Synthesis and structural characterization of (carbene)ruthenium complexes binding nucleobases

Article abstract of DOI:10.1002/1099-0682(200203)2002:4<935::AID-EJIC935>3.0.CO;2-I

The new (carbene)ruthenium(II) nucleobase derivatives fac,cis-[(PNP)RuCl{C(NHC₄ H₃N₂O₂)(CH₂Ph)}]Cl (5) and fac,cis-[(PNP)RuCl{C(NHC₅H₃N₄) (CH₂Ph)}]Cl (6) [PNP = CH₃CH₂CH₂N (CH₂CH₂PPh₂)₂] were synthesised by treating (vinylidene)ruthenium(II) complex fac,cis-[(PNP)RuCl₂{C= C(H)Ph}] (1) with 5-aminouracil or adenine, respectively. Both complexes were characterized by spectroscopic techniques (IR and NMR) and elemental analyses, which confirmed the formation of the aminocarbene moieties incorporating 1 equiv. of the nucleobase in the complex framework. Crystal and molecular structure determination by X-ray diffraction analysis of the uracil derivative 5 revealed a very unusual O-coordination of the exocyclic C=O group on the C(4) atom of the uracil ring to the ruthenium atom leading to an unprecedented six-membered aminocarbene metallacycle. Wiley-VCH Verlag GmbH, 69451 Weinheim, Germany, 2002.

Full text of DOI:10.1002/1099-0682(200203)2002:4<935::AID-EJIC935>3.0.CO;2-I

FULL PAPER
Synthesis and Structural Characterization of (Carbene)ruthenium Complexes
Binding Nucleobases
[
a]
[b]
[b]
[c]
Jean-Luc Fillaut,* Isaac de los Rios, Dante Masi, Antonio Romerosa,
[b]
[b]
Fabrizio Zanobini, and Maurizio Peruzzini*
Keywords: Carbenes / Ruthenium / Adenine / Uracil / X-ray crystallography / Aminophosphanes
The new (carbene)ruthenium(II) nucleobase derivatives
rating 1 equiv. of the nucleobase in the complex framework.
Crystal and molecular structure determination by X-ray dif-
fraction analysis of the uracil derivative 5 revealed a very
fac,cis-[(PNP)RuCl{C(NHC
fac,cis-[(PNP)RuCl{C(NHC
4
H
H
3
N
3
N
2
2
O
2
)(CH
2
Ph)}]Cl (5) and
5
4
)(CH Ph)}]Cl (6) [PNP
2
=
3
CH CH
2
CH
2
N(CH
2
CH
2
PPh
2
)
] were synthesised by treating unusual O-coordination of the exocyclic C=O group on the
(
vinylidene)ruthenium(II) complex fac,cis-[(PNP)RuCl
2
{C=
C(4) atom of the uracil ring to the ruthenium atom leading to
an unprecedented six-membered aminocarbene metalla-
cycle.
C(H)Ph}] (1) with 5-aminouracil or adenine, respectively.
Both complexes were characterized by spectroscopic tech-
niques (IR and NMR) and elemental analyses, which con-
( Wiley-VCH Verlag GmbH, 69451 Weinheim, Germany,
firmed the formation of the aminocarbene moieties incorpo- 2002)
Introduction
ruthenium anticancer agent showing promising activity
against otherwise resistant tumours and a low systemic tox-
The chemistry of organotransition metal complexes con- icity has recently entered clinical trials.[ Remarkably, bio-
taining biologically important molecules as ligands consti- organometallic compounds conjugating nucleobases with
tutes a recent research field of general interest relevant to typical metalϪcarbon multiple bond species such as carb-
7]
[1]
aspects such as DNA condensation, heavy metal toxicity enes and carbynes have not yet been described in spite of
[
2]
[8]
and mutagenicity, and, in a broader sense, to topics re- the enormous interest in this class of compounds and the
lated to the subject of supramolecular architectures where steadily increasing attention paid to the search of new
metal-to-ligand coordination bonds are intimately com- routes to ruthenium species bio-conjugated with nucleo-
bined with H-bonding interactions. These supramolecular bases.
bio-organometallic aggregates have potential implications
Herein, we wish to report on our results in this area de-
for the design of new metal-based drugs as well as in ma- scribing the first examples of transition metal carbenes in-
[3]
[
4]
terial chemistry.
corporating nucleobases in their molecular structure. No-
The presence of metal ions in these systems introduces ticeably, an unprecedented bonding mode of the uracil moi-
additional variables, whose effects remain largely to be ex- ety to a transition metal ion has been ascertained by X-
plored in detail. These include inter alia the overall charge ray analysis.
of the complex, the oxidation state of the metal atom, the
electronic and steric properties of the coligands and also, in
charged compounds, the nature of the counterion.[
5]
Results and Discussion
Among transition metal ions, ruthenium has unique prop-
[6]
erties making it particularly useful in drug design.
