<?xml version="1.0" encoding="ASCII"?>
<!DOCTYPE article PUBLIC "-//BEILSTEIN-INSTITUT//DTD Journal Article DTD v0.3.8 20091009//EN" "http://www.beilstein-journals.org/bjoc/content/xml/journalarticle.v038.dtd">
<article locale="en" public-id="1860-5397-6-3" publisher="Beilstein-Institut" journal="Beilstein Journal of Organic Chemistry" journal-abbreviated="Beilstein J. Org. Chem." journal-code="bjoc" issn="1860-5397" coden="BJOCBH" year="2010" volume="6" article="3" type="full-research-paper">
<author first-name="Carolin" last-name="Rether" affiliations="a1"/>
<author first-name="Wilhelm" last-name="Sicking" affiliations="a1"/>
<author first-name="Roland" last-name="Boese" affiliations="a2"/>
<author first-name="Carsten" last-name="Schmuck" email="carsten.schmuck@uni-due.de" affiliations="a1" corresponding-author="yes"/>
<affiliation id="a1">Institute of Organic Chemistry, Faculty of Chemistry, University of Duisburg-Essen, Universit&#228;tsstra&#223;e 7, 45141 Essen, Germany</affiliation>
<affiliation id="a2">Institute of Inorganic Chemistry, Faculty of Chemistry, University of Duisburg-Essen, Universit&#228;tsstra&#223;e 7, 45141 Essen, Germany</affiliation>
<editor first-name="Christoph" middle-names="A" last-name="Schalley" role="guest-editor"/>
<submission-date day="28" month="10" year="2009"/>
<acceptance-date day="4" month="1" year="2010"/>
<publication-date day="14" month="1" year="2010"/>
<title>
<chunk>Self-association of an indole based guanidinium-carboxylate-zwitterion: formation of stable dimers in solution and the solid state</chunk>
</title>
<keyword>
<chunk>dimerisation</chunk>
</keyword>
<keyword>
<chunk>molecular recognition</chunk>
</keyword>
<keyword>
<chunk>self-assembly</chunk>
</keyword>
<keyword>
<chunk>supramolecular chemistry</chunk>
</keyword>
<keyword>
<chunk>zwitterions</chunk>
</keyword>
<abstract-section>
<paragraph>
<chunk>The indole based zwitterion </chunk>
<chunk bold="yes">2</chunk>
<chunk> forms stable dimers held together by H-bond assisted ion pairs. Dimerisation was confirmed in the solid state and studied in solution using dilution NMR experiments. Even though zwitterion </chunk>
<chunk bold="yes">2</chunk>
<chunk> forms very stable dimers even in DMSO, their stability is lower than of an analogous pyrrole based zwitterion </chunk>
<chunk bold="yes">1</chunk>
<chunk>. As revealed by the X-ray crystal structure the two binding sites in </chunk>
<chunk bold="yes">2</chunk>
<chunk> cannot be planar due to steric interactions between the guanidinium group and a neighbouring aromatic CH. Hence the guanidinium moiety is twisted out of planarity from the rest of the molecule forcing the two monomers in dimer </chunk>
<chunk bold="yes">2</chunk>
<chunk>&#183;</chunk>
<chunk bold="yes">2</chunk>
<chunk> to interact in a non-ideal orientation. Furthermore, the acidity of the NHs is lower than in </chunk>
<chunk bold="yes">1</chunk>
<chunk> (as determined by UV-pH-titration) also leading to less efficient binding interactions.</chunk>
</paragraph>
</abstract-section>
<abstract-graphic public-id="1860-5397-6-3-graphical-abstract"/>
<external-link type="doi" public-id="10.3762/bjoc.6.3"/>
<section>
<title>
<chunk>Introduction</chunk>
</title>
<paragraph>
<chunk>The vast majority of supramolecular self-assembling systems known so far form stable assemblies only in non polar solvents such as chloroform, as they mainly rely on hydrogen bonds </chunk>
<link target="b1"/>
<link target="b2"/>
<link target="b3"/>
<link target="b4"/>
<chunk>. The design of self-complementary molecules that assemble even in polar solvents is still a challenging task despite all the progress made in this field in recent years. The use of metal-ligand coordination and hydrophobic interactions has proven especially useful in this context </chunk>
<link target="b5"/>
<link target="b6"/>
<link target="b7"/>
<link target="b8"/>
<link target="b9"/>
<link target="b10"/>
<link target="b11"/>
<chunk>. We are interested in developing self-complementary zwitterions that from stable aggregates in polar solution based on H-bond assisted ion pair formation. A few years ago we introduced the guanidiniocarbonyl pyrrole carboxylate zwitterion </chunk>
<chunk bold="yes">1</chunk>
<chunk> which forms extremely stable dimers not only in the solid state but also in polar solution </chunk>
<link target="b12"/>
<chunk>. In DMSO the stability is too large to evaluate with an estimated association constant of </chunk>
<chunk italic="yes">K</chunk>
<chunk subscript="yes">ass</chunk>
<chunk>&gt; 10</chunk>
<chunk superscript="yes">10</chunk>
<chunk> M</chunk>
<chunk superscript="yes">&#8722;1</chunk>
<chunk>. Even in water dimerisation still takes place (</chunk>
<chunk italic="yes">K</chunk>
<chunk subscript="yes">ass</chunk>
<chunk> = 170 M</chunk>
<chunk superscript="yes">&#8722;1</chunk>
<chunk>) </chunk>
<link target="b13"/>
<chunk>. The stability of the dimer </chunk>
<chunk bold="yes">1</chunk>
<chunk>&#183;</chunk>
<chunk bold="yes">1</chunk>
<chunk> is significantly larger than the simple Coulomb-interactions of point charges, suggesting that indeed the formation of directed, H-bond assisted salt-bridges is crucial. Zwitterion </chunk>
<chunk bold="yes">1</chunk>
<chunk> combines in a near perfect fit geometrical self-complementarity with the possibility to form two salt-bridges assisted by a network of six H-bonds. The superior stability of </chunk>
<chunk bold="yes">1</chunk>
<chunk>&#183;</chunk>
<chunk bold="yes">1</chunk>
<chunk> compared to analogous zwitterions based on other aromatic scaffolds such as benzene or furan instead of pyrrole or with an amidinium cation instead of a guanidinium cation was also confirmed by DFT calculations </chunk>
<link target="b14"/>
<chunk>. Zwitterion </chunk>
<chunk bold="yes">1</chunk>
<chunk> has thus found widespread application in the formation of self-assembled nanostructures such as vesicles or supramolecular polymers </chunk>
<link target="b15"/>
<link target="b16"/>
<link target="b17"/>
<chunk>.</chunk>
</paragraph>
<paragraph>
<chunk>We have now synthesized and studied the indole based zwitterion </chunk>
<chunk bold="yes">2</chunk>
<chunk>, a close analogue of </chunk>
<chunk bold="yes">1</chunk>
<chunk>. In </chunk>
<chunk bold="yes">2</chunk>
<chunk> the guanidinium group is not acylated as in </chunk>
<chunk bold="yes">1</chunk>
<chunk> but conjugated to an aromatic ring. Compared to the parent guanidinium cation, in both cases the acidity of the NHs is significantly increased due to the &#8722;M effect of the carbonyl group or the aromatic ring, respectively, thus facilitating the formation of H-bond assisted ion pairs </chunk>
<link target="b18"/>
<link target="b19"/>
<chunk>. Apart from the increased acidity of the NHs in </chunk>
<chunk bold="yes">1</chunk>
<chunk> and </chunk>
<chunk bold="yes">2</chunk>
<chunk>, also the geometric shape of </chunk>
<chunk bold="yes">2</chunk>
<chunk> is very similar to </chunk>
<chunk bold="yes">1</chunk>
<chunk> at least based on the inspection of simple models. It was therefore expected that the new zwitterion </chunk>
<chunk bold="yes">2</chunk>
<chunk> might form dimers with similar stability to </chunk>
<chunk bold="yes">1</chunk>
<chunk>, increasing our repertoire of self-complementary binding motifs that efficiently self-assemble in polar solution. And indeed we could show that zwitterion </chunk>
<chunk bold="yes">2</chunk>
<chunk> is able to form highly stable dimers in polar solution and in the solid state as well. However, dimer </chunk>
