The search for a potentially prebiotic synthesis of nucleotides via arabinose-3-phosphate and its cyanamide derivative

Article abstract of DOI:10.1002/chem.200701351

For the RNA world hypothesis to be accepted, the constitutional self-assembly of RNA will have to be demonstrated. Conceptually, the simplest route to RNA involves nucleotide polymerisation. Activated pyrimidine nucleotides can be derived from arabinose-3

Full text of DOI:10.1002/chem.200701351

FULL PAPER
DOI: 10.1002/chem.200701351
The Search for a Potentially Prebiotic Synthesis of Nucleotides via
Arabinose-3-phosphate and Its Cyanamide Derivative
Carole Anastasi, Fabien F. Buchet, Michael A. Crowe, Madeleine Helliwell,
Jim Raftery, and John D. Sutherland*[a]
Abstract: For the RNA world hypothesis to be accepted, the constitutional self-as-
sembly of RNA will have to be demonstrated. Conceptually, the simplest route to
RNA involves nucleotide polymerisation. Activated pyrimidine nucleotides can be
derived from arabinose-3-phosphate under potentially prebiotic conditions, but the
prebiotic synthesis of this sugar phosphate has not hitherto been investigated. The
results of synthetic approaches involving phosphorylation, phosphate migration
Keywords: aldol
diastereoselectivity · nucleotides ·
phosphorylation · prebiotic · RNA
reaction
·
ꢀ
and 2,3-C C bond construction are described herein.
Introduction
by stepwise nucleobase assembly on a sugar–phosphate scaf-
fold is etiologically noteworthy for a number of reasons:
1) It involves the selection of the furanose ring system from
a starting material that exists predominantly in pyranose (p)
forms, 2) the b-configuration at C(1’) is established, 3) inver-
sion of configuration at C(2’) takes place and 4) the phos-
phate group is activated from a monoester to a diester. We
recently showed that deactivation of 2, by hydrolysis to the
2’- and 3’-monophosphates, can be reversed by the action of
cyanoacetylene, the very reagent used in the second stage of
nucleobase assembly.[2] This continuous reactivation was
seen as strengthening the case for the involvement of nu-
cleoside-2’,3’-cyclic phosphates, such as 2, in the prebiogene-
sis of RNA. Our work on the potential constitutional self-as-
sembly of RNA has been guided by the use of matrices that
make clear the many possible routes to RNA from its con-
stituent prebiotic feedstock molecules. By using a constitu-
tional self-assembly matrix for pyrimidine RNA (Figure 1),
we now sought to extend the sequence 1!3!2 such that 2
could be accessed from simple feedstock molecules.
As part of an ongoing investigation into the prebiotic origin
of RNA, we recently showed that d-arabinose-3-phosphate
(1) could be converted into b-d-cytidine-2’,3’-cyclic phos-
phate (2) by way of the aminooxazoline 3 (Scheme 1).[1]
Being an activated nucleotide, 2 is a monomer with the po-
tential to undergo polymerisation to RNA, and its synthesis
Pentose–phosphate derivatives can be produced by aldoli-
sation of mono- or bis(glycolaldehyde) phosphate and form-
aldehyde,[3,4] or by direct phosphorylation of the free pento-
ses.[5,6] As the aldolisation route produces pentose-2,4-di-
phosphates, or 2,4-cyclic phosphates, and our target 1 is a
pentose-3-phosphate, we first considered the direct phos-
phorylation route. Inoue et al. have investigated the phos-
phorylation of the d-aldopentoses with cyclotriphosphate 4
at high pH, and reported that d-arabinose gives a-d-arabi-
nopyranose-1-triphosphate 5 in low yield (Scheme 2).[5] Ac-
cording to these authors, other phosphorylated products
Scheme 1. Stepwise pyrimidine nucleobase assembly on a sugar-phos-
phate template.
[a] Dr. C. Anastasi, F. F. Buchet, M. A. Crowe, Dr. M. Helliwell,
Dr. J. Raftery, Prof. Dr. J. D. Sutherland
School of Chemistry, The University of Manchester
Oxford Road, Manchester M13 9PL (UK)
Fax : (+44)161-275-4939
E-mail: john.sutherland@manchester.ac.uk
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Figure 1. This constitutional self-assembly matrix makes clear the many
potential routes to RNA from prebiotic feedstocks. The synthesis that
has normally been assumed (blue lines) involves oxygenous chemistry
from formaldehyde to ribose, and nitrogenous chemistry leading to nucle-
obases. Attachment of the nucleobases to ribose is followed by phosphor-
ylation, activation and polymerisation. Despite extensive efforts, this
route has not been experimentally demonstrated and this has prompted
us to explore other routes suggested by the matrix, such as ones including
the sequence 1!3!2 (green lines). For simplicity, only the assembly op-
tions for pyrimidine RNA are shown, but similar matrices can be con-
structed for assembly of purine RNA.
Scheme 3. Intramolecular phosphorylation by transient tethering in the
ribo series.
behave similarly to ribose.[6] The formation of 8 and 9 from
d-ribose and 7 presumably proceeds via the acyclic adduct
10. Dehydration of 10 and ring closure could give the mono-
cyclic adduct 11 in either furanose or pyranose forms, but
the former are expected to predominate, if kinetic control is
operative, because closure to the furanose ring is faster.[11]
The a-furanose form of 11 is then predisposed towards cycli-
sation, giving the phosphoramidate 12, presumably by
means of nucleophilic displacement of ammonia from an N-
protonated form of 11 (a-f). Ring opening of 12 to 13, via
imine or oxonium ion intermediates, is then followed by re-
cyclisation to a mixture of 8 and 9. As the 1,2-cyclic phos-
phate is only formed in the furanose form 8, it can be infer-
red that it results from closure of the a-furanose form of 13.
This suggests that 9 (f) is initially produced from furanose
forms of 13, and then equilibrates with 9 (p). Krishnamurthy
et al. then went on to show that the mixture of 8 and 9
could be hydrolysed in a separate step, at low pH, to a mix-
ture of d-ribose-2-phosphate and d-ribose-3-phosphate.[6]
The formation of d-ribose-3-phosphate, albeit as the minor
product, attracted our attention as it suggested that it might
be possible to make the arabino-analogue 1 in a similar
manner. Although the trans-2,3 stereochemistry of d-arabi-
nose would prevent formation of d-arabinose-2,3-cyclic
phosphate in furanose forms, it potentially allows the forma-
tion of this material in (strained) pyranose forms. We, there-
fore, decided both to investigate the phosphorylation of d-
arabinose by using DAP 7, and to try and identify the other
Scheme 2. Direct phosphorylation by using cyclotriphosphate.
were formed, suggesting low selectivity, but the nature of
these byproducts could not be determined due to their low
yield. Krishnamurthy et al. investigated the phosphorylation
of the d-aldotetroses and d-ribose by amidotriphosphate
(AmTP) 6 and diamidophosphate (DAP) 7 at neutral pH
(Scheme 3).[6] AmTP[7] and DAP[8] can be produced by am-
monolysis of 4 and are viewed as prebiotically plausible
phosphorylating agents (or analogues thereof). By using
either reagent, d-ribose was converted to the 1,2- and 2,3-
cyclic phosphates 8 and 9, respectively, with the latter exist-
ing in equilibrating b-pyranose and a- and b-furanose
forms.[9,10] The chemistry was more efficient with DAP (8+
9, 71%) than with AmTP (8+9, 29%), however, and this
was ascribed to faster equilibration of intermediate adducts
with the former reagent. In the case of AmTP, “exploratory
experiments” suggested that the other three aldopentoses
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Prebiotic Synthesis of Nucleotides
FULL PAPER
products observed by Inoue et al. in their phosphorylation
of d-arabinose by using cyclotriphosphate 4.[5] We also plan-
ned to study the possible interconversion of the various ara-
binose phosphates, and so decided to first use conventional
synthesis to prepare standards for comparison.
Results and Discussion
Conventional synthesis of arabinose phosphates: Synthesis
of d-arabinose-2-phosphate 14 started from benzyl 3,4-O-
isopropylidene-b-d-arabinopyranoside 15 (Scheme 4).[12]
Phosphorylation of 15, by using amidite chemistry, gave
phosphate triester 16 in good yield. We had hoped to global-
ly deprotect 16 to 14 by treatment with Me3SiBr followed by
aqueous acid workup, but these conditions left the anomeric
benzyl protecting group in place in 17, and subsequent hy-
drogenolysis was necessary to give 14.
The synthesis of d-arabinose-3,4-cyclic phosphate 18 also
commenced with 15, and first involved protecting group ma-
nipulation to give the dibenzyl derivative 19. Cyclophos-
phorylation of 19 by using the conditions of Pitsch et al.[10]
gave the protected cyclic phosphate 20, and hydrogenolysis
of this material followed by ion-exchange gave 18.
Scheme 4. Conventional synthesis of d-arabinose-2-phosphate 14 and d-
arabinose-3,4-cyclic phosphate 18. a) (BnO)2PNiPr2, 1H-tetrazole,
MeCN; b) tBuOOH, H2O; c) Me3SiBr, CH2Cl2; d) 1m HCl; e) Na+-
Dowex-50, H2O; f) H2, Pd/C, THF/H2O; g) NaH, BnBr, THF/DMF;
h) 1m HCl/THF 1:1; i) POCl3, py.; j) Et3N, H2O; k) H2, Pd(OH)2/C,
EtOH. py: pyridine.
Our next target was arabinose-4-phosphate 21
(Scheme 5). This compound was synthesised in the l-series
because in a related project we had need of xylose-4-phos-
phate 22, and we envisaged that both l-21 and d-22 could
be prepared from the l-arabinose derivative 23.[12] In our
subsequent investigation of the reaction of 21 with cyana-
mide, characterisation of the product was facilitated by com-
parison to the product formed from 22 and cyanamide, and,
accordingly, the synthesis of 22 is also given herein.
Phosphorylation of 23 by using tetrabenzylpyrophos-
phate[13] gave the fully protected phosphate 24, which was
deprotected by sequential hydrogenolysis and acidic hydrol-
ysis to give, after neutralisation, 21. Conversion of 23 into a
d-xylose derivative was achieved through inversion at the 4-
position by a Mitsunobu reaction whereupon the para-nitro-
benzoate 25 was formed in quantitative yield. The inversion
of stereochemistry associated with this reaction was proved
by an X-ray crystallographic analysis of 25 (Scheme 5).[14]
Ammonolysis of 25 then gave the alcohol 26 which was con-
verted to 22, by way of the protected phosphate 27, by using
the same chemistry employed for the conversion of 23 to 21.
d-Arabinose-3-phosphate 1 was prepared by the route we
have previously described.[15]
Scheme 5. Conventional synthesis of l-arabinose-4-phosphate 21 and d-
xylose-4-phosphate 22.
(BnO)2P(O)OP(O)AHCTRE(GNU OBn)2; b) H2, Pd(OH)2/C, MeOH; c) 90% TFA,
a) tBuOK,
THF,
RT!ꢀ408C,
CH2Cl2 then pH!7 (NaOH aq.); d) pNO2BzOH, Ph3P, iPrO2CN=
NCO2iPr, THF; e) NH3, MeOH/CH2Cl2. TFA: trifluoroacetic acid.
Potentially prebiotic phosphorylation of d-arabinose: We
first investigated the phosphorylation of arabinose with
DAP 7 according to the procedure of Krishnamurthy et al.[6]
An aqueous solution of d-arabinose and 7 was stirred at
room temperature over a period of days, with aliquots being
ly to neutralise the mixture. It was also necessary to add fur-
ther portions of 7 to drive the reaction. By comparison with
literature values for the chemical shift of the anomeric pro-
tons of products from the phosphorylation of d-ribose[6] and
from analysis of coupling constants, it was possible to identi-
fy the different components of the reaction mixture by
1H NMR spectroscopy (see Figure 2a, Scheme 6 and
1
taken at regular intervals for H NMR spectroscopic analy-
sis. During the phosphorylation, ammonia was released
causing the pH to rise and slowing down the reaction.[6] To
counter this, acidic ion-exchange resin was added periodical-
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J. D. Sutherland et al.
Table 1). The signals for the
anomeric proton of the 1,2-
cyclic phosphoramidate 28 and
the furanose 1,2-cyclic phos-
phate 29 were identified by
comparison to the correspond-
ing signals of 12 and 8 in the
ribo series. Relative to that
series, there was also an addi-
tional downfield-shifted anome-
1
ric signal in the H NMR spec-
trum. This signal showed a cou-
pling to phosphorus, and we
assign it to the pyranose form
of the 1,2-cyclic phosphate 30
on the basis of the small value
for J1,2. The amount of 28 was
seen to rise and then fall as 29
and 30 increased. This latter ob-
servation is also consistent with
the structural assignment for
30, as 29 is presumably formed
from 28 via the 2-phosphorami-
date 31, and this compound is
expected to exist in both fura-
nose and pyranose forms, with
one of the latter, 31 (b-p), setup
to cyclise to 30. The lack of
such a pyranose-1,2-cyclic phos-
phate in the phosphorylation of
d-ribose is presumably due to
the increased propensity for d-
ribose to exist in furanose
forms.[11] The generation of 1,2-
cyclic phosphates from d-arabi-
nose was slower and less effi-
cient than from d-ribose, and
Figure 2. 1H NMR analysis of the direct phosphorylation of arabinose and the attempted cyclisation of the 2-
phosphate to the 2,3-cyclic phosphate. a) Products of reaction of arabinose and DAP 7, b) products of reaction
of arabinose and cyclotriphosphate 4, and c) products of reaction of d-arabinose-2-phosphate 14 with cyano-
acetylene in D2O.
