Effect of substituents in the molecular and supramolecular architectures of 1-ferrocenyl-2-(aryl)thioethanones

Article abstract of DOI:10.1039/c5ce00149h

We discuss here a comprehensive solid state approach to the influence of diverse molecular functionalities present in a group of 1-ferrocenyl-2-(aryl)thioethanones [aryl = phenyl, 2-, 3-, and 4-chlorophenyl, 3- and 4-methoxyphenyl, 4-nitrophenyl, and 2-na

Full text of DOI:10.1039/c5ce00149h

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Effect of substituents in the molecular and
supramolecular architectures of 1-ferrocenyl-2-
Cite this: CrystEngComm, 2015, 17,
IJaryl)thioethanones†
3089
*
J. L. Ferreira da Silva, Shrika G. Harjivan, André P. Ferreira, Karina Shimizu,
M. Matilde Marques and M. Teresa Duarte
We discuss here a comprehensive solid state approach to the influence of diverse molecular functionalities
present in a group of 1-ferrocenyl-2-IJaryl)thioethanones [aryl = phenyl, 2-, 3-, and 4-chlorophenyl, 3- and
4-methoxyphenyl, 4-nitrophenyl, and 2-naphthyl] on their molecular structures, intermolecular contacts
and subsequent supramolecular arrangements. Ab initio calculations provide electrostatic charge distribu-
tions and electron density isosurface maps to assist this analysis. Atomic point charges are used to evaluate
the best acceptors and donors in the molecules. The absence of good hydrogen donors increases the
influence of close packing factors on the crystal network for the majority of these compounds. However
the characteristics of each substituent, like the donor–acceptor ability of the methoxy group, electronic
anisotropy of chlorine or electronic resonance of the nitro group, also play important roles in the self-
assembly processes. A systematic and detailed analysis is presented.
Received 22nd January 2015,
Accepted 8th March 2015
DOI: 10.1039/c5ce00149h
www.rsc.org/crystengcomm
organometallic benzo[b]thiophene derivatives and of interme-
diate IV included a preliminary study of the supramolecular
Introduction
This paper reports analysis of molecular and supramolecular
structures of a series of 1-ferrocenyl-2-IJphenyl)thioethanones:
unsubstituted 1-ferrocenyl-2-IJphenyl)thioethanone (I) and
1-ferrocenyl-2-ij(naphthalen-2-yl)thio]ethanone (II), methoxy
arrangements of these compounds.
Analogous synthetic procedures, involving different benz-
enethiolates, were later used to prepare other 1-ferrocenyl-2-
IJaryl)thioethanones similar to IV, with the aim of preparing
diverse starting materials for the synthesis of new raloxifene-
like compounds and of studying the effect of different aryl
substituents on their molecular and supramolecular struc-
tures. The focus of this paper is to understand how the intro-
duced substituents interplay in the design and structural con-
trol of these particular molecular packing.
The eight molecules studied are all composed of a
ferrocenyl group, an oxoethylthio bridge, and finally an aryl
ring to which the different substituents are bonded. In terms
of molecular interactions, the main feature of these
substituted
(III) and 1-ferrocenyl-2-ij3-IJmethoxyphenyl)thio]ethanone (IV),1
chloro substituted 1-ferrocenyl-2-ij4-IJchlorophenyl)thio]-
1-ferrocenyl-2-ij4-IJmethoxyphenyl)thio]ethanone
ethanone (V), 1-ferrocenyl-2-ij3IJchlorophenyl)thio]ethanone
(VI) and 1-ferrocenyl-2-ij2-IJchlorophenyl)thio]ethanone (VII)
and finally nitro substituted 1-ferrocenyl-2-ij4-IJnitrophenyl)-
thio]ethanone (VIII) (Fig. 1).
In a previous paper,1 we reported synthesis and characteri-
zation of
a
series of raloxifen-like 2-benzoyl-3-
ferrocenylbenzoijb]thiophene derivatives containing several
terminal alkylamino groups bonded to a benzoyl substituent,
which displayed interesting activity against several tumor cell
lines in vitro. Compound IV, an intermediate in the synthesis
of these benzo[b]thiophene compounds, was prepared by a
Friedel–Crafts-type acylation of ferrocene with chloroacetyl
chloride, followed by
a nucleophilic substitution with
3-methoxybenzenethiolate. The characterization of the novel
Centro de Química Estrutural, Instituto Superior Técnico, Universidade de Lisboa,
Av. Rovisco Pais, 1049-001 Lisboa, Portugal. E-mail: joao.luis@ist.utl.pt;
Fax: +351 218417246; Tel: +351 218419282
† Electronic supplementary information (ESI) available. CCDC 1044508–1044513
and 1051170. For ESI and crystallographic data in CIF or other electronic format
see DOI: 10.1039/c5ce00149h
Fig. 1 Structures of the 1-ferrocenyl-2-IJaryl)thioethanones discussed
in the paper. I, R = H; III, R = 4-methoxy; IV, R = 3-methoxy; , R =
4-Cl; , R = 3-Cl; VII, R = 2-Cl; and VIII, R = NO2.
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molecules is the absence of hard hydrogen donors. The for-
mation of hydrogen bonds is, therefore, almost limited to C–
H⋯O interactions mainly with the carbonyl group, a group
that is recognized as one of the best acceptors in this type of
weak hydrogen bonds.2 One of the objectives of this work is
to establish that in this series of molecules, the C–
H⋯Ocarbonyl interactions are determinant in the design of the
supramolecular networks, an assumption commonly
acknowledged in the absence of stronger donors and
acceptors.3,4
a complete comparison of the structural characteristics for
the whole series of compounds analysed herein.
