Influence of quadrupolar interactions on the crystal packing of organic compounds: The pentafluorophenyl ester of a tricyclic α,β-unsaturated-γ-amino acid

Article abstract of DOI:10.1016/S0022-2860(02)00351-4

The single crystal X-ray diffraction structure of (-)-pentafluorophenyl(Z,S,S)-2-(6-oxo-1,3,4,6,11,11a-hexahydro-2H-pyrido[1, 2-b]isoquinolin-11-yliden)acetate (1) is reported. We have found that the crystal packing of the α,β-unsaturated-γ-amino acid derivative 1 is mainly determined by the interaction between the two aromatic rings, namely the benzenic type and the pentafluorinated ring. The crystal packing of 1 shows a herringbone (zig-zag) structure, that is quite typical of aromatic compound with intermolecular arene-arene interactions. The benzenic and the fluorinated phenyl rings in 1 are in a matched face-to-face arrangement. The origin of this interaction can be ascribed to a favourably quadrupolar interaction between both types of aromatic ring. The results reported in the present paper indicate that the pentafluorophenyl ester functionality can be a useful building block in crystal engineering.

Full text of DOI:10.1016/S0022-2860(02)00351-4

Journal of Molecular Structure 641 (2002) 101–107
www.elsevier.com/locate/molstruc
Influence of quadrupolar interactions on the crystal packing of
organic compounds: the pentafluorophenyl ester of a tricyclic
a,b-unsaturated-g-amino acid
a
Enrique Mann , Jose Mahıa , Miguel A. Maestro , Bernardo Herradon
b
b
a,
*
´
´
´
a
´ ´
Instituto de Quımica Organica General, C.S.I.C., Juan de la Cierva 3, E-28006 Madrid, Spain
b
´ ´
Servicios Xerais de Apoio a Investigacion, Campus da Zapateira s/n, Universidade da Corun˜a, E-15071 A Corun˜a, Spain
Received 25 April 2002; revised 1 July 2002; accepted 1 July 2002
Abstract
The single crystal X-ray diffraction structure of (2)-pentafluorophenyl(Z,S,S )-2-(6-oxo-1,3,4,6,11,11a-hexahydro-2H-
pyrido[1,2-b]isoquinolin-11-yliden)acetate (1) is reported. We have found that the crystal packing of the a,b-unsaturated-g-
amino acid derivative 1 is mainly determined by the interaction between the two aromatic rings, namely the benzenic type and
the pentafluorinated ring. The crystal packing of 1 shows a herringbone (zig-zag) structure, that is quite typical of aromatic
compound with intermolecular arene–arene interactions. The benzenic and the fluorinated phenyl rings in 1 are in a matched
face-to-face arrangement. The origin of this interaction can be ascribed to a favourably quadrupolar interaction between both
types of aromatic ring. The results reported in the present paper indicate that the pentafluorophenyl ester functionality can be a
useful building block in crystal engineering. q 2002 Elsevier Science B.V. All rights reserved.
Keywords: Arene–arene interaction; Quadrupolar interaction; Crystal structure; Polyannular heterocycle; a,b-Unsaturated-g-amino acid
1. Introduction
electrostatic multipole moment, magnetic ring
current, etc) [5–7], that render them very active
to participate in numerous interactions. Aromatic
moieties have been reported to interact with other
chemical entities, including other aromatics
(arene–arene interactions) [8–12], electron-donat-
ing groups [13], hydrogen-bond donors [14,15],
hydrocarbonated fragments [16,17], amides [18,
19], halogens [20,21], and cations [22–24].
Intermolecular interactions play key roles in the
structure, reactivity, and properties of organic
compounds [1,2]. The strength of the interaction
depends on the type (electrostatic, dispersion,
charge-transfer, etc) as well as on the relative
orientation of the interacting species [3,4]. Aro-
matic compounds possess several properties (elec-
The structure (both molecular and supramolecu-
lar), the reactivity, and the properties (physical,
physico-chemical, technological, and biological) of
the aromatic compounds are modulated by the nature
of the substituents [25–27]. From an electronic point
tron
charge
distribution,
non-vanishing
*
Corresponding author. Tel.: þ34-91-561-8806; fax: þ34-91-
564-4853.