Scheme 6. Intramolecular phosphorylation by transient tethering in the arabino series.
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Prebiotic Synthesis of Nucleotides
FULL PAPER
Table 1. Partial 1H NMR spectroscopic data for the various species
formed during the phosphorylation of d-arabinose by DAP 7.
ribose-2-phosphate can be formed by hydrolysis of the 1,2-
cyclic phosphate 8,[6] it seems reasonable to assume that d-
arabinose-2-phosphate 14 could be similarly formed from
the 1,2-cyclic phosphates 29 and 30. Thus, even though 29
and 30 are minor products in the phosphorylation of d-ara-
binose by 4 or 7, there existed the possibility that the 3-
phosphate 1 might be formed from the 2-phosphate 14 by
phosphate migration. We had in mind a sequence whereby
14 was somehow cyclised to the 2,3-cyclic phosphate 35
which could then undergo hydrolysis to 1 and (back to) 14
[a]
ꢀ
Compound
d H C(1) [ppm]
J1,2 [Hz]
JH-P [Hz]
28
29
30
32 (a-p)
5.47
5.95
5.70
4.12
5.0
4.4
3.7
8.3
18.3
13.8
4.3
8.3
[a] Spectra were recorded in D2O and the chemical shifts were found to
be very pD dependent, those given here are taken from a single spec-
trum.
(Scheme 7). Any success in demonstrating such
a se-
extensive accumulation of the a-pyranosyl adduct 32 (a-p)
was also observed. This compound was identified by com-
parison of J1,2 and JH,P to the corresponding coupling con-
stants of 5, and by its subsequent very slow conversion back
to the starting sugar. We assume that this conversion pro-
ceeds by means of hydrolysis to the monoamidate adduct 33
(a-p), and, at the later stages of the reaction, we also ob-
served low-intensity signals tentatively assigned to 33 (a-p),
slightly upfield-shifted relative to 32 (a-p). The pyranose
and furanose adducts 32 presumably all derive from the
open-chain adducts 34. The formation, persistence and then
hydrolysis of the pyranose adducts 32 (a-p) and 33 (a-p) are
presumably the major contributory factors to the inefficient
phosphorylation of d-arabinose relative to d-ribose. Not
only was the phosphorylation of d-arabinose found to be
slow and inefficient, but the 2,3-cyclic phosphate (from
which 1 might have been accessed by hydrolysis) was not
detected. After 5 d, the reaction mixture comprised unreact-
ed d-arabinose, 28 (7%), 29 (13%), 30 (11%) and 32 (a-p;
51%).
Scheme 7. Potential formation of a 3-phosphate from a 2-phosphate by
phosphate migration in the arabino series.
We next investigated the products formed in the phos-
phorylation of d-arabinose by using cyclotriphosphate 4 at
high pH. Inoue et al. had found that the 1-triphosphate 5
was the major phosphorylated product,[5] and we were able
to confirm these findings observing 5 in 15% yield (Fig-
ure 2b)). In addition to 5, and by comparison to the prod-
ucts of phosphorylation by using DAP 7, we were able to
identify the 1,2-cyclic phosphates 29 and 30 as products of
phosphorylation by using 4. These latter compounds were
both formed in very low yield (ꢁ1–2%) along with an un-
quence—particularly if the hydrolysis of 35 showed selectivi-
ty for the formation of 1—would then have been followed
by a search for a more-efficient synthesis of 14 via 29 and
30. At the outset, we were not particularly hopeful because
the previously noted formation of the 1,2-cyclic phosphates
29 and 30 (eg. from 31 (b-f) and 31 (b-p) in the phosphoryla-
tion of d-arabinose with DAP 7 (Scheme 6)) suggested that
any form of activation of 14 would result in cyclisation to
the 1,2-cyclic phosphates rather than the 2,3-cyclic phos-
phate 35. However, for the sake of completeness, and to
more fully explore the RNA constitutional self-assembly
matrix (Figure 1), we treated 14 with cyanoacetylene in an
attempt to make 35. In our earlier work using cyanoacety-
lene to (re)cyclise b-d-cytidine-2’(3’)-phosphates to 2,[2] we
had found that five to ten equivalents of this electrophile
were required to obtain the highest yields of cyclised prod-
uct. However, in the attempted cyclisation of 14 to 35, we
first conducted an experiment in D2O by using two equiva-
ꢀ
identified product characterised by a dd signal for H C(1)
at d=5.60 ppm. As it can be assumed that 30 is derived by
cyclisation of the b-anomer of 5, and that 29 is derived by
cyclisation of the b-furanose isomer of 5, then it is reasona-
ble to assume that the a-furanose isomer of 5 is also
formed. Like 5 itself, the a-furanose isomer of 5 cannot un-
dergo cyclisation, and so we tentatively assign the dd signal
at d=5.60 ppm to this latter species. Whatever the case, it is
clear that the phosphorylation of d-arabinose by using 4 at
high pH is inefficient. Furthermore, the 3-phosphate 1 is
again not formed, so we were forced to consider less direct
ways in which this compound could be produced under po-
tentially prebiotic conditions.
1
lents of cyanoacetylene and H NMR spectroscopy to deter-
mine whether the reaction followed the desired course or
not (Figure 2c). Had 35 been produced, we would have opti-
mised conditions for its production, but, in the event, it was
not, and the 1,2-cyclic phosphates 29 and 30 were detected
ꢀ
instead. In addition to clear signals for the H C(1) of 29
and 30, small signals of similar appearance to the signals for
ꢀ
Potential formation of d-arabinose-3-phosphate 1 by phos-
phate migration: As Krishnamurthy et al. showed that d-
H C(1) of the various forms of residual 14, but ꢁ0.3 ppm
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J. D. Sutherland et al.
downfield-shifted were apparent. In previous work, we have
shown that cyanoacetylene reacts with phosphate monoest-
ers to give Z cyanovinyl adducts, so it seems reasonable to
ꢀ
suggest that these additional H C(1) signals are due to the
various forms of 36, the deuterated Z-cyanovinyl adduct of
14. The cyanovinyl group of 36 is deuterated because, in
D2O, the proton of cyanoacetylene rapidly exchanges for a
deuteron, and the incipient vinyl anion resulting from phos-
phate addition is quenched with a deuteron.[15] The cyclisa-
tion of the b-anomers of 36 to 29 and 30 confirms our earlier
suspicion that any form of activation of the phosphate group
of 14 will result in this mode of cyclisation.
Unable to find a route from the 2-phosphate of arabinose
to the 3-phosphate, but intrigued by the possibility of phos-
phate migration, we next considered a route to the 3-phos-
phate from the 4-phosphate. In pyranose forms of arabi-
nose-4-phosphate, the 3’-OH is the only hydroxyl group
available for cyclisation; furthermore, it is cis-configured rel-
ative to the 4-phosphate group. Before exploring potentially
prebiotic routes to the 4-phosphate, we, therefore, decided
to investigate the possible 4’- to 3’-phosphate migration ex-
perimentally by using material prepared by conventional
synthesis. As mentioned previously, we prepared the 4-phos-
phate 21 in the l-series (Scheme 5), but as we planned to
1
use H NMR spectroscopy to monitor the potential conver-
sion to the 3-phosphate via the 3,4-cyclic phosphate, it did
not matter that our standard samples of the latter two com-
pounds were prepared in the d-series. Encouraged by early
experiments in which 21 was treated with a few equivalents
of cyanoacetylene, and the 3,4-cyclic phosphate 18 appeared
to be formed, we optimised the reaction, and found that
when three equivalents were used, 60% conversion to l-18
could be achieved (Figure 3a–c). Then, to our delight, we
found that acidic hydrolysis of our synthetic standard of d-
18 proceeded quantitatively, and showed selectivity in
favour of the 3-phosphate over the 4-phosphate, with 1 and
d-21 being formed in a 2:1 ratio (Figure 3c–f). Thus, if expo-
sure to cyanoacetylene and subsequent hydrolysis can be
deemed to be etiologically relevant, we have formally dem-
onstrated the prebiotic conversion of arabinose-4-phosphate
to the 3-phosphate in 40% overall yield, and, accordingly,
we now sought a prebiotically plausible route to the 4-phos-
phate.
Figure 3. 1H NMR spectroscopic analysis of the migration of the arabi-
nose-4-phosphate to the 3-phosphate via the 3,4-cyclic phosphate. a) l-
Arabinose-4-phosphate 21, b) products of the reaction of 21 with cyano-
acetylene in D2O, c) authentic standard of d-arabinose-3,4-cyclic phos-
phate 18, d) products of acid-catalysed hydrolysis of 18 in D2O, e) as
d) but spiked with an authentic standard of d-arabinose-3-phosphate 1,
and f) authentic standard of 1.
Potential formation of arabinose-4-phosphate, or derivatives
ꢀ
thereof, by C(2) C(3) bond-forming processes: Because
arabinose-4-phosphate is not formed by direct phosphoryla-
tion of the free sugar, we initially considered several aldoli-
sation routes to the (rac-)pentose-4-phosphates. Ostensibly,
the simplest route involves the hetero-aldolisation of glyco-
laldehyde and glyceraldehyde-2-phosphate 37 with the
former acting as donor, and the latter as acceptor
(Scheme 8). Although this route looks simple on the face of
it, it relies upon a specific hetero-aldolisation, and homo-al-
dolisation of either component, or the alternative hetero-al-
dolisation could not be ruled out a priori. Therefore, before
evaluating this route experimentally, we also considered
other options. The 4-phosphates could conceivably also be
produced by hydrolysis of the 2,4-diphosphates which them-
selves have been shown to be accessible by hetero-aldolisa-
tion of glycolaldehyde phosphate 38 and 37.[3] rac-Arabi-
nose-2,4-diphosphate was a minor kinetic product of such an
aldolisation, but the major component when the products
were subsequently allowed to equilibrate under the same
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Prebiotic Synthesis of Nucleotides
FULL PAPER
Scheme 8. (Potential) aldolisation and hydrolysis routes to pentose-4-
phosphates.
basic conditions of the reaction.[3] Despite this predisposed
formation of arabinose-2,4-diphosphate, we did not pursue
this route further because of the perceived difficulty of hy-
drolysing the 2-phosphate selectively. The (presumed) easier
hydrolysis of cyclic phosphate diesters temporarily attracted
our attention to arabinose-2,4-cyclic phosphate, but the in-
tramolecular aldolisation of the acyclic diester 39, from
which this could derive, has been shown to give predomi-
nantly the ribo- and xylo-configured products.[4] With cou-
pled aldolisation and hydrolysis routes to the 4-phosphate
ruled out, we were forced to focus our attention on the first
possible aldolisation route—the hetero-aldolisation of glyco-
laldehyde and glyceraldehyde-2-phosphate 37. Investigation
of this route demanded more conventional synthesis
(Scheme 9). Firstly, we needed a synthesis of 37, and, sec-
ondly, we decided to synthesise ribose- and lyxose-4-phos-
phates 40 and 41 so that, along with 21 and xylose-4-phos-
Scheme 9. Conventional synthesis of rac-glyceraldehyde-2-phosphate 37,
l-ribose-4-phosphate 40 and d-lyxose-4-phosphate 41. a) tBuOK, THF,
RT!ꢀ408C, (BnO)2P(O)OP(O)
ACHTRE(UNG OBn)2; b) H2, Pd/C, dioxane/H2O;
c) D2O, pD ꢁ2.2, 508C, 2 d then H2O pH!7 (NaOH aq.), d) H2, Pd/C,
MeOH then pH!1 (HCl aq.), 408C, 3 h then pH!7 (NaOH aq.);
e) CrO3, py, Ac2O, CH2Cl2; f) NaBH4, EtOH, 08C; g) H2, Pd/C, MeOH
then pH!7 (NaOH aq.).
mer of a known l-lyxose derivative.[17] Phosphorylation of
44 by using tetrabenzylpyrophosphate gave protected d-
lyxose-4-phosphate 45. Hydrogenolytic debenzylation of 45
was followed by acid treatment to hydrolyse the acetal, and
neutralisation and lyophilisation to give 41 as a sodium salt.
An oxidation–reduction sequence—via ketone 46—served
to convert 44 to the l-ribose derivative 47, the structure of
which was confirmed by X-ray crystallography.[14] Phosphor-
ylation of 47 then gave protected l-ribose-4-phosphate 48.
In this case, hydrogenolysis effected removal of the three
benzyl protecting groups and the isopropylidene group, the
latter presumably catalysed by the liberated monoalkyl
phosphoric acid without the need for addition of exogenous
acid. Finally, neutralisation with sodium hydroxide, and lyo-
phiisation afforded l-40 as a sodium salt.
