Zero-, one- and two-dimensional hydrogen-bonded structures in the 1:1 proton-transfer compounds of 4,5-dichloro-phthalic acid with the monocyclic heteroaromatic Lewis bases 2-amino-pyrimidine, nicotin-amide and isonicotinamide

Article abstract of DOI:10.1107/S0108270109004405

The structures of the anhydrous 1:1 proton-transfer com-pounds of 4,5-dichloro-phthalic acid (DCPA) with the mono-cyclic heteroaromatic Lewis bases 2-amino-pyrimidine, 3-(am-ino-carb-onyl)pyridine (nicotinamide) and 4-(amino-carbon-yl)pyridine (isonicotin

Full text of DOI:10.1107/S0108270109004405

organic compounds
Acta Crystallographica Section C
Crystal Structure
acid is generally associated with the planar DCPA anion
species.
Communications
ISSN 0108-2701
Comment
The 1:1 proton-transfer compounds of the acid salts of 4,5-
dichlorophthalic acid (DCPA) with aromatic and heteroaro-
matic nitrogen Lewis bases generally show low-dimensional
hydrogen-bonded structure types (Smith et al., 2008a), with
the occurrence of three-dimensional structures limited to the
compounds with the bifunctional examples 3- and 4-amino-
benzoic acid (Smith et al., 2008b). In these two examples, the
primary hydrogen-bonded cation–anion ‘heterodimer’ (Etter
& Adsmond, 1990) is extended into sheet substructures
through further anion–cation interactions, then into a three-
dimensional framework via cyclic R22(8) cation carboxylic acid
hydrogen bonds (Etter et al., 1990). In these examples, the
DCPA anions are nonplanar, whereas in the low-dimensional
structure types, the DCPA anion species are essentially planar
with the planarity achieved through short intramolecular
carboxyl–carboxylate O—Hꢀ ꢀ ꢀO hydrogen bonds [typically
Zero-, one- and two-dimensional
hydrogen-bonded structures in the
1:1 proton-transfer compounds of
4,5-dichlorophthalic acid with the
monocyclic heteroaromatic Lewis
bases 2-aminopyrimidine, nicotin-
amide and isonicotinamide
Graham Smith,a* Urs D. Wermuthb and Jonathan M.
Whitec
aSchool of Physical and Chemical Sciences, Queensland University of Technology,
GPO Box 2434, Brisbane, Queensland 4001, Australia, bSchool of Biomolecular and
Physical Sciences, Griffith University, Nathan, Queensland 4111, Australia, and
cBIO-21 Molecular Science and Biotechnology, University of Melbourne, Parkville,
Victoria 3052, Australia
˚
2.441 (3) A in the brucinium DCPA compound (Smith et al.,
2007)]. There is also a low incidence of hydrates among the
structures of the 1:1 proton-transfer compounds of DCPA
when prepared in aqueous alcohol solution, with the only
three known examples limited to the salts with quinaldic acid
(a monohydrate) (Smith et al., 2008a), 2-aminobenzoic acid
(a dihydrate) (Smith et al., 2008b), hexamethylenetetramine
(a monohydrate) (Smith et al., 2009) and the drug quinacrine
(a tetrahydrate) (Smith & Wermuth, 2009).
Correspondence e-mail: g.smith@qut.edu.au
Received 10 January 2009
Accepted 6 February 2009
Online 21 February 2009
The 1:1 stoichiometric reaction of DCPA with the substi-
tuted monocyclic heteroaromatic bases 2-aminopyrimidine,
3-(aminocarbonyl)pyridine (nicotinamide) and 4-(aminocar-
bonyl)pyridine (isonicotinamide) in methanol gave the an-
hydrous compounds 2-aminopyrimidinium 2-carboxy-4,5-di-
chlorobenzoate, (I), 3-(aminocarbonyl)pyridinium 2-carboxy-
4,5-dichlorobenzoate, (II), and the unusual adduct 4-(amino-
carbonyl)pyridinium 2-carboxy-4,5-dichlorobenzoate–methyl
2-carboxy-4,5-dichlorobenzoate (1/1), (III). This set of
compounds shows examples of zero-, one- and two-dimen-
sional hydrogen-bonded structures.