<chunk bold="yes">2</chunk>
<chunk>&#183;</chunk>
<chunk bold="yes">2</chunk>
<chunk> is significantly less stable than dimer </chunk>
<chunk bold="yes">1</chunk>
<chunk>&#183;</chunk>
<chunk bold="yes">1</chunk>
<chunk>. Possible reasons for this decreased stability are discussed.</chunk>
</paragraph>
<float target="f1"/>
</section>
<section>
<title>
<chunk>Results and Discussion</chunk>
</title>
<paragraph>
<chunk>The indole zwitterion </chunk>
<chunk bold="yes">2</chunk>
<chunk> was prepared by a four-step synthesis (</chunk>
<link target="s1"/>
<chunk>). Commercially available 7-nitro-1</chunk>
<chunk italic="yes">H</chunk>
<chunk>-indole-2-carboxylate </chunk>
<chunk bold="yes">3</chunk>
<chunk> was reduced by reaction with hydrogen in the presence of Pd/C to provide the amine </chunk>
<chunk bold="yes">4</chunk>
<chunk> in a yield of 98%. For the next stept, first, thiourea was </chunk>
<chunk italic="yes">N</chunk>
<chunk>-Boc-protected at both amino-functions following a literature procedure </chunk>
<link target="b20"/>
<chunk>. Thiourea was deprotonated with sodium hydride and afterwards reacted with di-</chunk>
<chunk italic="yes">tert</chunk>
<chunk>-butyl dicarbonate to give the di-Boc-protected thiourea </chunk>
<chunk bold="yes">5</chunk>
<chunk> in 79% yield. The di-Boc-protected thiourea </chunk>
<chunk bold="yes">5</chunk>
<chunk> was then reacted with the amine </chunk>
<chunk bold="yes">4</chunk>
<chunk> in the presence of Mukaiyama&#8217;s reagent </chunk>
<link target="b21"/>
<chunk> and triethylamine as a base, which provided </chunk>
<chunk bold="yes">6</chunk>
<chunk> in a yield of 71% </chunk>
<link target="b22"/>
<chunk>. Deprotection of the two Boc-groups was achieved by treatment with TFA and the guanidinium salt </chunk>
<chunk bold="yes">7</chunk>
<chunk> was obtained quantitatively. In the last reaction step the ethyl ester in </chunk>
<chunk bold="yes">7</chunk>
<chunk> was hydrolysed with lithium hydroxide in a THF/water mixture (THF/water = 4/1). Zwitterion </chunk>
<chunk bold="yes">2</chunk>
<chunk> was then obtained after adjustment of the pH to 6 with 1M HCl in a yield of 84% as a light brown crystalline solid.</chunk>
</paragraph>
<float target="s1"/>
<paragraph>
<chunk>For the spectroscopic characterisation and as a reference compound also the picrate salt of </chunk>
<chunk bold="yes">2</chunk>
<chunk> was prepared by treating a methanolic solution of </chunk>
<chunk bold="yes">2</chunk>
<chunk> with picric acid (</chunk>
<link target="s2"/>
<chunk>). The picrate salt </chunk>
<chunk bold="yes">2</chunk>
<chunk>&#183;</chunk>
<chunk bold="yes">H</chunk>
<chunk bold="yes" superscript="yes">+</chunk>
<chunk> was isolated in form of a yellow, crystalline solid in 89% yield.</chunk>
</paragraph>
<float target="s2"/>
<paragraph>
<chunk>While the picrate salt </chunk>
<chunk bold="yes">2</chunk>
<chunk>&#183;</chunk>
<chunk bold="yes">H</chunk>
<chunk bold="yes" superscript="yes">+</chunk>
<chunk> is moderately soluble in methanol and water, the zwitterionic form of </chunk>
<chunk bold="yes">2</chunk>
<chunk> is virtually insoluble in all solvents except DMSO and DMSO-containing solvent mixtures, such as DMSO&#8211;MeOH or DMSO&#8211;CHCl</chunk>
<chunk subscript="yes">3</chunk>
<chunk>, so that the dimerisation studies in solution were limited to DMSO. The </chunk>
<chunk superscript="yes">1</chunk>
<chunk>H NMR spectrum (</chunk>
<link target="f2"/>
<chunk>) of the protonated zwitterion </chunk>
<chunk bold="yes">2</chunk>
<chunk>&#183;</chunk>
<chunk bold="yes">H</chunk>
<chunk bold="yes" superscript="yes">+</chunk>
<chunk> (picrate salt in [D</chunk>
<chunk subscript="yes">6</chunk>
<chunk>]DMSO) shows the signals expected for an aromatic guanidinium cation </chunk>
<link target="b23"/>
<chunk>. The four guanidinium NH</chunk>
<chunk subscript="yes">2</chunk>
<chunk> protons have a chemical shift of &#948; = 7.19, whereas the NH of the guanidinium group shows up at &#948; = 9.21 and the indole NH at &#948; = 12.06. The signals were assigned based on 2D NMR experiments.</chunk>
</paragraph>
<float target="f2"/>
<paragraph>
<chunk>The </chunk>
<chunk superscript="yes">1</chunk>
<chunk>H NMR spectrum of zwitterion </chunk>
<chunk bold="yes">2</chunk>
<chunk> is significantly different. Especially the NH signals are shifted downfield. The indole NH is shifted downfield by 0.2 ppm and appears at &#948; = 12.26 and the four guanidinium NH</chunk>
<chunk subscript="yes">2</chunk>
<chunk> are shifted to &#948; = 8.00 ppm. Most significantly the NH of the guanidinium group is shifted downfield by nearly 4 ppm from &#948; = 9.21 to &#948; = 13.07 pm. A similar dramatic downfield shift was observed for the guanidinium amide NH of zwitterion </chunk>
<chunk bold="yes">1</chunk>
<chunk> upon dimer formation </chunk>
<link target="b12"/>
<link target="b13"/>
<chunk>.</chunk>
</paragraph>
<paragraph>
<chunk>Hence, the downfield shifts in the spectrum of zwitterion </chunk>
<chunk bold="yes">2</chunk>
<chunk> relative to the protonated form </chunk>
<chunk bold="yes">2</chunk>
<chunk>&#183;</chunk>
<chunk bold="yes">H</chunk>
<chunk bold="yes" superscript="yes">+</chunk>
<chunk> are most likely also due to the formation of a H-bonded ion pair which can only take place intermolecularly due to the rigidity of </chunk>
<chunk bold="yes">2</chunk>
<chunk>. The similarity of the shift changes with those of zwitterion </chunk>
<chunk bold="yes">1</chunk>
<chunk> suggests that dimerisation takes place.</chunk>
</paragraph>
<paragraph>
<chunk>The stability of these dimers was determined by an NMR dilution experiment. To obtain the binding constant for the dimerisation, we studied the concentration dependence of the </chunk>
<chunk superscript="yes">1</chunk>
<chunk>H NMR spectrum of </chunk>
<chunk bold="yes">2</chunk>
<chunk> in a concentration range from 0.25 to 100 mM in [D</chunk>
<chunk subscript="yes">6</chunk>
<chunk>]DMSO. The </chunk>
<chunk superscript="yes">1</chunk>
<chunk>H NMR shifts are concentration-dependent as expected for a dimerisation (</chunk>
<link target="f3"/>
<chunk>).</chunk>
</paragraph>
<float target="f3"/>
<paragraph>
<chunk>As the binding isotherms show (</chunk>
<link target="f4"/>
<chunk>), even at concentrations &gt; 10 mM dimerisation is mostly complete. This suggests very large stability of the dimers even in DMSO. In agreement with this, a quantitative data analysis provided a dimerisation constant </chunk>
<chunk italic="yes">K</chunk>
<chunk subscript="yes">ass</chunk>
<chunk> &gt; 10</chunk>
<chunk superscript="yes">5</chunk>
<chunk> M</chunk>
<chunk superscript="yes">&#8722;1</chunk>
<chunk>, too large to be measured accurately by NMR techniques. Similar observations were made earlier for zwitterion </chunk>
<chunk bold="yes">1</chunk>
<chunk>. However, for </chunk>
<chunk bold="yes">1</chunk>
<chunk> the estimated stability in DMSO was even higher. Interestingly, at higher concentrations the formation of larger aggregates also seems to occur. For example, the signal for the guanidinium NH</chunk>
<chunk subscript="yes">2</chunk>
<chunk> protons shows a second shift change at concentrations &gt; 20 mM. First, the signal is shifted to lower field due to the dimerisation, and then a smaller upfield shift is observed (</chunk>
<link target="f5"/>
<chunk>). This could be indicative of a second association process in which the dimers </chunk>
<chunk bold="yes">2</chunk>
<chunk>&#183;</chunk>
<chunk bold="yes">2</chunk>
<chunk> start to interact at concentration &gt; ca. 15 mM. However, the exact nature of these larger aggregates is unclear at the moment.</chunk>
