Synthesis and coordination chemistry of pyrimidine-substituted phosphine ligands

Article abstract of DOI:10.1016/j.ica.2011.10.058

Reaction of PPh₂H with UrI (Ur = uracil) in the presence of Pd(OAc)₂ affords PPh₂Ur. In the solid state, PPh ₂Ur crystallises as a methanol solvate in the monoclinic space group P2₁/c. Reaction of PPh₂Ur with CuI in dry and deoxygenated THF solution results in the formation of [Cu₄(μ₃-I) ₄(PPh₂Ur)₄]. A single crystal X-ray diffraction study demonstrated that this species contains a distorted tetrahedral core of copper atoms, with facially-capping iodides. The uracil groups in the clusters are engaged in hydrogen bonding to groups on neighbouring molecules to form an extended array. A similar reaction between PPh₂Ur and CuI in unpurified THF allows for the isolation of the phosphine oxide P(O)PPh ₂Ur. The synthesis of the benzyl-protected phosphine PPh ₂Ur^P is also described [Ur^P = 2,4-bis(benzyloxy)pyrimidine]. Reaction of PPh₂Ur^P with [Ru(η⁵-C₅H₅)(NCMe)₃]PF ₆ allows for isolation of [Ru(η⁵-C₅H ₅)(NCMe)(PPh₂Ur^P)₂]PF₆.

Full text of DOI:10.1016/j.ica.2011.10.058

Inorganica Chimica Acta 380 (2012) 252–260
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Synthesis and coordination chemistry of pyrimidine-substituted phosphine ligands
⇑
Tracy D. Nixon, Aimee J. Gamble, Robert J. Thatcher, Adrian C. Whitwood, Jason M. Lynam
Department of Chemistry, University of York, Heslington, York YO10 5DD, UK
a r t i c l e i n f o
a b s t r a c t
Article history:
Available online 29 October 2011
Reaction of PPh2H with UrI (Ur = uracil) in the presence of Pd(OAc)2 affords PPh2Ur. In the solid state,
PPh2Ur crystallises as a methanol solvate in the monoclinic space group P21/c. Reaction of PPh2Ur with
CuI in dry and deoxygenated THF solution results in the formation of [Cu4(l3-I)4(PPh2Ur)4]. A single crys-
Young Investigator Award Special Issue
tal X-ray diffraction study demonstrated that this species contains a distorted tetrahedral core of copper
atoms, with facially-capping iodides. The uracil groups in the clusters are engaged in hydrogen bonding
to groups on neighbouring molecules to form an extended array. A similar reaction between PPh2Ur and
CuI in unpurified THF allows for the isolation of the phosphine oxide P(O)PPh2Ur. The synthesis of the
benzyl-protected phosphine PPh2UrP is also described [UrP = 2,4-bis(benzyloxy)pyrimidine]. Reaction of
Keywords:
Phosphine ligands
Hydrogen bonding
Ruthenium half sandwich
PPh2UrP with [Ru( 5-C5H5)(NCMe)3]PF6 allows for isolation of [Ru( 5-C5H5)(NCMe)(PPh2UrP)2]PF6.
g g
Ó 2011 Elsevier B.V. All rights reserved.
1. Introduction
For example, reaction of ruthenium half sandwich compounds
with HC„CUr may be employed to prepare the vinylidene-con-
Phosphorus(III) ligands play a pivotal role as co-ligands in tran-
sition metal chemistry [1]. Variation of the substituents in the PR3
framework allows for direct control over the steric and electronic
effects exerted by the ligand and, therefore, the properties of any
resulting metal complex. Indeed metrics such as cone angle and
the Tolman electronic parameter have ensured that phospho-
rus(III) ligands may be used to develop well-defined structure–
activity relationships [2]. Furthermore, a number of additional
approaches to determining the steric and electronic influence of
these ligands have been developed [3].
The introduction of additional functional groups into the ligand
framework may be employed to generate more diverse control
over the reactivity of transition metal compounds. For example,
the introduction of N-heterocycles into the P(III) ligand may be
used to position a Brønsted basic site in close proximity to the me-
tal [4]. This basic position has subsequently been shown to facili-
tate proton transfer reactions in organic ligands bound to the
metal. Furthermore, phosphorus-based ligands that may engage
in mutually complementary hydrogen-bonding in the coordination
sphere of the metal have been shown to increase both the selectiv-
ity in rhodium-catalysed hydroformylation [5] and the anti-Mark-
ovnikov hydration of terminal alkynes [6].
taining complex [Ru(g
5-C5H5)(@C@CHUr)(PPh3)2][PF6] which, in
the solid state, self-assembles to give a remarkable hexameric mo-
tif [8]. The presence of the uracil substituent does not profoundly
alter the underlying organometallic chemistry of the half-sand-
wich compound. For example complexes containing carbene, alky-
nyl and alkenyl ligands, all containing pendant uracil groups, may
be prepared in a similar vein to their phenyl-substituted analogues
[9]. In addition, this method may be applied to the preparation of
square-planar and half-sandwich rhodium compounds, again with
the uracil dictating assembly in both the solid state and solution
[10].
Given that suitable phosphine ligands may employ non-covalent
interactions to dictate the behaviour of transition metal compounds,
we sought to expand this methodology to phosphorus-based li-
gands containing pendant uracil groups. The methodology which
we had developed using HC„CUr as a substrate had demonstrated
that an appropriate choice of metal would ensure that selective
binding to the alkyne occurred, it was envisaged that a similar strat-
egy might translate to phosphorus-based ligands. The synthesis of
the uracil-substituted phosphine PPh2Ur was therefore targeted. It
is important to note that Kamer and co-workers have demonstrated
that it is possible to incorporate PPh2 groups into the backbone of
deoxyuridine units that are part of an oligonucleotide [11]. This
phosphine ligand is able to introduce a measure of enantiocontrol
in palladium-mediated allylic-substitution reactions.