E-mail address: herradon@iqog.csic.es (B. Herradon).
´
0022-2860/02/$ - see front matter q 2002 Elsevier Science B.V. All rights reserved.
PII: S0022-2860(02)00351-4

102
E. Mann et al. / Journal of Molecular Structure 641 (2002) 101–107
of view, they can be either electron-donor or electron-
acceptor through resonance or inductive effect;
furthermore, a sterically demanding substituent can
distort the planarity of the aromatic systems.
2.79 (distorted dt, J ¼ 12:8; 2.9, 1H), 2.00–1.40 (m,
6H). IR (KBr) n 3380, 2900, 1720, 1620, 1595, 1570,
1490, 1350, 1205, 1085, 970. MS (ES, positive
ionization mode) m=z 446 (Mþ þ Na). Anal. calcd.
for C21H14F5NO3: C, 59.57; H, 3.33; N, 3.31. Found:
C, 59.38; H, 3.12; N, 3.31.
Another important characteristic of arenes is that
most of them, besides having a permanent dipole
moments, possess non-vanishing higher-order elec-
trostatic moments [28], that allows them to
participate in a variety of electrostatic interactions.
The potential (sign and value) of an electrostatic
interaction depends on the distance and the relative
orientation of the dipole/multipole(s).
2.2. Crystal structure of (2)
pentafluorophenyl(Z,S,S )-2-(6-oxo-1,3,4,6,11,11a-
hexahydro-2H-pyrido[1,2-b]isoquinolin-11-
yliden)acetate (1)
In this paper, we report the crystal structure of (2)
pentafluorophenyl(Z,S,S )-2-(6-oxo-1,3,4,6,11,11a-
hexahydro-2H-pyrido[1,2-b ]isoquinolin-11-yliden)
acetate (1); this molecule possesses both a benzenic
type aromatic ring and a pentafluorinated phenyl ring.
The molecular structure of this molecule is quite
suitable to assess the relative importance of diverse
interactions on the crystal packing. Due to the
relevance of aromatic building blocks in the field of
crystal engineering [29], the analysis of the crystal
structure of compound 1 is useful to understand the
different factors influencing the crystal packing of
aromatic compounds [30,31].
Single crystals of 1 were obtained by crystal-
lization from hexane–ethyl acetate. A suitable crystal
(block, white, dimensions 0.50 £ 0.45 £ 0.40 mm3)
was used for the structure determination. X-ray data
were collected using a Bruker SMART CCD area
detector single-crystal diffractometer with graphite
ꢀ
monochromated Mo Ka radiation ðl ¼ 0:71073 AÞ
by the phi-omega scan method. A total of 1271 frames
of intensity data were collected. The integration
process yields a total of 10,382 reflections of which
4576 were independent ½RðintÞ ¼ 0:0402ꢀ: Absortion
corrections were applied using the SADABS program
[33] (maximum and minimum transmission coeffi-
cients, 1.000 and 0.456). The structure was solved
using the Bruker SHELXTL-PC software [34] by direct
methods on F 2. Hydrogen atoms were included in
calculated positions and refined in the riding mode.
The convergence was reached at a final R1 ¼ 0:0441
(for I . 2sðIÞ), wR2 ¼ 0:1304 (for all data), 272
parameters, with allowance for the thermal anisotropy
for all non-hydrogen atoms. The weighting scheme
2. Experimental
2.1. Synthesis of (2)-pentafluorophenyl(Z,S,S )-2-
(6-oxo-1,3,4,6,11,11a-hexahydro-2H-pyrido
[1,2-b]isoquinolin-11-yliden)acetate (1)
C6F5OH (1.04 g, 5.7 mmol), dicyclohexylcarbo-
diimide (DCC, 625 mg, 3 mmol), and 4-dimethyla-
minopyridine (DMAP, 50 mg, 0.40 mmol) were
sequentially added to a solution of acid 2 [32]
(500 mg, 1.9 mmol) in CH2Cl2 (60 ml). The mixture
was stirred at room temperature for 7 h. Then, the
solution was washed with 5% aqueous HCl, water,
saturated aqueous NaHCO3, brine and dried (MgSO4).
