Supporting information
Crystallographic Information File (CIF) https://doi.org/10.1107/S1600536807027407/fj2037sup1.cif | |
Structure factor file (CIF format) https://doi.org/10.1107/S1600536807027407/fj2037Isup2.hkl |
CCDC reference: 654974
Key indicators
- Single-crystal X-ray study
- T = 298 K
- Mean (N-C) = 0.001 Å
- R factor = 0.042
- wR factor = 0.128
- Data-to-parameter ratio = 18.1
checkCIF/PLATON results
No syntax errors found
Alert level C PLAT250_ALERT_2_C Large U3/U1 Ratio for Average U(i,j) Tensor .... 2.29
0 ALERT level A = In general: serious problem 0 ALERT level B = Potentially serious problem 1 ALERT level C = Check and explain 0 ALERT level G = General alerts; check 0 ALERT type 1 CIF construction/syntax error, inconsistent or missing data 1 ALERT type 2 Indicator that the structure model may be wrong or deficient 0 ALERT type 3 Indicator that the structure quality may be low 0 ALERT type 4 Improvement, methodology, query or suggestion 0 ALERT type 5 Informative message, check
Guanamine was purchased from Sigma Aldrich (99% purity). and used as obtained. Crystals of guanamine were grown from a hot water solution (0.25 mmol in ca 10 ml) by slow evaporation of the solvent.
All H atoms were found in a difference Fourier map. Positional and isotropic displacement parameters of all H atoms were independently refined (C—H = 0.972 (13) Å, N—H = 0.851 (16)–0.903 (18) Å).
As a part of our continuing study of crystal adducts of DNA/RNA pyrimidine bases coupled with amino-derivatives of aromatic N-heterocycles via multiple hydrogen bonds to mimic the base-pairing of nucleic acids (Portalone et al., 1999; Brunetti et al., 2000, 2002; Portalone et al., 2002; Portalone & Colapietro, 2004a,b; Portalone & Colapietro, 2006; Portalone & Colapietro, 2007a,b,c,d) we became interested in guanamine (I), as a good candidate to be associated in the crystal with pyrimidinic nucleobases.
The asymmetric unit of (I) comprises a planar molecule and is shown in Fig. 1. With regard to the aromatic ring, the bond lengths and angles are normal and conform within experimental error to C2v symmetry (Table 1). The H-bonding scheme involves all H atoms of the NH2 groups (Fig. 2) and consists entirely of N—H··· N intermolecular interactions (Table 2). These interactions delineate patterns in which rings are the most prominent features. Besides the intermolecular N—H··· N hydrogen bonds, two small rings of descriptor R22(8) are formed by centrosymmetric molecules. Infinite C22(6) chains are then generated by the 21 screw axis running along the b direction,
For related literature describing crystal adducts of DNA/RNA pyrimidine bases coupled with amino derivatives of aromatic N-heterocycles via multiple hydrogen bonds to mimic the base-pairing of nucleic acids, see: Portalone et al. (1999, 2002); Brunetti et al. (2000, 2002); Portalone & Colapietro (2004a,b, 2006, 2007a,b,c,d).
Data collection: XCS (Colapietro et al., 1992); cell refinement: XCS; data reduction: XCS; program(s) used to solve structure: SIR97 (Altomare et al., 1999); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: ORTEP-3 (Farrugia, 1997); software used to prepare material for publication: SHELXL97.
C3H5N5 | F(000) = 232 |
Mr = 111.12 | Dx = 1.575 Mg m−3 |
Monoclinic, P21/c | Mo Kα radiation, λ = 0.71069 Å |
Hall symbol: -P 2ybc | Cell parameters from 87 reflections |