</paragraph>
<float target="f4"/>
<float target="f5"/>
<paragraph>
<chunk>We were able to determine the solid state structure of </chunk>
<chunk bold="yes">2</chunk>
<chunk>. X-ray quality crystals of compound </chunk>
<chunk bold="yes">2</chunk>
<chunk> were obtained by slow evaporation of a dimethyl sulfoxide solution. X-ray crystallography confirmed the formation of head-to-tail dimers, which are held together by the formation of two salt bridges assisted by a network of six hydrogen bonds (</chunk>
<link target="f6"/>
<chunk>). The hydrogen bond distances between the aromatic N</chunk>
<chunk superscript="yes">...</chunk>
<chunk>O (2.703 &#197;), the guanidinium N</chunk>
<chunk superscript="yes">...</chunk>
<chunk>O (2.942 &#197;) and the indole N</chunk>
<chunk superscript="yes">...</chunk>
<chunk>O (2.935 &#197;) are all rather short.</chunk>
</paragraph>
<float target="f6"/>
<paragraph>
<chunk>However, the distances are larger than the corresponding distances in dimer </chunk>
<chunk bold="yes">1</chunk>
<chunk>&#183;</chunk>
<chunk bold="yes">1</chunk>
<chunk>: the amide N</chunk>
<chunk superscript="yes">...</chunk>
<chunk>O (2.679 &#197;), the guanidinium N</chunk>
<chunk superscript="yes">...</chunk>
<chunk>O (2.854 &#197;), and the pyrrole N</chunk>
<chunk superscript="yes">...</chunk>
<chunk>O (2.731 &#197;) distances in dimer </chunk>
<chunk bold="yes">1</chunk>
<chunk>&#183;</chunk>
<chunk bold="yes">1</chunk>
<chunk> are even shorter than in dimer </chunk>
<chunk bold="yes">2</chunk>
<chunk>&#183;</chunk>
<chunk bold="yes">2</chunk>
<chunk>. The main difference between </chunk>
<chunk bold="yes">1</chunk>
<chunk>&#183;</chunk>
<chunk bold="yes">1</chunk>
<chunk> and </chunk>
<chunk bold="yes">2</chunk>
<chunk>&#183;</chunk>
<chunk bold="yes">2</chunk>
<chunk> is however that the dimers </chunk>
<chunk bold="yes">2</chunk>
<chunk>&#183;</chunk>
<chunk bold="yes">2</chunk>
<chunk> are not completely planar. Zwitterion </chunk>
<chunk bold="yes">2</chunk>
<chunk> itself is not planar, but the guanidinium group is twisted out of planarity by 48.75&#176; (</chunk>
<link target="f7"/>
<chunk>). Also the two molecules within the dimer are not within the same plane but slightly offset (by 1.050 pm). This is a consequence of the twisted guanidinium group. To allow optimal interaction of the carboxylate with the NHs of the guanidinium group the second molecule has to be a little bit out of plane of the first, which results in longer hydrogen bond distances for the guanidinium N</chunk>
<chunk superscript="yes">...</chunk>
<chunk>O and the indole N</chunk>
<chunk superscript="yes">...</chunk>
<chunk>O (</chunk>
<link target="f7"/>
<chunk>) and less favorable H-bond angles within the dimer (164.78&#176; for the outer and 148.97&#176; for the inner guanidinium NH-bonds and 141.37&#176; for the indole NH-bond).</chunk>
</paragraph>
<float target="f7"/>
<paragraph>
<chunk>Within the crystal lattice the molecules of </chunk>
<chunk bold="yes">2</chunk>
<chunk> are arranged in parallel planes held together most likely by aromatic stacking interactions: The centroid-centroid distance of two indoles is 3.636 &#197;. Furthermore, the &#8220;backside&#8221; of the out of plane twisted guanidinium cation also interacts with the carboxylate group one plane below (</chunk>
<link target="f8"/>
<chunk>). The corresponding hydrogen bond distances are 2.790 &#197; and 2.922 &#197;, respectively, and are therefore similar to the hydrogen bond distances within the dimer.</chunk>
</paragraph>
<float target="f8"/>
<paragraph>
<chunk>The main difference between the pyrrole zwitterion </chunk>
<chunk bold="yes">1</chunk>
<chunk> and the indole zwitterion </chunk>
<chunk bold="yes">2</chunk>
<chunk> is hence the non-planar, twisted structure of the latter. This is most likely due to steric interactions with the neighboring aromatic C-H bond (</chunk>
<link target="s3"/>
<chunk>). In the pyrrole zwitterion </chunk>
<chunk bold="yes">1</chunk>
<chunk> this position is occupied by the carbonyl oxygen which forms an H-bond to the guanidinium moiety and thus actually helps to keep the molecule planar. This amide group in </chunk>
<chunk bold="yes">1</chunk>
<chunk> is replaced by the aromatic benzene ring in </chunk>
<chunk bold="yes">2</chunk>
<chunk>, thereby replacing an attractive H-bond with a repulsive steric interaction.</chunk>
</paragraph>
<float target="s3"/>
<paragraph>
<chunk>This twisted, non-planar structure of dimer </chunk>
<chunk bold="yes">2</chunk>
<chunk>&#183;</chunk>
<chunk bold="yes">2</chunk>
<chunk> is also reproduced by DFT calculations. Geometry optimizations were performed with the Gaussian03 program package using the M05-2X/6-311+G** basis set </chunk>
<link target="b24"/>
<chunk>. In all calculations DMSO as a solvent was included (CPCM, </chunk>
<inline-float target="i1"/>
<chunk> = 48) </chunk>
<link target="b25"/>
<link target="b26"/>
<chunk>. The optimization revealed the twisted dimer, which fits quite well to the X-ray structure. Though the calculated structure of dimer </chunk>
<chunk bold="yes">2</chunk>
<chunk>&#183;</chunk>
<chunk bold="yes">2</chunk>
<chunk> is not completely symmetric like the X-ray structure, all the hydrogen bond distances, as well as the torsion angle match pretty well (</chunk>
<link target="f9"/>
<chunk>). In the solid state structure, the hydrogen bond distances between the aromatic N</chunk>
<chunk superscript="yes">...</chunk>
<chunk>O (2.703 &#197;), the guanidinium N</chunk>
<chunk superscript="yes">...</chunk>
<chunk>O (2.942 &#197;) and the indole N</chunk>
<chunk superscript="yes">...</chunk>
<chunk>O (2.935 &#197;) are quite short, as mentioned above. The torsion angle between the aromatic scaffold and the guanidinium group is 48.75&#176;. The DFT calculation give an average dihedral angle of 53.57&#176; and lead to the following averaged hydrogen bond distances: 2.738 &#197; (aromatic N</chunk>
<chunk superscript="yes">...</chunk>
<chunk>O), 2.931 &#197; (guanidinium N</chunk>
<chunk superscript="yes">...</chunk>
<chunk>O) and 2.850 (indole N</chunk>
<chunk superscript="yes">...</chunk>
<chunk>O).</chunk>
</paragraph>
<float target="f9"/>
<paragraph>
<chunk>Hence, the good agreement of the observed structure in the solid state and the calculated structure obtained from DFT calculations suggests that the level of theory used in these calculations describes the dimer with sufficient accuracy. We therefore also calculated the enthalpy values for the dimerisation process of zwitterion </chunk>
<chunk bold="yes">2</chunk>
<chunk> and of </chunk>
<chunk bold="yes">1</chunk>
<chunk>, respectively, as the experimental values were too large to measure them accurately in DMSO (as mentioned above). The calculated stability of dimer </chunk>
<chunk bold="yes">2</chunk>
<chunk>&#183;</chunk>
<chunk bold="yes">2</chunk>
<chunk> is significantly lower than for the pyrrole zwitterion&#160;</chunk>
<chunk bold="yes">1</chunk>
<chunk>: &#916;H &#8722;54 kJ/mol and &#8722;85 kJ/mol, respectively. Hence, even though the bonding interactions in dimer </chunk>
<chunk bold="yes">1</chunk>
<chunk>&#183;</chunk>
<chunk bold="yes">1</chunk>
<chunk> and </chunk>
<chunk bold="yes">2</chunk>
<chunk>&#183;</chunk>
<chunk bold="yes">2</chunk>
<chunk> are temptingly similar the latter is only two third as stable as the former.</chunk>
</paragraph>
<paragraph>
<chunk>This difference in stability is most likely due to the non-ideal geometry of the H-bonded ion pairs and reflects the importance of planarity in zwitterion </chunk>
