Supra-molecular association in proton-transfer adducts containing benz-amidinium cations. I. Four mol-ecular salts with uracil derivatives

Article abstract of DOI:10.1107/S0108270110016252

Four organic salts, namely benzamidinidium orotate (2,6-di-oxo-1,2,3,6- tetra-hydro-pyrimidine-4-carboxyl-ate) hemi-hydrate, C₇H ₉N₂⁺·C₅H₃N ₂O₄^-·0.5H₂O (BenzamH ⁺·Or^-), (I), benzamidinium isoorotate (2,4-dioxo-1,2,3,4-tetra-hydro-pyrimidine-5-carboxyl-ate) trihydrate, C ₇H₉N₂⁺·C₅H ₃N₂O₄^-·3H₂O (BenzamH⁺·Isor^-), (II), benzamidinium diliturate (5-nitro-2,6-dioxo-1,2,3,6-tetra-hydro-pyrimidin-4-olate) di-hydrate, C ₇H₉N₂⁺·C₄H ₂N₃O₅^-·2H₂O (BenzamH⁺·Dil^-), (III), and benzamidinium 5-nitro-uracilate (5-nitro-2,4-dioxo-1,2,3,4-tetra-hydro-pyrimidin-1-ide), C₇H₉N₂⁺·C₄H ₂N₃O₄^- (BenzamH⁺· Nit^-), (IV), have been synthesized by a reaction between benzamidine (benzene-carboximidamide or Benzam) and the appropriate carboxylic acid. Proton transfer occurs to the benzamidine imino N atom. In all four acid-base adducts, the asymmetric unit consists of one tautomeric amino-oxo anion (Or^-, Isor^-, Dil^- and Nit^-) and one monoprotonated benzamidinium cation (BenzamH⁺), plus one-half (which lies across a twofold axis), three and two solvent water mol-ecules in (I), (II) and (III), respectively. Due to the presence of protonated benzamidine, these acid-base complexes form supra-molecular synthons characterized by N⁺- H...O^- and N⁺-H...N^- (±)-charge-assisted hydrogen bonds (CAHB).

Full text of DOI:10.1107/S0108270110016252

organic compounds
Acta Crystallographica Section C
Crystal Structure
al., 1995), allowing reasonably good control over the resulting
structures.
Communications
It has been observed that the strength of directional forces
depends on the nature and polarity of the donor and acceptor
groups. Enhancement of hydrogen-bond strength by reson-
ance or ionic charge has long been recognized (Ferretti et al.,
ISSN 0108-2701
Supramolecular association in proton-
transfer adducts containing benz-
amidinium cations. I. Four molecular
salts with uracil derivatives
´
´
ˇ
2004; Ward, 2005; Kojic-Prodic & Molcanov, 2008, and refer-
ences therein). The protonated form of benzamidine appears
to be a very promising building block in supramolecular
chemistry because its multiple hydrogen-bond donors can
interact with anions having multiple acceptor sites, such as
carboxylates. Although it is difficult to predict the formation
of a hydrogen bond between a potential donor D—H group
and a potential acceptor A in a given system, a probability of
formation (Pm) can be defined. This is the fraction of D—
Hꢀ ꢀ ꢀA hydrogen bonds (or hydrogen-bond arrays) out of the
total number of such hydrogen bonds that could be formed.
From the probabilities of formation of 75 bimolecular ring
motifs that have been determined (Allen et al., 1999), the
rather poor performance of the amidinium–carboxylate
heterodimer (Pm = 0.51) can be explained by strong compe-
tition of alternative motifs. In contrast, in the case of salts
containing the benzamidinium cation, although only a few
structures have been reported, the R22(8) (Etter et al., 1990;
Bernstein et al., 1995; Motherwell et al., 1999) one-dimensional
heterosynthon with carboxylate or other oxygenate anions
Gustavo Portalone
Chemistry Department, ‘Sapienza’ University of Rome, Piazzale A. Moro 5,
I-00185 Rome, Italy
Correspondence e-mail: g.portalone@caspur.it
Received 3 March 2010
Accepted 3 May 2010
Online 13 May 2010
Four organic salts, namely benzamidinidium orotate (2,6-dioxo-
1,2,3,6-tetrahydropyrimidine-4-carboxylate) hemihydrate,
+
C7H9N2 ꢀC5H3N2O4ꢁꢀ0.5H2O (BenzamH+ꢀOrꢁ), (I), benzami-
dinium isoorotate (2,4-dioxo-1,2,3,4-tetrahydropyrimidine-5-
+
carboxylate) trihydrate, C7H9N2 ꢀC5H3N2O4ꢁꢀ3H2O (Benz-
amH+ꢀIsorꢁ), (II), benzamidinium diliturate (5-nitro-2,6-di-
´
predominates (Kratochvıl et al., 1987; Portalone, 2008a; Kolev
+
oxo-1,2,3,6-tetrahydropyrimidin-4-olate) dihydrate, C7H9N2 ꢀ-
et al., 2009). These acid–base complexes are usually arranged
in a dimeric motif, similar to that found in carboxylic acid
dimers, via N+—Hꢀ ꢀ ꢀOꢁ (ꢂ)-charge-assisted hydrogen bonds
(CAHB) (Gilli & Gilli, 2009), provided that ÁpKa [ÁpKa =
pKa(base) ꢁ pKa(acid), where the pKa are for aqueous solu-
tions] is sufficiently large. The value of ÁpKa is often used to
predict whether a salt or cocrystal can be expected for two
components (Johnson & Rumon, 1965; Childs et al., 2007), but
some exceptions have been reported (Herbstein, 2005;
Molcanov & Kojic-Prodic, 2010). A value of ÁpKa < 0 is
generally considered to be associated with systems that form
cocrystals, ÁpKa > 3 results in salts, while 0 < ÁpKa < 3 can
produce cocrystals, salts or mixed ionization complexes.
