On the existence of the chair conformation in six-membered ring phosphates bearing an aryl group axially oriented at the C4 position: Cyclic nucleotides as model compounds for cyclic phosph(on)ate and phosphoramide prodrugs

Article abstract of DOI:10.1021/jo100863n

A series of cyclic nucleotide analogues to HepDirect prodrugs were prepared by a three-component reaction of protected thymine, phosphoryl chloride, and 5-aryl-α-d-xylofuranoses derivatives. One of the cyclic nucleotides showed NMR data that suggest a predominant twisted conformation; however, in spite of having an aryl group at the C4 position within the crystal lattice, the cyclic nucleotide had a chair conformation with the aryl group axially oriented. By analyzing the unprecedented X-ray structure, it was observed that the oxygen atom from the phoshoryl group (P=O) is found in close proximity to the o-hydrogen atom of the aryl group (2.51 A), suggesting thus an attractive nonbonding electrostatic interaction, which might be the driving force that overcomes the steric diaxial interactions imposed by the aryl group. Theoretical studies (NBO) for two model compounds showed that there are indeed interactions between filled (donor) Lewis-type NBOs and empty (acceptor) non-Lewis NBOs corresponding to the nO→φ_C-H interaction. Additionally, conversion of a diastereomeric mixture of cyclic nucleotides into the more stable diastereomeric cyclic nucleotide was observed and explained by spontaneous isomerization in the phosphorinane ring. This finding supports the recently established hypothesis for the mode of action of prodrug cleavage, for which the anomeric effect plays an important role.

Full text of DOI:10.1021/jo100863n

pubs.acs.org/joc
On the Existence of the Chair Conformation in Six-Membered Ring
Phosphates Bearing an Aryl Group Axially Oriented at the C4 Position:
Cyclic Nucleotides As Model Compounds for Cyclic Phosph(on)ate and
Phosphoramide Prodrugs
†
Leticia Quintero, Mario Sanchez-Vazquez, Silvano Cruz-Gregorio,* and
‡
,†
ꢀ
Fernando Sartillo-Piscil*,†
†
´
Centro de Investigacioꢀn de la Facultad de Ciencias Quımicas, BUAP. 14 Sur Esq. San Claudio, San Manuel.
72570, Puebla, Mexico, and Centro de Investigacion en Materiales Avanzados, S. C. Alianza Norte 202,
‡
ꢀ
ꢀ
Carretera Monterrey-Aeropuerto Km. 10, PIIT, C. P. 66600, Apodaca NL, Meꢀxico
fsarpis@siu.buap.mx
Received May 1, 2010
A series of cyclic nucleotide analogues to HepDirect prodrugs were prepared by a three-component
reaction of protected thymine, phosphoryl chloride, and 5-aryl-R-D-xylofuranoses derivatives. One
of the cyclic nucleotides showed NMR data that suggest a predominant twisted conformation;
however, in spite of having an aryl group at the C4 position within the crystal lattice, the cyclic
nucleotide had a chair conformation with the aryl group axially oriented. By analyzing the
unprecedented X-ray structure, it was observed that the oxygen atom from the phoshoryl group
(PdO) is found in close proximity to the o-hydrogen atom of the aryl group (2.51 A), suggesting thus
an attractive nonbonding electrostatic interaction, which might be the driving force that overcomes
the steric diaxial interactions imposed by the aryl group. Theoretical studies (NBO) for two model
compounds showed that there are indeed interactions between filled (donor) Lewis-type NBOs and
empty (acceptor) non-Lewis NBOs corresponding to the nOfσ*C-H interaction. Additionally,
conversion of a diastereomeric mixture of cyclic nucleotides into the more stable diastereomeric
cyclic nucleotide was observed and explained by spontaneous isomerization in the phosphorinane
ring. This finding supports the recently established hypothesis for the mode of action of prodrug
cleavage, for which the anomeric effect plays an important role.
Introduction
emerged as an excellent strategy for drug administration into
the body.1-9 In this regard, six-membered ring phosph(on)-
ates represent a new prodrug strategy for treating liver
diseases such as hepatitis B and C, and hepatocellular
In the search for new antiviral and anticancer candidate
drugs, the use of site-selective drug deliveries (prodrugs) has
*To whom correspondence should be addressed. Phone/fax: þ52 2222
2955500, ext. 7391.
(1) Hecker, S. J.; Erion, M. D. J. Med. Chem. 2008, 51, 2328–2345.