<chunk bold="yes">1</chunk>
<chunk> for an effective dimerisation. Due to the twisted guanidinium groups in </chunk>
<chunk bold="yes">2</chunk>
<chunk> the two monomers in dimer </chunk>
<chunk bold="yes">2</chunk>
<chunk>&#183;</chunk>
<chunk bold="yes">2</chunk>
<chunk> are not in-plane, which leads to less efficient interactions. Also as mentioned above, the guanidinium group in zwitterion </chunk>
<chunk bold="yes">2</chunk>
<chunk> is directly attached to the aromatic indole scaffold, whereas it is acylated in </chunk>
<chunk bold="yes">1</chunk>
<chunk>. Though the overall structure looks similar, this replaces an attractive H-bond which also help to planarize zwitterion </chunk>
<chunk bold="yes">1</chunk>
<chunk> by a repulsive steric interaction in </chunk>
<chunk bold="yes">2</chunk>
<chunk>, which is responsible for its non-planar structure.</chunk>
</paragraph>
<paragraph>
<chunk>Furthermore, the p</chunk>
<chunk italic="yes">K</chunk>
<chunk subscript="yes">a</chunk>
<chunk> value of the two guanidinium groups as well is an important factor for the stability of the dimers. While simple guanidinium cations as in arginine have a p</chunk>
<chunk italic="yes">K</chunk>
<chunk subscript="yes">a</chunk>
<chunk> of 13.5, the p</chunk>
<chunk italic="yes">K</chunk>
<chunk subscript="yes">a</chunk>
<chunk> of the acylguanidinium group in </chunk>
<chunk bold="yes">1</chunk>
<chunk> was measured by UV-pH-titration to be 6.3 &#177; 0.1. Analysis of the pH dependent UV spectral changes was performed using the Specfit/32 software program from Spectrum Software Associates. However, the p</chunk>
<chunk italic="yes">K</chunk>
<chunk subscript="yes">a</chunk>
<chunk> of the guanidinium group in </chunk>
<chunk bold="yes">2</chunk>
<chunk> also obtained from a UV-pH-titration is significantly larger with p</chunk>
<chunk italic="yes">K</chunk>
<chunk subscript="yes">a</chunk>
<chunk> = 10.6 &#177; 0.1. Hence, the lower acidity of the NHs in </chunk>
<chunk bold="yes">2</chunk>
<chunk> is a second important factor leading to the overall reduced stability of dimer </chunk>
<chunk bold="yes">2</chunk>
<chunk>&#183;</chunk>
<chunk bold="yes">2</chunk>
<chunk>.</chunk>
</paragraph>
</section>
<section>
<title>
<chunk>Conclusion</chunk>
</title>
<paragraph>
<chunk>In conclusion, we have presented the synthesis of a new indole based zwitterion </chunk>
<chunk bold="yes">2</chunk>
<chunk>, a close analogue of the 5-(guanidiniocarbonyl)-1</chunk>
<chunk italic="yes">H</chunk>
<chunk>-pyrrole-2-carboxylate (</chunk>
<chunk bold="yes">1</chunk>
<chunk>) which we recently introduced as one of the most stable self-complementary simple molecules known so far. Both dimers rely on the same intermolecular interactions, two salt-bridges assisted by a very similar network of six H-bonds. We could show here that zwitterion </chunk>
<chunk bold="yes">2</chunk>
<chunk> also self-assembles into stable dimers in the solid state and also solution (</chunk>
<chunk italic="yes">K</chunk>
<chunk subscript="yes">ass</chunk>
<chunk> &gt; 10</chunk>
<chunk superscript="yes">5</chunk>
<chunk> M</chunk>
<chunk superscript="yes">&#8722;1</chunk>
<chunk> in DMSO). However, DFT calculations suggest that the dimers are significantly less stable than dimer </chunk>
<chunk bold="yes">1</chunk>
<chunk>&#183;</chunk>
<chunk bold="yes">1</chunk>
<chunk> despite the overall similarity of the binding interactions. The calculated dimerisation enthalpy for dimer </chunk>
<chunk bold="yes">2</chunk>
<chunk>&#183;</chunk>
<chunk bold="yes">2</chunk>
<chunk> is only 66% of that for dimer </chunk>
<chunk bold="yes">1</chunk>
<chunk>&#183;</chunk>
<chunk bold="yes">1</chunk>
<chunk>. This is most likely due to two reasons. As the solid state structure shows, the two binding sites in </chunk>
<chunk bold="yes">2</chunk>
<chunk>&#183;</chunk>
<chunk bold="yes">2</chunk>
<chunk> are not coplanar, but the guanidinium moiety is twisted out of plane of the aromatic ring. This forces the two zwitterions in the dimer also to be out of plane leading to less efficient interactions between them. Furthermore, the NHs in </chunk>
<chunk bold="yes">2</chunk>
<chunk> are significantly less acidic than in </chunk>
<chunk bold="yes">1</chunk>
<chunk> which also reduces the stability of H-bonded ion pairs. Hence, geometric as well as electronic fit is the important factor controlling the stability of aggregates obtained from such self-complementary molecules. Nevertheless, zwitterion </chunk>
<chunk bold="yes">2</chunk>
<chunk> is an efficient self-assembling molecule. This indole guanidinium cation might also be an interesting binding motif for the recognition of oxoanions by indole based receptors </chunk>
<link target="b27"/>
<link target="b28"/>
<link target="b29"/>
<chunk>, similar to our guanidiniocarbonyl pyrrole cation </chunk>
<link target="b30"/>
<link target="b31"/>
<link target="b32"/>
<chunk>.</chunk>
</paragraph>
</section>
<section>
<title>
<chunk>Experimental</chunk>
</title>
<paragraph>
<chunk bold="yes">General Remarks:</chunk>
<chunk> Solvents were dried and distilled before use. The starting materials and reagents were used as obtained from Aldrich or Fluka. </chunk>
<chunk superscript="yes">1</chunk>
<chunk>H and </chunk>
<chunk superscript="yes">13</chunk>
<chunk>C NMR spectra were recorded with a Bruker Avance 400 spectrometer. The chemical shifts are reported relative to the deuterated solvents. The ESI-mass spectra were recorded with a Finnigan MAT 900 S spectrometer. IR spectra were recorded by measuring the Attenuated Total Reflectance (ATR). Melting points are not corrected. The pH values were measured with a Knick pH meter 766 Calimatic at 25 &#176;C. UV spectra were measured in 10 mm rectangular cells with a Jasco V660 spectrometer.</chunk>
</paragraph>
<paragraph>
<chunk bold="yes">Ethyl 7-amino-1</chunk>
<chunk bold="yes" italic="yes">H</chunk>
<chunk bold="yes">-indole-2-carboxylate (4):</chunk>
<chunk> A mixture of ethyl 7-nitro-1</chunk>
<chunk italic="yes">H</chunk>
<chunk>-indole-2-carboxylate (</chunk>
<chunk bold="yes">3</chunk>
<chunk>; 200 mg, 0.85 mmol) and Pd/C (20&#160;mg) in methanol (40 mL) was hydrogenated at ambient temperature for 1.5 h. The mixture was filtered over Celite to remove Pd/C, and the solvent was evaporated to give the desired product </chunk>
<chunk bold="yes">4</chunk>
<chunk> (170&#160;mg, 0.83&#160;mmol, 98%) as a colourless solid: mp 146 &#176;C; </chunk>
<chunk superscript="yes">1</chunk>
<chunk>H NMR (400 MHz, [D</chunk>
<chunk subscript="yes">6</chunk>
<chunk>]DMSO, 25 &#176;C): &#948; = 1.34 (t, 3H), 4.34 (q, 2H), 5.38 (s, 2H), 6.41 (dd, 1H), 6.78-6.86 (m, 2H), 7.02 (d, 1H), 11.40 (bs, 1H) ppm; </chunk>
<chunk superscript="yes">13</chunk>
<chunk>C NMR (100 MHz, [D</chunk>
<chunk subscript="yes">6</chunk>
<chunk>]DMSO, 25 &#176;C): &#948; = 14.3, 60.3, 106.5, 108.1, 109.5, 121.5, 126.2, 127.3, 127.6, 134.6, 161.5; IR (KBr): &#957; = 3329 (s), 2996 (w), 2939 (w), 1668 (s), 1250 (s), 1215(s) cm</chunk>
<chunk superscript="yes">&#8722;1</chunk>
<chunk>; HR-MS (ESI) calcd for [M+H]</chunk>
<chunk superscript="yes">+</chunk>
<chunk>: 205.0972; found 205.0979.</chunk>
</paragraph>
<paragraph>
<chunk bold="yes" italic="yes">N</chunk>
<chunk bold="yes">,</chunk>
<chunk bold="yes" italic="yes">N</chunk>
<chunk bold="yes">&#8217;-Di-(</chunk>
<chunk bold="yes" italic="yes">tert</chunk>
<chunk bold="yes">-butoxycarbonyl)thiourea (5):</chunk>
