Ruthenium-thiobase complexes: Synthesis, spectroscopy, density functional studies for trans,cis,cis-[RuII(AsPh3)2 (N,S-2-Thiopyrimidinato)2] and structural analysis of selected weak C-H?N and C-H?S interactions

Article abstract of DOI:10.1016/j.ica.2007.07.026

The reaction of trans-[Ru^III(AsPh₃)₂Cl ₃(CH₃OH)] (green powder) with 2-thiopyrimidine-1,3, HTPYM, in ethanol, produced red crystals of trans,cis,cis-[Ru^II(AsPh₃)₂(N,S-

Full text of DOI:10.1016/j.ica.2007.07.026

Available online at www.sciencedirect.com
Inorganica Chimica Acta 362 (2009) 1011–1021
www.elsevier.com/locate/ica
Ruthenium-thiobase complexes: Synthesis, spectroscopy,
density functional studies for trans,cis,cis-[RuII(AsPh3)2
(N,S-2-Thiopyrimidinato)2] and structural analysis of selected weak
C–Hꢀ ꢀ ꢀN and C–Hꢀ ꢀ ꢀS interactions
a,
*
a
a
b
b
Gabriella Tamasi , Sandra Defazio , Luisa Chiasserini , Alessandro Sega , Renzo Cini
a
Department of Chemical and Biosystem Sciences and Technologies, University of Siena, Via Aldo Moro 2, I-53100 Siena, Italy
b
Department of Medicinal Chemistry, University of Siena, Via Aldo Moro 2, I-53100 Siena, Italy
Received 5 April 2007; accepted 21 July 2007
Available online 6 August 2007
This study is dedicated to Professor Dr. Bernhard Lippert, University of Dortmund
Abstract
The reaction of trans-[RuIII(AsPh3)2Cl3(CH3OH)] (green powder) with 2-thiopyrimidine-1,3, HTPYM, in ethanol, produced red crys-
tals of trans,cis,cis-[RuII(AsPh3)2(N,S-2-thiopyrimidinato)2]. The compound has two TPYMꢁ chelating anions in the equatorial plane,
whereas the As atoms occupy the apical positions. It is stable in the solid state but the yellow chloroform solutions turn to green quickly
˚
in air atmosphere. The Ru–As, Ru–S and Ru–N bond distances average 2.432(1), 2.440(2) and 2.078(6) A, respectively. The AsPh3
ligands assume a semi-trefoil C1 arrangement and have C–Hꢀ ꢀ ꢀS intra-molecular hydrogen bond type interactions to TPYMꢁ ligands.
These latter ligands are also involved in C–Hꢀ ꢀ ꢀN and C–Hꢀ ꢀ ꢀS interactions that pair two thiobase ligands via an unusual way. Density
functional computational studies on [Ru(AsH3)2(N,S-TPYM)2] model molecules show that the cis,cis,trans isomer is more stable than the
trans,cis,cis one by some 5 kcal molꢁ1
.
ꢀ 2007 Elsevier B.V. All rights reserved.
Keywords: Ruthenium complex; Thiobase; DFT; XRD; Hydrogen bonds
1. Introduction
of inorganic chemists in the past half century. Selected
fields that were related to these species are basic coordina-
tion chemistry, catalysis, electrochemistry, spectroscopy
and bio-inorganic chemistry. In spite of the very many sci-
entific reports, much work remains to be done, at least
from preparative, spectroscopy, theoretical and reactivity
with bio-molecules stand points.
It is known that thiobases like thiopurines and thiopyr-
imidines have anti-cancer, anti-viral properties by their
own [6–9]. Thus, the combination of such ligands with met-
als like ruthenium and other ‘‘block-d’’ metals could hope-
fully produce pharmacologically active complexes whose
action comes from synergic effects by the metal and the
ligand, once the coordination molecule dissociates in the
target tissue [2a,10–12].
The synthesis of new ‘‘platinum group’’ complexes with
purine/pyrimidine derivatives as ligands or the synthesis of
complexes able to react with bio-molecules like aminoac-
ids, nucleobases, proteins, and nucleic acids is a matter that
attracts much efforts nowadays because the well-known
anti-cancer, anti-metastase, anti-bacterial activity shown
by several of analogous species in the past [1–5]. Further-
more, the chemistry of Ru–XR3 derivatives, where X is a
pnictogen element, has much fascinated the community
*
Corresponding author.
E-mail address: cini@unisi.it (R. Cini).
0020-1693/$ - see front matter ꢀ 2007 Elsevier B.V. All rights reserved.
doi:10.1016/j.ica.2007.07.026

1012
G. Tamasi et al. / Inorganica Chimica Acta 362 (2009) 1011–1021
a
b
S
SH
S
2
3
H
H
N
H
H
N
N
N
-H+
N
6
N
1
-
4
H
H
H
H
H
H
H
5
H
H
H
c
H
H
H
H
H
As
As
As
S
H
S
S
N
Ru
N
H
N
Ru
As
N
S
N
N
N
H
H
H
H
H
H
H
H
H
N
H
H
H
H
H
Ph
e
d
Ph
Ph
Ph
As
Ph
As
As
S
Ph
Ph
Ph
Ph
S
Ru
N
N
S
N
S
H
Ru
N
N
N
N
H
H
H
N
H
As
Ph
H
Ph
Ph
H
H
H
H
H
Scheme 1. Sketches for the selected molecules studied in this work. The molecules were also optimized via DFT-B3LYP methods in this work. (a) 2-
thiopyrimidine-1,3 (HTPYM). (b) trans,cis,cis-[Ru(AsH3)2(N,S-TPYM)2]. (c) cis,cis,trans-[Ru(AsH3)2(N,S-TPYM)2]. (d) trans,cis,cis-[Ru(AsPh3)2(N,S-
TPYM)2] (Ph = phenyl). (e) cis,cis,trans-[Ru(AsPh3)2(N,S-TPYM)2].
Furthermore, arsenic derivatives (mostly arsenic triox-
ide and arsenites, but even arsenic sulfides like As4S4) are
much investigated for their anti-leukemia properties [13].
An important finding that came from structural studies at
the solid state for several metal-nucleobase complexes was
the existence of unexpected hydrogen bond type interactions
as unusual base-pairing schemes. This fact had major contri-
butions from Lippert’s group [see for example: 1g,14].