The structures of the anhydrous 1:1 proton-transfer com-
pounds of 4,5-dichlorophthalic acid (DCPA) with the
monocyclic heteroaromatic Lewis bases 2-aminopyrimidine,
3-(aminocarbonyl)pyridine (nicotinamide) and 4-(aminocarbon-
yl)pyridine (isonicotinamide), namely 2-aminopyrimidinium
+
2-carboxy-4,5-dichlorobenzoate, C4H6N3 ꢀC8H3Cl2O4ꢁ, (I),
3-(aminocarbonyl)pyridinium 2-carboxy-4,5-dichlorobenzoate,
C6H7N2O+ꢀC8H3Cl2O4ꢁ, (II), and the unusual salt adduct
4-(aminocarbonyl)pyridinium 2-carboxy-4,5-dichlorobenzo-
ate–methyl 2-carboxy-4,5-dichlorobenzoate (1/1), C6H7N2O+ꢀ-
C8H3Cl2O4ꢁꢀC9H6Cl2O4, (III), have been determined at
130 K. Compound (I) forms discrete centrosymmetric
hydrogen-bonded cyclic bis(cation–anion) units having both
R22(8) and R21(4) N—Hꢀ ꢀ ꢀO interactions. In (II), the primary
N—Hꢀ ꢀ ꢀO-linked cation–anion units are extended into a two-
dimensional sheet structure via amide–carboxyl and amide–
carbonyl N—Hꢀ ꢀ ꢀO interactions. The structure of (III) reveals
the presence of an unusual and unexpected self-synthesized
methyl monoester of the acid as an adduct molecule, giving
one-dimensional hydrogen-bonded chains. In all three struc-
tures, the hydrogen phthalate anions are essentially planar
with short intramolecular carboxyl–carboxylate O—Hꢀ ꢀ ꢀO
˚
hydrogen bonds [Oꢀ ꢀ ꢀO = 2.393 (8)–2.410 (2) A]. This work
Figure 1
The molecular conformation and atom-numbering scheme for the
2-aminopyrimidinium cation and the 2-carboxy-4,5-dichlorobenzoate
anion in (I), showing the cyclic R22(8) inter-species hydrogen-bonding
associations as dashed lines. Non-H atoms are shown as 50% probability
displacement ellipsoids.
provides examples of low-dimensional 1:1 hydrogen-bonded
DCPA structure types, and includes the first example of a
discrete cyclic ‘heterotetramer.’ This low dimensionality in the
structures of the 1:1 aromatic Lewis base salts of the parent
Acta Cryst. (2009). C65, o103–o107
doi:10.1107/S0108270109004405
# 2009 International Union of Crystallography o103

organic compounds
All three compounds have at least one direct hetero-ring
N+—Hꢀ ꢀ ꢀOcarboxyl hydrogen-bonding interaction (Figs. 1–3
and Tables 1–3), and all show low-dimensional hydrogen-
bonded overall structures, viz. two-dimensional in (II), one-
dimensional in (III) and the first example of a cyclic zero-
dimensional bis(cation–anion) species in (I) (Figs. 4–6).
Associated with all of these DCPA structure types is the
essentially planar monoanion species, which is found in ca
50% of the known 1:1 acid salts of DCPA with aromatic Lewis
bases (Smith et al., 2008a). However, structures (I)–(III) are
sufficiently different as to be described separately.
methyl monoester of DCPA, arising from self-synthesis in the
methanol solvent under the conditions of the reaction. This
phenomenon has no precedence among the proton-transfer
compounds prepared under similar conditions in our labora-
Figure 2
The molecular conformation and atom-numbering scheme for the
3-(aminocarbonyl)pyridinium cation and the 2-carboxy-4,5-dichloro-
benzoate anion in (II). The dashed lines indicate the inter-species
hydrogen bonds, while non-H atoms are shown as 50% probability
displacement ellipsoids.
With compound (I), the primary cation–anion association is
an asymmetric cyclic R22(8) pyrimidinium–carboxyl Nꢀ ꢀ ꢀO,O0
association (Fig. 1). This is the high-probability type 4
hydrogen-bonding structural motif described by Allen et al.
