Birmingham Selective nitrate recognition by a halogen-bonding four-station [3]rotaxane molecular shuttle

: The synthesis of the first halogen bonding [3]rotax-ane host system containing a bis-iodo triazolium-bis-naphtha-lene diimide four station axle component is reported. Proton NMR anion binding titration experiments revealed the halogen bonding rotaxane is selective for nitrate over the more basic acetate, hydrogen carbonate and dihydrogen phosphate oxoanions and chloride, and exhibits enhanced recognition of anions relative to a hydrogen bonding analogue. This elaborate interlocked anion receptor functions via a novel dynamic pincer mechanism where upon nitrate anion binding, both macrocycles shuttle from the naphthalene diimide stations at the periphery of the axle to the central halogen bonding iodo-triazolium station anion recognition sites to form a unique 1:1 stoichiometric nitrate anion–rotaxane sandwich complex. Molecular dynamics simulations carried out on the nitrate and chloride halogen bonding [3]rotaxane complexes corrob-orate the 1 H NMR anion binding results. sandwich complex, corroborated by MD simulations. design and synthesis of dynamic higher-order interlocked host systems for anion switchable and sensory applications

SelectiveN itrate Recognitionb yaHalogen-Bonding Four-Station [3]RotaxaneM olecular Shuttle Timothy A. Barendt, Andrew Docker,I gor Marques,Vítor FØlix, and Paul D. Beer* Abstract: The synthesis of the first halogen bonding [3]rotaxane host system containing abis-iodo triazolium-bis-naphthalene diimide four station axle component is reported. Proton NMR anion binding titration experiments revealed the halogen bonding rotaxane is selective for nitrate over the more basic acetate,hydrogen carbonate and dihydrogen phosphate oxoanions and chloride,and exhibits enhanced recognition of anions relative to ah ydrogen bonding analogue.T his elaborate interlocked anion receptor functions via an ovel dynamic pincer mechanism where upon nitrate anion binding,b oth macrocycles shuttle from the naphthalene diimide stations at the periphery of the axle to the central halogen bonding iodotriazolium station anion recognition sites to form aunique 1:1 stoichiometric nitrate anion-rotaxane sandwich complex. Molecular dynamics simulations carried out on the nitrate and chloride halogen bonding [3]rotaxane complexes corroborate the 1 HNMR anion binding results.
The prevalence of negatively charged species in biology and in the environment has deemed the development of synthetic anion receptors capable of their strong and selective recognition an important field of chemical research. [1][2][3] Thenitrate anion in particular is an environmental pollutant when leeched into lakes and rivers resulting from anthropogenic overuse of fertilizers or by acid rain. [4] Medically,a no ver exposure to nitrate via contaminated drinking water is associated with the formation of carcinogenic nitrosamines and ar ange of diseases such as methemoglobinemia (blue baby syndrome) in infants. [5] Thedesign of synthetic receptors capable of the selective recognition of nitrate is ac hallenge because of the anions inherent low affinity for hydrogen bonds and high energy of solvation. [6] To date only arelatively small number of nitrateselective tripodal acyclic,m acrocyclic and cage-like host systems have been reported that utilise convergent hydrogen bonding (HB) and/or anion-p interactions to recognise the oxoanion in polar organic solvents. [7][8][9][10][11][12][13][14][15][16][17][18][19] Thec hallenge of developing synthetic receptors that can rival the anion recognition properties of biotic systems relies upon the arrangement of at hree-dimensional convergent array of numerous HB donor groups in an optimized geometry for recognition of the complementary guest. [20,21] To meet this challenge we have exploited anion-templation to construct interlocked host structures [22,23] whose unique threedimensional cavities encapsulate anionic guest species.
