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Four organic salts, namely benzamidinidium orotate (2,6-di­oxo-1,2,3,6-tetra­hydro­pyrimidine-4-carboxyl­ate) hemi­hydrate, C7H9N2+·C5H3N2O4·0.5H2O (BenzamH+·Or), (I), benzamidinium isoorotate (2,4-dioxo-1,2,3,4-tetra­hydro­pyrimidine-5-carboxyl­ate) trihydrate, C7H9N2+·C5H3N2O4·3H2O (BenzamH+·Isor), (II), benzamidinium diliturate (5-nitro-2,6-dioxo-1,2,3,6-tetra­hydro­pyrimidin-4-olate) di­hydrate, C7H9N2+·C4H2N3O5·2H2O (BenzamH+·Dil), (III), and benzamidinium 5-nitro­uracilate (5-nitro-2,4-dioxo-1,2,3,4-tetra­hydro­pyrimidin-1-ide), C7H9N2+·C4H2N3O4 (BenzamH+·Nit), (IV), have been synthesized by a reaction between benzamidine (benzene­carboximidamide 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 amino­oxo 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 mol­ecules in (I), (II) and (III), respectively. Due to the presence of protonated benzamidine, these acid–base complexes form supra­molecular synthons characterized by N+—H...O and N+—H...N (±)-charge-assisted hydrogen bonds (CAHB).

Supporting information

cif

Crystallographic Information File (CIF) https://doi.org/10.1107/S0108270110016252/fn3053sup1.cif
Contains datablocks global, I, II, III, IV

hkl

Structure factor file (CIF format) https://doi.org/10.1107/S0108270110016252/fn3053Isup2.hkl
Contains datablock I

hkl

Structure factor file (CIF format) https://doi.org/10.1107/S0108270110016252/fn3053IIsup3.hkl
Contains datablock II

hkl

Structure factor file (CIF format) https://doi.org/10.1107/S0108270110016252/fn3053IIIsup4.hkl
Contains datablock III

hkl

Structure factor file (CIF format) https://doi.org/10.1107/S0108270110016252/fn3053IVsup5.hkl
Contains datablock IV

CCDC references: 782536; 782537; 782538; 782539

Comment top

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 non-covalent 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 al., 1995), allowing reasonably good control over the resulting structures.

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 resonance or ionic charge has long been recognized (Ferretti et al., 2004; Ward, 2005; Kojić-Prodić & Molčanov, 2008, and references 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—H···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 competition 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 predominates (Kratochvíl et al., 1987; Portalone, 2008a; Kolev et al., 2009). These acid–base complexes are usually arranged in a dimeric motif, similar to that found in carboxylic acid dimers, via N+—H···O- (±)-charge-assisted hydrogen bonds (CAHB) (Gilli & Gilli, 2009), provided that Δpka [Δpka = pka(base) - pka(acid), where the pka are for aqueous solutions] is sufficiently large. The value of Δpka is often used to predict whether a salt or co-crystal can be expected for two components (Johnson & Rumon, 1965; Childs et al., 2007), but some exceptions have been reported (Herbstein, 2005; Molčanov & Kojić-Prodić, 2010). A value of Δpka < 0 is generally considered to be associated with systems that form co-crystals, Δpka > 3 results in salts, while 0 < Δpka < 3 can produce co-crystals, salts or mixed ionization complexes.

Another possibility is offered by coupling benzamidinium cations with counterions 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, CC—H and C—Hal) (Robinson et al., 2000; Thallapally et al., 2003; Thomas et al., 2005). Consequently, 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.

In this study, an analysis of solid-state heteromeric and homomeric hydrogen-bond interactions has been carried out in four acid–base complexes formed by benzamidine (Benzam) with orotic acid (Or), isoorotic acid (Isor), dilituric 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 biological 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 Δpka 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).

In these four 1:1 proton-transfer compounds, protonation occurs at the Benzam 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+—H···O- and N+—H···N- (±)-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+.Or-, (I), and favours aggregation into dimers. In BenzamH+.Isor- and BenzamH+.Dil-, (II) and (III), the lack of hydrogen-bond acceptors with respect to imino hydrogen-bond donors gives rise to the formation of bifurcated hydrogen bonds.

Compound (I) crystallizes in the monoclinic space group C2/c, with one tautomeric aminooxo anion (Or-), one monoprotonated benzamidinium cation (BenzamH+) and one-half of a solvent water molecule (which lies across a screw 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 dihedral angles are 29.3 (2) and 29.2 (2)°, respectively], close to the values observed in benzamidine [22.7 (3) and 20.9 (3)°; Barker et al., 1996] and benzdiamidine [25.3 (2) and 23.8 (2)°; Jokić 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 Or- anion the pyrimidine ring is essentially planar and the carboxylate group is rotated 15.4 (2)–15.7 (2)° 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+—H···O- (±)-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 (Isor-), one BenzamH+ cation and three solvent water molecules in the asymmetric unit (Fig. 2). In the non-planar BenzamH+ cation the amidinium group is twisted out of the mean plane of the benzene ring by 23.2 (3) and 22.5 (3)°. Comparison of the geometric parameters of the Isor- 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 bifurcated N+—H···O- (±)-CAHB hydrogen bonds. The Isor- anion acts as an acceptor of bifurcated hydrogen bonds of descriptor R12(6) and R21(6) through one O atom of the carboxylate group and the adjacent carbonyl O atom (Table 3).

Compound (III) also crystallizes in the monoclinic space group P21/n, with one planar tautomeric aminooxo anion (Dil-), one BenzamH+ cation and two solvent water molecules in the asymmetric unit (Fig. 3). At variance with the previous adducts, (I) and (II), in (III) the BenzamH+ cation is planar [N4—C14—C8—C13 and N5—C14—C8—C9 dihedral angles are 0.5 (2) and 0.7 (2)°, 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 conformation is the planar one (Li et al., 2009). In the planar Dil- anion, the release of an H atom from the hydroxyl O atom causes a redistribution of π-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 R12(6) and R21(6) bifurcated N+—H···O- (±)-CAHB hydrogen bonds, but the Dil- 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 phenylbiguanide and dilituric acid monohydrate (Portalone & Colapietro, 2007a).

Compound (IV) crystallizes in the triclinic space group P1, with one planar tautomeric aminooxo anion (Nit-) 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 dihedral angles are 29.7 (4) and 30.4 (3)°, respectively]. Of the different sites available in the 5-nitrouracil molecule, deprotonation occurs at the more acidic ring N atom meta to the C atom bearing the nitro group (Portalone & Colapietro, 2007b) and this causes a redistribution of π-electron density in Nit-. 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 contributor. The two ions are connected by two R12(6) N+—H···O hydrogen bonds, and the carbonyl atom O1 of the Nit- anion acts as a bifurcated acceptor (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+—H···O, N+—H···O- and N+—H···N- (±)-CAHB hydrogen bonds. Analysis of the resulting supramolecular 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.

In the supramolecular structure of (I), which is a stoichiometric monohydrate, 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 in 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).

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—H···O and six O—H···O bonds (Table 3). Two coplanar subunits form centrosymmetric R22(8) and R23(8) rings via double intermolecular N+—H···O and N—H···O hydrogen bonds. These pairs further self-organize through double intermolecular OW—H···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—H···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+—H···O and N—H···O hydrogen bonds. In this case, however, these pairs further self-organize through an intermolecular R22(8) N—H···O interaction formed around an inversion centre, to give 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). There are auxiliary C—H···O interactions between two C—H groups of the benzamidinium cation, and carbonyl atom O1 of the Dil- anion and one water molecule (Table 4).

The molecules of (IV) are linked by a combination of five N+—H···O and N+—H···N- (±)-CAHB (Table 5). Neighbouring subunits form a sheet-like structure via three structurally significant hydrogen bonds (Fig. 8). Two centrosymmetric subunits are linked by two independent N+—H···O hydrogen bonds, forming fused centrosymmetric rings with graph-set motifs R33(12) and R22(8). An N+—H···N- homonuclear (±)-CAHB then connects these two subunits in a adjoining centrosymmetric R44(12) ring. Propagation by inversion of these subunits suffices to link all the molecules into a sheet approximately along the [010] direction [A sheet needs a plane, not a direction]. Formation of the sheet is reinforced by three intermolecular C—H···O interactions.

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?; 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 counterions 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 consequences 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 investigation.

Related literature top

For related literature, see: Allen (2002); Allen et al. (1999); Barker et al. (1996); Bernstein et al. (1994, 1995); Bis et al. (2007); Childs et al. (2007); Etter (1990); Etter, MacDonald & Bernstein (1990); Ferretti et al. (2004); Gagnon et al. (2007); Gilli & Gilli (2009); Gregson et al. (2000); Grzesiak et al. (2000); Herbstein (2005); Johnson & Rumon (1965); Jokić et al. (2001); Kojić-Prodić & Molčanov (2008); Kolev et al. (2009); Kolotuchin et al. (1995); Kratochvíl et al. (1987); Leiserowitz (1976); Li et al. (2009); Molčanov & Kojić-Prodić (2010); Motherwell et al. (1999); Nangia & Desiraju (1998); Pereira Silva, Domingos, Ramos Silva, Paixão & Matos Beja (2008); Portalone (2008a, 2008b); Portalone & Colapietro (2007a, 2007b, 2009); Powers & Harper (1999); Robinson et al. (2000); Sarma et al. (2009); Shattock et al. (2008); Thallapally et al. (2003); Thomas et al. (2005); Tidwell & Boykin (2003); Ward (2005).

Experimental top

BenzamH+.Or-, (I), BenzamH+.Isor-, (II), BenzamH+.Dil-, (III), and BenzamH+.Nit-, (IV), were obtained as white powders from equimolar mixtures (1 mmol 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 slowly warmed and then left to evaporate under ambient conditions. Small transparent single crystals were deposited after two weeks.

Refinement top

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 Å and Uiso = 1.2Ueq(C). All other H atoms, including those of the water molecules, were refined freely. In the case of BenzamH+.Nit-, (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.

Structure description top

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 non-covalent 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 al., 1995), allowing reasonably good control over the resulting structures.