Through the works carried out on some ruthenium-thio-
base complexes in this laboratory in the past, it appeared
that starting complexes that contain XR3 ligands are versa-
tile materials to obtain definite, crystalline compounds with
ligands of biological interest like purines and pyrimidines.
Most of the data collected in the field of Ru–XR3 species
by others and by some of us were relevant to phosphines
(X = P) as co-ligands, whereas corresponding complexes
with arsines and stibines were not much investigated. It
was shown that thiopurines react with [Ru(AsPh3)2Cl3-
(CH3OH)] in a way to cause the reduction of the metal cen-
ter and to form bis-chelates via Ru–S6/N7 coordinate
bonds. The complexes were characterized via spectroscopy
but resisted several efforts aimed at growing single crystals
suitable for X-ray diffraction studies.
On the basis of these premises, the research work on Ru–
XR3-thiobase complexes continued in this laboratory, by
extending the investigations to thiopyrimidines and by pay-
ing special attention to unusual weak hydrogen bond type
interactions and unusual base pairings [12b]. Here we wish
to report on the synthesis, X-ray structure, spectroscopy
and theoretical analysis for a Ru(II) complex with 2-thio-
pyrimidine-1,3 (HTPYM) (Scheme 1a) and AsPh3 ligands.
2. Experimental
2.1. Materials
The compounds RuCl3 Æ 3H2O (Ega), AsPh3 (Merck),
HTPYM (Sigma) were used without any further purifica-
tion. Absolute ethanol, methanol and acetonitrile were
analytical grade products from Merck.
2.2. Synthesis
[RuIII(AsPh3)2Cl3(CH3OH)] (1). The compound was
prepared from RuCl3 Æ 3H2O and AsPh3 as previously
described by others [15].

G. Tamasi et al. / Inorganica Chimica Acta 362 (2009) 1011–1021
1013
trans,cis,cis-[Ru(AsPh3)2(N,S-TPYM)2] (2). Fifty-six
2.4. X-ray crystallography
milligrams of HTPYM (0.50 mmol) was mixed with abso-
lute ethanol (10 mL). The yellow suspension was de-aer-
ated by bubbling ultra-pure nitrogen for 15 min and then
1 was added (217 mg, 0.40 mmol). The mixture was heated
up to reflux and maintained refluxing and stirring, under
nitrogen (ca. 1 bar), in the dark (3 h). A brown–red suspen-
sion was obtained, from which a small portion was col-
lected and tested for reactivity with air. No apparent
change occurred to the aerated suspension over a period
of 6 h. Then, the hot suspension was filtered and the
green–brown solid was taken off. The deep brown red fil-
trate was cooled down to room temperature and left con-
centrating through spontaneous solvent evaporation (in
the dark). Deep-red crystals suitable for X-ray diffraction
analysis formed within 24 h. They were collected, washed
by using small volumes of cold absolute ethanol and then
stored in air. Yield, 71 mg (30%). Anal. Calc. for
C44H36As2N4RuS2 (MW = 935.83): C, 56.47; H, 3.88; N,
5.99. Found: C, 56.07; H, 3.96; N, 6.32%. UV–Vis. (CHCl3,
the crystals are slightly soluble): 0.348 nm (e, 6500 cmꢁ1
molꢁ1 L), shoulder 402 nm (e, 5800 cmꢁ1 molꢁ1 L). The
chloroform solution became green upon heating at 50 ꢁC
for 60 s, or at 25 ꢁC after a few hours; the chromatographic
analysis (TLC) of the green solution showed the presence
of two main components: a yellow one RF 0.87 and a blue
one RF 0.82. The green solution has an absorption maxi-
mum at 597 nm (estimated absorption coefficient for the
blue component, 2000 cmꢁ1 molꢁ1 L) and a shoulder at
ca. 300 nm. IR for 2 (KBr matrix): 1534 cmꢁ1 (medium
m), 1480 cmꢁ1 (weak w), 1436 cmꢁ1 (m), 1371 cmꢁ1
(strong, s), 1180 cmꢁ1 (w), 1158 cmꢁ1 (w), 1077 cmꢁ1 (w),
1000 cmꢁ1 (w), 739 cmꢁ1 (m), 695 cmꢁ1 (s), 668 cmꢁ1 (s),
A well formed dark-red parallelepiped of dimensions
0.80 · 0.15 · 0.15 mm was selected under the polarizing
microscope and then mounted on a glass capillary. The Sie-
mens P4 four circle automatic diffractometer at CIADS
(Centro Interdipartimentale di Analisi e Determinazioni
Strutturali, University of Siena) was used for the XRD
measurements. Cell dimensions were obtained through
the least-squares technique from 43 high angle
(10 < 2h < 38ꢁ), randomly selected, relatively strong reflec-
tions (Table 1). The analysis of intensities for groups of
reflections revealed a mmm Laue symmetry. A total of
5001 reflections were collected at 293 2 K in the range
(2.8 < 2h < 50ꢁ), 4754 of which were unique and 3459 were
considered observed (I > 2r(I)). Three check reflections
were measured every 97 reflections, no decaying was
recorded during the data collection. The data set was cor-
rected for Lorentz-polarization effects. The absorption cor-
rection was applied to the data set by using the w-scan
method based on the values of four reflections.
The structure solution and refinement were performed
via the direct methods and series of 12 difference-Fourier
and least-squares cycles that located all the non-hydrogen
atoms by using the crystallographic program SHELX-97
[16] implemented in WINGX [17].
The hydrogen atoms were set in calculated positions via
the HFIX/AFIX options of SHELX-97 and they were left to
ride on the atoms to which they are linked in the subse-
quent refinement cycles. All the non-hydrogen atoms were
refined with anisotropic thermal parameters, whereas the
hydrogen atoms were considered isotropically. The final
conventional agreement factors were R1 = 0.0435 and
wR2 = 0.0725 for the observed reflections.
1
477 cmꢁ1 (m). H NMR for 2 (CDCl3, freshly prepared):
7.99–7.97 ppm from TMS (1H, multiplet m, H6), 7.62–
7.60 ppm (1H, m, H4), 7.31–7.09 ppm (15H, m, AsPh3),
6.07–6.05 ppm (1H, m, H5). 1H NMR for TPYMꢁ
(CDCl3): 8.27–8.23 ppm (2H, d, H4,H6), 6.55–6.60 ppm
(1H, t, H5).
