All‐cis 1,2,4,5‐tetrakis (trifluoromethyl)‐ and all‐cis 1,2,3,4,5,6‐hexakis (trifluoromethyl)‐ cyclohexanes were prepared by direct aryl hydrogenation. All‐cis 1,2,3,4,5,6‐hexakis(trifluoromethyl)cyclohexane has a high barrier to ring inversion (ΔG≠=27 kcal mol−1) and a Janus face profile with a large diffuse negative density on the fluorine face, and a focused positive density on the hydrogen face which coordinates carbonyls and halides.

We report counter‐intuitive axial preferences in non‐stereochemically biased, selectively fluorinated methoxycyclohexanes. These pseudo‐anomeric effects are apparent when electronegative CF2 groups are placed at the C‐2, C‐4 and C‐6 positions of the cyclohexane ring to render the C‐3/5 axial hydrogen atoms electropositive. The electrostatic interaction between these axial hydrogen atoms and the ‐OMe oxygen is stabilising. The effect is explored using high‐level ab initio and DFT calculations in the framework of NBO, QTAIM and NCI analysis across a range of derivatives, and experimentally (19F{1H}‐NMR at −80 °C) for some illustrative examples. The effect is significant in energy terms for a weak interaction, and illustrates a new stereoelectronic aspect attributed to selective fluorine substitution in organic chemistry., Fluorine chemistry: Selective fluorination in methoxycyclohexanes induces an electrostatic 1,3‐diaxial interaction favouring a counter‐intuitive axial preference.

Authors thank the Leverhulme Trust, EPSRC and the Sinfonia consortium of the EU for grants as well as the Chinese Scholarship Council for a Studentship (YC), all of which helped to support this work. Genome homology and the presence of a putative biosynthetic gene cluster identified Streptomyces aureorectus DSM 41692 and Streptomyces virens DSM 41465 as candidate producers of the antibiotic nucleocidin 1. Indeed when these bacterial strains were cultured in a medium supplemented with fluoride (4 mM) they each produced nucleocidin 1 and the previously identified 4'-fluoro-3'-O-β-glucosylated adenosine 2 and its sulfamylated derivative 3. In both of these cases 4'-fluoroadenosine 9 is also identified as a natural product although it has never been observed during fermentations of Streptomyces calvus, the original source of nucleocidin 1. The identity of 4'-fluoroadenosine 9 was confirmed by a total synthesis as well as by its in vitro enzymatic conversion to metabolite 2 using the glucosyl transferase enzyme, NucGT. Postprint Postprint

We thank EPSRC for a grant (EP/R013799/1) and Studentships (JLC) through the EPSRC CRITICAT CDT programme and also the Chinese Scholarship Council (CY). Monoalkylated derivatives of the unusually polar all- cis 2,3,4,5,6- pentafluorocyclohexyl (Janus face) motif are prepared starting from an aryl hydrogenation of 2,3,4,5,6- pentafluorophenylacetate methyl ester 15 . The method used Zeng's Rh(CAAC) carbene catalyst 4 in the hydrogenation following the protocol developed by Glorius. The resultant Janus pentafluorocyclohexylacetate methyl ester 16 was converted to the corresponding alcohol 18 , aldehyde 13 , bromide 29 and azide 14 through functional group manipulations, and some of these building blocks were used in Ugi-multicomponent and Cu-catalysed click reactions. NBoc protected pentafluoroarylphenylalanine methyl ester 35 was also subject to an aryl hydrogenation, and then deprotection to generate the Janus face ß-pentafluorocyclohexyl-alanine amino acid 15 , which was incorporated into representative members of an emerging class of candidate antiviral compounds. Log P measurements demonstrate that the all- cis 2,3,4,5,6-pentafluorocyclohexyl ring system is more polar than a phenyl ring. In overview the paper introduces new building blocks containing this Janus ring and demonstrates their progression to molecules typically used in bioactives discovery programmes. Publisher PDF

Authors thank the Engineering and Physical Sciences Research Council (EPSRC) for funding and we are grateful to the EPSRC Mass Spectroscopy Service at the University of Swansea for carrying out some of the accurate mass analysis of prepared compounds. A series of five 12-dodecanolides have been synthesised containing CF2 groups at C5, C6, C7, C8 and in one case a double substitution at C5 & C8, as a strategy to bias the conformational space accessed by these macrocycles, and to assess if the analogues may act as mimetics for 12-decenolide pheromones associated with the Emerald Ash Borer. Accordingly individual syntheses of 5,5-difluoro- 5, 6,6-difluoro- 6, 7,7-difluoro- 7, 8,8-difluoro- 8 and 5,5,8,8-tetrafluoro- 9, 12-decanolides is outlined and X-ray structural data was obtained for three (5, 8 and 9) of these compounds. The structures show clearly that the CF2 groups occupy ‘corner’ locations in the macrocycle consistent with their ability to bias accessible conformations. The fluorine containing 12-dodecanolides all generated an electro-antennogram response in female beetles. Postprint