The solvent was removed under vacuum and the crude
residue was chromatographed (hexane–EtOAc, 4:1)
to give pure pentafluorophenyl ester 1 (730 mg, 91%).
White solid. Mp 147–149 8C. [a ]D ¼ 2324 (CHCl3,
2
employed was w ¼ ½s2ðFo2 þ 0:0712PÞ ꢀ and P ¼
ðlFol2 þ 2lFcl2Þ=3 and the goodness of fit on F 2 was
1.039 for all the observed reflections. The details of
the data collection and refinement are summarized in
Table 1. Table 2 shows the atomic coordinates and
isotropic displacement parameters for non-hydrogen
atoms. The structure drawings were prepared using
1
2
PLATON and ORTEP-3 programs.
1
c ¼ 0:6). H NMR (300 MHz, 303 K, CDCl3) d 8.33
1
Web address: http://www.cryst.chem.uu.nl/platon/
2
(m, 1H), 7.82 (m, 1H), 7.63 (m, 2H), 6.66 (s, 1H), 5.43
(broad d, J ¼ 11:0; 1H), 4.89 (broad d, J ¼ 13:1; 1H),
Web address: http://www.chem.gla.ac.uk/~louis/software/
ortep3/

E. Mann et al. / Journal of Molecular Structure 641 (2002) 101–107
103
Table 1
Table 2
Atomic coordinates ( £ 104) and equivalent isotropic displacement
Crystal data and structure refinement for 1
2
3
˚
parameters (A £ 10 ) for 1. U(eq) is defined as one third of the
Empirical formula
C21H14F5NO3
trace of the orthogonalized Uij tensor
Fw
423.33
Space group
Crystal system
Z
˚
a (A)
˚
b (A)
P2(1)2(1)2(1)
Orthorhombic
4
x
y
z
U(eq)
F(1)
7780(2)
8089(3)
6583(4)
4726(3)
4399(2)
8273(2)
7218(2)
5832(2)
7968(2)
8854(2)
8012(2)
7022(2)
6191(2)
7132(2)
6336(2)
5879(2)
6551(2)
7668(2)
6189(2)
5133(3)
4441(2)
4798(2)
6034(3)
6465(3)
6086(2)
7027(2)
7168(3)
6392(4)
5490(3)
5335(2)
25366(2)
26245(2)
25329(2)
3607(2)
10,837(1)
12,311(2)
13,476(1)
13,187(1)
11,740(1)
7669(1)
128(1)
179(1)
176(1)
150(1)
115(1)
72(1)
89(1)
82(1)
49(1)
56(1)
60(1)
63(1)
56(1)
48(1)
51(1)
51(1)
50(1)
52(1)
61(1)
69(1)
67(1)
59(1)
66(1)
66(1)
56(1)
72(1)
93(1)
97(1)
83(1)
68(1)
9.8700(2)
10.9262(3)
17.1709(4)
90
F(2)
F(3)
˚
c (A)
F(4)
a ¼ b ¼ g (deg)
F(5)
22749(2)
1230(2)
3
˚
V (A )
1851.74(8)
1.518
O(1)
O(2)
O(3)
N(1)
C(1)
r (calc) (g/cm3)
22058(2)
23656(2)
397(1)
10,689(1)
10,510(1)
8862(1)
mcalc (mm21
)
0.135
˚
Radiation (Mo Ka) (A)
T (K)
0.70173
298(2)
1304(2)
9232(1)
Q range for data collection (deg)
a
2.21–28.27
R1 ¼ 0.0441
wR2 ¼ 0.1304
0.216 and 20.239
C(2)
2266(2)
9643(1)
Final R1 indices ½I . 2sðIÞꢀ
C(3)
1674(2)
10,214(1)
9838(1)
Final wR2 indices (all data)a
C(4)
661(2)
23
)
˚
Largest diff. peak and hole (eA
C(5)
2263(2)
21301(2)
21124(2)
2278(2)
513(2)
9433(1)
P
P
P
C(6)
9071(1)
a
R1 ¼ llFol 2 lFcll= lFol and wR2 ¼ { ½wðFo2 2 Fc2Þ ꢀ=
2
P
C(7)
8262(1)
2
½wðFo2Þ ꢀ}1=2
:
C(8)
7793(1)
C(9)
8099(1)
3. Results and discussion
C(10)
C(11)
C(12)
C(13)
C(14)
C(15)
C(16)
C(17)
C(18)
C(19)
C(20)
C(21)
2134(2)
2815(2)
21636(2)
21796(2)
22314(2)
22586(2)
24030(2)
24936(2)
25373(2)
24905(3)