1
phate 22, we would have H NMR spectroscopic standards
for all four pentose-4-phosphates.[16] We wanted a full set of
standards of potential products in case the desired hetero-al-
dolisation was found to operate, but with a strong stereo-
chemical selectivity against the arabino-configured product
rac-21. Furthermore, there would have been other etiologi-
cal implications had rac-40 been produced selectively, and,
anyway, we had in mind an additional use for 40 and 41 in a
later part of this work.
Krishnamurthy et al. synthesised d-37 by phosphorylation
of d-glyceraldehyde by using 6, but their procedure involved
an ion-exchange chromatography step that limited scale
up.[6] As enantiomeric purity of the product was unimpor-
tant for the applications we planned, we developed a route
to racemic material by starting from the known acetal 42.
Phosphorylation by using tetrabenzylpyrophosphate gave
the dibenzyl phosphate 43 which was deprotected to rac-37
by hydrogenolysis, and acid hydrolysis. The hydrolysis was
carried out in D2O to enable convenient monitoring of reac-
With standards of the four potential pentose-4-phosphate
products in hand (albeit in enantiomerically pure rather
than racemic form), we next investigated the aldol reaction
of glycolaldehyde and 37. When a 0.2m solution in both gly-
colaldehyde and rac-37 was incubated at pH 11 for 3 h at
1
608C, a complex mixture resulted. By H NMR spectroscop-
1
tion progress by H NMR spectroscopy so that a slower sub-
ic analysis, it was clear that a substantial amount of the ini-
tial 37 remained, but signals for residual glycolaldehyde
were not apparent. Suspecting that glycolaldehyde had pre-
dominantly undergone homoaldolisation, and that 37 had
sequent acid-catalysed destruction of 37 could be avoided.
We synthesised ribose-4-phosphate in the l-series, and
lyxose-4-phosphate in the d-series from 44, the d-enantio-
Chem. Eur. J. 2008, 14, 2375 – 2388
ꢀ 2008 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim
www.chemeurj.org
2381

J. D. Sutherland et al.
been largely unreactive under the conditions used, we sub-
jected the two compounds to the same conditions individual-
ly. These experiments confirmed our suspicion—the glyco-
laldehyde was converted into a complex mixture of products
whilst 37 was unchanged. We investigated several other
aldol reaction conditions, but on no occasion found any evi-
dence, by comparison of NMR spectra to those of the stand-
ards, for the synthesis of any of the pentose-4-phosphates. It
can thus be concluded that whilst arabinose-3-phosphate 1
can be obtained from arabinose-4-phosphate 21 by phos-
phate migration, the 4-phosphate (and, indeed, any other
pentose-4-phosphate) cannot be produced by a simple aldo-
lisation process.
be induced to migrate from the 4’-position to the 3’-posi-
tion—the successful conversion of 21 to 1 auguring well in
this regard—then the resultant pyranose aminooxazoline 53
should be able to equilibrate with the furanose form 3. The
possibility of bypassing 1, and forming 3 in this way was ex-
tremely appealing, and so we proceeded to treat 37 with 49
in the same way as we did with glyceraldehyde-3-phosphate.
Upon examining the reaction products by 1H NMR spectros-
copy, it was apparent that both components of the reaction
had been consumed, and a complex mixture had formed,
but we were unable to detect any signals that we could attri-
bute to pentose-4-phosphate aminooxazolines. Assuming
that addition of 49 to 37 had taken place as envisaged, but
that the adducts had not undergone cyclisation and had in-
stead hydrated, we heated the reaction products in an at-
tempt to bring about dehydration. Subsequent 1H NMR
spectroscopic analysis revealed that further reaction had
taken place, but aminooxazolines had still not been formed,
and instead signals consistent with two diastereoisomeric
aminooxazoles presumed to be 54 and 55 (Scheme 11) were
We recently showed that pentose aminooxazoline deriva-
tives can be produced in an aldol-type reaction in which the
ꢀ
2’,3’-C C bond is constructed (Scheme 10). The ribo-, arabi-
Scheme 11. Formation of pentose-aminooxazole-4’-phosphates.
observed. By integration of the signals assumed to be due to
these aminooxazoles relative to signals for all other species
present, it could be estimated that the two products were
formed in a 5:1 ratio and a combined yield of 60%. To gain
support for the assigned structures, and to determine the rel-
ative stereochemistry of the most abundant product, we
next investigated the reaction of the pentose-4-phosphates
21, 40, 22 and 41 with cyanamide. Our reasoning was that 21
and 40 should give one of the diastereoisomeric aminooxa-
zoles, and 22 and 41 should give the other. The aminooxa-
zole products from these cyanamide reactions would pre-
sumably be enantiopure in contrast to the racemic products
from the addition of 49 to 37, but the NMR data would of
course be comparable. In the event, it was found that ami-
nooxazole products were formed in moderate to good yield
by heating the pentose-4-phosphates with cyanamide in
aqueous solution (Scheme 11). The major product 54 in the
addition of 49 to 37 corresponded to the aminooxazole
Scheme 10. Potential formation of pentose-aminooxazoline-3’-phosphates
ꢀ
by 2’,3’-C C bond formation, giving the corresponding 4’-phosphates, and
subsequent phosphate migration.
no- and xylo-configured aminooxazolines exist in furanose
forms, but the lyxo-configured derivative was shown to exist
as an equilibrating mixture of furanose and pyranose forms.
2-Aminooxazole 49 functions as a glycolaldehyde enolate
equivalent at neutral pH in this reaction, and adds to the
carbonyl group of glyceraldehyde with good facial selectivi-
ty. As we have also recently found that 49 will add to glycer-
aldehyde-3-phosphate, we now wondered whether it would
add to the 2-phosphate 37. If such an addition took place,
the resultant adducts 50 would be incapable of ring closure
to furanose aminooxazoline derivatives, but there remained
the possibility that the pyranose aminooxazolines 51 could
form. If the phosphate of the arabinose derivative 52 could
2382
www.chemeurj.org
ꢀ 2008 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim
Chem. Eur. J. 2008, 14, 2375 – 2388

Prebiotic Synthesis of Nucleotides
FULL PAPER
product formed from 21 or 40 and cyanamide, and the
minor product 55 corresponded to the aminooxazole formed
from 22 or 41 and cyanamide. It thus appears that the pen-
tose-4-phosphate aminooxazolines 51 (including 52) are
strained and unstable relative to the isomeric aminooxazoles
54 and 55. In the reaction of 49 with 37, it is not possible to
say whether 54 derives from arabino- or ribo-configured ini-
tial addition products, or whether 55 derives from xylo- or
lyxo-configured addition products because stereochemistry
at C(2’) is lost in the subsequent conversion to aminooxa-
zoles. However, the stereoselective formation of 54 in 50%
yield in water at neutral pH is chemically noteworthy. From
an etiological point of view, the successful construction of
1’,2’-cis-relationship in the aminooxazoline intermediates
means that stereochemical inversion at the 2’-position (from
b-arabino-intermediates) or the 1’-position (from a-ribo-in-
termediates) is necessary. The fact that our previously dem-
onstrated sequence involving 2’-inversion cannot be extend-
ed back to prebiotically plausible starting materials now
makes further investigation of processes involving 1’-inver-
sion an important objective.[18] Only when the constitutional
self-assembly matrix for RNA has been fully explored
(Figure 1) will it be possible to draw firm conclusions about
the likelihood of a prebiotic origin of this nucleic acid.
ꢀ
the 2’,3’-C C bond in 54 is offset by the lack of opportunity
Experimental Section
the open chain structure affords for regioselective phosphate
migration. If the phosphate could undergo migration to the
3’-position, then protonation at C(2’) would give an arabino-
or ribo-configured intermediate with the potential to
become the corresponding furanose aminooxazoline. In con-
trast to the demonstrated situation with the predominantly
pyranose arabinose-4-phosphate 21, and the presumed situa-
tion with the pyranose 52, the open-chain structure of 54
suggests that if the phosphate were activated, both 3’,4’- and
4’,5’-cyclic phosphates would be formed. Furthermore, cycli-
sation would be expected to be slower than it was with 21
because of the bond rotation allowed by the open chain
structure of 54. We thus did not hold out much hope when
we treated 54 with cyanoacetylene, and we were not sur-
prised to observe a complex mixture of products by NMR
spectroscopic analysis. We did not attempt to resolve this
mixture or characterise any of its components and simply
concluded that an efficient conversion to the 3’,4’-cyclic
phosphate is not possible by using cyanoacetylene in this
case.
General: Reagents and solvents are from Fluka, Aldrich, and Lancaster.
Petroleum ether (40–60) was used. TLC: Merck Kieselgel 60 F254; detec-
tion by UV or by dipping plates in EtOH/anisaldehyde/concentrated
H2SO4/AcOH 180:10:10:2 or 5% (w/v) ammonium molybdate in H2SO4
(1.0m) followed by heating with a heat gun. Flash chromatography: Sor-
bisil C60 silica gel. M.p.: Sanyo Gallenkamp, uncorrected. FTIR: AT1
Mattson Genesis series spectrophotometer (KBr disc, Nujol mull, film or
solution), n˜ in cmꢀ1. NMR: Varian INOVA 300E, Varian INOVA 400,
Varian UNITY 500; d in ppm, J in Hz, assignments by COSY, HMBC,
HMQC (app.: apparent, br: broad). EIMS/CIMS: Micromass Trio 2000;
ESIMS, APCIMS: Micromass Platform; HRMS: Thermofinnigan
MAT95XP. HPLC: Gilson semi-preparative system: Rainin Dynamax-
60 Š Si83-141-C, Rainin Dynamax-60 Š C18 21.2 mm”25 cm; Gilson 115
UV detector, 255 nm.
1-O-Benzyl-3,4-O-isopropylidene-b-d-arabinopyranoside-2-O-dibenzyl-
phosphate (16): A sample of 15[12] was dried over P2O5 overnight under
high vacuum. A mixture of 15 (400 mg, 1.43 mmol), powdered dried 3 Š
molecular sieves (600 mg) and (BnO)2PNiPr2 (0.94 mL, 2.86 mmol) in an-
hydrous MeCN (8 mL) was stirred at RT for 20 min under N2. Then a so-
lution of 1H-tetrazole in MeCN (0.45m, 25.4 mL, 11.44 mmol) was added
and the reaction mixture left to stir at RT. After 4 h, tBuOOH (70%
(aq.), 6.5 mL, 4.60 mmol) was added and stirring was continued for a fur-
ther 1 h. The mixture was then filtered through Celite and the filtrate
concentrated in vacuo. The residue was dissolved in EtOAc (50 mL),
washed with NaHCO3 (aq. saturated, 3”30 mL), then brine (30 mL). The
organic layer was dried (MgSO4) and concentrated in vacuo. Purification
first by flash chromatography (cyclohexane/EtOAc 8:2 then 7:3), and
then by normal phase HPLC (hexane/EtOAc 1:1), gave 16 as a white
solid (500 mg, 65%). 1H NMR (300 MHz, CDCl3): d=1.39 (3H, s; Me),
1.53 (3H, s; Me), 3.98–4.08 (2H, m; H2C(5)), 4.27 (1H, app. d; J=
Conclusion
The results described in this paper suggest that the previous-
ly reported conversion of arabinose-3-phosphate 1 to b-cyti-
dine-2’,3’-cyclic phosphate 2 is not of direct etiological rele-
vance. Direct phosphorylation of arabinose does not give 1,
neither can the 2-phosphate 14, which is accessible, be con-
verted to 1. The 4-phosphate 21 can be efficiently converted
to 1, but direct formation of 21 is not possible, nor is forma-
ꢀ
ꢀ
ꢀ
5.3 Hz; H C(4)), 4.39–4.48 (1H, m; H C(3)), 4.50–4.58 (1H, m; H
ꢀ
C(2)), 4.52–4.75 (2H, AB q, J=12.0 Hz; PhCH2), 5.04 (d, J=7.5 Hz; H
C(1)), 5.06–5.15 (4H, m; 2”PhCH2OP), 7.30–7.41 ppm (10H, m; Ar);
13C NMR (75.4 MHz, CDCl3): d=26.68 (Me), 28.35 (Me), 59.13 (PhCH2),
69.37 (d, J=5.4 Hz; PhCH2OP), 69.73 (d, J=5.7 Hz; PhCH2OP), 70.10
(C(5)), 74.03 (C(4)), 74.34 (d, J=6.6, C(3)), 76.57 (d, J=5.9, C(2)), 96.56
(C(1)), 109.65 (Me2C), 127.82–128.85, 136.06, 136.13, 136.16, 136.23,
137.26 ppm (Ar); ESIMS (pos., MeCN): m/z (%): 541 (10) [M+H]+, 563
(100) [M+Na]+.
ꢀ
tion by a 2’,3’-C C bond construction process involving al-
dolisation of glycolaldehyde and glyceraldehyde-2-phos-
phate 37. Formation of a cyanamide derivative of 21, by ad-
dition of 2-aminooxazole 49 to 37, is possible, but regioselec-
tive phosphate migration in this derivative is not possible.