<chunk> To a stirred solution of thiourea (570 mg, 7.50 mmol) in dry tetrahydrofuran (150 mL) sodium hydride (1.35 g, 33.80 mmol, 60% in mineral oil) was added under argon atmosphere at 0 &#176;C (ice bath). After 5 min the ice bath was removed and the mixture was stirred for additional 10 min at ambient temperature. The mixture was cooled to 0 &#176;C again and di-</chunk>
<chunk italic="yes">tert</chunk>
<chunk>-butyl dicarbonate (3.60 g, 16.50 mmol) was added. After 40 min of stirring at 0 &#176;C the ice bath was removed and the mixture was stirred for additional 3 h at ambient temperature. The reaction was quenched by adding an aqueous saturated solution of NaHCO</chunk>
<chunk subscript="yes">3</chunk>
<chunk> (10 mL). Water (200 mL) was added and the reaction mixture was extracted with ethyl acetate (3 &#215; 75 mL). The collected organic layers were dried over MgSO</chunk>
<chunk subscript="yes">4</chunk>
<chunk>, filtered and evaporated to dryness. The white solid was purified by flash column chromatography on silica gel (hexane/ethyl acetate&#160;= 1&#160;:&#160;1 + 0.5% triethylamine) to give </chunk>
<chunk italic="yes">N</chunk>
<chunk>,</chunk>
<chunk italic="yes">N</chunk>
<chunk>&#8217;-di-(</chunk>
<chunk italic="yes">tert</chunk>
<chunk>-butoxycarbonyl)thiourea (</chunk>
<chunk bold="yes">5</chunk>
<chunk>, 1.63&#160;g, 5.92&#160;mmol, 79%) as a colourless solid: mp 130 &#176;C; </chunk>
<chunk superscript="yes">1</chunk>
<chunk>H NMR (400 MHz, [D</chunk>
<chunk subscript="yes">6</chunk>
<chunk>]DMSO, 25 &#176;C): &#948; = 1.44 (s, 9H), 1.45 (s, 9H), 8.96 (s, 1H), 9.14 (s, 1H) ppm; </chunk>
<chunk superscript="yes">13</chunk>
<chunk>C NMR (100 MHz, [D</chunk>
<chunk subscript="yes">6</chunk>
<chunk>]DMSO, 25 &#176;C): &#948; = 27.6, 82.5, 150.5, 178.7; IR (KBr): &#957; = 3160 (s), 2987 (m), 2933 (m), 1767 (m), 1718 (m), 1128 (s) cm</chunk>
<chunk superscript="yes">&#8722;1</chunk>
<chunk>; HR-MS (ESI) calcd for [M+H]</chunk>
<chunk superscript="yes">+</chunk>
<chunk>: 277.1217; found 277.1056.</chunk>
</paragraph>
<paragraph>
<chunk bold="yes">Ethyl 7-{</chunk>
<chunk bold="yes" italic="yes">N</chunk>
<chunk bold="yes">,</chunk>
<chunk bold="yes" italic="yes">N</chunk>
<chunk bold="yes">&#8217;-bis-[</chunk>
<chunk bold="yes" italic="yes">tert</chunk>
<chunk bold="yes">-(butoxycarbonyl)guanidino]}-1</chunk>
<chunk bold="yes" italic="yes">H</chunk>
<chunk bold="yes">-indole-2-carboxylate (6):</chunk>
<chunk> To a solution of ethyl 7-amino-1</chunk>
<chunk italic="yes">H</chunk>
<chunk>-indole-2-carboxylate (</chunk>
<chunk bold="yes">4</chunk>
<chunk>, 130 mg, 0.65 mmol), </chunk>
<chunk italic="yes">N</chunk>
<chunk>,</chunk>
<chunk italic="yes">N</chunk>
<chunk>&#8217;-di-(</chunk>
<chunk italic="yes">tert</chunk>
<chunk>-butoxycarbonyl)thiourea (</chunk>
<chunk bold="yes">5</chunk>
<chunk>, 185 mg, 0.65 mmol) and triethylamine (0.35 mL, 2.44 mmol) in dry dichloromethane (30 mL) was added 2-chloro-1-methyl-pyridinium iodide (297 mg, 1.14 mmol) at 0&#176; C and the mixture was stirred for 30 min. The ice bath was removed and the reaction mixture was stirred at ambient temperature for 24 h. The solvent was removed under reduced pressure, and the residue was purified by flash column chromatography on silica gel (ethyl acetate/hexane = 2:3) to give </chunk>
<chunk bold="yes">6</chunk>
<chunk> (206&#160;mg, 0.46&#160;mmol, 71%) as a colourless solid: mp 144 &#176;C; </chunk>
<chunk superscript="yes">1</chunk>
<chunk>H NMR (400 MHz, [D</chunk>
<chunk subscript="yes">6</chunk>
<chunk>]DMSO, 25 &#176;C): &#948; = 1.28 (s, 9H), 1.34 (t, 3H), 1.54 (s, 9H), 4.36 (q, 2H), 7.09 (t, 1H), 7.20 (d, 2H), 7.60 (d, 1H), 9.73 (s, 1H), 11.56 (bs, 1H), 11.95 (bs, 1H) ppm; </chunk>
<chunk superscript="yes">13</chunk>
<chunk>C NMR (100 MHz, [D</chunk>
<chunk subscript="yes">6</chunk>
<chunk>]DMSO, 25 &#176;C): &#948; = 14.3, 27.8, 27.8, 60.5, 78.4, 82.9, 108.4, 120.2, 120.9, 121.8, 122.8, 127.8, 128.3, 133.5, 152.0, 155.0, 161.2, 162.8; IR (KBr): &#957; = 3136 (w), 2974 (w), 2930 (w), 1717 (m), 1636 (m), 1360 (m) cm</chunk>
<chunk superscript="yes">&#8722;1</chunk>
<chunk>; HR-MS (ESI) calcd for [M+Na]</chunk>
<chunk superscript="yes">+</chunk>
<chunk>: 469.2058; found 469.2096.</chunk>
</paragraph>
<paragraph>
<chunk bold="yes">2-(Ethoxycarbonyl)-1</chunk>
<chunk bold="yes" italic="yes">H</chunk>
<chunk bold="yes">-indole-7-guanidinium&#160;trifluoroacetate&#160;(7):</chunk>
<chunk> Trifluoroacetic acid (3 mL) was added to the ethyl 7-[</chunk>
<chunk italic="yes">N</chunk>
<chunk>,</chunk>
<chunk italic="yes">N</chunk>
<chunk>&#8217;-bis-(</chunk>
<chunk italic="yes">tert</chunk>
<chunk>-butoxycarbonyl)guanidino]-1</chunk>
<chunk italic="yes">H</chunk>
<chunk>-indole-2-carboxylate (</chunk>
<chunk bold="yes">6</chunk>
<chunk>, 170 mg, 0.39 mmol), and the reaction mixture was stirred at room temperature for 2&#160;h. The excess trifluoroacetic acid was removed in vacuo to give </chunk>
<chunk bold="yes">7</chunk>
<chunk> as a colourless solid (140&#160;mg, 0.39 mmol, 100%): mp &gt; 240&#160;&#176;C; </chunk>
<chunk superscript="yes">1</chunk>
<chunk>H NMR (400 MHz, [D</chunk>
<chunk subscript="yes">6</chunk>
<chunk>]DMSO, 25 &#176;C): &#948; = 1.35 (t, 3H), 4.36 (q, 2H), 7.13-7.26 (m, 7H), 7.69 (d, 1H), 9.29 (s, 1H), 12.11 (s, 1H) ppm; </chunk>
<chunk superscript="yes">13</chunk>
<chunk>C NMR (100 MHz, [D</chunk>
<chunk subscript="yes">6</chunk>
<chunk>]DMSO, 25 &#176;C): &#948; = 14.3, 60.6, 108.7, 112.0, 120.7, 121.8, 122.8, 128.3, 128.9, 133.5, 156.4, 161.1; IR (KBr): &#957; = 3298 (w), 3193 (w), 3101 (w), 2955 (w), 1699 (m), 1671 (s), 1255 (s) cm</chunk>
<chunk superscript="yes">&#8722;1</chunk>
<chunk>; HR-MS (ESI) calcd for [M+H]</chunk>
<chunk superscript="yes">+</chunk>
<chunk>: 247.1190; found 247.1215.</chunk>
</paragraph>
<paragraph>
<chunk bold="yes">7-Guanidinio-1</chunk>
<chunk bold="yes" italic="yes">H</chunk>
<chunk bold="yes">-indole-2-carboxylate (2):</chunk>
<chunk> To a solution of the trifluoroacetate salt </chunk>
<chunk bold="yes">7</chunk>
<chunk> (130 mg, 0.53 mmol) in water/THF (1/4; 15 mL) LiOH&#183;H</chunk>
<chunk subscript="yes">2</chunk>
<chunk>O (223 mg, 5.30 mmol) was added. The reaction mixture was heated to 40&#160;&#176;C and stirred for 8 h. The solvent was removed under reduced pressure and the residue was dissolved in water (20&#160;mL). The solution was acidified dropwise with hydrochloric acid (0.1 molar) until a yellow solid precipitated at a pH&#160;=&#160;6. The solid was filtered and to remove inorganic salts again suspended in water (25&#160;mL), some dioxane (5&#160;mL) was added. The mixture was heated to reflux for 40&#160;min. The residue was filtered, and washed with water and afterwards with diethyl ether. The residue was dried in vacuo to give </chunk>
<chunk bold="yes">2</chunk>
<chunk> as a light brown solid (98 mg, 0.44 mmol, 84%): mp &gt; 240 &#176;C; </chunk>
<chunk superscript="yes">1</chunk>
<chunk>H NMR (400 MHz, [D</chunk>
<chunk subscript="yes">6</chunk>
<chunk>]DMSO, 25 &#176;C): &#948; = 6.82 (s, 1H), 7.05 (t, 1H), 7.15 (d, 1H), 7.43 (d, 1H), 7.99 (bs, 4H), 12.26 (bs, 1H), 13.07 (bs, 1H) ppm; </chunk>
<chunk superscript="yes">13</chunk>
<chunk>C NMR (100 MHz, [D</chunk>
<chunk subscript="yes">6</chunk>
<chunk>]DMSO, 25 &#176;C): &#948; = 103.4, 113.0, 118.1, 119.7, 122.0, 128.1, 129.6, 135.9, 155.9, 166.4; IR (KBr): &#957; = 3327 (m), 3086 (m), 3724 (m), 1397 (s), 737 (s) cm</chunk>
<chunk superscript="yes">&#8722;1</chunk>
<chunk>; HR-MS (ESI) calcd for [M+H]</chunk>
<chunk superscript="yes">+</chunk>