A
Synthesis and Characterization
of the (Carbene)ruthenium Nucleobase Derivatives fac,cis-
[
a]
Institut de Chimie de Rennes, UMR 6509 CNRS Ϫ Universite´
[
(PNP)RuCl{C(NHC H N O )-(CH Ph)}]Cl (5) and
de Rennes 1,
4 3 2 2 2
35042 Rennes, France
fac,cis-[(PNP)RuCl{C(NHC H N )(CH Ph)}]Cl (6)
5 3 4 2
Fax: (internat.) ϩ 33-2/99286939
E-mail: jean-luc.fillaut@univ-rennes1.fr
ISSECC CNR,
In recent years, some of us reported that the reaction of
the (vinylidene)ruthenium(II) complex fac,cis-[(PNP)-
[
[
b]
c]
Via Jacopo Nardi, 39, 50132 Firenze, Italy
Fax: (internat.) ϩ 39-055/247-8366
E-mail: peruz@fi.cnr.it
RuCl
{CϭC(H)Ph}] (1) [PNP
ϭ
CH CH CH N-
2
3 2 2
(
CH CH PPh ) ] with a variety of primary amines is a
2
2
2 2
´
Area de Qu ´ı mica Inorg a´ nica, Facultad de Ciencias, Universidad
simple general method to synthesising the neutral amino-
de Almer ´ı a,
Almer ´ı a, Spain
carbene complexes fac,cis-[(PNP)RuCl {C(NHR)(CH Ph)}]
2
2
Eur. J. Inorg. Chem. 2002, 935Ϫ942

WILEY-VCH Verlag GmbH, 69451 Weinheim, Germany, 2002 1434Ϫ1948/02/0404Ϫ0935 $ 17.50ϩ.50/0
935

J.-L. Fillaut, I. de los Rios, D. Masi, A. Romerosa, F. Zanobini, M. Peruzzini
FULL PAPER
(
2) in excellent yields via the intermediary aminoalkynyl
[
9]
compounds 3. The aminocarbene complexes are air- and
thermally stable in the solid state but slowly decompose in
boiling THF eliminating toluene and forming the corre-
sponding isocyanide complexes fac,cis-[(PNP)RuCl2-
(CϵNR)] (4) (Scheme 1).
Scheme 2
nucleobase and the formation of the expected aminocar-
bene moiety in the complex framework of both 5 and 6,
precious information that shed light on their structures was
inferred from chemical tests. A complete X-ray diffraction
analysis was also obtained for 5 (see below).
Scheme 1
We were intrigued by the generality of the reaction of
Unambiguous evidence for the presence of the aminocar-
1
with primary amines, and so decided to investigate the bene ligands in 5 and 6 was provided by NMR spectroscopy
13
possibility of introducing biologically relevant molecules ([D ]DMSO) that showed the typical C NMR absorptions
such as 5-aminouracil and adenine into the skeleton of the of the aminocarbene carbon atom at δ ϭ 257.9 (t, J
6
2
ϭ
C,P
2
rutheniumϪcarbene moiety. The incorporation of both 5- 13.9 Hz) for 5 and δ ϭ 284.5 (t, JC,P ϭ 19.2 Hz) for 6.
aminouracil and adenine in the ruthenium complex would The magnitude of the coupling constants, which are in the
lead to the building of bifunctional organometallic moieties expected range for Fischer-type (carbene)ruthenium(II)
that could exploit their potential to act as ligands capable complexes points to a trans disposition of the carbene li-
of recognising complementary nucleobases trough hydrogen gand and the nitrogen donor atom of the PNP ligand. The
bond interactions.
IR spectra contained a broad absorption in the NϪH
Ϫ1
With these ideas in mind, we have examined the reactivity stretching region (3500Ϫ3400 cm ), while the uracil deriv-
of the vinylidene complex 1 with a slight excess of 5-amino- ative, in addition, exhibited medium-to-strong bands at
Ϫ1
uracil or adenine. This was done by adapting our general 1720, 1643 and 1621 cm , which were assigned to the
preparation of the aminocarbene complexes 2 for both the stretching of the oxo groups in position 2 and 4 and to the
insolubility of these nucleobases in common organic sol- C(5)ϪC(6) double bond in the uracil residue, respectively.
1
vents and the reluctance of these weak bases to interact In the H NMR spectra, the hydrogen atoms of the benzyl
with the RuϭCϭC fragment under less forceful conditions. substituents are diastereotopic and thus give rise to an AB
A straightforward reaction was obtained by allowing 1 to multiplet, whereas the NH proton of the aminocarbene
react with an excess of either 5-aminouracil or adenine in moiety appears as a very broad singlet at δ ϭ 11.70 (5)
distilled dimethylformamide at ca. 110 °C where both the and δ ϭ 13.90 (6) due to the presence of the quadrupolar
14
nucleobases and the ruthenium precursors are soluble
N-nucleus.
enough. Concentration of the hot solution to dryness under
In keeping with a facial arrangement of the PNP ligand
vacuum left a yellowish residue which was taken up with a and an inequivalent chemical environment of the two phos-
mixture of dichloromethane/ethanol to yield, after workup, phane ends, the 31P{ H} NMR spectra in [D ]DMSO
1
6
a crop of light-yellow microcrystals of fac,cis-[(PNP)- showed slightly perturbed second-order AB splitting pat-
2
RuCl{C(NHC H N O )(CH Ph)}]Cl (5) or orange platelets terns with homonuclear geminal coupling constants J
4
3
2
2
2
P,P
of fac,cis-[(PNP)RuCl{C(NHC H N )(CH Ph)}]Cl (6), re- equal to 32.5 and 27.5 Hz, respectively. The inequivalence
5
3
4
2
spectively (Scheme 2). The uracil derivative could be recrys- of the two P-donor atoms in both 5 and 6 was quite unex-
tallized in air as lemon-yellow needles suitable for an X- pected in view of the facial geometry adopted by the amino-
[10]
ray diffraction study from dichloromethane/petroleum ether diphosphane ligand (δ Ͼ 39) and of the absence of any
P
mixtures. In contrast, several attempts to grow crystals of 6 chiral element in the frame of the nucleobases incorporated
either as chloride or tetraphenylborate salt) were unsuc- in the complexes.[ While a P NMR singlet could be an-
9]
31
(
cessful.
