Self-Assembly of N3-Substituted Xanthines in the ... - ACS Publications

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Self-assembly of N3-substituted xanthines in the solid state and at the solid-liquid interface Artur Ciesielski, Sebastien Haar, Attila Bényei, Gabor Paragi, C. Fonseca Guerra, F. Matthias Bickelhaupt, Stefano Masiero, János Szolomájer, Paolo Samori, Gian Piero Spada, and Lajos Kovács Langmuir, Just Accepted Manuscript • DOI: 10.1021/la304540b • Publication Date (Web): 01 Jan 2013 Downloaded from http://pubs.acs.org on January 10, 2013

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SELF-ASSEMBLY OF N3-SUBSTITUTED XANTHINES IN THE SOLID STATE AND AT THE SOLID-LIQUID INTERFACE Artur Ciesielski,a Sébastien Haar,a Attila Bényei,b Gábor Paragi,c Célia Fonseca Guerra,d F. Matthias Bickelhaupt,d,e Stefano Masiero,f János Szolomájer,g Paolo Samorì,*,a Gian Piero Spada,*,f Lajos Kovács*,g a

Nanochemistry Laboratory, ISIS & icFRC, Université de Strasbourg & CNRS, 8 allée Gaspard Monge, 67000 Strasbourg, France. b

c

University of Debrecen, Department of Physical Chemistry, Egyetem tér 1, 4010 Debrecen, Hungary.

Research Group of Supramolecular and Nanostructured Materials of the Hungarian Academy of Sciences, Dóm tér 8, 6720 Szeged, Hungary. d

Department of Theoretical Chemistry and Amsterdam Center for Multiscale Modeling (ACMM), VU University Amsterdam, De Boelelaan 1083, NL-1081 HV Amsterdam, The Netherlands. e

Radboud University Nijmegen, Institute for Molecules and Materials, Heyendaalseweg 135, NL-6525 AJ Nijmegen, The Netherlands.

f

Alma Mater Studiorum – Università di Bologna, Dipartimento di Chimica “G. Ciamician” Via San Giacomo 11 – 40126 Bologna, Italy. g

University of Szeged, Department of Medicinal Chemistry, Dóm tér 8, 6720 Szeged, Hungary.

KEYWORDS. Xanthine, hydrogen bonding, interfaces, purine, self-assembly. ABSTRACT Self-assembly of small molecular modules interacting through non-covalent forces is increasingly being used to generate functional structures and materials for electronic, catalytic,

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and biomedical applications. The greatest control over the geometry in H-bond supramolecular architectures, especially in H-bonded supramolecular polymers, can be achieved by exploiting the rich programmability of artificial nucleobases undergoing self-assembly through strong Hbonds. Here N3-functionalized xanthine modules are described, which are capable of selfassociating through self-complementary H-bonding patterns to form H-bonded supramolecular ribbons. The self-association of xanthines through directional H-bonding between neighboring molecules allows the controlled generation of highly compact 1D supramolecular polymeric ribbons on graphite. These architectures have been characterized by scanning tunneling microscopy at the solid–liquid interface, corroborated by dispersion-corrected density functional theory (DFT) studies and X-ray diffraction.

INTRODUCTION The self-assembly of small molecular modules into non-covalently linked polymeric nanostructures is a subject of continuous interest.1 In particular, supramolecular structures with a high degree of order can be obtained through the self-association of organic molecules on flat solid surfaces.2 Such structures can be used as scaffolds to position with sub-nm precision electrically/optically active groups in pre-determined locations in 2D,3 thereby paving the way towards a wide range of applications, e.g. in electronic and optical devices.4 Among weak interactions, H-bonding5 offers high control over the process of molecular self-assembly because it combines reversibility, directionality, specificity and cooperativity. The great deal of effort devoted so far towards the generation of H-bonded polymeric structures via self-assembly from small molecular modules is instrumental as it illustrates a variety of general design principles employed in supramolecular engineering of hydrogen-bond mediated self-assembly.2e, 6