We have previously demonstrated that the incorporation of
pendant uracil groups into the coordination sphere of metal com-
pounds may be used to dictate the assembly of both organometal-
lic and coordination compounds in the solid state and solution [7].
The synthesis of the uracil-substituted phosphine PPh2Ur is
now reported with the resulting copper(I)iodide complex, along
with the corresponding oxide, P(O)Ph2Ur. Furthermore the prepa-
ration of a phosphine ligand containing a protected uracil group,
⇑
Corresponding author. Tel.: +44 (0) 1904 322534; fax: +44 (0) 1904 322516.
E-mail address: jason.lynam@york.ac.uk (J.M. Lynam).
0020-1693/$ - see front matter Ó 2011 Elsevier B.V. All rights reserved.
doi:10.1016/j.ica.2011.10.058

T.D. Nixon et al. / Inorganica Chimica Acta 380 (2012) 252–260
253
PPh2UrP, and the ruthenium complex [Ru(
g
5-C5H5)(NCMe)(P-
shorter than those to the phenyl groups [C(5)–P(1) 1.8365(15) Å,
C(11)–P(1) 1.8291(16) Å].
Ph2UrP)2][PF6] are also described. In a preliminary communication
we have shown that the gold phosphine complex AuCl(PPh2Ur)
self-assembles in the solid state to give a crystalline structure with
large solvent-accessible areas [12]. This solid state structure is dic-
tated by hydrogen bonding interactions between uracil groups on
neighbouring molecules. The resulting array is robust and it ap-
peared to be possible to remove and replace the solvent from these
areas without substantial degradation in the quality of the crystal-
line material.
As shown in Fig. 2a, the uracil groups of the phosphine ligands
engage in complementary hydrogen-bonding between the N–H
group in the 1-position of the uracil and the carbonyl group in
the 2-position [N(2)–H(19)ÁÁÁO(2) 2.771(2) Å; H(19)ÁÁÁO(2)
1.89(2) Å]. In addition the remaining N–H and carbonyl groups in
the uracil are involved in hydrogen bonding with the oxygen and
hydrogen of the OH group of the methanol respectively [N(1)–
H(18)ÁÁÁO(3) 2.742(2) Å, H(18)ÁÁÁO(3) 1.86(3) Å, O(3)–H(3A)ÁÁÁO(1)
2.763(2) Å, H(3A)ÁÁÁO(1) 1.96(3) Å]. The combination of these inter-
actions results in the formation of stacks of dimeric PPh2Ur units
linked by methanol molecules. Neighbouring stacks run in orthog-
onal directions. A space-filing model of the structure of PPh2Ur
(Fig. 2b) viewed down the c-axis of the unit cell illustrates the polar
domains (containing the uracil and methanol groups) and non-po-
lar areas (the phenyl groups of the phosphine).
2. Results and discussion
2.1. Synthesis of PPh2Ur
The uracil-substituted phosphine PPh2Ur may conveniently be
prepared by the palladium-catalysed coupling of PPh2H with 5-
iodouracil in DMF solution at 60 °C in the presence of triethyl-
amine (Scheme 1). The compound was obtained as colourless crys-
tals that proved to be soluble in DMSO, THF, warm MeOH and
acetone, partially soluble in CHCl3 and insoluble in water, hexane,
toluene and diethylether. Crystals of PPh2Ur suitable for study by
X-ray crystallography were obtained from a methanol solution of
the phosphine. The resulting structure determination revealed that
PPh2Ur had crystallised as a methanol solvate and the asymmetric
unit is shown in Fig. 1. An examination of the structure revealed
that the PPh2Ur unit possessed the expected connectivity, with
the PPh2 group being attached to the 5-position of the uracil. The
introduction of the uracil group only introduces small distortions
in the structure of the phosphine ligand. For example, the bond an-
gles surrounding phosphorus are similar [(C(4)–P(1)–C(11)
103.09(7)°,
C(4)–P(1)–C(5)
101.03(7)°,
C(11)–P(1)–C(5)
101.04(7)°], although the sum of the angles at phosphorus
[305.19(12)°] is somewhat less than that seen in PPh3
[308.21(13)° [13] 308.57(10)° [14] and 308.18(14)° [15]]. There is
some asymmetry in the P–C bonds with that between the phos-
phorus and the uracil group [C(4)–P(1) 1.8208(15) Å] being notably
Fig. 2. (a) Hydrogen bonding interactions in the structure of PPh2UrÁMeOH. (b)
Space filling diagram of PPh2UrÁMeOH.
Scheme 1. (i) +Pd(OAc)2, +NEt3, À[NHEt3]I, DMF, 60 °C 1 h.
Fig. 1. Molecular structure of PPh2Ur as the methanol solvate as determined by single crystal X-ray diffraction. Thermal ellipsoids are shown at the 50% probability level.