(1998). The cation–anion pairs so formed repeat across
inversion centres via cyclic three-centre R21(4) amine–carboxyl
N+—Hꢀ ꢀ ꢀO,O0 associations, enclosing R66(12) rings, giving
discrete four-molecule ‘heterotetramer’ structural units
(Fig. 4). Although other zero-dimensional structures are
known among the DCPA proton-transfer compounds [others
Figure 3
The molecular conformation and atom-numbering scheme for the
4-(aminocarbonyl)pyridinium cation, the 2-carboxy-4,5-dichlorobenzoate
anion and the methyl 2-carboxy-4,5-dichlorobenzoate adduct molecule in
(III). The dashed lines indicate the inter-species hydrogen bonds, while
non-H atoms are shown as 50% probability displacement ellipsoids.
being discrete cation–anion ‘heterodimers’ (Etter
&
Adsmond, 1990), with brucine (Smith et al., 2007), hexa-
methylenetetramine and 1,10-phenanthroline (Smith et al.,
2009)], the formation of this bis(cation–anion) structure type
is driven more by the interactive features of the 2-amino-
pyrimidine molecular synthon and finds a small incidence
among its 1:1 salts with the aromatic acids, e.g. (3,4-dichloro-
phenoxy)acetic acid (Lynch et al., 1994) and phthalic acid
(Smith et al., 1995).
With (II), the nicotinamide cations form chain structures
through homomeric amide–carbonyl N31—Hꢀ ꢀ ꢀO inter-
actions. These chains are linked along the b cell direction by
associations involving H-atom donors of both the amide N and
the primary pyridinium groups to carboxyl O-atom acceptors
of the anions (Table 2), giving a sheet parallel to (100) (Fig. 5).
Compound (III) is an example of a 1:1:1 cation–anion
adduct structure with the adduct molecule an unexpected
Figure 4
Hydrogen-bonding in the discrete cyclic centrosymmetric bis(cation–
anion) ‘heterotetramer’ structural units in (I), shown as dashed lines.
Non-interacting H atoms have been omitted. See Table 1 for symmetry
code.
ꢁ
ꢂ
o104 Smith et al. Three C8H3Cl2O4 salts
Acta Cryst. (2009). C65, o103–o107

organic compounds
tory. In (III), the primary pyridinium–carboxyl N+—Hꢀ ꢀ ꢀO
hydrogen-bonded unit is extended into a zigzag chain along
[101] via an amide–carboxyl N—Hꢀ ꢀ ꢀO association (Fig. 6).
The second amide N atom, together with the amide carbonyl
O atom, is involved in an asymmetric cyclic R22(8) association
with the peripherally linked DCPA methyl monoester adduct
molecule (B).
compounds with 3- and 4-aminobenzoic acids (Smith et al.,
2008a). The occurrence of this phenomenon, particularly in
dichloro-substituted aromatic compounds, has previously
been described (Sarma & Desiraju, 1986). However, in all
three structures there are short Clꢀ ꢀ ꢀOcarboxyl associations [for
ii
˚
(I): Cl4ꢀ ꢀ ꢀO22 = 3.0683 (14) A; symmetry code: (ii) ꢁx + 1,
ii
˚
ꢁy + 2, ꢁz + 1; for (II): Cl4ꢀ ꢀ ꢀO11 = 3.1583 (15) A; symmetry
iii
1
2
5
2
There is an absence in (I)–(III) of short intermolecular
Clꢀ ꢀ ꢀCl interactions such as has been found in the DCPA
code: (iii) ꢁx + 1, y + , ꢁz + ; for (III): Cl4ꢀ ꢀ ꢀO22
=
1
2
˚
2.983 (5) A; symmetry code: (iii) x, ꢁy + 1, z ꢁ ].
With the DCPA anions in this series, the essential planarity
is the result of the presence of short intramolecular hydrogen
bonds between the carboxyl groups [Oꢀ ꢀ ꢀO distances range
˚
˚
from 2.393 (8) A in (III) to 2.410 (2) A in (II)]. The torsion
angles associated with these groups (C2—C1—C11—O11 and
C1—C2—C21—O22) are ꢁ170.16 (16) and ꢁ179.70 (16)ꢃ,
respectively, for (I), ꢁ178.73 (19) and 172.53 (18)ꢃ for (II), and
173.0 (7) and ꢁ178.5 (7)ꢃ for (III). The planarity also means
that there are short intramolecular aromatic ring C—
Hꢀ ꢀ ꢀOcarboxyl contacts [typically, the Cꢀ ꢀ ꢀO distances are C6—
˚
˚
H6ꢀ ꢀ ꢀO11 = 2.676 (2) A and C3—H3ꢀ ꢀ ꢀO22 = 2.643 (2) A in
(I)]. With the methyl ester adduct molecule in (III), the
carboxylic acid group provides hydrogen-bonding links to the
cation–anion chain structure rather than forming an intra-
molecular hydrogen bond and is therefore rotated out of the
molecular plane [C2B—C1B—C11B—O11B = ꢁ151.6 (6)ꢃ].