24033(3)
23594(2)
7013(1)
6707(1)
In connection with our continuous interest on
aromatic compounds [35–38] and on peptide–arene
hybrids3 [39], we have prepared the tricyclic a,b-
unsaturated-g-amino acid 2 (Scheme 1) [32,40], that
has been used as precursor for the synthesis of the
peptide-heterocyclic hybrids of type 3. An intermedi-
ate for the synthesis of 3 is the pentafluorophenyl ester
1 (Scheme 1), that bears a benzenic type ring and a
pentafluorophenyl ring in its structure.
7177(1)
7942(1)
9472(1)
10,270(1)
11,261(1)
11,419(2)
12,177(2)
12,755(2)
12,604(2)
11,871(2)
It is known that benzene and hexafluorobenzene
form a 1:1 complex that have a higher melting point
that either of their components [41]. Although
previous work rationalized this behaviour to different
grounds, it is currently accepted that the origin of this
interaction is through a quadrupole–quadrupole
interaction between the two aromatic compounds
[42].
arrangement of both rings very favourable by
quadrupolar interactions. Two face-to-face aromatic
rings can be totally aligned or they can have their
mass centres displaced each other (offset). The
magnitude of the offset depends on some steric and
electrostatic factors. It has been shown, from both
theoretical [46] and experimental [47] points of view,
that the higher the quadrupolar interaction is, lower is
the offset.
The zz components (perpendicular to the ring
plane) of the quadrupole moment tensors of the
pentafluorinated phenyl ring and of the benzenic-type
ring of 1 are large in magnitude and with opposite
signs [43–45]; this fact makes a face-to-face
On the basis of these premises, we reasoned that
the crystal structure of compound 1 can give
information on the relative importance of different
intermolecular interactions in the crystal packing of
organic compounds. Some putative interactions in the
crystal packing of 1 include arene–arene interactions
3
The hybrids peptide–arene are compounds having one or
several peptidic chain(s) linked to a conformationally rigid scaffold
(either aromatic carbocyclic or heterocyclic).

104
E. Mann et al. / Journal of Molecular Structure 641 (2002) 101–107
Scheme 1.
(and the relative orientation of the aromatic rings),
and fluorine-mediated interactions (fluorine–hydro-
gen, fluorine–arene, and so on) [48,49].
packing. It is worth mentioning that an alternative
arrangement (with the pentafluorophenyl and the
tricyclic system in a coplanar conformation) would
place a fluorine atom and the oxygen carbonyl in the
same plane (and quite close), probably resulting in a
destabilizing interaction from an electrostatic point of
view.
The molecular solid state structure of 1 is shown in
Fig. 1. A selection of geometrical parameters is
indicated in Table 3.