254
T.D. Nixon et al. / Inorganica Chimica Acta 380 (2012) 252–260
ment of the copper and iodine atoms: [Cu4(l3-I)4(PEt3)4] has a reg-
ular cubane core [18]. Selected bond lengths for each of these
species are also presented in Table 1. The different structural mo-
tifs adopted by these copper iodide complexes have been associ-
ated with the relative steric demands of the phosphine ligands,
with larger ligands preferring the chair conformation. In the case
Scheme 2. (i) +CuI, purified THF; (ii) +CuI, reagent-grade THF.
of [Cu4(l3-I)4(PPh2Ur)4], where the phosphine ligand possess a
similar steric demand to PPh3, the effect of the hydrogen-bonding
network (q.v.) cannot be ignored.
2.2. Reaction of PPh2Ur with CuI
In this solid state structure the [Cu4(l3-I)4(PPh2Ur)4] molecules
are linked by a hydrogen bonding array which arises from interac-
tions between uracil groups on neighbouring clusters. The uracil
groups attached to the P(2) and P(3) edge of the Cu4 tetrahedron
interact via multiple hydrogen bonds with the groups attached to
P(1) and P(4) (Fig. 3c). Considering the uracil group attached to
P(4), the N–H group in the 3-position of the ring is engaged in
hydrogen bonding to the carbonyl group in the 2-position of the
uracil attached to P(2) [N(8)–H(8A)ÁÁÁO(4) 2.784(4) Å]. The oxygen
atom of the carbonyl group in the 2-position of the uracil group at-
tached to P(4) is involved in bifurcated hydrogen bonding to the N–
H group in the 3-position of the uracil attached to P(2) [N(3)–
H(3)ÁÁÁO(8) 2.744(4) Å] and N–H group in the 1-position attached
to P(3) [N(6)–H(6A)ÁÁÁO(8) 3.007(4) Å]. On the basis of the bond
lengths, however, there is considerable asymmetry in this bifur-
cated arrangement. The N–H group in the 3-position of the uracil
attached to P(4) is engaged in hydrogen-bonding to the carbonyl
group in the 2-position of the uracil attached to P(3) [N(7)–
H(7A)ÁÁÁO(6) 2.776(4) Å]. Additionally the carbonyl group in the
2-position of the uracil attached to P(1) is engaged in hydrogen
bonding with the N–H group in the 3-position of the uracil at-
tached to P(3) [N(5)–H(5)ÁÁÁO(2) 2.854(4) Å]. The sum of these
interactions is to create a one-dimensional hydrogen bonded
strand which is propagated into a two-dimensional network by
The reaction of CuI with PPh2Ur in THF solution resulted in the
formation of a tetrameric complex [Cu4(l3-I)4(PPh2Ur)4]. In order
for the reaction to be successful it was imperative to employ puri-
fied THF as the use of reagent grade solvent only allowed for the
phosphine oxide P(O)PPh2Ur to be isolated, Scheme
Section 2.3).
2 (see
The copper complex was isolated as colourless crystals suitable
for study by X-ray diffraction. The resulting structural determina-
tion demonstrated that [Cu4(l3-I)4(PPh2Ur)4] had co-crystallised
as a THF solvate. Unfortunately, due to problems with disorder
only two of the THF molecules in the asymmetric unit could be
successfully modelled. The structure of the copper core of this sys-
tem is shown in Fig. 3a, and the hydrogen bonded network in
Fig. 3b.
The [Cu(l3-I)P]4 core of the complex may be considered to be a
distorted tetrahedron of copper atoms each bound to a terminal
phosphine ligand with facially capping iodide ligands: selected
bond lengths are presented in Table 1. There are considerable devi-
ations from an ideal tetrahedron with CuÁÁÁCu distances ranging
from 3.0361(6) Å [Cu(1)ÁÁÁCu(3)] to 2.8235(6) Å [Cu(2)ÁÁÁCu(4)].
The distorted tetrahedral copper core is similar to that reported
by Churchill and Rotella [16] for [Cu4(
l3-I)4(PPh2Me)4] but differs
from [Cu4( 3-I)4(PPh3)4] [17] which possesses a chair-like arrange-
l
Fig. 3. (a) [Cu(l3-I)P]4 core of [Cu4(l3-I)4(PPh2Ur)4], thermal ellipsoids shown at the 50% probability level (b) hydrogen bonding network (THF molecules omitted for clarity).
(c) Intermolecular hydrogen bonding motif. Copper atoms shown in dark blue, iodine in purple and phosphorus in orange. (For interpretation of the references to colours in
this figure legend, the reader is referred to the web version of this article.)

T.D. Nixon et al. / Inorganica Chimica Acta 380 (2012) 252–260
255
Table 1
Selected bond lengths (Å) for complexes [Cu4(
l
3-I)4(PR3)4]. [Cu4(
l
3-I)4(PEt3)4] has crystallographic Td symmetry, [Cu4(
l
3-I)4(PMe2Ph)4] crystallographic C2 symmetry and
[Cu4(l3-I)4(PPh3)4] crystallographic Ci symmetry.