This present series provides a set of low-dimensional
hydrogen-bonded structure types in the series of 1:1 proton-
transfer compounds of 4,5-dichlorophthalic acid with aromatic
Lewis bases. This low dimensionality is largely associated with
planarity in the internally hydrogen-bonded hydrogen
phthalate anion species.
Figure 5
Hydrogen-bonding in the homomeric cation chains and the peripheral
cation–anion extensions in the sheet structure in a perspective view of the
unit cell of (II). Non-interacting H atoms have been omitted, and
hydrogen bonds are shown as dashed lines. See Table 2 for symmetry
codes.
Experimental
Compounds (I)–(III) were synthesized by heating together, for
10 min under reflux, 1 mmol quantities of 4,5-dichlorophthalic acid
and, respectively, 2-aminopyrimidine, nicotinic acid and isonicotinic
acid in methanol (50 ml). All compounds were obtained as small
colourless plates or needles [m.p. (I) 334 K; (II) 455–457 K; (III) 433–
434 K] after partial room-temperature evaporation of the solvent.
Compound (I)
Crystal data
+
ꢁ
C4H6N3 ꢀC8H3Cl2O4
ꢂ = 109.473 (5)ꢃ
3
˚
Mr = 330.12
Triclinic, P1
a = 6.9738 (4) A
V = 650.50 (7) A
Z = 2
˚
˚
Cu Kꢀ radiation
ꢃ = 4.70 mmꢁ1
T = 180 K
0.40 ꢄ 0.25 ꢄ 0.06 mm
b = 9.4413 (4) A
˚
c = 10.8900 (7) A
ꢀ = 97.420 (4)ꢃ
ꢁ = 100.527 (5)ꢃ
Data collection
Figure 6
The zigzag hydrogen-bonded chains formed by extension of the cation–
anion pairs and the peripherally attached methyl monoester adduct B
molecules in the structure of (III), in a perspective view of the unit cell.
Oxford Diffraction Gemini-S Ultra
CCD-detector diffractometer
Absorption correction: multi-scan
(SADABS; Sheldrick, 1996)
Tmin = 0.263, Tmax = 0.750
4955 measured reflections
2542 independent reflections
2300 reflections with I > 2ꢄ(I)
Rint = 0.020
1
Non-interacting H atoms have been omitted. [Symmetry code: (ii) x ꢁ ,
2
1
2
y + 32, z ꢁ ; see Table 3 for symmetry code (i).]
ꢁ
ꢂ
Acta Cryst. (2009). C65, o103–o107
Smith et al. Three C8H3Cl2O4 salts o105

organic compounds
Refinement
Data collection
R[F2 > 2ꢄ(F2)] = 0.033
wR(F2) = 0.095
S = 1.09
2542 reflections
206 parameters
H atoms treated by a mixture of
independent and constrained
refinement
Oxford Diffraction Gemini-S Ultra
CCD-detector diffractometer
Absorption correction: multi-scan
(SADABS; Sheldrick, 1996)
Tmin = 0.454, Tmax = 0.710
6097 measured reflections
3034 independent reflections
2530 reflections with I > 2ꢄ(I)
Rint = 0.045
ꢁ3
˚
Áꢅmax = 0.33 e A
ꢁ3
˚
Áꢅmin = ꢁ0.27 e A
Refinement
Table 1
Hydrogen-bond geometry (A, ) for (I).