<chunk>: 219.0877; found 219.0884.</chunk>
</paragraph>
<paragraph>
<chunk bold="yes">(2-Carboxy-1</chunk>
<chunk bold="yes" italic="yes">H</chunk>
<chunk bold="yes">-indole-7-yl)guanidinium picrate (2&#183;H</chunk>
<chunk bold="yes" superscript="yes">+</chunk>
<chunk bold="yes">):</chunk>
<chunk> To a suspension of the zwitterion </chunk>
<chunk bold="yes">2</chunk>
<chunk> (20&#160;mg, 0.09&#160;mmol) in methanol (4&#160;mL) a saturated solution of picric acid in water (6&#160;mL) was added and the mixture was stirred for 24&#160;h at ambient temperature. The picrate salt crystallized and was filtered, washed several times with methanol, and dried to provide the yellow solid </chunk>
<chunk bold="yes">2</chunk>
<chunk>&#183;</chunk>
<chunk bold="yes">H</chunk>
<chunk bold="yes" superscript="yes">+</chunk>
<chunk> (35 mg, 0.08 mmol, 89%): mp &gt; 240 &#176;C; </chunk>
<chunk superscript="yes">1</chunk>
<chunk>H NMR (400 MHz, [D</chunk>
<chunk subscript="yes">6</chunk>
<chunk>]DMSO, 25 &#176;C): &#948; = 7.11-7.20 (m, 8H), 7.67 (d, 1H), 8.58 (s, 2H), 9.21 (s, 1H), 12.02 (s, 1H), 13.23 (bs, 1H) ppm; </chunk>
<chunk superscript="yes">13</chunk>
<chunk>C NMR (100 MHz, [D</chunk>
<chunk subscript="yes">6</chunk>
<chunk>]DMSO, 25 &#176;C): &#948; = 120.5, 124.1, 125.2, 129.1, 129.2, 141.9, 156.3, 160.9; IR (KBr): &#957; = 3200(w), 1674 (w), 1554 (m), 1336 (m) cm</chunk>
<chunk superscript="yes">&#8722;1</chunk>
<chunk>; HR-MS (ESI) calcd for [M+H]</chunk>
<chunk superscript="yes">+</chunk>
<chunk>: 219.0877; found 219.0884.</chunk>
</paragraph>
<section>
<title>
<chunk>X-ray Crystallographic Data</chunk>
</title>
<paragraph>
<chunk bold="yes">Crystal structure of 2:</chunk>
<chunk> C</chunk>
<chunk subscript="yes">10</chunk>
<chunk>H</chunk>
<chunk subscript="yes">10</chunk>
<chunk>N</chunk>
<chunk subscript="yes">4</chunk>
<chunk>O</chunk>
<chunk subscript="yes">2</chunk>
<chunk>, colourless crystals, dimensions 0.16 &#215; 0.13 &#215; 0.10 mm</chunk>
<chunk superscript="yes">3</chunk>
<chunk>, measured with a Bruker D8 KAPPA series II with APEX II area detector system at 100 K; </chunk>
<chunk italic="yes">a</chunk>
<chunk> = 12.1695 (5) &#197;, </chunk>
<chunk italic="yes">b</chunk>
<chunk> = 7.1061 (3) &#197;, </chunk>
<chunk italic="yes">c</chunk>
<chunk> = 12.3061 (4) &#197;, </chunk>
<chunk italic="yes">V</chunk>
<chunk> = 985.45 (7) &#197;</chunk>
<chunk superscript="yes">3</chunk>
<chunk>, </chunk>
<chunk italic="yes">Z</chunk>
<chunk> = 4, </chunk>
<chunk italic="yes">&#961;</chunk>
<chunk> = 1.471 g/cm</chunk>
<chunk superscript="yes">3</chunk>
<chunk>, space group </chunk>
<chunk italic="yes">P</chunk>
<chunk>2</chunk>
<chunk subscript="yes">1</chunk>
<chunk>/</chunk>
<chunk italic="yes">n</chunk>
<chunk>, 7030 intensities measured (&#952;</chunk>
<chunk subscript="yes">max</chunk>
<chunk> = 28.33&#176;), 2458 independent (</chunk>
<chunk italic="yes">R</chunk>
<chunk subscript="yes">(int)</chunk>
<chunk> = 0.0279), 2061 observed, structure solution by direct methods and refinement of 145 parameters on </chunk>
<chunk italic="yes">F</chunk>
<chunk italic="yes" superscript="yes">2</chunk>
<chunk> with the Bruker software package SHELXTL Vers. 2008/4/(c) 2008, </chunk>
<chunk italic="yes">R</chunk>
<chunk subscript="yes">1</chunk>
<chunk> = 0.0485, </chunk>
<chunk italic="yes">&#969;R</chunk>
<chunk subscript="yes">2</chunk>
<chunk> (all data) = 0.1111, Gof = 1.053, max electron density 0.407 e &#197;</chunk>
<chunk superscript="yes">&#8722;3</chunk>
<chunk>.</chunk>
</paragraph>
</section>
</section>
<album-graphics>
<graphic public-id="1860-5397-6-3-1"/>
<graphic public-id="1860-5397-6-3-i1"/>
<graphic public-id="1860-5397-6-3-i2"/>
</album-graphics>
<inline-graphics>
<graphic id="i1" public-id="1860-5397-6-3-i4"/>
</inline-graphics>
<figures>
<figure id="f1">
<caption>
<paragraph>
<chunk>Self-assembly of zwitterion </chunk>
<chunk bold="yes">1</chunk>
<chunk> to give dimer </chunk>
<chunk bold="yes">1</chunk>
<chunk>&#183;</chunk>
<chunk bold="yes">1</chunk>
<chunk> and self-assembly of zwitterion </chunk>
<chunk bold="yes">2</chunk>
<chunk> to give dimer </chunk>
<chunk bold="yes">2</chunk>
<chunk>&#183;</chunk>
<chunk bold="yes">2</chunk>
<chunk> &#8211; both using the same intermolecular interactions: a pattern of six H-bonds and two salt bridges.</chunk>
</paragraph>
</caption>
<graphic public-id="1860-5397-6-3-1"/>
</figure>
<figure id="f2">
<caption>
<paragraph>
<chunk superscript="yes">1</chunk>
<chunk>H NMR spectra of zwitterion </chunk>
<chunk bold="yes">2</chunk>
<chunk> (bottom) and its protonated form </chunk>
<chunk bold="yes">2</chunk>
<chunk>&#183;</chunk>
<chunk bold="yes">H</chunk>
<chunk bold="yes" superscript="yes">+</chunk>
<chunk> (top).</chunk>
</paragraph>
</caption>
<graphic public-id="1860-5397-6-3-2"/>
</figure>
<figure id="f3">
<caption>
<paragraph>
<chunk>Part of the </chunk>
<chunk superscript="yes">1</chunk>
<chunk>H NMR spectrum of </chunk>
<chunk bold="yes">2</chunk>
<chunk> in [D</chunk>
<chunk subscript="yes">6</chunk>
<chunk>]DMSO showing the complexation-induced shifts of the indole CH protons (concentration from bottom to top: 0.4, 1, 6, 12, 25 and 50 mM).</chunk>
</paragraph>
</caption>
<graphic public-id="1860-5397-6-3-3"/>
</figure>
<figure id="f4">
<caption>
<paragraph>
<chunk>Representative binding isotherm of the aromatic proton d (left) and the indole NH proton (right).</chunk>
</paragraph>
</caption>
<graphic public-id="1860-5397-6-3-4"/>
</figure>
<figure id="f5">
<caption>
<paragraph>
<chunk>Binding isotherm of the guanidinium NH</chunk>
<chunk subscript="yes">2</chunk>
<chunk> protons.</chunk>
</paragraph>
</caption>
<graphic public-id="1860-5397-6-3-5"/>
</figure>
<figure id="f6">
<caption>
<paragraph>
<chunk>Crystal structure of dimer </chunk>
<chunk bold="yes">2</chunk>
<chunk>&#183;</chunk>
<chunk bold="yes">2</chunk>
<chunk> with hydrogen bond distances (&#197;) and dihedral angles.</chunk>
</paragraph>
</caption>
<graphic public-id="1860-5397-6-3-6"/>
</figure>
<figure id="f7">
<caption>
<paragraph>
<chunk>Side view of dimer </chunk>
<chunk bold="yes">2</chunk>
<chunk>&#183;</chunk>
<chunk bold="yes">2</chunk>
<chunk> in the solid state.</chunk>
</paragraph>
</caption>
<graphic public-id="1860-5397-6-3-7"/>
</figure>
<figure id="f8">
<caption>
<paragraph>
<chunk>Part of the crystal lattice of zwitterion </chunk>
<chunk bold="yes">2</chunk>
<chunk>.</chunk>
</paragraph>
</caption>
<graphic public-id="1860-5397-6-3-8"/>
</figure>
<figure id="f9">
<caption>
<paragraph>
<chunk>Energy-minimized structure for dimer </chunk>
<chunk bold="yes">2</chunk>
<chunk>&#183;</chunk>
<chunk bold="yes">2</chunk>
<chunk> with hydrogen bond distances (&#197;) and dihedral angles.</chunk>
</paragraph>
</caption>
<graphic public-id="1860-5397-6-3-9"/>
</figure>
</figures>
<schemes>
<scheme id="s1">
<caption>
<paragraph>
<chunk>Synthesis of zwitterion </chunk>
<chunk bold="yes">2</chunk>
<chunk>.</chunk>
</paragraph>
</caption>
<graphic public-id="1860-5397-6-3-i1"/>
</scheme>
<scheme id="s2">
<caption>
<paragraph>
<chunk>Synthesis of compound </chunk>
<chunk bold="yes">2</chunk>
<chunk>&#183;</chunk>
<chunk bold="yes">H</chunk>
<chunk bold="yes" superscript="yes">+</chunk>
<chunk>.</chunk>
</paragraph>
</caption>
<graphic public-id="1860-5397-6-3-i2"/>
</scheme>
<scheme id="s3">
<caption>
<paragraph>
<chunk>An attractive H-bond in </chunk>
<chunk bold="yes">1</chunk>
<chunk> (left) is replaced by a repulsive steric interaction in </chunk>
<chunk bold="yes">2</chunk>
<chunk> (right).</chunk>