[Cu4I4(PPh2Ur)4]
[Cu4I4(PEt3)4] [17]
2.9272(20)
[Cu4I4(PMe2Ph)4] [16]
[Cu4I4(PPh3)4] [18]
Cu(1)
Cu(1)
Cu(2)
Cu(2)
Cu(3)
Cu(1)
Cu(2)
Cu(3)
Cu(4)
Cu(1)
Cu(1)
Cu(1)
Cu(2)
Cu(2)
Cu(2)
Cu(3)
Cu(3)
Cu(3)
Cu(4)
Cu(4)
Cu(4)
I(1)
Cu(3)
Cu(4)
Cu(3)
Cu(4)
Cu(4)
P(1)
P(2)
P(3)
P(4)
I(1)
I(2)
I(3)
I(1)
I(2)
I(4)
I(1)
I(3)
I(4)
3.0361(6)
2.8278(7)
2.9571(7)
2.8235(6)
2.8800(6)
2.2622(10)
2.2529(10)
2.2558(10)
2.2560(10)
2.6810(5)
2.6869(5)
2.6876(5)
2.6968(5)
2.6789(5)
2.6508(5)
2.6816(5)
2.7003(5)
2.6453(5)
2.6782(5)
2.6297(6)
2.7111(5)
4.5090(4)
4.2774(4)
4.2988(4)
4.3906(4)
4.3933(4)
4.4190(4)
3.0095(13)
2.83595(13)
2.9620(18)
2.9202(18)
2.8345(29)
4.2949(29)
3.4040(36)
2.2538(27)
2.6837(13)
2.2500(20)
2.2498(20)
2.2277(47)
2.2418(39)
2.7262(11)
2.6440(11)
2.7157(12)
2.7591(11)
2.6108(11)
2.7333(12)
2.5273(22)
2.5913(24)
2.6203(23)
2.7281(23)
2.7073(22)
I(2)
I(3)
I(4)
I(2)
4.3800(11)
4.2973(12)
4.4883(8)
4.4188(9)
4.3253(12)
4.3842(17)
4.2044(18)
4.2375(22)
I(1)
I(3)
I(1)
I(4)
I(2)
I(3)
I(2)
I(4)
I(3)
I(4)
hydrogen bonding between the NH in the 1-position of the uracil
group attached to P(2) and the carbonyl in the 4-position on P(1)
on neighbouring strands [N(4)–H(4A)ÁÁÁO(1) 2.857(4) Å].
It should also be noted that neither of the NH groups on the ura-
cil groups attached to P(1) are involved in hydrogen bonding to an-
other nucleobase. The two THF molecules that could be
successfully modelled as part of the structural solution are located
close in-space to these NH groups, although the nature of the dis-
order means that the nature of any interactions must be treated
with considerable caution.
complementary hydrogen bonding through N(1)–H and O(2) to
an identical neighbour [N(1)–H(1)ÁÁÁO(2) 2.836(2) Å; H(1)ÁÁÁO(2)
1.97(2) Å, N(1)–H(1)ÁÁÁO(2) 176(2)°]. The oxygen attached to P(1)
exhibits a hydrogen bond to a N–H group on the other phosphine
oxide molecule in the asymmetric unit, specifically to the N–H
group in the 1-position of the uracil group [O(3)ÁÁÁH(4)–N(4)
2.738(2) Å, H(4)ÁÁÁO(3) 1.90(2) Å, O(3)ÁÁÁH(4)–N(4) 170(2)°]. The
only remaining hydrogen-bonding interaction involving the uracil
group attached to P(2) is between the N–H group in the 3-position
and the THF of crystallisation, [N(3)–H(3)ÁÁÁO(7) 2.840(1) Å,
H(3)ÁÁÁO(7) 1.90(2) Å, N(3)–H(3)ÁÁÁO(7) 177(2)°]. However the oxy-
gen attached to the phosphorus atom P(2) is engaged in hydrogen
bonding to the N–H group in the 1-position of the uracil group at-
tached to P(1) [O(6)ÁÁÁH(1)–N(1) 2.670(1) Å, O(6)ÁÁÁH(1) 1.85(2),
O(6)ÁÁÁH(1)–N(1) 177(2)°]. The net effect of these interactions is
to produce a linear hydrogen bonded strand (Fig. 4b), which addi-
In a similar vein to [Cu4(l3-I)4(PPh3)4], one might expect the
uracil-substituted copper complex to adopt a chair-like conforma-
tion on the basis of steric arguments. However it is tempting to ar-
gue that the effects of the hydrogen bonding network may affect
the ultimate geometry of the complex. In cases such as this, where
the copper core may form one several structural types with only
small variations in energy, then the most favourable arrangement
of the non-covalent interactions may play a role in dictating the
global geometry. Therefore, although it is possible that the chair
conformation may be favoured on steric grounds, the observed dis-
torted tetrahedral shape might allow for hydrogen bonding inter-
actions to be optimised.
tionally exhibits some mutual p–p interactions between the uracil
groups attached to P(2) [C(25)ÁÁÁN(3) 3.110(2) Å, C(26)ÁÁÁO(5)
3.112(2) Å] (Fig. 4c). As may be seen from the space filling diagram
(Fig. 4d), the polar nucleobase and P–O units form a distinct do-
main surrounded by the non-polar aromatic groups. This is also
the case in the structure of PPh2Ur.
The strongest hydrogen bonds in the structure of P(O)Ph2Ur ap-
pear to be those involving the phosphine oxide functionality [19],
at least on the basis of the observed bond lengths. Hydrogen bonds
of the N–HÁÁÁO@P type have been observed previously and that be-
tween O(6) and H–N(1) [2.6682(3) Å] is an example of an extre-
mely short interaction of this type [20].
2.3. Synthesis of P(O)Ph2Ur
The reaction of CuI with PPh2Ur using THF which had not been
deoxygenated and dried did not form the tetrameric copper com-
plex [Cu4(l3-I)4(PPh2Ur)4]. In this instance colourless crystals of
the phosphine oxide P(O)Ph2Ur were isolated. In addition to NMR
spectroscopy and mass spectrometry, the structure of this oxide
was determined by single crystal X-ray diffraction.