ticipated for a fac,cis-PNP(carbene)Ru complex, the occur-
Apart from conventional spectroscopic techniques (IR rence of an AB system could not be simply explained. On
and NMR spectroscopy) and elemental analysis (see Exp. the basis of the elemental analysis, confirming two chloride
Sect.), which confirmed the incorporation of one equiv. of ligands for each ruthenium atom, a reasonable structural
936
Eur. J. Inorg. Chem. 2002, 935Ϫ942

(Carbene)ruthenium Complexes Binding Nucleobases
FULL PAPER
hypothesis suggested that one of the two chloride ligands Table 1. Selected bond lengths [ A˚ ] and angles [°] for
was no longer coordinated to the metal centre, therefore fac-[(PNP)RuCl{C(NHC
)(CH Ph)}]Cl·CH OH·H O
2
4
H
3
N
2
O
2
2
3
(
3 2
5·CH OH·H O)
acting as the counteranion in a charged complex. In agree-
ment with this hypothesis, both 5 and 6 readily exchanged
one of the two chloride ions with tetraphenylborate when
Ru(1)ϪC(12)
Ru(1)ϪO(1)
Ru(1)ϪP(2)
1.956(6)
2.126(4)
C(12)ϪRu(1)ϪO(1)
C(12)ϪRu(1)ϪP(2)
91.99(19)
100.27(17)
165.25(11)
98.58(17)
85.37(11)
100.71(6)
176.0(2)
84.19(15)
83.33(12)
82.42(12)
86.94(17)
81.15(11)
91.28(6)
165.61(6)
91.20(12)
124.2(4)
128.6(5)
123.9(5)
127.5(5)
118.0(5)
118.3(5)
123.7(5)
121.7(5)
124.3(6)
123.0(6)
112.6(5)
117.5(5)
126.6(5)
115.9(5)
107.5(5)
123.1(4)
128.8(4)
their solutions in CH Cl /EtOH were treated with excess
2
2
2.2792(17) O(1)ϪRu(1)ϪP(2)
2.2847(17) C(12)ϪRu(1)ϪP(1)
2.352(5)
NaBPh . Elemental analysis, IR and NMR spectroscopy, as Ru(1)ϪP(1)
4
Ru(1)ϪN(1)
O(1)ϪRu(1)ϪP(1)
well as solution conductivities (1,2-dichloroethane) clearly
Ru(1)ϪCl(1)
indicated that the tetraphenylborate complexes fac,cis-
O(1)ϪC(11)
2.4631(17) P(2)ϪRu(1)ϪP(1)
1.240(6)
1.203(7)
1.349(7)
1.415(7)
1.368(8)
1.372(7)
1.371(7)
1.386(7)
1.352(7)
1.430(8)
1.528(8)
C(12)ϪRu(1)ϪN(1)
O(1)ϪRu(1)ϪN(1)
P(2)ϪRu(1)ϪN(1)
P(1)ϪRu(1)ϪN(1)
C(12)ϪRu(1)ϪCl(1)
O(1)ϪRu(1)ϪCl(1)
P(2)ϪRu(1)ϪCl(1)
P(1)ϪRu(1)ϪCl(1)
N(1)ϪRu(1)ϪCl(1)
C(11)ϪO(1)ϪRu(1)
C(12)ϪN(2)ϪC(8)
C(10)ϪN(3)ϪC(9)
C(11)ϪN(4)ϪC(10)
C(9)ϪC(8)ϪN(2)
C(9)ϪC(8)ϪC(11)
N(2)ϪC(8)ϪC(11)
C(8)ϪC(9)ϪN(3)
O(2)ϪC(10)ϪN(3)
O(2)ϪC(10)ϪN(4)
N(3)ϪC(10)ϪN(4)
O(1)ϪC(11)ϪN(4)
O(1)ϪC(11)ϪC(8)
N(4)ϪC(11)ϪC(8)
N(2)ϪC(12)ϪC(13)
N(2)ϪC(12)ϪRu(1)
C(13)ϪC(12)ϪRu(1)
[
(PNP)RuCl{C(NHC H N O )(CH Ph)}]BPh
(5-BPh4)
4
3
2
2
2
4
O(2)ϪC(10)
and fac,cis-[(PNP)RuCl{C(NHC H N )(CH Ph)}]BPh (6- N(2)ϪC(12)
5
3
4
2
4
BPh ), were quantitatively produced by metathetical chlo- N(2)ϪC(8)
4
N(3)ϪC(10)
N(3)ϪC(9)
N(4)ϪC(11)
N(4)ϪC(10)
C(8)ϪC(9)
C(8)ϪC(11)
C(12)ϪC(13)
ride substitution.
Crystal Structure of fac,cis-[(PNP)RuCl{C(NHC H N O )-
4
3
2
2
(
CH Ph)}]Cl·CH OH·H O (5·CH OH·H O)
2 3 2 3 2
The easy formation of the tetraphenylborate salts of 5
and 6 raised the question of which structure is attributed to C(13)ϪC(1*5) 1.518(6)
carbenes 5 and 6 where a nucleobase is incorporated with
a (carbene)ruthenium moiety. This makes it of paramount
importance to attain single crystals suitable for an X-ray
diffraction analysis. While for 6 we were unable to grow
well-shaped crystals, the thermal and air robustness of the
uracil derivative makes it feasible to grow crystals of 5 for
the diffraction study from a saturated dichloromethane/
methanol solution in air. Thus, in order to collect geomet-
rical information on this class of aminocarbenes, an X-ray
analysis was carried out on a single crystal of 5. An ORTEP
drawing of the complex is shown in Figure 1 with the ad-
opted atomic numbering scheme. A list of selected bond
lengths and angles is given in Table 1.