Another possibility is offered by coupling benzamidinium
cations with counter-ions containing the NO2 group as
hydrogen-bond acceptor in complementary bimolecular
(DD)ꢀ(AA) heterosynthons. Although nitro groups are
intrinsically poorer acceptors of hydrogen bonds than
carboxylates (Gagnon et al., 2007), they form a variety of weak
supramolecular synthons with different types of donors (e.g.
O—H, aniline N—H, C C—H and C—Hal) (Robinson et al.,
2000; Thallapally et al., 2003; Thomas et al., 2005). Conse-
quently, the preference of a particular class of donor, such as
the protonated analogues of benzamidine, to form symmetric
motifs with nitro groups could rely on the characteristics of the
hydrogen-bond donor.
C4H2N3O5ꢁꢀ2H2O (BenzamH+ꢀDilꢁ), (III), and benzamidin-
ium 5-nitrouracilate (5-nitro-2,4-dioxo-1,2,3,4-tetrahydro-
+
ꢁ
pyrimidin-1-ide), C7H9N2 ꢀC4H2N3O4
(BenzamH+ꢀNitꢁ),
(IV), have been synthesized by a reaction between benzami-
dine (benzenecarboximidamide or Benzam) and the appro-
priate carboxylic acid. Proton transfer occurs to the
benzamidine imino N atom. In all four acid–base adducts,
the asymmetric unit consists of one tautomeric aminooxo
anion (Orꢁ, Isorꢁ, Dilꢁ and Nitꢁ) and one monoprotonated
benzamidinium cation (BenzamH+), plus one-half (which lies
across a twofold axis), three and two solvent water molecules
in (I), (II) and (III), respectively. Due to the presence of
protonated benzamidine, these acid–base complexes form
supramolecular synthons characterized by N+—Hꢀ ꢀ ꢀOꢁ and
N+—Hꢀ ꢀ ꢀNꢁ (ꢂ)-charge-assisted hydrogen bonds (CAHB).
ˇ
´
´
Comment
An invaluable approach for supramolecular synthesis is the
exploitation of the principles of molecular self-assembly. This
relies heavily on the ability of certain functional groups to self-
interact in a noncovalent fashion and to retain a specific and
persistent pattern or motif, the supramolecular synthon.
Among the functional groups used most frequently for
supramolecular synthesis and crystal engineering are carboxyl
groups and their derivatives. These functions are capable of
forming robust and directional hydrogen bonds, and aggregate
in the solid state as dimers, catemers and double-bridged
motifs (Leiserowitz, 1976; Bernstein et al., 1994; Kolotuchin et
In this study, an analysis of solid-state heteromeric and
homomeric hydrogen-bond interactions has been carried out
on four acid–base complexes formed by benzamidine
(Benzam) with orotic acid (Or), isoorotic acid (Isor), dilituric
Acta Cryst. (2010). C66, o295–o301
doi:10.1107/S0108270110016252
# 2010 International Union of Crystallography o295

organic compounds
acid (Dil) and 5-nitrouracil (Nit). Benzamidine derivatives
such as pentamidine and propamidine are very simple DNA
binders that show good stability, A/T sequence selectivity, and
excellent cell-transport properties in a variety of cell lines
(Tidwell & Boykin, 2003). Benzamidine itself also has biolo-
gical and pharmacological relevance (Powers & Harper, 1999;
Grzesiak et al., 2000). With this in mind, the acids Or, Isor, Dil
and Nit were selected to react with benzamidine as they
possess appreciable acidity and are structurally related to
thymine (2,4-dihydroxy-5-methylpyrimidine). In these four
complexes, (I)–(IV), the ÁpKa values are 9.5, 7.4, 10.8 and 5.9,
respectively, so salts are expected. In situations where both
anion and cation are derived from organic acids and bases, the
term molecular salt has been proposed (Sarma et al., 2009).
Figure 1
The asymmetric unit of (I), showing the atom-labelling scheme and
hydrogen bonding (dashed lines). The asymmetric unit was selected so
that the two ions are linked by N+—Hꢀ ꢀ ꢀOꢁ (ꢂ)-CAHB hydrogen bonds.
