Transoid-to-Cisoid Conformation Changes of Single Molecules on Surfaces Triggered by Metal Coordination
Sara Freund, Rémy Pawlak, Lucas Moser, Antoine Hinaut, Roland Steiner, Nathalie Marinakis, Edwin C. Constable, Ernst Meyer, Catherine E. Housecroft, Thilo Glatzel
TTransoid-to-Cisoid Conformation Changes ofSingle Molecules on Surfaces Triggered byMetal Coordination
Sara Freund, † Rémy Pawlak, ∗ , † Lucas Moser, † Antoine Hinaut, † Roland Steiner, † Nathalie Marinakis, ‡ Edwin C. Constable, ‡ Ernst Meyer, † Catherine E.Housecroft, ‡ and Thilo Glatzel † † University of Basel, Department of Physics, Klingelbergstrasse 82, CH-4056 Basel,Switzerland ‡ University of Basel, Department of Chemistry, Mattenstrasse 24a, BPR 1096, CH-4058Basel, Switzerland
E-mail: [email protected]
Abstract
Conformational isomers are stereoisomers that can interconvert over low potentialbarriers by rotation around a single bond. However, such bond rotation is hampered bygeometrical constraints when molecules are adsorbed on surfaces. Here we show thatthe adsorption of 4,4 (cid:48) -bis(4-carboxyphenyl)-6,6 (cid:48) -dimethyl-2,2 (cid:48) -bipyridine molecules onsurfaces leads to the appearance of pro-chiral single-molecules on NiO(001) and to enan-tiopure supramolecular domains on Au(111) surfaces containing the transoid moleculeconformation. Upon additional Fe adatom deposition, molecules undergo a controlledinterconversion from a transoid to cisoid conformation as a result of coordination ofthe Fe atoms to the 2,2 (cid:48) -bipyridine moieties. As confirmed by atomic force microscopy a r X i v : . [ c ond - m a t . m e s - h a ll ] O c t mages and X-ray photoelectron spectroscopy measurements, the resulting molecularstructures become irreversibly achiral. Introduction
An enantiomer is "one of a pair of molecular entities which are mirror images of each otherand non-superposable". Atropisomerism is a particular class of axial enantiomerism whichresults from hindered rotation about a single bond. In such compounds, enantiomer inter-conversions are mediated only by bond rotations between isomers (in contrast to interconver-tions that involve covalent bond breaking). Thus, the stability of "long-lived" atropisomersin three-dimensions usually requires steric hindrance in order to constrain internal bond rota-tions using peripheral chemical substitutions . To impose chirality, another approach consistsin the confinement of molecules onto a crystalline surface. Over the last couple of decades,this strategy has enabled the formation of enantiopure self-assemblies or chiral molecularcompounds from on-surface chemical reactions.
Accessing chiral molecular surfaces furtherallows a vast range of novel properties to emerge including the amplification of non-linearoptical properties and the asymmetric scattering of spin-polarized electrons. Moreover,the control of chiral-achiral transitions in surface-stabilized molecular networks could alsohelp designing chirality sensors, molecular switches and motors.
If a good alternative forstabilizing relies in their geometrical frustration on a surface, a step further would be tocontrol the bond rotation and thus the molecule conformation.In this work, we investigate the adsorption of achiral 4,4 (cid:48) -di(4-carboxyphenyl)-6,6 (cid:48) -dimethyl-2,2 (cid:48) -bipyridine molecules (DCPDMbpy) by means of atomic force microscopy (AFM), scan-ning tunneling microscopy (STM) and X-ray photoelectron spectroscopy (XPS) on NiO(001)and Au(111). Our work is motivated by our recent hierarchical assembly strategy "surfaces-as-ligands surfaces-as-complexes" (SALSAC) approach focusing on designing novel molec-ular compounds having (i) anchoring groups such as carboxylic or phosphonic acids that2nable a strong anchoring of the molecule to surfaces and (ii) metal-binding moieties suchas 2,2 (cid:48) -bipyridine ( bpy ) to facilitate the assembly of surface-bound metal coordination com-pounds either through sequential addition of metal ions and an ancillary ligand, or through aligand-exchange reaction between the anchoring ligand and a homoleptic metal complex. In a previous work, we investigated the first step of the DCPDMbpy assembly pro-cess using AFM operated in ultrahigh vacuum (UHV) conditions. We showed that theDCPDMbpy molecule systematically adopts two prochiral transoid -conformations ( α and β , Figure 1a) when adsorbed onto an atomically clean NiO(001) crystal surface. In contrast,the cisoid -conformation was not observed even upon annealing up to 420 K close to thedesorption temperature of the molecule. This can be explained by the high energy barrierneeded to be overcome in order to induce a bond rotation about the interannular C–C bondas well as the energy to partially desorb