ꢃ
R[F2 > 2ꢄ(F2)] = 0.046
wR(F2) = 0.128
S = 0.97
3034 reflections
363 parameters
1 restraint
H atoms treated by a mixture of
independent and constrained
refinement
˚
D—Hꢀ ꢀ ꢀA
D—H
Hꢀ ꢀ ꢀA
Dꢀ ꢀ ꢀA
D—Hꢀ ꢀ ꢀA
ꢁ3
˚
Áꢅmax = 0.32 e A
ꢁ3
˚
Áꢅmin = ꢁ0.43 e A
O12—H12ꢀ ꢀ ꢀO21
1.02 (4)
0.87 (2)
0.86 (2)
0.86 (2)
0.92 (3)
1.38 (3)
1.79 (2)
2.18 (3)
2.47 (3)
2.02 (3)
2.4037 (19)
2.6609 (19)
3.038 (2)
2.971 (2)
2.929 (2)
177 (3)
Absolute structure: Flack (1983),
576 Friedel pairs
Flack parameter: 0.03 (2)
N1A—H1Aꢀ ꢀ ꢀO22
N21A—H21Aꢀ ꢀ ꢀO11i
N21A—H21Aꢀ ꢀ ꢀO12i
N21A—H22Aꢀ ꢀ ꢀO21
178.8 (19)
173 (3)
117 (2)
169.4 (19)
Symmetry code: (i) ꢁx ꢁ 1; ꢁy þ 1; ꢁz.
Table 3
Hydrogen-bond geometry (A, ) for (III).
ꢃ
˚
D—Hꢀ ꢀ ꢀA
D—H
Hꢀ ꢀ ꢀA
Dꢀ ꢀ ꢀA
D—Hꢀ ꢀ ꢀA
Compound (II)
O12—H12ꢀ ꢀ ꢀO21
0.81 (8)
0.93 (8)
0.83 (7)
0.82 (8)
0.85 (9)
1.60 (9)
1.70 (7)
2.05 (8)
2.14 (8)
1.81 (8)
2.394 (10)
2.620 (8)
2.866 (9)
2.935 (6)
2.661 (7)
166 (11)
169 (5)
166 (5)
167 (10)
174 (8)
N1A—H1Aꢀ ꢀ ꢀO22i
N41A—H41Aꢀ ꢀ ꢀO12B
N41A—H42Aꢀ ꢀ ꢀO11
O11B—H11Bꢀ ꢀ ꢀO41A
Crystal data
C6H7N2O+ꢀC8H3Cl2O4
ꢁ
3
˚
V = 1432.06 (6) A
Z = 4
Cu Kꢀ radiation
ꢃ = 4.36 mmꢁ1
T = 130 K
Mr = 357.14
Monoclinic, P21=c
˚
1
3
1
a = 11.4303 (3) A
Symmetry code: (i) x þ ; ꢁy þ ; z ꢁ .
2
2
2
˚
b = 13.7933 (3) A
˚
c = 9.2082 (2) A
0.50 ꢄ 0.25 ꢄ 0.07 mm
ꢁ = 99.454 (2)ꢃ
H atoms potentially involved in hydrogen-bonding interactions in
all compounds were located by difference methods and their posi-
tional and isotropic displacement parameters were refined. Other H
Data collection
Oxford Diffraction Gemini-S CCD-
detector diffractometer
Absorption correction: multi-scan
(SADABS; Sheldrick, 1996)
Tmin = 0.340, Tmax = 0.740
6939 measured reflections
˚
atoms were included at calculated positions (C—H = 0.93–0.96 A)
2798 independent reflections
2237 reflections with I > 2ꢄ(I)
Rint = 0.026
and treated as riding [with Uiso(H) = 1.2Ueq(C) or 1.5Ueq(methyl C)].
For compound (III), the correct orientation of the structure with
respect to the polar-axis directions was established by means of the
Flack (1983) x parameter.
Refinement
For all compounds, data collection: CrysAlis CCD (Oxford
Diffraction, 2008); cell refinement: CrysAlis RED (Oxford Diffrac-
tion, 2008); data reduction: CrysAlis RED; program(s) used to solve
structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine
structure: SHELXL97 (Sheldrick, 2008); molecular graphics:
PLATON (Spek, 2009); software used to prepare material for
publication: PLATON.