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Modified purine bases play an important role in biology, and they are interesting systems from biochemical, pharmacological, and chemical points of view.7 In particular, xanthine (X) found in most human body tissues and fluids as well as in other organisms. Its 9-glycosylated nucleosides, nucleotides and alkyl derivatives play a decisive role in a variety of intracellular metabolic pathways as substrates and/or intermediates of numerous enzymes or enzyme systems.8 Xanthine is also one of the purines which could have been present on a primitive, prebiotic Earth, possibly being formed in frozen ammonium cyanide solutions9 or being brought to Earth by carbonaceous chondrite meteorites.10 Many xanthine derivatives are naturally occurring drugs which find use as central nervous system stimulants, and the best known is caffeine, one of the most widely consumed, pharmacologically active substances.11 N3-substituted xanthines, in particular N3methylxanthine, an intermediate in the metabolism of methylxanthine alkaloids (caffeine, theophylline, theobromine),12 possess an interesting properties such as bronchodilator effect,13 and have been employed to study the dynamics of theophylline-binding RNA aptamers.14 N3methylxanthine has been found to self-assemble in the presence of metal cations in gas and solution phases into planar tetrameric and bilayered octameric aggregates.15 In recent years, the self-assembly of nucleobases into superstructures on solid surfaces has attracted much attention and has been the subject of both experimental and theoretical explorations,16 due to their possible applications in the key area of nanotechnology. The adsorption of xanthine molecules on inorganic surfaces is therefore of interest for the fundamental understanding of prebiotic biosynthesis17 and may be of relevance to the origin and evolution of life as well.18 In particular, the self-assembly of xanthine molecules on solid surfaces has been studied by scanning tunneling microscopy (STM) under ultrahigh vacuum (UHV),19 and was found that xanthine self-assembles into two extended homochiral networks


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tiled by two types of di-pentamer units and stabilized by intermolecular double hydrogen bonding. Despite the published X-ray single crystal analysis20 of N3-methylxanthine (Cambridge Structural Database Ref. code: FADCUI), the knowledge on the self-assembly of N3-alkylated xanthines is still relatively poor. Scanning tunneling microscopy is a most powerful tool to investigate the structure of molecular assemblies at surfaces under various environmental conditions with a sub-molecular resolution. It is therefore an important method to unravel the self-assembly phenomena and 2D crystal engineering with a high degree of precision. The STM application at the solid–liquid interfaces also allows the study of dynamic processes21 such as reactivity,22 making this tool very precious for nanochemistry investigations. Herein, we present a sub-molecularly resolved STM study of the self-assembly of N3 substituted xanthine derivatives at a solid–liquid interface on highly oriented pyrolytic graphite (HOPG) surface, corroborated with X-ray crystal structure analysis and density functional theory (DFT) calculations. We focused our attention on two N3-alkylated xanthine derivatives, i.e. N3methylxanthine15 (1) and N3-octadecylxanthine (2) (Scheme 1).

Scheme 1. Chemical representation of investigated xanthine derivatives.

Experimental Section


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Materials. Unless otherwise noted, solvents and reagents were reagent grade from commercial suppliers and used without further purification. Pearlman’s catalyst refers to Pd(OH)2/C with 20 % Pd content, Alfa Aesar cat. no. 042578. All moisture-sensitive reactions were performed under an argon atmosphere using oven-dried glassware. All the reactions were monitored by TLC on Kieselgel 60 F254 plates (Merck) with detection by UV. Flash column chromatography was carried out using silica gel (particle size 40–63 µm). Melting points (uncorrected): Electrothermal IA 8103 apparatus. Elementary analyses: Perkin-Elmer CHN analyzer model 2400. 1H and

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C NMR spectra were recorded in DMSO-d6 and C2D2Cl4 using a Varian Unity

INOVA 600 MHz instrument equipped with a reverse probe. ESI-MS: Finnigan MAT TSQ 7000 (negative mode) and Micromass ZMD-4000 spectrometer (positive mode).