2.4. Synthesis of PPh2UrP
As shown in Fig. 4a, the asymmetric unit contained two crystal-
lographically-independent molecules of P(O)Ph2Ur and a THF of
crystallisation. The bond lengths within the two independent mol-
ecules were in general found to be statistically identical, yet two
different hydrogen bonding motifs are present. In the case of the
phosphine containing atom P(1), the uracil group is engaged in
A further phosphine ligand, based on the pyrimidine group, was
targeted in which the hydrogen-bonding capability of the uracil
group had been removed by suitable protecting groups. The syn-
thetic procedure employed is shown in Scheme 3 and it was envis-
aged that such a ligand might be able to act as Brønsted base in a
similar way to the more well-known pyridyl-substituted

256
T.D. Nixon et al. / Inorganica Chimica Acta 380 (2012) 252–260
Fig. 4. (a) Asymmetric unit for P(O)Ph2Ur, thermal ellipsoids shown at the 50% probability level and selected hydrogen atoms omitted for clarity. (b) Hydrogen bonded
network (c) interaction between uracil groups (d) space filling diagram.
p–p
phosphines. Reaction of 5-bromouracil with POCl3 results in the
formation of 5-bromo-2,4-dichloropyrimidine. Subsequent reac-
tion with benzyl-alcohol and NaH results in the generation of 5-
bromo-2,4-bis(benzyloxy)pyrimidine. The final step in the reaction
procedure to prepare PPh2UrP utilised the low temperature lithia-
tion of 5-bromo-2,4-bis(benzyloxy)pyrimidine with LinBu followed
by addition of PClPh2.
In addition to characterisation by NMR spectroscopy and
mass spectrometry, the structure of PPh2UrP (Fig. 5) was deter-
mined by single crystal X-ray diffraction. The resulting structure
determination demonstrated that PPh2UrP had crystallised in the
chiral space group P21. The phosphorus atom in the PPh2UrP is
coordinated to two phenyl group and the benzyl-protected pyri-
mindine at the 5-position of the ring. Again the introduction of
the pyrimidine group does not profoundly affect the structure
of the phosphine when compared to PPh3. For example, the
sum of the angles at phosphorus is 305.72(14)° [C(13)–P(1)–
C(1) 100.47(8)°, C(13)–P(1)–C(7) 102.02(8)°, C(1)–P(1)–C(7)
103.23(8)°] with the two angles involving the pyrimidine group
slightly more acute that the remaining one between the two
phenyls. Furthermore, the P–C bonds to the two phenyl groups
are similar [C(7)–P(1) 1.8321(19) Å, C(1)–P(1) 1.830(2) Å]
whereas that to the pyrimidine is somewhat shorter [C(13)–
P(1) 1.8216(18) Å].
2.5. Synthesis of [Ru(g
5-C5H5) (NCMe)(PPh2UrP)2]PF6
The half-sandwich complex [Ru(g
5-C5H5)(NCMe)(PPh2UrP)2]PF6
was prepared in order to investigate the potential of PPh2UrP to di-
rect the ruthenium-mediated hydration of alkynes. The reaction of
[Ru(g
5-C5H5)(NCMe)3]PF6 with two equivalents of PPh2UrP was
initially investigated by NMR spectroscopy in CDCl3 solution. The
resulting 31P{1H} NMR spectrum exhibited a new singlet resonance
at d 30.7 corresponding to the formation of the cation [Ru(g
5-C5H5)
(NCMe)(PPh2UrP)2]+. Slow diffusion of Et2O into this solution re-
sulted in the formation of yellow crystals of the complex suitable
Scheme 3. (i) +POCl3; (ii) +NaH, +HOCH2Ph; (iii) +LinBu (À85°); (iv) +PClPh2.

T.D. Nixon et al. / Inorganica Chimica Acta 380 (2012) 252–260
257
Fig. 5. Structure of PPh2UrP in the solid state. Thermal ellipsoids are shown at the 50% probability level, hydrogen atoms omitted for clarity.
Fig. 6. (a) Structure of the cation [Ru(g
5-C5H5)(NCMe)(PPh2UrP)2]+. Thermal ellipsoids shown at the 50% probability level and hydrogen atoms omitted for clarity. (b)
Coordination environments of the PPh2UrP ligands.
for study by X-ray diffraction. The resulting study demonstrated
that the complex had crystallised as a mixed Et2O/CDCl3 solvate
in the triclinic space group P1: the structure of the cation is shown
Unfortunately, only a slow reaction occurred and the major prod-
uct proved to be the linear dimer of the alkyne, E-1,4-diphenyl-
1-buten-3-yne [21]: only trace amount of hydration products were
observed.
ꢀ
in Fig. 6a.
The structure determination demonstrated that the complex
did indeed contain two PPh2UrP ligands with the remaining coordi-
nation sites being occupied by cyclopentadienyl and acetonitrile li-
gands. The phosphine ligands are both arranged so that the two
phenyl groups are directed towards the cyclopentadienyl ligand,
thus the benzyl-protected pyrimidine groups provide a sterically-
hindered region around the remaining faces of the complex,
Fig. 6(b). There is a close contact between the pyrimidine rings
3. Conclusions
The solid-state structure of the phosphine PPh2Ur and its oxide
P(O)Ph2Ur show a number of common features, most notably the
clustering of polar and non-polar domains. In some respects the
topology may be compared to that of double strand nucleic acids
with the bases contained with a sheath of (in this instance) a very
non-polar aromatic region or (in the case of nucleic acids) a water-
solubilising phosphate backbone. Clearly, by removing the N–H
and carbonyl functionality by protection with benzyl-groups the
potential for the pyrimidine to engage in hydrogen bonding is all
[C(21)–C(53) 3.247(3) Å] which may be indicative of a p–p interac-
tion. This may, at least in the solid-state, assist in defining the
topology of the coordination sphere of the metal.