R[F2 > 2ꢄ(F2)] = 0.035
wR(F2) = 0.095
S = 0.96
2798 reflections
224 parameters
H atoms treated by a mixture of
independent and constrained
refinement
ꢁ3
˚
Áꢅmax = 0.34 e A
ꢁ3
˚
Áꢅmin = ꢁ0.22 e A
Table 2
Hydrogen-bond geometry (A, ) for (II).
ꢃ
˚
The authors acknowledge financial support from the School
of Physical and Chemical Sciences, Queensland University of
Technology, the School of Biomolecular and Physical Sciences,
Griffith University, and the School of Chemistry, University of
Melbourne.
D—Hꢀ ꢀ ꢀA
D—H
Hꢀ ꢀ ꢀA
Dꢀ ꢀ ꢀA
D—Hꢀ ꢀ ꢀA
O12—H12ꢀ ꢀ ꢀO21
0.99 (4)
0.96 (2)
0.88 (3)
0.89 (3)
1.43 (4)
1.62 (2)
2.04 (3)
2.06 (3)
2.410 (2)
2.571 (2)
2.908 (2)
2.869 (2)
180 (6)
178 (3)
171 (2)
151 (2)
N1A—H1Aꢀ ꢀ ꢀO22
N31A—H31Aꢀ ꢀ ꢀO31Ai
N31A—H32Aꢀ ꢀ ꢀO11ii
3
2
1
2
Symmetry codes: (i) x; ꢁy þ ; z þ ; (ii) x; y þ 1; z.
Supplementary data for this paper are available from the IUCr electronic
archives (Reference: GD3270). Services for accessing these data are
described at the back of the journal.
Compound (III)
References
Crystal data
C6H7N2O+ꢀC8H3Cl2O4ꢁꢀC9H6Cl2O4
Allen, F. H., Raithby, P. R., Shields, G. P. & Taylor, R. (1998). Chem. Commun.
pp. 1043–1044.
Etter, M. C. & Adsmond, D. A. (1990). J. Chem. Soc. Chem. Commun. pp. 589–
591.
Etter, M. C., MacDonald, J. C. & Bernstein, J. (1990). Acta Cryst. B46, 256–262.
Flack, H. D. (1983). Acta Cryst. A39, 876–881.
Lynch, D. E., Smith, G., Freney, D., Byriel, K. A. & Kennard, C. H. L. (1994).
Aust. J. Chem. 47, 1097–1115.
3
˚
V = 2458.39 (15) A
Z = 4
Cu Kꢀ radiation
ꢃ = 4.90 mmꢁ1
T = 130 K
Mr = 606.18
Monoclinic, Cc
a = 11.9645 (4) A
˚
˚
b = 26.1393 (6) A
˚
c = 9.3213 (3) A
0.56 ꢄ 0.14 ꢄ 0.07 mm
ꢁ = 122.509 (3)ꢃ
ꢁ
ꢂ
o106 Smith et al. Three C8H3Cl2O4 salts
Acta Cryst. (2009). C65, o103–o107

organic compounds
Oxford Diffraction (2008). CrysAlis CCD and CrysAlis RED. Versions
1.171.32.5. Oxford Diffraction Ltd, Abingdon, Oxfordshire, England.
Sarma, J. A. R. P. & Desiraju, G. R. (1986). Acc. Chem. Res. 19, 222–228.
Sheldrick, G. M. (1996). SADABS. University of Go¨ttingen, Germany.
Sheldrick, G. M. (2008). Acta Cryst. A64, 112–122.
Smith, G. & Wermuth, U. D. (2009). Acta Cryst. C65. Submitted.
Smith, G., Wermuth, U. D. & White, J. M. (2007). Acta Cryst. E63, o4276–
o4277.
Smith, G., Wermuth, U. D. & White, J. M. (2008a). Acta Cryst. C64, o180–o183.
Smith, G., Wermuth, U. D. & White, J. M. (2008b). Acta Cryst. C64, o532–o536.
Smith, G., Wermuth, U. D. & White, J. M. (2009). Unpublished data.
Spek, A. L. (2009). Acta Cryst. D65, 148–155.
Smith, G., Gentner, J. M., Lynch, D. E., Byriel, K. A. & Kennard, C. H. L.
(1995). Aust. J. Chem. 48, 1151–1166.
ꢁ
ꢂ
Acta Cryst. (2009). C65, o103–o107
Smith et al. Three C8H3Cl2O4 salts o107