Synthesis N3-methylxanthine (1). N3-methylxanthine was synthesized according to a literature procedure.15 N3-octadecylxanthine (2). N7-Benzylxanthine23 (2.0 g, 8.26 mmol) was dissolved in anhydrous DMF (50 mL) and sonicated in ultrasonic bath. K2CO3 was added (1.37 g, 9.91 mmol, 1.2 equiv.) and the obtained heterogeneous mixture was heated with vigorous stirring at 50 °C for 1 h. The obtained potassium salt was treated dropwise with octadecyl bromide (8.26 mmol, 2.75 g, 2.82 mL, 1.0 equiv.) in anhydrous DMF (50 mL) and the reaction mixture was stirred at 50 °C overnight. The obtained heterogeneous mixture was filtered and the filtrate was evaporated in vacuo and co-evaporated successively with EtOH (2×) and CH3CN (2×). The residue was dissolved in EtOAc (200 mL) and extracted with H2O (5 × 100 mL). The organic layer was dried on Na2SO4, filtered and evaporated in vacuo. The crude product was purified by column


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chromatography using the solvent system: CH2Cl2 : EtOAc (9 : 1, v/v) to give N7-benzyl-N3octadecylxanthine (1.50 g, 37%) as a white powder which was used without any further purification in the next step.

Scheme 2. Synthesis of N3-octadecylxanthine (2) N7-Benzyl-N3-octadecylxanthine (1.3 g, 2.62 mmol) was dissolved in a mixture of 1,4-dioxane and AcOH (50 mL each) and Pearlman’s catalyst [Pd(OH)2/C , 1.30 g] was added. The batch reactor was filled with hydrogen at 75-100 bar and the reaction mixture was heated with vigorous stirring at 95°C for 24h. The obtained mixture was filtered, the filtrate was evaporated in vacuo and coevaporated with MeCN (3×). The purification of the crude product was achieved by column chromatography using the solvent system toluene : 2-propanol (9 : 1, v/v) to give the final compound (750 mg, 71%). The molecule (2) was insoluble in most organic solvents with the exception of a mixture of 10% (v/v) 2-propanol in toluene and neat MeOH. A sample was obtained by crystallisation from MeOH. Mp. 232 °C (sinters), 238-239 °C. Anal calcd. for C23H40N4O2 (404.589): C, 68.28; H, 9.97; N, 13.85%, found: C, 68.40; H, 9.90; N, 13.71%. 1H NMR and

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C NMR spectra are reported in Supporting Information (SI, Figs. S1-S6). ESI-MS

(negative mode, m/z) (403.07, [M-H]-, 100). ESI-MS (positive mode, C2H2Cl4/CHCl3 solution with a small amount of formic acid, m/z) (405, [M+H]+, 100; 427, [M+Na]+, 85; 443, [M+K]+, 100; 831, [2M+Na]+, 60; 1236, [3M+Na]+, 12; 1640, [4M+Na]+, 45, Fig. S7).


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X-ray crystal structure analysis. Single crystals were grown from water solution of N3methylxanthine (1) by keeping the temperature at 40 °C. The quality of the crystals was rather low, nevertheless a suitable colorless prism crystal with dimensions of 0.54 mm × 0.33 mm × 0.2 mm was found and fixed on the tip of a glass capillary using epoxy glue. Diffraction intensity data collection was carried out at 293(2) K on a Bruker-Nonius MACH3 diffractometer equipped with a point detector using graphite-monochromated Mo-Kα radiation (λ = 0.71073 Å). The structure was solved by SIR-92 program24 and refined by full-matrix least-squares method on F2, with all non-hydrogen atoms refined with anisotropic thermal parameters using the SHELXL-97 package.25 Publication material was prepared with the WINGX suite.26 All hydrogen atoms were located geometrically and refined in the riding mode, except protons at nitrogen atoms which could be found at the difference electron density map but their distance to the nitrogen atoms should be restrained.

STM investigation. Scanning Tunneling Microscopy (STM) measurements were performed using a Veeco scanning tunneling microscope (multimode Nanoscope III, Veeco) at the interface between highly oriented pyrolitic graphite (HOPG) and a supernatant solution, by using a scanner A (Veeco), therefore by mapping a maximum area of 1µm × 1µm. Diluted solutions of 1 and/or 2 were applied to the basal plane of the surface. For STM measurements the substrates were glued on a magnetic disk and an electric contact is made with silver paint (Aldrich Chemicals). The STM tips were mechanically cut from a Pt/Ir wire (90/10, diameter 0.25 mm). The raw STM data were processed through the application of background flattening and the drift was corrected using the underlying graphite lattice as a reference. The latter lattice was visualized by lowering the bias voltage to 20 mV and raising the current to 65 pA. Mother