(2) He, G.-X.; Krise, J. P.; Oliyai, R. Prodrugs of Phosphonates, Phos-
phinates, and Phosphates. Prodrugs: Challenges and Rewards; Springer: New
York, 2007; pp 223-264.
(3) Ariza, M. E. Drug Des. Rev. 2005, 2, 273–387.
(4) Mackman, R. L.; Cihlar, T. Annu. Rep. Med. Chem. 2004, 39, 305–
321.
(5) Schultz, C. Bioorg. Med. Chem. 2003, 11, 885–898.
(6) Anastasi, C.; Quelever, G.; Burlet, S.; Garino, C.; Souard, F.; Kraus,
J.-L. Curr. Med. Chem. 2003, 10, 1825–1843.
5852 J. Org. Chem. 2010, 75, 5852–5859
Published on Web 08/10/2010
DOI: 10.1021/jo100863n
r
2010 American Chemical Society

Quintero et al.
JOCArticle
SCHEME 1. Proposed Mechanistic Mode of Action for Six-
Membered Ring P-Heterocyclic Prodrugs A
SCHEME 2. Anomeric and Steric Effects Involved in the
Spontaneous Conversion of Cyclic Phosphates (E f F)
carcinoma.1,2,8,9 Erion’s gruop10-12 has successfully intro-
duced HepDirect prodrugs (I and II) for the treatment of the
above-mentioned diseases. Similarly, cyclic aryl phosphor-
amides (III)13,14 represent another class of prodrugs for
cancer therapy.
presence of an aryl group at the C4 position, but also by the
cis-configuration of the P-heterocycle; however, it was rela-
tively independent of the nucleoside and absolute stereo-
chemistry at C4.10 This suggests that the stereochemistry and
conformation of the P-heterocycle plays a key role in the
prodrug cleavage. With this information in mind, it was
recently proposed, based on simple model phosphates, that
the anomeric effect is involved in the spontaneous cleavage
of cyclic phosph(on)ate prodrugs.15 The spontaneous con-
version of unstable cyclic phosphates (E) to their most stable
cyclic phosphates (F) demonstrates that isomerization is
favored by natural hyperconjugation between the nO non-
bonding and σ*-P-X antibonding orbital (anomeric effect),
which generates the double-bonded non-bonding resonance
structure (G), thus weakening the O3-C4 bond and favoring
the selective and spontaneous cleavage of the phosphate ring
(G h H); finally, after a rapid collapse of the phosphate
group, the more stable cyclic phosphate Fis formed (Scheme 2).
Additionally, it was also postulated that the steric hindrance
caused by the 1,3-syn diaxial interaction between aryl and
phenoxy groups influences the O3-C4 bond cleavage, even
though the chair conformation has been found to be less
favorable.
Crucial for the above findings was the previous conforma-
tional and configurational analysis of a series of conformation-
ally restricted 4-substituted-1,3,2-dioxaphosphorinanes.15-18
NMR spectroscopic and X-ray diffraction have shown that
the conformational equilibria for the phosphorinane ring
depended on both the configuration at the phosphorus atom
and the substituent at the C5 atom (or C4 according to the
nomenclature for 1,3,2-dioxaphosphorinanes). For cyclic
phosphates with RP configuration and bearing an equatorially
oriented aryl group at the C4 position, a chair h boat
equilibrium (C1 h B1) was observed, whereas a chair h twist
equilibrium (C1 h T) was observed for the SP-epimers.
Conformers C2 and B2 (of which B2 has been proposed for
related cyclic phosphates)20,21 were not considered in the study:
first, because equilibrium C1 h B1 was supported having
trapped both conformers in the solid state within the same
crystal lattice (for R = Ph, equatorially oriented in C1),18
second, because equilibrium C1 h T could be established
For cyclic phosphoramides, selective prodrug cleavage is
caused by delocalization of the electron density from the
aromatic ring toward the P-heterocycle (A f B), affording
thus ionic species for the cross-linkage of DNA strands, thus
producing high cytotoxity.13 On the contrary, Erion’s Hep-
Direct prodrugs10-12 suffer a selective oxidation (A f C)
catalyzed by a specific enzyme, followed by cleavage of the
O3-C4 bond (C f D), thus leading to an increment of the
concentration of nucleoside triphosphates (NTPs) within the
living cell, which interfere with the viral replication mechan-
ism (Scheme 1).