Thus, we have been able to solve the 4’- to 3’-phosphate mi-
Sodium 1-O-benzyl-b-d-arabinopyranoside-2-O-phosphate (17): Me3SiBr
(0.33 mL, 2.58 mmol) was added dropwise under N2 to a stirred solution
of 16 (348 mg, 0.64 mmol) in anhydrous CH2Cl2 (10 mL). After stirring
for 1 h, the solution was concentrated, and the residue stirred in H2O
(6 mL, pH!1) overnight. The pH was then adjusted to 6.5 by addition of
a concentrated solution of NaOH aq., and the mixture was lyophilised to
furnish 17 (205 mg, quant.). 1H NMR (500 MHz, D2O): d=3.40 (1H,
ꢀ
ꢀ
gration or the 2’,3’-C C bond construction problems, but
not both in the same sequence. The stepwise assembly of
pyrimidine nucleobases via aminooxazoline intermediates
remains etiologically attractive, however, particularly as
direct ribosylation of cytosine and uracil has not proved pos-
sible under prebiotically plausible conditions. The obligate
ABXdd,
JAB =12.6,
JAX =1.8 Hz;
H
C(5)), 3.64 (1H, ABXbrd, J=
ꢀ
ꢀ
12.6 Hz; H C(5’)), 3.71 (1H, dd, J=10.2, 3.5 Hz; H C(3)), 3.75 (1H, m;
ꢀ
ꢀ
H C(4)), 4.03 (1H, dt, J=9.5, 3.7 Hz, H C(2)), 4.39–4.48 (2H, ABq, J=
ꢀ
11.7 Hz; PhCH2), 4.93 (1H, d, J=3.9 Hz; H C(1)), 7.14–7.25 ppm (5H,
Chem. Eur. J. 2008, 14, 2375 – 2388
ꢀ 2008 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim
www.chemeurj.org
2383

J. D. Sutherland et al.
m; Ar); 13C NMR (125.7 MHz, D2O): d=62.61 (PhCH2), 69.12 (C(4)),
70.25 (C(5)), 71.03 (C(3)), 98.28 (d, J=26.5 Hz; C(1)), 128.56–129.02,
137.26 ppm (Ar); 31P NMR (121.5 MHz, D2O): d=4.29 ppm (brs);
ESIMS (neg., H2O): m/z (%): 319 (100) [M+H]ꢀ, 341 (5) [M+Na]ꢀ; HR-
ESIMS: (neg., H2O): m/z: calcd for C12H16O8P: 319.0588; found:
319.0588.
m; H C(3), H C(4)), 4.62–4.76 (2H, ABq, J=11.7 Hz; PhCH2OC(2)),
ꢀ
ꢀ
4.89 (1H, d, J=3.1 Hz; H C(1)), 7.25–7.38 ppm (10H, m; Ar); 13C NMR
ꢀ
(75.4 MHz, CD3OD): d=59.41 (C(5)), 69.24, 73.02 (PhCH2), 74.70
(C(4)), 77.34 (C(3)), 77.35 (C(2)), 96.19 (C(1)), 127.54–128.28, 137.51,
137.78 ppm (Ar); 31P NMR (121.5 MHz, CD3OD): d=17.96 ppm (s);
ESIMS (neg., MeOH): m/z (%): 391 (100) [M]ꢀ; HR-ESIMS (neg.,
MeOH): m/z: calcd for C19H20O7P: 391.0952; found: 391.0953.
Sodium d-arabinose-2-phosphate (14): Pd/C (10% Pd, 100 mg) was
added to a solution of 17 (195 mg, 0.61 mmol) in H2O/THF (1:1, 14 mL).
After degassing (N2), the mixture was stirred under H2 overnight at RT.
Filtration through Celite and lyophilisation of the filtrate afforded 14
(167 mg, quant.) as a white solid. 1H NMR (300 MHz, D2O): d=3.61–
Sodium d-arabinose-3,4-cyclic phosphate (18): Pd(OH)2 (20% on C,
40 mg) was added to a solution of 20 (85 mg, 0.19 mmol) in EtOH
(10 mL). After degassing (N2), the mixture was stirred under H2 for 2 d
at RT. Filtration through Celite, treatment with Na+-Dowex-50 resin and
ꢀ
ꢀ
ꢀ
ꢀ
ꢀ
3.80 (2H, m; H C(4), H C(5)), 3.84–4.17 (3H, m; H C(2), H C(3), H
lyophilisation of the filtrate gave 18 (37 mg, 82%) as a white powder.
1
ꢀ
ꢀ
C(5’)), 4.54 (0.47H, d, J=7.4 Hz; H C(1) (a-p)), 5.26 (0.43H, d, J=
H NMR (500 MHz, D2O): d=3.64 (0.6H, app.t, J=8.2 Hz; H C(2)
3.4 Hz; H C(1) (b-p)), 5.35 ppm (0.1H, 2”app.s; H C(1) (f)); 13C NMR
(75.4 MHz, D2O): d=62.45, 66.19, 68.21, 71.45, 72.80, 74.92 (C(2), C(3),
C(4), C(5) (a, b)), 92.33 (d, J=5.3 Hz; C(1) (b-p)), 96.66 ppm (d, J=
5.4 Hz; C(1) (a-p)); 31P NMR (121.5 MHz, D2O): d=3.82 (s), 4.46 ppm
(s); ESIMS (neg., H2O): m/z (%): 229 (100) [M+H]ꢀ; ESIMS (pos.,
H2O): m/z: 253 (35) [M+Na+2H]+, 275 (25) [M+2Na+H]+, 297 (100)
[M+3Na]+; HR-ESIMS (neg., H2O): m/z: calcd for C5H10O8P: 229.0119;
found: 229.0124.
(a)), 3.79 (0.6H, ddd, J=14.5, 4.1, 2.2 Hz; H C(5) (a)), 3.88 (0.4H, d,
ꢀ
ꢀ
ꢀ
ꢀ
ꢀ
J=14.2 Hz; H C(5) (b)), 3.92 (0.4H, dd, J=8.4, 3.6 Hz; H C(2) (b)),
4.11 (0.4H, dt, J=14.2, 3.2 Hz; H C(5’) (b)), 4.17 (0.6H, d, J=14.5 Hz;
H C(5’) (a)), 4.31–4.38 (0.6H, m; H C(3) (a)), 4.39–4.46 (0.4H, m; H
C(3) (b)), 4.48 (0.6H, d, J=8.5 Hz; H C(1) (a)), 4.50–4.53 (0.6H, m; H
ꢀ
ꢀ
ꢀ
ꢀ
ꢀ
ꢀ
ꢀ
C(4) (a)), 4.57–4.60 (0.4H, m; H C(4) (b)), 5.17 ppm (0.4H, d, J=
3.5 Hz; H C(1) (b)); 13C NMR (75.4 MHz, D2O): d=58.73, 63.50, 64.00
ꢀ
(C(5) (a, b)), 69.14 (C(2) (b)), 73.01 (C(2) (a)), 74.48, 74.66 (C(4) (a,
b)), 77.13 (C(3) (b)), 79.94 (C(3) (a)), 92.03 (C(1) (b)), 95.44 (C(1) (a));
1H-decoupled 31P NMR (161.9 MHz, D2O): d=15.75 (s); ESIMS (pos.,
H2O): m/z: 235 (15) [M+Na+H]+, 257 (10) [M+2Na]+; HR-ESIMS
(pos., H2O): m/z: calcd for C5H8O7Na2P: 256.9798; found: 256.9795.
1,2-Di-O-benzyl-b-d-arabinopyranoside (19): NaH (60% in oil, 429 mg)
was added to a stirred solution of 15 (2.00 g, 7.14 mmol) in anhydrous
THF (10 mL), and stirring was then continued for 30 min at RT. A solu-
tion of PhCH2Br (1.20 mL, 9.99 mmol) in anhydrous DMF (5 mL) was
then added dropwise, and the mixture was stirred at RT overnight. The
reaction was quenched with AcOH then concentrated in vacuo. The resi-
due was dissolved in EtOAc, washed with saturated NaHCO3 aq. and
then brine. The organic phase was dried (MgSO4) and concentrated in
vacuo. Purification by flash chromatography (cyclohexane/EtOAc 95:5
then 90:10) gave 1,2-di-O-benzyl-3,4-O-isopropylidene-b-d-arabinopyra-
1-O-Benzyl-2,3-(2,3-dimethoxybut-2,3-diyl)-b-l-arabinopyranoside-4-O-
dibenzylphosphate (24): A solution of tBuOK in THF (1m, 0.94 mL) was
added dropwise at RT to a solution of 23 (1.52 g, 4.28 mmol) in anhy-
drous THF (30 mL) under N2. After 20 min, the solution was cooled to
ꢀ408C before addition of
a solution of ((BnO)2P(O))2O (3.46 g,
6.42 mmol) in anhydrous THF (8 mL). After 20 min at ꢀ408C, the solu-
tion was allowed to warm to 08C for 1 h, then for 2 h at RT before
AcOH (0.2 mL) was added. After concentration in vacuo, the residue
was diluted with EtOAc, washed with H2O and brine and then dried
(Na2SO4). Purification by flash chromatography (cyclohexane/EtOAc 4:1
then 7:3) afforded 24 (2.82 g, quant.) as a colourless oil. Rf =0.53 (cyclo-
hexane/EtOAc 1:1); [a]D24 =+33 (c=0.7 in CHCl3); 1H NMR (500 MHz,
CDCl3): d=1.22 (3H, s; Me), 1.32 (3H, s; Me), 3.19 (3H, s; OMe), 3.26
1
noside (2.36 g, 90%) as a white powder. H NMR (300 MHz, CDCl3): d=
1.43 (3H, s; Me), 1.50 (3H, s; Me), 3.61 (1H, dd, J=7.8, 3.4 Hz; H
C(2)), 3.95–4.07 (2H, m; H2C(5)), 4.28 (1H, app.d, J=5.3 Hz; H C(4)),
4.46 (1H, dd, J=7.8, 5.8 Hz; H C(3)), 4.59–4.80 (2H, ABq, J=12.4 Hz;
ꢀ
ꢀ
ꢀ
PhCH2OC(2)), 4.70–4.80 (2H, ABq, J=12.6 Hz; PhCH2OC(1)), 4.93
(1H, d, J=3.4 Hz; H C(1)), 7.33–7.47 ppm (10H, m; Ar); 13C NMR
ꢀ
(125.7 MHz, CDCl3): d=24.30 (Me), 27.42 (Me), 57.52 (PhCH2), 67.62
(PhCH2), 70.56 (C(5)), 72.14 (C(4)), 74.09 (C(3)), 75.50 (C(2)), 94.39
(C(1)), 107.18 (Me2C), 126.08–126.94, 136.03, 137.02 ppm (Ar); ESIMS
(pos., MeOH): m/z (%): 393 (100) [M+Na]+; HR-ESIMS (pos., MeOH):
m/z: calcd for C22H26O5Na: 393.1672; found: 393.1667. To a solution of
this compound (2 g, 5.41 mmol) in THF (20 mL) was added a solution of
1m HCl. The mixture was stirred at 308C overnight, then concentrated in
vacuo to give 19 (1.71 g, 96%). 1H NMR (300 MHz, CDCl3): d=3.76
(1H, ABXdd, JAB =12.6, JAX =1.9 Hz; H C(5)), 3.78 (1H, dd, J=9.5,
3.6 Hz; H C(2)), 3.91 (1H, ABXbrd, JAB =12.6 Hz; H C(5’)), 4.05 (1H,
m; H C(4)), 4.12 (1H, dd, J=9.5, 3.3 Hz; H C(3)), 4.52–4.77 (2H, ABq,
J=12.1 Hz; PhCH2OC(1)), 4.54–4.60 (2H, ABq, J=11.5 Hz;
ꢀ
(3H, s; OMe), 3.71 (1H, ABXdd, JAB =13.1, JAX =1.7 Hz; H C(5)), 3.83
ꢀ
ꢀ
ꢀ
(1H, ABXd, JAB =13.1 Hz; H C(5’)), 4.20 (2H, m; H C(2), H C(3)),
ꢀ
4.71–4.76 (2H, ABq, J=12.6 Hz; PhCH2OC), 4.76 (1H, m; H C(4)),
4.97 (1H, d, J=3.1 Hz; H C(1)), 5.08 (1H, ABXdd, JAB =11.8, JAX
ꢀ
=
7.5 Hz; PhCH2OP), 5.11 (1H, ABXdd,
JAB =11.8,
JBX =7.2 Hz;
PhCH2OP), 5.18 (1H, ABXdd, JAB =12.0, JAX =6.2 Hz; PhCH2OP), 5.23
(1H, ABXdd, JAB =12.0, JBX =6.4 Hz; PhCH2OP), 7.28–7.42 ppm (15H,
m; Ar); 13C NMR (75.4 MHz, CDCl3): d=17.73 (Me), 17.75 (Me), 47.84
ꢀ
ꢀ
ꢀ
ꢀ
(OMe), 48.07 (O Me), 62.71 (C(5)), 64.47 (C(2)), 65.17 (C(3)), 69.13
ꢀ
ꢀ
(PhCH2OP), 69.25 (PhCH2OP), 69.57 (PhCH2OC), 74.55 (C(4)), 96.83
ꢀ
ꢀ
(C(1)), 99.96 (C OMe), 100.10 (C OMe), 127.60, 127.69, 127.86, 127.89,
128.16, 128.28, 128.34, 128.41, 128.46, 137.50 ppm (Ar); 1H-decoupled
31P NMR (161.9 MHz, CDCl3): d=ꢀ4.01 ppm (s); elemental analysis
calcd (%) for C32H39O10P: C 62.53, H 6.40, P 5.04; found: C 62.33, H
6.60, P 5.24; APCIMS (pos., MeOH): m/z (%): 583 (100) [MꢀCH3O]+,
638 (15) [M+H+Na]+; HR-ESIMS (pos., MeOH): m/z: calcd for
C32H39O10NaP: 637.2173; found: 637.2173.
