Synthesis and Structural Evaluation of 5-Methyl-6-acetyl Substituted Indole and Gramine

The synthesis and crystal structures of 1-(5-methyl-1H-indol-6-yl)ethan-1-one (7), C11H11NO, and 1-{3-[(dimethylamino)methyl]-5-methyl-1H-indol-6-yl}ethan-1-one (8), C14H18N2O, are reported. The synthesis is based on the Diels–Alder cycloaddition of a substituted 2H-pyran-2-one derivative, followed by an acid-catalyzed cyclization and concomitant deprotection (the last two steps were carried out as a one-pot domino process) yielding substituted indole 7, which was further derivatized via Mannich reaction to the gramine derivative 8. Both structures 7 and 8 were determined on the basis of IR, H NMR and mass spectroscopy, as well as by the elemental analysis and melting point determination. According to the single-crystal X-Ray diffraction analysis, the structure 7 has a single unique molecule in the asymmetric unit whereas the structure 8 contains four unique molecules in the asymmetric unit. Molecules 7 are linked via N–H···O hydrogen bonds between the secondary amine group and carbonyl moiety of the acetyl group of adjacent molecules, whereas molecules 8 are linked via N–H···N hydrogen bonds between the secondary and tertiary amine groups of adjacent molecules. Both structures are further stabilized by weak C–H···O, C–H···π and π···π interactions.


Introduction
Gramine, 3-(N,N-dimethylaminomethyl)indole, is a simple indole derivative with important functions in the plant world.The essential amino acid tryptophan and its derivatives are biosynthesized from gramine.Gramine was isolated for the first time from the giant cane (Arundo donax), has a role as an alkaloid in barley (Hordeum vulgare) and is of importance in many other plants. 1,2urthermore, gramine represents a valuable precursor for further derivatizations towards other targets, for example for the preparation of 1,3-disubstituted β-carbolines by the reaction of gramines with α-(alkylidenamino)nitriles in the presence of tributylphosphine 3 and for the synthesis of the 2-prenyl tryptophan core of the tryprostatins A and B. 4 For the quaternary gramine derivatives it was shown that they can be used as suitable sources of the 3-methylindole fragment in various diastereoselective alkylations, as recently described by Reinfelds et al. 5 Gramine has also found utility as a part of N-substituted phosphines that were used as ligands in Suzuki-Miyaura coupling reactions of aryl halogenides, conducted at room temperature in a suitable ionic liquid, thus achieving in-creased yields in comparison with standard ligands containg amine groups. 6ramine derivatives also possess various biological activites; recently it was found that a gramine derivative (i.e.N-[(1H-indol-3-yl)(pyridin-2-yl)methyl]benzo [d]  thiazol-2-amine) having a pyridine and a benzothiazole moiety in its structure selectively inhibits human enterovirus 71 (EV71), a known agent of hand, foot and mouth disease in children associated with severe neurological problems, including death; on the other hand, the parent gramine does not inhibit EV71. 7he synthetic approach used toward gramine and its derivatives is most often Mannich reaction 8 of the corresponding indoles: the position 3 of the indole framework (being the most nucleophilic) attacks an intermediate formed from formaldehyde and a secondary amine.The reaction can be accelerated by the application of suitable additives, Dai et al. 9 have successfully applied zinc chloride among various other options.Such synthesis generally takes place at room temperature and is finished in a relatively short time (typically 90 min).
The scope of such reaction can be further broadened by the application of various aromatic aldehydes (instead Kukuljan et al.: Synthesis and Structural Evaluation ... of formaldehyde) and various heterocyclic compounds (instead of secondary amines) as demonstrated by Ke and co-workers. 10During their synthetic protocol there was no need to use any catalysts or solvents.
Analogues of gramine can be also prepared by the reaction between substituted 1,4-piperazines, 1H-indole and formaldehyde.With such an approach, Köksal Akkoç et al. 11 were able to synthesize compounds with increased cytotoxicity against human carcinoma cells compared with the other commercially available agents, such as the standard drug 5-fluorouracil.
Herein we present a straightforward approach towards a substituted gramine based on a Diels-Alder reaction between a corresponding 2H-pyran-2-one (acting as a diene) and a suitable dienophile (i.e.(Z)-1-methoxybut-1-en-3-yne) yielding a cycloadduct that is in the next step transformed into the desired indole, which is further derivatized via Mannich reaction to the substituted gramine.

1. Materials and Measurements
Melting points were determined on a micro hot stage apparatus and are uncorrected. 1H NMR spectra were recorded with a Bruker Avance DPX 300 spectrometer at 29 °C and 300 MHz using Me 4 Si as an internal standard.IR spectra were obtained with a Bio-Rad FTS 3000MX as KBr pellets.MS spectra were recorded with a VG-Analytical AutoSpec Q instrument.Elemental analyses (C, H, N) were performed with a Perkin Elmer 2400 Series II CHNS/O Analyzer.TLC was carried out on Fluka silicagel TLC-cards.All reagents and solvents were used as received from commercial suppliers.

Crystallography
Single-crystal X-ray diffraction data were collected at room temperature on an Agilent Technologies SuperNova Dual diffractometer using Cu-Kα radiation (λ = 1.54184Å).The data were processed by CrysAlis Pro. 13 Structures were solved by direct methods implemented in Superflip 14 and refined by a full-matrix least-squares procedure based on F 2 using SHELX2014. 15All non-hydrogen atoms were refined anisotropically.Hydrogen atoms were readily located in a difference Fourier maps and were subsequently treated as riding atoms in geometrically idealized positions, with C-H = 0.93 (aromatic), 0.97 (methylene) or 0.96 Å (CH 3 ), N-H = 0.86 Å and with U iso (H) = k-U eq (C or N), where k = 1.5 for methyl groups, which were permitted to rotate but not to tilt, and 1.2 for all other H atoms. Crystallographic data are listed in Table 1.
where n is the number of reflections and p is the total number of parameters refined.