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 resonance or ionic charge has long been recognized (Ferretti et al., 2004; Ward, 2005; Kojić-Prodić & Molčanov, 2008, and references 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—H···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 competition 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 predominates (Kratochvíl et al., 1987; Portalone, 2008a; Kolev et al., 2009). These acid–base complexes are usually arranged in a dimeric motif, similar to that found in carboxylic acid dimers, via N+—H···O- (±)-charge-assisted hydrogen bonds (CAHB) (Gilli & Gilli, 2009), provided that Δpka [Δpka = pka(base) - pka(acid), where the pka are for aqueous solutions] is sufficiently large. The value of Δpka is often used to predict whether a salt or co-crystal can be expected for two components (Johnson & Rumon, 1965; Childs et al., 2007), but some exceptions have been reported (Herbstein, 2005; Molčanov & Kojić-Prodić, 2010). A value of Δpka < 0 is generally considered to be associated with systems that form co-crystals, Δpka > 3 results in salts, while 0 < Δpka < 3 can produce co-crystals, salts or mixed ionization complexes.

Another possibility is offered by coupling benzamidinium cations with counterions 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, CC—H and C—Hal) (Robinson et al., 2000; Thallapally et al., 2003; Thomas et al., 2005). Consequently, 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.

In this study, an analysis of solid-state heteromeric and homomeric hydrogen-bond interactions has been carried out in four acid–base complexes formed by benzamidine (Benzam) with orotic acid (Or), isoorotic acid (Isor), dilituric 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 biological 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 Δpka 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).

In these four 1:1 proton-transfer compounds, protonation occurs at the Benzam 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+—H···O- and N+—H···N- (±)-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+.Or-, (I), and favours aggregation into dimers. In BenzamH+.Isor- and BenzamH+.Dil-, (II) and (III), the lack of hydrogen-bond acceptors with respect to imino hydrogen-bond donors gives rise to the formation of bifurcated hydrogen bonds.

Compound (I) crystallizes in the monoclinic space group C2/c, with one tautomeric aminooxo anion (Or-), one monoprotonated benzamidinium cation (BenzamH+) and one-half of a solvent water molecule (which lies across a screw 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 dihedral angles are 29.3 (2) and 29.2 (2)°, respectively], close to the values observed in benzamidine [22.7 (3) and 20.9 (3)°; Barker et al., 1996] and benzdiamidine [25.3 (2) and 23.8 (2)°; Jokić 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 Or- anion the pyrimidine ring is essentially planar and the carboxylate group is rotated 15.4 (2)–15.7 (2)° 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+—H···O- (±)-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 (Isor-), one BenzamH+ cation and three solvent water molecules in the asymmetric unit (Fig. 2). In the non-planar BenzamH+ cation the amidinium group is twisted out of the mean plane of the benzene ring by 23.2 (3) and 22.5 (3)°. Comparison of the geometric parameters of the Isor- 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 bifurcated N+—H···O- (±)-CAHB hydrogen bonds. The Isor- anion acts as an acceptor of bifurcated hydrogen bonds of descriptor R12(6) and R21(6) through one O atom of the carboxylate group and the adjacent carbonyl O atom (Table 3).

Compound (III) also crystallizes in the monoclinic space group P21/n, with one planar tautomeric aminooxo anion (Dil-), one BenzamH+ cation and two solvent water molecules in the asymmetric unit (Fig. 3). At variance with the previous adducts, (I) and (II), in (III) the BenzamH+ cation is planar [N4—C14—C8—C13 and N5—C14—C8—C9 dihedral angles are 0.5 (2) and 0.7 (2)°, 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 conformation is the planar one (Li et al., 2009). In the planar Dil- anion, the release of an H atom from the hydroxyl O atom causes a redistribution of π-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 R12(6) and R21(6) bifurcated N+—H···O- (±)-CAHB hydrogen bonds, but the Dil- 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 phenylbiguanide and dilituric acid monohydrate (Portalone & Colapietro, 2007a).

Compound (IV) crystallizes in the triclinic space group P1, with one planar tautomeric aminooxo anion (Nit-) 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 dihedral angles are 29.7 (4) and 30.4 (3)°, respectively]. Of the different sites available in the 5-nitrouracil molecule, deprotonation occurs at the more acidic ring N atom meta to the C atom bearing the nitro group (Portalone & Colapietro, 2007b) and this causes a redistribution of π-electron density in Nit-. 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 contributor. The two ions are connected by two R12(6) N+—H···O hydrogen bonds, and the carbonyl atom O1 of the Nit- anion acts as a bifurcated acceptor (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+—H···O, N+—H···O- and N+—H···N- (±)-CAHB hydrogen bonds. Analysis of the resulting supramolecular 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.

In the supramolecular structure of (I), which is a stoichiometric monohydrate, 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 in 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).

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—H···O and six O—H···O bonds (Table 3). Two coplanar subunits form centrosymmetric R22(8) and R23(8) rings via double intermolecular N+—H···O and N—H···O hydrogen bonds. These pairs further self-organize through double intermolecular OW—H···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—H···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+—H···O and N—H···O hydrogen bonds. In this case, however, these pairs further self-organize through an intermolecular R22(8) N—H···O interaction formed around an inversion centre, to give 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). There are auxiliary C—H···O interactions between two C—H groups of the benzamidinium cation, and carbonyl atom O1 of the Dil- anion and one water molecule (Table 4).

The molecules of (IV) are linked by a combination of five N+—H···O and N+—H···N- (±)-CAHB (Table 5). Neighbouring subunits form a sheet-like structure via three structurally significant hydrogen bonds (Fig. 8). Two centrosymmetric subunits are linked by two independent N+—H···O hydrogen bonds, forming fused centrosymmetric rings with graph-set motifs R33(12) and R22(8). An N+—H···N- homonuclear (±)-CAHB then connects these two subunits in a adjoining centrosymmetric R44(12) ring. Propagation by inversion of these subunits suffices to link all the molecules into a sheet approximately along the [010] direction [A sheet needs a plane, not a direction]. Formation of the sheet is reinforced by three intermolecular C—H···O interactions.

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?; 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 counterions 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 consequences 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 investigation.

For related literature, see: Allen (2002); Allen et al. (1999); Barker et al. (1996); Bernstein et al. (1994, 1995); Bis et al. (2007); Childs et al. (2007); Etter (1990); Etter, MacDonald & Bernstein (1990); Ferretti et al. (2004); Gagnon et al. (2007); Gilli & Gilli (2009); Gregson et al. (2000); Grzesiak et al. (2000); Herbstein (2005); Johnson & Rumon (1965); Jokić et al. (2001); Kojić-Prodić & Molčanov (2008); Kolev et al. (2009); Kolotuchin et al. (1995); Kratochvíl et al. (1987); Leiserowitz (1976); Li et al. (2009); Molčanov & Kojić-Prodić (2010); Motherwell et al. (1999); Nangia & Desiraju (1998); Pereira Silva, Domingos, Ramos Silva, Paixão & Matos Beja (2008); Portalone (2008a, 2008b); Portalone & Colapietro (2007a, 2007b, 2009); Powers & Harper (1999); Robinson et al. (2000); Sarma et al. (2009); Shattock et al. (2008); Thallapally et al. (2003); Thomas et al. (2005); Tidwell & Boykin (2003); Ward (2005).

Computing details top

For all compounds, data collection: CrysAlis CCD (Oxford Diffraction, 2006); cell refinement: CrysAlis RED (Oxford Diffraction, 2006); data reduction: CrysAlis RED (Oxford Diffraction, 2006); program(s) used to solve 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).

Figures top
[Figure 1] Fig. 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+—H···O- (±)-CAHB hydrogen bonds. Displacement ellipsoids are drawn at the 50% probability level and H atoms are shown as small spheres of arbitrary radii.
[Figure 2] Fig. 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+—H···O- (±)-CAHB hydrogen bonds. Displacement ellipsoids are drawn at the 50% probability level and H atoms are shown as small spheres of arbitrary radii.
[Figure 3] Fig. 3. 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+—H···O- (±)-CAHB hydrogen bonds. Displacement ellipsoids are drawn at the 50% probability level and H atoms are shown as small spheres of arbitrary radii.
[Figure 4] Fig. 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+—H···O hydrogen bonds. Displacement ellipsoids are drawn at the 50% probability level and H atoms are shown as small spheres of arbitrary radii.
[Figure 5] Fig. 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 6] Fig. 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 7] Fig. 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 8] Fig. 8. Part of the crystal structure of (IV), showing the formation of a hydrogen-bonded sheet approximately along the [010] direction [A sheet needs a plane, not a direction]. All atoms are shown as small spheres of arbitrary radii. For the sake of clarity, H atoms bonded to C have been omitted. Hydrogen bonding is indicated by dashed lines.
(I) benzamidinidium 2,6-dioxo-1,2,3,6-tetrahydropyrimidine-4-carboxylate hemihydrate top
Crystal data top
C7H9N2+·C5H3N2O4·0.5H2OF(000) = 1192
Mr = 285.27Dx = 1.495 Mg m3
Monoclinic, C2/cMo Kα radiation, λ = 0.71070 Å
Hall symbol: -C 2ycCell parameters from 37429 reflections
a = 27.2046 (6) Åθ = 2.8–32.6°
b = 7.3566 (2) ŵ = 0.12 mm1
c = 12.6687 (3) ÅT = 298 K
β = 91.621 (2)°Tablet, colourless
V = 2534.41 (11) Å30.30 × 0.20 × 0.15 mm
Z = 8
Data collection top
Oxford Xcalibur S CCD area-detector
diffractometer
4342 independent reflections
Radiation source: Enhance (Mo) X-ray source3512 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.043
Detector resolution: 16.0696 pixels mm-1θmax = 32.0°, θmin = 2.9°
ω and φ scansh = 4039
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]
k = 1010
Tmin = 0.956, Tmax = 0.983l = 1818
119911 measured reflections
Refinement top
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.065Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.152H atoms treated by a mixture of independent and constrained refinement
S = 1.20 w = 1/[σ2(Fo2) + (0.0673P)2 + 0.8406P]
where P = (Fo2 + 2Fc2)/3
4342 reflections(Δ/σ)max < 0.001
214 parametersΔρmax = 0.36 e Å3
0 restraintsΔρmin = 0.18 e Å3
Crystal data top
C7H9N2+·C5H3N2O4·0.5H2OV = 2534.41 (11) Å3
Mr = 285.27Z = 8
Monoclinic, C2/cMo Kα radiation
a = 27.2046 (6) ŵ = 0.12 mm1
b = 7.3566 (2) ÅT = 298 K
c = 12.6687 (3) Å0.30 × 0.20 × 0.15 mm
β = 91.621 (2)°
Data collection top
Oxford Xcalibur S CCD area-detector
diffractometer
4342 independent reflections
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]
3512 reflections with I > 2σ(I)
Tmin = 0.956, Tmax = 0.983Rint = 0.043
119911 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0650 restraints
wR(F2) = 0.152H atoms treated by a mixture of independent and constrained refinement
S = 1.20Δρmax = 0.36 e Å3
4342 reflectionsΔρmin = 0.18 e Å3
214 parameters
Special details top

Experimental. CrysAlis RED, Oxford Diffraction Ltd., Version 1.171.31.7 (release 18-10-2006 CrysAlis171 .NET) (compiled Oct 18 2006,16:28:17) Empirical absorption correction using spherical harmonics, implemented in SCALE3 ABSPACK scaling algorithm.