</paragraph>
</caption>
<graphic public-id="1860-5397-6-3-i3"/>
</scheme>
</schemes>
<end-section>
<title>
<chunk>Acknowledgements</chunk>
</title>
<paragraph>
<chunk>Financial support by the Deutsche Forschungsgemeinschaft and the Fonds der Chemischen Industrie is gratefully acknowledged.</chunk>
</paragraph>
</end-section>
<reference id="b1" type="book" publisher-name="Oxford University Press" publisher-location="New York">
<reference-author first-name="G" middle-names="A" last-name="Jeffrey"/>
<source>
<chunk>An Introduction to Hydrogen Bonding</chunk>
</source>
<publication-date year="1997"/>
</reference>
<reference id="b2" type="article" volume="116" first-page="7072" last-page="7080">
<reference-author first-name="T" middle-names="R" last-name="Kelly"/>
<reference-author first-name="M" middle-names="H" last-name="Kim"/>
<source>
<chunk>J. Am. Chem. Soc.</chunk>
</source>
<publication-date year="1994"/>
<external-link type="doi" public-id="10.1021/ja00095a009"/>
</reference>
<reference id="b3" type="article" volume="119" first-page="3780" last-page="3783">
<reference-author first-name="J" middle-names="L" last-name="Cook"/>
<reference-author first-name="C" middle-names="A" last-name="Hunter"/>
<reference-author first-name="C" middle-names="M R" last-name="Low"/>
<reference-author first-name="A" last-name="Perez-Velasco"/>
<reference-author first-name="J" middle-names="G" last-name="Vinter"/>
<source>
<chunk>Angew. Chem.</chunk>
</source>
<publication-date year="2007"/>
<external-link type="doi" public-id="10.1002/ange.200604966"/>
</reference>
<reference id="b4" type="article" volume="46" first-page="3706" last-page="3709">
<reference-author first-name="J" middle-names="L" last-name="Cook"/>
<reference-author first-name="C" middle-names="A" last-name="Hunter"/>
<reference-author first-name="C" middle-names="M R" last-name="Low"/>
<reference-author first-name="A" last-name="Perez-Velasco"/>
<reference-author first-name="J" middle-names="G" last-name="Vinter"/>
<source>
<chunk>Angew. Chem., Int. Ed.</chunk>
</source>
<publication-date year="2007"/>
<external-link type="doi" public-id="10.1002/anie.200604966"/>
</reference>
<reference id="b5" type="article" volume="100" first-page="853" last-page="908">
<reference-author first-name="S" last-name="Leininger"/>
<reference-author first-name="B" last-name="Olenyuk"/>
<reference-author first-name="P" middle-names="J" last-name="Stang"/>
<source>
<chunk>Chem. Rev.</chunk>
</source>
<publication-date year="2000"/>
<external-link type="doi" public-id="10.1021/cr9601324"/>
</reference>
<reference id="b6" type="article" volume="35" first-page="972" last-page="983">
<reference-author first-name="S" middle-names="R" last-name="Seidel"/>
<reference-author first-name="P" middle-names="J" last-name="Stang"/>
<source>
<chunk>Acc. Chem. Res.</chunk>
</source>
<publication-date year="2002"/>
<external-link type="doi" public-id="10.1021/ar010142d"/>
</reference>
<reference id="b7" type="article" volume="38" first-page="369" last-page="378">
<reference-author first-name="M" last-name="Fujita"/>
<reference-author first-name="M" last-name="Tominaga"/>
<reference-author first-name="A" last-name="Hori"/>
<reference-author first-name="B" last-name="Therrien"/>
<source>
<chunk>Acc. Chem. Res.</chunk>
</source>
<publication-date year="2005"/>
<external-link type="doi" public-id="10.1021/ar040153h"/>
</reference>
<reference id="b8" type="article" volume="106" first-page="3520" last-page="3560">
<reference-author first-name="M" last-name="Kruppa"/>
<reference-author first-name="B" last-name="K&#246;nig"/>
<source>
<chunk>Chem. Rev.</chunk>
</source>
<publication-date year="2006"/>
<external-link type="doi" public-id="10.1021/cr010206y"/>
</reference>
<reference id="b9" type="article" volume="43" first-page="6724" last-page="6727">
<reference-author first-name="J" middle-names="R" last-name="Nitschke"/>
<reference-author first-name="M" last-name="Hutin"/>
<reference-author first-name="G" last-name="Bernardinelli"/>
<source>
<chunk>Angew. Chem., Int. Ed.</chunk>
</source>
<publication-date year="2004"/>
<external-link type="doi" public-id="10.1002/anie.200461308"/>
</reference>
<reference id="b10" type="article" volume="73" first-page="7132" last-page="7136">
<reference-author first-name="M" middle-names="D" last-name="Pluth"/>
<reference-author first-name="R" middle-names="G" last-name="Bergman"/>
<reference-author first-name="K" middle-names="N" last-name="Raymond"/>
<source>
<chunk>J. Org. Chem.</chunk>
</source>
<publication-date year="2008"/>
<external-link type="doi" public-id="10.1021/jo800991g"/>
</reference>
<reference id="b11" type="article" volume="130" first-page="14966" last-page="14967">
<reference-author first-name="J" last-name="Baram"/>
<reference-author first-name="E" last-name="Shirman"/>
<reference-author first-name="N" last-name="Ben-Shirit"/>
<reference-author first-name="A" last-name="Ustinov"/>
<reference-author first-name="H" last-name="Weissman"/>
<reference-author first-name="I" last-name="Pinkas"/>
<reference-author first-name="S" middle-names="G" last-name="Wolf"/>
<reference-author first-name="B" last-name="Rybtchinski"/>
<source>
<chunk>J. Am. Chem. Soc.</chunk>
</source>
<publication-date year="2008"/>
<external-link type="doi" public-id="10.1021/ja807027w"/>
</reference>
<reference id="b12" type="article" first-page="2397" last-page="2403">
<reference-author first-name="C" last-name="Schmuck"/>
<source>
<chunk>Eur. J. Org. Chem.</chunk>
</source>
<publication-date year="1999"/>
<external-link type="doi" public-id="10.1002/(SICI)1099-0690(199909)1999:9&lt;2397::AID-EJOC2397&gt;3.0.CO;2-3"/>
</reference>
<reference id="b13" type="article" volume="125" first-page="452" last-page="459">
<reference-author first-name="C" last-name="Schmuck"/>
<reference-author first-name="W" last-name="Wienand"/>
<source>
<chunk>J. Am. Chem. Soc.</chunk>
</source>
<publication-date year="2003"/>
<external-link type="doi" public-id="10.1021/ja028485+"/>
</reference>
<reference id="b14" type="article" volume="127" first-page="11115" last-page="11124">
<reference-author first-name="S" last-name="Schlund"/>
<reference-author first-name="C" last-name="Schmuck"/>
<reference-author first-name="B" last-name="Engels"/>
<source>
<chunk>J. Am. Chem. Soc.</chunk>
</source>
<publication-date year="2005"/>
<external-link type="doi" public-id="10.1021/ja052536w"/>
</reference>
<reference id="b15" type="article" volume="46" first-page="1693" last-page="1697">
<reference-author first-name="C" last-name="Schmuck"/>
<reference-author first-name="T" last-name="Rehm"/>
<reference-author first-name="K" last-name="Klein"/>
<reference-author first-name="F" last-name="Gr&#246;hn"/>
<source>
<chunk>Angew. Chem., Int. Ed.</chunk>
</source>
<publication-date year="2007"/>
<external-link type="doi" public-id="10.1002/anie.200603629"/>
</reference>
<reference id="b16" type="article" volume="128" first-page="1430" last-page="1431">
<reference-author first-name="C" last-name="Schmuck"/>
<reference-author first-name="T" last-name="Rehm"/>
<reference-author first-name="F" last-name="Gr&#246;hn"/>
<reference-author first-name="K" last-name="Klein"/>
<reference-author first-name="F" last-name="Reinhold"/>
<source>
<chunk>J. Am. Chem. Soc.</chunk>
</source>
<publication-date year="2006"/>
<external-link type="doi" public-id="10.1021/ja056465c"/>
</reference>
<reference id="b17" type="article" first-page="698" last-page="700">
<reference-author first-name="G" last-name="Gr&#246;ger"/>
<reference-author first-name="V" last-name="Stepanenko"/>