Bond lengths and angles are similar in all eight molecules
and well within the expected range, as judged from extensive
analysis of the values included in the CSD.13,14 The main dif-
ferences in the geometric parameters of the compounds lie
in the relative values of the CIJ11)–CIJ12)–SIJ1)–CIJ13) torsion
angle whose values range from 71 to 85° for compounds I to
VII, while compound VIII exhibits values of 174–177° (see
Table 2).
The presence of a sulphur atom in the molecules creates
the possibility of C–H⋯S and OC⋯S interactions.5–7 The
aromatic rings present can be involved in C–H⋯π and π–π
contacts.8,9
This angle defines the relative orientation between the aryl
ring and the cyclopentadienyl (Cp) rings of the ferrocenyl
moiety, a feature that divides these compounds in three clas-
ses: compound I, where the phenyl-containing moiety is
rotated around the CH2–S bond towards the unsubstituted
Cp ring; compounds II–VII, in which the aromatic group also
rotates around the same bond, but in the opposite direction,
i.e. away from the unsubstituted Cp ring, and finally com-
pound VIII, where a NO2 group occupies the para position in
the phenyl and the ring lies almost coplanar to the
substituted Cp ring. The rationale for these different molecu-
lar orientations will be analysed together with the study of
the supramolecular arrangements, since they are both based
on the intra- and intermolecular contacts.
A notable structural feature that differentiates compounds
II to VII is the angle β (see Fig. S1 – ESI†) between the plane
of the aryl ring and the plane bisecting the ferrocenyl moiety
(containing atoms C(1), Fe(1) and C(6)) that decreases from
ortho- to meta-substituted compounds and from these to
para-substituted compounds (see Table 2). Two arguments
will be used to explain these differences: charge repulsion
between the aryl and the carbonyl groups and steric hin-
drance; both will be addressed in the next section.
Introducing substituents with acceptor characteristics
might create other regions in the molecules that are active
for supramolecular interactions and can be strong competi-
tors against the carbonyl group for the dominant role in the
definition of the supramolecular arrangement. Our originally
studied compound IV contained a methoxy group bonded to
the meta position of the phenyl ring with its oxygen atom
involved in C–H⋯O hydrogen bonds.1 This study analyses
the effect on the network that results from removing this sub-
stituent or moving it to the para position, as well as from
inserting another good acceptor, the nitro group, in the same
position. The other substituent to be examined is chlorine, a
choice based on the various types of interactions in which
this atom can get involved (C–H⋯X, type I and type II halo-
gen bonds),10–12 and their characteristic bonding parameters,
whose high directionality12 can strongly influence the crystal
frameworks. Finally, we also discuss the effect of replacing
the phenyl ring with the naphthyl group, which is a more
extended aromatic system.
The electrostatic contribution to most of the mentioned
intermolecular contacts suggests that the calculation of point
charges for the atoms present in these molecules can be use-
ful in the analyses of preferential interaction places. This esti-
mate is achieved herein by DFT computations and the results
are also used to represent electrostatic potential maps that
can be utilized to explain repulsions between major molecu-
lar electronic density areas and their influence on the supra-
molecular structures.
Electrostatic charge distribution
The electrostatic charge distributions in each compound were
evaluated by ab initio calculations (see the Experimental sec-
tion). These distributions were used to map electrostatic
potentials onto electron density isosurfaces (Fig. 4) for the
eight compounds. The calculated point charges for the indi-
vidual atoms will be mentioned in the text whenever relevant
and are displayed in totality in Table S2 (see the ESI†).
The skeleton of compounds I and II is limited to the
ferrocenyl group, the bridge, and an aromatic group (phenyl
or naphthyl). The aromatic groups contain the largest con-
centration of electronic density in these molecules, apart
from the bridge (which includes the carbonyl group and a
sulphur atom) (Fig. 4, I and II). In compound II, the larger
aromatic ring results in both more pronounced steric
restraints that prevent the folding of the molecule onto itself
and higher charge density. In combination, these features
force the naphthyl group to move away from the carbonyl,
resulting in values of 144.51IJ37)° (molecule 1) and
147.06IJ31)° (molecule 2) for the β angle, as opposed to
129.30IJ9)° in compound I.
Results and discussion
X-ray diffraction studies
Single crystal X-ray diffraction analysis allowed us to fully
characterize the eight 1-ferrocenyl-2-IJaryl)thioethanone com-
pounds (Fig. 2 and 3). Some of their crystal parameters are
reported in Table 1, while selected geometrical parameters
are presented in Table 2 (see also Table S1 – ESI†). We have
previously reported the molecular structure of compound IV
and a preliminary survey of its supramolecular arrangement.1
Nonetheless, the main features of IV are depicted in the
tables and figures included in this section in order to achieve
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Fig. 2 ORTEP diagram, drawn with 50% probability ellipsoids, showing the atomic labelling scheme for 1-ferrocenyl-2-IJphenyl)thioethanone (I),
1-ferrocenyl-2-ij(naphthalen-2-yl)thio]ethanone (II), 1-ferrocenyl-2-ij4-IJmethoxyphenyl)thio]ethanone (III) and 1-ferrocenyl-2-ij3-IJmethoxyphenyl)-
thio]ethanone (IV).1
Compounds III and IV have a methoxy group in the para
and meta positions of the phenyl group, respectively (Fig. 2).
Its oxygen atom displays a negative point charge (−41 and
−40 atomic charge unit percentage (acu%) for III and IV,
respectively) similar to that of the carbonyl oxygen (−50 acu%
for both molecules) (Fig. 4), and therefore these two groups
should repel each other. This effect is not very strong in III,
due to the para position of the methoxy substituent, and so
the β angle is smaller IJ133.17IJ7)°) than those observed in I
and II; in IV, however, the meta substituent is closer to the
carbonyl, compelling the phenyl ring to rotate and the angle
between the two planes to open IJ155.68IJ8)°).
