PALAU‘AMINE 26 June 2017 | Faculty of Chemistry | B.Sc. Biomolecular Engineering | Prof. Dr.

Wolf-Dieter Fessner | Juliane Müller, Duc Le Ngoc, Jan Krumbach, Lara Kopp

The Structure and its Revision: Palau’amin was discovered in a sea sponge family

named Stylotella agminata found in the southwest

Pacific Ocean. This chemical substance is believed

to be poisonous and was first isolated and

described in 1993. Palau’amin contains nine

nitrogen atoms making it very difficult to define its

structure precisely. Therefore, the configuration -

which has been found before - was still being

researched. Until 2007, the highly complex

structure of the molecule was once again pinned down and officially confirmed in 2010.

Defining a 100% correct structure of an organic substance is not an easy job. It requires a

combination of many researching methods such as NMR-Spectroscopy, and especially time

(here, nearly a decade). In the case of Palau’amin, the researchers could not interact directly

with the molecule and had to work with other derivatives or substances likely to have similar

atomic structures.

While working with the molecule, scientists discovered that the coupling constant between

the protons H11 and H12 (14,1 Hz) was too big for a cis-conjunction. However, it matched

the experimental records of the already known spiro-annulated 5-rings. Considering this

inconsistency, they didn’t stop there, and a lot of different experiments were continuously

performed. Finally, it showed that the structure published in 1993 is false - the conjunction of

H11, H12 must be trans.

So why did they think that the cis-conjunction is more likely?

The explanation for this assumption is that the energetic difference between cis- and trans-

conjunctions is 27 kJ/mol, making the cis-conjunction more stable and thus preferred by the

molecule. Furthermore, not so many trans-conjunctions have been documented up to that

time to make a good comparison.

The revision of the atomic structure of Palau’amine was done with the research of the

distance between protons (H-atoms) by Dr. Achim Grube and Dr. Matthias Köck. They did

some experiments on Tetrabromstyloguanidin and the results were processed and presented

in form of a diagram. The distances of 1,3-protons of the revised structure strongly matched

with the experimental records. Besides,

the conformation of the cyclopentane

ring in the new structure is in “envelope”

form and the chlorine atom is in

equatorial position. In contrast to the

revised form, the conformation of the

older one is in “twist” form and the

chlorine atom is in axial position. It is very

possible that this change in conformation

leads to the difference of the distance

between protons H12/H17, explained

through the interaction of one atom to

the other.

2007 1993

Key

Black Bar: Old Configuration

White Bar: Revised Configuration

Grey Bar: Experimental Figures

In 2010, three years later, the atomic structure of Palau’amin was once again confirmed

thanks to the cooperation of Dr. Köck and Dr. Volker Schmidts (AK Thiele, Technical

University of Darmstadt). A method called “residual dipolar couplings” (in short, RDCs) was

used. The molecule in question (Dibrompalau’amin) is surrounded by a liquid crystal or an

aligned medium (in this case: PAN Gel) leading to the interaction between the molecule and

the medium. In other words, the effect is the “partial orientation with respect to the magnetic

field” [http://www.chemie.tu-darmstadt.de/thiele/forschung_9/nmrspektroskopie/rdc/rdc.en.jsp,

19.06.2017, 11:35 am].

The Biosynthesis of Palau’amine: Up to this point the biosynthesis of Palau’amine has not been studied in living organisms . The

most prominent hypothesis assumes that many Pyrrole-Imidazole-Alkaloids are formed out

of an intermediate product - the so called Preaxellinamine - during the synthesis in living

organisms.

The Preaxinellamine is most likely synthesised in three different ways:

The first two mechanisms are based on ring modifications (expansion and contraction,

respectively) of alkaloids; the third assumes a linear dimerization.

1) The Ring Expansion:

The ring expansion of the alkaloid sceptrin consists of the assembly of a positively charged

oxygen atom at the aminoimidazole-ring. In consecutive rearrangements of electrons, the

neighbouring cyclobutane-ring transforms into a cyclopentane-ring.

❖ twisted-form ❖ old conformation

❖ envelope-form ❖ new conformation

2) The Ring Contraction:

The ring contraction of Ageliferin is very similar to the ring expansion in its general order of

reaction. A hydroxy- and chloride group are added during the process. Instead of a ring

expansion of cyclobutane, the process is concluded after a ring contraction of a neighbouring

cyclohexane.

Ageliferin and Sceptrin have been found in organisms producing pyrrole-immidazole-

alkaloids, which supports the first two theses.

3) The Linear Dimerization:

Two linear oroidine-molecules dimerize in an enantio- and stereoselective way. A chloride

and a hydroxy-group are added and induce a cyclisation of a pentane-ring.

The linear dimerization hypothesis can be seen as the missing link between relatively simple

molecules (Oroidine) and complex pyrrole-imidazole alkaloids.

Finally, the actual Palau’amine synthesis consists of the oxidation of an amino-imidazole-ring

and consecutive internal rearrangements. After the separation of a pyrrole-remnant the

synthesis is concluded.