Apparently, the aryl or pyridyl group at the C4 position is
responsible for the selective O3-C4 bond cleavage. Erion
observed that the prodrug cleavage is favored not only by the
(7) Wagner, C. R.; Iyer, V. V.; McIntee, E. J. Med. Res. Rev. 2000, 20,
417–451.
(8) Freeman, S.; Ross, K. C. Prog. Med. Chem. 1997, 34, 112–142.
(9) Krise, J. P.; Stella, V. J. Adv. Drug Delivery Rev. 1996, 19, 287–310.
(10) Erion, M. D.; Reddy, K. R.; Boyer, S. H.; Matelich, M. C.; Gomez-
Galeno, J.; Lemus, R. H.; Ugarkar, B. G.; Colby, T. J.; Schanzer, J.; van
Poelje, P. D. J. Am. Chem. Soc. 2004, 126, 5154–5163.
(11) Erion, M. D.; van Poelje, P. D.; Mackenna, D. A.; Colby, T. J.;
Montag, A. C.; Fujitaka, J. M.; Linemeyer, D. L.; Bullough, D. A.
J. Pharmacol. Exp. Ther. 2005, 312, 554–560.
(12) Hecker, S. J.; Reddy, K. R.; van Poelje, P. D.; Sun, Z.; Huang, W.;
Varkhedkar, V.; Reddy, M. V.; Fujitaki, J. M.; Olsen, D. B.; Koeplinger,
K. A.; Boyer, S. H.; Linemeyer, D. L.; MacCoss, M.; Erion, M. D. J. Med.
Chem. 2007, 50, 3891–3896.
€
´
guez-Palacios, V.; Hopfl, H.; Quintero, L.;
(13) Hu, L.; Yu, C.; Jiang, Y.; Han, J.; Li, Z.; Browne, P.; Race, P. R.;
Knox, R. J.; Searle, P. F.; Hyde, E. I. J. Med. Chem. 2003, 46, 4818–4821.
(14) Li, Z.; Han, J.; Jiang, Y.; Browne, P.; Knox, R. J.; Hu, L. Bioorg.
Med. Chem. 2003, 11, 4171–4478.
(15) Cruz-Gregorio, S.; Rodrı
Sartillo-Piscil, F. J. Org. Chem. 2009, 74, 197–205.
ꢀ
ꢀ
(16) Cruz-Gregorio, S.; Sanchez, M.; Clara-Sosa, A.; Bernes, S.;
Quintero, L.; Sartillo-Piscil, F. J. Org. Chem. 2005, 70, 7107–7113.
J. Org. Chem. Vol. 75, No. 17, 2010 5853

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SCHEME 3. Conformational Equilibria for 4-Substituted-1,3,2-dioxaphosphorinanes Containing the 1,2-O-Isopropylidene-R-D-xylo-
furanose Template
based on NMR data, and third because conformation T was
corroborated by an X-ray crystallographic study for R = p-Cl-
Ph (Scheme 3).15,18
SCHEME 4. Synthetic Strategy for the Synthesis of HepDirect
Analogues 1
The four above-mentioned conformations were estab-
lished in solution and corroborated by X-ray crystallo-
graphic studies for phosphates with both RP and SP
configuration, and having an equatorial oriented R group.
The only conformation that has not been corroborated by
X-ray diffraction analysis is that having an axially oriented
aryl group at the C4 position. Many authors have considered
that an aryl group at the C4 position can only have an
equatorial or pseudo-equatorial orientation, and based on
the idea of a locked chair conformation they have taken
advantage of this anchoring element for stereoselective
chemical transformations.19,22-25
In the present contribution, the first crystal structure of a
six-membered ring phosphate bearing an axially oriented
aryl group at the C4 position with a chair conformation is
reported. Additionally, with the expectation to provide
further experimental and theoretical evidence that supports
the above-mentioned proposal related to the selective pro-
drug-cleavage, the synthesis and the conformational study of
cyclic nucleotide analogues to HepDirect prodrugs are also
reported.
Thus, thymine 5 was selectively protected in one step at the
20,30-positions by treatment with an excess of 2,2-dimethox-
ypropene and catalytic amounts of p-TSA at room tempera-
ture for 24 h under solvent-free conditions. It is important to
note that after 2 h of reaction, the starting material 5 was
consumed and two compounds were observed by TLC
(presumably the two possible protected isomers); however,
after a further 22 h of reaction at room temperature, the
presence of 2 as the sole product was observed.
