Diplomová Práce

MASARYKOVA UNIVERZITA PŘÍRODOVĚDECKÁ FAKULTA ÚSTAV CHEMIE

Diplomová práce

Brno 2016 Jan Sokolov

MASARYKOVA UNIVERZITA PŘÍRODOVĚDECKÁ FAKULTA ÚSTAV CHEMIE

Supramolekulární hostitelské molekuly vycházející z glykolurilového dimeru

Diplomová práce

Jan Sokolov

Vedoucí práce: doc. Ing. Vladimír Šindelář, Ph.D. Brno 2016

Bibliografický záznam

Autor: Bc. Jan Sokolov Přírodovědecká fakulta, Masarykova univerzita Ústav chemie Supramolekulární hostitelské molekuly vycházející Název práce: z glykolurilového dimeru

Studijní program: Chemie

Studijní obor: Organická chemie

Vedoucí práce: doc. Ing. Vladimír Šindelář, Ph.D.

Akademický rok: 2015/2016

Počet stran: 87+33 Klíčová slova: Supramolekulární chemie, Glykolurily, Glykolurilové dimery, Molekulární klipsy

Bibliographic Entry

Author Bc. Jan Sokolov Faculty of Science, Masaryk University Department of Chemistry Supramolecular host molecules based on glycoluril Title of Thesis: dimers

Degree programme: Chemistry

Field of Study: Organic Chemistry

Supervisor: doc. Ing. Vladimír Šindelář, Ph.D.

Academic Year: 2015/2016

Number of Pages: 87+33 Keywords: Supramolecular chemistry, Glycolurils, Glycoluril dimers, Molecular clips

Abstrakt

Tato diplomová práce se zaměřuje na syntézu nových glykolurilových dimerů, které se skládají ze dvou oddělených glykolurilových jednotek. Tyto dimery byly využity pro syntézu hostitelských molekul se dvěma vazebnými místy. V rámci práce byly syntetizovány dimery molekulární klips rozpustných ve vodě, které jsou schopné vázat dvě molekuly hosta současně. Kromě toho byla objevena nová sloučenina, která vytváří ve vodě supramolekulární polymer.

Abstract This thesis focuses on synthesis of new glycoluril dimers, which are composed of two separated glycoluril moieties. These dimers were used for synthesis of new host molecules with two binding sites. Within the scope of this thesis, new dimeric water- soluble molecular clips were synthesized, which can bind two guest molecules simultaneously. Furthermore, a new compound, which forms supramolecular polymer in aqueous solution, was discovered.

Poděkování

Chtěl bych poděkovat svému školiteli doc. Ing. Vladimíru Šindelářovi, Ph.D., za možnost pracovat na zajímavém projektu, za jeho cenné připomínky a hlavně za volnost, kterou mi na práci poskytl.

Dále bych chtěl poděkovat Lauře Gilberg, Dr. rer. nat. za praktické rady při práci v laboratoři, RNDr. Václavu Havlovi za podnětné diskuze a rady a také za pomoc s měřením ITC.

Také bych rád poděkoval Mgr. Lukáši Maierovi, Ph.D. za měření NMR spekter a zejména za změření mnoha nestandardních vzorků a za měření při vysokých teplotách, Mgr. Lukáši Ustrnulovi za to, že mi vysvětlil, jak měřit DOSY, Mgr. Janu Novotnému, Ph.D. za konzultace týkající se studia konformačních vlastností, Mgr. Tomáši Lízalovi za optimalizované struktury a Mgr. Miroslavě Bittové, Ph.D. za HR-MS analýzy.

Závěrem bych chtěl poděkovat celému kolektivu naší výzkumné skupiny za přátelskou atmosféru v laboratoři.

Prohlášení Prohlašuji, že jsem svou diplomovou práci vypracoval samostatně s využitím informačních zdrojů, které jsou v práci citovány.