Compounds V, VI and VII have a chlorine atom occupying
the para, meta and ortho positions in the phenyl ring,
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Fig. 3 ORTEP diagram, drawn with 50% probability ellipsoids, showing the atomic labelling scheme for 1-ferrocenyl-2-ij4-IJchlorophenyl)thio]-
ethanone (V), 1-ferrocenyl-2-ij3-IJchlorophenyl)thio]ethanone (VI), 1-ferrocenyl-2-ij2-IJchlorophenyl)thio]ethanone (VII) and 1-ferrocenyl-2-
ij4-IJnitrophenyl)thio]ethanone (VIII).
respectively. Two important conclusions can be drawn from
Fig. 4, and the most noticeable one is that the chlorine atoms
show a negative charge, although their point charges (−15,
−14 and −11 acu%, respectively) are not as intense as those
of the methoxy oxygens. The second feature is the anisotropic
charge density at the halogen atoms, originally referred by
Metrangolo et al.,12 that consists of an electron deficient “cyl-
inder” along the C–halogen bond axis (the area on the top of
the atom in green), surrounded by an electronegative ring
(the area in yellow). As for the methoxy substituted com-
pounds, the β angle increases from the para- IJ115.06IJ27)–
117.24IJ30)°) to the meta-substituted compound IJ142.09IJ20)°),
with the larger value observed for the ortho compound
IJ177.37IJ16)°). This trend can again be rationalized as a
consequence of the growing repulsion between the carbonyl
group and the chlorine. It should be noted that the angles
for the para- and meta-substituted compounds are smaller
with chlorine than those with methoxy substituents due, in
part, to the higher point charges of the methoxy oxygens; in
addition, the larger relative volume of the methoxy substitu-
ent may also be a factor.
The electron density surface of compound VIII (Fig. 4)
shows the existence of two areas with a large density of
electronic charge: the carbonyl oxygen and the nitro group.
The main feature that distinguishes this molecule from the
other seven is the almost planar arrangement of the entire
atomic framework spanning from the substituted Cp to the
nitro group. This group acts as a strong electron attractor by
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Table 1 Crystal parameters for compounds I–VIII
a (Å)
b (Å)
c (Å)
α (°)
β (°)
γ (°)
Packing
index
(%)
Space
group
Chem. formula
C18H16Fe1O1S1
Cryst. system
Z
Z′
I
Monoclinic
Orthorhombic
Triclinic
C2/c
18.895(5)
5.769(3)
26.820(6)
10.570(5)
7.329(4)
90
90.989(5)
90
90
90
90
112.724(5)
94.083(8)
94.391(10)
90
97.571(2)
90
90
90
8
1
71.9
68.6
71.1
70.7
70.7
71.0
II
C22H18Fe1O1S1
Pca21
8
2
4
8
4
4
4
2
1
1
2
1
1
2
45.553(8)
5.706(3)
¯
P1
III
IV1
V
C19H18Fe1O2S1
11.339(5)
13.634(5)
21.5959(8)
7.3570(3)
10.2431(3)
24.794(5)
5.846(3)
21.572(4)
7.6287(18)
23.333(6)
9.210(2)
7.119(3)
23.6200(8)
9.661(2)
6.0532(19)
34.587(8)
7.827(2)
C19H18Fe1O2S1
Monoclinic
Orthorhombic
Monoclinic
Monoclinic
Monoclinic
P21/c
Pna21
P21/c
P21/n
P21
C18H15Fe1O1S1Cl1
C18H15Fe1O1S1Cl1
C18H15Fe1O1S1Cl1
C18H15Fe1O3S1N1
90
90
VI
VII
VIII
108.146(9)
90
90
108.071(7)
90
90
71.3
a
101.767(9)
90
a
Could not be calculated due to disorder in the Cp ring.
Table 2 Selected geometrical parameters for compounds I–VIII
Angles (°)
I
II
III
IV
V
VI
VII
VIII
CIJ7)–CIJ6)–CIJ11)–CIJ12)
−179.38IJ18) −4.1IJ14),
−167.2IJ8)
157.44(13) 165.09(18) 167.3(7),
178.5(5)
−164.7IJ4) −171.4IJ8),
−165.6IJ6)
173.2(7)
CIJ10)–CIJ6)–CIJ11)–CIJ12)
CIJ11)–CIJ12)–SIJ1)–CIJ13)
7.0(3)
168.8(8), 7.5(14)
−17.8IJ2)
−9.0IJ3)
−4.6IJ9), 5.3(9)
−4.1IJ8)
9.4(6)
−1.3IJ13),
1.9(13)
74.00(17)
76.7(8), −76.8IJ7)
−71.04IJ12) 73.92(17) 85.3(5), −82.9IJ6)
−74.0IJ4)
78.9(3)
177.8(6),
−174.8IJ6)
0.4(13), 3.0(10)
−0.8IJ13),
10.9(11)
CIJ15)–CIJ16)–NIJ1)–OIJ3)
CIJ17)–CIJ16)–NIJ1)–OIJ2)
—
—
—
—
—
—
—
—
—
—
—
—
—
—
CIJ15)–CIJ16)–OIJ2)–CIJ19)
CIJ17)–CIJ16)–OIJ2)–CIJ19)
CIJ16)–CIJ15)–OIJ2)–CIJ19)
CIJ14)–CIJ15)–OIJ2)–CIJ19)
β ijCIJ1)–FeIJ1)–CIJ6)/-
—
—
—
—
—
—
—
—
−1.2IJ2)
179.36(15)
—
—
—
—
—
—
—
—
—
—
—
—
—
—
—
—
—
—
−170.8IJ2)
—
8.9(3)
129.30(9)
144.51IJ37),
147.06(31)
133.17(7) 155.68(8) 115.06IJ27),
142.09(20) 177.37(16) 79.88(35)a
aromatic ring]
117.24(30)
a
Could not be calculated due to disorder in the Cp ring.
both induction and resonance, thereby promoting the estab-
lishment of an extended conjugated π-system that causes the
whole molecular moiety containing the phenyl ring to adopt
this geometry.
candidate for the best hydrogen bond acceptor, while only
carbon atoms can act as hydrogen donors. So it is not sur-
prising that weak C–H⋯Ocarbonyl hydrogen bonds are the
main intermolecular interactions. The intermolecular contact
structural parameters are listed in Table S3 (the ESI†).