ꢀ
PhCH2OC(2)), 5.00 (1H, d, J=3.3 Hz; H C(1)), 7.30–7.45 ppm (10H, m;
Ar); 13C NMR (75.4 MHz, CDCl3): d=62.32 (PhCH2), 68.77 (C(4)), 69.17
(C(3)), 69.41 (C(5)), 72.52 (C(2)), 95.66 (C(1)), 128.15–128.92, 137.51,
138.05 ppm (Ar); ESIMS (pos., MeOH): m/z (%): 353 (100) [M+Na]+;
HR-ESIMS (pos., MeOH): m/z: calcd for C19H22O5Na: 353.1359; found:
353.1365.
Triethylammonium
1,2-di-O-benzyl-b-d-arabinopyranoside-3,4-cyclic
Sodium l-arabinose-4-phosphate (21): A solution of 24 (1.11 g,
phosphate (20): A sample of 19 was dried over P2O5 overnight under
high vacuum. To a stirred solution of 19 (1.00 g, 3.03 mmol) in anhydrous
pyridine (7.6 mL) was added POCl3 (0.565 mL, 6.06 mmol), and stirring
was then continued at 258C overnight. A mixture of Et3N (6 mL) and
H2O (6 mL) was added, and the resultant mixture was stirred at 258C for
1 h before being concentrated in vacuo. Purification by flash chromatog-
raphy (CH2Cl2/MeOH 8:2, 1% Et3N), and then by reverse-phase HPLC
(H2O for 15 min, then MeCN/H2O 1:1), followed by lyophilisation gave
20 as a white powder (755 mg, 56%). 1H NMR (500 MHz, CD3OD): d=
1.80 mmol) in MeOH (15 mL) that contained Pd(OH)2 (180 mg,
0.09 mmol) was frozen, degassed and thawed three times. The mixture
was then stirred under H2 at RT overnight. Filtration through Celite, fol-
lowed by concentration in vacuo afforded 2,3(2,3-dimethoxybut-2,3-diyl)-
b-l-arabinopyranoside-4-phosphoric acid as a colourless foam (660 mg,
quant.). [a]1D2 =ꢀ19 (c=1.0 in MeOH). The a/b ratio was 7:3 in CD3OD
according to 1H NMR spectroscopic integration. 1H NMR (500 MHz,
CD3OD): d=1.26 (3H, s; Me), 1.29 (3H, s; Me), 3.23 (3H, s; OMe), 3.25
ꢀ
(3H, s; OMe), 3.67 (0.3H, d, J=13.2 Hz; H C(5) (b)), 3.73 (0.3H, dd,
ꢀ
ꢀ
ꢀ
1.23 (t, J=7.0 Hz; N
3.94 (2H, ABq, J=13.7 Hz; H2C(5)), 4.03 (1H, dd, J=8.4, 3.3 Hz; H
C(2)), 4.44–4.67 (2H, ABq, J=12.1 Hz; PhCH2OC(1)), 4.47–4.57 (2H,
A
G
J=10.4, 7.8 Hz; H C(2) (b)), 3.83 (1H, m; H C(3) (b), H C(5) (a)),
ꢀ
ꢀ
ꢀ
ꢀ
3.99 (0.7H, d, J=13.2 Hz; H C(5) (a)), 4.09 (1.7H, m; H C(5) (b), H
ꢀ
ꢀ
C(2) (a), H C(3) (a)), 4.34 (0.3H, brd, J=7.3 Hz; H C(4) (b)), 4.39
2384
www.chemeurj.org
ꢀ 2008 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim
Chem. Eur. J. 2008, 14, 2375 – 2388

Prebiotic Synthesis of Nucleotides
FULL PAPER
ꢀ
ꢀ
(0.7H, brd, J=6.9 Hz, H C(4) (a)), 4.65 (0.3H, d, J=7.9 Hz; H C(1)
(2H, d, J=7.4 Hz; Ar); 13C NMR (75.4 MHz, CDCl3): d=17.64 (Me),
17.78 (Me), 47.82 (OMe), 47.89 (OMe), 62.11 (C(5)), 67.98 (C(2)), 68.14
(b)), 5.23 ppm (0.7H, d, J=3.5 Hz; H C(1) (a)); 13C NMR (125.7 MHz,
ꢀ
ꢀ
CD3OD): d=18.08 (Me), 18.10 (Me), 18.16 (Me), 18.18 (Me), 48.33
(OMe), 48.40 (OMe), 48.47 (OMe), 48.49 (OMe), 62.95 (C(5) (b)), 65.73
(C(5) (a)), 66.88 (C(2) (b)), 67.22 (C(2) (a)), 69.58 (C(3) (b)), 70.08
(C(3) (a)), 74.05 (C(4) (b)), 74.83 (C(4) (a)), 92.73 (C(1) (a)), 96.80
(C(4)), 69.08 (PhCH2), 69.93 (C(3)), 96.10 (C(1)), 99.43 (MeO C), 99.84
ꢀ
(MeO C), 127.53, 127.90, 128.23, 137.37 ppm (Ar); IR (film, CH2Cl2):
n˜ =3469–3399 cmꢀ1 (brOH); CIMS (pos., MeOH): m/z (%): 372 (60)
[M+NH4]+; HR-CIMS (pos., MeOH): m/z: calcd for C18H30O7N:
372.2017; found: 372.2020.
ꢀ
ꢀ
ꢀ
(C(1) (b)), 101.08 ((C OMe) (a)), 101.36 ((C OMe) (a)), 101.40 ((C
OMe) (b)), 101.47 ppm ((C OMe) (b)); 31P NMR (161.9 MHz, CD3OD):
ꢀ
1-O-Benzyl-2,3-(2,3-dimethoxybut-2,3-diyl)-a-d-xylopyranoside-4-O-di-
benzylphosphate (27): Synthesised from 26 (130 mg, 0.37 mmol) by the
same procedure as 24 was from 23. Purification by flash chromatography
(PhMe/EtOAc 4:1) afforded 27 as a colourless oil (230 mg, quant.). Rf =
0.60 (cyclohexane/EtOAc 1:1); [a]2D1 =ꢀ20 (c=1.2 in CHCl3); 1H NMR
(500 MHz, CDCl3): d=1.24 (3H, s; Me), 1.32 (3H, s; Me), 3.23 (3H, s;
d=3.36 ppm (s); ESIMS (neg., MeOH): m/z (%): 325 (15)
[MꢀH2OꢀH]ꢀ, 343 (100) [MꢀH]ꢀ; HR-ESIMS (neg., MeOH): calcd for
C11H20O10P: 343.0805; found: 343.0800. To a solution of this compound
(124 mg, 0.36 mmol) in CH2Cl2 (5 mL) was added TFA (90%, aq.,
0.25 mL) at RT and the mixture was left for 24 h. After separation of a
white syrup, the yellow organic phase was removed. The white syrup was
triturated with CH2Cl2 (5 mL) and dried in vacuo to give the free acid
form of 21 (88 mg) which was dissolved in D2O and neutralised with
NaOD solution The resultant solution was lyophilised to afford 21 as a
white powder (114 mg, quant.). The a/b ratio was 2:1 in D2O according
ꢀ
OMe), 3.27 (3H, s; OMe), 3.58 (1H, t, J=10.8 Hz; Hax C(5)), 3.73 (1H,
ꢀ
ꢀ
dd, J=11.1, 5.5 Hz; Heq C(5)), 3.74 (1H, dd, J=10.1, 3.6 Hz; H C(2)),
ꢀ
ꢀ
4.12 (1H, t, J=9.8 Hz; H C(3)), 4.40 (1H, m; H C(4)), 4.60–4.75 (2H,
ꢀ
ABq, J=12.2 Hz; PhCH2OC), 4.88 (1H, d, J=3.5 Hz; H C(1)), 5.13
(4H, m; PhCH2OP), 7.30–7.42 ppm (15H, m; Ar); 13C NMR (75.4 MHz,
CDCl3): d=17.57 (Me), 17.69 (Me), 47.78 (OMe), 47.90 (OMe), 60.43
(C(5)), 67.76 (C(3)), 68.09 (C(2)), 69.12 (PhCH2), 69.25, 69.29
1
1
to H NMR spectroscopic integration. H NMR (500 MHz, D2O): d=3.54
(0.66H, dd, J=9.7, 7.8 Hz; H C(2) (a)), 3.63 (0.66H, m; H C(3) (a)),
3.64 (0.66H, d, J=13.4 Hz; Heq C(5) (a)), 3.81 (0.33H, dd, J=12.9,
3.0 Hz; H C(2) (b)), 3.87 (0.66H, m; H C(5) (b)), 4.00 (0.33H, dd, J=
ꢀ
ꢀ
ꢀ
ꢀ
ꢀ
(PhCH2OP), 72.98 (C(4)), 95.76 (C(1)), 99.51 (C OMe), 99.88 (C OMe),
127.62, 127.69, 127.88, 128.01, 128.27, 128.40, 128.50, 135.66, 135.75,
137.18 ppm (Ar); 31P NMR (161.9 MHz, CDCl3): d=ꢀ1.26 ppm (sextet,
J=7.3 Hz); APCIMS (pos., MeOH): m/z (%): 583 (20) [MꢀCH3O]+,
637 (85) [M+Na]+; HR-ESIMS (pos., MeOH): m/z: calcd for
C32H39O10NaP: 637.2173; found: 637.2175.
ꢀ
ꢀ
ꢀ
ꢀ
12.7, 1.0 Hz; H C(3) (b)), 4.05 (0.66H, dd, J=13.1, 2.2 Hz; Hax C(5)
ꢀ
ꢀ
(a)), 4.33 (0.66H, m; H C(4) (a)), 4.39 (0.33H, m; H C(4) (b)), 4.51
ꢀ
ꢀ
(0.66H, d, J=7.7 Hz; H C(1) (a)), 5.22 ppm (0.33H, d, J=3.3 Hz; H
C(1) (b)); 13C NMR (125.7 MHz, D2O): d=61.84 (C(2) (a)), 65.50 (C(5)
(a)), 68.57 (C(3) (b)), 68.91 (C(5) (b)), 72.20 (C(2) (b)), 72.40 (C(4) (a)),
72.72 (C(4) (b)), 92.72 (C(1) (b)), 96.87 ppm (C(1) (a)); 31P NMR
(161.9 MHz, D2O): d=0.80 (s), 1.67 ppm (s); ESIMS (neg., H2O): m/z
(%): 229 (100) [Mꢀ2Na+H]ꢀ; HR-ESIMS (neg., H2O): m/z: calcd for
C5H10O8P: 229.0119; found: 229.0115.
Sodium d-xylose-4-phosphate (22): A solution of 27 (709 mg, 1.15 mmol)
in MeOH (10 mL) that contained Pd(OH)2 (40 mg, 0.06 mmol) was
frozen, degassed and thawed twice. The mixture was then stirred under
H2 at RT overnight. Filtration through Celite followed by concentration
in vacuo afforded the ketal, 2,3-(2,3-dimethoxybut-2,3-diyl)-a-d-xylopyra-
noside-4-phosphoric acid, and fully deprotected material in a 4:1 ratio as
a colourless foam. Data for the ketal: 1H NMR (500 MHz, CD3OD): d=
1.27 (1.5H, s; Me), 1.28 (1.5H, s; Me), 1.29 (3H, 2”s; 2”Me), 3.24
(1.5H, s; OMe), 3.27 (1.5H, s; OMe), 3.28 (1.5H, s; OMe), 3.29 (1.5H, s;
1-O-Benzyl-2,3-(2,3-dimethoxybut-2,3-diyl)-4-(4-nitrobenzoyl)-a-d-xylo-
pyranoside (25): Compound 23 (727 mg, 2.05 mmol), PPh3 (1.61 g,
6.15 mmol) and 4-nitrobenzoic acid (1.03 g, 6.15 mmol) were stirred in
anhydrous THF (10 mL) under N2 at RT. (iPrOC(O)N)2 (1.21 mL,
6.15 mmol) was added dropwise and the resultant solution stirred at RT.
After 2 d. The solution was concentrated in vacuo and the resulting
yellow oil was purified by flash chromatography (cyclohexane/EtOAc
85:15) to give the product as a white powder. Recrystallisation from
CH2Cl2/heptane gave 25 as yellow orthorhombic crystals (1.03 g, quant.).