Table 1
Selected crystallographic data for trans,cis,cis-[Ru(AsPh3)2(N,S-TPYM)2]
(2)
Parameter
Value
2.3. Spectroscopy
Empirical formula
C44H36As2N4RuS2
Formula weight
Crystal system, space group
935.83
orthorhombic, P212121, #
19
UV–Vis. The spectra were recorded through a Lambda
EZ Perkin–Elmer Spectrophotometer working under
PESSW (Ver. 1.2, Rev. 3) software. The spectra were
obtained by using quartz cuvettes, 1 cm path-length at 25 ꢁC.
IR. The spectra were recorded at the solid state from
KBr matrixes at 25 ꢁC by using the Perkin–Elmer 1600
FT-IR spectrometer.
Unit cell dimensions
˚
a (A)
10.999(2)
12.536(2)
29.165(4)
4021.4(11)
4, 1.546
2.164
5001/4754 [0.0559]
3459/0/478
R1 = 0.0435, wR2 = 0.0725
R1 = 0.0750, wR2 = 0.0821
0.301 and ꢁ0.359
˚
b (A)
˚
c (A)
3
˚
Volume (A )
Z, Calculated density (Mg mꢁ3
)
1H NMR. The spectra were recorded by using CDCl3 at
99.8 atom D%, concentrations of the compounds
0.01 mol Lꢁ1 for 2 and TPYMꢁ and <0.01 mol Lꢁ1 for
HTPYM (because of the low solubility at 22 2 ꢁC). The
1H NMR spectrum of TPYMꢁ was recorded from a CDCl3
solution of HTPYM after the addition of an equivalent of
pure triethylamine. The spectrometer was a Bruker
Advance operating at 400 MHz.
Absorption coefficient (mmꢁ1
)
Reflection collected/unique [Rint
Data/restraint/parameters
Final R indexes [I > 2r(I)]
Final R indexes (all data)
]
ꢁ3
˚
Largest differences in peak and hole (e A
)
Cell measurements and data collection performed at 293 2 K, through
radiation Mo Ka, k = 0.71073 A.
˚

1014
G. Tamasi et al. / Inorganica Chimica Acta 362 (2009) 1011–1021
The analysis of the molecular structure and molecular
3.2. X-ray crystallography
graphic computations were performed via PARST-97 [18]
and ORTEP-3 [19]. All the software programs were imple-
mented under the WINGX package and the Microsoft Win-
dows-XP operating system.
3.2.1. The coordination sphere
The molecular structure for trans,cis,cis-[Ru(AsPh3)2-
(N,S-TPYM)2] (2), is represented in Fig. 1, whereas the
selected geometrical parameters are listed in Tables 2 and
3. The coordination sphere is distorted octahedral, and
the two chelating N,S-TPYM ligands occupy the equato-
rial positions and have a cis,cis arrangement, so that the
sulfur atoms are facing each other. The strained four-mem-
ber fully hetero-atom RuSCN(Ru) chelate rings cause the
largest distortions from an idealized octahedron. Two
arsenic atoms from the triphenylarsine ligands occupy the
apical sites. The Ru–S bond distances are equal within
one time the estimated standard deviation and average
2.5. Computational studies
All the computations were performed using the GUS-
SIAN03 package [20] implemented on IBM-SP5 clusters
of computers at CINECA (Inter-University Consortium
for Scientific Computation, Casalecchio di Reno, Bolo-
gna, Italy). The molecules investigated were trans,cis,-
cis-[Ru(AsH3)2(N,S-TPYM)2],
cis,cis,trans-[Ru(AsH3)2-
(N,S-TPYM)2], trans,cis,cis-[Ru(AsPh3)2(N,S-TPYM)2],
and cis,cis,trans-[Ru(AsPh3)2(N,S-TPYM)2], (Scheme 1).
The level of theory used to compute the structures was
B3LYP/(Lanl2DZ, Ru; Lanl2DZ, d, As; 6-31G, CHN;
6-31G**, S) and B3LYP/(Lanl2DZ, AsRu; 6-31G,
CHNS) [21] for AsH3 and AsPh3 derivatives, respec-
tively, and the structure optimization was continued up
to the threshold values implemented in GAUSSIAN03:
(maximum force 0.000450 mdyne, rms – root mean
square – force 0.000300 mdyne, maximum displacement
˚
2.440(2) A, and are in perfect agreement with the corre-
˚
sponding value (2.451(1) A) previously found in this labo-
ratory for trans,cis,cis-[Ru(PPh3)2(N,S-TPYM)2] (3) [12b].
The two apical Ru–As vectors found for 2 (lengths:
˚
2.428(1) and 2.436(1) A) are expectedly longer than the
˚
Ru–P vectors (2.369(1) A) found for the corresponding
PPh3 derivative. The Ru–N bond distances (average,
˚
2.078(6) A) are in good agreement with the value previ-
˚
ously found for 3 (2.063(3) A). One can note that for both
2 and 3 the corresponding bond distances at coordination
sphere have very close values; that does not happen for cis,-
cis,trans-[Ru(PPh3)2(N,S-TPYM)2] (4). The Ru–S(trans to
N) bond distance found for [Ru(6-methyl-2-thiopyrimidi-
˚
˚
0.001800 A, rms displacement 0.001200 A). No negative
frequency for the optimized structures were revealed
from the analysis of the hessian. Molecular drawings
were obtained by using the GAUSSVIEW3.0 software pack-
age [22].
+
ꢁ
nato){bis(2,20-bipyridine)}2] ClO4 is 2.408(2) A [24] in
agreement with a lower trans influence by N with respect
to S.
˚
3. Results and discussion
The bond angle between the apical vectors As1–Ru1–
As2 (168.45(4)ꢁ) deviates significantly from the idealized
value, 180ꢁ, and the deviation (11.55(4)ꢁ) is even larger
3.1. Synthesis
The reaction of [RuIII(AsPh3)2Cl3(CH3OH)] (1), with
2-thiopyrimidine-1,3, HTPYM (ligand:Ru molar ratio,
1.25:1), in refluxing ethanol produced a dark-brown
suspension. The red filtrate produced trans,cis,
cis-[Ru(AsPh3)2(N,S-TPYM)2] (2), in the form of single
crystals. As it happened for the reaction of 1 with 6-thi-
opurine (H2TP) [23], a reduction from Ru(III) to Ru(II)
occurred even with the ligand HTPYM (this work) that
undergoes deprotonation followed by chelation. In case
the closed shell d6 configuration is stabilized by ligands
that posses high-field donors (like S, P, As, Sb, etc.)
the Ru(II) center is much stabilized even in the solution
phase.