the molecule from the surface to allow the rotation.Theoretical studies of the conformational change from transoid to cisoid for a bpy in thegas phase have estimated an energy of about 320 meV (31 kJ · mol − ). The high rota-tional barrier was found to arise from the electrostatic repulsion between the lone pairs of thebipyridine units. This repulsive interaction also leads to the transoid conformation in favorof the cisoid one in gas phase as well as during its adsorption on surfaces. Note that thisbarrier is much higher than the available thermal energy at room temperature or even uponsurface annealing ( i.e. at 1000K, the available energy is about 80 meV (8 kJ · mol − ) whichimplies that the molecule desorb before changing its conformation to the cisoid one). How-ever, the activation energy to promote the conformational change can be overcome whenforming a complex between a metal atom and a bpy unit, theoretically delivering about4.66 eV (450 kJ · mol − ). Metal coordination might thus enable the emergence of the cisoid form on surfaces.Here, we investigated DCPDMbpy molecules in the presence of metallic adatoms onboth NiO(001) and Au(111) surfaces. The achiral cisoid geometry is observed after ad-sorption of prochiral DCPDMbpy on a NiO(001) surface previously partially covered with3igure 1:
T ransoid and
Cisoid
Conformations of The DCPDMbpy And Fe-DCPDMbpyMolecules. Upon adsorption, the DCPDMbpy adopts two prochiral conformations α and β . Upon coordination with Fe, the molecule can undergo a conformational change to the cisoid -conformation.Fe atoms, demonstrating the Fe-DCPDMbpy complex formation through coordination be-tween Fe atoms and bpy moieties. Furthermore, upon Fe adatom deposition on prochiralDCPDMbpy assemblies formed on Au(111), the molecules undergo an interconversion from transoid to cisoid on the surface, which is triggered by the same metal-coordination mech-anism as shown by AFM images and XPS measurements. Results and discussion
The Conformations of The DCPDMbpy And Fe-DCPDMbpy Moleculeson NiO(001) at Room Temperature.
To demonstrate the control of such chiral-achiral transitions on surfaces, we first investigatedDCPDMbpy molecules on a NiO(001) substrate. Figure 2a shows a representative AFM to-pographic image of the NiO(001) surface after deposition of 0.2 monolayer of DCPDMbpyat room temperature (RT). In the following, we define a monolayer (ML) as one layer ofmolecules fully covering the surface, 0.2 ML corresponds to a surface coverage of 20 % . Largeterraces are separated by mono-atomic steps and are covered with single molecules as wellas molecular aggregates. The step edges are saturated on both upper and lower sides indi-cating that these are preferential adsorption sites. The relatively short distance between the4igure 2: T ransoid - And
Cisoid -Conformations of DCPDMbpy Molecules Adsorbed onNiO(001). Large-scale AFM topographic images of NiO(001): (a) after deposition ofDCPDMbpy molecules and (b) after deposition of Fe and DCPDMbpy molecules (scanparameters: A = 4 nm, ∆ f = − Hz and ∆ f = − Hz, respectively). (c) and (d)AFM topographic images of flat-lying single-molecules adsorbed before and after Fe deposi-tion, respectively. The images were acquired using the first scanning pass (scan parameters: A = 4 nm, ∆ f = − . Hz and ∆ f = 29 Hz, respectively). (e) and (f) Corresponding ∆ f images acquired with the second scanning pass, i.e. with open feedback, using offsets of ∼ -350 pm and -280 pm. The molecules are in transoid - and cisoid - conformation, respectively.(g) and (h) structural models of both DCPDMbpy geometries on NiO(001).molecules (3.9 ± where molecular diffusionas a function of the substrate annealing temperature was studied.In order to trigger the emergence of metal complexes, 0.1 ML of Fe atoms were depositedat RT on the bare surface of NiO. DCPDMbpy molecules were then subsequently adsorbedonto this surface. To favour the coordination complex formation, the sample was annealedto 420 K after sublimation of molecules. Figure 2b shows an AFM topographic image of thissurface. To unambiguously confirm the DCPDMbpy-Fe complex formation on NiO(001),we focused on imaging of the molecule conformations at RT using a silicon cantilever (seeMethods), employing the multipass technique which has proven to deliver submolecular5esolution at RT. The method consists of recording a first line scan with a closed feedbackloop at a relative tip-sample distance Z st regulated for a particular set-point ∆ f andacquiring a second pass along the same scan line with the feedback open and at a closertip-sample distance Z nd = Z st - Z off ( Z off is in the order of 200 to 400 pm).Figures 2c and 2d show such AFM images of the DCPDMbpy molecules on NiO(001)without