Results and Discussions
On the other hand, the diasteroisomeric 1,3-diols 4a-d and
4a0-d0 were obtained by applying a Sequential Hydrolysis-
Oxidation-Grignard Reagent Addition procedure15,17,18 to dia-
cetone-R-D-glucose 6 (Scheme 5). Then, protected thymine 2
and 1,3-diols 4a-d and 4a0-d0were treated with phosphoryl
chloride 3 in the presence of triethylamine (in the case of 4d and
The synthetic strategy for the preparation of the HepDir-
ect analogues was based on a three-component reaction
between protected thymine 2, phosphoryl chloride 3, and
5-aryl-R-D-xylofuranoses 4a-d (Scheme 4).
ꢀ
(17) Sartillo-Piscil, F.; Cruz-Gregorio, S.; Sanchez, M.; Quintero, L.
Tetrahedron 2004, 60, 3001–3008.
(18) Sartillo-Piscil, S.; Cruz-Gregorio, S.; Sanchez, M.; Hopfl, H.; Anaya
(26) We have assigned, here and previously, the stereochemistry at
phosphorus atom by considering the oxygen atom of the phosphoryl group
with the highest priority (as a PdO multiple bond, not as a P;O single
bond). We understand that, the PdO bond should not be taken like the
conventional double bond of carbon to oxygen, the reactivity of both groups
is totally different. However, due to the controversy of the role for the
phosphorus 3d-orbital into the phosphoryl group, in which, according to
Cahn, Ingold, and Prelog assignment rules, contributions by d-orbital to
bonds of quadriligants atoms are neglected, hence the PdO bond should be
taken as a P;O single bond with the assignment of the least priority (see:
Venukadasula, P. K. M.; Chegondi, R.; Maitra, S.; Hanson, P. R. Org. Lett.
2010, 12, 1556-1559. ), we decided to take the concept of the phosphoryl
multiple bonding only for representative purposes but with the understand-
ꢀ
de Parrodi, C.; Quintero, L. Tetrahedron 2003, 59, 4077–4083.
ꢀ
(19) Sartillo-Piscil, F.; Meza-Leon, R.; Quintero, L. Rev. Soc. Quim.
Meꢀx. 2002, 330.
(20) Hermans, R. J. M.; Buck, H. M. J. Org. Chem. 1988, 53, 2077–2084.
(21) Neeser, J.-T.; Tronchet, J. M. J.; Charollais, E. J. Can. J. Chem. 1983,
61, 1387–1396.
(22) Jankowski, S.; Marczak, J.; Olczak, A.; Glowka, M. L. Tetrahedron
Lett. 2006, 47, 3341–3344.
(23) Ten Hoeve, W.; Wynberg, H. J. Org. Chem. 1985, 50, 4508–4514.
(24) Hulst, R.; Zijlstra, R. W. J.; de Vries, N. K.; Feringa, B. L. Tetra-
hedron: Asymmetry 1994, 5, 1701–1710.
(25) Hulst, R.; Visser, J. M.; de Vries, N. K.; Zijlstra, R. W. J.; Kooijman,
H.; Smeets, W.; Spek, A. L.; Feringa, B. L. J. Am. Chem. Soc. 2000, 122,
3135–3150.
ing of its real meaning. For a better discussion on this matter, please see: A
Guide to Organophosphorus Chemistry; Quin, L. D., Ed.; Wiley-Interscience:
New York, 2000.
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SCHEME 5. Preparation of Protected Nucleoside 2and 1,3-Diols 4a-d and 4a0-d0
a
SCHEME 6. Three-Component Reaction for the Synthesis of Cyclic Nucleotides 1a-d and 1a0-d0
aUnless otherwise noted, yields were determined after chromatography. An asterisk indicates that yields were determined by 1H and 31P NMR.
4d0, a stronger base such as t-BuOK and low temperature were
needed), giving an almost equimolar mixture of cyclic nucleotides
(RP)-1a-d/(SP)-1a-d and (RP)-1a0-d0/(SP)-1a0-d0 in moderate
to good yields (Scheme 6).