The isolation and structure characterization of trans,cis,
cis-[Ru(AsPh3)2(N,S-TPYM)2] from this work (see below
for structural details) is in agreement with the equatorial
arrangement proposed for [Ru(AsPh3)(H2TP)2(CH3OH)]2+
and [Ru(DMSO)2(H2TP)2]2+ [23], (DMSO = dimethylsulf-
oxide) for which the very many crystal growth attempts were
unsuccessful, so far. The arrangement of the AsPh3 ligands
is the semi-trefoil C1, Stf-C1, defined in Scheme 4e of Ref.
[12b].
Fig. 1. Ortep style drawing of trans,cis,cis-[Ru(AsPh3)2(N,S-TPYM)2] (2).
The labeling scheme is reported for the selected not-hydrogen atoms only,
for the sake of clarity. Ellipsoids enclose 50% probability.

G. Tamasi et al. / Inorganica Chimica Acta 362 (2009) 1011–1021
1015
3.2.2. The TPYMꢁ ligands
Table 2
˚
The coordination mode shown by TPYMꢁ ligands for 2
is the common one represented as VIII in Scheme 1a in
Selected experimental bond distances (A) for trans,cis,cis-
[Ru(AsPh3)2(N,S-TPYM)2] (2)
Vector
Length
˚
Ref. [12b]. The S–C bond distances average 1.706(8) A in
Ru1–As1
Ru1–As2
Ru1–S11
Ru1–S12
Ru1–N11
Ru1–N12
S11–C21
S12–C22
N11–C21
N12–C22
N11–C61
N12–C62
N31–C21
N32–C22
N31–C41
N32–C42
C41–C51
C42–C52
C51–C61
C52–C62
As1–C111
As1–C121
As1–C131
As2–C112
As2–C122
As2–C132
2.436(1)
2.428(1)
2.441(2)
2.438(2)
2.076(6)
2.079(6)
1.714(8)
1.699(10)
1.376(9)
1.349(9)
1.321(9)
1.345(10)
1.315(9)
1.344(11)
1.343(11)
1.325(12)
1.374(11)
1.379(13)
1.386(10)
1.375(11)
1.956(8)
1.962(7)
1.954(9)
1.971(9)
1.935(9)
1.944(8)
agreement with an intermediate character between the thi-
one and thiol types. The N1x–C2x vectors included in the
coordination rings have lengths that average 1.362(9) A,
˚
whereas the other six N–C bond lengths average
˚
1.332(9) A. Even though the difference between the two sets
of N–C bond lengths is ca. within twice the esd, a lengthen-
ing effect on N1–C2 bonds by the coordination is reason-
able. Distances relevant to the C–C bonds have normal
˚
values and average 1.379(10) A.
As expected, the (Ru)N1–C–S(Ru) bond angles (average
109.6(6)ꢁ) are much smaller than the N3–C–S(Ru) angles
(126.3(7)ꢁ) in agreement with a strong N,S chelation by
TPYMꢁ. It has to be noted that the sulfur atoms deviate
significantly from the least-squares plane defined by the
˚
endo-cyclic atoms (0.135(2) and 0.069(2) A). The two
least-squares planes defined by endo-cyclic atoms from
TPYMꢁ are twisted by 8.9(3)ꢁ. The metal coordination
to N1 reflects in a significant widening of the two C–N1–
C bond angles (119.2(7)ꢁ) with respect to the C–N3–C ones
(115.6(8)ꢁ).
Intra-molecular contacts that involve TPYMꢁ ligands
are of hydrogen bond type and pꢀ ꢀ ꢀp stacking type.
Note worthy, both the sulfur atoms are hydrogen accep-
tors from phenyl rings, namely C212–Hꢀ ꢀ ꢀS11 (Cꢀ ꢀ ꢀS,
Table 3
˚
ˆ
3.50(1) A; H, 133(1)ꢁ) and C231–Hꢀ ꢀ ꢀS12 (Cꢀ ꢀ ꢀS,
Selected experimental bond angles (ꢁ) for trans,cis,cis-[Ru(AsPh3)2(N,S-
TPYM)2] (2)
˚
ˆ
3.63(1) A; H, 136(1)ꢁ); this datum has to be compared to
the bending of the Ru–As vectors towards the sulfur
region.
Vectors
Angle
As2–Ru1–As1
N11–Ru1–S11
N12–Ru1–S12
S12–Ru1–S11
N11–Ru1–N12
168.45(4)
67.5(2)
66.8(2)
118.49(9)
107.4(3)
Stacking interaction occurs between the N11/C61
TPYMꢁ system and the C121/C621 phenyl-ring; in fact,
C21ꢀ ꢀ ꢀC621 and N11ꢀ ꢀ ꢀC121 contact distances are 3.33(1)
˚
and 3.39(1) A, respectively, and the dihedral angle between
the two least-squares planes is 27.2(3)ꢁ. A similar interac-
tion occurs between the N12/C62 TPYMꢁ and the C122/
C622 ring systems for which the dihedral angle between
N11–C21–S11
N12–C22–S12
N31–C21–S11
N32–C22–S12
N31–C21–N11
N32–C22–N12
C61–N11–C21
C62–N12–C22
C21–N31–C41
C42–N32–C22
109.2(6)
110.0(7)
126.4(7)
126.3(7)
124.4(7)
123.7(9)
118.8(6)
119.6(8)
115.6(8)
115.6(9)
the least-squares planes is 30.3(3)ꢁ and short contact dis-
˚
tances
are
C22ꢀ ꢀ ꢀC622
(3.28(1)A),
N12ꢀ ꢀ ꢀC122
˚
˚
(3.40(1) A) and S12ꢀ ꢀ ꢀC622 (3.61(1) A).