and with Fe atoms, respectively. The two AFM images acquired during the first scansuggest that both molecules are lying flat on the surface ( ∼ transoid and cisoid conformations of both molecules is observed as illustrated in Figures 2g and h.Upon adsorption and without Fe atoms, the DCPDMbpy molecules are adsorbed in theprochiral transoid conformation whereas successive deposition of Fe and molecules results inthe formation of the Fe-DCPDM(bpy) units possessing the cisoid conformation within the bpy units. Although the adoption of the cisoid -conformation is due to the coordination toa metal centre, we cannot clearly confirm its presence by AFM imaging. Metal atoms aregenerally difficult to observe by AFM in metal-ligand complexes at surfaces. Structure Resolution by Low Temperature AFM With CO-TerminatedTips.
To further improve the resolution, we measured the DCPCMbpy molecules on Au(111)at 4.7 K using AFM with a CO-terminated tip. Compared to the NiO(001) samples,Au(111) surfaces were prepared with similar molecule and Fe atom coverages (see Methods).Figures 3a and 3b show STM topographies of both DCPDMbpy conformations and thecorresponding constant-height AFM image acquired with a CO-terminated tip at 4.7 K. The transoid - and cisoid -conformations are unambiguously observed and a clear distinction ofthe phenyl rings of the molecules as well as the methyl groups attached to the bpy units againconfirms that the molecules lie flat on the surface (see qualitative models in Figures 3c). For6igure 3: High-Resolution Imaging of The
T ransoid - And
Cisoid - Conformations ofDCPDMbyp And Fe-DCPDMbpy With CO-Terminated Tips. (a) STM image of themolecules in transoid - and cisoid - conformation. (b) Corresponding AFM image of thetwo same molecules with intra-molecular resolution. (c) Structural models of DCPDMbypin transoid - and Fe-DCPDMbpy in cisoid -conformations. (d) Self-assemblies of transoid -DCPDMbpy on Au(111) leading to two enantiopure domains denoted and , respectively.(e) Tentative structural model of H-bonded enantiopure molecular domains superimposedto an AFM image of the assembly with a CO-terminated tip. (f) STM image of the molecularnetwork obtained by adding Fe atoms on Au(111). The pro-chirality of the molecule domainis lost due to the metal-complex formation. (g) Tentative structural model an AFM imageof the H-bonded Fe-DCPDMbpy molecules in their cisoid -conformation on Au(111). (Scanparameters: STM images: I t = 1 pA, V = -0.15 V and AFM images: A = 50 pm, V = 0 V).the cisoid -conformation, the Fe atom bound to the bpy moieties is again not visible in theimage. This observation, in addition to the fact that the methyl groups of the Fe-DCPDMbpyappear with a brighter contrast in comparison to transoid -DCPDMbpy, suggest that the Featom is hidden under the molecule with the result that the latter undergoes a slight bending(Figures 3c).The diffusion of the DCPDMbpy on Au(111) in comparison to what is observed onNiO(001) plays an important role. Indeed, in contrast to NiO, large DCPDMbpy self-assemblies can be formed at the gold surface at room temperature even at low coverage ( ≤ . ML) as shown in Figure 3d. In other words, the diffusion of each product of the reaction andconsequently also the formation of supramolecular structures can be hindered or facilitated7s function of the host substrate. On Au(111), two enantiopure domains denoted and coexist as a direct consequence of the prochirality of the DCPDMbpy molecule. As shownin the AFM image and highlighted by green lines in the structural model of Figure 3e,the self-assembly process is governed by hydrogen bonding between carboxylic groups ofadjacent enantiomers and forms extended close-packed molecular domains. The additionaldeposition of Fe atoms onto these chiral molecular domains on Au(111) leads to the formationof extended chain-like structures (Figure 3f and Figure 4d). By interacting with the lonepairs of the bipyridine unit, the Fe atom in the Fe-DCPDMbpy complex imposes the cisoid conformation. This conformation is achiral on the surface and, thus, induces the loss ofchirality of the molecular domains.In analogy to the self-assembly of transoid molecules, the assembly of cisoid Fe-DCPDMbpycomplex is driven by hydrogen bonding between their carboxylic groups (O-H...O) leadingto the formation of chain-like assemblies (Figures 3f and 4d) as well as trimers (Figure 3g).Note that the coordination of more than one DCPDMbpy ligand to Fe was never observedon the surface. We attribute this to the steric hindrance that would occur between the 6,6’-dimethyl groups of adjacent DCPDMbpy ligands in a Fe(DCPDMbpy) species that wasconstrained to a planar conformation on a surface. XPS Study of The Complex on Au(111).