Displacement ellipsoids are drawn at the 50% probability level and H
atoms are shown as small spheres of arbitrary radii.
one-half of a solvent water molecule (which lies across a
twofold axis) in the asymmetric unit (Fig. 1). The BenzamH+
cation is not planar. The amidinium group has a synclinal
disposition with respect to the benzene ring [N4—C14—C8—
C13 and N5—C14—C8—C9 torsion angles are 29.3 (2) and
29.2 (2)ꢃ, respectively], close to the values observed in
benzamidine [22.7 (3) and 20.9 (3)ꢃ;ꢃBarker et al., 1996] and
´
benzdiamidine [25.3 (2) and 23.8 (2) ; Jokic et al., 2001]. This
disposition is a consequence of an overcrowding effect, i.e.
steric hindrance between the H atoms of the aromatic ring and
the amidine moiety. In the Orꢁ anion, the pyrimidine ring is
essentially planar and the carboxylate group is rotated
15.4 (2)–15.7 (2)ꢃ out of the plane of the uracil fragment. For
this anion, the bond lengths and angles of the heteroaromatic
ring are in accord with values obtained for orotic acid
monohydrate (Portalone, 2008b). The two ions are joined by
two N+—Hꢀ ꢀ ꢀOꢁ (ꢂ)-CAHB hydrogen bonds to form a dimer
with graph-set motif R22(8) (Table 2).
Compound (II) crystallizes in the monoclinic space group
P21/n, with one almost planar tautomeric aminooxo anion
(Isorꢁ), one BenzamH+ cation and three solvent water mol-
ecules in the asymmetric unit (Fig. 2). In the nonplanar
BenzamH+ cation, the amidinium group is twisted out of the
In these four 1:1 proton-transfer compounds, protonation
occurs at the benzamidine imino N atom as a result of proton
transfer from the acidic hydroxy [compounds (I)–(III)] and
amino groups [compound (IV)]. These acid–base complexes
are linked by N+—Hꢀ ꢀ ꢀOꢁ and N+—Hꢀ ꢀ ꢀNꢁ (ꢂ)-CAHB. The
amidinium fragments are completely delocalized (Table 1) and
can be described as carrying a half-positive formal charge on
the two N atoms. The same delocalization occurs within the
carboxylate group in BenzamH+ꢀOrꢁ, (I), and favours
aggregation into dimers. In BenzamH+ꢀIsorꢁ, (II), and
BenzamH+ꢀDilꢁ, (III), the lack of hydrogen-bond acceptors
with respect to imino hydrogen-bond donors gives rise to the
formation of bifurcated hydrogen bonds.
Figure 2
The asymmetric unit of (II), showing the atom-labelling scheme and
hydrogen bonding (dashed lines). The asymmetric unit was selected so
that the two ions are linked by N+—Hꢀ ꢀ ꢀOꢁ (ꢂ)-CAHB hydrogen bonds.
Displacement ellipsoids are drawn at the 50% probability level and H
atoms are shown as small spheres of arbitrary radii.
Compound (I) crystallizes in the monoclinic space group
C2/c, with one tautomeric aminooxo anion (Orꢁ), one
monoprotonated benzamidinium cation (BenzamH+) and
+
o296 Gustavo Portalone C7H9N2 ꢀC5H3N2O4ꢁꢀ0.5H2O and three analogues
Acta Cryst. (2010). C66, o295–o301
ꢄ

organic compounds
Figure 4
The asymmetric unit in (IV), showing the atom-labelling scheme and
hydrogen bonding (dashed lines). The asymmetric unit was selected so
that the two ions are linked by N+—Hꢀ ꢀ ꢀO hydrogen bonds. Displace-
ment ellipsoids are drawn at the 50% probability level and H atoms are
shown as small spheres of arbitrary radii.
Figure 3
phenylbiguanide and dilituric acid monohydrate (Portalone &
Colapietro, 2007a).
The asymmetric unit in (III), showing the atom-labelling scheme and
hydrogen bonding (dashed lines). The asymmetric unit was selected so
that the two ions are linked by N+—Hꢀ ꢀ ꢀOꢁ (ꢂ)-CAHB hydrogen bonds.
Displacement ellipsoids are drawn at the 50% probability level and H
atoms are shown as small spheres of arbitrary radii.
Compound (IV) crystallizes in the triclinic space group P1,
with one planar tautomeric aminooxo anion (Nitꢁ) and one
BenzamH+ cation in the asymmetric unit (Fig. 4). Again, the
BenzamH+ cation is not planar. The amidinium group, as in
(I), has a synclinal disposition with respect to the benzene ring
[N4—C14—C8—C13 and N5—C14—C8—C9 torsion angles
are 29.7 (4) and 30.4 (3)ꢃ, respectively]. Of the two sites
available for ionization in the heterocyclic ring of the
5-nitrouracil molecule (N1 and N3), deprotonation occurs at
the more acidic N1 (Portalone & Colapietro, 2007b), and this
causes a redistribution of ꢀ-electron density in the Nitꢁ anion.
The resulting distortions in the molecular geometry of the
anion (Table 1), which have been observed in the only
reported structure containing the 5-nitrouracilate unit
(Pereira Silva et al., 2008), point to the importance of the
charge-separated quininoid form (VI) as a significant contri-
butor. The two ions are connected by two N+—Hꢀ ꢀ ꢀO
hydrogen bonds, and the carbonyl atom O1 of the Nitꢁ anion
acts as a bifurcated acceptor, thus generating an R12(6) motif
(Table 5).