1-Ferrocenyl-2-IJphenyl)thioethanone (I). The electrostatic
potential map of this compound (Fig. 4) displays an area with
large electron density, involving the carbonyl group and the
sulphur–methylene bridge and centred at the oxygen atom
(−51 acu%).
Supramolecular arrangements
The structural characteristics of compounds I–VIII, the types
of substituents present, and the point charges (see Table S2 –
ESI†) indicate that the carbonyl oxygen is the strongest
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in opposite directions along b (as growing direction, we con-
sider the orientation of the
C
Ph–H⋯Ocarbonyl hydrogen
bonds). These double chains interact along c through parallel
displaced π–π stacking interactions9 involving the substituted
Cp rings (Fig. 6).
1-Ferrocenyl-2-ij(naphthalen-2-yl)thio]ethanone (II). Com-
pound II is expected to present a similar supramolecular
arrangement to that of I, because a non-substituted aromatic
system is connected to the sulphur atom. As anticipated, the
primary motif is again composed of linear C(7) chains
formed by Caryl–H⋯Ocarbonyl hydrogen bonds, growing along
b; however, as the compound displays Z′ = 2, these chains are
formed separately by type 1 and type 2 molecules (Fig. 7).
Hydrogen atoms have very similar point charges, so the
choice of those involved in the interactions is once again
determined by their relative position, leading towards a more
compact structure.15
The aromatic system in II is larger than that in I,
favouring π interactions but imposing more steric restraints.
Actually, a “V”-structured double chain is formed based on
Caryl–H⋯πaryl interactions with type 1 molecules acting as
hydrogen donors (Fig. 7 and S2†). In order to attain this her-
ringbone arrangement, the S-aryl group rotates around the
SIJ1)–CIJ12) bond, but in the direction opposite that observed
in I, positioning the π-system away from the ferrocenyl group
and allowing greater freedom for supramolecular interactions.
These “V”-chains align on top of each other in alternated
directions, forming an angle of 81.8° between the axes of
ferrocenyl moieties (see the ESI,† Fig. S3). The aromatic
groups are not stacked, so this arrangement results mainly
from Cmethylene–H⋯πaryl contacts.
Fig.
4 Electrostatic potential mapped onto an electron density
isosurface for compounds I to VIII. Positively or negatively charged
regions are indicated by color gradients changing from blue to red,
respectively.
1-Ferrocenyl-2-ij4-IJmethoxyphenyl)thio]ethanone
(III).
Despite the presence of the methoxy group, the carbonyl oxy-
gen remains the strongest hydrogen bond acceptor in this
molecule. The supramolecular arrangement of the
para-methoxy compound (III) involves, as a primary motif,
The presence of a dispersed negative charge on the phenyl
ring, together with the possibility of rotation of the S–phenyl
group around the SIJ1)–CIJ12) bond, in order to leave the ring
facing one C–H bond of the unsubstituted Cp ring, CIJ1)–HIJ1),
enables the formation of a CCp–H⋯πPh intramolecular bond.
The formation of this intramolecular bond essentially
explains the different molecular structures of this compound
when compared to the others (II–VIII) included in this survey.
the formation of
a –
bifurcated16 hydrogen bond: CPh
H⋯Ocarbonyl and CCp–H⋯Ocarbonyl. This results from competi-
tion for the best acceptor between the two hydrogen atoms
with higher point charges that are geometrically better posi-
tioned to engage in C–H⋯Ocarbonyl hydrogen bonds, H(10)
(18 acu%) and H(18) (13 acu%); these bifurcated hydrogen
bonds form chains along a (Fig. 8 and S4†).
Compound
I
displays
a
supramolecular arrangement
Two of these chains, growing in opposite directions, inter-
act forming again a double chain, also along a, by means of
based on CPh–H⋯Ocarbonyl C(7) chains, involving CIJ18)–H-
IJ18)⋯OIJ1) hydrogen bonds (Fig. 5). DFT calculations show
that H(5) is the hydrogen atom with a more positive point
charge (+15 acu%), while H(18) displays a slightly smaller
value (+11 acu%). Thus, the choice of donor atoms must be
based on other factors besides electrostatic reasons. Had the
C–H⋯Ocarbonyl hydrogen bond involved the H(5) atom, the
resulting structure would not be as compact (with a packing
index (PI) of 71.9%).
C
methylene–H⋯Ocarbonyl hydrogen bonds, reinforced by CCp
H⋯S contacts (Fig. 8). So the oxygen atom of the carbonyl
group is actually involved in a trifurcated hydrogen bond,19
–
a
situation explained by the H(12) point charge (12.8 acu%),
the largest value found for methylene hydrogens in all the
eight compounds studied.
The presence of a group that can act as both an acceptor
and a donor will certainly influence the crystal packing of
this compound. The growth on the bc plane is based on inter-
The electrophilic character of the carbonyl C atom, C(11)
(+50 acu%), brings about its participation in weak S⋯CIJπ)O
interactions7 (S(1) = −31 acu%) between two chains “growing”
actions that precisely involve the methoxy group: CCp
–
H⋯Omethoxy hydrogen bonds and methoxy–H⋯πCp short
C
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Fig. 5 Intramolecular CCp–H⋯π hydrogen interaction in I (left); chains of molecule I growing along b (right) through CPh–H⋯Ocarbonyl (in red).