While during the past two decades HB has been widely exploited in anion receptor design, halogen bonding (XB), [24][25][26][27] the attractive highly directional interaction between an electron-deficient halogen atom and aL ewis base,h as only recently begun to be utilised for anion recognition. Of the relatively few examples of XB anion receptors reported to date,i ti sn oteworthy that all display promising,a nd significantly contrasting, anion recognition behaviour when compared to HB analogues,byvirtue of their comparable bond strengths and more strict linear geometry preference. [28][29][30][31][32][33][34][35][36][37][38][39][40][41][42] Importantly in as ignificant step forward for highlighting the potential importance of halogen bonding in anion supramolecular chemistry,w eh ave recently demonstrated the first examples of solution phase halogen bonding being exploited to control and facilitate the anion-templated assembly of interlocked structures [43][44][45][46][47] and demonstrated that the incorporation of halogen bond donor atoms into a [ 2]rotaxane host cavity dramatically improves the anion recognition capabilities of the XB interlocked receptor. [48][49][50][51] Herein, we report the synthesis of the first halogen bonding [3]rotaxane host system, containing ab is-iodo triazolium-bis-naphthalene diimide four station axle component, which employs multiple cooperative XB and HB interactions to exhibit enhanced recognition of anions relative to an all-HB analogue and, impressively,i sf ound to be selective for nitrate over other oxoanions and chloride. Integrated into the extremities of the axle component of the [3]rotaxane are two electron deficient naphthalene diimide (NDI) groups that act as recognition sites (or stations) for each macrocycle component in the absence of acoordinating anion by donor-acceptor charge-transfer interactions.T his produces an exotic anion receptor that functions via an ovel dynamic pincer mechanism in which both macrocycles shuttle from the periphery of the axle component towards the central halogen bonding bis-iodo-triazolium recognition sites to form au nique 1:1s toichiometric nitrate anion-rotaxane sandwich complex ( Figure 1). Therefore,this adaptable receptor is also an example of acomplex molecular switch, since it produces reversible pincer-like molecular motion, through changes in the relative positions of the macrocycle components at the recognition sites on the axle upon exposure to anionic chemical stimuli.
Thed icationic HB and XB axle components 1·(Cl) 2 and 2·(Cl) 2 were synthesised using amultistep procedure shown in Scheme S1 in the Supporting Information (SI), incorporating two NDI motifs,asmacrocycle stations,each separated from the central bis-triazolium anion recognition site by ar igid biphenyl spacer unit.
Both rotaxanes were characterised by 1 Ha nd 13 CNMR spectroscopy and by high resolution mass spectrometry (see SI). Thei nterlocked nature of the rotaxane species was confirmed by two-dimensional 1 HR OESY NMR spectroscopy which also provided evidence for the co-conformations depicted in Scheme 1. Cross coupling correlations between the mechanically bonded macrocycle (H g,g' and H e,e' )a nd diagnostic protons of the bis triazolium station of the axle components (H n ,H k, H l and H o )i ndicate both macrocycles symmetrically occupying the central recognition site courtesy of convergent HB and/or XB to each of the chloride counter anions ( Figures S1 and S2). An absence of cross coupling between the macrocycle and NDI station protons (Figures S1 and S2) and small differences between d(H e,e' )inthe 1 HNMR spectra of [3]rotaxanes 4·(Cl) 2 and 5·(Cl) 2 and the bis-chloride salts of their corresponding axles indicates there are negli-gible interactions between macrocycles and the NDI stations ( Figures S3 and S4).
Anion exchange to the corresponding PF 6 À salts was achieved by repeatedly passing as olution of the rotaxane chloride salt through an Amberlite ion exchange column. A comparison of the resulting 1 HNMR spectra in CDCl 3 of rotaxanes 4·(PF 6 ) 2 and 5·(PF 6 ) 2 with their respective chloride salts 4·(Cl) 2 and 5·(Cl) 2 indicates ac hange in the coconformation has occurred as ar esult of shuttling of the macrocycle components to symmetrically occupy the peripheral NDI stations of the axle (Figures 2a nd S5). This is inferred by significant upfield shifts of the macrocycle hydroquinone protons H g,g' ,indicative of stronger aromatic donoracceptor charge-transfer interactions between the axles electron deficient NDI and macrocycle hydroquinone motifs.T he changes to the co-conformations are further evidenced by the two-dimensional 1 HROESYNMR spectra of 4·(PF 6 ) 2 and 5·(PF 6 ) 2 ,t hat both show the appearance of new correlations between resonance signals arising from the macrocycle protons H g,g' and H e,e' with the NDI protons H e,e' (Figures S6 and S7). Acomparison of the 1 HNMR spectra of 4·(PF 6 ) 2 and 5·(PF 6 ) 2 with the bis-hexafluorophosphate salts of their respective axle components also revealed the macrocycle components interact significantly with the NDI stations ( Figures S8 and S9).