3.2.3. AsPh3 ligand
˚
The As–C bond distances average 1.954(13) A and range
˚
1.935(9)–1.971(9) A. The values compare well with those
reported for trans-[RhI(AsPh3)2Cl(CO)] [25]. Correspond-
than the corresponding one found for 3 (8.00(4)ꢁ). On the
other hand the N–Ru–S bond angles that insist on the same
TPYMꢁ ligand average 67.2(2)ꢁ and are in perfect agree-
ment with the value for 3 (67.51(8)ꢁ). Similarly, bond angle
values in the equatorial plane for N11–Ru1–N12,
107.4(3)ꢁ, and S12–Ru1–S11, 118.49(9)ꢁ are in perfect
agreement with the corresponding ones found for 3
(106.1(1)ꢁ and 119.12(4)ꢁ, respectively).
ing values found for P–C bonds in trans,cis,cis-
˚
[Ru(PPh3)2(N,S-TPYM)2] are 1.833(4) A, range 1.828(4)–
˚
1.837(4) A. The analysis of the bond angles is as follows:
Ru–As–C, average 116.4ꢁ (esds from the six values 1.6ꢁ),
range 113.6–117.3(2)ꢁ; C–As–C, average 101.7(18)ꢁ, range
99.6(4)–104.2(4)ꢁ. Corresponding values for the Ru–P–C
and C–P–C angles in trans,cis,cis-[Ru(PPh3)2(N,S-TPYM)2]
are average 113.5(23)ꢁ, range 111.4(1)–115.9(1)ꢁ, and aver-
age 105.1(45)ꢁ, range 101.0(2)–109.9(2)ꢁ. The data show that
C–As–C angles are smaller than the C–P–C ones in agree-
The metal atom lies on the least-squares plane defined
by the four donor atoms from the TPYMꢁ ligands.

1016
G. Tamasi et al. / Inorganica Chimica Acta 362 (2009) 1011–1021
ment with a smaller cone angle for AsPh3 than for PPh3. The
examination of the Ru–S bond distances for trans,cis,cis-
[Ru(XPh3)2(N,S-TPYM)2] (reported above) suggests a lar-
ger cis influence for X = P when compared to X = As.
3.2.4. Inter-molecular contacts
Some C–Hꢀ ꢀ ꢀN hydrogen-bond type interactions occur
between C–H functions and the non-coordinate nitrogen
atoms. For example, C232 and N31 related by a screw-axis
parallel to a cell edge have contact parameters: C(x + 1/2,
˚
ˆ
ꢁy + 1/2, ꢁz)ꢀ ꢀ ꢀN, 3.58(1) A, and H, 148(1)ꢁ; C411 and
N32 related by a screw-axis parallel to b cell edge have
˚
parameters C(ꢁx, +y + 1/2, ꢁz + 1/2)ꢀ ꢀ ꢀN, 3.78(1) A
ˆ
and H, 138(1)ꢁ. On examining possible base pairings, it
appears that C51 and S11 have distances and angles as fol-
˚
ˆ
lows: C(x + 1/2, ꢁy + 1/2, ꢁz)ꢀ ꢀ ꢀS, 3.65(1) A and H,
Fig. 3. The diagram shows selected intra-molecular hydrogen bond type
interactions that involve a TPYMꢁ ligand.
113(1)ꢁ, whereas C61 and N31 from the same unit have
˚
ˆ
Cꢀ ꢀ ꢀN, 3.72(1) A and H, 119(1)ꢁ. Thus, the arrangement
of the two bases is such to look like a base pairing
(Fig. 2a), even though the linkage is reasonably weak
because the two pyrimidine rings do not lie on the same
plane (Fig. 2b). The N12/C62 pyrimidine system is not
involved in such a type of baseꢀ ꢀ ꢀbase interaction. Instead
the S12 atom is hydrogen acceptor from C412(ꢁx + 1,
1.0
0.9
0.8
0.7
0.6
0.5
0.4
0.3
0.2
0.1
0.0
˚
ˆ
+y ꢁ 1/2, ꢁz + 1/2) (Cꢀ ꢀ ꢀS, 3.58(1) A; H, 138(1)ꢁ) and
from C512(ꢁx + 1, +y ꢁ 1/2, ꢁz + 1/2) (Cꢀ ꢀ ꢀS,
˚
ˆ
3.79(1) A; H, 117(1)ꢁ), whereas the N32 atom is hydrogen
acceptor from C422(ꢁx, +y ꢁ 1/2, ꢁz + 1/2) (Cꢀ ꢀ ꢀS,
˚
ˆ
3.48(1) A; H, 113(1)ꢁ) and from C522(ꢁx, +y ꢁ 1/2,
˚
ˆ
ꢁz + 1/2) (Cꢀ ꢀ ꢀS, 3.51(1) A; H, 112(1)ꢁ), and from
˚
ˆ
C411(ꢁx, +y + 1/2, ꢁz + 1/2) (Cꢀ ꢀ ꢀS, 3.78(1) A; H,
138(1)ꢁ) (Fig. 3). It is worthy of note that weak
C–Hꢀ ꢀ ꢀN, C–Hꢀ ꢀ ꢀS and C–Hꢀ ꢀ ꢀCl hydrogen bond type
interactions play important roles in coordination and orga-
nometallic compounds, as previously shown from this lab-
oratory and from others [26–30].
300
400
500
600
700
800
nm
Fig. 4. Absorption UV–Vis spectrum for trans,cis,cis-[Ru(AsPh3)2(N,S-
TPYM)2] (4.3 · 10ꢁ5 M) in chloroform (fresh solution).
absorption band at 348 nm (e, 16000 cmꢁ1 molꢁ1 L) and
the shoulder at 402 nm (e, 14300 cmꢁ1 molꢁ1 L) compare
well with the values previously found for trans,cis,cis-
[Ru(PPh3)2(N,S-TPYM)2] and show a shift towards lower
energy for the arsine derivative. The absorptions in the
3.2.5. Spectroscopy
UV–Vis. The spectrum of a freshly prepared solution of
2 in CHCl3 (4.3 · 10ꢁ5 M) is reported in Fig. 4. The
a
b
Fig. 2. The diagram shows the way two thiopyrimidine ligands are arranged in a pairing-type fashion through weak C–Hꢀ ꢀ ꢀS and C–Hꢀ ꢀ ꢀN interactions:
(a) the view is almost perpendicular to the least-squares planes that are defined by the endo-cyclic atoms; (b) the view is almost parallel to the same planes.
The Ru atom and the atoms from TPYMꢁ only are pictured for the sake of clarity.

G. Tamasi et al. / Inorganica Chimica Acta 362 (2009) 1011–1021
1017
UVA region are assigned to ligand (TPYMꢁ)-to-metal
charge transfer on the basis of computations reported in
[12b]. The absorption band at kmax 597 nm recorded from
the solution of 2 in chloroform after 24 h from the prepa-
ration is responsible for the green color of the solution.