C(1*5)ϪC(13)ϪC(12) 118.6(5)
In
the
structure
of
fac,cis-[(PNP)RuCl{C-
(5·CH OH·
(
NHC H N O )(CH Ph)}]Cl·CH OH·H O
4
3
2
2
2
3
2
3
H O), formed by fac,cis-[(PNP)RuCl{C(NHC H N O )-
2
4
3
2
2
ϩ
vate molecules of methanol and water in a 1:1:1:1 ratio, the
arrangement of the non-hydrogen atoms about the metal
atom in the cation is approximately octahedral with the
aminodiphosphane ligand occupying three facial coordina-
tion sites. A chloride ligand and one aminocarbene group
incorporating the 5-aminouracil fragment and located trans
to the PNP nitrogen donor, are also coordinated to the
metal centre. The coordination polyhedron about the ruthe-
nium atom is completed by O-coordination from the exo-
cyclic CϭO group on the C(4) atom of the uracil ring. The
arrangement found in 5 does not significantly differ from
that established in the related aminocarbene derivative
(
CH Ph)}] cations, chloride anions and interspersed sol-
2
fac,cis-[(PNP)RuCl {C[NH(S)-(Ϫ)-CH(Me)(1-naphthyl)]-
2
(
CH Ph)}], which was also authenticated by X-ray
2
[9]
methods, as well as in other PNPruthenium(II) com-
plexes.[
10,11]
Bond lengths and angles match well with the
data reported for other (aminocarbene)ruthenium com-
plexes.[
9,12]
Cocrystallised molecules of methanol and water,
the latter likely taken from the air, contribute to the stability
of the crystal lattice. As a matter of fact, a net of hydrogen
bonding interactions involves the uracil N(4), the methanol
O(3) and the water O(4) atoms, the most important con-
tacts being N(4)···O(3) 2.79 A and O(3)···O(4) 2.72 A. Ad-
ditionally, the O(4) water atom shows weak interactions
Figure 1. ORTEP drawing of the complex cation fac,cis-
ϩ
[
4 3 2 2 2
(PNP)RuCl{C(NHC H N O )(CH Ph)}] ; only the ipso-carbon
˚
˚
atoms of the PNP phenyl substituents are shown for the sake of
clarity
Eur. J. Inorg. Chem. 2002, 935Ϫ942
937

J.-L. Fillaut, I. de los Rios, D. Masi, A. Romerosa, F. Zanobini, M. Peruzzini
˚
FULL PAPER
˚
with both chlorine atoms [3.24 A with Cl(1), 3.31 A with distances pertaining to the uracil residue in 5, which rules
Cl(2)].
out the occurrence of a ketoimine equilibrium involving
The most notable feature of the crystal structure of 5 is N(4) and O(2). The closeness of two positive charges in V
the unexpected metallation of the CϭO group at the 4-posi- also agrees with this observation. In accordance with a sig-
1
tion of the uracil moiety, that, therefore, behaves as an η - nificant contribution from the structures II and III, both
monodentate ligand through the exocyclic oxygen atom. C(9)ϪN(3) and C(11)ϪN(4) bond lengths are slightly
The complexation of one of the carbonyl groups of the ur- shorter in 5 than in the free uracil while the separations
acil ligand to the ruthenium centre was quite surprising and C(9)ϪC(8) and C(8)ϪC(11) are longer and shorter, respec-
has no precedents in this series of PNP(carbene)Ru deriva- tively, with respect to the free nucleobase. On the basis of
tives. In this regard, it is remarkable to underline that the all these findings, it is conceivable that form I corresponds
reaction of 1 with several α,ω-diamines parallels that estab- to the closest representation of the cationic complex 5.
lished for simple monoamines and resulted in the synthesis
Although one of the two carbonyl groups of the uracil
of (aminocarbene)ruthenium complexes with a pendant, moiety is blocked by coordination to the ruthenium centre,
noncoordinated, amino arm.[
13]
preventing H-bonding, 5 still presents a potential hydrogen
Although few examples of transition metal complexes bond donor/hydrogen bond acceptor/hydrogen bond donor
containing uracil residues have been described so far,[
5a,14a]
arrangement (DAD), capable of forming hydrogen bonds
[16]
the arrangement found in 5, where the nucleobase with molecules containing complementary ADA or AD
metallates through one carbonyl group, is unpreceden- ends (Scheme 4).
[
14]
˚
ted. The C(11)ϪO(1) bond length [1.240(6) A] of the car-
bonyl group involved in the intramolecular interaction with
the ruthenium atom [the O(1)ϪRu separation is 2.126(4)
˚
˚
[15]
A], even if longer than in free uracil [1.227(2) A],
does
not significantly differ from that observed in the known
uracil derivatives containing metal complexes.[
5a,14a]
This
points to a weak interaction between the uracil moiety and
the ruthenium centre. The two rings deriving from the Scheme 4
adopted geometry of the (aminocarbene)ruthenium com-
The formation of centrosymmetric [2ϩ2] ‘‘dimer pairs’’
plex with 5-aminouracil are virtually planar. In order to
analyse the influence of the coordination of one uracil car-
bonyl group to the ruthenium centre, the bond lengths of
the uracil ring in 5 have been compared with those deter-
by association of NϪH···O hydrogen bonds between an
amide NϪH group of one molecule of 5 with the ‘‘free’’
carbonyl oxygen atom of a second molecule of 5 and vice
versa could be expected. Actually, the analysis of the crystal
packing of 5 does not permit us to detect any links via
hydrogen bonds between independent molecules, even if
geometrical complementarity is unaltered.
mined for the free ligand.[15] Five different valence isomers
may be drawn in which the positive charge is moved from
the metal atom to the nitrogen atoms N(3) and N(4)
(Scheme 3).
NMR Spectroscopic Studies of the H-Binding Properties of
the (Aminocarbene)ruthenium Complexes 5 and 6
Because of coordination to the metal centre in 5 (and 6),
it is evident that the ‘‘usual’’ H bonding at the uracil (or
adenine) fragment is not possible. Nevertheless, the new
aminocarbenes 5 and 6 bear appropriate hydrogen bonding
molecular recognition sites, which could, in principle, still
form non-covalent host-guest assemblies with suitable sub-
strates.[
5a,17]
Therefore, in order to assess this property, we
1
decided to study how the H NMR chemical shift of the
NϪH protons of 5 and 6 change as a function of the sample
concentration and of the presence of substrates with com-
Scheme 3. Structure of the possible valence isomers for the metal
modified uracil ring in 5
[18]
plementary hydrogen-bonding recognition sites.