<reference-author first-name="F" last-name="W&#252;rthner"/>
<reference-author first-name="C" last-name="Schmuck"/>
<source>
<chunk>Chem. Commun.</chunk>
</source>
<publication-date year="2009"/>
<external-link type="doi" public-id="10.1039/b820281h"/>
</reference>
<reference id="b18" type="article" volume="118" first-page="11237" last-page="11243">
<reference-author first-name="Y-J" last-name="Zheng"/>
<reference-author first-name="R" middle-names="L" last-name="Ornstein"/>
<source>
<chunk>J. Am. Chem. Soc.</chunk>
</source>
<publication-date year="1996"/>
<external-link type="doi" public-id="10.1021/ja960041o"/>
</reference>
<reference id="b19" type="article" volume="62" first-page="2763" last-page="2787">
<reference-author first-name="B" last-name="Dietrich"/>
<reference-author first-name="D" middle-names="L" last-name="Fyles"/>
<reference-author first-name="T" middle-names="M" last-name="Fyles"/>
<reference-author first-name="J-M" last-name="Lehn"/>
<source>
<chunk>Helv. Chim. Acta</chunk>
</source>
<publication-date year="1979"/>
<external-link type="doi" public-id="10.1002/hlca.19790620827"/>
</reference>
<reference id="b20" type="article" volume="66" first-page="4206" last-page="4213">
<reference-author first-name="A" last-name="Exp&#243;sito"/>
<reference-author first-name="M" last-name="Fern&#225;ndez-Su&#225;rez"/>
<reference-author first-name="T" last-name="Iglesias"/>
<reference-author first-name="L" last-name="Mu&#241;oz"/>
<reference-author first-name="R" last-name="Riguera"/>
<source>
<chunk>J. Org. Chem.</chunk>
</source>
<publication-date year="2001"/>
<external-link type="doi" public-id="10.1021/jo010076t"/>
</reference>
<reference id="b21" type="article" volume="18" first-page="707" last-page="721">
<reference-author first-name="T" last-name="Mukaiyama"/>
<source>
<chunk>Angew. Chem., Int. Ed. Engl.</chunk>
</source>
<publication-date year="1979"/>
<external-link type="doi" public-id="10.1002/anie.197907073"/>
</reference>
<reference id="b22" type="article" volume="128" first-page="14528" last-page="14536">
<reference-author first-name="F" last-name="Sansone"/>
<reference-author first-name="M" last-name="Dudi&#269;"/>
<reference-author first-name="G" last-name="Donofrio"/>
<reference-author first-name="C" last-name="Rivetti"/>
<reference-author first-name="L" last-name="Baldini"/>
<reference-author first-name="A" last-name="Casnati"/>
<reference-author first-name="S" last-name="Cellai"/>
<reference-author first-name="R" last-name="Ungaro"/>
<source>
<chunk>J. Am. Chem. Soc.</chunk>
</source>
<publication-date year="2006"/>
<external-link type="doi" public-id="10.1021/ja0634425"/>
</reference>
<reference id="b23" type="article" volume="6" first-page="4925" last-page="4927">
<reference-author first-name="A" last-name="Porcheddu"/>
<reference-author first-name="G" last-name="Giacomelli"/>
<reference-author first-name="A" last-name="Chighine"/>
<reference-author first-name="S" last-name="Masala"/>
<source>
<chunk>Org. Lett.</chunk>
</source>
<publication-date year="2004"/>
<external-link type="doi" public-id="10.1021/ol047926m"/>
</reference>
<reference id="b24" type="article" volume="2" first-page="364" last-page="382">
<reference-author first-name="Y" last-name="Zhao"/>
<reference-author first-name="N" middle-names="E" last-name="Schultz"/>
<reference-author first-name="D" middle-names="G" last-name="Truhlar"/>
<source>
<chunk>J. Chem. Theory Comput.</chunk>
</source>
<publication-date year="2006"/>
<external-link type="doi" public-id="10.1021/ct0502763"/>
</reference>
<reference id="b25" type="article" volume="102" first-page="1995" last-page="2001">
<reference-author first-name="V" last-name="Barone"/>
<reference-author first-name="M" last-name="Cossi"/>
<source>
<chunk>J. Phys. Chem. A</chunk>
</source>
<publication-date year="1998"/>
<external-link type="doi" public-id="10.1021/jp9716997"/>
</reference>
<reference id="b26" type="article" volume="24" first-page="669" last-page="681">
<reference-author first-name="M" last-name="Cossi"/>
<reference-author first-name="N" last-name="Rega"/>
<reference-author first-name="G" last-name="Scalmani"/>
<reference-author first-name="V" last-name="Barone"/>
<source>
<chunk>J. Comput. Chem.</chunk>
</source>
<publication-date year="2003"/>
<external-link type="doi" public-id="10.1002/jcc.10189"/>
</reference>
<reference id="b27" type="article" volume="72" first-page="8921" last-page="8927">
<reference-author first-name="G" middle-names="W" last-name="Bates"/>
<reference-author last-name="Triyanti"/>
<reference-author first-name="M" middle-names="E" last-name="Light"/>
<reference-author first-name="M" last-name="Albrecht"/>
<reference-author first-name="P" middle-names="A" last-name="Gale"/>
<source>
<chunk>J. Org. Chem.</chunk>
</source>
<publication-date year="2007"/>
<external-link type="doi" public-id="10.1021/jo701702p"/>
</reference>
<reference id="b28" type="article" volume="7" first-page="3505" last-page="3511">
<reference-author first-name="D" last-name="Makuc"/>
<reference-author first-name="M" last-name="Lenar&#269;i&#269;"/>
<reference-author first-name="G" last-name="Bates"/>
<reference-author first-name="P" middle-names="A" last-name="Gale"/>
<reference-author first-name="J" last-name="Plavec"/>
<source>
<chunk>Org. Biomol. Chem.</chunk>
</source>
<publication-date year="2009"/>
<external-link type="doi" public-id="10.1039/b908947k"/>
</reference>
<reference id="b29" type="article" first-page="4854" last-page="4866">
<reference-author first-name="D" last-name="Makuc"/>
<reference-author last-name="Triyanti"/>
<reference-author first-name="M" last-name="Albrecht"/>
<reference-author first-name="J" last-name="Plavec"/>
<reference-author first-name="K" last-name="Rissanen"/>
<reference-author first-name="A" last-name="Valkonen"/>
<reference-author first-name="C" middle-names="A" last-name="Schalley"/>
<source>
<chunk>Eur. J. Org. Chem.</chunk>
</source>
<publication-date year="2009"/>
<external-link type="doi" public-id="10.1002/ejoc.200900721"/>
</reference>
<reference id="b30" type="article" volume="127" first-page="10486" last-page="10487">
<reference-author first-name="C" last-name="Schmuck"/>
<reference-author first-name="L" last-name="Geiger"/>
<source>
<chunk>J. Am. Chem. Soc.</chunk>
</source>
<publication-date year="2005"/>
<external-link type="doi" public-id="10.1021/ja052699k"/>
</reference>
<reference id="b31" type="article" volume="127" first-page="3373" last-page="3379">
<reference-author first-name="C" last-name="Schmuck"/>
<reference-author first-name="M" last-name="Schwegmann"/>
<source>
<chunk>J. Am. Chem. Soc.</chunk>
</source>
<publication-date year="2005"/>
<external-link type="doi" public-id="10.1021/ja0433469"/>
</reference>
<reference id="b32" type="article" volume="72" first-page="6832" last-page="6839">
<reference-author first-name="C" last-name="Schmuck"/>
<reference-author first-name="V" last-name="Bickert"/>
<source>
<chunk>J. Org. Chem.</chunk>
</source>
<publication-date year="2007"/>
<external-link type="doi" public-id="10.1021/jo070981z"/>
</reference>
<copyright year="2010" holder="Rether et al; licensee Beilstein-Institut." link="http://creativecommons.org/licenses/by/2.0">
<paragraph>
<chunk>This is an Open Access article under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.</chunk>
</paragraph>
<paragraph>
<chunk>The license is subject to the </chunk>
<chunk italic="yes">Beilstein Journal of Organic Chemistry</chunk>
<chunk> terms and conditions: (http://www.beilstein-journals.org/bjoc)</chunk>
</paragraph>
</copyright>
</article>