The solid state conformation of the fused tricyclic
system of 1 is quite similar to the one found in
solution (1H NMR evidence in CDCl3) and analogous
to other derivatives of pyrido[1,2-b]isoquinoline [32,
50]. The conformation of the saturated ring of 1 is a
nearly perfect chair with a slight pyramidalization at
the nitrogen atom. An interesting structural feature of
the conformation of the molecule 1 is that the
pentafluorophenyl ring is nearly perpendicular to the
mean plane of the pyrido[1,2-b]isoquinoline ring
system (dihedral angle between the two rings is 848);
this relative orientation is suitable to maximize the
number of intermolecular interactions in the crystal
The most interesting structural feature of the
pentafluorophenyl ester 1 is its crystal packing (Fig.
2). The molecules of 1 are arranged in a herringbone
(zig-zag) supramolecular structure, with an antipar-
allel array of two contiguous molecules (Fig. 3). The
main intermolecular interaction is arene–arene
between the pentafluorophenyl ring and the benzenic
type ring of the two adjacent molecules. The distance
˚
between the geometrical centres of both rings is 4.3 A,
and they are almost perfectly aligned: the offset
˚
between rings is less than 0.2 A, and the angle
between both rings is ca. 68.
Fig. 1. Molecular structure of (2)-pentafluorophenyl(Z,S,S)-2-(6-oxo-1,3,4,6,11,11a-hexahydro-2H-pyrido[1,2-b]isoquinolin-11-yliden)ace-
tate (1). Thermal ellipsoids are represented at 50% probability.

E. Mann et al. / Journal of Molecular Structure 641 (2002) 101–107
105
Table 3
Selected torsion angles (deg) for compound 1
Torsion
Torsion
C(9)–N(1)–C(1)–C(2)
C(5)–N(1)–C(1)–C(2)
N(1)–C(1)–C(2)–C(3)
C(1)–C(2)–C(3)–C(4)
C(2)–C(3)–C(4)–C(5)
C(9)–N(1)–C(5)–C(6)
C(1)–N(1)–C(5)–C(6)
C(9)–N(1)–C(5)–C(4)
C(1)–N(1)–C(5)–C(4)
C(3)–C(4)–C(5)–N(1)
C(3)–C(4)–C(5)–C(6)
N(1)–C(5)–C(6)–C(14)
C(4)–C(5)–C(6)–C(14)
N(1)–C(5)–C(6)–C(7)
C(4)–C(5)–C(6)–C(7)
C(14)–C(6)–C(7)–C(8)
C(5)–C(6)–C(7)–C(8)
C(14)–C(6)–C(7)–C(13)
C(5)–C(6)–C(7)–C(13)
C(6)–C(7)–C(8)–C(10)
C(13)–C(7)–C(8)–C(9)
C(6)–C(7)–C(8)–C(9)
96.9(2)
262.0(2)
54.3(2)
C(1)–N(1)–C(9)–O(1)
C(5)–N(1)–C(9)–O(1)
C(1)–N(1)–C(9)–C(8)
C(5)–N(1)–C(9)–C(8)
C(10)–C(8)–C(9)–O(1)
C(7)–C(8)–C(9)–O(1)
C(10)–C(8)–C(9)–N(1)
C(7)–C(8)–C(9)–N(1)
C(9)–C(8)–C(10)–C(11)
C(6)–C(7)–C(13)–C(12)
C(7)–C(6)–C(14)–C(15)
C(5)–C(6)–C(14)–C(15)
C(16)–O(3)–C(15)–O(2)
C(16)–O(3)–C(15)–C(14)
C(6)–C(14)–C(15)–O(2)
C(6)–C(14)–C(15)–O(3)
C(15)–O(3)–C(16)–C(21)
C(15)–O(3)–C(16)–C(17)
O(3)–C(16)–C(17)–F(1)
O(3)–C(16)–C(17)–C(18)
O(3)–C(16)–C(21)–F(5)
O(3)–C(16)–C(21)–C(20)
12.0(3)
168.06(18)
2168.01(16)
211.9(3)
22.6(3)
251.1(3)
52.4(2)
29.2(3)
177.98(19)
177.42(18)
22.0(3)
2173.24(17)
294.7(2)
62.87(19)
256.8(2)
178.49(17)
148.8(2)
2177.93(19)
2177.4(2)
178.6(2)
23.1(4)
2.6(4)
288.9(2)
232.8(2)
89.5(2)
2177.9(2)
26.9(5)
173.7(2)
2159.6(2)
22.0(3)
86.1(3)
19.4(3)
299.6(3)
6.2(3)
2159.06(18)
176.69(18)
177.15(17)
23.9(3)
2174.0(2)
23.7(3)
174.0(2)
All the bond lengths and angles have standard values. The two aromatic rings are planar, having dihedral angles of either 0 or ^1808 being
the deviation from planarity lower than 28.