Rf =0.64 (cyclohexane/EtOAc 7:3); m.p. 171–1738C; [a]2D5 =ꢀ83 (c=1.0
in CHCl3); 1H NMR (500 MHz, CDCl3): d=1.27 (3H, s; Me), 1.35 (3H,
s; Me), 3.25 (3H, s; OMe), 3.30 (3H, s; OMe), 3.65 (1H, t, J=10.7 Hz;
Hax C(5)), 3.87 (1H, dd, J=10.2, 3.6 Hz; H C(2)), 3.94 (1H, dd, J=10.8,
5.8 Hz; Heq C(5)), 4.39 (1H, t, J=10.0 Hz; H C(3)), 4.71–4.80 (2H,
ABq, J=12.5 Hz; PhCH2O), 4.93 (1H, d, J=3.6 Hz; H C(1)), 5.20 (1H,
dt, J=10.3, 5.8 Hz; H C(4)), 7.30 (1H, t, J=7.3 Hz; Ar), 7.36 (2H, t, J=
7.4 Hz; Ar), 7.43 (2H, d, J=7.3 Hz; Ar), 8.17 (2H, d, J=8.9 Hz; Ar),
8.29 ppm (2H, d, J=8.9 Hz; Ar); 13C NMR (75.4 MHz, CDCl3): d=17.58
(Me), 17.71 (Me), 47.70 (OMe), 47.93 (OMe), 59.16 (C(5)), 66.56 (C(3)),
68.27 (C(2)), 69.46 (PhCH2), 70.58 (C(4)), 96.04 (C(1)), 99.61 (MeO C),
99.94 (MeO C), 123.51, 123.57, 127.67, 127.88, 128.28, 128.79, 130.72,
ꢀ
OMe), 3.38 (0.5H; H C(2) (b) partially obscured), 3.41 (0.5H, dd, J=
ꢀ
ꢀ
11.7, 9.8 Hz; H C(5) (b)), 3.63 (0.5H, dd, J=10.1, 3.8 Hz; H C(2) (a)),
ꢀ
ꢀ
3.73 (0.5H, app.t, J=9.7 Hz; H C(3) (b)), 3.81 (1H, m; H C(5) (a)),
4.06 (0.5H, app.t, J=9.6 Hz; H C(3) (a)), 4.12 (0.5H, dd, J=11.7,
5.4 Hz; H C(5) (b)), 4.23 (1H, m; H C(4) (a,b)), 4.60 (0.5H, d, J=
ꢀ
ꢀ
ꢀ
ꢀ
ꢀ
7.9 Hz;
H C(1) (b)), 5.05 ppm (0.5H, d, J=3.5 Hz; H C(1) (a));
13C NMR (75.4 MHz, CD3OD): d=17.95 (Me), 18.05 (Me), 47.36 (OMe),
48.24 (OMe), 48.31 (OMe), 48.36 (OMe), 61.63 (C(5)), 68.92–70.04 (over-
lapping C(2), C(3)), 71.91 (C(2)), 72.46 (C(4)), 101.08 (C(1) (b)),
101.36 ppm (C(1) (a)); 31P NMR (161.9 MHz, CD3OD): d=2.30 (d, J=
8.6 Hz, (b)), 2.36 (d, J=8.6 Hz, (a)); ESIMS (neg., MeOH): m/z: 343
(100) [MꢀH]ꢀ; HR-ESIMS (neg., MeOH): m/z: calcd for C11H20O10P:
343.0800; found: 343.0802. To a solution of all of this mixture in CH2Cl2
(5 mL) was added TFA (90%, aq., 0.25 mL). The mixture was left at RT
for 24 h. After separation of a white syrup, the yellow organic phase was
removed. The white syrup was triturated with CH2Cl2 (5 mL) and dried
in vacuo. The residue was dissolved in D2O and neutralised with NaOD
solution, and the resultant solution lyophilised to afford 22 as a white
powder (295 mg, 96%). [a]2D4 =+30 (c=1.1 in H2O). The a/b ratio was
1:2 in D2O according to 1H NMR spectroscopic integration. 1H NMR
ꢀ
ꢀ
ꢀ
ꢀ
ꢀ
ꢀ
ꢀ
ꢀ
135.09, 137.19, 150.58 (Ar), 163.72 ppm (C=O); IR (film, CH2Cl2): n˜ =
1732 (CO), 1529, 1350 cmꢀ1 (N=O); elemental analysis calcd (%) for
C25H29O10N: C 59.64, H 5.81, N 2.78; found: C 59.87, H 5.91, N 2.75;
APCIMS (neg., MeOH): m/z (%): 503 (50) [M]ꢀ, 504 (100) [M+H]ꢀ.
ꢀ
(500 MHz, D2O): d=3.27 (0.66H, dd, J=9.0, 8.0 Hz; H C(2) (b)), 3.34
1-O-Benzyl-2,3-(2,3-dimethoxybut-2,3-diyl)-a-d-xylopyranoside (26):
A
ꢀ
(0.66H, dd, J=11.2, 10.6 Hz; Hax C(5) (b)), 3.56 (0.66H, t, J=9.1 Hz;
methanolic NH3 solution (saturated, 60 mL) was added to a solution of
25 (8.12 g, 16.12 mmol) in CH2Cl2 (25 mL) and the resultant mixture was
kept at 608C overnight After concentration in vacuo, the resulting yellow
powder (10 g) was purified by flash chromatography (EtOAc/cyclohexane
1:3) to afford 26 (5.35 g, 93%) as a yellow-glassy syrup. Rf =0.25 (cyclo-
hexane/EtOAc 7:3); [a]D21 =ꢀ27 (c=1.0 in CHCl3); 1H NMR (500 MHz,
CDCl3): d=1.33 (3H, s; Me), 1.35 (3H, s; Me), 3.24 (3H, s; OMe), 3.30
ꢀ
ꢀ
H C(3) (b)), 3.57 (0.33H, dd, J=9.2, 3.2 Hz; H C(2) (a)), 3.70 (0.33H,
ꢀ
ꢀ
t, J=10.9 Hz; Hax C(5) (a)), 3.76 (0.33H, t, J=9.1 Hz; H C(3) (a)), 3.81
ꢀ
ꢀ
(0.33H, dd, J=11.3, 5.6 Hz; Heq C(5) (a)), 3.97 (1H, m, H C(4) (a,b)),
ꢀ
4.05 (0.66H, dd, J=11.4, 5.6 Hz; Heq C(5) (b)), 4.57 (0.66H, d, J=
ꢀ
ꢀ
7.9 Hz;
H
C(1) (b)), 5.16 ppm (0.33H, d, J=3.7 Hz;
H
C(1) (a));
13C NMR (125.7 MHz, D2O): d=58.88 (C(5) (a)), 64.16 (C(5) (b)), 71.05
(C(2) (a)), 71.85 (C(4) (a, b)), 72.14 (C(3) (a)), 73.64 (C(2) (b)), 75.30
(C(3) (b)), 91.70 (C(1) (a)), 96.17 ppm (C(1)(b)); 31P NMR (161.9 MHz,
D2O): d=3.87 ppm (s, (a)), 4.01 (s, (b)); ESIMS (neg., H2O): m/z (%):
229 (100) [Mꢀ2Na+H]ꢀ; HR-ESIMS (pos., H2O): m/z: calcd
C5H10O8Na2P: 274.9903; found: 274.9904.
ꢀ
(3H, s; OMe), 3.57 (1H, app.t, J=10.7 Hz; Hax C(5)), 3.67 (1H, app.t,
ꢀ
ꢀ
J=5.4 Hz; Heq C(5)), 3.70 (1H, dd, J=10.3, 3.6 Hz; H C(2)), 3.85 (1H,
ꢀ
ꢀ
dt, J=9.9, 5.7 Hz; H C(4)), 4.04 (1H, dd, J=10.2, 9.3 Hz; H C(3)),
4.67–4.77 (2H, ABq, J=12.5 Hz; PhCH2O), 4.86 (1H, d, J=3.6 Hz; H
ꢀ
C(1)), 7.29 (1H, t, J=7.5 Hz; Ar), 7.27 (2H, t, J=7.5 Hz; Ar), 7.35 ppm
Chem. Eur. J. 2008, 14, 2375 – 2388
ꢀ 2008 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim
www.chemeurj.org
2385

J. D. Sutherland et al.
Reaction of sodium d-arabinose-2-phosphate (14) with cyanoacetylene:
A solution of 14 (30 mg, 0.11 mmol) in D2O (0.6 mL) at pD 7 was pre-
pared. A solution of cyanoacetylene in D2O (1m, 0.22 mL, 0.22 mmol,
2 equiv) was then added, and the resultant mixture was allowed to stand
at RT. The reaction was monitored by 1H NMR spectroscopy with the
spectra being recorded after 1 h, 5 h, 1 d and 4 d.
tion lyophilised to afford glyceraldehyde-2-phosphate 37 as the sodium
1
ꢀ
salt (244 mg, 94%). H NMR (500 MHz, D2O): d=3.64 (2H, m; H
ꢀ
ꢀ
C(3)), 3.96 (1H, m; H C(2)), 4.94 ppm (1H, d, J=3.8 Hz; H C(1));
13C NMR (75.4 MHz, D2O): d=61.64 (C(3)), 77.25 (C(2)), 89.48 ppm
(C(1)); 1H-decoupled 31P NMR (161.9 MHz, D2O): d=5.30 ppm (s);
ESIMS (neg., H2O): m/z (%): 169 (100) [M]ꢀ; HR-ESIMS (neg., H2O):
m/z: calcd for C3H6O6P: 168.9907; found: 168.9910.
Reaction of sodium l-arabinose-4-phosphate (21) with cyanoacetylene:
A solution of cyanoacetylene in D2O (1m, 0.21 mL, 0.21 mmol, 3 equiv),
was added to a solution of 21 (18 mg, 0.07 mmol) in D2O (0.5 mL; final
pD 6.49). After 20 h at 608C, the solution was lyophilised to give a red
powder (22 mg) which was redissolved in D2O. 1H NMR spectroscopic
analysis showed 60% conversion to the 3,4-cyclic-phosphate 18
(Figure 3).
1-O-Benzyl-2,3-O-isopropylidene-a-d-lyxopyranoside-4-O-dibenzylphos-
phate (45): A solution of tBuOK (274 mg, 2.45 mmol) in THF (5 mL)
was added dropwise at RT to a solution of 44 (489 mg, 1.75 mmol) in an-
hydrous THF (15 mL) under N2. After 20 min, the solution was cooled to
ꢀ408C before a solution of ((BnO)2P(O))2O (1.50 g, 2.79 mmol) in anhy-
drous THF (5 mL) was added. After 40 min at ꢀ408C, the solution was
allowed to warm to 08C for 1 h and then RT for 4 h. NH4Cl (aq., 50%
saturated, 10 mL) was added, and the mixture was extracted with EtOAc
(10 mL). The aqueous phase was extracted with EtOAc (15 mL) and the
combined organic phases were washed with NaHCO3 aq. (50% saturat-
ed, 15 mL), H2O (10 mL) and brine (20 mL). The resulting mixture was
dried (MgSO4) before filtration and the concentrated in vacuo. The resul-
tant yellow oil was purified by flash chromatography (petroleum ether/
EtOAc 3:1) to afford 45 (779 mg, 83%) as a colourless oil. Rf =0.66 (pe-
troleum ether/EtOAc 3:2); [a]2D4 =+26 (c=1.0 in CHCl3); 1H NMR
(500 MHz, CDCl3): d=1.33 (3H, s; Me), 1.42 (3H, s; Me), 3.68 (1H,
Hydrolysis of sodium d-arabinose-3,4-cyclic phosphate (18): A solution
of 18 (10.5 mg, 0.043 mmol) in D2O (1 mL) was prepared and the pD ad-
justed to 2 with a solution of DCl. The volume was then adjusted to
1.5 mL with D2O. The mixture was kept at RT, and the progress of the
reaction was monitored by 1H NMR spectroscopy. After 4 d, the starting
material was observed to have been consumed. Spiking of the 1H NMR
spectroscopic sample with authentic standards of d-arabinose-3-phos-
phate (1) and l-arabinose-4-phosphate (21) enabled the hydrolysis prod-
ucts to be identified as 1 and 21 in a ratio of 0.67:0.33 (Figure 3).