a = 9.8631 (9) Å | θ = 21–27° |
b = 3.7180 (3) Å | µ = 0.12 mm−1 |
c = 12.9609 (9) Å | T = 298 K |
β = 99.643 (9)° | Tablet, colourless |
V = 468.57 (7) Å3 | 0.15 × 0.12 × 0.10 mm |
Z = 4 |
Huber CS four-circle diffractometer | Rint = 0.026 |
Radiation source: X-Ray tube | θmax = 32.5°, θmin = 2.1° |
Graphite monochromator | h = 0→14 |
ω scans | k = 0→5 |
2088 measured reflections | l = −19→19 |
1684 independent reflections | 3 standard reflections every 97 reflections |
1450 reflections with I > 2σ(I) | intensity decay: 1% |
Refinement on F2 | Primary atom site location: structure-invariant direct methods |
Least-squares matrix: full | Secondary atom site location: difference Fourier map |
R[F2 > 2σ(F2)] = 0.042 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.128 | All H-atom parameters refined |
S = 1.07 | w = 1/[σ2(Fo2) + (0.0865P)2 + 0.0407P] where P = (Fo2 + 2Fc2)/3 |
1684 reflections | (Δ/σ)max = 0.001 |
93 parameters | Δρmax = 0.35 e Å−3 |
0 restraints | Δρmin = −0.22 e Å−3 |
C3H5N5 | V = 468.57 (7) Å3 |
Mr = 111.12 | Z = 4 |
Monoclinic, P21/c | Mo Kα radiation |
a = 9.8631 (9) Å | µ = 0.12 mm−1 |
b = 3.7180 (3) Å | T = 298 K |
c = 12.9609 (9) Å | 0.15 × 0.12 × 0.10 mm |
β = 99.643 (9)° |
Huber CS four-circle diffractometer | Rint = 0.026 |
2088 measured reflections | 3 standard reflections every 97 reflections |
1684 independent reflections | intensity decay: 1% |
1450 reflections with I > 2σ(I) |
R[F2 > 2σ(F2)] = 0.042 | 0 restraints |
wR(F2) = 0.128 | All H-atom parameters refined |
S = 1.07 | Δρmax = 0.35 e Å−3 |
1684 reflections | Δρmin = −0.22 e Å−3 |
93 parameters |
Geometry. All e.s.d.'s (except the e.s.d. in the dihedral angle between two l.s. planes) are estimated using the full covariance matrix. The cell e.s.d.'s are taken into account individually in the estimation of e.s.d.'s in distances, angles and torsion angles; correlations between e.s.d.'s in cell parameters are only used when they are defined by crystal symmetry. An approximate (isotropic) treatment of cell e.s.d.'s is used for estimating e.s.d.'s 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. |
x | y | z | Uiso*/Ueq | ||
N1 | 0.61517 (7) | 0.0133 (2) | 0.89333 (5) | 0.02784 (18) | |
N3 | 0.79107 (7) | 0.0531 (2) | 0.78800 (5) | 0.02702 (18) | |
N5 | 0.83121 (7) | 0.2817 (2) | 0.96284 (5) | 0.02508 (18) | |
N7 | 0.99658 (8) | 0.3212 (2) | 0.85938 (6) | 0.03028 (19) | |
N8 | 0.66293 (9) | 0.2167 (3) | 1.06320 (6) | 0.0387 (2) | |
C2 | 0.66676 (8) | −0.0349 (3) | 0.80627 (6) | 0.02765 (19) | |
C4 | 0.87077 (8) | 0.2155 (2) | 0.87067 (6) | 0.02206 (17) | |
C6 | 0.70459 (8) | 0.1707 (2) | 0.97155 (6) | 0.02440 (18) | |
H2 | 0.6089 (13) | −0.151 (3) | 0.7476 (10) | 0.032 (3)* | |
H71 | 1.0272 (14) | 0.261 (4) | 0.8030 (12) | 0.048 (4)* | |
H72 | 1.0486 (19) | 0.421 (4) | 0.9162 (13) | 0.049 (4)* | |
H81 | 0.5800 (17) | 0.144 (4) | 1.0735 (12) | 0.043 (3)* | |
H82 | 0.7201 (16) | 0.298 (4) | 1.1143 (12) | 0.051 (4)* |
U11 | U22 | U33 | U12 | U13 | U23 | |
N1 | 0.0212 (3) | 0.0393 (4) | 0.0235 (3) | −0.0077 (3) | 0.0052 (2) | −0.0031 (2) |
N3 | 0.0238 (3) | 0.0369 (4) | 0.0211 (3) | −0.0032 (3) | 0.0061 (2) | −0.0024 (2) |
N5 | 0.0201 (3) | 0.0352 (4) | 0.0210 (3) | −0.0061 (2) | 0.0063 (2) | −0.0026 (2) |
N7 | 0.0219 (3) | 0.0442 (4) | 0.0269 (4) | −0.0066 (3) | 0.0102 (3) | −0.0025 (3) |
N8 | 0.0279 (4) | 0.0668 (6) | 0.0238 (4) | −0.0178 (4) | 0.0114 (3) | −0.0114 (3) |
