Essential reactive intermediates in nucleoside chemistry: Cyclonucleoside cations

Article abstract of DOI:10.1039/c2ob25868d

DFT-based modeling as well as experimental examination of model keto nucleosides have revealed that high susceptibility of these compounds to acids is due to formation of intermediate cyclonucleoside cations of low energy. Theoretically established chemical structures of these previously overlooked intermediates explain the reaction courses for a cluster of nucleoside reactions.

Full text of DOI:10.1039/c2ob25868d

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Essential reactive intermediates in nucleoside chemistry: cyclonucleoside
cations†
Anatoly M. Belostotskii,* Elisheva Genizi and Alfred Hassner
Received 6th May 2012, Accepted 3rd July 2012
DOI: 10.1039/c2ob25868d
DFT-based modeling as well as experimental examination of
model keto nucleosides have revealed that high susceptibility
of these compounds to acids is due to formation of interme-
diate cyclonucleoside cations of low energy. Theoretically
established chemical structures of these previously over-
looked intermediates explain the reaction courses for a
cluster of nucleoside reactions.
Chemical transformations of unnatural nucleoside derivatives
can allow us to discern new aspects of the chemistry of naturally
occurring nucleosides and, consequently, of key biopolymers –
DNA and RNA. In this context, keto nucleosides are interesting.
These compounds are often used as synthetic precursors of
C-branched,1 methylene substituted1,2 and non-ribo3 nucleo-
sides, many derivatives of which are pharmacologically
active.1a,4 However, synthetic reports often mention an increased
lability of keto nucleosides both under basic and acidic con-
ditions3,5 – these ketones bear a β-positioned hetero substituent
(the amino base or alkoxy/ester group) and undergo β-elimi-
nation, e.g., 1a→2a.3,5d–f Their susceptibility to acids may be
extremely high: sometimes, contact with silica is sufficient to
cause the nucleobase elimination.3a
The reason for the unusual ease of this acid-promoted
decomposition of keto nucleosides is not entirely clear. Such an
elimination for a β-substituted ketone includes three sequential
elementary reactions: protonation of the carbonyl moiety, proto-
tropic rearrangement in triad OvC–C (i.e., enolization) and an
anionotropic rearrangement in triad CvC–C (i.e., enone for-
mation) as shown in Scheme 1 for 3′-oxo compound 1a whose
decomposition gives enone 2a. This general scheme does not
disclose molecular structural factors that impart to keto nucleo-
sides the considered distinctive lability. Nevertheless, the nucleo-
side cation (oxacarbenium ion; Scheme 1) is a remarkable
intermediate in this reaction sequence. Strong intramolecular
interactions between nucleobases and the sugar ring take place
in nucleoside cations as theoretical modeling shows for the
Scheme 1 Acid-catalyzed elimination of the amino base in 3′-oxo-2′-
deoxythymidine 1a [(i) carbonyl protonation, (ii) enolization (α-deproto-
nation), (iii) eliminative migration of the double bond].
3′-dehydro derivative of thymidine 3′,5′-diphosphate – this
cation has a cyclonucleoside backbone.6 If similar tricyclic
cations exist for CvO-protonated keto nucleosides, could they
be responsible for the lability of the parent nucleosidic ketones?
Herein, we examine this hypothesis by means of theoretical and
synthetic models. We establish chemical structures of tricyclic
cations of keto and non-keto (“normal”) nucleosides in order to
understand whether the considered instability reflects a unique
chemistry inherent in keto nucleosides or points out some cluster
of nucleoside reactions.
In our theoretical modeling [non-empirical calculations at the
B3LYP/6-31+G(d,p) level with approximation of water solution
within the limits of the PCM model; see ESI† for details], we
located both anti and syn conformers 3anti and 3syn of a cation of
nucleoside 1a whose chemical structure corresponds to the pro-
tonated carbonyl moiety (Fig. 1). These cations are oxacar-
benium ions: their C3′⋯O3′ interatomic distances are longer
than the “normal” CvO bond in aliphatic ketones (0.121 nm),
but shorter than the C–O bond in aliphatic alcohols (0.143 nm).
By converting the East-South geometry (envelope 1E) of the
furanose ring of syn structure 3syn into the North geometry (twist
3T2) and using the resulting structure as the initial one in energy
minimization, we succeeded in locating isomeric cation 3iso that
has a C3′,2-O-cyclonucleoside structure. Similar cyclonucleoside
Department of Chemistry, Bar-Ilan University, Ramat-Gan 52900,
Israel. E-mail: belostot@biu.ac.il; Fax: +972 3738 4053
†Electronic supplementary information (ESI) available: Cartesian
coordinates, energies, Wiberg indexes and atomic CHELPG charges of
optimized structures as well as 1H, 13C NMR and HRMS spectral
data of new compounds. See DOI: 10.1039/c2ob25868d
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Fig. 2 Optimized geometries, LUMOs and chemical structures of
C2′,2-O-anhydrocytidine cation 5iso of salt 5 and C2′,2-O-anhydrouri-
dine cation 6iso. Small numbers show calculated orders of selected
bonds. The given Lewis structure of 5iso (top, in the middle) may be rep-
resented by two highly-weighted resonance forms shown below.