2-Dibenzylphosphoryl-3-triphenylmethylglyceraldehyde diethyl acetal
(42): A solution of tBuOK (473 mg, 4.22 mmol) in THF (9 mL) was
added dropwise at RT to a solution of 41[19] (1.23 g, 3.01 mmol) in anhy-
drous THF (15 mL) under N2. After stirring for 20 min, the solution was
cooled to ꢀ408C and a solution of ((BnO)2P(O))2O (2.60 g, 4.83 mmol)
in anhydrous THF (6 mL) was added. After 40 min at ꢀ408C, the solu-
tion was allowed to warm to 08C and stirred for 1 h then at RT for a fur-
ther 3 h. NH4Cl aq. (50% saturated, 15 mL) and EtOAc (15 mL) were
added to the mixture. The aqueous phase was extracted with EtOAc (2”
10 mL) and the combined organic phases were washed sequentially with
NaHCO3 aq. (50% saturated, 20 mL), H2O (20 mL) and brine (20 mL),
and was then dried (MgSO4), filtered and concentrated in vacuo. Purifi-
cation by flash chromatography (petroleum ether/EtOAc 4:1) afforded
42 as a colourless oil (1.99 g, 99%). Rf =0.26 (petroleum ether/EtOAc
7:2); 1H NMR (500 MHz, CDCl3): d=1.08 (3H, t, J=7.1 Hz; Me), 1.18
ꢀ
ABXq, JAB =11.4, JAX =8.8 Hz; Hax C(5)), 3.74 (1H, ABXq, JAB =11.6,
ꢀ
ꢀ
J
BX =4.7 Hz; Heq C(5)), 4.14 (1H, dd, J=5.4, 1.9 Hz; H C(2)), 4.22 (1H,
ꢀ
ꢀ
app.t, J=5.8 Hz; H C(3)), 4.49 (1H, m; H C(4)), 4.55–4.77 (2H, ABq,
J=11.8 Hz; PhCH2OC), 4.91 (1H, d, J=1.9 Hz; H C(1)), 5.07 (2H, d,
ꢀ
J=7.5 Hz; PhCH2OP), 5.09 (2H, dd, J=7.8, 3.3 Hz; PhCH2OP), 7.31–
7.39 ppm (15H, m; Ar); 13C NMR (125.7 MHz, CDCl3): d=26.27 (Me),
27.74 (Me), 59.46 (C(5)), 69.30 (PhCH2OP), 69.35 (PhCH2OC), 69.50
(PhCH2OP), 75.35 (C(4)), 75.71 (C(2)), 75.77 (C(3)), 96.84 (C(1)), 109.72
(Me2C), 127.89, 127.95, 127.98, 128.47, 128.50, 128.51, 135.61, 135.67,
135.72, 136.74 ppm (Ar); 1H-decoupled 31P NMR (161.9 MHz, CDCl3):
d=ꢀ3.32 ppm (s); elemental analysis calcd (%) for C29H33O8P: C 64.44,
H 6.15, P 5.73; found: C 64.23, H 6.43, P 5.75; ESIMS (pos., MeOH): m/z
(%): 563 (100) [M+Na]+, 564 (40) [M+H+Na]+; HR-ESIMS (pos.,
MeOH): m/z: calcd for C29H33O8NaP: 563.1805; found: 563.1809.
ꢀ
Sodium d-lyxose-4-phosphate (41): A solution of 45 (323 mg, 0.60 mmol)
in MeOH (10 mL) with Pd/C (5% Pd, 32 mg) was frozen, degassed and
thawed. The mixture was then stirred under H2 at RT overnight. After
this time, the mixture was filtered through Celite and the plug was rinsed
with MeOH (5 mL). The pH was adjusted to 1 with HCl aq. and the solu-
tion was warmed for 3 h at 408C. After neutralization to pHꢁ6 (NaOH),
the solution was partially concentrated in vacuo then lyophilised to
afford 41 as a white powder (124 mg, 75%). The b/a ratio was 3:1 in
D2O according to 1H NMR spectroscopic integration. 1H NMR
(3H, t, J=6.9 Hz; Me), 3.34 (1H, dd, J=10.6, 5.2 Hz; H C(3)), 3.50
ꢀ
(1H, qd, J=9.1, 7.1 Hz; CH2CH3), 3.53–3.61 (2H, m; CH2CH3, H C(3)),
3.64 (1H, qd, J=9.1, 7.1 Hz; CH2CH3), 3.73 (1H, qd, J=9.1, 7.1 Hz;
ꢀ
ꢀ
CH2CH3), 4.62 (1H, m; H C(2)), 4.81 (1H, d, J=5.7 Hz; H C(1)), 5.04
(2H, ABXdt, AB =12.0, AX =JBX =7.3 Hz; PhCH2OP), 5.10 (2H,
J
J
ABXdt, JAB =12.0, JAX =JBX =7.3 Hz; PhCH2OP), 7.20–7.37 (19H, m;
Ar), 7.46–7.51 ppm (6H, m; Ar); 13C NMR (125.7 MHz, CDCl3): d=
15.05 (Me), 15.17 (Me), 62.74 (OCH2CH3), 62.76, 62.79 (C(3)), 63.67
(OCH2CH3), 68.98 (2 PhCH2OP), 77.78 (C(2)), 86.67 (CPh3), 100.81
(C(1)), 126.93, 127.67, 127.72, 127.76, 128.18, 128.37, 127.38, 128.71,
135.95, 136.04, 143.64 ppm (Ar); 31P NMR (161.9 MHz, CDCl3): d=
ꢀ0.41 ppm (sextet, J=8.5 Hz); elemental analysis calcd for C40H43O7P: C
72.06, H 6.50, P 4.65; found: C 72.02, H 6.70, P 4.43; ESIMS (pos.,
MeOH): m/z (%): 684 (20) [M+NH4]+, 689 (100) [M+Na]+, 690 (40)
[M+Na+H]+; HR-ESIMS (pos., MeOH): m/z: calcd for C40H43O7NaP:
689.2639; found: 689.2639.
ꢀ
(300 MHz, D2O): d=3.29 (0.25H, dd, J=12.0, 8.3 Hz; H C(5) (a)), 3.42
ꢀ
ꢀ
(0.75H, dd, J=5.8, 3.2 Hz; H C(2) (b)), 3.69 (0.25H, m; H C(3) (a)),
ꢀ
3.70 (0.75H, dd, J=12.3, 5.0 Hz; H C(5) (b)), 3.81 (0.75H, dd, J=12.3,
2.8 Hz; H C(5) (b)), 3.82 (0.25H, m; H C(2) (a)), 3.94 (0.75H, dd, J=
5.7, 3.5 Hz; H C(3) (b)), 3.99 (0.25H, dd, J=12.6, 4.4 Hz; H C(5) (a)),
4.13 (1H, m; H C(4) (a), H C(4) (b)), 4.79 (0.25H, d, J=1.6 Hz; H
ꢀ
ꢀ
ꢀ
ꢀ
ꢀ
ꢀ
ꢀ
ꢀ
C(1) (a)), 4.81 ppm (0.75H, d, J=6.0 Hz;
H
C(1) (b)); 13C NMR
(500 MHz, D2O): d=61.14 (C(5) (a)), 62.28 (C(5) (b)), 68.89 (C(2) (a)),
69.49 (C(3) (b)), 69.70 (C(2) (b)), 69.78 (C(3) (a)), 72.32 (C(4) (b)),
73.37 (C(4) (a)), 92.70 (C(1) (a)), 93.36 ppm (C(1) (b)); 1H-decoupled
31P NMR (161.9 MHz, D2O): d=ꢀ3.32 ppm (s); ESIMS (neg., H2O): 229
(90) [MꢀH]ꢀ; HR-ESIMS (neg., H2O): calcd for C5H10O8P: 229.0119;
found: 229.0112.
Sodium glyceraldehyde-2-phosphate (37):
A solution of 42 (829 mg,
1.24 mmol) in dioxane/H2O (2:1, 15 mL) that contains Pd/C (5% Pd,
66 mg) was frozen, degassed and thawed three times before being stirred
under H2 at RT overnight. H2O (5 mL) was then added and the mixture
was filtered through Celite. After rinsing the Celite with dioxane/H2O
(1:1, 40 mL), the combined filtrates were lyophilised. CH2Cl2 (10 mL)
and H2O (5 mL) were added to the lyophilisate, and the resulting mixture
shaken to effect dissolution of solids. After separation, the organic phase
was extracted with H2O (3”10 mL) and the combined aqueous phases
were washed with CH2Cl2 (2”10 mL). The aqueous phase was then
lyophilised and the resulting colourless oil (276 mg) was dissolved in D2O
(2.7 mL) and filtered through a 0.2 mm filter. The pD was adjusted to 2.2
(NaOD) and the solution was then warmed at 508C for 2 d. The hydroly-
1-O-Benzyl-2,3-isopropylidene-b-l-erythropent-4-ulose (46):
A mixture
of CrO3 (3.82 g, 38.18 mmol), anhydrous pyridine (6.10 mL, 76.37 mmol)
and anhydrous CH2Cl2 (130 mL) was stirred for 15 min under N2 at RT.
A solution of 44 (2.67 g, 9.54 mmol) in anhydrous CH2Cl2 (6 mL) was
added immediately followed by Ac2O (3.6 mL, 38.18 mmol). After
30 min, EtOAc (100 mL) was added and the mixture was then poured
into PhMe (100 mL) and filtered through a short pad of silica gel, which
was then rinsed with EtOAc (2”100 mL). The combined filtrates were
concentrated in vacuo, and the residue co-evaporated with PhMe
1
sis was monitored by H NMR spectroscopic analysis. After complete hy-
drolysis of the acetal, the pD was adjusted to ꢁ6 (NaOD) and the solu-
2386
www.chemeurj.org
ꢀ 2008 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim
Chem. Eur. J. 2008, 14, 2375 – 2388

Prebiotic Synthesis of Nucleotides
FULL PAPER
ꢀ
ꢀ
(50 mL) to give 46 as a yellow oil (2.52 g, 95%) which could be used
without further purification. An analytical sample was prepared in the
following way: the ketone was dissolved in EtOAc (30 mL) and washed
with CuSO4 aq.(saturated, 2”50 mL) and brine (20 mL). The mixture
was dried (MgSO4), filtered and then concentrated in vacuo to give a
pale-yellow solid (2.12 g, 80%); 1H NMR (300 MHz, CDCl3): d=1.38
(3H, s; Me), 1.52 (3H, s; Me), 4.17–4.24 (2H, ABq, J=16.7 Hz;
d, J=2.0 Hz; H C(1) (a)), 4.82 ppm (0.66H, d, J=6.9 Hz; H C(1) (b));
13C NMR (125.7 MHz, D2O): d=60.72 (C(5)), 67.53 (C(3)), 68.42 (C(2)),
69.38 (C(4)), 91.91 (C(1) (a)), 92.26 ppm (C(1) (b)); 31P NMR
(161.9 MHz, D2O): d=0.41 (d, J=8.6 Hz; (b)), 0.76 ppm (d, J=8.6 Hz;
(a)); ESIMS (neg., H2O): m/z (%): 229 (100) [M]ꢀ; HR-ESIMS (neg.,
H2O): m/z: calcd for C5H10O8P: 229.0119; found: 229.0115.
Attempted aldol reaction of sodium glyceraldehyde-2-phosphate (37)
with glycolaldehyde: Compound 37 (20 mg, 0.10 mmol) and glycolalde-
hyde (5.6 mg, 0.10 mmol) were dissolved in H2O (0.5 mL) and the pH
was adjusted to ꢁ11 (NaOH). The resultant solution was heated at 508C
for 3 h and was then cooled to RT, adjusted to pH ꢁ7 (HCl), and lyophi-
lized. The resulting residue was dissolved in D2O and analysed by
1H NMR spectroscopy.
ꢀ
ꢀ
H2C(5)), 4.43–4.50 (2H, m; H C(3), H C(2)), 4.59–4.80 (2H, ABq, J=
ꢀ
11.9 Hz; OCH2Ph), 4.99 (1H, d, J=1.5; H C(1)), 7.32–7.39 ppm (5H, m;
Ar); 13C NMR (75.4 MHz, CDCl3): d=25.31 (Me), 26.66 (Me), 65.87
(C(5)), 70.03 (OCH2Ph), 75.26 (C(3)), 77.68 (C(2)), 96.42 (C(1)), 111.87
(Me2C), 128.08, 128.24, 128.59, 136.17 (Ar), 203.14 ppm (C(4)); IR (film,
CH2Cl2): n˜ =1743 cmꢀ1 (CO); ESIMS (neg., MeOH): m/z (%): 277 (100)
[MꢀH]ꢀ; HR-ESIMS (neg., MeOH): m/z: calcd for C15H17O5: 277.1081;
found: 277.1089.
In control experiments, 37, glycolaldehyde, threose, and erythrose were
separately subjected to the same reaction conditions.
1-O-Benzyl-2,3-isopropylidene-b-l-ribopyranose (47): NaBH4 (686 mg,
18.14 mmol) was added in portions to a solution of 46 (2.52 g, 9.07 mmol)
in EtOH (20 mL) at 08C. After stirring for 1 h, the mixture was allowed
to warm to RT for 5 h and was then quenched with NH4Cl aq. (50% sa-
turated, 20 mL). After addition of EtOAc (10 mL) and separation, the
aqueous phase was extracted with EtOAc (3”20 mL). The combined or-
ganic phases were washed with H2O (20 mL) and brine (20 mL), and
were then dried (MgSO4), filtered, and concentrated in vacuo to afford a
colourless oil (2.06 g). Crystallization (petroleum ether/Et2O) gave white
monoclinic crystals (1.51 g, 62%). Rf =0.55 (petroleum ether/EtOAc
3:2); m.p. 60–648C; [a]D26 =+105 (c=1.0 in CHCl3); 1H NMR (500 MHz,
CDCl3): d=1.38 (3H, s; Me), 1.50 (3H, s; Me), 3.63 (1H, dd, J=11.4,
Reaction of 2-aminooxazole (49) with sodium glyceraldehyde-2-phos-
phate (37): Compound 37 (40 mg, 0.19 mmol) and 49 (16 mg, 0.19 mmol)
were dissolved in D2O (0.75 mL) and the pD was adjusted to 7.2
(NaOD). The solution was then heated to 408C and occasionally moni-
tored by H NMR spectroscopic analysis. According to integration of the
signals at d=4.65–4.72 and 3.45–3.60 ppm, the ratio of rac-54/rac-55 was
1
5:1 after 24 h.