The potential for [Ru(
catalyst for the hydration of phenyl acetylene was investigated.
g
5-C5H5)(NCMe)(PPh2UrP)2]PF6 to act as a

258
T.D. Nixon et al. / Inorganica Chimica Acta 380 (2012) 252–260
but removed as demonstrated by the structures of PPh2UrP and its
ruthenium complex.
4.3. Synthesis of P(O)Ph2Ur
In a similar vein to Kamer and co-workers [11], we have also
shown that it is possible to use palladium-mediated methods to
prepare uracil functionalised phosphine ligands and, in addition,
that a salt-elimination method may be used to prepare pyrimi-
dine-substituted phosphine PPh2UrP. Therefore, the preparation
of related functionalised phosphorus(III) ligands should be possible
by extension of these synthetic methods and thus expand the li-
brary of ligands that may engage in hydrogen bonding for both cat-
alytic and structural purposes.
P(O)PPh2Ur was prepared using an identical procedure to
[Cu4(l3-I)4(PPh2Ur)4] with the exception that the THF employed
was not purified prior to use. Yield 9 mg (38%) 1H NMR (d6-DMSO)
d 10.78 (br. s, 1H, NH), 10.51 (s, 1H, NH), 6.80 (d, JHP = 10.9 Hz, 1H,
CH), 6.85 (ddd, 3JHP = 12.8 Hz, 3JHH = 7.5, 4JHH = 1.0 Hz, 4H, Ph), 6.70
3
4
3
(dd, JHH = 7.5 Hz, JHH = 1.0 Hz, 2H, Ph), 6.62 (td, JHH = 7.5 Hz,
4JHP = 2.8 Hz, 4H, Ph). 31P{1H} NMR (d6-DMSO) d 22.3 (s). 13C{1H}
d
J
162.7 (d, JPC = 10.5 Hz, C@O), 151.2 (s, C@O), 150.9 (d,
PC = 12.8 Hz, CH), 132.5 (d, JPC = 110 Hz, Ph), 131.9 (d, JPC = 3.0 Hz,
Ph), 131.4 (d, JPC = 10.5 Hz, Ph), 128.4 (d, JPC = 12.5 Hz, Ph), 103.1
(br, Ur C5). Mass spectrum 313.0736 (M+H+ expected for
C16H14N2O3P 313.0737), 335.0552 (M+Na+ expected for
4. Experimental
C
16H13N2NaO3P 335.0556) IR (ATR/cmÀ1) 3469 (br, w), 3271 (br,
Unless otherwise stated, all reactions were performed under an
atmosphere of dry nitrogen using standard Schlenk line and glove
box techniques. THF was distilled from sodium/benzophenone,
NEt3 was distilled from sodium and degassed before use, Et2O
was purified using an Innovative Technology anhydrous solvent
engineering system. CDCl3 was dried over CaH2 and vacuum trans-
w), 2962 (br, w), 1768 (m) 1714 (m) 1611 (w), 1483 (w), 1407
(m), 1165 (m), 1036 (m), 990 (w), 694 (w). Elemental Anal. Calc.
for C16H13N2O3PÁ(THF)0.5: C, 62.07; H, 4.92; N, 8.04. Found: C,
62.18; H, 5.24; N, 7.88%.
4.4. Synthesis of PPh2UrP
ferred prior to use. 5-iodouracil, [Ru(g
5-C5H5)(NCMe)3][PF6] and
DMF (anhydrous) were purchased from Aldrich. 5-Bromo-2,4-
dichloropyrimidine [22] and 5-bromo-2,4-bis(benzyloxy)pyrimi-
dine [23] were prepared according to literature procedures.
NMR spectra were recorded on either a Bruker AV500 (operat-
ing frequencies 1H 500.13 MHz, 31P 202.50 MHz, 13C
125.77 MHz), or JEOL EX400 (operating frequencies 1H
A dry 100 ml flask, equipped with a septum, inlet, low temper-
ature thermometer, and magnetic stirrer bar was flushed with ar-
gon. A solution of 5-bromo-2,4-bis(benzyloxy)pyrimidine (0.5 g,
1.3 mmol) in THF (35 ml) was introduced and the flask and cooled
to À95 °C. A pre-cooled solution of n-BuLi (2.5 M solution in hex-
anes, 1.6 mmol) was added at such a rate that the internal temper-
ature did not exceed À85 °C. The yellow solution was stirred for
400.13 MHz, 31P 161.83 MHz, 13C 100.60 MHz) spectrometers.
(n+2)
N = nJPC
+
J . Mass spectra were acquired using the ESI tech-
PC
5 min then chlorodiphenylphosphine (313 ll, 1.7 mmol) was
nique on a Bruker Daltronic microTOF instrument.
added and temperature maintained for a further 20 min then al-
lowed to warm to room temperature over 2 h. The solution was
evaporated to dryness and the residue extracted with methanol.
The resulting solution was concentrated in vacuo, cooling to
À20 °C resulted in the formation of colourless crystals.
Yield = 247 mg (40%).