At first,
we noticed that, independently from the solvent used,
A perusal of the bond lengths listed in Table 1, suggests (CD Cl or CD CN), the NϪH chemical shift of both 5
2
2
3
that both IV and V, in which the oxygen atom O(2) bears a and 6 is not concentration-dependent. Whereas this fact is
negative charge, do not provide a major contribution to the quite intriguing and suggests that dimerisation of these nu-
representation of 5, and, in keeping with this hypothesis, cleobase aminocarbenes does not occur through hydrogen
˚
the ‘‘distal’’ C(10)ϪO(2) separation (1.203 A), which is typ- bonding, it can be related with the information derived
ical of a CϭO double bond, is shorter in 5 than in the free from the X-ray study of 5. This behaviour does not have a
˚
[15]
uracil molecule [1.218(2) A]. In contrast, the C(10)ϪN(4) clear explanation as electrostatic repulsions between cat-
bond length is definitely longer than all the other CϪN ionic organometallic species, steric hindrance due to the
938
Eur. J. Inorg. Chem. 2002, 935Ϫ942

(Carbene)ruthenium Complexes Binding Nucleobases
FULL PAPER
presence of bulky ancillary ligands,[19] or even changes in
the electronic distribution in the metal-bounded nucleo-
[
20]
bases, could be responsible. In order to understand better
this piece of evidence, we unsuccessfully attempted to detect
1
by H NMR spectroscopy the formation of hydrogen bond-
ing adducts of 5 in the presence of adenine. The latter could
indeed act as a neutral sterically nondemanding molecule
with a DA (DA ϭ donor/acceptor)[ motif capable of ut-
ilising only one hydrogen bond acceptor and donor motif
of the uracil derivative 5 in a WatsonϪCrick manner.[
This negative result could suggest that either electrostatic
repulsions or steric hindrance at the approaching of a com-
plementary motif to the metal-modified uracil are not de-
cisive. In any case, it can be anticipated that O-binding of
the uracil ring to a metal ion significantly disturbs its elec-
tronic complementarity with the adenine partner.
16]
16,17]
Mechanism of the Formation of the Nucleobase Carbene
Complexes
The mechanism accounting for the formation of the vast
family of PNP aminocarbene derivatives by nucleophilic at-
tack of primary amines to the (vinylidene)ruthenium com-
plex 1 encompasses a well-established pathway requiring 2
Scheme 5
[
9,10]
In summary, the first amine equivalent tion at 2050 cmϪ1 assigned to the phenylethynyl ligand in
equiv. of amine.
deprotonates the vinylidene C carbon atom, while the se- 7. Heating the [D ]DMSO solution of 7 at 65 °C turns the
β
6
cond one coordinates the metal centre prior to be trans- light yellow colour to greenish yellow as 7 transforms into
ferred, by an intramolecular nucleophilic attack, on the Cα a new compound still exhibiting an AB spin system in the
carbon atom of the alkynyl intermediate (Scheme 1).
The synthetic route to both 5 and 6 most likely goes species, assigned to the nonmetallated neutral (amino-
through a related pathway with the obvious changes ex- carbene)ruthenium
complex fac,cis-[(PNP)RuCl {C-
pected by the formation of the metallated aminocarbenes. (NHC H N )(CH Ph)}] (8), is accompanied by the appear-
phosphorus NMR spectrum. The formation of this latter
2
5
3
4
2
In the case of 6, the N(7) atom of the adenine is responsible ance of the final metallated derivative 6. In keeping with
for chelation at the ruthenium centre affording the unpre- the accepted mechanistic hypothesis, on transforming 7 into
cedented cyclic adeninylcarbene 6. Remarkably, once 8 (and then into 6), the informative AB system of the dia-
formed, 5 is much more robust than 6 indicating that the stereotopic benzylic CH protons and the featureless NH
2
1
RuϪOϭC interaction involving the uracil system is much signal of the aminocarbene (δ ϭ 11.91) rises in the H
more stable than the RuϪN(7) interaction of the aminocar- NMR spectrum indicating that the intramolecular ruthe-
bene deriving from adenine.
Monitoring the reaction between 1 and adenine in an curred along the CϭC moiety of the vinylidene ligand. The
nium-mediated attack of the adenine-NH end has just oc-
2
1
31
NMR tube via H and P NMR spectroscopy is a straight- conversion of 8 into 6 is not completed at 65 °C in 1 d and
forward method to providing experimental evidence for the goes to completion only after prolonged heating at 95 °C.
proposed mechanism as well as confirming that for 6, the A perusal of the collected pieces of evidence makes it rea-
final reaction product is an N(7)-metallated adeninylcar- sonable to assign 6 to a structure similar to that ascertained
bene (Scheme 5). In the case at hand, when 2 equiv. of aden- in 5 by X-ray methods.