Brno 16. 5. 2016 ……………………………… Jan Sokolov

Contents

1 Introduction ...... 10 2 Theoretical part ...... 11 2.1 Supramolecular chemistry ...... 11 2.1.1 Host-guest chemistry ...... 11 2.1.2 Determination of stoichiometry ...... 12 2.1.3 Measurement of binding constants ...... 12 2.2 Glycoluril ...... 13 2.2.1 Glycolurils substituted in methine positions ...... 13 2.2.2 N-substituted glycolurils ...... 14 2.3 Glycoluril molecular clips and baskets ...... 16 2.4 Acyclic glycoluril oligomers...... 19 2.4.1 Synthesis of glycoluril oligomers ...... 19 2.4.2 Water soluble glycoluril oligomers ...... 23 2.5 Cucurbit[n]urils ...... 28 2.5.1 Cucurbit[n]uril derivatives ...... 29 3 Results and discussion ...... Chyba! Záložka není definována. 3.1 Aims of thesis ...... Chyba! Záložka není definována. 3.2 Synthesis of glycoluril dimers and corresponding cyclic ethers ...... Chyba! Záložka není definována. 3.3 Synthesis of molecular clips ...... Chyba! Záložka není definována. 3.3.1 Chloroform-soluble clips ...... Chyba! Záložka není definována. 3.3.2 Water-soluble clips ...... Chyba! Záložka není definována. 3.4 Synthesis of “dimeric glycoluril dimer” ...... Chyba! Záložka není definována. 3.5 Conformational properties of certain compounds...... Chyba! Záložka není definována. 3.6 Interactions of water-soluble clips with organic cations ... Chyba! Záložka není definována. 3.7 Self-association of glycoluril dimers ...... Chyba! Záložka není definována. 4 Summary ...... Chyba! Záložka není definována. 5 Experimental part ...... Chyba! Záložka není definována. 5.1 General information ...... Chyba! Záložka není definována. 5.2 Synthetic procedures ...... Chyba! Záložka není definována. 6 List of abbreviations ...... 83 7 References ...... 84 8 Supplementary information ...... Chyba! Záložka není definována. 8.1 NMR and IR spectra of new compounds ..... Chyba! Záložka není definována.

8.2 Temperature dependent spectra NMR of selected compounds . Chyba! Záložka není definována. 8.3 NMR titrations ...... Chyba! Záložka není definována. 8.4 ITC measurements ...... Chyba! Záložka není definována. 8.5 Calculation of polymerization degree ...... Chyba! Záložka není definována.

1 Introduction

Glycoluril and its derivatives are rigid bicyclic compounds and they are widely used for synthesis of supramolecular host molecules. Cucurbit[n]urils, which can bind cations, and bambus[n]urils, which prefer binding of anions, are well-known glycoluril-based macrocyclic hosts. Molecular clips and acyclic glycoluril oligomers are also capable of binding of a large variety of organic guests. This thesis focuses on synthesis on glycoluril dimers which consist of two isolated glycoluril moieties. The main goal of this work was to use these glycoluril dimers for synthesis of new host molecules with two binding sites and to investigate their supramolecular properties.

2 Theoretical part

2.1 Supramolecular chemistry

Supramolecular chemistry is a multidisciplinary field of chemistry that focuses on non- covalent interactions (hydrogen bonding,  interactions, ion-dipole or dipole-dipole interactions, solvophobic effect etc.) between molecules, which are responsible for formation of complexes and molecular assemblies.1

Today, supramolecular chemistry can be divided into many branches like host-guest chemistry, molecular recognition, crystal engineering, self-association processes, mechanically interlocked molecules (rotaxanes, catenanes) and molecular devices.

2.1.1 Host-guest chemistry

The experimental part of this thesis focuses on synthesis and supramolecular propertes of new glycoluril-based host molecules, therefore host-guest chemistry is introduced in more detail than the other branches of supramolecular chemistry.

In host-guest chemistry one molecule (host) binds another one (guest) to produce supramolecular complex.1

Host is usually a large molecule with a central hole or cavity, where the guest can be encapsulated. Host molecule can be either acyclic (molecular clips or tweezers) or cyclic (crown ethers, cyclodextrins, calix[n]arenes etc.). Guest can be simple metal cation or inorganic anion as well as neutral organic molecule.

The stability of the supramolecular complex is characterized by binding (association) constant Ka. The formation of the complex can be described by equation (1).

푎퐻 + 푏퐺 ⇆ 퐶 (1)

퐻, 퐺 and 퐶 are concentrations of host, guest and complex 푎 and 푏 stoichiometry. Ka is the equilibrium constant of this reaction and can be calculated from equation (2).

퐶 (2) 퐾 = 푎 퐻푎 ∙ 퐺푏

2.1.2 Determination of stoichiometry

Before the binding constant of the supramolecular complex can be calculated, it is necessary to identify the stoichiometry of the complex.1, 2 In this chapter basic principles of the continuous variation method, which was used in the experimental part of this thesis to determine the stoichiometry of supramolecular complexes, are explained.

In order to determine the stoichiometry using the continuous variation methods, it is necessary to make a set of samples with different ratios of guest and host total concentrations ([G]t and [H]t). Sum of concentrations [G]t + [H]t has to maintain constant in all samples. After the measurement of the appropriate physical quantity (usually absorbance for UV-Vis or chemical shift for NMR experiment), the data are treated using

Job's plot (Fig. 1), where the x-axis is [G]t / ([G]t + [H]t) and the y-axis is the concentrateion of the complex [C]. The x-value of maximum on the Job's curve corresponds to the stoichiometry, e.g. if x = 0.5 (shown in Fig. 1), then the stoichiometry of the complex is 1 : 1, if x = 0.66, the stoichiometry is 2 : 1 etc.