As previously mentioned, due to their protonated base, the
supramolecular aggregations in compounds (I)–(IV) are
dominated by an extensive series of hydrogen bonds, which
include N+—Hꢀ ꢀ ꢀO, N+—Hꢀ ꢀ ꢀOꢁ and N+—Hꢀ ꢀ ꢀNꢁ
(ꢂ)-CAHB hydrogen bonds. Analysis of the resulting supra-
molecular structures is greatly eased by the use of the
substructure approach (Gregson et al., 2000), as in each of (I)–
(IV) it is possible to identify a basic structural subunit built
from the ion pairs of the asymmetric unit.
mean plane of the benzene ring [N4—C14—C8—C13 and
N5—C14—C8—C9 torsion angles are 23.2 (3) and 22.5 (3)ꢃ,
respectively]. Comparison of the geometric parameters of the
Isorꢁ anion in (II) with those reported for the isoorotate anion
in the 1:1 proton-transfer adduct between cytosine and
isoorotic acid (Portalone & Colapietro, 2009) shows that the
corresponding bond lengths and angles are equal within
experimental error. The two ions are connected by three N+—
Hꢀ ꢀ ꢀOꢁ (ꢂ)-CAHB hydrogen bonds, which include one
bifurcated donor and one bifurcated acceptor interaction. The
Isorꢁ anion accepts two of these hydrogen bonds through one
O atom of the carboxylate group and the third through the
adjacent carbonyl O atom. These interactions generate graph-
set motifs of R12(6) and R21(6) (Table 3).
Compound (III) also crystallizes in the monoclinic space
group P21/n, with one planar tautomeric aminooxo anion
(Dilꢁ), one BenzamH+ cation and two solvent water mol-
ecules in the asymmetric unit (Fig. 3). At variance with
adducts (I) and (II), in (III) the BenzamH+ cation is planar
[N4—C14—C8—C13 and N5—C14—C8—C9 torsion angles
are 0.5 (2) and 0.7 (2)ꢃ, respectively]. This conformation is
rather unusual, as only the nonplanar arrangement has been
observed in previous small-molecule structures. Quite the
opposite is true in benzamidinium-containing macromolecular
structures, in which the most frequently encountered confor-
mation is the planar one (Li et al., 2009). In the planar Dilꢁ
anion, the release of an H atom from the hydroxy O atom
causes a redistribution of ꢀ-electron density so that the
geometry of the anion (Table 1) approaches mirror symmetry
through a mirror plane along the line joining atoms C2 and C5
[form (V)]. As with the previous case, the two ions are
connected by bifurcated N+—Hꢀ ꢀ ꢀOꢁ (ꢂ)-CAHB hydrogen
bonds, which generate R21(6) and R21(6) motifs, but the Dilꢁ
anion acts as an acceptor through one O atom of the nitro
group and the adjacent carbonyl O atom (Table 4). A similar
hydrogen-bond pattern has been observed in the 1:1 salts of
In the supramolecular structure of (I), which is a stoichio-
metric hemihydrate, seven hydrogen bonds link the molecular
components into a three-dimensional framework structure
(Table 2). One subunit generates a centrosymmetric R22(8)
hydrogen-bonding motif. Two centrosymmetric subunits are
then linked into a two-dimensional network via multiple
hydrogen bonds, forming two adjoining hydrogen-bonded
rings with graph-set motifs R33(14) and R44(18). The formation
of the final three-dimensional array is facilitated by the water
molecules, which act as bridges between structural subunits
linked into R34(12) hydrogen-bonded rings (Fig. 5).
+
C7H9N2 ꢀC5H3N2O4ꢁꢀ0.5H2O and three analogues o297
ꢄ
Acta Cryst. (2010). C66, o295–o301
Gustavo Portalone

organic compounds
Figure 5
A crystal packing diagram for (I), viewed approximately down the b axis.
All atoms are shown as small spheres of arbitrary radii. For the sake of
clarity, carbon-bound H atoms have been omitted. Hydrogen bonding is
indicated by dashed lines.
Figure 7
A crystal packing diagram for (III), viewed approximately down the b
axis. All atoms are shown as small spheres of arbitrary radii. For the sake
of clarity, carbon-bound H atoms have been omitted. Hydrogen bonding
is indicated by dashed lines.
Figure 6
A crystal packing diagram for (II), viewed approximately down the b axis.
All atoms are shown as small spheres of arbitrary radii. For the sake of
clarity, carbon-bound H atoms have been omitted. Hydrogen bonding is
indicated by dashed lines.
Figure 8
Part of the crystal structure of (IV), showing the formation of a hydrogen-
bonded ribbon approximately along [110]. All atoms are shown as small
spheres of arbitrary radii. For the sake of clarity, carbon-bound H atoms
have been omitted. Hydrogen bonding is indicated by dashed lines.
In the crystal structure of (II), which is a stoichiometric
trihydrate, the hydrogen-bonding scheme is rather complex
and involves all available hydrogen donor and acceptor sites.
In total, the supramolecular structure of (II) is characterized
by 13 hydrogen bonds, namely seven N—Hꢀ ꢀ ꢀO and six O—
Hꢀ ꢀ ꢀO bonds (Table 3). Two coplanar subunits form centro-
symmetric R22(8) and R23(8) rings via double intermolecular
N+—Hꢀ ꢀ ꢀO and N—Hꢀ ꢀ ꢀO hydrogen bonds. These pairs
further self-organize through double intermolecular OW—
Hꢀ ꢀ ꢀO hydrogen bonds with a water molecule, to generate
infinite chains of rings running approximately parallel to the
[100] direction (Fig. 6). The hydrogen bonds so far discussed in
the two-dimensional arrays in the ac plane are bridged by the
remaining water molecules via OW—Hꢀ ꢀ ꢀO interactions.