To test the ability of the HB and XB [3]rotaxanes to behave as translational molecular shuttles stimulated by the chemical recognition of an oxoanion such as nitrate,o ne equivalent of (tetrabutylammonium)NO 3 was added to the rotaxanes 4·(PF 6 ) 2 and 5·(PF 6 ) 2 in CDCl 3 solution. The resulting 1 HNMR spectra are almost identical to that of their respective chloride salts indicating that both systems undergo ac oncerted molecular pincer motion of the macrocycles from the peripheral NDI stations into the centre of the axle to participate in binding of the nitrate anion at the bistriazolium station via formation of a1 :1 sandwich complex (Figures 2a nd S5). This change in co-conformation of both [3]rotaxane systems was confirmed using two-dimensional 1 H ROESY NMR which indicated the re-emergence of cross coupling between the macrocycle protons H g,g' and H e,e' and the axle protons associated with the bis-triazolium station (Figures S10 and S11). Importantly the spectra show no cross coupling interactions between the macrocycle hydroquinone protons H g,g' and the NDI aromatic protons H e,e' implying that any interactions with this station prior to nitrate addition have since been reduced. Thes ame conclusion can also be drawn from ac omparison of the 1 HNMR spectra of 4·(NO 3 )·(PF 6 ) and 5·(NO 3 )·(PF 6 ) with their respective axle components ( Figures S3 and S4). Theoperational cycle of the [3]rotaxane molecular shuttles is completed upon anion exchange of 4·(NO 3 )·(PF 6 ) and 5·(NO 3 )·(PF 6 ) back to their bis-hexafluorophosphate salts using NaPF 6(s) (Figures S5 and S12).
Additional evidence for the dynamic behaviour exhibited by these systems comes from a"naked eye" colour change of the [3]rotaxane in CHCl 3 that occurs on addition of acoordinating anion ( Figure 3). As the non-coordinating PF 6 À salt the [3]rotaxanes produce as trongly coloured orange solution courtesy of the donor-acceptor charge-transfer interactions that dominate between the NDI stations of the axle and the hydroquinone motifs of the macrocycle components. Upon addition of ac oordinating anion, the solution becomes colourless indicating that the macrocycles have moved away from the NDI groups and occupy the central bis-triazolium anion recognition sites resulting in al oss of the charge-transfer interactions,a ne ffect that can be easily monitored by UV/Vis spectroscopy (Figure S13). This means that these [3]rotaxane host systems have the propensity to act as optical sensors for anions by exploiting the novel dynamic behaviour of their constituent parts stimulated by anion recognition.
Theanion binding properties of the [3]rotaxanes were investigated by 1 HNMR titration experiments in the competitive solvent mixture of 1:1 CDCl 3 :CD 3 OD.U pon the addition of anions to the respective rotaxane bis-hexafluorophosphate salts,s ignificant downfield chemical shift perturbations of the methylene protons H o adjacent to the triazolium recognition sites were observed as well as similar changes to the macrocycles acidic internal isophthalamide proton H b (Figures S14 to S22). These proton perturbations are diagnostic of anion binding occurring at the charged triazolium stations aided by hydrogen bonding interactions from the macrocycles to achieve encapsulation of the anion within the unique cavity created by the three components as shown in Figure 3. WinEQNMR2 analysis of the titration data, [52] monitoring either protons H o or H b ,e nabled the determination of the anion association constants shown in Table 1. Importantly all were found to exhibit 1:1s toichiometry [53,54] apart from chloride (1:2 host:guest model), presumably because of the propensity for the larger oxoanions to bridge the bis-triazolium recognition site and to form as andwich complex via favourable HB interactions between the macrocycle components.
Both [3]rotaxanes exhibit as ignificant selectivity for nitrate over the more basic oxoanions (acetate,h ydrogen carbonate and dihydrogen phosphate) and chloride.T he latter is an important result considering the fact that our previous nitrate-designed HB [2] rotaxane and [2]catenane Scheme 1. Synthesis of the HB and XB multi-station [ 3]rotaxanes 4·(Cl) 2 and 5·(Cl) 2 ,indicating the predicted co-conformation of the molecules as their chloride salts.