Figure 1. Example of Job's plot for 1 : 1 complex.

2.1.3 Measurement of binding constants

Binding constants of supramolecular complex in solution can be determined using any technique that can yield information about the concentration of the complex as a function of the concentration of host or guest.

Typically, in such an experiment, concentration of one of the components is variable, while the concentration of the other one is maintained constant. Theoretical binding

isotherm is fitted to the experimental data and from the isotherm the binding constant is calculated.

Common techniques for determination of binding constants are NMR, UV-Vis and fluorescence titrations, isothermal titration calorimetry, potentiometric titration or extraction methods.

2.2 Glycoluril

Glycoluril (2,4,6,8-tetraazabicyclo[3.3.0]octane-3,7-dione) 1 (Fig. 2) is a rigid bicyclic heterocycle synthetized by acid-catalyzed condensation of glyoxal with urea.3 Glycoluril and its derivatives have been proven useful in fields of pharmaceutical and supramolecular chemistry.

Figure 2. Structure of glycoluril.

In pharmaceutical chemistry some glycoluril derivatives can be used as neurotropic drugs, 2,4,6,8-tetramethylglycoluril (mebicar) has been already introduced to medical practice in Russia as a tranquilizer.4

In supramolecular chemistry glycoluril and its derivatives are building blocks for synthesis of macrocycles,5, 6 acyclic oligomers,7, 8 molecular clips9 and other compounds, which can bind various guest molecules.

This thesis focuses on the application of glycoluril-based compounds in supramolecular chemistry.

2.2.1 Glycolurils substituted in methine positions

Glycolurils substituted in methine positions (positions 1 and 5) 2 are synthetized from urea and vicinal dicarbonyl compounds dissimilar to glyoxal (Scheme 1).3 If the functional groups are not very sterically demanding (alkyl groups, e.g. methyl, ethyl,

butane-1,4-diyl), the reaction proceeds at room temperature. In case of bulky substituents (phenyl, ethoxycarbonyl) the reaction mixture must be heated.

Scheme 1. Synthesis of 1,5-disubstituted glycolurils.

2.2.2 N-substituted glycolurils

Nitrogen atoms of the glycoluril can be alkylated and acylated by common agents (dimethyl sulfate, benzyl bromide, acetic anhydride).10, 11 Halogenation by elemental chlorine and bromine is also known.12

Derivatization of glycolurils with formaldehyde is widely used. Treating glycoluril with formaldehyde in acidic media at room temperature leads to tetracyclic products known as glycoluril diethers 3.3 Reaction at basic pH give tetrakishydroxymethylated glycolurils 4 (Scheme 2).13 Both derivatives react with nucleophiles and are used as precursors for synthesis of substituted cucurbit[n]urils,14,15 glycoluril oligomers,8,16 and molecular clips.9

Scheme 2. Synthesis of glycoluril diethers 3 and hydroxylmethylglycolurils 4.

Another method for the synthesis of N-substituted glycolurils is based reaction of glyoxal with urea derivatives.4 Condensation of N-alkylurea with glyoxal gives a mixture of 2,6- dialkylglycoluril 5 and 2,8-dialkylglycoluril 6 (Scheme 3). Derivative 5 is major product due to steric effects.

Scheme 3. Reaction of glyoxal with N-alkylurea.

On the other hand, glycolurils 6 can be selectively prepared by reaction of glyoxal with diureas 7 (Scheme 4).7 These glycolurils have been successfully used for selective synthesis of glycoluril oligomers.

Scheme 4. selective synthesis of 2,8-dialkyl glycolurils

2,4-Dialkylglycolurils 8 are prepared in two-step synthesis (Scheme 5).4 First step is a basic condensation of urea with glyoxal, which leads to 4,5-dihydroxyimidazolidinone 9. Compound 9 further reacts with N,N'-dialkylurea in presence of the acid catalyst to give 2,4-dialkylglycoluril.

Scheme 5. Synthesis of 2,4-dialkylglycolurils.

This class of glycoluril serves as a starting material for synthesis of bambus[n]uril macrocycles (BU[n]) – neutral anion receptors (Fig. 3).6

Figure 3. Structure of BU[6] with an included chloride anion.6

2.3 Glycoluril molecular clips and baskets

Glycoluril molecular clips were first synthetized in late 1980s by Roeland Nolte.17 Molecular clips contain one glycoluril unit, which is flanked by two aromatic units (benzene 10 or naphthalene 11) (Fig. 4). These compounds are synthetized from glycoluril cyclic diethers 3 (or tetrakishydroxymehyl glycolurils 4) and aromatic compounds, which are activated by electron donating groups (typically OH and OMe).

These reactions proceed in acidic media; in (CH2Cl)2 in presence of PTSA, in TFA or in

TFA/Ac2O mixture.