From a topological point of view, the crystal structure of
(III), which is a stoichiometric dihydrate, shows similarities
with that of (II). Two coplanar subunits form centrosymmetric
R22(8) and R23(8) rings via intermolecular N+—Hꢀ ꢀ ꢀO and N—
Hꢀ ꢀ ꢀO hydrogen bonds. In this case, however, these pairs
further self-organize through an intermolecular R22(8) N—
Hꢀ ꢀ ꢀO interaction formed around an inversion centre, giving
infinite chains of rings running approximately parallel to the
[100] direction. The formation of this two-dimensional array is
then reinforced by two water molecules (Fig. 7).
The molecules of (IV) are linked by a combination of five
N+—Hꢀ ꢀ ꢀO and N+—Hꢀ ꢀ ꢀNꢁ (ꢂ)-CAHB (Table 5). Neigh-
bouring subunits form a sheet-like structure via three struc-
turally significant hydrogen bonds (Fig. 8). Two centrosym-
metric subunits are linked by two independent N+—Hꢀ ꢀ ꢀO
hydrogen bonds, forming fused centrosymmetric riꢁngs with
graph-set motifs R33(12) and R22(8). An N+—Hꢀ ꢀ ꢀN homo-
nuclear (ꢂ)-CAHB then connects these two subunits to
produce an adjoining centrosymmetric R44(12) ring. Propaga-
tion by inversion of these subunits suffices to link all the
molecules into a ribbon approximately along [110].
+
o298 Gustavo Portalone C7H9N2 ꢀC5H3N2O4ꢁꢀ0.5H2O and three analogues
Acta Cryst. (2010). C66, o295–o301
ꢄ

organic compounds
From a supramolecular retrosynthesis perspective, only
those synthons that occur repeatedly in crystal structures,
namely robust synthons of a particular set of functional
groups, are useful in crystal design (Nangia & Desiraju, 1998).
Moreover, hydrogen bonds are often formed in a hierarchical
fashion (Etter, 1990; Allen et al., 1999; Bis et al., 2007; Shattock
et al., 2008), and there is a need to ascertain the prevalence of
a particular heterosynthon over another in a competitive
environment. From the results reported here, only the crystal
structure of (I) is consistent with the R22(8) supramolecular
heterosynthon persistence exhibited by the benzamidinium
adducts that have been archived in the Cambridge Structural
Database (CSD, Version 5.30; Allen, 2002). Consequently, it
would be of interest to pursue crystal engineering studies that
provide possible correlations between the synthons used and
the topology of the hydrogen bonds in benzamidinium-
containing molecular salts. Moreover, such proton-transfer
adducts are ideally suited to studying the competition between
different supramolecular heterosynthons if the counter-ions in
benzamidinium salts are from molecules having acceptor
groups whose nature is modified in a graded manner through
chemical synthesis. Work in this laboratory has begun to tackle
this issue, and a systematic analysis of the structural conse-
quences for solid-state assembly in benzamidinium proton-
transfer adducts as a function of the hydrogen-bond acceptor
properties of the coupling agents is currently under investi-
gation.
Refinement
R[F2 > 2ꢄ(F2)] = 0.065
wR(F2) = 0.152
S = 1.20
4342 reflections
214 parameters
H atoms treated by a mixture of
independent and constrained
refinement
ꢁ3
˚
Áꢅmax = 0.36 e A
ꢁ3
˚
Áꢅmin = ꢁ0.18 e A
Compound (II)
Crystal data
+
3
C7H9N2 ꢀC5H3N2O4ꢁꢀ3H2O
˚
V = 1525.84 (5) A
Z = 4
Mr = 330.30
Monoclinic, P21=n
Mo Kꢂ radiation
ꢃ = 0.12 mmꢁ1
T = 298 K
0.18 ꢅ 0.14 ꢅ 0.09 mm
˚
a = 11.3562 (2) A
˚
b = 6.0402 (1) A
˚
c = 22.3763 (4) A
ꢁ = 96.221 (2)ꢃ
Data collection
Oxford Xcalibur S CCD area-
detector diffractometer
implemented in the SCALE3
ABSPACK scaling algorithm]
Tmin = 0.918, Tmax = 0.990
218566 measured reflections
5260 independent reflections
3884 reflections with I > 2ꢄ(I)
Rint = 0.073
Absorption correction: multi-scan
[CrysAlis RED (Oxford Diffrac-
tion, 2006); empirical (using
intensity measurements) correc-
tion using spherical harmonics
Table 1
Selected bond distances (A) for (I)–(IV).