ine are dissolved in a 5-mm NMR tube containing a solu-
tion of 1 in [D ]DMSO and the solution is monitored by
6
31
P NMR spectroscopy, a neat reaction takes place at room Conclusions
temperature affording a single compound displaying a well-
resolved AB spin system at δ ϭ 53.90 and 52.01 with JP,P
5.2 Hz. The latter derives from the chemical inequivalence transition metal carbenes incorporating nucleobases such as
of the two PPh groups in the adenine complex fac,cis- adenine and 5-aminouracil. Surprisingly these novel bio-or-
ϭ
In this paper we have described the first examples of
3
2
[
(PNP)RuCl(CϵCPh)(NH C H N )}] (7) that forms after ganometallic derivatives exploit a new coordination mode
2
5
3
4
the substitution of one chloride ligand by an amine. At- towards a ruthenium centre. Thus, in the 5-aminouracil de-
tempts to isolate 7 by stripping off DMSO at room temper- rivative a six-membered ring is closed by metallation of the
ature leave a yellowish residue whose 3 P NMR spectrum oxo group on C(4) while in the adenine complex the amino-
denies a simple analysis owing to the accompanying pres- carbene uses the nitrogen atom N(7) to coordinate the
ence of several unidentified products. Nevertheless, the IR ruthenium atom. This behaviour is quite surprising and has
spectrum of this solid species exhibits a sharp IR absorp- no precedents either in the series of PNP(carbene)Ru
1
Eur. J. Inorg. Chem. 2002, 935Ϫ942
939

J.-L. Fillaut, I. de los Rios, D. Masi, A. Romerosa, F. Zanobini, M. Peruzzini
FULL PAPER
2
1
derivatives, or, to the best of our knowledge, in the coor- system: δ
ϭ 55.24, δ
]DMSO, 299.94 MHz): δ ϭ 12.4 [br, 2 H, NH(uracil)],
1.70 [s, 1 H, NH(aminocarbene)], 8.04 [s, 6-H, 1 H, CH(uracil)],
B A B
ϭ 50.14, J(P ,P ) ϭ 32.5 Hz. H NMR
A
(
22 °C, [D
6
dination chemistry of these nucleobases. As a final consid-
eration, it can be stressed that the present coordination
mode of the two nucleobases has an important influence on
their hydrogen-bonding pattern.
1
5
3
13
1
.13 (CH
2
Ph), 4.75 [AB system, JH,H ϭ 16.9 Hz, 2 H]. C{ H}
]DMSO, 75.42 MHz): δ ϭ 257.9 [t, 2JC,P
3.9 Hz, RuϭC], 161.3 [CϭO(uracil)], 149.1 (s, C-2 and C-4), 118.0
NMR (22 °C, [D
1
6
ϭ
3
[
s, C-6, CϭCH(uracil)], 66.0 [br d, JC,P ϭ 2.2 Hz, CH
2
Ph].
Synthesis of fac,cis-[(PNP)RuCl{C(NHC )(CH Ph)}]Cl (6): A
threefold excess of adenine (0.22 g, 1.63 mmol) was added at room
5
H
3
N
4
2
Experimental Section
temperature to a stirred suspension of the vinylidene complex 1
General Procedures: Dimethylformamide (DMF), n-hexane and
dichloromethane were purified by distillation under nitrogen over
(
0.40 g, 0.53 mmol) in 20 mL of DMF. The reaction mixture was
stirred for 10 min and then gently heated to about 110 °C. Heating
was continued for 30 min to afford a light orange solution, which
was concentrated to dryness under vacuum. The crude orange ma-
terial was combined with two portions (10 mL each) of hot di-
chloromethane and the excess of unchanged adenine was separated
by filtration through a cotton plug. Addition of n-hexane (8 mL)
and concentration of the orange solution under nitrogen gave or-
ange yellowish crystals of the aminocarbene complex 6 that were
recrystallised from dichloromethane/n-hexane (2:1). Yield ca. 74%.
2 5
molecular sieves, sodium and P O , respectively. Adenine and 5-
aminouracil were purchased from Aldrich and used as received. All
the other reagents and chemicals were reagent grade and, unless
otherwise stated, were used as received from commercial suppliers.
All reactions and manipulations were routinely performed under
dry nitrogen by using standard Schlenk-tube techniques. The solid
complexes were collected on sintered glass-frits and washed with
light petroleum ether (b.p. 40Ϫ60 °C) before being dried in a stream
(PNP)[
3 2 2 2 2 2 2
CH CH N(CH CH PPh )
21]
of nitrogen. The ligand CH
and the vinylidene complex fac,cis-[(PNP)RuCl
44 2 6 2
C H46Cl N P Ru (892.81): calcd. C 59.19, H 5.19, N 9.41; found
2
{CϭC(H)Ph}]
were prepared as described in the literature. [D ]DMSO
for NMR measurements (Aldrich) was dried with molecular sieves
Ϫ1
˜
ϭ 3480Ϫ3350 cm
(br, νNH).
[
10b]
C 58.87, H 5.20, N 9.22. IR: ν
(1),
6
3
1
1
P{ H} NMR (22 °C, [D
6
]DMSO, 81.01 MHz): AB system: δ
) ϭ 27.5 Hz. H NMR (22 °C, [D
A
2
1
1
13
1
47.74, δ
B
39.21, J(P
A
,P
B
6
]DMSO,
(
0.4 nm). H and C{ H} NMR spectra were recorded with Varian
2
99.94 MHz): δ ϭ 13.9 [br. d, JH,P ϭ 12.4 Hz, 1 H, NH(aminocar-
VXR 300 or Bruker AC200 spectrometers operating at 299.94 or
1
13
bene)], 8.75 [s, 1 H, NH(adenine)], 8.62 [CH(adenine)], 7.90 (s, 2
2
00.13 MHz ( H) and 75.42 or 50.32 MHz ( C), respectively. Peak
3
H, 2-H ϩ 8-H), 5.88 (CH
2
Ph), 5.25 [AB system, JH,H ϭ 16.8 Hz,
positions are relative to tetramethylsilane and were calibrated
1
3
1
1
2 H]. C{ H} NMR (22 °C, [D ]DMSO, 75.42 MHz): δ ϭ 284.5
[t, JC,P ϭ 19.2 Hz, RuϭC ], 154.7 [s, C-5(adenine)], 152.6 [s, C-
6
against the residual solvent resonance ( H) or the deuterated solv-
2
13
13
ent multiplet ( C). C-DEPT-135 experiments were run with the
Bruker AC200 spectrometer. 3 P{ H} NMR spectra were recorded
1
1
2(adenine)], 146.8 [s, C-4(adenine)], C-8(adenine) not observed,
likely masked by aromatic resonances, 56.3 (s, CH Ph).