The chemical synthesis of Palau’amine:

It has been very difficult to find a way to synthesize the

molecule because of its daunting structural and physical

attributes, which are consisting of nine nitrogen atoms, eight

contiguous stereogenic centres, a lot of reactive

(hemi)aminals, oxidation-prone pyrroles and highly polar, non-

crystalline morphologies.

Compared to its’ two structural family members, the

axinellamines and massadines, Palau’amine additionally

possesses a very unique chemical challenge: The pyrrole-

amide sidechain embedded in a hexacyclic core architecture

containing a highly strained trans substructure (aka: the 5,5’-fused system) - which is

unprecedented among natural products and has always been a problem with Palau’amine

(see: the revision from cis to trans).

This structure possesses a high degree of

strain, and thus there have been many

thwarted attempts at a biomimetic or

stepwise closure. In the paper “Total

Synthesis of Palau’amine” by the lab of

Prof Dr Phil Baran – who, after years of

research, proceeded to be the first lab to

synthesize Palau’amine - was even written:

“Many well-founded and logical plans to

secure the peculiar trans-5,5 core of

Palau'amine in our laboratory resulted in

unfortunate outcomes” [p. 1, line 24 f.].

They secured their victory in the run for the chemical synthesis of Palau’amine in 25 precise

steps, outgoing from commercial material. Here, we describe the final and most important

steps through which Baran accomplished the complicated ring closure beginning from a

similar intermediate to his 2007 total synthesis of the axinellamines, which features a readily

available cyclopentane core.

The teams first move was to install the sole hydroxyl group using silver(II)-picolinate; this

entailed the stereo- and chemoselective transformation targeting only the secondary amine.

The next aim was to build the second 2-aminoimidazole ring, which has been done by adding

cyanamide in brine. Other solvents would have most likely resulted into the secondary

chloride of the molecule to be replaced; also, having a load of chloride ions in solution is told

to favour the desired side of the reaction step equilibrium.

Following this was the bromination of the new aminoimidazole ring, as it provides a functional

handle for the next fragment coupling – a masked pyrrole synthesis; or more specifically,

done with a pyrrole surrogate and masked by the amidine tautomer of the molecule.

To complete the C-N linkage, an alkylation followed by a series of acid mediated methanol

eliminations to obtain the aromatic heterocycle has been done; this has been conveniently

achieved with the free acid functional group.

A hydrogenation using palladium acetate in a hydrogen atmosphere then reduced the azide

groups to a pair of primary amines, and the following treatment of the amino acid system with

EDC (1-ethyl-3-(3-dimethylaminopropyl)carbodiimide)/HOBt (N-hydrobenzotriazole)

formed a macrolactone, presumably favouring the nine-member ring over the ten; this

macrocycle, named ‘macro-palau’amine‘ by Baran was the key to his synthesis.

Finally, it just needed the addition of acid, which promoted a transannular cyclisation

between amide nitrogen N-14 and imine C-10 - and astoundingly, this particular reaction is

selective for the trans-configured 5,5′-fused system, and thereby completes the synthesis of

Palau’amine.

We want to thank Dr Volker Schmidts of the TU Darmstadt Thielelab for his help and cooperation

with us for this project.

REFERENCES:

Research Papers:

▪ The Total Synthesis of Palau‘amine, Published: 29 December 2009 by Phil S. Baran Prof. Dr.

et.al. in „Angewandte Chemie“

Weblink:

http://onlinelibrary.wiley.com/store/10.1002/ange.200701798/asset/6706_ftp.pdf;jsessionid=

E150E2434FAF6317DE82C911005F3B7B.f01t01?v=1&t=j3q00g75&s=3ed52a9128aef0

5873d70ef1196dbf51954dcf9f

▪ Die Jagd auf Palau‘amin, Published: 24 April 2007 von Matthias Köck, Achim Grube et.al. in

„Angewandte Chemie“

Weblink:

http://onlinelibrary.wiley.com/doi/10.1002/ejoc.201001392/epdf

Other Articles:

▪ http news.softpedia.com/news/Excalibur-Compound-Finally-Synthesized-132182.shtml

▪ http://www.chemie.tu-darmstadt.de/thiele/forschung_9/nmrspektroskopie/rdc/rdc.en.jsp

Graphics:

▪ https://www.macfound.org/media/photos/baran_2013_hi-res-download_2_1.jpg

▪ https://www.wired.com/images_blogs/wiredscience/2010/01/palausponge.jpg

▪ https://i.ytimg.com/vi/7Kna4xhxSHA/maxresdefault.jpg

▪ http://onlinelibrary.wiley.com/enhanced/figures/doi/10.1002/ange.200701798#figure-viewer-

sch1

▪ https://www.chemie.tu-darmstadt.de/thiele/gruppe/mitarbeiter_10/volkerschmidts/index.de.jsp

▪ http://i1-news.softpedia-static.com/images/news2/Excalibur-Compound-Finally-Synthesized-

2.jpg