˚
Bond
(I)
(II)
(III)
(IV)
O1—C2
O2—C4
O3—C7
O4—C7
O3—N7
O4—N7
O5—C6
N1—C2
N1—C6
N3—C2
N3—C4
C4—C5
C5—C6
C5—C7
C5—N7
C6—C7
N4—C14
N5—C14
C8—C14
C8—C9
C8—C13
C9—C10
C12—C13
C10—C11
C11—C12
1.2179 (16)
1.2289 (16)
1.2483 (15)
1.2400 (17)
1.225 (2)
1.2293 (19)
1.230 (2)
1.273 (2)
1.2215 (18)
1.2364 (16)
1.232 (3)
1.224 (3)
Experimental
1.2385 (16)
1.2364 (17)
1.2287 (17)
1.3605 (18)
1.3848 (18)
1.3652 (17)
1.3835 (17)
1.4416 (18)
1.4478 (17)
1.229 (2)
1.232 (2)
BenzamH+ꢀOrꢁ, (I), BenzamH+ꢀIsorꢁ, (II), BenzamH+ꢀDilꢁ, (III),
and BenzamH+ꢀNitꢁ, (IV), were obtained as white powders from
equimolar mixtures (1 mmol of each compound) in ethanol solutions
(20 ml) of benzamidine (Fluka, 95%) and orotic acid (Sigma Aldrich,
98%), isoorotic acid (Sigma Aldrich, 95%), dilituric acid (Sigma
Aldrich, 95%) and 5-nitrouracil (Sigma Aldrich, 98%), respectively.
The 1:1 molecular adducts were recrystallized from water. The
solutions were warmed slowly and then left to evaporate under
ambient conditions. Small transparent single crystals were deposited
after two weeks.
1.3664 (16)
1.3673 (16)
1.3717 (18)
1.3765 (16)
1.4431 (17)
1.3385 (18)
1.370 (2)
1.352 (2)
1.371 (2)
1.389 (2)
1.455 (2)
1.355 (2)
1.500 (2)
1.366 (3)
1.316 (3)
1.371 (3)
1.382 (3)
1.443 (3)
1.381 (3)
1.3945 (17)
1.421 (3)
1.5225 (17)
1.3118 (17)
1.3106 (18)
1.4763 (18)
1.3901 (18)
1.386 (2)
1.386 (2)
1.386 (2)
1.377 (3)
1.375 (2)
1.318 (2)
1.312 (2)
1.483 (2)
1.395 (3)
1.393 (3)
1.387 (3)
1.384 (3)
1.376 (3)
1.379 (3)
1.3083 (19)
1.321 (2)
1.4843 (19)
1.391 (2)
1.389 (2)
1.389 (2)
1.386 (2)
1.377 (3)
1.372 (3)
1.309 (3)
1.302 (3)
1.478 (3)
1.384 (3)
1.387 (4)
1.375 (4)
1.394 (4)
1.368 (4)
1.373 (5)
Compound (I)
Crystal data
+
3
C7H9N2 ꢀC5H3N2O4ꢁꢀ0.5H2O
˚
V = 2534.41 (11) A
Z = 8
Mo Kꢂ radiation
ꢃ = 0.12 mmꢁ1
T = 298 K
Mr = 285.27
Monoclinic, C2=c
˚
a = 27.2046 (6) A
˚
b = 7.3566 (2) A
Table 2
Hydrogen-bond geometry (A, ) for (I).
˚
c = 12.6687 (3) A
0.30 ꢅ 0.20 ꢅ 0.15 mm
ꢃ
˚
ꢁ = 91.621 (2)ꢃ
D—Hꢀ ꢀ ꢀA
D—H
Hꢀ ꢀ ꢀA
Dꢀ ꢀ ꢀA
D—Hꢀ ꢀ ꢀA
Data collection
N1—H1ꢀ ꢀ ꢀO2i
N3—H3ꢀ ꢀ ꢀO1ii
N4—H4Aꢀ ꢀ ꢀO4
N4—H4Bꢀ ꢀ ꢀO3i
N5—H5Aꢀ ꢀ ꢀO3
N5—H5Bꢀ ꢀ ꢀO2iii
O5—H51ꢀ ꢀ ꢀO2
0.82 (2)
0.96 (2)
0.97 (2)
0.91 (2)
0.92 (2)
0.89 (2)
0.85 (3)
2.24 (2)
1.90 (2)
1.82 (2)
2.00 (2)
1.95 (2)
2.06 (2)
2.35 (3)
3.0013 (16)
2.8491 (15)
2.7809 (16)
2.9036 (17)
2.8638 (16)
2.9357 (16)
3.1345 (14)
153.5 (18)
168.0 (19)
170.6 (18)
171.4 (18)
178 (2)
Oxford Xcalibur S CCD area-
detector diffractometer
Absorption correction: multi-scan
[CrysAlis RED (Oxford
Diffraction, 2006); empirical
(using intensity measurements)
absorption correction using
spherical harmonics implemented
in the SCALE3 ABSPACK
scaling algorithm]
Tmin = 0.956, Tmax = 0.983
119911 measured reflections
4342 independent reflections
3512 reflections with I > 2ꢄ(I)
Rint = 0.043
170.0 (17)
154 (3)
1
2
1
2
1
2
Symmetry codes: (i) x; ꢁy þ 1; z þ ; (ii) ꢁx; ꢁy þ 1; ꢁz; (iii) ꢁx þ ; ꢁy þ ; ꢁz.
+
C7H9N2 ꢀC5H3N2O4ꢁꢀ0.5H2O and three analogues o299
ꢄ
Gustavo Portalone
Acta Cryst. (2010). C66, o295–o301

organic compounds
Table 3
Hydrogen-bond geometry (A, ) for (II).
Table 4
Hydrogen-bond geometry (A, ) for (III).