Reaction of the pentose-4-phosphate sodium salts with cyanamide: Cyan-
amide was added to a solution of the pentose-4-phosphate sodium salt in
D2O/H2O, and the pD/pH was adjusted to
a value near neutrality
(NaOD/NaOH). After heating, the reaction was cooled down and ana-
lysed by 1H NMR spectroscopy either directly or after lyophilisation and
(re)dissolution in D2O.
ꢀ
ꢀ
7.9 Hz; Heq C(5)), 3.86 (1H, dd, J=11.0, 4.4 Hz, Hax C(5)), 4.06 (1H, dt,
ꢀ
ꢀ
J=7.9, 4.4 Hz, H C(4)), 4.16 (1H, dd, J=6.5, 3.3 Hz; H C(2)), 4.62
ꢀ
(1H, dd, J=6.3, 4.4 Hz; H C(3)), 4.58–4.81 (2H, ABq, J=11.8 Hz;
PhCH2O), 4.79 (1H, d, J=3.2 Hz; H C(1)), 7.31 (1H, m; Ar), 7.36 ppm
Data for l-54 as prepared from 21: Conditions: 21 (35 mg, 0.15 mmol)
and cyanamide (16 mg, 0.38 mmol) in H2O (0.8 mL), pH 7, 28 h at 608C,
followed by lyophilisation and dissolution in D2O. Yield: ꢁ30% residual
21+ ꢁ70% l-54; 1H NMR (500 MHz, D2O): d=3.61 (1H, brd, J=
ꢀ
(4H, m; Ar); 13C NMR (125.7 MHz, CDCl3): d=25.29 (Me), 26.54 (Me),
62.34 (C(5)), 64.20 (C(4)), 69.73 (PhCH2O), 72.92 (C(3)), 75.01 (C(2)),
97.61 (C(1)), 109.94 (Me2C), 127.88, 128.08, 128.44, 137.07 ppm (Ar); IR
(film, CH2Cl2): n˜ =3446 cmꢀ1 (OH); elemental analysis calcd (%) for
C15H20O5: C 64.27, H 7.19; found: C 64.30, H 7.12; CIMS (pos., MeOH):
m/z: 298 [M+NH4]+; HR-CIMS (pos., MeOH): m/z: calcd for
C15H24O5N: 298.1649; found: 298.1646.
ꢀ
ꢀ
ꢀ
2.5 Hz; H C(5)), 3.62 (1H, brd, J=4.5 Hz; H C(5)), 4.32 (1H, m; H
ꢀ
ꢀ
C(4)), 4.72 (1H, d, J=3.5 Hz; H C(3)), 6.69 ppm (1H, s; H C(1));
13C NMR (100.6 MHz, D2O): d=61.76 (C(5)), 68.78 (C(3)), 75.63 (C(4)),
122.85 (C(1)), 143.38 (C(2)), 161.31 ppm (C(6)); 31P NMR (161.9 MHz,
D2O): d=4.39 ppm (d, J=8.0 Hz); ESIMS (neg., H2O): m/z (%): 253
(30) [M]ꢀ; HR-ESI-MS (neg., H2O): calcd for C6H10N2O7P: 253.0231;
found: 253.0234.
1-O-Benzyl-2,3-O-isopropylidene-b-l-ribopyranoside-4-O-dibenzylphos-
phate (48): Procedure as for 45. By starting from 47 (762 mg, 2.72 mmol),
48 (1.40 g, 96%) was obtained as a white oil. Rf =0.66 (petroleum ether/
EtOAc 3:2); [a]2D1 =+58 (c=1.0 in CHCl3); 1H NMR (500 MHz, CDCl3):
Data for l-54 as prepared from 40: Conditions: 40 (20.5 mg, 0.07 mmol)
and cyanamide (6.2 mg, 0.15 mmol) in D2O (0.75 mL), pD 7.2, 20 h at
608C, followed by lyophilisation and redissolution in D2O. Yield: ꢁ25%
residual 40 and ꢁ75% l-54; 1H NMR (300 MHz, D2O): d=3.54 (1H,
ꢀ
d=1.31 (3H, s; Me), 1.45 (3H, s; Me), 3.77 (2H, m; H C(5)), 4.07 (1H,
ꢀ
ꢀ
dd, J=6.3, 3.8 Hz; H C(2)), 4.47 (1H, dd, J=6.3, 3.8 Hz; H C(3)), 4.62
ꢀ
(1H, d, J=3.8 Hz; H C(1)), 4.70 (2H, ABq, J=12.1 Hz; PhCH2OC),
4.83 (1H, m; H C(4)), 5.07 (2H, m; PhCH2OP), 7.34 ppm (15H, m; Ar);
ꢀ
ꢀ
brd, J=1.5 Hz; H C(5)), 3.55 (1H, brd, J=2.2 Hz; H C(5)), 4.25 (1H,
ꢀ
ꢀ
ꢀ
ꢀ
m; H C(4)), 4.66 (1H, d, J=3.9 Hz; H C(3)), 6.63 ppm (1H, s; H
C(1)); 13C NMR (100.6 MHz, D2O): d=62.04 (C(5)), 69.69 (C(3)), 75.99
(C(4)), 120.14 (C(1)), 143.69 (C(2)), 163.05 ppm (C(6)); 31P NMR
(161.9 MHz, D2O): d=1.47 ppm (brs); ESIMS (neg., H2O): 253 (50)
[M]ꢀ; HR-ESIMS (neg., H2O): calcd for C6H10N2O7P: 253.0231; found:
253.0219.
13C NMR (125.8 MHz, CDCl3): d=25.52 (Me), 26.61 (Me), 60.40 (C(5)),
69.48 (PhCH2OP), 69.86 (PhCH2OC), 69.96 (C(4)), 72.40 (C(3)), 75.80
(C(2)), 98.18 (C(1)), 127.93, 127.96, 128.02, 128.07, 128.47, 128.53, 128.59,
128.61, 128.64 ppm (Ar); 31P NMR (161.9 MHz, CDCl3): d=ꢀ1.59
(sextet, J=20.1 Hz); elemental analysis calcd (%) for C29H33O8P: C
64.44, H 6.15, P 5.73; found: C 64.42, H 6.24, P 5.76; ESIMS (pos.,
MeOH): m/z (%): 563 (100) [M+Na]+, 564 (30) [M+Na+H]+; HR-
ESIMS (pos., MeOH): m/z: calcd for C29H39O8P: 541.1986; found:
541.1983.
Data for d-55 as prepared from 22: Conditions: 22 (30 mg, 0.13 mmol)
and cyanamide (11 mg, 0.26 mmol) in H2O (0.8 mL), pH 7.4, 38 h at
608C, followed by lyophilisation and dissolution in D2O. Yield: ꢁ14%
residual 22 and ꢁ56% d-55; 1H NMR (500 MHz, D2O): d=3.48 (1H,
Sodium l-ribose-4-phosphate (40): A solution of 48 (1.13 g, 2.08 mmol)
in MeOH (20 mL) that contained Pd/C (209 mg, 0.21 mmol) was stirred
under H2 at RT overnight. The mixture was then filtered through Celite
and the plug was rinsed with MeOH (5 mL). H2O (5 mL) was added
before the solution was neutralised to pHꢁ6 (NaOH). The solution was
partially concentrated in vacuo, and was then lyophilised to afford 40 as
a white powder (571 mg, quant.). The b/a ratio was 2:1 in D2O according
ꢀ
ꢀ
dd, J=12.3, 5.1 Hz; H C(5)), 3.65 (1H, dd, J=12.3, 3.2 Hz; H C(5)),
ꢀ
ꢀ
4.34 (1H, tdd, J=8.2, 5.0, 3.2 Hz; H C(4)), 4.71 (1H, d, J=8.1 Hz; H
C(3)), 6.75 ppm (1H, s; H C(1)); 13C NMR (125.7 MHz, D2O): d=62.07
(C(5)), 65.73 (C(3)), 75.69 (C(4)), 123.56 (C(1)), 142.77 (C(2)),
161.60 ppm (C(6)); 31P NMR (121.5 MHz, D2O): d=5.08 ppm (d, J=
8.4 Hz); ESIMS (neg., H2O): 253 (100) [M]ꢀ; IR (solid): n˜ =1636 cmꢀ1
(C=N); HR-ESIMS (neg., H2O): m/z: calcd for C6H10N2O7P: 253.0231;
found: 253.0235.
ꢀ
1
1
to H NMR spectroscopic integration. H NMR (500 MHz, D2O): d=3.42
ꢀ
(0.66H, dd, J=6.8, 3.0 Hz; H C(2) (b)), 3.57 (0.33H, dd, J=12.2, 2.9 Hz;
ꢀ
ꢀ
Data for d-55 as prepared from 41: Conditions: 41 (24.4 mg, 0.10 mmol)
and cyanamide (8.9 mg, 0.21 mmol) in D2O (0.75 mL), pD 6.9, 50 h at
608C. Yield: ꢁ40% d-55; 1H NMR (300 MHz, D2O): d=3.44 (1H, dd,
H C(5) (a)), 3.68 (0.66H, dd, J=11.5, 4.4 Hz; H C(5) (b)), 3.69 (0.33H,
ꢀ
ꢀ
m; H C(2) (a)), 3.82 (0.66H, dd, J=11.5, 4.6 Hz; H C(5) (b)), 3.93
(0.33H, m; H C(3) (a)), 3.97 (0.33H, dd, J=12.5, 5.5 Hz; H C(5) (a)),
4.11 (0.66H, m; H C(4) (b)), 4.16 (0.66H, m; H C(3) (b)), 4.78 (0.33H,
ꢀ
ꢀ
ꢀ
ꢀ
ꢀ
ꢀ
J=12.3, 5.0 Hz; H C(5)), 3.60 (1H, dd, J=12.3, 2.8 Hz; H C(5)), 4.29
Chem. Eur. J. 2008, 14, 2375 – 2388
ꢀ 2008 Wiley-VCH Verlag GmbH & Co. KGaA, Weinheim
www.chemeurj.org
2387

J. D. Sutherland et al.
ꢀ
ꢀ
ꢀ
(1H, m; H C(4)), 4.67 (1H, d, J=7.9 Hz; H C(3)), 6.70 ppm (1H, s; H
C(1)).
[11] The kinetic preference for closure to furanoses is especially pro-
nounced in the case of ribose and its derivatives. This is presumably
related to the high propensity of ribose to exist in furanose forms
((p)/(f): d-ribose 4:1, d-arabinose 10:1, d-lyxose 42:1, d-xylose
60:1): K. N. Drew, J. Zajicek, G. Bondo, B. Bose, A. S. Serianni, Car-
bohydr. Res. 1998, 308, 199.
[12] Preparation of the enantiomer of 15 has been reported: T. K. M.
Shing, Y. C. Leung, K. W. Yeung, Tetrahedron 2003, 59, 2159.
[13] P. Raboisson, A. Baurand, J.-P. Cazenave, C. Gachet, M. Retat, B.
Spiess, J.-J Bourguignon, J. Med. Chem. 2002, 45, 962.
[14] Crystallographic data (excluding structural factors) for 25 and 47
have been deposited with the Cambridge Crystallographic Data
Centre as deposition nos. CCDC 641481 (2) and 641482 (4) contain
the supplementary crystallographic data for this paper. These data
can be obtained free of charge from The Cambridge Crystallograph-
ic Data Centre via www.ccdc.cam.ac.uk/data_request/cif.
[15] V. Borsenberger, M. A. Crowe, J. Lehbauer, J. Raftery, M. Helliwell,
K. Bhutia, T. Cox, J. D. Sutherland, Chem. Biodiversity 2004, 1, 203.
[16] Pitsch et al. have prepared d-40 along with other ribose phosphates
in a divergent synthesis from d-ribose, but the individual yield of
each derivative was (necessarily) low (ref. [10]).
Acknowledgements
This work was carried out as part of EU COST action D27 “Prebiotic
Chemistry and Early Evolution” and was funded by the Engineering and
Physical Sciences Research Council through the provision of studentships
to F.F.B. and M.A.C. and a postdoctoral fellowship to C.A.
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[17] G. E. Keck, D. F. Kachensky, E. J. Enholm, J. Org. Chem. 1985, 50,
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[18] M. W. Powner, C. Anastasi, M. A. Crowe, A. L. Parkes, J. Raftery,
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[9] It has been shown that 9 does not adopt the a-pyranose form to a
detectable extent, and only the b-pyranose (27%), a-furanose
(20%), and b-furanose (53%) forms are observed in neutral aque-
ous solution (ref. [10]).
Received: August 28, 2007
[10] S. Pitsch, C. Spinner, K. Atsumi, P. Ermert, Chimia 1999, 53, 291.
Published online: January 18, 2008
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