Geometry. All esds (except the esd in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds involving l.s. planes.

Refinement. Refinement of F2 against ALL reflections. The weighted R-factor wR and goodness of fit S are based on F2, conventional R-factors R are based on F, with F set to zero for negative F2. The threshold expression of F2 > σ(F2) is used only for calculating R-factors(gt) etc. and is not relevant to the choice of reflections for refinement. R-factors based on F2 are statistically about twice as large as those based on F, and R- factors based on ALL data will be even larger.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
O10.02755 (4)0.4965 (2)0.12107 (9)0.0493 (3)
O20.10134 (4)0.32241 (16)0.17858 (7)0.0365 (3)
O30.23893 (3)0.40803 (18)0.10565 (8)0.0406 (3)
O40.19075 (4)0.4125 (2)0.24542 (8)0.0479 (3)
N10.10987 (4)0.44659 (18)0.12752 (10)0.0308 (3)
H10.1124 (7)0.480 (3)0.1895 (16)0.044 (5)*
C20.06493 (5)0.4533 (2)0.07669 (11)0.0322 (3)
N30.06541 (4)0.40698 (18)0.02815 (9)0.0317 (3)
H30.0342 (8)0.423 (3)0.0643 (16)0.054 (6)*
C40.10600 (4)0.35802 (18)0.08405 (10)0.0268 (3)
C50.15181 (4)0.35577 (18)0.02380 (10)0.0275 (3)
H50.18210.32090.05720.033*
C60.15233 (4)0.40213 (18)0.07840 (10)0.0253 (2)
C70.19839 (4)0.40846 (19)0.14941 (11)0.0289 (3)
N40.26467 (4)0.4543 (2)0.39963 (11)0.0384 (3)
H4A0.2378 (7)0.453 (3)0.3477 (16)0.051 (5)*
H4B0.2597 (7)0.493 (3)0.4665 (16)0.047 (5)*
N50.31367 (5)0.3631 (2)0.26730 (10)0.0383 (3)
H5A0.2896 (8)0.374 (3)0.2157 (17)0.056 (6)*
H5B0.3416 (7)0.316 (3)0.2457 (14)0.048 (5)*
C80.35047 (4)0.39310 (19)0.44155 (11)0.0286 (3)
C90.39765 (5)0.4217 (2)0.40563 (12)0.0379 (3)
H90.40250.45000.33190.045*
C100.43776 (6)0.4098 (3)0.47517 (14)0.0489 (4)
H100.47070.42890.45000.059*
C110.43083 (6)0.3706 (3)0.58001 (15)0.0482 (4)
H110.45890.36350.62880.058*
C120.38423 (6)0.3416 (2)0.61574 (13)0.0423 (4)
H120.37960.31280.68950.051*
C130.34375 (5)0.3533 (2)0.54708 (12)0.0348 (3)
H130.31090.33360.57280.042*
C140.30793 (5)0.40428 (19)0.36685 (11)0.0292 (3)
O50.00000.1534 (3)0.25000.0624 (5)
H510.0239 (11)0.228 (5)0.244 (3)0.127 (13)*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
O10.0254 (5)0.0917 (10)0.0312 (6)0.0122 (5)0.0037 (4)0.0106 (6)
O20.0299 (5)0.0569 (7)0.0227 (5)0.0019 (4)0.0005 (4)0.0060 (4)
O30.0224 (4)0.0694 (8)0.0301 (6)0.0012 (4)0.0016 (4)0.0047 (5)
O40.0289 (5)0.0901 (10)0.0247 (5)0.0004 (5)0.0009 (4)0.0001 (6)
N10.0228 (5)0.0483 (7)0.0212 (6)0.0038 (4)0.0007 (4)0.0043 (5)
C20.0226 (5)0.0477 (8)0.0263 (7)0.0041 (5)0.0012 (5)0.0025 (6)
N30.0214 (5)0.0493 (7)0.0242 (6)0.0043 (5)0.0006 (4)0.0032 (5)
C40.0232 (5)0.0338 (6)0.0237 (6)0.0003 (5)0.0022 (4)0.0002 (5)
C50.0207 (5)0.0362 (6)0.0255 (6)0.0011 (5)0.0024 (4)0.0003 (5)
C60.0203 (5)0.0306 (6)0.0249 (6)0.0005 (4)0.0010 (4)0.0029 (5)
C70.0230 (5)0.0378 (7)0.0257 (6)0.0008 (5)0.0012 (4)0.0020 (5)
N40.0261 (5)0.0578 (8)0.0311 (7)0.0074 (5)0.0003 (5)0.0107 (6)
N50.0285 (6)0.0601 (8)0.0263 (6)0.0086 (5)0.0001 (5)0.0078 (6)
C80.0247 (5)0.0328 (6)0.0282 (7)0.0003 (5)0.0007 (5)0.0052 (5)
C90.0287 (6)0.0542 (9)0.0308 (7)0.0052 (6)0.0030 (5)0.0066 (6)
C100.0282 (7)0.0730 (12)0.0456 (10)0.0073 (7)0.0001 (6)0.0131 (8)
C110.0363 (7)0.0620 (11)0.0456 (9)0.0020 (7)0.0127 (7)0.0097 (8)
C120.0454 (8)0.0514 (9)0.0297 (8)0.0036 (7)0.0051 (6)0.0012 (7)
C130.0317 (6)0.0412 (7)0.0315 (7)0.0007 (5)0.0035 (5)0.0002 (6)
C140.0257 (5)0.0338 (6)0.0282 (7)0.0008 (5)0.0018 (5)0.0034 (5)
O50.0494 (11)0.0713 (14)0.0671 (14)0.0000.0124 (10)0.000
Geometric parameters (Å, º) top
O1—C21.2179 (16)N5—C141.3106 (18)
O2—C41.2289 (16)N5—H5A0.92 (2)
O3—C71.2483 (15)N5—H5B0.89 (2)
O4—C71.2400 (17)C8—C131.386 (2)
N1—C21.3664 (16)C8—C91.3901 (18)
N1—C61.3673 (16)C8—C141.4763 (18)
N1—H10.82 (2)C9—C101.386 (2)
C2—N31.3717 (18)C9—H90.9700
N3—C41.3765 (16)C10—C111.377 (3)
N3—H30.96 (2)C10—H100.9700
C4—C51.4431 (17)C11—C121.375 (2)
C5—C61.3385 (18)C11—H110.9700
C5—H50.9700C12—C131.386 (2)
C6—C71.5225 (17)C12—H120.9700
N4—C141.3118 (17)C13—H130.9700
N4—H4A0.97 (2)O5—H510.85 (3)
N4—H4B0.91 (2)
C2—N1—C6123.39 (12)C14—N5—H5A124.4 (13)
C2—N1—H1119.2 (13)C14—N5—H5B121.0 (12)
C6—N1—H1117.2 (13)H5A—N5—H5B114.6 (17)
O1—C2—N1122.64 (13)C13—C8—C9119.74 (13)
O1—C2—N3122.88 (12)C13—C8—C14120.53 (12)
N1—C2—N3114.48 (11)C9—C8—C14119.73 (12)
C2—N3—C4126.37 (11)C10—C9—C8120.01 (14)
C2—N3—H3113.5 (12)C10—C9—H9120.0
C4—N3—H3119.9 (12)C8—C9—H9120.0
O2—C4—N3119.67 (11)C11—C10—C9119.97 (15)
O2—C4—C5125.22 (11)C11—C10—H10120.0
N3—C4—C5115.10 (11)C9—C10—H10120.0
C6—C5—C4119.60 (11)C12—C11—C10120.18 (15)
C6—C5—H5120.2C12—C11—H11119.9
C4—C5—H5120.2C10—C11—H11119.9
C5—C6—N1121.02 (11)C11—C12—C13120.48 (15)
C5—C6—C7124.42 (11)C11—C12—H12119.8
N1—C6—C7114.56 (11)C13—C12—H12119.8
O4—C7—O3127.63 (12)C8—C13—C12119.63 (13)
O4—C7—C6114.97 (11)C8—C13—H13120.2
O3—C7—C6117.40 (12)C12—C13—H13120.2
C14—N4—H4A116.6 (12)N5—C14—N4120.12 (13)
C14—N4—H4B122.8 (12)N5—C14—C8119.44 (12)
H4A—N4—H4B120.5 (17)N4—C14—C8120.44 (12)
C6—N1—C2—O1178.56 (15)C5—C6—C7—O315.7 (2)
C6—N1—C2—N31.6 (2)N1—C6—C7—O3164.98 (13)
O1—C2—N3—C4179.51 (15)C13—C8—C9—C100.2 (2)
N1—C2—N3—C40.7 (2)C14—C8—C9—C10179.42 (15)
C2—N3—C4—O2178.82 (14)C8—C9—C10—C110.4 (3)
C2—N3—C4—C50.4 (2)C9—C10—C11—C120.6 (3)
O2—C4—C5—C6178.18 (14)C10—C11—C12—C130.7 (3)
N3—C4—C5—C60.96 (19)C9—C8—C13—C120.2 (2)
C4—C5—C6—N11.9 (2)C14—C8—C13—C12179.37 (14)
C4—C5—C6—C7178.78 (12)C11—C12—C13—C80.5 (2)
C2—N1—C6—C52.3 (2)C13—C8—C14—N5150.40 (15)
C2—N1—C6—C7178.29 (13)C9—C8—C14—N529.2 (2)
C5—C6—C7—O4163.94 (14)C13—C8—C14—N429.3 (2)
N1—C6—C7—O415.40 (19)C9—C8—C14—N4151.05 (15)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N1—H1···O2i0.82 (2)2.24 (2)3.0013 (16)153.5 (18)
N3—H3···O1ii0.96 (2)1.90 (2)2.8491 (15)168.0 (19)
N4—H4A···O40.97 (2)1.82 (2)2.7809 (16)170.6 (18)
N4—H4B···O3i0.91 (2)2.00 (2)2.9036 (17)171.4 (18)
N5—H5A···O30.92 (2)1.95 (2)2.8638 (16)178 (2)
N5—H5B···O2iii0.89 (2)2.06 (2)2.9357 (16)170.0 (17)
O5—H51···O20.85 (3)2.35 (3)3.1345 (14)154 (3)
Symmetry codes: (i) x, y+1, z+1/2; (ii) x, y+1, z; (iii) x+1/2, y+1/2, z.
(II) benzamidinium 2,4-dioxo-1,2,3,4-tetrahydropyrimidine-5-carboxylate trihydrate top
Crystal data top
C7H9N2+·C5H3N2O4·3H2OF(000) = 696
Mr = 330.30Dx = 1.438 Mg m3
Monoclinic, P21/nMo Kα radiation, λ = 0.71070 Å
Hall symbol: -P 2ynCell parameters from 39574 reflections
a = 11.3562 (2) Åθ = 2.7–32.6°
b = 6.0402 (1) ŵ = 0.12 mm1
c = 22.3763 (4) ÅT = 298 K
β = 96.221 (2)°Tablet, colourless
V = 1525.84 (5) Å30.18 × 0.14 × 0.09 mm
Z = 4
Data collection top
Oxford Xcalibur S CCD area-detector
diffractometer
5260 independent reflections
Radiation source: Enhance (Mo) X-ray source3884 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.073
Detector resolution: 16.0696 pixels mm-1θmax = 32.0°, θmin = 3.1°
ω and φ scansh = 1616
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]
k = 98
Tmin = 0.918, Tmax = 0.990l = 3333
218566 measured reflections
Refinement top
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.087Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.186H atoms treated by a mixture of independent and constrained refinement
S = 1.24 w = 1/[σ2(Fo2) + (0.0799P)2 + 0.1594P]
where P = (Fo2 + 2Fc2)/3
5260 reflections(Δ/σ)max < 0.001
256 parametersΔρmax = 0.36 e Å3
0 restraintsΔρmin = 0.25 e Å3
Crystal data top
C7H9N2+·C5H3N2O4·3H2OV = 1525.84 (5) Å3
Mr = 330.30Z = 4
Monoclinic, P21/nMo Kα radiation
a = 11.3562 (2) ŵ = 0.12 mm1
b = 6.0402 (1) ÅT = 298 K
c = 22.3763 (4) Å0.18 × 0.14 × 0.09 mm
β = 96.221 (2)°
Data collection top
Oxford Xcalibur S CCD area-detector
diffractometer
5260 independent reflections
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]
3884 reflections with I > 2σ(I)
Tmin = 0.918, Tmax = 0.990Rint = 0.073
218566 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0870 restraints
wR(F2) = 0.186H atoms treated by a mixture of independent and constrained refinement
S = 1.24Δρmax = 0.36 e Å3
5260 reflectionsΔρmin = 0.25 e Å3
256 parameters
Special details top