Fig. 6 Double chains of compound I molecules along b, formed by S–Ccarbonyl interactions (in black) (left). π–π interactions along c are depicted in
purple (right).
contacts (Fig. 9). These latter interactions do not result from
a large positive point charge in H(19A), but rather from the
global positive charge of the methyl group (25 acu%), a situa-
tion that can be visualized with the blue area around this
group in Fig. 4.
1-Ferrocenyl-2-ij3-IJmethoxyphenyl)thio]ethanone (IV). The
main motif in compound IV is again C(7) chains along the b
axis involving CPh–H⋯Ocarbonyl hydrogen bonds (Fig. 10). The
choice of H(18) (14 acu%) is not based on electrostatic rea-
sons. H(14) displays a larger point charge value (21 acu%);
however, the stereochemical hindrance imposed on the
CIJ14)–HIJ14) bond by the two ortho substituents precludes its
participation in the intermolecular contacts.
Due to the relative positioning of the phenyl ring and the
methoxy group, the C–H⋯O chains form a planar network of
double chains on plane ab with the creation of very stable
R22(8) synthons (Fig. 10).
Despite the different secondary motifs, molecules III and IV
display similar packing indexes (71.1 and 70.7%, respectively).
1-Ferrocenyl-2-ij4-IJchlorophenyl)thio]ethanone (V). In the
para-chlorophenyl substituted compound (Z′ = 2), the most
negative point charge is again located in the carbonyl oxygen
(−49 and −50 acu%) and not in the chlorine (−15 and −14
acu%), suggesting that the molecules should organize again
in linear chains formed by the CCp–H⋯Ocarbonyl interactions
both in type 1 and in type 2 molecules. The Cp hydrogen
atoms involved (C(10) and C(10A)) are the ones displaying
the larger point charges (18 and 17 acu%) in each type of
molecule.
Fig. 7 Chains of compound II along b, formed via Caryl–H⋯Ocarbonyl
hydrogen bonds (on the left are type I molecules and on the right are
type II molecules). Caryl–H⋯πaryl interchain contacts are represented in
purple.
These chains grow in opposite directions along b and they
interact with each other, forming a double chain (Fig. 11).
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Fig. 8 Chains of molecule III along a (left), with the CPh–H⋯Ocarbonyl and CCp–H⋯Ocarbonyl hydrogen bonds represented in red; details of the
double chains formed through Cmethylene–H⋯Ocarbonyl hydrogen bonds (blue) and CCp–H⋯S contacts (green) (right).
Fig. 9 Supramolecular arrangement of compound III on plane bc, based on methoxy group interactions: CCp–H⋯Omethoxy hydrogen bonds (black)
and Cmethoxy–H⋯πCp contacts (purple).
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It is worth noting that the values of the H⋯Cl–C angles
are close to 100°, which are in good agreement with study by
Glaser et al. who reported several CIJsp2)–H⋯Cl–CIJsp2) inter-
actions with H⋯Cl distances in the range 3.00–3.41 Å and
H⋯Cl–C angles in the range 79.7–143°.10
It is well known that halogen intermolecular contacts
heavily depend on the charge density anisotropy around the
halogen nuclei.11,12,17,18 This charge distribution allows the
atom to act both as a donor and as an acceptor of electron
density. As a donor, it can intervene in C–H⋯X hydrogen
bonds.18–20 The small angles obtained are in good agreement
with a donor–acceptor interaction between the electronega-
tive ring of the halogen and an electronic deficient atom like
hydrogen.
The compact arrangement (PI = 70.7%) in V is due to both
Cl⋯Cl interactions between molecules in different double
chains and the
C
Cp–H⋯Cl contacts mentioned above,
forming bifurcated bonds involving each chlorine atom.
These Cl⋯Cl contacts display C–X⋯X angles that fall into
Desiraju's definition of type I halogen bonds,11 with van der
Waals interactions between the negative belts of two halo-
gens (see Fig. 12).
1-Ferrocenyl-2-ij3-IJchlorophenyl)thio]ethanone (VI). The
packing of VI shows, as a primary motif, a zigzag chain,
along c, formed by CCp–H⋯Ocarbonyl involving a hydrogen
atom from the unsubstituted Cp ring. This chain is shaped
not only by these hydrogen bonds but also by bifurcated C–
H⋯πCp interactions (see Table S3†). The supramolecular
motif grows along b through bifurcated C–H⋯Cl between
two chains in reversed orientation (Fig. 13).
Fig. 10 Supramolecular arrangement of compound IV on plane ab,
formed by
C
Ph–H⋯Ocarbonyl (red) and
C
Ph–H⋯Omethoxy hydrogen
bonds (blue).
The role of halogen atoms in directing molecular self-
assembly phenomena has been discussed since 1970 (ref. 21)
and reported in the literature for various types of halogen
(particularly chlorine) contacts.22 The supramolecular
arrangement of VI is determined by competition between C–
H⋯O and C–H⋯Cl hydrogen bonds, and instead of a C–
H⋯O linear chain, a zigzag chain supported by a C–H⋯Cl
network is obtained. This C–H⋯O zigzag chain no longer
involves the hydrogen with the larger electronic point charge
This arrangement involves
C
Cp–H⋯Cl reinforced by
Cmethylene–H⋯πPh contacts. The Cmethylene–H⋯πPh interac-
tions result from the unusually high point charges for
the methylene H(12A) (10 acu%) and H(12D) (11 acu%)
and from the relative positioning of the phenyl ring and
the ferrocene moiety.