After a careful separation of the diastereoisomeric pairs
(RP)-1a-d/(SP)-1a-d and (RP)-1a0-d0/(SP)-1a0-d0, determi-
nation of the absolute stereochemistry at the phosphorus
atom was achieved with the aid of NMR spectroscopy and
single-crystal X-ray diffraction analysis.26 In the case of
compounds (RP)-1d/(SP)-1d and (RP)-1d0/(SP)-1d0, NMR
data were obtained from the crude reaction mixture because
these compounds spontaneously isomerize at room tempera-
ture (see Figure 1 and Table 2 in Supporting Information
for a description of the rate of isomerization). Following
Gorenstein’s criteria,27-29 the cyclic nucleotides giving upfield
shifted NMR signals (31P NMR) were assigned the absolute
configuration SP.30,31 The vicinal coupling constants, such as
3JH5-P for nucleotides (RP)-1a-d and (SP)-1a-d, showed
values in the range of 0.5-1.0 Hz, indicating that the aryl
group at the C5 position is oriented equatorially or pseudoe-
quatorially (absolute configuration S), meanwhile values in the
range of 9.2-10.4 Hz for (RP)-1a0-d0and (SP)-1a0-d0 (absolute
configuration R) suggested that the aryl group was axially or
pseudoaxially oriented. These coupling constants are almost
identical with those previously observed for 2-phenoxy-1,3,2-
dioxaphaphosphorinanes derived from 1,2-O-isopropylidene-
R-D-xylofuranoses.15,18 Apparently, no significant conforma-
tional changes occur when the OPh group is switched by the
nucleosyl group at the P-atom. Therefore, in agreement with
the general conformational equilibria shown in Scheme 3,
chair-boat equilibria (C1 h B1) for (RP)-1a-d and (RP)-
1a0-d0, andchair-twist equilibria (C1 h T) for(SP)-1a-d, and
(SP)-1a0-d0 can be proposed.
(27) Gorenstein, D. G.; Rowell, R. J. Am. Chem. Soc. 1979, 101, 4925–
4928.
(28) Gorenstein, D. G.; Rowell, R.; Findlay, J. J. Am. Chem. Soc. 1980,
102, 5077–5081.
(29) Majoral, J. P.; Pujol, R.; Navech, J. Bull. Soc. Chim. Fr. 1972, 2, 606–
610.
(30) Bentrude, W. G.; Setzer, W. N. Stereospecificity in 31P-Element
Coupling: Proton-Phosphorus Coupling. In Phosphorus-31 NMR Spectros-
copy in Stereochemical Analysis; Verkade, J. G., Quin, L. D., Eds.; VCH:
Weinheim, Germany, 1987.
(31) For a detailed description of the important NMR data, see Table 1 in
the Supporting Information.
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equatorially oriented aryl group at C4 is insufficient to freeze
the chair conformation.
What force overcomes the strong syn-1,3-diaxial steric
interactions and thus allowed the revelation of this unprece-
dented molecular structure? When examining the molecular
structure of (RP)-1c0 we found an intramolecular C-H
O
hydrogen bonding interaction between the PdO bond and
3 3 3
the o-hydrogen atom of the aryl group at the C4 atom (C-H,
0.93 A; H O, 2.51 A; C O, 3.39 A; C-H O, 159°,
3 3 3 3 3 3 3 3 3
Figure 2). It is important to mention that this interaction is
within the previously established limits for such contacts.36,37
To investigate this interaction, theoretical calculations for
model structure J using density functional theory (B3LYP/6-
31þG(d,p)) were realized.38 In model J, the nucleoside
moiety was replaced by a methyl group. This, besides saving
computational time, permitted evaluation of whether the
nucleoside moiety imposes any interactions that could facil-
itate the chair conformation or whether the axial aryl ring
contributed to this electrostatic interaction. Although the
experimental chair conformation was slightly flattened, the
calculated chair conformation in J showed a similar value for
aryl-H to PdO distance (2.25 A).
To further demonstrate the above-mentioned interaction,
we examined the filled (donor) Lewis-type NBOs and empty
(acceptor) non-Lewis NBOs of the nO f σ*C-H interaction
(Figure 3).39 Additionally, to establish whether the chlorine
atom in the para-position influences the formation of the
FIGURE 1. Perspective view of the molecular structure of (RP)-1c0
showing that it possesses C1 conformation and crystal structure
previously reported that it possesses twist T conformation.
C-H O hydrogen bonding interaction, the Jb structure
3 3 3
was also analyzed, in which the chlorine atom was replaced
by a hydrogen atom. As for structure J, the stereoelectronic
nO f σ*C-H interaction was observed also in this case, with a
similar distance (2.28 A). These results suggest that the C1 h
T equilibria for 4-aryl-1,3,2-dioxaphosphorinanes do not
depend on the presence of the chlorine atom; therefore, the
same conformational equilibrium could be readily accessible
for other 4-aryl-1,3,2-dioxaphosphorinane compounds, at
least for those having 1,3-cis oriented PdO and aryl groups.