Figure 4. Structure of molecular clips 10 and 11.

These clips can bind dihydroxybenzenes – resorcinols or catechols in chloroform and tetrachloromethane (Fig. 5).9 Two interactions contribute to the binding; (i) hydrogen bonding between the carbonyl oxygens of the glycoluril moiety and the hydroxyl groups of the guest, (ii)  interaction between the host and the guest.

Figure 5. Complex of clip 10b with resorcinol.9

To demonstrate the role of both interactions, binding resorcinol by compounds 12 and 3a was investigated.18 Compound 12 contains sulfur atoms instead of carbonyl oxygens and it cannot act as a hydrogen bond acceptor, it can bind resorcinol only by  interaction.

On the other hand, cyclic ether 3a can form hydrogen bonds with resorcinol, but it cannot stabilize the complex by  interaction.

Figure 6. Three different resorcinol receptors.

Molecular clip 10b can bind via both hydrogen bonds and  interactions, therefore it has higher affinity towards resorcinol than compounds 12 and 3a (Tab. 1)

Table 1. Association constants of complexes between resorcinol and hosts 10b, 12 and 3a (in chloroform).18

-1 Host Ka [M ] 10b 2600 ± 200 12 51 ± 4 3a 25 ± 10

In order to modify the binding properties of the molecular clips, they can be derivatized with crown ether 13 or aza-crown ether 14 moieties (Fig. 7).19

Figure 7. Molecular baskets.

These compounds are thanks to their shape called molecular baskets thanks to their shape. In chloroform these baskets bind alkali metal and ammonium cations and forming very stable complexes with association constants above 1 ∙ 109 M-1.

2.4 Acyclic glycoluril oligomers

Acid catalyzed reaction of glycoluril (or its derivatives) with paraformaldehyde usually leads to a mixture of oligomers20, 21 and it can be difficult to isolate the products in the pure form. Therefore, selective methods for synthesis of glycoluril oligomers, which make the isolation much easier, have been developed.

This chapter is divided into two main parts; the first one describes methods for synthesis of glycoluril oligomers and also their supramolecular properties. The other part focuses on a relatively new class of oligomers bearing water-solubilizing groups.

2.4.1 Synthesis of glycoluril oligomers

2.4.1.1 Synthesis based on 2,8-dialkylglycolurils

2,8-Dialkylglycolurils 6 can be used for synthesis of glycoluril dimers 15. Dimers can be synthesized by three methods22 – condensation of glycolurils 6 with formaldehyde, condensation of glycoluril ethers 16 or heterocondensation of a glycoluril 6 with a glycoluril cyclic ether 16 (Scheme 6).

Scheme 6. Synthesis of glycoluril dimers 15.

Glycoluril dimers exist in two diastereomeric forms – C-shaped, which is thermodynamically more stable, and S-shaped.23 In presence of acid catalyst the dimers can isomerize (Scheme 7).

Scheme 7. Isomerization of glycoluril dimers 15.

C-shaped glycoluril dimers are also capable of self-association. Dimers with hydrogen atoms on their convex face form assemblies in solid state,7 while derivatives with carboxylic groups in methine positions of glycoluril units self-associate in water (Fig. 8).24

Figure 8. Self-association of dimers 15.7, 24

A selective method for synthesis of glycoluril trimers 17 was developed by Sindelar et al.16 It is based on reaction of a glycoluril protected in positions 2 and 8 with another glycoluril derivative bearing hydroxymethyl groups 4a or glycoluril cyclic ether 3b, which acts as a connecting block (Scheme 8). The reaction proceeds only in anhydrous methanesulfonic acid. In aqueous hydrochloric acid hydroxymethyl or cyclic ether groups are hydrolyzed and the major products of the reaction are glycoluril dimers 15.

Scheme 8. synthesis of glycoluril trimer 17.

Glycoluril trimers 17a and 17b are capable of binding pyridinium guests 18 and 19 in water with 1 : 1 stoichiometry. However, in the solid state guest 19 interacts with two trimer molecules (Fig. 9).

Figure 9. Structure of pyridinium guests 18 and 19 and crystal structure of complex 16 17b2·191.

The synthesis of glycoluril tetramer 20 is analogous to the synthesis of trimers.25 The only difference is that tetrakis(hydroxymehyl)glycoluril dimer 21 was used as a connecting block (Scheme 9).

Scheme 9. Synthesis of glycoluril tetramer 20.

Tetramer is poorly soluble in water, therefore its supramolecular properties were studied in DCOOD/D2O 1 : 1 (v/v). Tetramer can bind not only pyridinium guests, but also aliphatic diammonium cations, which are typical guests for CB[6]. On the other hand, the complexes of tetramer are about one order of magnitude less stable than the CB[6] complexes.