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solutions of N3-methylxanthine (1) and N3-ocadecylxanthine (2) were dissolved in 1,2,4trichlorobenzene (TCB) at 95 ºC and diluted to give 100 µM and 10 µM solutions. STM imaging was carried out in constant height mode yet without turning off the feedback loop, to avoid tip crashes. Monolayer pattern formation was achieved by applying onto freshly cleaved HOPG 4µL of a solution that was heated at 60-70 ºC to improve the solubility. Noteworthy, study of this system in different solvents, i.e. 1-phenyloctane, nonanoic acid and tetradecane, did not produced any ordered monolayers, which can be attributed to the low solubility of molecules 1 and 2 in those solvents. The STM images were recorded at room temperature after achieving a negligible thermal drift. By using lower temperature during the heating process, small precipitating agglomerates were observed. On the other hand, in-situ STM experiments at variable temperature cannot be performed using our set-up. All of the molecular models were minimized with Chem3D at the MM2 level and processed with QuteMol visualization software.27

Theoretical Calculations Computational Details. All calculations were performed using the Amsterdam Density Functional (ADF),28 and the QUantum-regions Interconnected by Local Descriptions (QUILD) program developed by Swart and Bickelhaupt.29 The applied level of theory was density functional theory (DFT) using the BLYP functional,30 with TZ2P basis set and dispersion corrections were taken into account according to Grimme’s method (BLYP-D).31 This approach has been shown to yield excellent structures and energies for multiply-hydrogen bonded DNAbase oligomers.32 Equilibrium structures were optimized using analytical gradient techniques and under constraint of Cs symmetry. This planar restraint mimics the presence of a surface and it


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seems to be a suitable approximation to compare the interaction between neighboring monomers in case of the simplest xanthine derivative, i.e. N3-methylxanthine (1) and guanine (G) ribbons. The N9-methylguanine ribbons (see Fig. S8 in SI) were calculated as reference system since the ribbon forming capacity of N9-octadecylguanine on a surface has been demonstrated experimentally before.33

Bonding Analyses. The overall bond energy ∆Ebond is made up of two major components [Eq. (1)]: (1)

∆Ebond = ∆Edef + ∆Eint

The deformation energy ∆Edef is the amount of energy required to deform the individual monomer base from its equilibrium structure in the gas phase to the geometry that it acquires in the supramolecular ribbon. The interaction energy ∆Eint corresponds to the energy change when the geometrically deformed bases are associated to form the ribbon. Typically, the sum of deformation energies is one order of magnitude smaller than the interaction energy. In the present case, the deformation energies amounts to ca. 1-2 kcal/mol for an individual monomer.

RESULTS AND DISCUSSION X-ray structure analysis of N3-methylxanthine (1) A single crystal of N3-methylxanthine (1) was prepared from aqueous solution kept at 40 °C. X-ray diffraction measurements revealed the existence of a new polymorph featuring orthorhombic motif. Crystallographic and experimental details of crystal structure analysis are summarized in Table S1 in the Supporting Information. These analyses provided evidence for the existence of only one structural motif. Such a finding is very reasonable, in view of the rigid


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conformation of the starting molecule. Not surprisingly, the bond length and bond angle data analysis are the same as that of the literature structure within the error bars (Fig. 1 and Table S2), the only noticeable differences being the C4-C5 and C8-N9 distances. However, the structural motif in our new polymorph (Fig. 2a) when compared to that of FADCUI (Fig. 2b) is completely different as evidenced by their different crystal system and space group.

Figure 1. Thermal ellipsoid (ORTEP) plot of N3-methylxanthine (1) at 50% probability level.


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Figure 2. The orientation of N3-methylxanthine molecules in the crystals and their respective hydrogen bonding network: (a) new polymorph and (b) literature data (FADCUI).20 While in FADCUI structure the neighboring molecules in the supramolecular motif are coplanar, in our new polymorphic structure they adopt non-planar conformation. The reasons for such a different orientation are the markedly different H-bond pattern (Table S3) and the different π-π stacking (see Figs. S10 and S11). Moreover, the new polymorph crystallizes in a non-centrosymmetrical space group. The new polymorph is also characterized by different powder pattern (Fig. S9) indicating peaks for FADCUI structure at 2Θ = 9.7, 14.0, 14.6 and for the new polymorph at 2Θ = 16.3 and 17.4 degree, respectively. Unfortunately we have not been able so far to form single crystals suitable for XRD analysis of N3-octadecylxanthine, most likely because of its relatively high solubility if compared with N3methylxanthine.