Fig. 1 Optimized geometries and chemical structures of isomeric
cations 3anti, 3syn and 3iso of protonated keto nucleoside 1a as well as
cyclonucleoside cation 4iso of protonated keto nucleoside 1b. Arrows
show selected bonds whose lengths are indicated. Numbers in rectangles
display values of calculated relative energies (kcal mol−1), and small
numbers point out calculated orders of the related bonds.
and 6iso using the NBO (natural bond orbitals) approach8 to
chemical structures.
cations 4iso (Fig. 1), 5iso and 6iso (Fig. 2) also have been located
for a model purine keto compound, viz. C-3′-oxo-2′-deoxy gua-
nosine (1b) with the protonated C3′vO group, and natural pyri-
midine nucleosides (cytidine and uridine, respectively). Thus,
these calculations show that, in addition to trivial cations of
CvO-protonated purine and pyrimidine keto nucleosides (oxa-
carbenium ions), isomeric cyclonucleoside cations (e.g., 3iso),
which have the same chemical connectivity H–heteroatom as the
“normal” cations (e.g., 3anti or 3syn) have, do exist.
Similar cations of regular pyrimidine cyclonucleosides (i.e.,
non-oxo ribosides) are not new in nucleoside chemistry con-
siderations: they are supposed to be intermediates in acid-
mediated nucleophilic transformations cyclonucleoside–
“normal” nucleoside.7a–g In some cases, the corresponding salts
are stable and the molecular structure of salt 5 (Fig. 2) was deter-
mined by X-ray crystallography.7g–l However, their chemical
functionalities have only been assumed; e.g., an amidinium
structure is merely attributed to compound 5. In order to describe
reliably cyclonucleoside cations in terms of chemical functional-
ity, we calculated bond orders for structures 3syn, 3iso, 4iso, 5iso
Appreciable similarity of calculated orders for bonds N3–C4,
C4–C5, C5–C6, N1–C6 and C4–4-O in the furanose-centered
cation 3syn and aromatic ring-centered cations 3iso and 6iso
(Fig. 1 and 2) shows that cyclonucleoside cations are mainly
delocalized in the nitrogen-containing fragments of nucleobases.
Orders of the bonds in these fragments show that 3iso and 6iso
may be described as isouronium cations, and related cation 4iso
may be represented as a guanidinium cation. Disposition of the
NBO LUMO for 6iso supports this structural assignment. This
vacant orbital is centered on atoms 2-O, C2 and N3, with main
localization in the C2–N3 unit.
In contrast, according to the calculated bond orders, cation
5
iso, whose main delocalization domain includes both N1–
(C2vO)–N3 and N3–C4–4-N fragments (Fig. 2), cannot be
approximated by either amidinium or isouronium functionality.
Two resonance forms – amidinium and isouronium cations –
display a dual chemical functionality of cyclocytidine cation 5iso
.
Atoms N3, C4, and 4-N are centers of the NBO LUMO (loca-
lized mainly in the C4–4-N unit) of 5iso indicating that the
amidinium form is the major resonance structure.
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Modeled molecular geometries confirm these chemical assign-
ments. For instance, bonds N1–C2 and C2–N3 in tricyclic struc-
ture 3iso are shortened with respect to the same bonds in
“acyclic” structure 3syn (0.134 and 0.134 nm vs. 0.140 and
0.138 nm, respectively). The interatomic distance C3′⋯2-O in
3iso is longer than the same distance in 3syn (0.131 nm vs.
0.123 nm, respectively); however, it is shorter than the length
of the
expectable alterations of bond lengths characterize also cations
syn and 5syn
The above established chemical structures of model nucleo-
C
arom–O bond in anisole (0.142 nm9). Similar
Scheme 2 Stages of eliminative decomposition of 3′-keto nucleosides
shown for ketone 1a. The proposed scheme differs from that in
4
.
Scheme 1 by introducing a C3′,2-O-cyclonucleoside cation (here: 3iso
)
that produces an enol (here: 2b) via the C2′–H-deprotonating 1,2-elimin-
ation. “Non-productive” elimination in cation 3iso associated with depro-
tonation of the 3′-O–H moiety is shown in the frame.
side cations permit us to understand the relationship between
some known nucleoside transformations, as they reflect versatile
reaction ability of the core intermediates (cyclonucleoside
cations). For instance, drawing on isouronium chemistry,10 one
can predict that cyclothymidine cations should show “carbodi-
imide reactivity”, i.e., should easily add nucleophiles and release
the urea fragment (the leaving group), or, in terms of nucleoside
structure, undergo stereospecific α-addition to the furanose frag-
ment accompanied by anhydro ring opening. In contrast, the pre-
diction for cyclocytidine cations is that these species with less
isouronium character should be more stable toward nucleophiles.