2.4.1.2 Synthesis of glycoluril tetramer and trimer with ether groups Glycoluril tetramer terminated with cyclic ether groups 22 can be prepared in acceptable yield (36 %) by treating glycoluril dimer 23 (which can be prepared from glycoluril 1 and formaldehyde in one step)20 with excess of dimethylglycoluril cyclic ether 4b in anhydrous methanesulfonic acid (Scheme 10).8

Scheme 10. Synthesis of glycoluril tetramer 22.

Glycoluril trimer 24 was later prepared by analogous procedure from glycoluril 1 and cyclic ether 3b (Scheme 11),26 but the trimer can be isolated only in very poor yield (4 %).

Scheme 11 Synthesis of glycoluril trimer 24.

Both of these compounds proved useful for synthesis of water-soluble host molecules (see chapter 2.4.2).

2.4.1.3 Templated synthesis of glycoluril hexamer Acyclic glycoluril hexamer 25 can be prepared from glycoluril 1 and paraformaldehyde in presence of p-xylelene diammonium cation 26, which acts as a template (Scheme 12)27. The principle of this process is that the acyclic hexamer, which is formed under reaction conditions, binds p-xylelene diammonium and the resulting complex reacts with formaldehyde to give CB[6] more slowly than free hexamer. Therefore acyclic glycoluril hexamer can be isolated. The effect of the p-xylelene diammonium is called in the literature “negative template effect”.

Scheme 12. Templated synthesis of glycoluril hexamer 25.

Acyclic hexamer reacts with various aldehydes to give cucurbit[n]urils substituted on the methylene bridges, while the reaction of hexamer with glycoluril cyclic diethers leads to CB[7]14 or CB[8]28 derivatives.

2.4.2 Water soluble glycoluril oligomers Relative recently, Lyle Isaacs' group has published a series of articles,26, 29, 30, 31 which focus on the application of the acyclic glycoluril oligomers in medicinal chemistry as solubilizing agents for insoluble drug molecules. Acyclic oligomers are more flexible than cucurbit[n]uril macrocycles; therefore they can bind a large variety organic of guests. They bind aliphatic and aromatic ammonium cations (which are typical guests for cucurbit[n]urils), as well as large non-polar molecules like paclitaxel.

Oligomers with two, three and four glycoluril units have been synthetized. The row of glycoluril units is terminated with aromatic side-walls. The aromatic side-walls can be substituted with various functional groups, which provide the water solubility to the oligomer. Aromatic units can also participate in binding of the aromatic guests by  stacking.

Glycoluril tetramer 27a was the first example of these water soluble oligomers. Carboxylic functional groups were introduced on aromatic side-walls of 27a to induce its solubility in water (Scheme 13).8 Supramolecular properties were studied in the sodium phosphate buffer aqueous solution (pD 7.4).

Scheme 13. Synthesis of glycoluril tetramer with carboxylic groups.

The disadvantage of the host 27a is that the carboxylic groups are weakly acidic and the solubility in water depends on their degree of dissociation. For that reason, new derivatives 27b and 28 with sulfonate groups (Scheme 14), which are strongly acidic, were synthesized.29 Sulfonated analogs were isolated as neutral sodium salts, which are well soluble in water, and they do not require buffered media for supramolecular studies.

Scheme 14. Synthesis of glycoluril tetramers with sulfonate groups.

Aromatic side-wall can also be varied.30 Up to now, tetramers terminated with benzene, naphthalene, dimethylbenzene and tetralin moieties have been synthetized (Fig. 10).

Figure 10. Aromatic compounds, which can be attached to tetramer 22.

It was discovered, that oligomers 27b and 28 are potent solubilizing excipients for hydrophobic drugs.29 For example compound 27b can enhance solubility of paclitaxel in water 2750-fold.

Glycoluril trimers 29 with sulfonate groups share very similar properties with tetramers 27 and 28 and their solubilizing efficiency is comparable, but glycoluril dimers 30 and monomers 31 bind only certain drug molecules (camptothecin, -estradiol) and with lower affinity than trimers and tetramers.26 This result is expectable, due to the fact that the trimers and tetramers possess a well-defined cavity, while the cavity of the monomers and dimers is much more open and resembles molecular clip type receptors (Fig. 11).

Figure 11. Structures of the glycoluril oligomers, analogs with naphthalene side-walls have been synthesized as well.

Compounds 27 – 31 self-associate in aqueous solution. 26 This is an unsurprising fact because previously published water-soluble glycoluril clips (Fig. 12) are known to self- associate strongly (Tab. 2). 24, 32

Figure 12. Structures of self-associating water-soluble clips.

On the other hand compounds 27 – 31 possess negatively charged sulfonate groups which are located on the aromatic side walls and which are making the self-association less favorable than in case of compounds 10d and 15a. It is desirable to have weakly associating host molecules in this case because the self-association is a process which interferes with the guest binding.