It is worth mentioning that the arene–arene
intermolecular interaction is the only one detected in
the crystal packing of 1. Based on the facts
commented previously, the origin of this phenomenon
must be attributed to a favourable quadrupolar
interaction between both rings.
ties. On the basis of the known characteristics of
arenes, the molecules containing aromatic fragments
have been frequently used as building blocks to design
organic crystals. Although, the crystal structure of
some fluorinated arenes have been described [60–63],
this is the first report on the crystal structure of the
pentafluorophenyl esters of an amino acid derivative
(a g-amino acid).4
Since pentafluorophenyl esters are readily avail-
able synthetic intermediates, they can be useful
building blocks for the generation of defined crystal
structures, as well as a tool to document the relative
importance of the different intermolecular forces in
the crystal.
The quadrupole moment is a tensorial magnitude
that, at a molecular level, can be used as a
measurement of the distribution of charge relative
to a particular axis [51]. We [38,52] and others [10,
11,47,53–55] have shown that this property can be
used to rationalize the molecular and supramole-
cular structure of organic compounds both in
solution and in the solid state.
Incidentally, we have prepared compound 1 as an
intermediate for the synthesis of peptide-heterocyclic
hybrids of type 3 [39]; that, in turn, were designed
with the goal in mind to interact with biological
targets through the aromatic ring. The results reported
On the other hand, a current, highly appealing,
topic of research is crystal engineering: the design,
preparation, and structural characterization of mol-
ecules having defined crystal packing [29,56,57]. The
interest on this topic is twofold: to deep in the
knowledge of the factors that influence crystal
packing, and to synthesize materials with useful
technological [58] and pharmacological [59] proper-
4
The first report on the crystal structure of a pentafluorophenyl
ester (from 3-chloro-3-phenylpropanoate) has been recently
disclosed on electronic format [63].

106
E. Mann et al. / Journal of Molecular Structure 641 (2002) 101–107
in this paper reinforces the capacity of the aromatic
ring of the tricyclic scaffold to participate in
intermolecular interactions.
4. Conclusions
Summarizing, we have reported the crystal struc-
ture of compound 1, having an aromatic tricyclic a,b-
unsaturated-g-amino acid and a pentafluorophenyl
fragment. The crystal packing of 1 has a face-to-face
arrangement of both types of aromatic rings, that it is
stabilized by a favourably quadrupolar interaction
between the aromatic rings. Although other inter-
molecular interactions are possible in this compound
(i.e. fluorine atom with other fragment), they have not
been observed; what indicates the relatively high
importance of quadrupolar interactions in the crystal
packing of organic molecules.
Acknowledgments
Fig. 2. View along the c-axis of the crystal packing of (2)-
pentafluorophenyl(Z,S,S )-2-(6-oxo-1,3,4,6,11,11a-hexahydro-2H-
pyrido[1,2-b]isoquinolin-11-yliden)acetate (1).
Financial support from the Spanish Ministry of
Science and Technology (Project BQU2001-2270)
and Madrid Autonomous Community (Project
08.5/0056/2000-2) is gratefully acknowledged.
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