ꢃ
˚
ꢃ
˚
D—Hꢀ ꢀ ꢀA
D—H
Hꢀ ꢀ ꢀA
Dꢀ ꢀ ꢀA
D—Hꢀ ꢀ ꢀA
D—Hꢀ ꢀ ꢀA
D—H
Hꢀ ꢀ ꢀA
Dꢀ ꢀ ꢀA
D—Hꢀ ꢀ ꢀA
N1—H1ꢀ ꢀ ꢀO5i
N3—H3ꢀ ꢀ ꢀO2ii
N4—H4Aꢀ ꢀ ꢀO2
N4—H4Aꢀ ꢀ ꢀO3
N4—H4Bꢀ ꢀ ꢀO1ii
N5—H5Aꢀ ꢀ ꢀO3
N5—H5Bꢀ ꢀ ꢀO7iii
O5—H51ꢀ ꢀ ꢀO4
O5—H52ꢀ ꢀ ꢀO1iv
O6—H61ꢀ ꢀ ꢀO4
O6—H62ꢀ ꢀ ꢀO7v
O7—H71ꢀ ꢀ ꢀO4
O7—H72ꢀ ꢀ ꢀO6vi
0.92 (3)
0.89 (3)
0.92 (3)
0.92 (3)
0.84 (3)
0.92 (3)
0.88 (3)
0.90 (4)
0.83 (3)
0.91 (4)
0.80 (4)
0.86 (3)
0.84 (3)
2.05 (3)
1.95 (3)
2.22 (3)
2.08 (3)
2.24 (3)
1.92 (3)
2.03 (3)
1.91 (4)
2.00 (3)
1.94 (4)
2.09 (4)
1.89 (3)
1.88 (3)
2.760 (2)
2.8296 (18)
2.959 (2)
2.854 (2)
3.050 (2)
2.770 (2)
2.868 (2)
2.787 (2)
2.821 (2)
2.837 (3)
2.878 (3)
2.741 (2)
2.704 (3)
133 (2)
174 (2)
136 (2)
141 (2)
162 (2)
154 (2)
158 (2)
163 (3)
173 (3)
171 (3)
169 (4)
173 (3)
166 (3)
N1—H1ꢀ ꢀ ꢀO5i
N3—H3ꢀ ꢀ ꢀO2ii
N4—H4Aꢀ ꢀ ꢀO2
N4—H4Aꢀ ꢀ ꢀO3
N4—H4Bꢀ ꢀ ꢀO1ii
N5—H5Aꢀ ꢀ ꢀO3
N5—H5Bꢀ ꢀ ꢀO7iii
O6—H61ꢀ ꢀ ꢀO4
O6—H62ꢀ ꢀ ꢀO4iv
O7—H71ꢀ ꢀ ꢀO6
O7—H72ꢀ ꢀ ꢀO7iii
0.91 (2)
0.90 (2)
0.84 (2)
0.84 (2)
0.88 (2)
0.85 (3)
0.88 (3)
0.91 (5)
0.78 (4)
0.89 (3)
0.87 (4)
1.92 (2)
1.97 (2)
2.19 (2)
2.12 (2)
1.98 (2)
2.19 (3)
2.18 (3)
2.00 (5)
2.29 (4)
1.84 (3)
2.04 (4)
2.8359 (16)
2.8635 (16)
2.8581 (16)
2.8808 (18)
2.8514 (18)
2.9250 (19)
3.035 (2)
2.894 (2)
3.037 (3)
2.729 (3)
2.8940 (19)
178 (2)
178 (2)
135.5 (19)
150 (2)
168 (2)
146 (2)
164 (2)
167 (4)
160 (4)
173 (3)
169 (4)
1
1
Symmetry codes: (i) ꢁx þ 1; ꢁy þ 2; ꢁz þ 2; (ii) ꢁx; ꢁy þ 1; ꢁz þ 2; (iii) ꢁx þ ; y ꢁ ,
2
2
3
2
ꢁz þ ; (iv) x; y ꢁ 1; z.
1
2
1
2
1
2
Symmetry codes: (i) x; y þ 1; z; (ii) ꢁx þ 1; ꢁy þ 2; ꢁz; (iii) ꢁx þ ; y ꢁ ; ꢁz þ ; (iv)
1
1
1
2
ꢁx; ꢁy þ 2; ꢁz; (v) ꢁx þ ; y þ ; ꢁz þ ; (vi) x; y ꢁ 1; z.
2
2
Table 5
Hydrogen-bond geometry (A, ) for (IV).
ꢃ
˚
Refinement
D—Hꢀ ꢀ ꢀA
D—H
Hꢀ ꢀ ꢀA
Dꢀ ꢀ ꢀA
D—Hꢀ ꢀ ꢀA
R[F2 > 2ꢄ(F2)] = 0.087
wR(F2) = 0.186
S = 1.24
5260 reflections
256 parameters
H atoms treated by a mixture of
independent and constrained
refinement
N3—H3ꢀ ꢀ ꢀO2i
N4—H4Aꢀ ꢀ ꢀO1
N4—H4Bꢀ ꢀ ꢀN1ii
N5—H5Aꢀ ꢀ ꢀO1
N5—H5Bꢀ ꢀ ꢀO3i
0.92 (3)
0.92 (3)
0.87 (3)
0.89 (3)
0.86 (3)
1.98 (3)
2.07 (3)
2.03 (3)
2.05 (3)
2.23 (3)
2.899 (2)
2.890 (3)
2.886 (3)
2.853 (3)
3.084 (3)
176 (2)
148 (3)
170 (2)
149 (2)
169 (2)
ꢁ3
˚
Áꢅmax = 0.36 e A
ꢁ3
˚
Áꢅmin = ꢁ0.25 e A
Symmetry codes: (i) ꢁx þ 1; ꢁy þ 2; ꢁz; (ii) ꢁx; ꢁy þ 1; ꢁz.