2
with the same instruments operating at 121.42 and 81.01 MHz, re-
spectively. Chemical shifts were measured relative to external 85%
H PO with downfield values taken as positive. Infrared spectra
3 4
Synthesis of fac,cis-[(PNP)RuCl{C(NHC
4
H
3
N
2
O
2
)(CH
fac,cis-[(PNP)RuCl{C(NHC
): Metathetical reaction of 5 or
(2 equiv.) in CH Cl
tetraphenylborate salts fac,cis-[(PNP)RuCl{C(NHC
2
Ph)}]-
(
(
BPh
CH
4
)
(5-BPh
4
)
and
5
H
3
N
4
)-
6
were recorded as Nujol mulls with a PerkinϪElmer 1600 series FT-
IR spectrometer between KBr plates. The molar conductivities
were measured with an AMEL model 134 conductance cell con-
nected with a model 101 conductivity meter. The conductivity data
2
Ph)}](BPh
4
)
(6-BPh
4
with NaBPh
4
2
2
/EtOH (2:1) yielded the
)-
4
H
3
N
2
O
2
(
{
CH
C(NHC
yields. 5-BPh
.45, 4.81; found
66BClN Ru (1176.59): calcd. C 69.42, H 5.65, N 7.14; found
C 69.56, H 5.42, N 6.84. ΛM(5-BPh4) ϭ 26 Ω cm mol (295 K,
2
Ph)}](BPh
4
)
(5-BPh
Ph)}](BPh
63BClN
4
)
and
) (6-BPh
Ru (1165.54): calcd. C 69.04, H
fac,cis-[(PNP)RuCl-
) in almost quantitative
Ϫ3
were obtained at sample concentration of 10  in 1,2-dichloro-
5
H
3
N
4
)(CH
2
4
4
ethane solution at room temperature (22 °C). Elemental analyses
4
: C67
H
4
O
2
P
2
(C,H,N) were performed using a Carlo Erba model 1106 ele-
5
C
N
C
69.67, 5.65, 4.59. 6-BPh :
H
N
4
mental analyser.
68
H
6 2
P
Ϫ1
2
Ϫ1
4 3 2 2 2
Synthesis of fac,cis-[(PNP)RuCl{C(NHC H N O )(CH Ph)}]Cl (5):
Ϫ1
2
Ϫ1
in 1,2-dichloroethane). ΛM(6-BPh4) ϭ 24 Ω cm mol (295 K, in
1
A fourfold excess of 5-aminouracil (0.27 g, 2.12 mmol) was added
in small portions at room temperature to a stirred suspension of
the vinylidene complex 1 (0.40 g, 0.53 mmol) in 30 mL of dichloro-
methane. The reaction mixture was stirred for 30 min and then
DMF (15 mL) was added and the temperature gently raised to
evaporate all the dichloromethane and then to about 110 °C. Heat-
ing was continued for 30 min to afford a light yellow solution,
which was concentrated to dryness under vacuum. The crude yel-
lowish material was taken with two portions (10 mL each) of a 1:2
mixture of ethanol and dichloromethane and the excess of un-
changed 5-aminouracil was separated by filtration of the hot solu-
tions. The filtered yellow solutions were collected in an Erlenmeyer
flask and concentrated to ca. 5 mL. Addition of petroleum ether
,2-dichloroethane).[ IR: ν˜ ϭ 612 cmϪ1 (m, νBC).
22]
In situ NMR Spectroscopic Study of the Reaction of 1 and Adenine:
A 5-mm NMR tube was filled under nitrogen with 1 (20 mg,
0
(
.026 mmol), adenine (7 mg, 0.052 mmol) and [D
6
]DMSO
0.8 mL). P{ H} NMR monitoring of the reaction showed
the fast and complete conversion of into fac,cis-
(PNP)RuCl(CϵCPh)(NH )}] (7). After 2 h, when 7 was
31
1
1
[
2 5 3 4
C H N
the only ruthenium complex, the temperature of the probehead was
raised to 65 °C and the NMR analysis showed a slow conversion
of
7
into
Ph)}] (8) and 6 {after 12 h: 8 (68%), 6 (30%), mer,trans-
(CO)] (2%)}. Heating to 95 °C completed the trans-
2 5 3 4
a mixture of fac,cis-[(PNP)RuCl {C(NHC H N )-
(
CH
2
[(PNP)RuCl
2
(3 mL) and slow concentration in air gave lemon-yellow crystals of
formation of 8 into 6 in 24 h, but caused the formation of several
unidentified compounds {after 24 h at 95 °C: 6 (81%), 8 (5%),
mer,trans-[(PNP)RuCl (CO)] (3%), fac,cis-[(PNP)RuCl (CO)] (2%),
2 2
the aminocarbene complex 5 that were recrystallised from dichloro-
methane and methanol in air to yield the solvate salt
3 2 2 4 4 2
5·CH OH·H O. Yield ca. 82%. C44H49Cl N O P Ru (931.16):
unidentified compounds (9%, δ ϭ 46.9, 36.5, 34.9 all singlets)}.
calcd. C 56.72, H 6.01, N 5.30; found C 56.39, H 5.89, N 6.10. IR:
1
ν˜ ϭ 3400 (br, m, νNH), 1720 (s, νCϭO), 1643 (s, νCϭOϪRu), 1621 (sh, fac,cis-[(PNP)RuCl(CϵCPh)(NH
2
C
5
H
3
N
)}] (7): 31P{ H} NMR
4
Ϫ1 31
1
νCϭC) cm
.