4.1. Synthesis of PPh2Ur
A Schlenk tube containing a magnetic stirrer bar was charged
with 5-iodouracil (0.34 g, 1.41 mmol), DMF (10 ml), NEt3
(0.22 ml, 1.55 mmol) and PPh2H (0.26 ml, 1.55 mmol). Pd(OAc)2
(3 mol%, 9.5 mg) was added and the resulting deep purple solution
heated at 60 °C for 1 h. The solvent was removed under reduced
pressure and the residue purified by dissolution warm methanol,
any insoluble impurities were removed by filtration. Cooling the
solution to À20 °C resulted in the formation of a precipitate of
PPh2Ur which could be further recrystallized until the sample
was colourless. Yield 159 mg (38%).
3
1H NMR (CDCl3) d 7.67 (d, JHP = 2.8 Hz, 1H, CH), 7.46 (m, 2H,
Ph), 7.35 (m, 13H, Ph), 7.20 (m, 3H, Ph), 6.98 (m, 2H, Ph), 5.39 (s,
2H, CH2), 5.37 (s, 2H, CH2). 31P{1H} NMR (CDCl3) -23.5 (s).
2
13C{1H} NMR (CDCl3) 171.2 (d, JPC = 14.6 Hz, COCH2), 165.7 (s,
2
COCH2), 162.6 (d, JPC = 7.0 Hz, CH), 136.5 (s, CH2Ph, C1) 135.9 (s,
1
CH2Ph, C1), 134.7 (d, JCP = 9.8 Hz, PPh, C1), 134.0 (s, Ph), 133.8 (s,
3
Ph), 129.3 (s, Ph), 128.8 (d, JPC = 7.4 Hz, PPh, C3), 128.6 (s, Ph),
2
128.3 (d, JPC = 8.8 Hz, PPh, C2), 128.2 (s, CH2Ph, C4), 127.8 (s,
1
CH2Ph, C4), 127.4 (s, Ph), 110.8 (d, JPC = 17.8 Hz, UrP C5), 69.4 (s,
1H NMR (d6-DMSO) d 11.28 (s, 1H, NH), d 10.96 (s, 1H, NH), d
7.42–7.25 (10H, Ph), d 6.45 (1H, Ur CH). 31P{1H} NMR (d6-DMSO)
d À21.1 (s). 13C{1H} d 164.2 (d, JPC = 18.8 Hz, C@O), d 151.2 (s,
C@O), 144.5 (d, JPC = 9.9 Hz, CH) d 135.2 (d, JPC = 10.8 Hz, Ph), d
133.2 (d, JPC = 20.4 Hz, Ph), 129.1 (s, Ph) 128.7 (d, JPC = 6.8 Hz,
Ph), 107.4 (s, Ur C5). Mass spectrum 297.0788 (M+H+ expected
for C16H14N2O2P 297.0787), 319.0605 (M+Na+ expected for
CH2Ph), 68.4 (s, CH2Ph). Mass spectrum 477.1727 (M+H+ expected
for C30H26N2O2P 477.1726). IR (ATR/cmÀ1) 3066 (w), 1566 (m),
1444 (m) 1454 (m), 1410 (m), 1353 (m), 1267 (m), 1227 (m),
1098 (m), 1041 (m), 979 (m), 905 (w), 852 (w), 796 (m), 745 (m),
697 (s). Elemental Anal. Calc. for C30H25N2O2P: C, 75.62; H, 5.29;
N, 5.88. Found: C, 73.89; H, 4.93; N, 5.74%. Repeats of the analysis
gave similar results with good matches to predicted hydrogen and
nitrogen content, but less carbon than expected.
C
16H13N2NaO2P 319.0607). IR (ATR/cmÀ1) 3285 (br, m) 3126 (br,
w) 3031 (br, w), 2827 (w), 1779 (w), 1739 (m) 1699 (m), 1646
(s), 1607 (s), 1466 (m), 1423 (m), 1324 (m) 1215 (m), 1137 (s),
1048 (w) 939 (w) 886 (w) 850 (w), 776 (w) 756 (m), 732 (m)
635 (m). Elemental Anal. Calc. for C16H13N2O2P: C, 64.87; H, 4.42;
N, 9.46. Found: C, 64.57; H, 4.45; N, 9.35%.
4.5. Synthesis of [Ru(g
5-C5H5)(NCMe)(PPh2UrP)2][PF6]
[Ru(
g
5-C5H5)(NCMe)3][PF6] (30 mg, 6.91 Â 10À5 mol) and
PPh2UrP (66 mg, 1.39 Â 10À4 moles) were dissolved in CDCl3 in
an NMR tube fitted with a PTFE ampoule. A 31P{1H} NMR spectrum
was then recorded to ensure that the reaction had reached comple-
tion. The solution was transferred into an ampoule and Et2O al-
lowed to slowly diffuse into the solution to precipitate the
product which could subsequently isolated by filtration.
4.2. Synthesis of [Cu4(l3-I)4(PPh2Ur)4]
Copper iodide (13 mg, 0.09 mmol) and PPh2Ur (20 mg,
0.08 mmol) were added to dry THF (2 ml) and the mixture shaken.
Any insoluble residues were removed by filtration and hexane
(2 ml) was allowed to diffuse into the resulting solution resulting
1H NMR (CDCl3): d = 8.01 (s, 2H, CH), 7.5–6.5 (20 H, Ph) 5.40 (m,
4H, CH2Ph), 5.12 (m, 4H, CH2Ph), 4.23 (s, 5H, C5H5), 1.62 (s, 3H,
NCCH3), 31P{1H} NMR (CDCl3): d = 30.7 (s, PPh3), À133.3 (septet,
in the formation of colourless crystals of [Cu4(l3-I)4(PPh2Ur)4].

T.D. Nixon et al. / Inorganica Chimica Acta 380 (2012) 252–260
259
Table 2
Data collection and structural refinements details for single crystal X-ray diffraction studies of compounds reported.
