The aim of this chapter is to undertake a comprehensive kinetic analysis of an inter- connected system of two structurally-similar self-replicators, and to investigate how the selectivity for one replicator over another changes in the presence of instructing preformed template. The two replicators are connected by a shared nitrone building block,NF, which can react with a maleimideM1andM2through 1,3-dipolar cycload-
dition reactionsato form two replicators:T1andT2(Scheme 3.1). Previous work in
the Philp laboratory has demonstrated126,199that both of these replicators are capable of establishing efficient autocatalytic cycles. Nevertheless, these two replicators,T1and T2, have thus far never been examined under competition conditions—a situation where both maleimides are present in the reaction mixture simultaneously, competing for a limited amount of a shared nitrone starting material. Similarly, the ability ofT1andT2 replicators to template the synthesis of each otherviathe crosscatalytic pathways has not been investigated and will be probed through template instructed kinetic experiments in this chapter. Finally, the comprehensive kinetic analysis will be supplemented by kinetic fitting and simulations with the view to probing the resolution of a network of T1andT2replicators, thereby establishing the limits on selectivity in the competing replication processes in a closed reaction format, driven by kinetic selection.
N N H O N+ O- F N N O O O O CO2H C8H17 CO2H T2 T1 M2 M1 NF N N H O O N N F O O N N H O O N N F O O HO2C H H H H C8H17 HO2C
Scheme 3.1 Schematic representation ofT1–T2replicating network formed by 1,3-dipolar cycload- dition betweenM1andM2maleimides with nitroneNF. Throughout this chapter,T1 cycloadduct and the recognition-processes pertaining to it will be represented in red, while blue colour will be used to representT2.
3.2.1 Recognition and reaction processes in the system
ReplicatorsT1andT2are equipped with two recognition elements: an amidopyridine moiety and a carboxylic acid group. The main distinguishing feature of these two replicators is the position of the carboxylic acid group, located on each maleimide. In maleimideM1, and thus also replicatorT1, the carboxylic acid recognition site is a
aThe 1,3-dipolar cycloaddition reaction between a nitrone and a maleimide can give two diastereoiso- mers:trans and cis. Only the trans diastereoisomer is capable of taking part in template-directed replication processes in the network ofT1andT2replicators, and, thus, the notation of the cycloadduct products capable of replication will generally omit thetransnotation throughout this thesis (for example,
trans-T1will be generally referred to asT1), unless emphasis on the identity of the diastereoisomer is necessary.
phenylacetic acid present in positionpararelative to the maleimide ring (Figure 3.1). MaleimideM2, in comparison, is equipped with a benzoic acid functionality, in position
metawith respect to the maleimide ring—a feature that is conserved in replicatorT2 (Figure 3.1). The 6-methyl amidopyridine recognition site, originating from the shared nitrone building block, is identical in both replicators and was selected out of the various amidopyridine recognition units possible for its favourable solubility properties and the large difference between theKavalues determined for its association with a phenylacetic
acid and a benzoic acid based compounds. Therefore, the difference in the recognition processes within each replicator system, as well as the variation in the length of the formed template as a result of the position of the carboxylic acid, was envisaged to produce a network of two replicators, referred to as theT1–T2network, with interesting crosscatalytic behaviour. N N O H O O H N N N O H O O H C8H17 N O O O O CO2H Br Br CO2H N N O H O A 1020 830 680 3750 3320 2950 0 5 10 (a) (b) (c) M2 M1 NF NF Phenyl Benzoic Ka/M–1 Temp. / °C
Figure 3.1 The hydrogen-bonding-mediated recognition between a 6-methyl amidopyridine moiety on nitroneNFand carboxylic acid recognition site present in(a)phenylacetic acidM1 maleimide and(b)benzoic acid maleimideM2.(c)Association constants (Ka/ M 1) deter- mined for the interaction between aldehydeA(analogue ofNF) and 4-bromophenylacetic acid (analogue ofM1) and 4-bromobenzoic acid (analogue ofM2) at 0 C and 10 C.Ka values for temperature 5 C were determined through van’t Hoff plot and are highlighted in red (T1) and blue (T2).
The formation of the two replicators relies on the 1,3-dipolar cycloaddition reac- tion between a nitrone and a maleimide. The minimal model of self-replication was introduced and described in detail inChapter 1. The maleimide components bear a COOH recognition group which allows these components to associate with the ami- dopyridine moiety on the NF. The single point recognition event can mediate the
formation of binary complexes [M1·NF] and [M2·NF] which can produce a ‘closed’
template,cis-T1 and cis-T2, via the recognition-mediated binary complex reaction pathway. These closed cis products possess no free recognition sites and are thus catalytically-inactive. Alternatively, the maleimides can react with the nitrone through an uncatalysed and template-independent bimolecular pathway, to give both thecis
andtransdiastereoisomeric products of each replicator. Only thetranscycloadducts
assembly of the maleimide and nitrone components in to the catalytically-active ternary complex [T·M·NF] (whereMdenotes a maleimide).
The slight structural difference in the recognition element inT1andT2, crucial for the ability of these systems to take part in recognition-mediated reactions, is expected to manifest in their ability to template their own synthesis. Bringing the individual components, required for the formation of the two replicators together permits the formation of a system that can form both products simultaneously, and is responsive to addition of external stimulus (addition of preformed template), opening up the possibility of creating an instructable replicating network (Figure 3.2) that can be directed to make a particular replicator with increased selectivity, i.e. preferentially compared to the condition with no instruction. Nevertheless, the ability of each replicator to compete for the limited shared building block, and, therefore, the selectivity for one replicator over another will depend on the efficiency of the autocatalytic cycles present in the system as well as the activity and efficiency of the two crosscatalytic pathways available to the system. Crosscatalytic cycle Crosscatalytic cycle A u to ca ta ly ti c cy cl e M1 M2 NF NF T1 T2 A u to ca ta ly ti c cy cl e ?
Figure 3.2 Cartoon model of theT1–T2 replicating network, composed of three building blocks: maleimidesM1andM2, and nitroneNF. Thetrans-T1andtrans-T2replicators formed by the reaction of the nitrone with each maleimide.
In order to understand fully the catalytic efficiencies of the replicators, formation of T1and T2 replicators will be examined in isolation first,i.e. reaction of nitrone with one maleimide at a time. In order to establish the relative contribution of each bimolecular pathway, the kinetic analysis of each replicator will be undertaken using a recognition-disabled model maleimide. Subsequently, the kinetic behaviour of each replicator will be examined in isolation, under various conditions: in the absence of template and in the presence of preformed autocatalytic and crosscatalytic template, allowing the efficiencies of the catalytic pathways available toT1andT2replicators to be determined. Following the full characterisation of the individual catalytic pathways,
these two replicators will be examined in a competition environment, first in the absence of template and later using preformed template, added at the beginning of each reaction to instruct the network. Kinetic analysis, permitted by the presence of an aryl-fluorine tag in the nitroneNF, and, thus, also in each cycloadduct formed by the reaction with
this nitrone, will be performed using19F{1H}NMR spectroscopy as the key analytical
method.