Chromatographic analysis of the solution (TLC, reverse
phase C18, eluent CH3CN) revealed two components: RF
0.88 (yellow fraction) and RF 0.82 (blue fraction). The
molar absorbance was roughly estimated to be ca.
2000 cmꢁ1 molꢁ1 L. These data compare well with those
for trans,cis,cis-[RuIII(PPh3)2(N,S-TPYM)2]+ obtained via
electrochemical oxidation [12b].
Interestingly, the chemical shifts for the signals from
(C)H protons of TPYMꢁ undergo a net up-field change
upon metal chelation via N1 and (C2)S atoms. The effect
is ca. 0.27, 0.64 and 0.57 ppm for H6, H4 and H5,
respectively.
3.3. Computational studies
3.3.1. Structures
The structure for the model molecule trans,cis,cis-
[Ru(AsH3)2(N,S-TPYM)2] as optimized through the den-
sity functional methods (see Section 2.5) is represented in
Fig. 5a, whereas the selected geometrical parameters are
listed in Table 4. The computed Ru–As bond distances
1H NMR. The three signals relevant to the (C)H protons
from TPYM anions for 2 in CDCl3 are in agreement with a
Cs symmetry at metal (free rotation of AsPh3 around Ru–
As; 22 2 ꢁC). As expected, the local C2v symmetry for free
TPYMꢁ no longer exists for the ligand in 2. The chemical
shift values for 2 (average 7.98, 7.61, 6.06 ppm for H6, H4
and H5, respectively) are in good agreement with corre-
sponding values previously found for other compounds,
from here [RuII(PPh3)2(N,S-TPYM)2] [12b], and by other
workers [Pd(C1,N-2-(dimethylaminomethyl)phenyl)(l-N,S-
TPYM)]2 [31] and [M(CF3-N,S-TPYM)2(PPh3)2] (M =
Ru, Os) [32].
˚
2.455 A are very close to the experimental value found
for
trans,cis,cis-[Ru(AsPh3)2(N,S-TPYM)2]
(average,
˚
2.432(1) A). A similar good agreement is found for Ru–N
bond distances: computed 2.118 A, experimental
2.078(6) A, whereas the computed value for the corre-
sponding PH3 derivative was 2.113 A. The computed
˚
˚
˚
˚
Ru–S bond distances (2.516 A) compare well with the
experimental values (average found Ru–S distance,
˚
2.440(2) A). As expected, the choice of the basis set for
the soft atoms is very important in simulating this type
Fig. 5. GaussView style drawing for the optimized molecules: (a) trans,cis,cis-[Ru(AsH3)2(N,S-TPYM)2]; (b) cis,cis,trans-[Ru(AsH3)2(N,S-TPYM)2]; (c)
trans,cis,cis-[Ru(AsPh3)2(N,S-TPYM)2]; (d) cis,cis,trans-[Ru(AsPh3)2(N,S-TPYM)2]. The computations have been performed via DFT-B3LYP methods
(see text for basis sets and Table 4 for the selected computed geometrical parameters).

1018
G. Tamasi et al. / Inorganica Chimica Acta 362 (2009) 1011–1021
Table 4
This hypothesis is confirmed by the comparative analysis
of the computed bond angles at metal for the two isomers.
The angles for trans,cis,cis have larger deviations from
canonical idealized values of 90ꢁ and 180ꢁ than for cis,cis,-
trans: N–Ru–N deviates by 20.8ꢁ in trans,cis,cis and 3ꢁ in
cis,cis,trans, As–Ru–As deviates by 11.2ꢁ and 3.3ꢁ in
trans,cis,cis and cis,cis,trans, respectively, S–Ru–S deviates
by 25.3ꢁ in trans,cis,cis and by 21.3ꢁ in cis,cis,trans. From
this analysis it is reasonable to predict that the cis,cis,trans
isomer is more stable than the trans,cis,cis one (see section
3.3.2).
˚
Selected computed bond distances (A) and angles (ꢁ) for trans,cis,cis-
[Ru(AsH3)2(N,S-TPYM)2] (tcc), and cis,cis,trans-[Ru(AsH3)2(N,S-
TPYM)2] (cct) model isomers
Vector
Length
tcc
cct
2.445
Ru1–As2/3
Ru1–S4/5
Ru1–N6/8
2.455
2.516
2.118
1.731
1.399
1.353
1.358
1.354
1.413
1.405
1.525
1.516
2.514
2.101
1.736
1.393
1.350
1.358
1.355
1.412
1.406
1.524
S4/5–C10/17
N6/8–C10/17
N6/8–C15/22
N7/9–C10/17
N7/9–C11/18
C11/18–C13/20
C13/20–C15/22
As2/3–H
On comparing the differences between the computed
Ru–N bond distances for complex molecules that contain
PH3 and AsH3 it is evident that a larger trans influence
by phosphines occurs [25].
The structural parameters for the chelating TPYMꢁ
anions are the same within each isomer and do not deviate
much on passing from trans,cis,cis to cis,cis,trans. The S–C
bond is slightly longer for cis,cis,trans than for trans,cis,cis
As2/3–H
Vectors
Angle
168.8
67.0
115.3
110.8
110.4
126.6
123.0
118.8
117.4
As2–Ru1–As3
N6/8–Ru1–S4/5
S4–Ru–S5
N6–Ru1–N8
N6/8–C10/17–S4/5
N7/9–
N6/8–C10/C17–N7/9
C10/17–N6/8–C15/C22
C10/17–N7/9–C11/18
93.3
67.3
158.7
87.0
110.5
126.9
122.6
119.9
117.1
˚
(by 0.005 A), in agreement with a stronger chelation to the
metal for cis,cis,trans.