Fig. 11 Double chains of compound V: CCp–H⋯Ocarbonyl hydrogen bonds (red), CCp–H⋯Cl contacts (green) and Cmethylene–H⋯πPh contacts
(purple) (left); interaction between two double chains involving bifurcated halogen bonds (interchain Cl⋯Cl and intrachain CCp–H⋯Cl bonds)
(right).
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again a hydrogen atom of the unsubstituted Cp and a hydro-
gen atom of a methylenic moiety.
These chains interact with each other along b by CCp
H⋯Cl interactions forming a planar arrangement (Fig. 14).
–
Another planar motif is formed by zigzag chains involving
CCp–H⋯S interactions, reinforced by CCp–H⋯πPh contacts,
Fig. 12 Electrostatic potential mapped onto an electron density
isosurface for the Cl⋯Cl interaction between two molecules of V.
and CIJ9)–HIJ9)⋯ClIJ1) interactions (Fig. 14). The two planar
arrangements form an angle of 108.1° and they interact
through CIJ2)–HIJ2)⋯SIJ1) contacts (see Fig. S4†). Despite the
different crystalline arrangements, compounds VI and VII
show PI values (71.0 and 71.3%, respectively) identical to
those of the compounds discussed above.
1-Ferrocenyl-2-ij4-IJnitrophenyl)thio]ethanone (VIII). The
nitro group is a good hydrogen acceptor, but the carbonyl
oxygen is again the atom with the most negative point charge
(−45 and −47 acu% for molecules 1 and 2, respectively, with
values of −39 to −40 acu% for the nitro oxygens). Thus, the supra-
molecular arrangement of compound VIII shows, as a primary
motif, CCp–H⋯Ocarbonyl C(5) chains, formed separately by type 1
and type 2 molecules (Z′ = 2) (Fig. 15, red interactions).
The carbonyl oxygen in this compound is actually a bifur-
cated acceptor, contributing to the formation of ladders of
type 1 and type 2 molecules (Fig. 15, blue interactions).
The presence of a strong acceptor, like NO2, as a substitu-
ent in the phenyl ring plays a key role in the final crystal and
molecular structures of this compound. In order to achieve
more compact packing, this group promotes the interaction
between type 1 and type 2 molecules, with the formation of
two CCp–H⋯Onitro hydrogen bonds between one oxygen of
the nitro group and a hydrogen of the unsubstituted Cp ring
(Fig. 16). To facilitate these interactions, the two molecules
assume an orientation in which the phenyl ring, the bridging
group and the substituted Cp are nearly coplanar. The
electrostatic potential map of this dimer formation can be
visualized in Fig. 16, where the partial charge transfer
between the nitro and the unsubstituted Cp groups can be
clearly seen.
Fig. 13 Supramolecular arrangement of VI: zigzag chains formed by
C
Cp–H⋯Ocarbonyl hydrogen bonds (red), C–H⋯πCp contacts (purple)
and interchain C–H⋯Cl interactions (green).
((H(10) ~18 acu%) or any other hydrogen (like H(18) ~14
acu%) opposite the carbonyl group, but a hydrogen atom
with lower electronic density located in the upper Cp ring
(H(1) ~9.5 acu%) (Fig. 13).
1-Ferrocenyl-2-ij2-IJchlorophenyl)thio]ethanone (VII). As in
the previous compound, the driving crystal motif is a zigzag
chain formed by C–H⋯Ocarbonyl hydrogen bonds, but this
time (due to the relative orientation of the chlorophenyl ring
and the ferrocene moiety) the bifurcated interactions involve
Fig. 14 View along a of zigzag chains of compound VII: CCp–H⋯Ocarbonyl (red) and Cmethylene–H⋯Ocarbonyl (blue) hydrogen bonds (left) and
interactions involving CCp–H⋯S (yellow) and CCp–H⋯πPh (purple) contacts (right). CCp–H⋯Cl interactions are displayed in green.
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Fig. 15 Ladders of molecules VIII-type 1 (left) and VIII-type 2 (right), based on CCp–H⋯Ocarbonyl hydrogen bonds.
Fig. 16 Interactions between type 1 and type 2 molecules of compound VIII (left). Electrostatic potential mapped onto an electron density
isosurface for these interactions (right).
Conclusions
grouped in double chains; in these compounds, further
assemblage is promoted by S–CIJπ)O and C–H⋯π contacts.
Compounds III and IV have a methoxy group in the phe-
nyl ring in para and meta positions, respectively. From DFT
calculations, it could be inferred that the oxygen in this
group displays smaller values of negative point charge than
that in the carbonyl moiety. So the primary motif will be
again C(7) chains, using CIJ18)–HIJ18)⋯Ocarbonyl hydrogen
bonds, in both compounds. The different positioning of the
methoxy group dictates different crystal packing arrange-
ments. In III, due to its terminal para position, the formation
of double chains is allowed through C–H⋯S hydrogen bonds,
The eight compounds studied in the current manuscript dis-
play identical functionalities: the ferrocenyl moiety, the oxo-
ethylthio bridge and an aromatic system. The main distinc-
tion between them resides in the presence (or the absence) of
different substituents in various positions of the aromatic
system. It is possible to identify in these molecules five
groups that can interact by donor–acceptor recognition pro-
cesses: the carbonyl group, the sulphur atom, the π-ring sys-
tems, the substituent groups and the aromatic C–H bonds.
The strongest acceptor present is, undoubtedly, the carbonyl
oxygen atom, as confirmed by DFT calculations. Therefore, as
the carbon atoms are the only possible hydrogen donors, the
primary motifs expected in all supramolecular arrangements
are C–H⋯Ocarbonyl hydrogen bonds. Based on an electrostatic
approach, it is extremely difficult to predict where these bonds
should take place, in view of the very similar values of the
point charges in the various hydrogen atoms (see Table S2†).