Experimental. CrysAlis RED, Oxford Diffraction Ltd., Version 1.171.31.7 (release 18-10-2006 CrysAlis171 .NET) (compiled Oct 18 2006,16:28:17) Empirical absorption correction using spherical harmonics, implemented in SCALE3 ABSPACK scaling algorithm.

Geometry. All esds (except the esd in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds involving l.s. planes.

Refinement. Refinement of F2 against ALL reflections. The weighted R-factor wR and goodness of fit S are based on F2, conventional R-factors R are based on F, with F set to zero for negative F2. The threshold expression of F2 > σ(F2) is used only for calculating R-factors(gt) etc. and is not relevant to the choice of reflections for refinement. R-factors based on F2 are statistically about twice as large as those based on F, and R- factors based on ALL data will be even larger.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
O10.26236 (11)1.4201 (2)0.03821 (6)0.0409 (3)
O20.43826 (10)0.8013 (2)0.04372 (6)0.0398 (3)
O30.29919 (13)0.5324 (3)0.11227 (8)0.0589 (5)
O40.12458 (11)0.6721 (2)0.12812 (6)0.0427 (4)
N10.15370 (12)1.1941 (3)0.01643 (7)0.0358 (4)
H10.094 (2)1.297 (4)0.0115 (11)0.060 (7)*
C20.25451 (14)1.2515 (3)0.00842 (8)0.0308 (4)
N30.34525 (12)1.1024 (3)0.00255 (7)0.0309 (3)
H30.410 (2)1.136 (4)0.0146 (11)0.053 (7)*
C40.34696 (13)0.9121 (3)0.03751 (7)0.0273 (3)
C50.23792 (13)0.8678 (3)0.06406 (7)0.0282 (4)
C60.14801 (14)1.0140 (3)0.05187 (8)0.0319 (4)
H60.07510.98780.06970.038*
C70.22149 (15)0.6745 (3)0.10440 (8)0.0330 (4)
N40.53366 (15)0.3845 (3)0.09913 (8)0.0374 (4)
H4A0.470 (2)0.479 (4)0.0904 (12)0.060 (7)*
H4B0.592 (2)0.408 (4)0.0797 (11)0.055 (7)*
N50.43814 (15)0.1995 (3)0.16819 (8)0.0418 (4)
H5A0.376 (2)0.293 (4)0.1573 (12)0.060 (7)*
H5B0.442 (2)0.101 (4)0.1975 (11)0.049 (6)*
C80.63617 (15)0.0799 (3)0.15370 (7)0.0298 (4)
C90.62272 (17)0.1276 (3)0.17948 (9)0.0375 (4)
H90.54490.17840.18740.045*
C100.7211 (2)0.2612 (3)0.19376 (9)0.0441 (5)
H100.71190.40450.21220.053*
C110.83168 (19)0.1922 (4)0.18196 (10)0.0491 (5)
H110.89990.28740.19160.059*
C120.84547 (19)0.0126 (4)0.15639 (11)0.0500 (6)
H120.92360.06130.14830.060*
C130.74854 (17)0.1489 (3)0.14223 (9)0.0397 (4)
H130.75890.29280.12430.048*
C140.53215 (15)0.2267 (3)0.13968 (8)0.0294 (4)
O50.03586 (15)0.3885 (3)0.06362 (8)0.0550 (5)
H510.003 (3)0.499 (6)0.0845 (17)0.110 (14)*
H520.102 (3)0.447 (5)0.0593 (13)0.068 (8)*
O60.1476 (2)0.9933 (3)0.22115 (11)0.0669 (5)
H610.135 (3)0.901 (6)0.1891 (16)0.089 (11)*
H620.217 (4)0.975 (6)0.2296 (18)0.100 (14)*
O70.10895 (17)0.4328 (3)0.23105 (8)0.0546 (4)
H710.114 (3)0.497 (5)0.1971 (15)0.075 (9)*
H720.112 (2)0.297 (5)0.2232 (12)0.064 (8)*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
O10.0303 (6)0.0438 (8)0.0495 (8)0.0085 (6)0.0085 (6)0.0170 (6)
O20.0232 (6)0.0444 (8)0.0540 (8)0.0114 (5)0.0140 (5)0.0152 (6)
O30.0446 (8)0.0600 (10)0.0766 (11)0.0222 (7)0.0274 (8)0.0358 (9)
O40.0325 (7)0.0471 (8)0.0515 (8)0.0008 (6)0.0179 (6)0.0099 (7)
N10.0206 (6)0.0400 (9)0.0480 (9)0.0094 (6)0.0089 (6)0.0092 (7)
C20.0218 (7)0.0383 (10)0.0321 (8)0.0050 (7)0.0023 (6)0.0033 (8)
N30.0193 (6)0.0385 (8)0.0362 (8)0.0061 (6)0.0094 (5)0.0073 (6)
C40.0208 (7)0.0327 (9)0.0290 (8)0.0038 (6)0.0050 (6)0.0012 (7)
C50.0213 (7)0.0341 (9)0.0297 (8)0.0026 (6)0.0059 (6)0.0014 (7)
C60.0196 (7)0.0398 (10)0.0373 (9)0.0019 (7)0.0080 (6)0.0007 (8)
C70.0270 (8)0.0369 (10)0.0363 (9)0.0012 (7)0.0081 (7)0.0034 (8)
N40.0314 (8)0.0395 (9)0.0423 (9)0.0067 (7)0.0087 (7)0.0120 (7)
N50.0357 (8)0.0451 (10)0.0472 (10)0.0126 (8)0.0160 (7)0.0149 (8)
C80.0310 (8)0.0320 (9)0.0265 (8)0.0052 (7)0.0035 (6)0.0002 (7)
C90.0387 (10)0.0330 (10)0.0411 (10)0.0031 (8)0.0059 (8)0.0001 (8)
C100.0555 (12)0.0333 (10)0.0435 (11)0.0112 (9)0.0047 (9)0.0042 (9)
C110.0431 (11)0.0559 (14)0.0479 (12)0.0210 (10)0.0025 (9)0.0027 (10)
C120.0332 (10)0.0613 (15)0.0570 (13)0.0089 (9)0.0111 (9)0.0088 (11)
C130.0342 (9)0.0418 (11)0.0441 (10)0.0046 (8)0.0092 (8)0.0100 (9)
C140.0300 (8)0.0292 (9)0.0290 (8)0.0013 (7)0.0032 (6)0.0017 (7)
O50.0299 (7)0.0686 (11)0.0675 (11)0.0133 (8)0.0103 (7)0.0014 (9)
O60.0718 (14)0.0477 (11)0.0797 (14)0.0075 (9)0.0012 (11)0.0127 (10)
O70.0850 (13)0.0365 (9)0.0458 (9)0.0018 (8)0.0235 (8)0.0025 (7)
Geometric parameters (Å, º) top
O1—C21.225 (2)N5—H5B0.88 (3)
O2—C41.2293 (19)C8—C131.393 (3)
O3—C71.230 (2)C8—C91.395 (3)
O4—C71.273 (2)C8—C141.483 (2)
N1—C61.352 (2)C9—C101.387 (3)
N1—C21.370 (2)C9—H90.9700
N1—H10.92 (3)C10—C111.376 (3)
C2—N31.371 (2)C10—H100.9700
N3—C41.389 (2)C11—C121.379 (3)
N3—H30.89 (3)C11—H110.9700
C4—C51.455 (2)C12—C131.384 (3)
C5—C61.355 (2)C12—H120.9700
C5—C71.500 (2)C13—H130.9700
C6—H60.9700O5—H510.90 (4)
N4—C141.318 (2)O5—H520.83 (3)
N4—H4A0.92 (3)O6—H610.91 (4)
N4—H4B0.84 (3)O6—H620.80 (4)
N5—C141.312 (2)O7—H710.86 (3)
N5—H5A0.92 (3)O7—H720.84 (3)
C6—N1—C2122.46 (14)H5A—N5—H5B126 (2)
C6—N1—H1122.1 (16)C13—C8—C9119.25 (16)
C2—N1—H1114.9 (16)C13—C8—C14120.47 (16)
O1—C2—N1122.97 (15)C9—C8—C14120.27 (15)
O1—C2—N3123.09 (15)C10—C9—C8119.76 (18)
N1—C2—N3113.94 (16)C10—C9—H9120.1
C2—N3—C4127.51 (14)C8—C9—H9120.1
C2—N3—H3114.6 (15)C11—C10—C9120.6 (2)
C4—N3—H3117.9 (15)C11—C10—H10119.7
O2—C4—N3118.31 (14)C9—C10—H10119.7
O2—C4—C5126.76 (16)C10—C11—C12119.90 (19)
N3—C4—C5114.93 (13)C10—C11—H11120.0
C6—C5—C4117.00 (15)C12—C11—H11120.0
C6—C5—C7119.23 (14)C11—C12—C13120.4 (2)
C4—C5—C7123.76 (14)C11—C12—H12119.8
N1—C6—C5124.03 (15)C13—C12—H12119.8
N1—C6—H6118.0C12—C13—C8120.12 (19)
C5—C6—H6118.0C12—C13—H13119.9
O3—C7—O4124.90 (17)C8—C13—H13119.9
O3—C7—C5119.68 (15)N5—C14—N4119.82 (17)
O4—C7—C5115.42 (15)N5—C14—C8119.61 (16)
C14—N4—H4A121.6 (16)N4—C14—C8120.57 (16)
C14—N4—H4B123.2 (17)H51—O5—H5298 (3)
H4A—N4—H4B115 (2)H61—O6—H62100 (3)
C14—N5—H5A115.9 (16)H71—O7—H72104 (3)
C14—N5—H5B118.0 (15)
C6—N1—C2—O1176.40 (18)C6—C5—C7—O45.0 (3)
C6—N1—C2—N34.2 (3)C4—C5—C7—O4173.72 (16)
O1—C2—N3—C4177.21 (17)C13—C8—C9—C100.6 (3)
N1—C2—N3—C43.4 (3)C14—C8—C9—C10178.41 (18)
C2—N3—C4—O2177.76 (17)C8—C9—C10—C110.9 (3)
C2—N3—C4—C51.3 (3)C9—C10—C11—C120.8 (3)
O2—C4—C5—C6179.15 (18)C10—C11—C12—C130.3 (4)
N3—C4—C5—C60.2 (2)C11—C12—C13—C80.0 (3)
O2—C4—C5—C70.4 (3)C9—C8—C13—C120.1 (3)
N3—C4—C5—C7178.60 (16)C14—C8—C13—C12178.89 (19)
C2—N1—C6—C53.2 (3)C13—C8—C14—N5156.43 (19)
C4—C5—C6—N10.8 (3)C9—C8—C14—N522.5 (3)
C7—C5—C6—N1179.63 (17)C13—C8—C14—N423.2 (3)
C6—C5—C7—O3174.78 (19)C9—C8—C14—N4157.83 (17)
C4—C5—C7—O36.5 (3)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N1—H1···O5i0.92 (3)2.05 (3)2.760 (2)133 (2)
N3—H3···O2ii0.89 (3)1.95 (3)2.8296 (18)174 (2)
N4—H4A···O20.92 (3)2.22 (3)2.959 (2)136 (2)
N4—H4A···O30.92 (3)2.08 (3)2.854 (2)141 (2)
N4—H4B···O1ii0.84 (3)2.24 (3)3.050 (2)162 (2)
N5—H5A···O30.92 (3)1.92 (3)2.770 (2)154 (2)
N5—H5B···O7iii0.88 (3)2.03 (3)2.868 (2)158 (2)
O5—H51···O40.90 (4)1.91 (4)2.787 (2)163 (3)
O5—H52···O1iv0.83 (3)2.00 (3)2.821 (2)173 (3)
O6—H61···O40.91 (4)1.94 (4)2.837 (3)171 (3)
O6—H62···O7v0.80 (4)2.09 (4)2.878 (3)169 (4)
O7—H71···O40.86 (3)1.89 (3)2.741 (2)173 (3)
O7—H72···O6vi0.84 (3)1.88 (3)2.704 (3)166 (3)
Symmetry codes: (i) x, y+1, z; (ii) x+1, y+2, z; (iii) x+1/2, y1/2, z+1/2; (iv) x, y+2, z; (v) x+1/2, y+1/2, z+1/2; (vi) x, y1, z.
(III) benzamidinium 5-nitro-2,6-dioxo-1,2,3,6-tetrahydropyrimidin-4-olate dihydrate top
Crystal data top
C7H9N2+·C4H2N3O5·2H2OF(000) = 688
Mr = 329.28Dx = 1.478 Mg m3
Monoclinic, P21/nMo Kα radiation, λ = 0.71070 Å
Hall symbol: -P 2ynCell parameters from 109123 reflections
a = 10.7607 (3) Åθ = 3.0–32.7°
b = 5.0998 (2) ŵ = 0.13 mm1
c = 27.2412 (5) ÅT = 298 K
β = 98.2485 (11)°Tablet, colourless
V = 1479.46 (8) Å30.16 × 0.14 × 0.12 mm
Z = 4
Data collection top
Oxford Xcalibur S CCD area-detector
diffractometer
5116 independent reflections
Radiation source: Enhance (Mo) X-ray source4542 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.034
Detector resolution: 16.0696 pixels mm-1θmax = 32.0°, θmin = 3.0°
ω and φ scansh = 1616
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]
k = 77
Tmin = 0.908, Tmax = 0.991l = 4040
306312 measured reflections
Refinement top
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.064Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.165H atoms treated by a mixture of independent and constrained refinement
S = 1.17 w = 1/[σ2(Fo2) + (0.0635P)2 + 0.691P]
where P = (Fo2 + 2Fc2)/3
5116 reflections(Δ/σ)max = 0.001
248 parametersΔρmax = 0.40 e Å3
0 restraintsΔρmin = 0.24 e Å3
Crystal data top
C7H9N2+·C4H2N3O5·2H2OV = 1479.46 (8) Å3
Mr = 329.28Z = 4
Monoclinic, P21/nMo Kα radiation
a = 10.7607 (3) ŵ = 0.13 mm1
b = 5.0998 (2) ÅT = 298 K
c = 27.2412 (5) Å0.16 × 0.14 × 0.12 mm
β = 98.2485 (11)°
Data collection top
Oxford Xcalibur S CCD area-detector
diffractometer
5116 independent reflections
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]
4542 reflections with I > 2σ(I)
Tmin = 0.908, Tmax = 0.991Rint = 0.034
306312 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0640 restraints
wR(F2) = 0.165H atoms treated by a mixture of independent and constrained refinement
S = 1.17Δρmax = 0.40 e Å3
5116 reflectionsΔρmin = 0.24 e Å3
248 parameters
Special details top