3.3.2. Energy and modeling of the base-pairing type
interaction
The total electronic energy is ꢁ657.44121 and
ꢁ657.44903 hartrees for trans,cis,cis-[Ru(AsH3)2(N,S-
TPYM)2] and cis,cis,trans-[Ru(AsH3)2(N,S-TPYM)2] iso-
mers, respectively, showing that the order of stability pre-
dicted from the structural strains commented just above
was correct. The difference corresponds to 4.907 kcal
molꢁ1, and it is large enough to suggest a preponderance
of the cis,cis,trans isomer compared to trans,cis,cis in the
mother mixtures, provided that the starting complex con-
tains the AsR3 ligands in both the cis and trans arrange-
ments (or provided that the cis/trans inter-conversion has
a low energy barrier). It has to be recalled that the reaction
of [RuCl2(PPh3)3] with HTPYM produces the correspond-
ing cis,cis,trans-[Ru(PPh3)2(N,S-TPYM)2] as the major
product and trans,cis,cis-[Ru(PPh3)2(N,S-TPYM)2] in a
lower yield. In fact, [RuCl2(PPh3)3] has a pseudo-trigonal
bipyramidal arrangement with two chloride and a phos-
phorous atom in the equatorial plane and two triphenyl-
phosphine ligands almost trans each to other [33]. In this
latter case the coordination arrangement of the starting
material and the higher trans influence of P over As are
such to allow the formation of the two isomers at a molar
ratio that reflects the relative stability.
The computational method (see text) was the hybrid density functional
B3LYP and the basis set was: (Lanl2DZ, Ru; Lanl2DZ, d, As; 6-31G,
CHN; 6-31 G**, S). Average values are reported. The labeling of the atom
is that shown in Fig. 5.
of complexes. In fact, the same model structure as opti-
mized by using the 6-31G type functions for AsCHNS
atoms (Lanl2DZ for Ru) has longer Ru–As,S bond dis-
tances: computed Ru–As, and Ru–S are 2.478, and
˚
2.562 A. As a consequence of the increased coordination
distances for the heavier donors, the computed Ru–N dis-
˚
tances decrease and average 2.105 A.
On the basis of this analysis, the mixed basis set that has
more expanded functions for As and S only, and 6-31G-
type functions for CHN atoms were considered reliable
for estimating bond lengths.
The computed bond angles at metal center reproduce
very well the experimental values, for example S–Ru–N
chelation angles are 67.0ꢁ, whereas the average value for
the solid state structure is 67.2(2)ꢁ.
The same methodology was applied to compute the
structure
of
cis,cis,trans-[Ru(AsH3)2(N,S-TPYM)2]
On the contrary, in the case of the present work the
starting compound has a trans arrangement of the arsenic
atoms, whereas the more labile donors, alcohol oxygen
and chloride anions occupy the equatorial plane. That
arrangement seems to allow first the formation of the
two stable chelate systems in the equatorial plane and thus
the trans,cis,cis isomer; the subsequent isomerization to
cis,cis,trans albeit favored by a higher stability of cis,cis,-
trans over trans,cis,cis is not favored because of high energy
barriers. A similar behavior was found for a 6-thiopurine
(Fig. 5b), that has been selected as model for the corre-
sponding triphenylarsine derivative.
The computed Ru–As and –S bond distances for cis,-
cis,trans isomer do not differ appreciably from those rele-
vant to the corresponding ones for trans,cis,cis. However,
the Ru–N bond distances for cis,cis,trans are shorter by
˚
0.017 A with respect to those for trans,cis,cis; thus the che-
lation of Ru by TPYMꢁ seems to be stronger in the case
of the cis,cis,trans isomer when compared to trans,cis,cis.

G. Tamasi et al. / Inorganica Chimica Acta 362 (2009) 1011–1021
1019
ꢁ1
˚
H2TP derivative obtained from the reaction of trans-
[Ru(AsPh3)2Cl3(CH3OH)] with H2TP. In the case of bulk-
ier H2TP (when compared to TPYMꢁ) the bis-chelate
allows the presence of just one AsPh3 and the formation
of [Ru(AsPh3)(N,S-H2TP)2(CH3OH)]Cl2 [23] instead of
[Ru(AsPh3)2(N,S-H2TP)2]Cl2. Even for the H2TP deriva-
tive the arrangement of the two chelating thiobases is
equatorial.
The computed total electronic energies for trans,cis,cis-
and cis,cis,trans-[Ru(AsPh3)2(N,S-TPYM)2] performed at
the B3LYP/(Lanl2DZ, AsRu; 6-31G, CHNS) level have
the same trend as that presented above for the AsH3 deriv-
atives, the cis,cis,trans isomer being more stable by
4.060 kcal molꢁ1 than the trans,cis,cis one.
plane) have values: 201.39 cmꢁ1 (0.2058 mdyn Aꢁ1
,
,
1.9169 km molꢁ1), and 262.68 cmꢁ1 (0.4389 mdyn A
˚
0.3494 km molꢁ1). The asymmetric Ru–S stretching vibra-
tions associated with N–C–S in plane vibrations are mostly
defined by the computed frequence 292.5 cmꢁ1 (1.073 mdyn
˚
A
ꢁ1, 10.10 km molꢁ1). Computed vibrations that have con-
tributions from complex Ru–N stretching and N–C–S bend-
ꢁ1
ing motions have the values: 393.9 cmꢁ1 (0.624 mdyn A
,
˚
5.254 km molꢁ1). Computed infrared absorption that have
contributions from C–S stretching have frequencies: 472.5
cmꢁ1 (1.754 mdyn Aꢁ1, 8.382 km molꢁ1), 997.7 cmꢁ1 (5.131
˚
mdyn Aꢁ1, 41.289 km molꢁ1), 1173.2 cmꢁ1 (1.813 mdꢁy1n
˚
˚
A
ꢁ1, 38.513 km molꢁ1), and 1255.9 cmꢁ1 (4.203 mdyn A
,
˚
59.341 km molꢁ1). Intense computed absorption effects
occur at 1407.0 cmꢁ1, combinations of C–N stretching
and H–C–N bending in TPYMꢁ plane, 1586.7 cmꢁ1, combi-
nations of C–N and C–C stretching and H–C–N bending in
plane, 2208.8 cmꢁ1, and 220.4 cmꢁ1, As–H stretching
motions.
As regards the thiopyrimidine-pairing type interaction
mentioned above (Section 3.2.4), it has to be recalled that
previous computations relevant to the pairing for {cis-
[(NH3)2Pt(HTP- H1)ꢀ ꢀ ꢀ(H2TP)}+ aggregate assisted by a
N–Hꢀ ꢀ ꢀNꢁ and a C–Hꢀ ꢀ ꢀS interactions, estimated an
adduct formation energy of ca. ꢁ7 kcal molꢁ1 [28]. It is
reasonable to assume that the computed energy contribu-
tion for pairing interaction found in the structure of 2
(see above) can be approximated roughly to that magni-
tude for the gas phase and without any correction for the
basis set superposition error (BSSE). Furthermore, the
paired (Ru)TPYMꢁ moieties for 2 are not coplanar
(Fig. 2b); this fact should decrease the pairing energy.
