Organic Synthesis with a focus on calixarenes
Although the Arnott group has a general interest in synthetic organic chemistry, the research is currently directed towards the areas of calixarene and resorcinarene chemistry. Both these structures provide a platform for our strategies to elaborate and expand on the chemistry of these molecules who have found applications in
many different areas such as host-guest chemistry, molecular self-assembly, nanotechnology and many other areas. If one has never been exposed to these molecules, it can be surprising at first, since they have a definite 3D shape and cavity, but this is ultimately where the interest in these molecules come from. One advantage is that they are easy to synthesise and can be obtained in multi-gram quantities by even the most inexperienced lab student!
Our focus with these molecules is to develop the chemistry around inherent chirality. This can be a difficult concept ‘see’, but if you consider the picture on the left, you should realise that the two calixarenes are mirror images of each other and that they are non-superposable. This meets all the criteria for chirality, even though there are no typical sp3 chiral carbon atoms. This feature has been known in calixarenes for many years, but precious few methods for their synthesis exist. Indeed we were the first group to come up with a method that enables the synthesis of meta-substituted inherently chiral calixarenes. The method (see scheme below) relies on an ortholithiation strategy using a chiral oxazoline. One of the unusual results was that the diastereoselectivity of the reaction could be switched by simply changing an achiral additive in the reaction.

Our current work in this area seeks to expand the method in a number of directions. The first is to look at other methods that may also be used to synthesise inherently chiral calixarenes, such as ortholithiation directed by chiral sulfoxides. Secondly we are interested in extending the method to the other rings of the calixarene, and thirdly we are looking at applying the method to synthesise specific targets that could act as ligands in asymmetric catalytic processes.
Our work in resorcinarenes has its roots in the PhD work of Gareth Arnott. Like calixarenes, these too can have inherently chiral isomers, but our work for the moment has been on methods for the selective distal functionalization of these molecules. By distal, we mean that some functionality has been introduced on the aromatic rings that are opposite each other in the resorcinarene. We have been interested in whether suitably functionalised versions of these molecules may act as bidentate ligands in transition-metal catalysed processes. So far we have been successful in developing a method for the synthesis of distal functionalised resorcinarenes and we have recently been exploring N-heterocyclic carbene analogues.
Within the department of chemistry and polymer science, we are involved, or have been involved, in a number of collaborative projects, such as dithiadiazolyl chemistry with Delia Haynes, polymer functionalization with Bert Klumperman and Peter Mallon, and organic synthesis with Willem van Otterlo.
Current members of the Arnott group
M.Sc. (2018—2019)
Ph.D. (2020—)
Past members of the Arnott group
M.Sc. (2015—2017)
Ph.D. (2018—2022)
M.Sc. (2016—2017)
Ph.D. (2018—2021)
Postdoc (2019)
Ph.D. (2013—2019 )
M.Sc. (2017—2019)
Postdoc (2016—2017)
M.Sc. (2015—2017)
Ph.D. (2013—2016)
M.Sc. (2010—2012)
Ph.D. (2013—2016)
Postdoc (2015)
M.Sc. (2008—2009)
Ph.D. (2010—2015)
NRF Intern (2014—2015)
NRF Intern (2014)
M.Sc. (2011—2013)
M.Sc. (2010—2011)
Ph.D. (2008— )
Ph.D. (2008—2011)
Research Publications
Organic chemistry is notorious for being difficult to learn. Herein we describe a two-pronged approach to engage students in the ability to afford successful knowledge building. We have drawn on focus group interviews with students to show that the approach is appreciated by the students. The two prongs comprise peer learning in small groups and the use of knowledge stratification. This stratification is achieved via the epistemic assessment framework and distinguishes between different kinds of knowledge that are operational in teaching chemistry. Formal assessments can be visually categorized with the EAF allowing students to judge their progress. In the small group tutorials, self-assessment of their contribution to the final submission also supports reflection on their own understanding.
The in silico adsorption of 53 cyclic scaffolds to the fastest-growing (001) face of a β-hematin crystal identified the phenoxazine scaffold for further derivatization. A small library of 2- and 3-substituted amino-phenoxazine compounds with predicted β-hematin inhibitory activity were synthesized. P2a shows the most promising β-hematin inhibition and antiplasmodium activity.
Inherently chiral calix[4]arenes with C4-symmetry are extremely rare and difficult to synthesise, severely hampering any effort to expand on their potential as chiral supramolecular catalysts and building blocks. Herein we report a reaction of a tetracarbamate calix[4]arene with NBS which results in a high yield of an inherently chiral calix[4]arenes with C4-symmetry. Furthermore, employing a chiral N-Boc proline moiety allows for separation of the diastereomers formed, thus obtaining the pure enantiomers after hydrolysis. The enantiomers could be assigned based on the CD spectra and DFT calculated values.