These results provide structural and theoretical evidence
that a C4 aryl group can assume an axial orientation in six-
membered ring phosph(on)ates, either in the HepDirect or
cyclic phosphoramide prodrugs. Additionally, these results
also support the recently proposed hypothesis for the factors
contributing to phosphorinane ring C4 epimerization where
the stereochemistry and conformation are involved (i.e., the
anomeric effect). Thereby, the “unstable” chair conformation
An important contribution of this study is the determina-
tion of the molecular structure of (RP)-1c0 by single-crystal
X-ray analysis,32 which not only confirmed the assignment
of the absolute configuration at the P-atom for cyclic nucleo-
tides, but also revealed for the first time the existence of a
stable chair conformation of a six-membered ring phosphate
bearing an aryl group axially oriented at the C4 position
(Figure 1).
Moreover, the vicinal H-P coupling constant (3JH5-P
=
=
10.4 Hz) matches the vicinal H-P coupling constant (3JH5-P
10.4 Hz) for the cyclic phosphate with a crystal structure in the
twist (T) conformation previously reported (Figure 1).15 The
P-O-C4-H dihedral angles for the solid state structures in
twist conformation (previously reported) and chair conforma-
tion (RP)-1c0 are 52° and 149°, respectively. Indeed, a vicinal
H-P coupling constant within the range of 10-14 Hz does not
establish a higher population of non-chair conformation, but
may indicate an equimolar equilibrium of chair and twist
conformation in solution.33-35 Therefore, with this unprece-
dented X-ray chair conformation C1 and the previously deter-
mined twisted structured T, it can be possible now to establish
that C1 h T conformational equilibria are energetically
accessible for 4-aryl-1,3,2-dioxaphosphorinanes, and that an
(36) Desiraju, G. R. Acc. Chem. Res. 1996, 29, 441–449.
(37) Steiner, T. Chem. Commun. 1997, 727–734.
(38) Frisch, M. J.; Trucks, G. W.; Schlegel, H. B.; Scuseria, G. E.; Robb,
M. A.; Cheeseman, J. R.; Montgomery, J. A., Jr.; Vreven, T.; Kudin, K. N.;
Burant, J. C.; Millam, J. M.; Iyengar, S. S.; Tomasi, J.; Barone, V.; Mennucci,
B.; Cossi, M.; Scalmani, G.; Rega, N.; Petersson, G. A.; Nakatsuji, H.; Hada,
M.; Ehara, M.; Toyota, K.; Fukuda, R.; Hasegawa, J.; Ishida, M.; Nakajima,
T.; Honda, Y.; Kitao, O.; Nakai, H.; Klene, M.; Li, X.; Knox, J. E.;
Hratchian, H. P.; Cross, J. B.; Bakken, V.; Adamo, C.; Jaramillo, J.;
Gomperts, R.; Stratmann, R. E.; Yazyev, O.; Austin, A. J.; Cammi, R.;
Pomelli, C.; Ochterski, J. W.; Ayala, P. Y.; Morokuma, K.; Voth, G. A.;
Salvador, P.; Dannenberg, J. J.; Zakrzewski, V. G.; Dapprich, S.; Daniels,
A. D.; Strain, M. C.; Farkas, O.; Malick, D. K.; Rabuck, A. D.; Raghavachari,
K.; Foresman, J. B.; Ortiz, J. V.; Cui, Q.; Baboul, A. G.; Clifford, S.;
Cioslowski, J.; Stefanov, B. B.; Liu, G.; Liashenko, A.; Piskorz, P.; Komaromi,
I.; Martin, R. L.; Fox, D. J.; Keith, T.; Al-Laham, M. A.; Peng, C. Y.;
Nanayakkara, A.; Challacombe, M.; Gill, P. M. W.; Johnson, B.; Chen, W.;
Wong, M. W.; Gonzalez, C.; Pople, J. A. Gaussian 03, Revision E.01; Gaussian
Inc., Wallingford, CT, 2004.
(32) The crystallographic coordinates have been deposited with the Cam-
bridge Crystallographic Data Centre; deposition no. 737132. These data can
be obtained free of charge from the Cambridge Crystallographic Data
Centre, 12 Union Rd., Cambridge CB2 1EZ, UK or via www.ccdc.cam.ac.
uk/conts/retrieving.html.