In accordance with these predictions, salts of anhydro cytidines
(e.g., anticancer agent 5) are stable compounds that may be
treated in aqueous solutions,7g,l while intermediate salts of tri-
cyclic cation structure, e.g., of cation 6iso (Fig. 2), have never
been isolated or detected in acid-catalyzed nucleophilic conver-
sions of C2′,2-O- or C3′,2-O-anhydro pyrimidine nucleosides
into the corresponding 2′-α- or 3′-α-substituted “normal” nucleo-
sides.7a–g Also, some nucleoside transformations are understand-
able if formation of cyclonucleoside isouronium cations is
taken into account: e.g., nucleophilic substitution of the activated
2′-hydroxy group (and not exclusively elimination) occurred at
the tertiary 2′-carbon of a 2′-α-Me derivative of cytidine,11a
configuration retention in nucleophilic conversions of 2′-α-
OMes-N,N-diMe-ψU11b and formation of a cyclonucleoside in
acidic hydrolysis of a dinucleotide triester.11c
For cyclocytidine cations, Fig. 2 shows additional transform-
ations that the dual isouronium–amidinium functionality of these
intermediates suggests: they are addition–elimination reactions
of isoureas in alkaline solutions that lead to corresponding ureas
and amidinium salt hydrolysis that affords amides. Both alkaline
hydrolysis of anhydro cytidines to the corresponding “open”
ara-cytidines and conversion of such cyclonucleoside salts
into anhydro uridines do take place,7g,h,12 in line with this
suggestion.
Thus, transformations of O-alkylisoureas in the presence of
acids mimic chemical behaviour of the anhydro ring fragment of
cyclothymidines under acidic conditions. Acid-catalyzed reac-
tions of O-alkyl isoureas with nucleophiles include elimi-
nation.13 Acid-associated lability of keto nucleosides becomes
clear in this light. Isouronium cation 3iso is a very plausible inter-
mediate in the degradation of the model keto nucleoside 1a to
non-nucleosidic enone 2a. Indeed, our calculations show that
this tricyclic cation is drastically more stable than isomeric
“normal” nucleoside cations 3syn and 3anti (Fig. 1). Skeletal
rearrangements, which occur not disrupting high energy bonds
as well as not altering molecular geometry substantially, are low
barrier transformations. These two circumstances make it clear
Scheme 3 Synthesis of nucleoside analogs 7a,b and examination of
their stability towards acids. (a) TBSCl, Im, DMF, −10°, 18 h; (b) NaH,
BnBr, Bu4NI, THF, rt, 12 h; (c) thymine, LiH, DMF, Ar, 120°, 1 h, then
9a or 9b in DMF, 140°, 20 h; (d) (PyH+)2·Cr2O7−2, CHCl2, molecular
sieves, Ar, rt, 5 h; (e) Pd(OH)2/C, cyclohexene, EtOH, Ar, reflux, 6 h;
(f) silica gel, 30 min; (g) AcOH–THF–H2O (3 : 1 : 1), rt, 24 h; (h)
Zn(BF4)2–THF–H2O, rt, 48 h.
that “normal” cation 3syn is converted into tricyclic cation 3iso
rapidly and completely. As an isouronium cation, the resulting
intermediate 3iso is associated with 1,2-elimination. This elemen-
tary reaction leads to formation of enol 2b that is the precursor
of the final compound 2a in decomposition of 1a (Scheme 2).
The concurrent 1,2-elimination that arises from deprotonation of
the C3′-positioned OH group leads to the starting ketone 1a,
and, therefore, does not affect the thermodynamically dictated
conversion of 1a into 2a.
An alternative hypothesis suggests that the acid-mediated labi-
lity of keto nucleosides is due to protonation of the amino base.
In order to inspect it and evaluate involvement of isouronium
cations, we have prepared new keto carbonucleosides 7a,b with
a 1,2-positioned keto group and an amino base using a known
route to such compounds14 (see Scheme 3 and ESI† as well),
and examined their susceptibility towards acids.
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Fig. 3 Optimized structures of isomeric cations 12syn and 12iso of pro-
tonated ketone 7b. Numbers in rectangles indicate calculated relative
energies (kcal mol−1) of 12syn and 12iso
.
corresponding cyclonucleoside isouronium cation. Indeed, this
molecular geometry is intermediate in the path of minimal geo-
metrical changes, and this energy minimum lies significantly
lower than the minimum that corresponds to the initial cation.