To investigate the role of Fe adatoms in the assembly process, we further investigated byXPS the N1s binding energies (BE) of the DCPDMbpy molecules on Au(111) to reveal thechemical environment of the bpy moieties. The samples were prepared at RT with a coverage ≤ ML in the preparation chamber of the LT microscope and then transferred using a UHV-vacuum suitcase to the XPS chamber for analysis (see Methods). For this specific coverage,the N1s BE is at 398.2 eV (green curve in Figure 4a) which corresponds to supramolecularnetworks of the transoid -molecules (Figure 4b). Upon complex formation obtained by addi-tionally depositing Fe adatoms (blue curve in Figure 4a), the N1s BE significantly shifts by8 eV to higher values (BE = 399.2 eV) supporting the expected Fe complex formation andwith this also the switch to cisoid -conformation. In that case, the lone-pair of the N atoms ofthe bpy preferentially interact with an Fe adatom inducing a new chemical environmentfor the nitrogens (N...Fe...N). After annealing of the surface covered with DCPDM(bpy)molecules at 400 K (without Fe deposition), the N1s BE shifts slightly by 0.2 eV. Accordingto STM image (Figure 4c), the shift originates from a fraction of DCPDMbpy molecules thathave formed a complex with specific sites of the gold surface such as step edges, defects andelbows of the reconstruction ( black arrows in Figure 4c). Although two peaks are expectedhere, the first arising from the transoid-DCPDMbpy molecules and the second from the Au-DCPDMbpy coordination complexes (N...Au...N), the small amount of molecules (<1ML),e.g. low signal-to-noise ratio, does not allow a proper deconvolution of the N1s peaks andhence only one peak is observed. Moreover, the complex formation reaction only triggeredby temperature without additional metal atoms is less efficient since restricted to specificlocations of the Au(111) surface.Table 1 summarizes the DCPDMbpy conformation ratio as a function of the samplepreparations at a coverage ≤ . ML adsorbed on Au(111). This ratio could be determinedthrough analysis of a set of high resolution STM images. Upon deposition at RT, almost allthe DCPCMbpy molecules adsorbed on the Au(111) surface are in transoid -conformationand the ratio transoid : cisoid is measured to be ∼ ∼ demonstrated that molecules arenot affected by annealing and remain in transoid -conformation up to 493 K when they tend9igure 4: N1s Core Level Spectra. (a) XPS of one monolayer (ML) coverage of DCPDMbpyon Au(111) adsorbed at RT (green), after annealing at 400 K (red) and after annealing at400 K and Fe deposition (blue). The shown spectra are normalized and shifted vertically forcomparison. (b-d) Corresponding STM images of the surfaces after these preparations forcoverage ≤ ML (scan parameters: I t = 1 pA, V = -0.15 V).to desorb. In principle, the process is thus independent of the underlying surface as soonas metal adatoms are present as demonstrated on both Au(111) and NiO(001) surfaces. Asshown in our work, the diffusion and local reactive sites of the surfaces, however, influencesthe complex reaction and other metals might also form complexes. Finally, we emphasizethe irreversible character of this prochiral to achiral transition in single molecules as wellas in supramolecular networks since the opposite change, from cisoid to transoid , couldnot be experimentally achieved. Our results thus show the formation and suppression ofsurface-induced prochirality from the single molecule scale to the supramolecular networklevel. 10able 1: Effect of Fe And Annealing on The DCPDMbpy Conformation For Less Than 0.1Monolayer Coverage. without Fe without Fe with Fewithout annealing with annealing with annealing transoid
91% 52% 3% cisoid
9% 48% 97%
Conclusion