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Communications interlocked hosts displayed comparable affinities for chloride. [22,23,55] Thes uperior nitrate recognition of this new generation of [3]rotaxanes is ascribed to the complementarity of the three-dimensional cavity resulting from the bidentate bis-triazolium site of the axle component and two hydrogen bond-donating isophthalamide macrocycles.T he importance of the macrocyclic wheel components was demonstrated by the significantly weaker binding of nitrate by the HB and XB axle components 1·(BF 4 ) 2 and 2·(BF 4 ) 2 in the same solvent mixture (K Ass = 163 and 216 m À1 respectively,F igures S23 and S24). [56] Ac omparison of the association constants for each [3]rotaxane crucially reveals the XB system to demonstrate superior anion binding,f or all anions,r elative to the HB analogue,c ourtesy of strong halogen bond formation to the anionic guest. Importantly,tothe best of our knowledge this is the first time an XB interlocked host system has exhibited an enhanced association for oxoanionic guests,o ver acomparable HB only system. In addition to the strength of the halogen bond interactions inherent to the XB [3]rotaxane,i ts success can also be ascribed to the stricter preference for al inear bond geometry between an XB donating iodo-triazolium group and the anion guest, relative to that of ahydrogen bond from ap roto-triazolium motif,r esulting in am ore geometrically defined recognition site which may specifically aid binding of multidentate oxoanions within the cavity.T he Figure 3. Co-conformations of XB [3]rotaxanes 5·(Cl) 2 , 5·(PF 6 ) 2 and·5·(NO 3 )·(PF 6 ) and photographs showing the "naked eye" colour changes.

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Communications superior recognition of chloride by the XB [3]rotaxane over the HB analogue is in agreement with previously-reported XB interlocked hosts that also exhibit improved halide binding trends. [45,48] Further structural insights on XB [3]rotaxane assembly with NO 3 À and Cl À anions were obtained through molecular dynamics (MD) simulations carried out at the atomic level using the GAFF [57,58] within the AMBER14 suite, [59] using GPU cards. [60][61][62] Ther emaining computational details are given in the SI.
Following our previous work, [50,63] the XB interactions were simulated with the inclusion, in the force field parameterisation, of an extra-point of positive charge to represent the s-hole of each iodine atom of the triazolium binding units. [64] Thes tarting binding scenarios of 5·(Cl) 2 and 5·NO 3 À were built assembling the two macrocycles and the bis-iodotriazolium axle central motif in an interlocked orthogonal binding arrangement, in agreement with the structures of analogous XB [2]rotaxane hosts. [50,63] In addition, in 5·(Cl) 2 , the two chloride anions together with the two macrocycles were initially disposed in ap arallel manner with each anion establishing two hydrogen bonds with asingle isophthalamide binding cleft and one halogen bond with aiodo-triazolium XB binding unit, as shown in Figure 4. Henceforth, the coconformation adopted by the XB [3]rotaxane 5 in this binding arrangement is called A.I n5·NO 3 À the trigonal anion was placed in ap osition consistent with its simultaneous recognition by the two macrocycles and the bis-iodo-triazolium axle central motif.These two anion [3]rotaxane arrangements, illustrated in Figure S27, were subsequently immersed in periodic cubic boxes of as olvent mixture of 1:1 CHCl 3 :CH 3 OH and their dynamic behaviours were ascertained through three MD production runs of 100 ns each.
During the initial nanoseconds of the three independent MD runs carried out with 5·(Cl) 2 ,one chloride anion coupled with its macrocycle initiates ahalf-circumrotation, passing by an intermediate co-conformation B where the macrocycles are almost perpendicular to each other.C oncomitantly,t he iodo-triazolium ring halogen bonded to that chloride follows the rotating motion around the axles main axis,w hile preserving the p-p stacking interactions between the electron deficient iodo-triazolium XB binding unit and the electron rich macrocycle hydroquinone motifs,a sw ell as the XB interactions.A fter this relatively short simulation period, an ew binding arrangement appears,c haracterised by an antiparallel disposition of both macrocycles (co-conformation C)and both chlorides,and is maintained until the end of the simulation time.T he two concerted rotating movements described are illustrated in Figure 4a nd in Movie S1.