The computed pairing energy for a non-metal bound
{TPYMꢁ. . .HTPYM} planar system (the two bases linked
via C–Hꢀ ꢀ ꢀS and C–Hꢀ ꢀ ꢀN and kept constrained to move
in the plane) is ca. ꢁ19 kcal in the gas phase at the
As regards the cis,cis,trans derivative, the computed IR
spectrum is similar to that for the trans,cis,cis isomer both
for the frequencies and intensities. For example, computed
effects that come from C–S stretching motions are at
470.7 cmꢁ1, 1004.3 cmꢁ1, 1180.3 cmꢁ1, 1256.9 cmꢁ1. As a
consequence, infrared spectroscopy is not a suitable tech-
nique to discriminate between the two isomers.
The comparative analysis between the computed IR
spectrum for trans,cis,cis-[Ru(AsH3)2(N,S-TPYM)2] and
the experimental data found at the solid state for 2, in
the spectral region relevant to vibrations that involve
TPYMꢁ, shows a remarkable agreement (see Section 2.2).
B3LYP/(6-31G , CHNS) level, without any correction
**
for BSSE. The optimization did not meet the convergence
criteria implemented in GAUSSIAN03 and was halted when
three out of four criteria were satisfied. The maximum dis-
placement item being relatively high, 0.020298. The
selected contact distances for the partially optimized aggre-
4. Conclusion
In conclusion the work produced the new trans,cis,cis-
[Ru(AsPh3)2(N,S-TPYM)2] crystalline compound that
might be of interest for testing as an anti-cancer drug.
The X-ray diffraction analysis and the spectroscopy studies
confirm that the solid state and solution phase structures
are the same. The compound is stable for years at the solid
state in the air atmosphere, but might easily decompose
when in solution. Studies devoted to investigate the nature
of other products from the preparative reaction, and to
draw light on the mechanism for the reactivity in solution
are in progress in this laboratory. Preliminary results (via
HPLC) show that in chloroform, acetonitrile and methanol
solution, the first step of the reaction cascade is the disso-
ciation of Ru–AsPh3 bond(s).
5
6
˚
gate (H ꢀ ꢀ ꢀS and H ꢀ ꢀ ꢀN, 2.588 and 2.253 A) are signifi-
cantly shorter than experimental value for 2 (3.193 and
˚
3.175 A), thus that the estimated pairing energy for planar
{TPYMꢁ. . .HTPYM} is undoubtedly higher than the
value for the pairing of two complex molecules. The pair-
ing interaction seems to be electrostatic-type in 2; the
sum of Van der Waals radii for H and S, and H and N
˚
˚
atoms being 3.00–3.25 A, and 2.75–3.00 A, respectively
[34,35]. The selected Mulliken atomic charges computed
for {TPYMꢁ. . .HTPYM} planar system are S(ꢁ0.49
e)ꢀ ꢀ ꢀH5(0.17 e) and N3(ꢁ0.45 e)ꢀ ꢀ ꢀH6(0.17 e).
The cis,cis,trans-[Ru(AsPh3)2(N,S-TPYM)2] isomer is
predictably more stable than the corresponding trans,cis,-
cis, as shown via density functional computational tools;
nevertheless, it could not be isolated at the solid state nor
detected as a major component via spectroscopy or chro-
matography so far. The coordination arrangement of the
starting compound 1 that has two triphenylarsine ligands
trans to each other, or the different solubility in alcoholic
media of the two possible isomers, makes the isolation of
3.3.3. Vibration frequencies
The analysis of the vibrations for trans,cis,cis-
[Ru(AsH3)2(N,S-TPYM)2] shows that the symmetric
stretching of the two Ru–As bond has a computed fꢁre1-
quency of 182.09 cmꢁ1 (force constant, 0.3849 mdyn A
)
˚
and is predicted to be weak (IR intensity, 0.3002 km molꢁ1).
The corresponding asymmetric Ru–As stretching vibrations
(associated with oscillation for S atoms out of the TPYMꢁ

1020
G. Tamasi et al. / Inorganica Chimica Acta 362 (2009) 1011–1021
[2] (a) A. Dobrov, V.B. Arion, N. Kandler, W. Ginzinger, M.A. Jakupec,
trans,cis,cis at the solid state easier even though its overall
stability is lower.
Finally, the work revealed a tendency for two {Ru(N,S-
TPYM)} coordination systems to pair via unusual
C5–Hꢀ ꢀ ꢀS and C6–Hꢀ ꢀ ꢀN3 interactions.
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Acknowledgements
The authors are indebted to Prof. Dr. Bernhard Lippert
for having shown us the beauty and the importance of me-
tal-nucleobase compounds. His leading researches in the
field of bio-inorganic chemistry sustained the enthusiasm
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The authors thank University of Siena for funding
through the PAR (Piano di Ateneo per la Ricerca) and
`
Ministero dell’Universita e della Ricerca Scientifica e Tec-
nologica (MURST, Rome) through PRIN (Progetto di
Rilevante Interesse Nazionale) year 2004 (Contract No.
2004032118). Thanks are also expressed to Dr. Francesco
Berrettini for the X-ray diffraction data collection at
CIADS (Centro Interdipartimentale di Analisi e Determin-
azioni Strutturali, University of Siena).
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Appendix A. Supplementary material
CCDC 643223 contains the supplementary crystallo-
graphic data for trans,cis,cis-[Ru(AsPh3)2(N,S-TPYM)2].
These data can be obtained free of charge via http://
www.ccdc.cam.ac.uk/conts/retrieving.html, or from the
Cambridge Crystallographic Data Centre, 12 Union Road,
Cambridge CB2 1EZ, UK; fax: (+44) 1223-336-033; or e-
mail: deposit@ccdc.cam.ac.uk.
Tables of atomic coordinates of fully optimized complex
molecules trans,cis,cis- and cis,cis,trans-[Ru(AsH3)2(N,S-
TPYM)2], and trans,cis,cis- and cis,cis,trans-[Ru(AsPh3)2-
(N,S-TPYM)2], and ligand molecules HTPYM and
TPYMꢁ, and the partially optimized adduct {TPYMꢁ. . .
HTPYM} (seven Tables). Supplementary data associated
with this article can be found, in the online version, at
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