In summary, the 4,4 (cid:48) -di(4-carboxyphenyl)-6,6 (cid:48) -dimethyl-2,2 (cid:48) -bipyridine molecule (DCPDMbpy)adsorbs in a transoid geometry on both NiO(001) and Au(111) as single molecules andenantiopure domains, respectively. When adsorbed on NiO(001) partially covered with Feadatoms, the molecule shows a cisoid conformation demonstrating the formation of a metal-coordination complex (Fe-DCPDMbpy). On Au(111), we showed that the molecules un-dergo the interconversion from transoid to cisoid upon Fe adatom deposition on previouslyformed enantiopure DCPDMbpy assemblies. Using AFM imaging and XPS measurements,we demonstrated that the process is triggered by coordination complex formation betweenFe atoms and the bpy moieties of the molecule. Interestingly, the new Fe-DCPDMbpy supra-molecular networks on gold are achiral, which demonstrates the suppression of a surface-induced chirality in thin supramolecular networks via metal complex formation. Methods
Molecule Synthesis
DCPDMbpy was synthesized by Dr. Davood Zare (University of Basel) following the re-ported procedure. ample Preparation The NiO(001) crystals used in this study, purchased from SurfaceNet, consist of a rectangularrod with dimensions × × mm and a long axis in the [001] direction. The NiO(001) surfacewas prepared through in-situ cleavage ( UHV, p < × − mbar) with prior and subsequentannealing at about 800 K resulting in an atomically clean surface. An Au(111) single crystal,purchased from Mateck GmbH, was cleaned by several sputtering and annealing cycles inUHV conditions. DCPDMbpy molecules were thermally evaporated from a Knudsen cellheated up to 528 K on the surfaces kept at RT. The molecule rate was checked in-situ usinga quartz micro-balance. Fe adatom depositions were conducted using an e-beam evaporator.To promote complex formation, the sample was then annealed to 420 K during molecule andatom evaporation. For NiO(001), because of the low diffusion rate, we first sublimated theFe atoms and then DCPDMbpy molecules. For Au(111), the steps of the procedure wereinverted: molecules were deposited first and Fe atoms afterwards. A vacuum suitcase fromFerrovac GmbH was employed to transfer samples from the UHV LT AFM/STM setup tothe XPS chamber. AFM Imaging at Room Temperature
AFM measurements on NiO were conducted with a home built atomic force microscope(AFM) in UHV operated at RT. All AFM images were recorded in the non-contact mode(nc-AFM), using silicon cantilever (Nanosensors PPP-NCR stiffness k = 20 − N/m,resonance frequency f around 165 kHz and Q factor around 30000 with compensatedcontact potential difference (CPD). STM/AFM Imaging at Low Temperature
STM/AFM experiments were carried out at 4.7 K with an Omicron GmbH low-temperatureSTM/AFM operated with a Nanonis RC5 electronics. We used commercial tuning fork12ensors in the qPlus configuration ( f = 26 kHz, Q = 10000-25000, nominal spring constantk = 1800 N.m − ). The constant-height AFM images were acquired with CO-terminated tips.All voltages refer to the sample bias with respect to the tip. XPS Measurements
The samples were transferred in-situ using a vacuum suitcase to the XPS chamber directlyafter molecules and Fe atom deposition. The pressure in the XPS chamber was always ≤ − mbar and measurements were performed using a VG ESCALAB 210 system equippedwith a mono-chromatic Al K α radiation source. A pass energy of 20 eV was used for all narrowscan measurements and 100 eV pass energy for survey scans. Normal electron escape angleand a step size of 0.05 eV were used. The energy positions of the spectra were calibratedwith reference to the 4f 7/2 level of a clean gold sample at 84.0 eV binding energy. XPSfitting was performed with Unifit 2016 Software. Author Contributions
S.F., A.H., C.E.H. and T.G. conceived the experiment. S.F. measured the RT-AFM on NiO,R.P. measured with the LT-STM/AFM on Au(111). L.M. and R.S. performed the XPSmeasurements. S.F. wrote the manuscript with the help of R.P. All co-authors contributedto project concepts, discussion and read and commented on the manuscript.
Acknowledgement
This work was supported by the Swiss National Science Foundation (SNF) CR22I2-156236,the Swiss Nanoscience Institute (SNI) and the University of Basel.13 eferences (1) IUPAC. Basic terminology of stereochemistry.
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