Experimental. CrysAlis RED, Oxford Diffraction Ltd., Version 1.171.31.7 (release 18-10-2006 CrysAlis171 .NET) (compiled Oct 18 2006,16:28:17) Empirical absorption correction using spherical harmonics, implemented in SCALE3 ABSPACK scaling algorithm.

Geometry. All esds (except the esd in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds involving l.s. planes.

Refinement. Refinement of F2 against ALL reflections. The weighted R-factor wR and goodness of fit S are based on F2, conventional R-factors R are based on F, with F set to zero for negative F2. The threshold expression of F2 > σ(F2) is used only for calculating R-factors(gt) etc. and is not relevant to the choice of reflections for refinement. R-factors based on F2 are statistically about twice as large as those based on F, and R- factors based on ALL data will be even larger.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
O10.20675 (11)1.0305 (3)1.05258 (5)0.0443 (3)
O20.08156 (10)0.3367 (2)0.95529 (4)0.0362 (3)
O30.23715 (13)0.1631 (3)0.89742 (6)0.0590 (4)
O40.41060 (14)0.3588 (3)0.89454 (7)0.0695 (5)
O50.48272 (10)0.7389 (3)0.95592 (5)0.0435 (3)
N10.34360 (11)0.8703 (3)1.00466 (5)0.0322 (3)
H10.400 (2)0.994 (5)1.0182 (8)0.047 (6)*
C20.23149 (13)0.8694 (3)1.02225 (5)0.0296 (3)
N30.14927 (11)0.6774 (3)1.00394 (5)0.0313 (3)
H30.078 (2)0.674 (5)1.0176 (8)0.052 (6)*
C40.16764 (12)0.4934 (3)0.96836 (5)0.0262 (3)
C50.28619 (12)0.5111 (3)0.94975 (5)0.0262 (3)
C60.37880 (13)0.7058 (3)0.96863 (5)0.0290 (3)
N70.31216 (11)0.3390 (3)0.91275 (5)0.0331 (3)
N40.00024 (13)0.1025 (3)0.89387 (5)0.0336 (3)
H4A0.057 (2)0.007 (4)0.9031 (8)0.046 (6)*
H4B0.068 (2)0.102 (4)0.9086 (8)0.045 (5)*
N50.11348 (14)0.2591 (3)0.83616 (6)0.0442 (4)
H5A0.172 (2)0.151 (5)0.8455 (9)0.057 (7)*
H5B0.126 (2)0.373 (5)0.8130 (9)0.053 (6)*
C80.08858 (13)0.4616 (3)0.84180 (5)0.0283 (3)
C90.07573 (16)0.6385 (3)0.80398 (6)0.0378 (3)
H90.00130.63390.78770.045*
C100.16936 (18)0.8218 (3)0.78951 (6)0.0434 (4)
H100.15980.94460.76310.052*
C110.27553 (17)0.8307 (3)0.81227 (6)0.0427 (4)
H110.34030.96000.80220.051*
C120.28899 (18)0.6554 (4)0.84935 (7)0.0480 (4)
H120.36390.66070.86530.058*
C130.19668 (17)0.4708 (4)0.86416 (7)0.0437 (4)
H130.20760.34730.89030.052*
C140.01158 (13)0.2672 (3)0.85800 (5)0.0294 (3)
O60.4502 (2)0.1249 (5)0.84345 (7)0.0746 (5)
H610.443 (4)0.013 (9)0.8638 (16)0.121 (14)*
H620.454 (4)0.244 (9)0.8614 (15)0.115 (15)*
O70.31408 (19)0.0585 (4)0.75176 (8)0.0674 (5)
H710.363 (3)0.087 (7)0.7806 (12)0.082 (10)*
H720.272 (4)0.203 (9)0.7466 (15)0.112 (13)*
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
O10.0441 (6)0.0459 (7)0.0462 (6)0.0171 (5)0.0181 (5)0.0231 (5)
O20.0290 (5)0.0359 (6)0.0452 (6)0.0149 (4)0.0103 (4)0.0149 (5)
O30.0439 (7)0.0592 (8)0.0785 (10)0.0269 (6)0.0240 (6)0.0462 (8)
O40.0545 (8)0.0651 (10)0.0997 (12)0.0322 (7)0.0483 (8)0.0495 (9)
O50.0313 (5)0.0474 (7)0.0552 (7)0.0208 (5)0.0174 (5)0.0216 (6)
N10.0283 (5)0.0326 (6)0.0367 (6)0.0143 (5)0.0079 (4)0.0134 (5)
C20.0299 (6)0.0296 (6)0.0298 (6)0.0106 (5)0.0063 (5)0.0071 (5)
N30.0267 (5)0.0327 (6)0.0361 (6)0.0121 (5)0.0099 (4)0.0115 (5)
C40.0243 (5)0.0250 (6)0.0294 (6)0.0070 (5)0.0039 (4)0.0040 (5)
C50.0244 (5)0.0239 (6)0.0308 (6)0.0083 (5)0.0054 (4)0.0082 (5)
C60.0271 (6)0.0273 (6)0.0331 (6)0.0099 (5)0.0055 (5)0.0077 (5)
N70.0297 (5)0.0289 (6)0.0421 (6)0.0087 (5)0.0096 (5)0.0122 (5)
N40.0345 (6)0.0312 (6)0.0354 (6)0.0098 (5)0.0059 (5)0.0096 (5)
N50.0396 (7)0.0455 (8)0.0503 (8)0.0136 (6)0.0159 (6)0.0178 (7)
C80.0328 (6)0.0227 (6)0.0284 (6)0.0045 (5)0.0013 (5)0.0019 (5)
C90.0433 (8)0.0349 (8)0.0351 (7)0.0041 (6)0.0052 (6)0.0085 (6)
C100.0547 (10)0.0340 (8)0.0392 (8)0.0083 (7)0.0011 (7)0.0117 (6)
C110.0471 (9)0.0335 (8)0.0436 (8)0.0138 (7)0.0066 (7)0.0012 (7)
C120.0445 (9)0.0465 (10)0.0547 (10)0.0186 (8)0.0134 (8)0.0115 (8)
C130.0454 (8)0.0399 (8)0.0486 (9)0.0161 (7)0.0162 (7)0.0178 (7)
C140.0319 (6)0.0260 (6)0.0298 (6)0.0040 (5)0.0026 (5)0.0017 (5)
O60.1073 (16)0.0599 (11)0.0596 (10)0.0032 (11)0.0220 (10)0.0097 (9)
O70.0694 (11)0.0696 (11)0.0668 (11)0.0037 (9)0.0219 (9)0.0109 (9)
Geometric parameters (Å, º) top
O1—C21.2215 (18)N5—H5A0.85 (3)
O2—C41.2364 (16)N5—H5B0.88 (3)
O3—N71.2385 (16)C8—C131.389 (2)
O4—N71.2364 (17)C8—C91.391 (2)
O5—C61.2287 (17)C8—C141.4843 (19)
N1—C21.3605 (18)C9—C101.389 (2)
N1—C61.3848 (18)C9—H90.9700
N1—H10.91 (2)C10—C111.377 (3)
C2—N31.3652 (17)C10—H100.9700
N3—C41.3835 (17)C11—C121.372 (3)
N3—H30.90 (2)C11—H110.9700
C4—C51.4416 (18)C12—C131.386 (2)
C5—N71.3945 (17)C12—H120.9700
C5—C61.4478 (17)C13—H130.9700
N4—C141.3083 (19)O6—H610.91 (5)
N4—H4A0.84 (2)O6—H620.78 (4)
N4—H4B0.88 (2)O7—H710.89 (3)