PPh2UrÁMeOH
[Cu4(
l
3-I)4(PPh2Ur)4]Á2THF P(O)Ph2UrÁ0.5THF
PPh2UrP
[Ru(g
5-C5H5)(NCMe)(PPh2UrP)2]
[PF6](CHCl3)0.75(Et2O)0.25
Empirical formula
Formula weight
T (K)
C17H17N2O3P
328.30
100(2)
C72H59Cu4I4N8O10P4
2081.91
110
C18H17N2O3.5
348.31
110.0
P
C30H25N2O2P
476.49
100(2)
C68.75H61.25Cl2.25F6N5O4.25P3Ru
1413.22
110(2)
k (Å)
0.71073
monoclinic
P2(1)/c
17.7803(15)
5.4182(5)
18.4514(15)
90
Crystal system
Space group
a (Å)
b (Å)
c (Å)
monoclinic
P2(1)/n
12.9440(9)
24.1550(16)
30.384(2)
90
98.680(2)
90
9391.3(11)
4
monoclinic
C2/c
17.1552(17)
14.8765(15)
26.674(3)
90
102.987(2)
90
6633.3(12)
16
monoclinic
P2(1)
11.6311(13)
5.5875(6)
18.225(2)
90
95.554(2)°.
90
1178.9(2)
2
triclinic
ꢀ
P1
13.3175(9)
14.6515(10)
18.0383(12)
108.6640(10)°
93.0410(10)
102.6260(10)
3225.0(4)
2
a
(°)
b (°)
114.416(2)
90
1618.6(2)
4
1.347
0.186
c
(°)
V (Å3)
Z
Dcalc (mgmÀ3
)
1.472
2.327
4060
1.395
1.342
1.455
Absorption coefficient (mmÀ1
F(000)
)
0.188
0.148
0.482
688
2912
500
1448
Crystal size (mm3)
0.28 Â 0.12 Â 0.06 0.23 Â 0.11 Â 0.02
0.45 Â 0.10 Â 0.05 0.38 Â 0.12 Â 0.04 0.14 Â 0.06 Â 0.05
/ Range for data collection (°)
Index ranges
2.22–28.33
À23 6 h 6 23
À7 6 k 6 7
1.60–28.31
À17 6 h 6 17
0 6 k 6 32
0 6 l 6 40
23288
1.57–28.31
1.76–28.32
À15 6 h 6 15
À7 6 k 6 7
1.20–30.03
À22 6 h 6 22
À19 6 k 6 19
À35 6 l 6 35
33496
À18 6 h 6 18
À20 6 k 6 20
À25 6 l 6 24
36912
À24 6 l 6 24
15105
À24 6 l 6 24
12088
Reflections collected
Independent reflections (Rint
Completeness to theta
)
4020 (0.0327)
99.6 (to 28.33)
23288 (0.0542)
99.6 (to 28.31)
8225 (0.0238)
99.7 (to 28.31)
5843 (0.0292)
99.7 (to 28.32)
18195 (0.0275)
96.4 (to 30.03)
Absorption correction
Semi-empirical from equivalents
Max. and min. transmission
Refinement method
0.990 and 0.813
1.000 and 0.842
1.000 and 0.864
0.990 and 0.847
0.976 and 0.820
Full-matrix least-squares on F2
Data/restraints/parameters
4020/0/221
1.038
23288/18/965
0.921
8225/0/458
1.016
5843/1/316
1.004
18195/0/851
1.031
Goodness-of-fit (GOF) on F2
Final R indices [I > 2
R indices (all data)
r
(I)]
R1 = 0.0387
wR2 = 0.1000
R1 = 0.0555
wR2 = 0.1099
0.434/À0.279
R1 = 0.0364
wR2 = 0.0763
R1 = 0.0667
wR2 = 0.0829
1.108/À0.684
R1 = 0.0372
wR2 = 0.0944
R1 = 0.0443
wR2 = 0.0984
0.501/À0.281
R1 = 0.0414
wR2 = 0.0847
R1 = 0.0484
wR2 = 0.0877
0.311/À0.215
À0.03(8)
R1 = 0.0372
wR2 = 0.0877
R1 = 0.0571
wR2 = 0.0977
0.706/À0.895
Largest diff. peak and hole (eÅÀ3
Absolute structure parameter (Flack)
)
1JPF = 712.8 Hz, PF6), 13C{1H} NMR (CDCl3): d = 169.8 (s, COCH2),
166.4 (s, COCH2), 164.9 (t, N = 17 Hz, CH), 136.1 (s, C1, Ph), 134.6
(s C1, Ph) 133.1 (t, N = 10.2 Hz, Ph), 131.8 (t, N = 10.2 Hz, Ph),
131.5 (partially obscured C1, Ph), 130.5 (s, Ph, C4), 128.7 (s, Ph,
C4), 128.6 (m, Ph), 128.5 (m, Ph), 128.3 (s, Ph), 128.2 (s, Ph),
107.5 (t, N = 34.7 Hz, UrP C5) 84.3 (C5H5), 69.9 (CH2), 69.7 (CH2),
Appendix A. Supplementary material
Supplementary data associated with this article can be found, in
the online version, at doi:10.1016/j.ica.2011.10.058.
References
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-
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4.41; N, 4.00. Found: C, 58.58; H, 4.45; N, 3.84%.
: C, 59.01; H,
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We are grateful to the EPSRC (Grant EP/R02178) for funding of
this work and Dr. N.J. Wood for informative discussions.

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