Theoretical studies To provide a molecular understanding of xanthine self-assembly in 2D, and cast light onto the formation and stability of supramolecular structures, xanthine pre-assembled ribbons were modeled in silico. Prior to experimental investigations quantum chemical analyses were preformed, where N9-methylguanine ribbons W-shaped type and U-shaped type (Fig. S7 in SI) served as reference system. Two similar xanthine ribbon structures, i.e. the W-shaped type and the U-shaped type were optimized in both cases with increasing number of constituents, namely 4, 6, 8, 10 and 12 units long ribbons. In Figure 3 the different ribbon structures are displayed with six-units long examples, and total bonding and the average H-bond energies are presented


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in Figure 4 (and Table S4 in the SI). According to the total bonding energies neither the W nor the U ribbon arrangement are preferred exclusively in xanthine ribbons. Interestingly, bonding energies were also similar in case of W and U type of guanine assemblies, however the Wshaped structure is preferred. The higher energy in the case of the U-type guanine assembly is ascribed to unfavorable steric interaction between the CH(8) and N(9)-methyl groups (Fig. S7).

Figure 3. Representative equilibrium structures of type W- (a) and U-shaped (b) ribbons formed by N3-methylxanthine molecules, computed at the BLYP-D/TZ2P level of theory. a) The length of a vector is 1.13 nm Comparing the bonding energy terms (deformation and interaction energies; see methodological section), the total deformation energy in a guanine (G) ribbon is always slightly greater (a few kcal/mol) than in the xanthine (X) ribbon. This can be explained by the presence of the NH2 group in case of G assemblies, which converts from non-planar (in isolated guanine) to planar (in the ribbon) conformation. However, the continuously increasing total bonding energy difference seems surprising, at first sight. In a recent theoretical analysis,32c it was shown


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that such effects in guanine supramolecular structures stem from cooperativity between unidirectional hydrogen bonds caused by the charge separation in the σ-electron system. The average H-bonding energy shows very well the primary consequence of such cooperativity in guanine ribbons, i.e. the strength of a single H-bond increases as guanine ribbons become longer. At variance, the interaction between neighboring monomers remains nearly independent from the length of the ribbon in xanthine structures. These results draw attention again to the careful application of molecular mechanical simulations where such cooperativity effects are often not taken into account.

Figure 4. Calculated (BLYP-D/TZ2P level of theory) total bonding energies and average Hbonding energies (in kcal/mol) of 4, 6, 8, 10 and 12 units long optimized X and G ribbons. X – N3-methylxanthine, G – N9-methylguanine, W- and U-types of H-bonded ribbon.

STM characterization


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STM was used to probe the self-assembly behavior of N3-alkylated xanthines (1 and 2) at the solution–graphite interface. Figure 5a shows STM height image (viz. images recorded in constant-current mode) of the obtained physisorbed monolayer featuring a polycrystalline structure formed through the self-assembly of N3-methylxanthine (1) which consists of crystalline domains of hundreds of square nanometers that are stable over several hours (up to 3– 4 h). The unit cell parameters, a = (1.14 ± 0.02) nm, b = (1.73 ± 0.02) nm and α = (58 ± 2)°, lead to an area A = (1.67 ± 0.04) nm2. The unit cell contains two xanthine molecules 1. Thus, the area occupied by a single molecule of 1 corresponds to (0.84 ± 0.04) nm2. Considering the size of the unit cell, the empty space is most likely occupied by additional molecule of co-adsorbed solvent, i.e. 1,2,4-trichlorobenzene, although, owing to their highly dynamic nature, we are unable to resolve them and therefore to unambiguously assign their position and orientation in proposed 2D packing model (Fig. 5b). The supramolecular motif can be well described by the formation of a one-dimensional H-bonded ribbon involving the following pairing: the NH(1) – O(2) and NH(7) – O(6) (W-shaped ribbon). Noteworthy, observed supramolecular motif is slightly different if compared to one determined by the X-ray single crystal analysis. Not surprisingly, in case of STM measurements neighboring molecules adopt co-planar conformation, which can be explained by the molecule-HOPG interactions, which cause planarization of supramolecular motif. Interestingly, the length of the experimentally defined unit cell vector a (1.14 nm), is in good accordance with the theoretical value predicted by our DFT calculations (1.13 nm).