€
(33) Frank, E.; Wolfling, J. Curr. Org. Chem. 2007, 11, 1610–1623.
(34) Bentrude, W. G. Steric and Stereoelectronic Effects in 1,3,2-Dioxa-
phosphorinanes. In Methods in Stereochemical Analysis; Juaristi, E., Ed.;
VCH: New York, 1995.
(35) Gorenstein, D. G. In Phosphorus-31 NMR: Principles and Applica-
tions; Gorenstein, D. G., Ed.; Academic Press: New York, 1984.
(39) Reed, A. L.; Curtiss, L. A.; Weinhold, F. Chem. Rev. 1988, 88, 899–
926.
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FIGURE 2. Experimental (RP)-1c0 and theoretical structure J (calculated at the B3LYP/6-31þG(d,p) level of theory) showing the existence of
an intramolecular C-H O hydrogen bonding interaction that stabilizes the chair conformation of the 1,3,2-dioxaphosphorinane.
3 3 3
FIGURE 3. NBO analysis for structures J and Jb showing the nO f σ*C-H interaction.
with an axially oriented C4 aryl group was postulated as a key
intermediary for the phosphate ring cleavage.15
bond that leads to the transformations. The isomerization of
(RP)-1d0 to (SP)-1d is possible by both routes. In the σ* route,
conformation B1enables nO f σ*P-ONu hyperconjugation (K)
that weakens the O3-C4 bond to give zwitterion L, which after
recombination affords (SP)-1d. Following the π* route, con-
formation C1 enables now nOfπ*PdO hyperconjugation15,41,42
(M) to give zwitterion N, which scrambles before collapsing to
give the isomerizated product (SP)-1d. On the other hand, the
situation with (SP)-1d0 is somewhat less complicated because the
conversion only requires inversion of the C4 atom and must,
therefore, follow the σ* route, in which starting from conforma-
tion C1 zwitterion P is formed that rapidly collapses to afford
(SP)-1d (Scheme 7).
To examine the prodrug isomerization for the series of
compounds studied herein, we carried out the phosphorylation
reaction of diol 4d0 at -78 °C in the presence of t-BuOK as
base, and cyclic nucleotides (RP)-10d and (SP)-10d were mo-
mentarily observed by 31P NMR (-8.9 and -7.8 ppm,
respectively);31 however, after monitoring the crude reaction
mixture until reaching room temperature, it could be deter-
mined that both nucleotides are selectively transformed to the
most stable diastereomeric cyclic nucleotide (SP)-1d (-8.8
ppm) in approximately 4 and 6 h, respectively (Scheme 7).40
Conversion of (RP)-1d0 to (SP)-1d occurs faster than con-
version of (SP)-1d0 to (SP)-1d even though this conversion
requires the inversion of two stereogenic centers (at C4 and
the P-atom), meanwhile only one stereogenic center is in-
verted in the case of (SP)-1d0. These transformations are
readily explained by the σ* and the π* route. The naming of
the routes indicates which orbital is involved in the O3-C4
Conclusions
The X-ray crystallographic and theoretical studies re-
ported herein demonstrated the existence of a stable chair
ꢀ
(41) Hernandez, J.; Ramos, R.; Sastre, N.; Meza, R.; Hommer, H.; Salas,
(40) Please see the experimental procedure of ref 15 for details in the
determination of the conversion time.
M.; Gordillo, B. Tetrahedron 2004, 60, 10927–10941.
(42) Verkade, J. G. Phosphorus Sulfur 1976, 2, 251–281.
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SCHEME 7. Spontaneous and Selective Isomerization of (RP)-1d0 and (SP)-1d0 into (SP)-1d in solution (CDCl3)
1
conformation for 1,3,2-dioxaphosphorinanes bearing an
aryl group axially oriented at the C4 position. This analysis
Internal references (TMS) for H and 13C Chemical shifts are
stated in parts per million. COSY, HSQC, and NOESY experi-
ments have been carried out in order to assign the H and 13
C
1
revealed a C-H O hydrogen bonding interaction between
3 3 3
spectra completely in high resolution mass spectra (FABþ ion
mode).