Thus, these cyclizations occur in three stages: (i) carbonium ion
generation, (ii) cyclonucleoside cation formation and (iii) trans-
formation into the product. Formation of these cyclic reactive
intermediates explains why nucleophilic addition that sometimes
takes place instead of cyclization is stereospecific (from the
α-stereoface).16c
Thus, by establishing chemical structures of cyclonucleoside
cations, we introduce these reactive intermediates in reasoned
considerations of a cluster of related transformations of nucleo-
sides/nucleotides. Such transformations are not limited by now
explained elimination reactions of keto nucleosides or by nucleo-
philic additions to anhydronucleosides under acidic conditions.
Cyclonucleoside cations certainly are components of the equili-
brium of interconverting chemically isomeric nucleoside or
nucleotide cations localized at any fragment of the furanose–
nucleobase backbone. The finding that cations of sugar–nucleo-
base-bonded nucleosides are much more stable than the corres-
ponding “normal” cations may provide new, valuable insight
into the chemistry of oxidative17 or hydrodynamically induced18
breaks of DNA and RNA chains. For instance, cyclonucleoside
carbocations may assist in keeping the integrity of translocated
ssDNA (e.g., transposons, unpacked viral ssDNA in the cell).
If the 3′-C–O bond of a pyrimidine nucleotide unit of the
moving strand is heterolytically ruptured due to stretching, the
ultimately formed C3′,2-O-cyclonucleoside isouronium cation
may be captured in the solvent cage by the 5′-phosphate of the
5′ → 3′ scrap, restoring the strand in the original chemical con-
nectivity and stereochemistry as well.
Scheme 4 Chemical structures of isomeric cations 12syn and 12iso and
acid-promoted β-elimination in ketone 7b.
Ether protected β-hydroxy groups of keto carboanalogs of
hexopyranoses and pentofuranoses (including benzyl, silyl, iso-
propylidene and tert-Bu ethers) but lacking an amino base are
generally stable upon action of both weak bases and weak
acids.15 Neither has β-elimination been detected for the corres-
ponding OH derivatives (aldols) for these conditions. By con-
trast, 2-thymino cyclopentanones 7a,b show different behavior.
Both 3′-O-silyl 7a and 3′-O-benzyl 7b ethers are completely
transformed into elimination products 11a and 11b, respectively,
when in contact with silica gel. Also AcOH converts 7a into
enone 11a. A weak Lewis acid, Zn(BF4)2, causes the same
decomposition in the presence of water. Furthermore, transfer
hydrogenolysis of 7b leads to a mixture of nucleoside com-
pounds which, as expected, bear neither a benzyl nor a silyl
group. NMR shows no presence of compound 11c. However,
11c is obtained in 63% yield when this mixture is subjected to
chromatography on silica gel. Thus, secondary β-ether or
hydroxy ring substituents of carbocyclic keto nucleosides 7a,b
are eliminated under very mild conditions. This lability, which
does involve nucleobase elimination, demonstrates that it is
unnecessary to postulate amino base protonation.
Our calculations for oxacarbenium cations 12syn and 12anti as
well as isouronium cation 12iso of the CvO-protonated model
ketone 10b (Scheme 4; see ESI† for 12anti) support the above
conclusion that high stability of cyclonucleoside isouronium
cations is the driving force of nucleobase elimination reactions in
keto nucleosides.
As in the case of cations 3syn, 3anti and 3syn (Fig. 1), the iso-
uronium cation (i.e., 12iso) is much more stable than the isomeric
oxacarbenium cations. Both cations 12syn and 12anti of opposite
rotational orientation of the nucleobase, which are primary
intermediates in the acid-promoted elimination via enol
13 (Scheme 4), are higher in energy than 12iso by 11.5 and
9.7 kcal mol−1, respectively (Fig. 3).
Acknowledgements
We thank the Ministry of Science and Technology of Israel
(Grant 1471-1-99) as well as the Marcus Center for Medicinal
Chemistry at Bar-Ilan University for financial support.
This high relative stability of cyclonucleosidium cations also
is consequential for other reactions of nucleosides. Cyclizations
of some nucleoside derivatives into anhydronucleosides is
thought to occur via generation of a carbocation that is localized
in the sugar ring.16a,b It is obvious that, when bringing the carbo-
cationic ring carbon and the 2-positioned oxygen of the pyri-
midine base closer, the molecule is rearranged into the
Notes and references
‡In Ref. 6, an incorrect chemical structure has been assigned to the
modeled cation of a 3′-dehydro nucleotide derivative. Our analysis of
molecular structure of nucleotide cations that includes the correct chemi-
cal structure of such “3′-cations” will be published elsewhere.
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