N5—C141.321 (2)O7—H720.87 (4)
C2—N1—C6126.45 (11)C14—N5—H5B121.8 (16)
C2—N1—H1115.4 (14)H5A—N5—H5B117 (2)
C6—N1—H1118.1 (14)C13—C8—C9118.77 (13)
O1—C2—N1121.76 (12)C13—C8—C14120.68 (13)
O1—C2—N3122.48 (13)C9—C8—C14120.55 (13)
N1—C2—N3115.76 (12)C10—C9—C8120.09 (16)
C2—N3—C4126.32 (12)C10—C9—H9120.0
C2—N3—H3114.1 (15)C8—C9—H9120.0
C4—N3—H3119.6 (16)C11—C10—C9120.63 (15)
O2—C4—N3117.62 (12)C11—C10—H10119.7
O2—C4—C5127.13 (12)C9—C10—H10119.7
N3—C4—C5115.24 (11)C12—C11—C10119.48 (15)
N7—C5—C4119.59 (11)C12—C11—H11120.3
N7—C5—C6119.28 (11)C10—C11—H11120.3
C4—C5—C6121.12 (11)C11—C12—C13120.67 (17)
O5—C6—N1117.96 (12)C11—C12—H12119.7
O5—C6—C5127.02 (13)C13—C12—H12119.7
N1—C6—C5115.02 (12)C12—C13—C8120.37 (15)
O4—N7—O3118.56 (13)C12—C13—H13119.8
O4—N7—C5120.71 (12)C8—C13—H13119.8
O3—N7—C5120.73 (12)N4—C14—N5119.49 (14)
C14—N4—H4A120.1 (15)N4—C14—C8120.43 (13)
C14—N4—H4B121.1 (15)N5—C14—C8120.07 (13)
H4A—N4—H4B119 (2)H61—O6—H62103 (4)
C14—N5—H5A121.0 (17)H71—O7—H72104 (3)
C6—N1—C2—O1176.59 (16)C4—C5—N7—O4176.48 (17)
C6—N1—C2—N33.5 (2)C6—C5—N7—O43.2 (2)
O1—C2—N3—C4177.54 (15)C4—C5—N7—O33.5 (2)
N1—C2—N3—C42.6 (2)C6—C5—N7—O3176.81 (16)
C2—N3—C4—O2178.44 (15)C13—C8—C9—C100.7 (2)
C2—N3—C4—C50.2 (2)C14—C8—C9—C10179.22 (15)
O2—C4—C5—N70.3 (2)C8—C9—C10—C110.0 (3)
N3—C4—C5—N7178.20 (13)C9—C10—C11—C120.5 (3)
O2—C4—C5—C6180.00 (15)C10—C11—C12—C130.3 (3)
N3—C4—C5—C61.5 (2)C11—C12—C13—C80.4 (3)
C2—N1—C6—O5177.73 (15)C9—C8—C13—C120.8 (3)
C2—N1—C6—C52.0 (2)C14—C8—C13—C12179.05 (17)
N7—C5—C6—O50.7 (2)C13—C8—C14—N40.5 (2)
C4—C5—C6—O5179.63 (16)C9—C8—C14—N4179.40 (15)
N7—C5—C6—N1178.97 (13)C13—C8—C14—N5179.46 (17)
C4—C5—C6—N10.7 (2)C9—C8—C14—N50.7 (2)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N1—H1···O5i0.91 (2)1.92 (2)2.8359 (16)178 (2)
N3—H3···O2ii0.90 (2)1.97 (2)2.8635 (16)178 (2)
N4—H4A···O20.84 (2)2.19 (2)2.8581 (16)135.5 (19)
N4—H4A···O30.84 (2)2.12 (2)2.8808 (18)150 (2)
N4—H4B···O1ii0.88 (2)1.98 (2)2.8514 (18)168 (2)
N5—H5A···O30.85 (3)2.19 (3)2.9250 (19)146 (2)
N5—H5B···O7iii0.88 (3)2.18 (3)3.035 (2)164 (2)
O6—H61···O40.91 (5)2.00 (5)2.894 (2)167 (4)
O6—H62···O4iv0.78 (4)2.29 (4)3.037 (3)160 (4)
O7—H71···O60.89 (3)1.84 (3)2.729 (3)173 (3)
O7—H72···O7iii0.87 (4)2.04 (4)2.8940 (19)169 (4)
C9—H9···O7iii0.972.453.410 (2)172
C13—H13···O1ii0.972.243.204 (2)171
Symmetry codes: (i) x+1, y+2, z+2; (ii) x, y+1, z+2; (iii) x+1/2, y1/2, z+3/2; (iv) x, y1, z.
(IV) benzamidinidium 5-nitro-2,4-dioxo-1,2,3,4-tetrahydropyrimidin-1-ide top
Crystal data top
C7H9N2+·C4H2N3O4Z = 2
Mr = 277.25F(000) = 288
Triclinic, P1Dx = 1.497 Mg m3
Hall symbol: -P 1Mo Kα radiation, λ = 0.71070 Å
a = 4.3625 (4) ÅCell parameters from 2451 reflections
b = 10.4461 (11) Åθ = 2.7–28.7°
c = 13.8556 (12) ŵ = 0.12 mm1
α = 78.551 (7)°T = 298 K
β = 86.841 (8)°Tablet, colourless
γ = 84.051 (7)°0.15 × 0.08 × 0.05 mm
V = 615.13 (10) Å3
Data collection top
Oxford Xcalibur S CCD area-detector
diffractometer
2153 independent reflections
Radiation source: Enhance (Mo) X-ray source1427 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.034
Detector resolution: 16.0696 pixels mm-1θmax = 25.2°, θmin = 2.7°
ω and φ scansh = 55
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]
k = 1012
Tmin = 0.978, Tmax = 0.993l = 1516
4864 measured reflections
Refinement top
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.051Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.119H atoms treated by a mixture of independent and constrained refinement
S = 1.05 w = 1/[σ2(Fo2) + (0.059P)2 + 0.0569P]
where P = (Fo2 + 2Fc2)/3
2153 reflections(Δ/σ)max < 0.001
201 parametersΔρmax = 0.18 e Å3
0 restraintsΔρmin = 0.17 e Å3
Crystal data top
C7H9N2+·C4H2N3O4γ = 84.051 (7)°
Mr = 277.25V = 615.13 (10) Å3
Triclinic, P1Z = 2
a = 4.3625 (4) ÅMo Kα radiation
b = 10.4461 (11) ŵ = 0.12 mm1
c = 13.8556 (12) ÅT = 298 K
α = 78.551 (7)°0.15 × 0.08 × 0.05 mm
β = 86.841 (8)°
Data collection top
Oxford Xcalibur S CCD area-detector
diffractometer
2153 independent reflections
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]
1427 reflections with I > 2σ(I)
Tmin = 0.978, Tmax = 0.993Rint = 0.034
4864 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0510 restraints
wR(F2) = 0.119H atoms treated by a mixture of independent and constrained refinement
S = 1.05Δρmax = 0.18 e Å3
2153 reflectionsΔρmin = 0.17 e Å3
201 parameters
Special details top

Experimental. CrysAlis RED, Oxford Diffraction Ltd., Version 1.171.31.7 (release 18-10-2006 CrysAlis171 .NET) (compiled Oct 18 2006,16:28:17) Empirical absorption correction using spherical harmonics, implemented in SCALE3 ABSPACK scaling algorithm.