Table 2. Self-association constants of selected glycoluril clips and oligomers in aqueous sodium phosphate buffer24, 26, 32

-1 Compound Ka [M ]

10d 18401

15a 41700i

31 302

30 12ii

29 3ii

27 47ii

1 100 mM sodium phosphate buffer, pD = 7.4 2 20 mM sodium phosphate buffer, pD = 7.4

The influence of the solubilizing group on the binding properties of the tetramers was also investigated.32 Apart from the derivatives with anionic group 27a-d, tetramers with neutral hydroxyl groups (27e) and ammonium groups (27f) were synthesized (Fig. 13). It was discovered that the neutral and positively charged analogs the solubilizing groups form intramolecular hydrogen bonds with glycoluril carbonyl groups. Intramolecular  interaction was observed as well in both derivatives. Due to this intramolecular interaction, the cavity of cationic and neutral derivatives is less accessible to the drug molecules and they are less effective as solubilizing excipients than oligomers bearing anionic groups.

Figure 13. (a) Tetramers 27 with different solubilizing groups. (b) Crystal structures of 27e and 27f showing the intramolecular hydrogen bonds.31

The one of the most recent results in this field of chemistry is the synthesis of chiral molecular containers 27g and 27h based on glycoluril tetramers (Fig. 14)33. Asymmetric centers of these compounds are situated on the side arms and they do not affect the binding significantly. Introducing chiral groups to a closer position to the binding site could make this type of compounds more suitable for chiral recognition.

Figure 14. Structure of chiral tetramers 32 and 33.

2.5 Cucurbit[n]urils Cucurbit[n]urils (CB[n], also abbreviated as Q[n])34 (Fig. 15) are a group of macrocyclic compounds, formed by condensation of glycoluril 1 with formaldehyde catalyzed by strong mineral acids35,36. Characteristic feature of cucurbit[n]urils is barrel-like shape of their molecules and a hydrophobic cavity, which is framed by two rows of carbonyl groups. Carbonyl oxygen atoms are partially negatively charged, therefore, cucurbit[n]urils can bind cationic species by dipole – ion interaction, while nonpolar parts of the molecules can be encapsulated in the cavity due to hydrophobic forces.

Figure 15. Structure of CB[n] (n = 5 -8).36

Cucurbit[n]uril homologues, which are composed from 5 – 8, 1037 and 1438 glycoluril units, have been synthesized so far. Cucurbit[6]uril, which is the most thermodynamically stable representative, can be selectively prepared by the reaction of glycoluril with formaldehyde in concentrated sulfuric acid at temperature around 110 °C. Milder reaction conditions (use of concentrated hydrochloric acid or diluted sulfuric acid, temperature between 75 – 90 °C) lead to mixture of homologues.

Notable property of the cucurbit[n]urils is their great thermal stability. CB[5], CB[6] and CB[8] do not decompose at temperatures below 420 °C, only CB[7] starts decomposing at 370 °C. CB[n] (n = 5 – 7) are stable in concentrated hydrochloric acid at 100 °C for at least one day, CB[8] interconverts into smaller homologues.

It should also be mentioned that cucurbit[n]urils are insoluble in organic solvents and poorly soluble in water. Homologues with odd number of glycoluril units are more soluble than the ones with even number. Solubility increases after addition of salts to solution because of the coordination of cations by carbonyl groups of cucurbit[n]urils. Carbonyls can also be protonated; therefore, the solubility can be enhanced by addition of acid.

2.5.1 Cucurbit[n]uril derivatives Introduction of a functional group on the methine carbons or the methylene bridges of the cucurbit[n]urils can significantly affect their properties. Substituents can enhance solubility of the cucurbit[n]urils not only in water, but also in organic solvents.39, 40 Functional groups, which can be encapsulated in the cucurbit[n]uril cavity, make cucurbit[n]urils self-associate in the solution41. Even the shape of the cavity can be distorted by some substituents (Fig. 16).15

15 Figure 16. (a) Me4CB[6] possesses ellipsoidal cavity. (b) Self-association of 2- phenylethylCB[6] in solid state.41

There are three ways to modify cucurbit[n]urils. Reaction of glycolurils bearing substituents in positions 1 and 5 with formaldehyde leads to cucurbit[n]urils substituted on methine position.15, 42 If different aldehyde than formaldehyde is used for condensation with glycoluril, the resulting cucurbit[n]uril is substituted on methylene bridge.27, 41 It is also possible to modify cucurbit[n]urils directly by radical hydroxylation