1. Synthesis
7][18][19][20][21] Here we applied (Z)-1-methoxybut-1-en-3-yne (4) as the dienophile cycloadding on 2H-pyran-2one derivative 3 yielding a crucial intermediate 5, a substituted N-{2-[(Z)-2-methoxyethenyl]phenyl}benzamide (Scheme 1).This intermediate 5 has a strategically positioned methoxy group bound to the ethenyl fragment being in an ortho position to the benzamido group, therefore enabling a straightforward cyclization towards the indole ring (i.e. 6) already under mildly acidic conditions, as described previously. 12However, an indole 6 obtained in such a way still contains an N-benzoyl protection group that needs to be removed to yield the indole 7. One possibility to achieve this could be the application of aqueous NaOH in a mixture of water and acetonitrile with gentle heating. 22n the other hand, our strategy was to combine both steps described above, i.e. the cyclization (5 → 6) and the removal of the N-benzoyl group (6 → 7) into a single step.Even though the first step needs acidic conditions and the second takes place in an alkaline solution, with a suitable choice of reaction parameters we were able to implement both transformations as a one-pot domino procedure.Primary cycloadduct 5, N-{2-[(Z)-2-methoxyethenyl] phenyl}benzamide derivative, was thus dissolved in acetonitrile, aqueous HCl was added and the mixture was stirred at room temperatue; thereafter enough aqueous NaOH was added to neutralize the excess HCl and to increase the pH to an appropriately alkaline value (pH approx.10) for the deprotection to occur (upon gentle hea-ting).Such approach to 7 shortens the synthetic pathway towards 7 and increases its final yield (86% yield after a one-pot procedure 5 → 7 vs. 71% combined yield over two separate steps).
Resonances in the 1 H NMR spectrum of the indole 7 are in agreement with those expected: both methyl groups were observed as singlets (at δ 2.636 and 2.639 ppm), together with the four aromatic protons (in the range δ 6.50-7.84ppm) and the amino proton as a singlet at δ 8.38 ppm.In the IR spectrum of 7 bands correspond to the NH group at 3318 cm -1 and carbonyl group at 1642 cm -1 .
The starting indole 7 was thereafter derivatized under standard Mannich reaction conditions (with formaldehyde and dimethylamine in ethanol as the solvent and with zinc chloride as the additive) 8 to form the 6-acetyl-5methylgramine derivative 8.
For the gramine derivative 8 in the 1 H NMR spectrum appropriate signals were observed: all four methyl groups as singlets (dimethylamino group at δ 2.29 ppm and the remaining two methyl groups at δ 2.59 and 2.62 ppm), the methylene group as a singlet at δ 3.61 ppm, the three aromatic protons (in the range δ 7.22-7.73ppm) and the amino proton as a singlet at δ 8.88 ppm.In the IR spectrum of 8 bands correspond to the NH group at 3085 cm -1 and carbonyl group at 1669 cm -1 .

Conclusion
With the Diels-Alder reaction between a substituted 2H-pyran-2-one and (Z)-1-methoxybut-1-en-3-yne as the dienophile we have prepared a cycloadduct that was in the next, one-pot domino process cyclized and deprotected into the desired 5-methyl-6-acetyl substituted indole and further derivatized via Mannich reaction to the 5-methyl-6-acetylgramine.Single-crystal X-ray diffraction analysis of both compounds provided a valuable insight into their molecular structures as well as the mode of packing and crystal architecture showing that in the indole derivative the molecules are linked via N-H•••O hydrogen bonds between the secondary amine group and carbonyl moiety of the acetyl group of adjacent molecules, whereas the molecules of gramine are linked via N-H•••N hydrogen bonds between the secondary and tertiary amine groups of adjacent molecules.In both structures weak C-H•••O, C-H•••π and π•••π interactions were also observed.

Figure 1 .
Figure 1.Molecular structure and atom numbering scheme for 7. Probability ellipsoids are drawn at the 50% level.

Figure 2 .
Figure 2. View of unique molecules in the asymmetric unit of 8 with the atom numbering scheme.Probability ellipsoids are drawn at the 50% level.
These chains are cross-linked into sheets by weak C11-H11C•••O1(x, y + 1, z) hydrogen bonding between the hydrogen atom of the acetyl moiety of one molecule and carbonyl oxygen of the other molecule generating the graph set motif C(4).Furthermore, this 2D structure in 7 is stabilized by additional π•••π interactions between the five membered pyrrole ring N1/C1-C3/C8 (centroid Cg1) and the six membered C3-C8 ring (centroid Cg2) of the other molecule, with a Cg1•••Cg2(x, y + 1, z) centroid-to-centroid distance of 4.3536( Additional weak C-H•••π interactions between C9-H9A•••Cg2(x, y -1, z) with hydrogen-to-centroid distance 3.688(3) Å also stabilize the structure.In the crystal structure 8 four unique molecules are linked via N-H•••N hydrogen bonding between the indole NH group of one molecule and the tertiary nitrogen atom of the dimethylamino group of the adjacent molecule into infinite zig-zag chains generating the graph set motif C(6).In each zig-zag chain two out of four unique molecules are involved.Chains are stabilized by weak C-H•••π interactions between the CH group of the pyrrole moiety

Figure 3 .
Figure 3. Zig-zag chain formation via N1-H1•••O1 hydrogen bonding with graph set motif C(7) in 7. Hydrogen atoms not involved in the motif shown have been omitted for clarity.

Table 1 .
Crystal data and refinement parameters for the compounds 7 and 8.