This study uses X-ray crystallography, theory and Langmuir isotherm analysis to explore the conformations and molecular packing of alkyl all-cis 2,3,4,5,6-pentafluorocyclohexyl motifs, which are prepared by direct aryl hydrogenations from alkyl- or vinyl-pentafluoroaryl benzenes. Favoured conformations retain the more polar triaxial C–F bond arrangement of the all-cis 2,3,4,5,6-pentafluorocyclohexyl ring systems with the alkyl substituent adopting an equatorial orientation, and accommodating strong supramolecular interactions between rings. Langmuir isotherm analysis on a water subphase of a long chain fatty acid and alcohol carrying terminal all-cis 2,3,4,5,6-pentafluorocyclohexyl rings do not show any indication of monolayer assembly relative to their cyclohexane analogues, instead the molecules appear to aggregate and form higher molecular assemblies prior to compression. The study indicates the power and potential of this ring system as a motif for ordering supramolecular assembly., Theory and Langmuir isotherm analysis was used to explore the conformations and molecular packing of alkyl all-cis 2,3,4,5,6-pentafluorocyclohexyl motifs, which are prepared by direct aryl hydrogenations from alkyl- or vinyl-pentafluoroaryl benzenes.

In this theory study we demonstrate the dominance of non-classical 1,3-diaxial CH

Authors thank FAPESP, CONFAP and The UK Academies FAPESP for a São Paulo International Research Collaboration (FAPESP #2019/05028-7). FAPESP is also gratefully acknowledge for an undergraduate fellowship to BAP (#2019/03855-3), and a Young Research Award to RAC (#2018/03910-1). CENAPAD-SP, CESUP and SDumont are acknowledged for computational resources used in the theory calculations. We also thank EPSRC for a grant (EP/S030506/1). In this theory study we demonstrate the dominance of non-classical 1,3-diaxial CHax∙∙∙OC hydrogen bonds (NCHBs) dictating a ‘pseudo‘ anomeric effect in selectively fluorinated methoxycyclohexanes and also influencing the axial preference in the classical anomeric exhibitor 2-methoxytetrahydropyran, a phenomenon which is most often described as a consequence of hyperconjugation. Analogues of methoxycyclohexane where ring CH2’s are replaced by CF2 can switch to an axial preference and theory methods (NBO, QTAIM, NCI) indicate the dominance of 1,3- CHax∙∙∙OMe interactions over hyperconjugation. For 2-methoxytetrahydropyran, it is revealed that the global contribution to the anomeric effect is from electrostatic interactions including NCHBs, not hyperconjugation, although hyperconjugation (nO→σ *CO or nO →σ*CC) remains the main contributor to the exo-anomeric phenomenon. When two and three ether oxygens are introduced into the ring, then both the NCHB interactions and hyperconjugative contributions become weaker, not stronger as might have been anticipated, and the equatorial anomers progressively dominate. Postprint

M.M. thanks SULSA for a PhD studentship. We gratefully acknowledge financial support from the EPSRC (grant EP/I034793/1). We report the synthesis of five radiotracers incorporating different oxyamine spacers between the hypoxia‐reactive 2‐nitroimidazole moiety and the 5‐[18F]‐fluorodeoxyribose ([18F]FDR, 12 ) prosthetic group: three linear alkyl chains with 3, 5, 7 carbon atoms ( 15 a – c ), a cyclopropyl ring ( 15 d ) and a 1,4‐disubstituted‐1,2,3‐triazole ( 15 e ). Experiments in hypoxic cells showed that 15 d displays superior uptake kinetics – and similar selectivity for hypoxic cells – relative to the gold standard hypoxia tracers [18F]fluoroazomycin arabinoside ([18F]FAZA) and [18F]fluoromisonidazole ([18F]FMISO). Lipophilicity and structural rigidity have strong influence on the selectivity of tracers 15 towards hypoxic cells: the lead tracer 15 d displays a logP=0.38 and the most rigid spacer. A sixth radiotracer ( 15 f ), with a 2‐H‐imidazole replacing the 2‐nitroimidazole moiety of 15 d , was used to demonstrate that the cyclopropyl group does not play a meaningful role in the sensitivity towards hypoxia. Postprint

The isolation of three adenosine based metabolites 6-8 from

An unexpected and highly efficient reaction of dibenzo[a,e]cyclooctatetraene with Ag(i)F and N-bromosuccinamide in dichloromethane results in a sequential ring contraction pathway to generate bridged bicyclic α,α'-difluoroether isomers 10 and 11 where the ether oxygen is isotopically labelled from oxygen-18 water. In diethyl ether the same reaction generates the more classical vicinal difluoride isomers 13 and 14.

We thank the EPSRC for financial support. M. B. thanks the School of Chemistry and EaStCHEM for support. This study extends our interest in the synthesis and conformational behaviour of all-syn multivicinal fluoro alkane motifs. Specifically an all-syn 1,2,3,6,7,8-hexafluorooctane chain was assembled with a run of three fluorines, of the same stereochemical sense (syn) to the direction of the chain, on each side of an ethylene (–CH2CH2–) spacer to explore if the helical sense of the chain crosses the ethylene bridge. The solid state (X-ray) structure indicated a continuous helix however in solution (NMR) and by DFT computation, although the individual all-syn 1,2,3-trifluoro motifs maintain good helical integrity, the molecule is much more dynamic across the ethylene bridge. It was notable however that a low energy, non-helical conformer has a high molecular dipole (μ = 7.15 D) indicating a role for this skipped motif in soft materials such as liquid crystals or polar polymers. Postprint