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Figure 5. STM height images of self-assembled supramolecular H-bonded polymers of: a) N3methylxanthine (1) and c) N3-octadecylxanthine (2) at the 1,2,4-trichlorobenzene–graphite interface. Proposed molecular packing motifs are shown in (b) and (d), respectively. (a, c) Tunneling parameters: average tunneling current (It) = 25 pA, tip bias voltage (Vt) = 400 mV.


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We then extended our studies to the self-assembly of N3-octadecylxanthine (2) molecules. The STM height image of the obtained monolayer (Fig. 5c) shows a crystalline structure consisting of ribbon-like architectures, resulting from deposition of a drop (10 µM solution) of 2 in TCB on the HOPG surface. In this 2D crystal, the octadecyl side chains are physisorbed flat on the surface and are interdigitated between adjacent supramolecular ribbons. The unit cell parameters, a = (1.14 ± 0.02) nm, b = (2.75 ± 0.02) nm and α = (83 ± 2)°, leads to an area A = (3.11 ± 0.03) nm2, where each unit cell consists of two xanthine molecules (2). Thus, the area occupied by a single molecule 2 equals to (1.55±0.03) nm2. Similarly to N3-methylxanthine, supramolecular packing motif can be described by the formation of the NH(1) – O(2) and NH(7) – O(6)H-bonds.

CONCLUSIONS In summary, we have performed an STM study on the self-assembly at the HOPG–solution interface of substituted xanthines exposing in the N3-position alkyl side chains with different length. Both molecules were found to form monomorphic 2D crystals, which are stable on the several tens of minutes time scale and exceed various hundred of square nanometers. Dramatic changes in the length of the alkyl side-chains did not influence the xanthine supramolecular packing in 2D on graphite. Both derivatives self-assembled into linear H-bonded ribbons through NH(1)–O(2) and NH(7)–O(6) pairing with two molecules in the unit cell. Interestingly, X-ray crystal structure analysis of 1 led to the detection of a new polymorph of N3-methylxanthine. This is interesting since all new polymorphic forms of biologically active compounds can feature innovative biological activities.34 Quantum chemical studies predicted the existence of ribbon structures based on xanthine molecules. The averaged single H-bond energy in these xanthine ribbons was found to be close to the H-bond energy computed for guanine assemblies. However,


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at variance with the guanine structures, the xanthine ribbons do not show a cooperative effect, i.e. they do not show an increasing stabilization per H-bond as the number of units increases.

ASSOCIATED CONTENT Supporting Information. NMR spectra, ESI data as well as X-ray powder patterns have been included in SI. This material is available free of charge via the Internet at http://pubs.acs.org. AUTHOR INFORMATION Corresponding Author *E-mail: [email protected] (G. P. Spada), [email protected] (P. Samorì) and [email protected] (L. Kovács) ACKNOWLEDGMENT This work was financially supported by ERC project SUPRAFUNCTION (GA-257305), the International Center for Frontier Research in Chemistry (icFRC), the COST Action MP0802, the HPC-EUROPA2 228398, the European Commission - Capacities Area - Research Infrastructures, OTKA 73672, the Hungarian Academy of Sciences, TÁMOP 4.2.1/B09/1/KONV-2010-0007, MIUR (Italy) in the framework of the National Interest Research Program (PRIN 2009, grant 2009N5JH4F), the European Social Fund, the Netherlands Organization for Scientific Research (NWO-CW), and the National Research School Combination - Catalysis (NRSC-C).


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ABBREVIATIONS STM (scanning tunneling microscopy), HOPG (highly oriented pyrolitic graphite), TCB (1,2,4trichlorobenzene), Bn (benzyl), C2D2Cl4 (1,2-dideutero-1,1,2,2-tetrachloroethane), C2H2Cl4 (1,1,2,2-tetrachloroethane), CHCl3 (chloroform), CH2Cl2 (dichloromethane), DMF (N,Ndimethylformamide), DMSO-d6 (hexadeuterodimethyl sulfoxide), ESI-MS (electrospray ionisation mass spectrometry), EtOAc (ethyl acetate), MeOH (methanol), AcOH (acetic acid), K2CO3 (potassium carbonate), CH3CN (acetonitrile).

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