The ipso-bromination of calix[4]arenes using bromine has been investigated and provides a direct method to tetra-bromocalix[4]arene in a single step in excellent yield (>90%). The method is also applicable to directly forming tribromocalix[4]arene in appreciable amounts (>60%). It was found during this study that a number of important reaction variables were very important for success, namely exclusion of light, temperature control, purity of starting material, solvent used and rate of bromine addition.
C–H activation offers an intriguing access into inherently chiral calix[4]arenes, but has been little explored in the literature. In this article, we report our investigation into a published C–H activation method that uses carbamates to direct a palladium catalyzed C–H activation and subsequent reaction with N-bromosuccinimide. However,we show that this report is unfortunately flawed on a number of points. An earlier reported study revealed the more likely SEAr mechanism of the bromination reaction, which did not involve palladium catalysis. We nevertheless employed the SEAr bromination in an attempt to form inherently chiral calix[4]arenes, using a chiral (+)-menthyl carbamate as a directing group. Unfortunately, although the reaction was high yielding, the diastereomers formed were inseparable and we were unable to quantify their ratio. Subsequent removal of the chiral (+)-menthyl carbamate, returned a small positive optical rotation, suggesting that at least a level of asymmetric induction was achieved in the bromination to afford a non-racemic product.
A calix[4]arene boronic acid was synthesized and tested for catalysis in amide formation. The results were positive and paved the way for future designs, even though protodeboronation was observed under the conditions employed.
This article looks at the chemistry surrounding the concept of inherently chiral calixarenes (ICCs), whose synthesis and application have only recently being realised. One challenge in the area of ICC chemistry is the sheer breadth and scope for installing different aspects of inherent chirality. The aim of this article is not to cover every known method, but rather to give the reader an overview of the main themes that have emerged in this area, including more recent additions to the literature. This overview will also touch on the very limited reports on the applications of ICCs which give a glimpse into the potential these compounds may have in future studies.
In pursuit of nonracemic, inherently chiral calix[4]arenes, we describe herein the application of a chiral tert-butyl sulfoxide in asymmetrically directing ortholithiation on a calix[4]arene. We demonstrate good diastereoselectivity (dr = 95:5) in the reaction, and also provide proof of the major diastereomer through single-crystal X-ray diffraction.
The synthesis and characterization of a distally bridged, bidentate resorcinarene bis(carbene) palladium complex is described for the first time. Preliminary catalytic studies show promise for future developments along this framework.
A simple one pot orthogonal procedure for synthesizing α-aldehyde, ω-thiol heterotelechelic poly(N-vinylpyrrolidone) (PVP) is introduced. Firstly we designed a xanthate chain transfer agent with an acetal protected aldehyde functionality in the leaving group, then we synthesized α-acetal ω-xanthate end-functional PVP, via a RAFT-mediated polymerization. The end-groups were modified via a facile, modular protocol, by first aminolysing the ω-xanthate end-groups to form thiols, using an excess of a primary amine, and subsequently acidifying the reaction medium to simultaneously convert excess primary amine to its (non-interfering) quaternary ammonium salt form, as well as effect the acid-catalysed deprotection of the acetal into an aldehyde functionality, to access the α-aldehyde, ω-thiol-PVP. Finally, we demonstrated the utility of these end-groups by performing conjugations with model small molecules. This study establishes a facile procedure for accessing different and bio-relevant end-functional groups with a biocompatible vinyl polymer, suitable for making drug delivery vehicles.
Herein, we describe an improved method to synthesise mono-, di- and tetra-cyanocalix[4]arene and report their crystal structure determinations. We also report our attempts to further functionalise the cyanocalix[4]arenes into dithiadiazolyl-calix[4]arenes, and propose a hypothesis as to why the cyano group on a calix[4]arene is an extremely challenging group to modify.
A comprehensive review on the chemistry related to the isomerization of allylbenzene derivatives.
The diastereoselective oxazoline-directed lithiation of calix[4]arenes is reported with diastereoselective ratios of greater than 100:1 in some instances. Notably, it has been found that the opposite diastereomer can be accessed via this approach merely through the choice of an alkyllithium reagent. The inherently chiral oxazoline calix[4]arenes have also been preliminarily examined as ligands in the palladium-catalyzed Tsuji–Trost allylation reaction, returning results comparable to their planar chiral ferrocene counterparts pointing towards future application of these types of compounds.
A bis-frustrated Lewis pair based on a calix[4]arene skeleton is reported for the first time. Importantly, this system has been shown to activate two molecules of hydrogen, thereby establishing a proof of concept for multisite frustrated Lewis pair (FLP) design and synthesis. The complex [calixarene-(Mes2PH+)2][BH(C6F5)3–]2 (6) has been characterised by X-ray crystal structure analysis.