Geometry. All esds (except the esd in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell esds are taken into account individually in the estimation of esds in distances, angles and torsion angles; correlations between esds in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell esds is used for estimating esds involving l.s. planes.

Refinement. Refinement of F2 against ALL reflections. The weighted R-factor wR and goodness of fit S are based on F2, conventional R-factors R are based on F, with F set to zero for negative F2. The threshold expression of F2 > σ(F2) is used only for calculating R-factors(gt) etc. and is not relevant to the choice of reflections for refinement. R-factors based on F2 are statistically about twice as large as those based on F, and R- factors based on ALL data will be even larger.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
O10.1899 (4)0.68872 (17)0.01314 (12)0.0498 (5)
O20.7422 (4)0.98092 (16)0.10665 (12)0.0491 (5)
O31.0469 (4)0.88810 (18)0.27942 (13)0.0562 (5)
O41.0080 (5)0.68823 (18)0.34994 (13)0.0622 (6)
N10.4511 (5)0.61358 (19)0.15366 (15)0.0427 (6)
C20.3644 (5)0.7085 (2)0.07448 (17)0.0358 (6)
N30.4734 (4)0.82919 (19)0.06400 (15)0.0361 (5)
H30.414 (6)0.890 (3)0.009 (2)0.065 (9)*
C40.6652 (5)0.8690 (2)0.12624 (17)0.0345 (6)
C50.7458 (5)0.7654 (2)0.20896 (16)0.0316 (5)
C60.6324 (5)0.6451 (2)0.21636 (17)0.0387 (6)
H60.69180.57780.27290.046*
N70.9421 (5)0.7824 (2)0.28300 (14)0.0401 (5)
N40.1471 (6)0.6134 (2)0.13726 (18)0.0525 (7)
H4A0.040 (7)0.603 (3)0.080 (2)0.082 (10)*
H4B0.244 (5)0.550 (3)0.1495 (18)0.048 (8)*
N50.0940 (5)0.8307 (2)0.16192 (18)0.0453 (6)
H5A0.001 (6)0.817 (3)0.104 (2)0.056 (8)*
H5B0.092 (6)0.906 (3)0.201 (2)0.050 (8)*
C80.3422 (5)0.7507 (2)0.28649 (16)0.0369 (6)
C90.5120 (6)0.8683 (3)0.32222 (18)0.0469 (7)
H90.52970.93810.28480.056*
C100.6557 (7)0.8869 (3)0.4105 (2)0.0646 (9)
H100.77730.96910.43450.078*
C110.6273 (8)0.7896 (4)0.4643 (2)0.0732 (10)
H110.72780.80350.52680.088*
C120.4575 (8)0.6725 (4)0.4308 (2)0.0733 (10)
H120.43670.60440.46980.088*
C130.3150 (7)0.6514 (3)0.34063 (19)0.0526 (7)
H130.19810.56830.31600.063*
C140.1896 (5)0.7313 (2)0.19131 (17)0.0352 (6)
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
O10.0651 (12)0.0424 (11)0.0454 (11)0.0182 (9)0.0266 (9)0.0034 (8)
O20.0711 (12)0.0286 (10)0.0479 (11)0.0173 (9)0.0284 (9)0.0050 (8)
O30.0764 (13)0.0393 (11)0.0568 (12)0.0152 (10)0.0349 (10)0.0045 (9)
O40.0939 (15)0.0495 (12)0.0408 (11)0.0165 (11)0.0363 (10)0.0111 (9)
N10.0583 (13)0.0301 (12)0.0399 (12)0.0121 (10)0.0218 (10)0.0021 (9)
C20.0391 (13)0.0333 (14)0.0355 (13)0.0088 (11)0.0092 (11)0.0031 (11)
N30.0486 (12)0.0286 (11)0.0309 (11)0.0091 (9)0.0174 (10)0.0023 (9)
C40.0397 (14)0.0303 (14)0.0344 (13)0.0064 (11)0.0115 (11)0.0043 (11)
C50.0377 (13)0.0287 (13)0.0298 (12)0.0055 (10)0.0118 (10)0.0048 (10)
C60.0448 (14)0.0313 (14)0.0375 (14)0.0050 (11)0.0138 (12)0.0033 (11)
N70.0511 (13)0.0358 (13)0.0338 (11)0.0052 (10)0.0152 (10)0.0033 (10)
N40.0741 (17)0.0364 (14)0.0486 (14)0.0218 (12)0.0300 (13)0.0039 (11)
N50.0621 (15)0.0354 (14)0.0396 (13)0.0161 (11)0.0187 (11)0.0005 (11)
C80.0434 (14)0.0376 (14)0.0306 (13)0.0152 (12)0.0077 (11)0.0013 (11)
C90.0532 (16)0.0451 (17)0.0417 (15)0.0109 (13)0.0117 (13)0.0011 (12)
C100.0660 (19)0.069 (2)0.0515 (18)0.0125 (17)0.0226 (15)0.0136 (17)
C110.089 (2)0.093 (3)0.0386 (17)0.037 (2)0.0251 (17)0.0054 (18)
C120.111 (3)0.077 (2)0.0422 (18)0.042 (2)0.0111 (18)0.0166 (17)
C130.0737 (19)0.0445 (17)0.0423 (16)0.0198 (14)0.0098 (14)0.0051 (13)
C140.0413 (14)0.0317 (14)0.0325 (13)0.0117 (11)0.0065 (11)0.0001 (11)
Geometric parameters (Å, º) top
O1—C21.232 (3)N5—C141.302 (3)
O2—C41.224 (3)N5—H5A0.89 (3)
O3—N71.229 (2)N5—H5B0.86 (3)
O4—N71.232 (2)C8—C91.384 (3)
N1—C61.316 (3)C8—C131.387 (4)
N1—C21.366 (3)C8—C141.478 (3)
C2—N31.371 (3)C9—C101.375 (4)
N3—C41.382 (3)C9—H90.9700
N3—H30.92 (3)C10—C111.368 (4)
C4—C51.443 (3)C10—H100.9700
C5—C61.381 (3)C11—C121.373 (5)
C5—N71.421 (3)C11—H110.9700
C6—H60.9700C12—C131.394 (4)
N4—C141.309 (3)C12—H120.9700
N4—H4A0.92 (3)C13—H130.9700
N4—H4B0.87 (3)
C6—N1—C2117.3 (2)C14—N5—H5B120.8 (17)
O1—C2—N1121.8 (2)H5A—N5—H5B120 (2)
O1—C2—N3119.5 (2)C9—C8—C13119.6 (2)
N1—C2—N3118.7 (2)C9—C8—C14120.1 (2)
C2—N3—C4127.2 (2)C13—C8—C14120.3 (2)
C2—N3—H3116.2 (17)C10—C9—C8120.4 (3)
C4—N3—H3116.6 (17)C10—C9—H9119.8
O2—C4—N3119.4 (2)C8—C9—H9119.8
O2—C4—C5129.0 (2)C11—C10—C9120.0 (3)
N3—C4—C5111.6 (2)C11—C10—H10120.0
C6—C5—N7118.6 (2)C9—C10—H10120.0
C6—C5—C4119.3 (2)C10—C11—C12120.5 (3)
N7—C5—C4122.11 (19)C10—C11—H11119.7
N1—C6—C5125.9 (2)C12—C11—H11119.7
N1—C6—H6117.1C11—C12—C13120.0 (3)
C5—C6—H6117.1C11—C12—H12120.0
O3—N7—O4120.94 (19)C13—C12—H12120.0
O3—N7—C5120.62 (19)C8—C13—C12119.3 (3)
O4—N7—C5118.43 (19)C8—C13—H13120.4
C14—N4—H4A118.3 (19)C12—C13—H13120.4
C14—N4—H4B120.2 (17)N5—C14—N4120.1 (2)
H4A—N4—H4B121 (2)N5—C14—C8120.2 (2)
C14—N5—H5A118.8 (17)N4—C14—C8119.8 (2)
C6—N1—C2—O1178.4 (2)C6—C5—N7—O41.3 (3)
C6—N1—C2—N31.0 (4)C4—C5—N7—O4177.9 (2)
O1—C2—N3—C4178.8 (2)C13—C8—C9—C100.6 (4)
N1—C2—N3—C40.6 (4)C14—C8—C9—C10179.7 (2)
C2—N3—C4—O2179.9 (3)C8—C9—C10—C111.1 (4)
C2—N3—C4—C50.1 (3)C9—C10—C11—C120.5 (5)
O2—C4—C5—C6179.8 (3)C10—C11—C12—C130.7 (5)
N3—C4—C5—C60.5 (3)C9—C8—C13—C120.6 (4)
O2—C4—C5—N70.5 (4)C14—C8—C13—C12179.2 (2)
N3—C4—C5—N7179.7 (2)C11—C12—C13—C81.2 (4)
C2—N1—C6—C50.6 (4)C9—C8—C14—N530.4 (3)
N7—C5—C6—N1179.4 (2)C13—C8—C14—N5149.3 (2)
C4—C5—C6—N10.1 (4)C9—C8—C14—N4150.6 (2)
C6—C5—N7—O3179.7 (2)C13—C8—C14—N429.7 (4)
C4—C5—N7—O31.1 (3)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
N3—H3···O2i0.92 (3)1.98 (3)2.899 (2)176 (2)
N4—H4A···O10.92 (3)2.07 (3)2.890 (3)148 (3)
N4—H4B···N1ii0.87 (3)2.03 (3)2.886 (3)170 (2)
N5—H5A···O10.89 (3)2.05 (3)2.853 (3)149 (2)
N5—H5B···O3i0.86 (3)2.23 (3)3.084 (3)169 (2)
C9—H9···O2iii0.972.843.691 (3)147
C11—H11···O4iv0.972.653.487 (3)145
C13—H13···O4v0.972.843.685 (4)146
Symmetry codes: (i) x+1, y+2, z; (ii) x, y+1, z; (iii) x, y+2, z; (iv) x2, y, z1; (v) x+1, y+1, z.