Thec onversion of co-conformation A into C is accompanied by an increase of the distance between the chlorides by ca. 0.7 a nd ad ecrease of the distance between the two axles iodine atoms of ca. 0.8 , as evident from the evolution of these distances throughout the simulation time plotted in Figure S28 (see SI) for the three MD runs.T hroughout the MD simulation time,including the rotational events,both XB interactions are almost constantly maintained with high

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Communications directional character along the three replicates with average values for the I···Cl À distances and C-I···Cl À angles of 3.490 AE 0.136 a nd 173.9 AE 3.58 8,r espectively.M oreover,b oth chloride anions are also held by the isophthalamide macrocyclic clefts via two cooperative N-H···Cl À hydrogen bonds preserved during most of the MD simulation time.T he N···Cl À distances and N-H···Cl À angles are summarised in Tables S4  and S5 for each independent MD run, along with the I···Cl À distances and C-I···Cl À angles.T he conformational rotation observed in the three unrestrained MD simulations indicates that, in solution, 5·(Cl) 2 prefers co-conformation C.F urthermore,during long simulation periods the two phenyl rings of the isophthalamide macrocyclic binding clefts (rings 1 and 2) and the hydroquinone of the bis-iodo-triazolium axle central motif (ring 3)remain almost parallel at interplanar distances consistent with the existence of stabilizing p-p stacking interactions in co-conformation C.T his structural feature is particularly noticeable in two of the three MD replicates,a s can be seen in Figure S28, where the variations on distances from the centroid of 3 to centroids 1 and 2 for 100 ns are plotted along with the 1-3-2 angle.This spatial disposition can also induce the H o protons downfield chemical shift perturbations observed in the 1 HNMR chloride titration. Tw or epresentative snapshots of the MD simulations carried out with the assembly between the multidentate trigonal anion NO 3 À and interlocked [3]rotaxane host are presented in Figure 5. In contrast with 5·(Cl) 2 ,t he overall structure of 5·NO 3 À oscillates between co-conformations A (top view) and B (bottom view) along the three independent MD runs of 100 ns,w ith the nitrate anion tightly bonded to both macrocycles and bis-iodo-triazolium axle central core through HB and XB interactions,respectively.Inspite of the quarter of rotation of am acrocycle relatively to each other, the assembly between the oxoanion and the three rotaxane binding entities is uninterrupted as can be seen in Movie S2. Moreover,t he nitrate oxygen acceptors intermittently exchange between the isophthalamides NÀHb inding sites and CÀIt riazolium recognition sites,y ielding slightly long average N···O (4.168 AE 0.994 ) and I···O (4.036 AE 0.857 ) distances.The swap of the nitrates oxygen atoms between XB and HB binding sites is well depicted by the two peaks in Figures S29-S31 Thed ifferent dynamic behaviours of XB complexes 5·(Cl) 2 and 5·NO 3 À are highlighted with 3D histograms built with the positions occupied by the chloride and nitrate anions within the [3]rotaxane interlocked binding pockets throughout as ingle MD run and shown in Figure S32. Thet wo chloride anions display individual clouds of positions with almost hemicyclic shapes,d erived from their oscillating movements around the axle,a nd ag reater density of points mirroring the preference for the binding arrangement with 5·(Cl) 2 in co-conformation C.N O 3 À displays aw ell-defined cloud of points constricted to the binding region defined by the isophthalamide clefts and the two iodo-triazolium axle binding sites,w ith the [3]rotaxane in co-conformation A. Furthermore,t he comparison between these two graphical depictions suggests that the nitrate anion is more tightly bonded to the interlocked host than the chloride anions, which is in agreement with 1 HNMR experimental binding data.
In summary,w eh ave synthesised the first higher-order XB [3]rotaxane,containing afour station bis-iodo-triazoliumbis-naphthalene diimide axle and two HB-donating macrocycle components,c apable of recognising anions via an ovel dynamic shuttling mechanism. Proton NMR titration experiments revealed the XB [3]rotaxane to exhibit selectivity for nitrate over more basic acetate,h ydrogen carbonate and dihydrogen phosphate oxoanions,and notably chloride,and is as uperior anion host in comparison to aH B [ 3]rotaxane analogue.T he XB interlocked host achieves oxoanion recognition via both macrocycles shuttling from the peripheral NDI axle stations to the core XB iodo-triazolium anion binding sites in ap incer-like motion to form au nique 1:1 Figure 5. Co-conformations A (top) and B (bottom) of 5·NO 3 À showing the isophthalamide binding clefts almost facing each other and adopting an early perpendiculars patial disposition, respectively. The bulky stoppersw ere removed for clarity. stoichiometric sandwich complex, as corroborated by MD simulations.The design and synthesis of dynamic higher-order XB interlocked host systems for anion switchable and sensory applications is continuing in our laboratories.