Compounds I and II, where aryl substituents are absent,
display C(7) chains involving CIJ18)–HIJ18)⋯Ocarbonyl as the
primary motif. H(18) does not show the highest point charge
among the hydrogen atoms but it is correctly positioned in
the molecule inducing the formation of this stable supramo-
lecular arrangement, and allowing complementary inter-
molecular contacts that stabilize the energetics and reinforce
the compactness of the crystal. These C(7) chains are
completing the final 3D structure by means of CCp
–
H⋯Omethoxy and Cmethoxy–H⋯πCp short contacts. In IV, how-
ever, the meta position of the methoxy group induces the for-
mation of planar double chains, based on R22(8) homo-
synthons defined by C⋯Hphenyl⋯Omethoxy contacts.
Compounds V, VI and VII present chlorine atoms as phe-
nyl substituents in para, meta, and ortho positions, respec-
tively. The competition between C–H⋯O and C–H⋯X hydro-
gen bonds in directing molecular self-assembly phenomena
is well known (particularly for chlorine); to achieve this con-
trol over crystallization patterns halogen atoms make use of
the high directionality of their interactions. This suggests
that competition between C–H⋯O and C–H⋯Cl hydrogen
bonds will determine the supramolecular arrangement in
these compounds.
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In compound V, chlorine has a lower negative point
main driving force, the leading factor in the choice of donor
atoms involved in the interactions is not their electron charge
but their position in the molecule. This results in the optimi-
zation of the crystal packing compacity.
charge when compared to the carbonyl oxygen, but due to
their relative distance, the latter still dictates the primary
motif, that is again C–H⋯O chains. However, the chlorine
atoms not only promote the interactions involved in the sec-
ondary motifs (CCp–H⋯Cl and type
I
Cl⋯Cl contacts,
Experimental section
Syntheses
forming a double chain) but also cause the involvement of
C(10) instead of C(18) in the C–H⋯O chains in order to facili-
tate the halogen interactions, achieving an arrangement that
is favourable not only in terms of compactness but also ener-
getically due to the larger number of interactions formed.
In compounds VI and VII this C–H⋯O and C–H⋯Cl com-
petition, controlled by the positioning of the chlorine atom
together with its greater proximity to the carbonyl group, cre-
ates an intercrossing of C–H⋯O zigzag chains and C–H⋯Cl
chains. However, in these compounds, the hydrogen atom
involved in the C–H⋯O hydrogen bonds is located in the
unsubstituted Cp ring and, despite showing low electronic
density values, plays a central role in achieving a more com-
pact array.
Potassium t-butoxide (1.5 equiv.) was added to a solution of
benzenethiol (14 mmol) in 30 mL of anhydrous diethyl ether,
and the suspension was stirred at room temperature for ca.
1 h. 2-Chloro-1-ferrocenylethanone [5.6 g, 1.5 equiv.] was
added and the mixture was stirred overnight. The solid mate-
rials were then removed by filtration over Celite. The thio-
ether precipitated upon cooling, and the crystals were col-
lected by filtration and dried under vacuum.
The synthesis and spectral characterization (IR, 1H and
13C NMR, and MS) of 1-ferrocenyl-2-ij3-IJmethoxy)phenylthio]-
ethanone (IV) was reported in our previous study.1
The spectral characterization data for the remaining
1-IJferrocenyl)-2-IJaryl)thioethanones discussed in the current
paper is presented in detail in the ESI† file.
The absence of Cl–Cl bonds both in VI and VII may be
explained by the large volume and polarizability of the halo-
gen atom when compared to hydrogen. Thus, due to the meta
and ortho positions of the chlorine atom in relation to the
thioether substituent, C–H⋯X hydrogen bonds are favoured
over Cl⋯Cl interactions for steric reasons. This situation
does not exist in V, in which the greater exposure of the
para-chlorine atom favors the establishment of type I halogen
bonds.
X-Ray crystallographic analysis
X-ray crystallographic data for compounds I to VIII were col-
lected from crystals using an area detector diffractometer
(Bruker AXS-KAPPA APEX II) equipped with an Oxford
Cryosystem open-flow nitrogen cryostat at 150
K and
In compound VIII, the para-nitrophenyl substituted mole-
cule, the effect of the resonance characteristics of the nitro
group is immediately shown in the molecular structure of the
compound, causing the planarity of the bridge-phenyl-nitro
system. DFT calculations also proved that the oxygen atoms
in this group as acceptors are not as good as the carbonyl
oxygen. This fact creates the conditions for the supramolecu-
lar primary motif in VIII to be similar to those of compounds
I–IV. However, instead of C(7) chains containing C(18), the
arrangement is built upon C(5) chains involving C(10), which
is better placed for this purpose than the C(18) due to the
planarity of the aryl moiety. The nitro group acceptor capacity
also contributes to the final compact dimers formed by sec-
ondary hydrogen bonds with an H from the unsubstituted Cp
ring.
In conclusion, the overall crystalline structures of this
series of compounds are determined not only by weak
C–H⋯O hydrogen bonds but also by the presence of substitu-
ents. These functional groups play an important role in
directing the buildup of the crystalline framework, because
of their intrinsic donor–acceptor properties and their relative
positioning. Certain substituents, such as chlorine, also pres-
ent distinctive types of interactions that affect the molecular
self-assembly phenomena.
graphite-monochromated Mo Kα (λ = 0.71073 Å) radiation.
Cell parameters were retrieved using Bruker SMART software
and refined with Bruker SAINT23 on all observed reflections.
Absorption corrections were applied using SADABS.24 The
structures were solved by direct methods using SIR 97 (ref.