Experimental details

(I)(II)(III)(IV)
Crystal data
Chemical formulaC7H9N2+·C5H3N2O4·0.5H2OC7H9N2+·C5H3N2O4·3H2OC7H9N2+·C4H2N3O5·2H2OC7H9N2+·C4H2N3O4
Mr285.27330.30329.28277.25
Crystal system, space groupMonoclinic, C2/cMonoclinic, P21/nMonoclinic, P21/nTriclinic, P1
Temperature (K)298298298298
a, b, c (Å)27.2046 (6), 7.3566 (2), 12.6687 (3)11.3562 (2), 6.0402 (1), 22.3763 (4)10.7607 (3), 5.0998 (2), 27.2412 (5)4.3625 (4), 10.4461 (11), 13.8556 (12)
α, β, γ (°)90, 91.621 (2), 9090, 96.221 (2), 9090, 98.2485 (11), 9078.551 (7), 86.841 (8), 84.051 (7)
V3)2534.41 (11)1525.84 (5)1479.46 (8)615.13 (10)
Z8442
Radiation typeMo KαMo KαMo KαMo Kα
µ (mm1)0.120.120.130.12
Crystal size (mm)0.30 × 0.20 × 0.150.18 × 0.14 × 0.090.16 × 0.14 × 0.120.15 × 0.08 × 0.05
Data collection
DiffractometerOxford Xcalibur S CCD area-detectorOxford Xcalibur S CCD area-detectorOxford Xcalibur S CCD area-detectorOxford Xcalibur S CCD area-detector
Absorption correctionMulti-scan
[CrysAlis RED (Oxford Diffraction, 2006); empirical (using intensity measurements) absorption correction using spherical harmonics implemented in the SCALE3 ABSPACK scaling algorithm]
Multi-scan
[CrysAlis RED (Oxford Diffraction, 2006); empirical (using intensity measurements) absorption correction using spherical harmonics implemented in the SCALE3 ABSPACK scaling algorithm]
Multi-scan
[CrysAlis RED (Oxford Diffraction, 2006); empirical (using intensity measurements) absorption correction using spherical harmonics implemented in the SCALE3 ABSPACK scaling algorithm]
Multi-scan
[CrysAlis RED (Oxford Diffraction, 2006); empirical (using intensity measurements) absorption correction using spherical harmonics implemented in the SCALE3 ABSPACK scaling algorithm]
Tmin, Tmax0.956, 0.9830.918, 0.9900.908, 0.9910.978, 0.993
No. of measured, independent and
observed [I > 2σ(I)] reflections
119911, 4342, 3512 218566, 5260, 3884 306312, 5116, 4542 4864, 2153, 1427
Rint0.0430.0730.0340.034
(sin θ/λ)max1)0.7460.7460.7460.600
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.065, 0.152, 1.20 0.087, 0.186, 1.24 0.064, 0.165, 1.17 0.051, 0.119, 1.05
No. of reflections4342526051162153
No. of parameters214256248201
H-atom treatmentH atoms treated by a mixture of independent and constrained refinementH atoms treated by a mixture of independent and constrained refinementH atoms treated by a mixture of independent and constrained refinementH atoms treated by a mixture of independent and constrained refinement
Δρmax, Δρmin (e Å3)0.36, 0.180.36, 0.250.40, 0.240.18, 0.17

Computer programs: CrysAlis CCD (Oxford Diffraction, 2006), CrysAlis RED (Oxford Diffraction, 2006), SIR97 (Altomare et al., 1999), SHELXL97 (Sheldrick, 2008), ORTEP-3 (Farrugia, 1997), WinGX (Farrugia, 1999).

Hydrogen-bond geometry (Å, º) for (I) top
D—H···AD—HH···AD···AD—H···A
N1—H1···O2i0.82 (2)2.24 (2)3.0013 (16)153.5 (18)
N3—H3···O1ii0.96 (2)1.90 (2)2.8491 (15)168.0 (19)
N4—H4A···O40.97 (2)1.82 (2)2.7809 (16)170.6 (18)
N4—H4B···O3i0.91 (2)2.00 (2)2.9036 (17)171.4 (18)
N5—H5A···O30.92 (2)1.95 (2)2.8638 (16)178 (2)
N5—H5B···O2iii0.89 (2)2.06 (2)2.9357 (16)170.0 (17)
O5—H51···O20.85 (3)2.35 (3)3.1345 (14)154 (3)
Symmetry codes: (i) x, y+1, z+1/2; (ii) x, y+1, z; (iii) x+1/2, y+1/2, z.
Selected bond distances (Å) for (I)–(IV) top
Bond(I)(II)(III)(IV)
O1—C21.2179 (16)1.225 (2)1.2215 (18)1.232 (3)
O2—C41.2289 (16)1.2293 (19)1.2364 (16)1.224 (3)
O3—C71.2483 (15)1.230 (2)
O4—C71.2400 (17)1.273 (2)
O3—N71.2385 (16)1.229 (2)
O4—N71.2364 (17)1.232 (2)
O5—C61.2287 (17)
N1—C21.3664 (16)1.370 (2)1.3605 (18)1.366 (3)
N1—C61.3673 (16)1.352 (2)1.3848 (18)1.316 (3)
N3—C21.3717 (18)1.371 (2)1.3652 (17)1.371 (3)
N3—C41.3765 (16)1.389 (2)1.3835 (17)1.382 (3)
C4—C51.4431 (17)1.455 (2)1.4416 (18)1.443 (3)
C5—C61.3385 (18)1.355 (2)1.4478 (17)1.381 (3)
C5—C71.500 (2)
C5—N71.3945 (17)1.421 (3)
C6—C71.5225 (17)
N4—C141.3118 (17)1.318 (2)1.3083 (19)1.309 (3)
N5—C141.3106 (18)1.312 (2)1.321 (2)1.302 (3)
C8—C141.4763 (18)1.483 (2)1.4843 (19)1.478 (3)
C8—C91.3901 (18)1.395 (3)1.391 (2)1.384 (3)
C8—C131.386 (2)1.393 (3)1.389 (2)1.387 (4)
C9—C101.386 (2)1.387 (3)1.389 (2)1.375 (4)
C12—C131.386 (2)1.384 (3)1.386 (2)1.394 (4)
C10—C111.377 (3)1.376 (3)1.377 (3)1.368 (4)
C11—C121.375 (2)1.379 (3)1.372 (3)1.373 (5)
Hydrogen-bond geometry (Å, º) for (II) top
D—H···AD—HH···AD···AD—H···A
N1—H1···O5i0.92 (3)2.05 (3)2.760 (2)133 (2)
N3—H3···O2ii0.89 (3)1.95 (3)2.8296 (18)174 (2)
N4—H4A···O20.92 (3)2.22 (3)2.959 (2)136 (2)
N4—H4A···O30.92 (3)2.08 (3)2.854 (2)141 (2)
N4—H4B···O1ii0.84 (3)2.24 (3)3.050 (2)162 (2)
N5—H5A···O30.92 (3)1.92 (3)2.770 (2)154 (2)
N5—H5B···O7iii0.88 (3)2.03 (3)2.868 (2)158 (2)
O5—H51···O40.90 (4)1.91 (4)2.787 (2)163 (3)
O5—H52···O1iv0.83 (3)2.00 (3)2.821 (2)173 (3)
O6—H61···O40.91 (4)1.94 (4)2.837 (3)171 (3)
O6—H62···O7v0.80 (4)2.09 (4)2.878 (3)169 (4)
O7—H71···O40.86 (3)1.89 (3)2.741 (2)173 (3)
O7—H72···O6vi0.84 (3)1.88 (3)2.704 (3)166 (3)
Symmetry codes: (i) x, y+1, z; (ii) x+1, y+2, z; (iii) x+1/2, y1/2, z+1/2; (iv) x, y+2, z; (v) x+1/2, y+1/2, z+1/2; (vi) x, y1, z.
Hydrogen-bond geometry (Å, º) for (III) top
D—H···AD—HH···AD···AD—H···A
N1—H1···O5i0.91 (2)1.92 (2)2.8359 (16)178 (2)
N3—H3···O2ii0.90 (2)1.97 (2)2.8635 (16)178 (2)
N4—H4A···O20.84 (2)2.19 (2)2.8581 (16)135.5 (19)
N4—H4A···O30.84 (2)2.12 (2)2.8808 (18)150 (2)
N4—H4B···O1ii0.88 (2)1.98 (2)2.8514 (18)168 (2)
N5—H5A···O30.85 (3)2.19 (3)2.9250 (19)146 (2)
N5—H5B···O7iii0.88 (3)2.18 (3)3.035 (2)164 (2)
O6—H61···O40.91 (5)2.00 (5)2.894 (2)167 (4)
O6—H62···O4iv0.78 (4)2.29 (4)3.037 (3)160 (4)
O7—H71···O60.89 (3)1.84 (3)2.729 (3)173 (3)
O7—H72···O7iii0.87 (4)2.04 (4)2.8940 (19)169 (4)
C9—H9···O7iii0.972.453.410 (2)172.3
C13—H13···O1ii0.972.243.204 (2)171.1
Symmetry codes: (i) x+1, y+2, z+2; (ii) x, y+1, z+2; (iii) x+1/2, y1/2, z+3/2; (iv) x, y1, z.
Hydrogen-bond geometry (Å, º) for (IV) top
D—H···AD—HH···AD···AD—H···A
N3—H3···O2i0.92 (3)1.98 (3)2.899 (2)176 (2)
N4—H4A···O10.92 (3)2.07 (3)2.890 (3)148 (3)
N4—H4B···N1ii0.87 (3)2.03 (3)2.886 (3)170 (2)
N5—H5A···O10.89 (3)2.05 (3)2.853 (3)149 (2)
N5—H5B···O3i0.86 (3)2.23 (3)3.084 (3)169 (2)
C9—H9···O2iii0.972.843.691 (3)146.5
C11—H11···O4iv0.972.653.487 (3)144.9
C13—H13···O4v0.972.843.685 (4)145.6
Symmetry codes: (i) x+1, y+2, z; (ii) x, y+1, z; (iii) x, y+2, z; (iv) x2, y, z1; (v) x+1, y+1, z.
 

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