P{ H} NMR (22 °C, [D
6
]DMSO, 121.42 MHz): AB (22 °C, [D
6
]DMSO, 121.42 MHz): AB system: δ
A B
53.90, δ 52.01,
940
Eur. J. Inorg. Chem. 2002, 935Ϫ942

(Carbene)ruthenium Complexes Binding Nucleobases
FULL PAPER
2J(P
) ϭ 35.2 Hz. H NMR (22 °C, [D
1
]DMSO, 299.94 MHz): gen atoms were found through a series of F
6
A
,P
B
0
Fourier maps. Refine-
2
δ ϭ 3.21 (br. s, 2 H, NH , superimposed to aliphatic resonances of ment was done by full-matrix least-squares calculations, initially
PNP ligand), , 8.60 [NH(adenine) and CH(adenine)], 8.52, 7.85 (all
s, NH, 2-H, 8-H, 3 H).
with isotropic thermal parameters, and then, in the last least-
squares cycle, with anisotropic thermal parameters for all atoms,
except the solvents ones. All of the phenyl rings were treated as
1
fac,cis-[(PNP)RuCl
2
{C(NHC
5
H
3
N
4
)(CH
2
Ph)}] (8): 31P{ H} NMR
˚
rigid bodies with D6h symmetry and CϪC distances fixed at 1.39 A.
(
22 °C, [D ]DMSO, 121.42 MHz): AB system: δ
J(P ,P ) ϭ 28.0 Hz. H NMR (22 °C, [D
A B 6
6
A
49.69, δ
]DMSO, 299.94 MHz):
1.91 [br. s, 1 H, NH(aminocarbene)], , 8.88 [NH(adenine) ϩ
CH(adenine)], 8.56, 8.21 (all s, NH, 2-H, 8-H, 3 H), 5.04 (CH Ph),
.87 [AB system, JH,H ϭ 17.1 Hz, 2 H]. C{ H} NMR (22 °C,
]DMSO, 75.42 MHz): 279.9 [t, 2JC,P ϭ 13.6 Hz, RuϭC], 163.7
s, C-5(adenine)], 156.1 [s, C-2(adenine)], 141.3 [s, C-4(adenine)], C-
(adenine) and C-8(adenine) not observed, likely masked by aro-
B
37.99,
Hydrogen atoms of the PNP ligand were introduced in calculated
positions, but not refined. At an advanced stage of the refinement,
two solvent molecules, one of methanol and the other of water,
were located in the Fourier map and successfully refined. CCDC-
2
1
1
2
3
13
1
4
1
3 2
72155 (5·CH OH·H O) contains the supplementary crystallo-
[
[
D
6
graphic data for this paper. These data can be obtained free of
charge at www.ccdc.cam.ac.uk/conts/retrieving.html or from the
Cambridge Crystallographic Data Centre, 12, Union Road, Cam-
bridge CB2 1EZ, UK [Fax: (internat.) ϩ 44-1223/336-033; E-mail:
deposit@ccdc.cam.ac.uk].
6
3
matic resonances, 62.6 [t, JC,P ϭ 1.9 Hz, CH
2
Ph].
X-ray Diffraction Study of fac,cis-[(PNP)RuCl{C(NHC
4 3 2 2
H N O )-
(
CH Ph)}]Cl·CH OH·H (5·CH OH·H O): lemon-yellow
2
3
2
O
3
2
A
crystal of 5·CH OH·H
3
2
O was chosen for an X-ray analysis. A sum- Acknowledgments
mary of crystal and intensity data for the compound is presented
in Table 2. Experimental data were recorded at room temperature
with an ENRAF-NONIUS CAD4 diffractometer using graphite-
The authors wish to thank the COST Action D17/003 of the Euro-
pean Community for promoting this scientific activity and for a
travel grant to J. L. F. to Florence. This work was also supported
by the bilateral program ‘ ‘A zione Integrata’’ between the Univer-
sities of Ferrara (Italy) and Almeria (Spain) and NATO (project
PST.CLG.978521). Thanks are expressed to Dr. Annabella
Orlandini (ISSECC CNR, Florence, Italy) for helpful discussions.
α
monochromated Mo-K radiation. A set of 25 carefully centred
reflections in the range 7.5° Յ θ Յ 9° was used for determining
the lattice constants. As a general procedure, the intensity of three
standard reflections was measured periodically every 2 h for ori-
entation and intensity control. This procedure did not reveal any
decay of intensities. The data were corrected for Lorentz and po-
larisation effects. Atomic scattering factors were those tabulated by
Cromer and Waber with anomalous dispersion corrections taken
from ref. An empirical absorption correction was applied via Ψ
scan with transmission factors in the range 1.0Ϫ0.9. All the calcu-
lations were performed using the WINGX package
SHELX97
equivalent isotropic thermal parameters of all atoms and structure
factors are available as supplementary material. All the non-hydro-
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[
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(
(PNP)RuCl{C(NHC
5·CH OH·H O)
4
H
3
N
2
O
2
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2
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[
7] [7a]
Empirical formula
Formula mass
Temperature
Wavelength
Crystal system, space group
Unit cell dimensions
44 2 4 4 2
C H49Cl N O P Ru
931.16
7b]
293(2) K
0.71069 A
monoclinic, P2
˚
[
1
/n
K. H. Dötz, H. Fischer, P. Hoffmann, F. R. Kreissl, U.
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a ϭ 15.682(9) A
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c ϭ 19.748(2) A
4311(3) A
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3
Z, calculated density
Absorption coefficient
F(000)
Crystal size
θ range for data collection
Limiting indices
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Ϫ1
0.609 mm
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Յ k Յ 15, 0 Յ l Յ 21
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5596/0/443
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[14] [14a]
1.016
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0.893 and Ϫ0.484 eA
Ϫ3
Largest diff. peak and hole
4
Eur. J. Inorg. Chem. 2002, 935Ϫ942
941

J.-L. Fillaut, I. de los Rios, D. Masi, A. Romerosa, F. Zanobini, M. Peruzzini
FULL PAPER
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