the phosphoryl group (PdO) and the o-hydrogen atom of the
aryl group, which overcomes the strong steric axial interac-
tions imposed by the aryl group. We have also corroborated
that the conversion or isomerization at C4 of cyclic nucleo-
tides, which are analogues of HepDirect prodrugs, occurs
through a spontaneous and selective O3-C4 bond cleavage
of the phosphorinane ring, which is favored by the confor-
mation and steric anomeric effect. The implications of this
finding may not only have relevance on the understanding of
the mechanistic course of prodrug cleavage, but also on the
re-evaluation of the conformational equilibria of 4-aryl-
1,3,2-dioxaphosphorinanes that have been postulated to
rarely exhibit a chair conformation. Taking advantage of
the above-described findings, along with the introduction of
an elegant protocol for the synthesis of novel cyclic nucleo-
tides, we have initiated the synthesis of a series of new cyclic
nucleotide analogues to HepDirect that are suitable to
undergo oxidative cleavage by a cytochrome P450 enzyme
(CYP). Results will be published in due course.
20,30-O-Isopropylidene-5-methyluridine (2).43 Thymine 5 (2 g,
7.7 mmol) was dissolved in 25 mL of 2,2-dimethoxypropane and
catalytic amounts of p-toluenesulfonic acid (8 mg, 0.058 mmol)
were added. Although the starting material was consumed
within 2 h and two products were observed by TLC, the reaction
mixture was allowed to react for 24 h at room temperature,
whereafter only one product was observed. Excess 2,2-di-
methoxypropane was evaporated under reduced pressure and
the residue was purified by silica gel column chromatography (n-
hexane:ethyl acetate = 1:5) to afford 2 (3 g, 95%). White solid;
1
mp 132-134 °C; H NMR (400 MHz, CDCl3) δ 1.36 (s, 3H),
1.57 (s, 3H), 1.90 (d, J = 1.2 Hz, 3H), 3.80 (dd, J = 12.4, 3.6 Hz,
1H), 3.90 (dd, J = 12.4, 2.8 Hz, 1H), 4.26 (q, J = 3.2 Hz, 1H),
4.96 (dd, J = 6.0, 3.2 Hz, 1H), 5.06 (dd, J = 6.4, 2.8 Hz, 1H),
5.55 (d, J = 2.8 Hz, 1H); 13C NMR (75 MHz, CDCl3) δ 12.4,
25.3, 27.3, 62.5, 80.3, 83.4, 86.8, 95.7, 111.0, 114.2, 138.8, 150.4,
163.9.
General Procedure for the Three-Component Reaction of
Protected Thymine (2), Phosphoryl Chloride, and 5-Aryl-R-D-
xylofuranoses Derivatives. To a solution protected thymine 2
(0.50 mmol) and triethylamine (1.25 mmol) in dry CH2Cl2 (30 mL)
at 0 °C was added dropwise phosphoryl chloride (0.6 mmol)
dissolved in 2 mL of dry CH2Cl2. The reaction mixture was allowed
to react for 2 h before adding a solution of the corresponding
Experimental Section
General. The reagents were obtained from commercial
sources and used without purification. The solvents were used
as technical grade, and freshly distilled prior to use. NMR
studies were carried out with 400 and 300 MHz spectrometers.
(43) Chung, R.; Anderson, K. S. Tetrahedron Lett. 2006, 47, 8361–8363.
5858 J. Org. Chem. Vol. 75, No. 17, 2010

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JOCArticle
1,3-diol 4 (0.50 mmol) and triethylamine (1.25 mmol) in dry
CH2Cl2 (30 mL) at 0 °C. The reaction mixture was stirred for 3 h
and concentrated under reduced pressure; the residue was
washed with brine and extracted with ethyl acetate, dried over
Na2SO4, and concentrated under reduced pressure. The residue
was purified by silica gel column chromatography (230-400
mesh) with n-hexane-EtOAc 2/1 (v/v) to afford the correspond-
ing cyclic nucleotide (RP)-1a-d and (SP)-1a-d. For the case of
1,3-diol (4d0), t-BuOK was used as base and ethyl ether as
solvent at -78 °C.
Acknowledgment. We thank the CONACyT (grant no.
62203) for support this work. We also thank Dr. Angel
Mendoza for X-ray crystallographic analysis and Professor
€
Herbert Hopfl for stimulating discussion on this work.
Supporting Information Available: Spectroscopic data,
1H and 13C NMR spectra for new compounds, Cartesian co-
ordinates for J and Jb structures, and a CIF file for (RP)-1c0.
This material is available free of charge via the Internet at http://
pubs.acs.org.
J. Org. Chem. Vol. 75, No. 17, 2010 5859