6 List of abbreviations

Ac ...... Acetyl APCI ...... Atmospheric pressure chemical ionization ATR ...... Attenuated total reflectance BU[n] ...... Bambus[n]uril, n is the number of 2,4-dialkylglycoluril units CB[n] ...... Cucurbit[n]uril, n is the number of glycoluril units DMF ...... Dimethyl formamide DMSO ...... Dimethyl sulfoxide DOSY ...... Diffusion ordered spectroscopy HR-MS ...... High resolution mass spectrometry ESI ...... Electrospray ionization FTIR ...... Fourier transformation infrared spectrometer IR ...... Infrared spectroscopy ITC ...... Isothermal titration calorimetry Me ...... Methyl NMR ...... Nuclear magnetic resonance Ph ...... Phenyl PTSA ...... p-Toluene sulfonic acid RT ...... Room temperature TFA ...... Trifluoroacetic acid THF ...... Tetrahydrofuran TOF ...... Time of flight UV-Vis ...... Ultraviolet-visible spectroscopy

7 References

1. Steed, J. W. Supramolecular chemistry; 2nd ed.; Wiley: Chichester, UK, 2009.

2. Hirose, K. J. Incl. Phenom. Macrocycl. Chem. 2001, 39, 193.

3. Jansen, K.; Wego, A.; Buschmann, H.-J.; Schollmeyer, E.; Döpp, D. Designed Monomers & Polymers 2003, 6, 43.

4. Kravchenko, A. N.; Sigachev, A. S.; Maksareva, E. Y.; Gazieva, G. A.; Trunova, N. S.; Lozhkin, B. V.; Pivina, T. S.; Il’in, M. M.; Lyssenko, K. A.; Nelyubina, Y. V.; Davankov, V. A.; Lebedev, O. V.; Makhova, N. N.; Tartakovsky, V. A. Russ. Chem. Bull. 2005, 54, 691.

5. Kim, J.; Jung, I.-S.; Kim, S.-Y.; Lee, E.; Kang, J.-K.; Sakamoto, S.; Yamaguchi, K.; Kim, K. J. Am. Chem. Soc. 2000, 122, 540.

6. Svec, J.; Necas, M.; Sindelar, V. Angew. Chem. Int. Ed. 2010, 49, 2378.

7. Stancl, M.; Necas, M.; Taraba, J.; Sindelar, V. J. Org. Chem. 2008, 73 (12); 4671.

8. Ma, D.; Zavalij, P. Y.; Isaacs, L. J. Org. Chem. 2010, 75, 4786.

9. Sijbesma, R. P.; Kentgensf A. P. M.; Lutz E. T. G.; van der Maas, J. H.; Nolte R. J. M. J. Am. Chem. Soc. 1993,115. 8999

10. Nematollahi, J.; Ketcham, R. J. Org. Chem. 1963, 28, 2378.

11. Stancl, M.; Khan, M. S. A.; Sindelar, V. Tetrahedron 2011, 67, 8937.

12. Slezak, F.; Hirsch, A.; Rosen, I. J. Org. Chem. 1960, 25, 660.

13. Goodman, H. G. US 2697714, 1954

14. Vinciguerra, B.; Cao, L.; Cannon, J. R.; Zavalij, P. Y.; Fenselau, C.; Isaacs, L. J. Am. Chem. Soc. 2012, 134, 13133.

15. Zhao, Y.; Xue, S.; Zhu, Q.; Tao, Z.; Zhang, J.; Wei, Z.; Long, L.; Hu, M.; Xiao, H.; Day, A. Chin. Scie. Bull. 2004, 49, 1111.

16. Stancl, M.; Hodan, M.; Sindelar, V. Org. Lett. 2009, 11, 4184.

17. Smeets, J. W. H; Sijbesma, R. P.; Niele, F. G. M.; Wilberth, A. L. S; Smeets, J. J.; Nolte, R. J. M. J. Am. Chem. Soc. 1987, 109, 928

18. Reek, J. N. H.; Priem A. H.; Engelkamp, H.; Rowan, A. R.; Elemans, J. A. A. W.; Nolte R. J. M. J. Am. Chem. Soc. 1997, 119, 9956

19. Smeets, J. W. H.; Van Dalen, L.; Kaats-Richter, V. E. M.; Nolte, R. J. M. J. Org. Chem. 1990, 55, 454.

20. Huang W.-H., Zavalij P. Y., Isaacs L., J. Am. Chem. Soc., 2008, 130, 8446

21. Lagona J., Fettinger J. C., Isaacs L., J. Org. Chem., 2005, 70, 10381

22. Wu, A.; Chakraborty, A.; Witt, D.; Lagona, J.; Damkaci, F.; Ofori, M. A.; Chiles, J. K.; Fettinger, J. C.; Isaacs, L. J. Org. Chem. 2002, 67, 5817.