25) and refined with full-matrix least-squares refinement
against F2 using SHELXL-97.26 All the programs are included
in the WINGX package (version 1.70.01).27 All non-hydrogen
atoms were refined anisotropically, and the hydrogen atoms
were inserted in idealized positions, riding on the parent C
atom, except for the methoxy hydrogens, whose orientation
was refined from electron density, allowing the refinement of
both O–C torsion angles and C–H distances. Drawings were
made with ORTEP3 for Windows.28 Geometrical parameters
such as average bond lengths, distances to centroids, angles
between planes and intramolecular and intermolecular inter-
actions were calculated using Platon 310310.29 The same
interactions were visualized and analysed using Mercury
1.4.2 (Build 2).30 Compound VIII displayed disorder in the
CIJ1A)–CIJ5A) Cp ring; modelling this disorder led to site occu-
pancy factors (sof) of 0.67(3) and 0.33(3) and anisotropic
refinement of these atoms implied the use of EADP con-
straints; for reasons of intelligibility, atomic fractions with
smaller values of sof were omitted in all the figures and
tables presented in this work. The correct configuration of
VIII was confirmed reaching a Flack parameter of 0.09(4).
Relevant details of the X-ray data analysis are displayed in
The main result arising from the study of the supramolec-
ular arrangements and DFT calculations presented here is
that, in molecules in which weak hydrogen bonding is the
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Table 3 Crystal and structure refinement for compounds I–III and V–VIII
I
II
III
IV
V
VI
VII
ρcalcd. (g cm−3
)
1.528
1.169
1392
1.454
0.979
1600
1.508
1.071
380
1.575
1.266
1520
1.580
1.271
760
1.594
1.282
760
1.578
1.086
784
Absor. coef. (mm−1
F000
)
θ range (°)
Data collected (h,k,l)
2.62/27.93
2.92/25.46
3.00/28.42
−7 ≤ h ≤ 7
−15 ≤ k ≤ 15
1.89/25.37
2.49/25.26
3.13/25.74
−8 ≤ h ≤ 8
2.36/25.33
−7 ≤ h ≤ 7
−24 ≤ h ≤ 24 −7 ≤ h ≤ 12
−29 ≤ h ≤ 29 −9 ≤ h ≤ 9
−7 ≤ k ≤ 7
−35 ≤ l ≤ 35
25 681/3443
0.0770
−8 ≤ k ≤ 8
−54 ≤ l ≤ 54
15 329/6248
0.0860
−7 ≤ k ≤ 7
−27 ≤ k ≤ 28 −27 ≤ k ≤ 28 −41 ≤ k ≤ 35
−18 ≤ l < = 18 −26 ≤ l ≤ 25
−10 ≤ l ≤ 11
12 798/2769
0.1162
−11 ≤ l ≤ 11
9158/2914
0.0624
−9 ≤ l ≤ 9
11 966/5232
0.0881
Reflections collected/unique
RIJint)
12 012/4047
0.0329
20 655/5647
0.1109
Completeness to Θ max (%)
Max./min. transmission
Data/restraints/parameters
Goodness-of-fit on F2
Final R indices
98.2
99.2
99.2
99.6
98.1
98.4
99.3
0.7998/0.5406 0.9807/0.6955 0.6740/0.5659
3443/0/190
1.032
R1 = 0.0337
wR2 = 0.0718
R1 = 0.0509
wR2 = 0.0779
0.6314/0.4307 0.9750/0.8834 0.9748/0.7836 0.9786/0.8121
5647/13/398
0.756
R1 = 0.0443
wR2 = 0.0561
R1 = 0.0891
wR2 = 0.0637
0.52(3)
6248/1/429
0.975
4047/0/220
1.029
R1 = 0.0281
wR2 = 0.0679
R1 = 0.033
wR2 = 0.0708
2769/0/199
0.994
R1 = 0.0505
wR2 = 0.0984
R1 = 0.1293
wR2 = 0.1241
2914/0/199
1.047
R1 = 0.0513
wR2 = 0.1090
R1 = 0.0841
wR2 = 0.1203
5232/1/429
0.957
R1 = 0.0674
wR2 = 0.1260
R1 = 0.1350
wR2 = 0.1538
0.28(3)
0.0044(4)
0.382/−0.345
R1 = 0.0513
wR2 = 0.0760
R1 = 0.1061
wR2 = 0.0901
0.09(3)
[I > 2sigmaIJI)]
R indices (all data)
Absolute structure parameter
Extinction coefficient
Largest diff. peak/hole (e Å−3
)
0.392/−0.299
0.328/−0.252
0.544/−0.418
0.458/−0.497
0.636/−0.475
0.326/−0.582
Table 3. The crystallographic data for compounds I–III and
V–VIII were deposited with the Cambridge Crystallographic
Data Centre (CCDC 1044508, 1044509, 1044510, 1044511,
1044512, 1044513, and 1051170).
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Press, Oxford, 1999, pp. 293–338.
5 See [4], pp. 230–231.
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each atom in the molecules were calculated from the
electronic density function using an electrostatic surface
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isolated molecules obtained from the crystallographic data
were taken as the reference.
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Acknowledgements
We thank Conceição Oliveira for obtaining the HRMS data
and Agílio A. H. Pádua for allowing access to computer facili-
ties. Thanks are also due to the Portuguese NMR and MS Net-
works (IST-UL Center) for providing access to the facilities.
This work was supported in part by research grants from
Fundação para a Ciência e a Tecnologia (FCT), Portugal [UID/
QUI/00100/2013, RECI/QEQ-QIN/0189/2012, RECI/QEQ-MED/
0330/2012, and FCT-ANR/CTM-NAN/0135/2012], and by a post-
doctoral fellowship from FCT to KS (SFRH/BPD/94291/2013).
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