Compound (III)
Data collection
Crystal data
+
Oxford Xcalibur S CCD area-
detector diffractometer
Absorption correction: multi-scan
[CrysAlis RED (Oxford
Diffraction, 2006); empirical
(using intensity measurements)
absorption correction using
spherical harmonics implemented
in the SCALE3 ABSPACK
scaling algorithm]
3
C7H9N2 ꢀC4H2N3O5ꢁꢀ2H2O
˚
V = 1479.46 (8) A
Z = 4
Mo Kꢂ radiation
ꢃ = 0.13 mmꢁ1
T = 298 K
Mr = 329.28
Monoclinic, P21=n
Tmin = 0.978, Tmax = 0.993
4864 measured reflections
2153 independent reflections
1427 reflections with I > 2ꢄ(I)
Rint = 0.034
˚
a = 10.7607 (3) A
˚
b = 5.0998 (2) A
˚
c = 27.2412 (5) A
ꢁ = 98.2485 (11)ꢃ
0.16 ꢅ 0.14 ꢅ 0.12 mm
Data collection
Refinement
Oxford Xcalibur S CCD area-
detector diffractometer
Absorption correction: multi-scan
[CrysAlis RED (Oxford
Diffraction, 2006); empirical
(using intensity measurements)
absorption correction using
in the SCALE3 ABSPACK
scaling algorithm]
R[F2 > 2ꢄ(F2)] = 0.051
wR(F2) = 0.119
S = 1.05
2153 reflections
201 parameters
H atoms treated by a mixture of
independent and constrained
refinement
Tmin = 0.908, Tmax = 0.991
306312 measured reflections
5116 independent reflections
4542 reflections with I > 2ꢄ(I)
Rint = 0.034
ꢁ3
˚
Áꢅmax = 0.18 e A
ꢁ3
˚
Áꢅmin = ꢁ0.17 e A
spherical harmonics implemented
All H atoms were found in a difference map. The H atoms of the
benzene rings were positioned with idealized geometry and refined
˚
isotropically as riding on their parent atoms, with C—H = 0.97 A and
Refinement
R[F2 > 2ꢄ(F2)] = 0.064
wR(F2) = 0.165
S = 1.17
5116 reflections
248 parameters
H atoms treated by a mixture of
independent and constrained
refinement
Uiso(H) = 1.2Ueq(C). All other H atoms, including those of the water
molecules, were refined freely. In the case of BenzamH+ꢀIsorꢁ, (II),
the refinement converged at a rather high R value, despite the resi-
duals in the final difference map being comparable in this compound
with those of compounds (I), (III) and (IV); the crystal quality for (II)
was not high, as indicated by the merging index of 0.073. Apparently,
the reason why it was not possible to attain an R value lower than
0.087 refers to significant difficulties in selecting a better crystal to
improve the experimental data. The crystals of (II) normally form
aggregates from water and several attempts undertaken to obtain
better results from alternative polar solvents gave no crystalline
material. However, the data set collected for compound (II) appeared
satisfactory, as judged by the data completeness (99.7% at ꢇ = 32.0ꢃ).
Scrutiny of the resulting interatomic distances and the Uij values in
compound (II), and comparison with the corresponding geometrical
parameters in compounds (I), (III) and (IV) showed no anomalies. In
ꢁ3
˚
Áꢅmax = 0.40 e A
Áꢅmin = ꢁ0.24 e A
ꢁ3
˚
Compound (IV)
Crystal data
+
ꢁ
C7H9N2 ꢀC4H2N3O4
ꢆ = 84.051 (7)ꢃ
V = 615.13 (10) A
Z = 2
3
˚
Mr = 277.25
Triclinic, P1
a = 4.3625 (4) A
˚
Mo Kꢂ radiation
ꢃ = 0.12 mmꢁ1
T = 298 K
0.15 ꢅ 0.08 ꢅ 0.05 mm
˚
b = 10.4461 (11) A
˚
c = 13.8556 (12) A
ꢂ = 78.551 (7)ꢃ
ꢁ = 86.841 (8)ꢃ
+
o300 Gustavo Portalone C7H9N2 ꢀC5H3N2O4ꢁꢀ0.5H2O and three analogues
Acta Cryst. (2010). C66, o295–o301
ꢄ

organic compounds
the case of BenzamH+ꢀNitꢁ, (IV), diffraction from the very small
crystals was weak. Nevertheless, these data gave good structural
results, albeit with a lower data/parameter ratio than usual.
For all four compounds, data collection: CrysAlis CCD (Oxford
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structure: SIR97 (Altomare et al., 1999); program(s) used to refine
structure: SHELXL97 (Sheldrick, 2008); molecular graphics:
ORTEP-3 (Farrugia, 1997); software used to prepare material for
publication: WinGX (Farrugia, 1999).
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C7H9N2 ꢀC5H3N2O4ꢁꢀ0.5H2O and three analogues o301
ꢄ
Acta Cryst. (2010). C66, o295–o301
Gustavo Portalone