23. Chakraborty, A.; Wu, A.; Witt, D.; Lagona, J.; Fettinger, J. C.; Isaacs, L. J. Am. Chem. Soc. 2002, 124, 8297.

24. Isaacs, L.; Witt, D.; Lagona, J. Org. Lett. 2001, 3, 3221.

25. Stancl, M.; Gilberg, L.; Ustrnul, L.; Necas, M.; Sindelar, V. Supramol. Chem.2014, 26, 168.

26. Gilberg, L.; Zhang, B.; Zavalij, P. Y.; Sindelar, V.; Isaacs, L. Org. Biomol. Chem. 2015, 13, 4041.

27. Lucas, D.; Minami, T.; Iannuzzi, G.; Cao, L.; Wittenberg, J. B.; Anzenbacher, P.; Isaacs, L J. Am. Chem. Soc. 2011, 133, 17966.

28. Vinciguerra, B.; Zavalij, P. Y.; Isaacs, L. Org. Lett. 2015, 17 (20); 5068.

29. Ma, D.; Hettiarachchi, G.; Nguyen, D.; Zhang, B.; Wittenberg, J. B.; Zavalij, P. Y.; Briken, V.; Isaacs, L. Nat. Chem. 2012, 4, 503.

30. Zhang, B.; Isaacs, L. J. Med. Chem. 2014, 57 (22); 9554.

31. Zhang, B.; Zavalij, P. Y.; Isaacs, L. Org. Biomol. Chem. 2014, 12, 2413.

32. Isaacs, L.; Witt, D.; Fettinger, J. C.; Chem. Commun. 1999, 2549.

33. Lu, X.; Isaacs, L. Org. Lett. 2015, 17, 4038.

34. Day, A.; Arnold, A. P.; Blanch, R. J.; Snushall, B. J. Org. Chem. 2001, 66, 8094

35. Lagona, J.; Mukhopadhyay, P.; Chakrabarti, S.; Isaacs, L. Angew. Chem. Int. Ed. 2005, 44, 4844.

36. Lee, J. W.; Samal, S.; Selvapalam, N.; Kim, H.-J.; Kim, K. Acc. Chem. Res. 2003, 36, 621.

37. Day, A. I.; Blanch, R. J.; Arnold, A. P.; Lorenzo, S.; Lewis, G. R.; Dance, I. Angew. Chem. Int. Ed. 2002, 41, 275.

38. Cheng, X.-J.; Liang, L.-L.; Chen, K.; Ji, N.-N.; Xiao, X.; Zhang, J.-X.; Zhang, Y.-Q.; Xue, S.-F.; Zhu, Q.-J.; Ni, X.-L.; Tao, Z. Angew. Chem. Int. Ed. 2013, 52, 7252.

39. Zhao, J.; Kim, H.-J.; Oh, J.; Kim, S.-Y.; Jae Wook Lee; Sakamoto, S.; Yamaguchi, K.; Kim, K. Angew. Chem. Int. Ed. 2001, 40, 4233.

40. Jon, S. Y.; Selvapalam, N.; Oh, D. H.; Kang, J.-K.; Kim, S.-Y.; Jeon, Y. J.; Lee, J. W.; Kim, K. J. Am. Chem. Soc. 2003, 125, 10186.

41. Gilberg, L.; Khan, M. S. A.; Enderesova, M.; Sindelar, V. Org. Lett. 2014, 16, 2446.

42. Isobe, H.; Sato, S.; Nakamura, E. Org. Lett. 2002, 4, 1287.

43. Bakibaev, A. A.; Yagovkin, A. Yu.; Russ. J. Org. Chem. 1994, 30, 143

44. Jung, M. E.; Deng, G. Org. Lett. 2014, 16, 2142.

45. Francis P.; Kolodny, Nancy H. J. Chem Educ. 1997, 54, 258.

46. Sackett, D. L.; Saroff, H. A. FEBS Letters 1996, 397, 1.

47. Brunsveld, L.; Folmer, B. J. B.; Meijer, E. W.; Sijbesma, R. P. Chem. Rev. 2001, 101, 4071.

48. Gao, L.; Zhang, Z.; Dong, S.; Xue, M. Macromol. Rapid Commun. 2014, 35, 987.

49. Singh, V. K.; Sharma, H.; Singh, S. K.; Gangwar, L. Chem. Biol. Drug Des. 2013, 82, 119.

50. Unoh, Y.; Hirano, K.; Satoh, T.; Miura, M. Angew. Chem. Int.l Ed. 2013, 52, 12975.

51. Zhang, T.; Fan, H.; Zhou, J.; Liu, G.; Feng, G.; Jin, Q. Macromolecules 2006, 39, 7839.

52. Stuart, D. R.; Bertrand-Laperle, M.; Burgess, K. M. N.; Fagnou, K. J. Am. Chem. Soc. 2008, 130 , 16474.

53. Schüttler, C.; Li-Böhmer, Z.; Harms, K.; von Zezschwitz, P. Org. Lett. 2013, 15, 800.