The sense of asymmetric ortholithiation directed by a chiral oxazoline may be inverted simply by the choice of achiral ligand. Comparison of results with a number of ferrocenyl oxazoline derivatives suggests that lithiation takes place by coordination to the oxazoline nitrogen irrespective of the ligand used.
The development of an ortholithiation approach to distal-functionalised resorcinarenes is described, greatly simplifying the current strategies available.
Employing a chiral oxazoline as an ortholithiation directing group allows the synthesis of inherently chiral calix[4]arenes suitable for elaboration into planar chiral molecules. An important finding has been that the diastereoselectivity of the reaction can be tuned by the choice of additive. These results have bearing on the elucidation of the general mechanism of oxazoline-directed ortholithiation.
A novel distal bidentate S/S resorcinarene ligand has given the first crystal structure evidence for a bispalladium-µ-chloro-bridged complex bound to thioether ligands.
A general asymmetric synthesis of inherently chiral calix[4]arenes is described: using a chiral oxazoline derived from L-valine, an ortholithiation strategy is employed to give inherently chiral calix[4]arenes with high (93%) enantiomeric excesses. A crystal structure of a phosphine oxide intermediate has been obtained, unambiguously assigning the major diastereomer in the reaction; a mechanism explaining this result is proposed.
Treatment of N-arylisonicotinamides with trifluoromethanesulfonic anhydride triggers intramolecular nucleophilic attack of the aryl ring on the 4-position of the pyridinium intermediate. The products are spirocyclic dihydropyridines which can be converted to valuable spirocyclic piperidines related to biologically active molecules such as MK-677.
On activation by pyridine N-acylation, enolates of N-nicotinoyl and N-isonicotinoyl glycine and alanine derivatives cyclize to yield 6,5-azabicyclic or 6,4-azaspirocyclic lactams. With an N-α-methyl-p-methoxybenzyl group the cyclization is diastereoselective; hydrogenation and deprotection yields azabicyclic amino acids in 94:6 er.
The enantioselective addition of diethylzinc to benzaldehyde catalysed by a range of chiral bridged resorcinarenes has been studied, and the results used as a means of probing cooperative effects in the resorcinarene bowl. A structure–activity relationship has emerged in which bridged resorcinarenes with little available room in the bowl (e.g., 3b, 3c) favour R-enantioselectivity in the product, while those promoting cooperative effects in the bowl via coordination sites in the bridge (3e) or strong donor protecting groups (3j) favour S-enantioselectivity. A mechanistic hypothesis based on Noyori's model to account for these trends has been put forward in which stereoselectivity is dependent on two factors as the ratio of axially diastereomeric anti-zincoxazines as well as the exo or endo bias of active zinc. The model explains why ee's are never greater than around 50% and indicates asymmetric induction to be due to the axial chirality in the bowl as a result of chirality transfer from the bridge, rather than due to induction via the central chirality in the line of the bridge. As a result, the model stimulates some new fascinating possibilities in enzyme mimicry.
A full study of the synthesis of chiral, bridged resorcinarenes (3a–3l, 13a, 13b) is presented using Mannich condensation of C2v-tetraprotected resorcinarenes with chiral 1,n-diamines bearing homochiral α-methylbenzyl auxiliaries at each terminal nitrogen. The study has revealed the methodology to be applicable to preparing a broad range of bridged structures with varying lengths of bridge, different functionality in the bridge and various protecting groups on the upper rim. Reproducible and satisfactory yields in the reaction were only obtained with the pendant R group as methyl. The bridged adducts have been fully characterized by a range of spectroscopic techniques, and NMR has revealed varying trends in the way the various bridges protrude into the cavity. Low temperature NMR as well as X-ray structures of tetramesylate 15 and tetratoluate 3g has revealed hydrogen bonding to the amine nitrogens in the bridge to be an important control element for positioning the bridge relative to the cavity of the bowl. The derivatives provide chiral templates for asymmetric catalysis studies using cooperative effects in the bowl.
New methodology for 2-alkylation of 3-furoic acids is presented involving Wittig reactions of the 3-methoxycarbonyl-2-furanylmethylphosphonium salt. The methodology has been used to prepare a tethered 2-alkylated-UC-781/d4T conjugate as a potentially new type of HIV reverse-transcriptase inhibitor.
Methodology is presented for synthesis of the first examples of chiral, bridged resorcinarenes with functionality in the bridge as possible sites for intracavity asymmetric catalysis. A preliminary study comparing unfunctionalised with functionalised lines using the enantioselective addition of diethylzinc to benzaldehyde as a probe reaction, provides compelling evidence for intracavity catalysis.
Organic Chemistry @ Stellenbosch University