C2 | 0.0238 (4) | 0.0368 (4) | 0.0223 (3) | −0.0054 (3) | 0.0036 (3) | −0.0037 (3) |
C4 | 0.0200 (3) | 0.0259 (3) | 0.0209 (3) | −0.0007 (2) | 0.0054 (2) | 0.0020 (2) |
C6 | 0.0209 (3) | 0.0320 (4) | 0.0212 (3) | −0.0046 (3) | 0.0060 (3) | −0.0009 (2) |
N1—C2 | 1.3254 (10) | N7—H71 | 0.866 (16) |
N1—C6 | 1.3597 (10) | N7—H72 | 0.903 (18) |
N3—C2 | 1.3280 (11) | N8—C6 | 1.3313 (10) |
N3—C4 | 1.3596 (10) | N8—H81 | 0.893 (17) |
N5—C6 | 1.3378 (10) | N8—H82 | 0.851 (16) |
N5—C4 | 1.3401 (9) | C2—H2 | 0.972 (13) |
N7—C4 | 1.3329 (10) | ||
C2—N1—C6 | 113.55 (7) | N1—C2—N3 | 128.02 (7) |
C2—N3—C4 | 113.46 (7) | N1—C2—H2 | 117.9 (8) |
C6—N5—C4 | 115.72 (7) | N3—C2—H2 | 114.1 (8) |
C4—N7—H71 | 118.6 (10) | N7—C4—N5 | 117.34 (7) |
C4—N7—H72 | 116.3 (11) | N7—C4—N3 | 118.06 (7) |
H71—N7—H72 | 124.3 (14) | N5—C4—N3 | 124.59 (7) |
C6—N8—H81 | 121.4 (10) | N8—C6—N5 | 117.89 (7) |
C6—N8—H82 | 118.5 (11) | N8—C6—N1 | 117.51 (7) |
H81—N8—H82 | 119.7 (15) | N5—C6—N1 | 124.60 (7) |
C6—N1—C2—N3 | −0.52 (15) | C2—N3—C4—N5 | 0.49 (13) |
C4—N3—C2—N1 | −0.82 (15) | C4—N5—C6—N8 | 177.18 (8) |
C6—N5—C4—N7 | −179.75 (7) | C4—N5—C6—N1 | −2.70 (14) |
C6—N5—C4—N3 | 1.13 (13) | C2—N1—C6—N8 | −177.48 (9) |
C2—N3—C4—N7 | −178.62 (8) | C2—N1—C6—N5 | 2.40 (13) |
D—H···A | D—H | H···A | D···A | D—H···A |
N7—H71···N3i | 0.866 (16) | 2.549 (16) | 3.1811 (10) | 130.7 (13) |
N7—H72···N5ii | 0.903 (18) | 2.113 (18) | 3.0106 (12) | 172.3 (14) |
N8—H81···N1iii | 0.893 (17) | 2.123 (17) | 3.0150 (11) | 176.6 (14) |
N8—H82···N3iv | 0.851 (16) | 2.310 (15) | 3.0962 (11) | 153.9 (14) |
Symmetry codes: (i) −x+2, y+1/2, −z+3/2; (ii) −x+2, −y+1, −z+2; (iii) −x+1, −y, −z+2; (iv) x, −y+1/2, z+1/2. |
Experimental details
Crystal data | |
Chemical formula | C3H5N5 |
Mr | 111.12 |
Crystal system, space group | Monoclinic, P21/c |
Temperature (K) | 298 |
a, b, c (Å) | 9.8631 (9), 3.7180 (3), 12.9609 (9) |
β (°) | 99.643 (9) |
V (Å3) | 468.57 (7) |
Z | 4 |
Radiation type | Mo Kα |
µ (mm−1) | 0.12 |
Crystal size (mm) | 0.15 × 0.12 × 0.10 |
Data collection | |
Diffractometer | Huber CS four-circle |
Absorption correction | – |
No. of measured, independent and observed [I > 2σ(I)] reflections | 2088, 1684, 1450 |
Rint | 0.026 |
(sin θ/λ)max (Å−1) | 0.756 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.042, 0.128, 1.07 |
No. of reflections | 1684 |
No. of parameters | 93 |
H-atom treatment | All H-atom parameters refined |
Δρmax, Δρmin (e Å−3) | 0.35, −0.22 |
Computer programs: XCS (Colapietro et al., 1992), XCS, SIR97 (Altomare et al., 1999), SHELXL97 (Sheldrick, 1997), ORTEP-3 (Farrugia, 1997), SHELXL97.
D—H···A | D—H | H···A | D···A | D—H···A |
N7—H71···N3i | 0.866 (16) | 2.549 (16) | 3.1811 (10) | 130.7 (13) |
N7—H72···N5ii | 0.903 (18) | 2.113 (18) | 3.0106 (12) | 172.3 (14) |
N8—H81···N1iii | 0.893 (17) | 2.123 (17) | 3.0150 (11) | 176.6 (14) |
N8—H82···N3iv | 0.851 (16) | 2.310 (15) | 3.0962 (11) | 153.9 (14) |
Symmetry codes: (i) −x+2, y+1/2, −z+3/2; (ii) −x+2, −y+1, −z+2; (iii) −x+1, −y, −z+2; (iv) x, −y+1/2, z+1/2. |
As a part of our continuing study of crystal adducts of DNA/RNA pyrimidine bases coupled with amino-derivatives of aromatic N-heterocycles via multiple hydrogen bonds to mimic the base-pairing of nucleic acids (Portalone et al., 1999; Brunetti et al., 2000, 2002; Portalone et al., 2002; Portalone & Colapietro, 2004a,b; Portalone & Colapietro, 2006; Portalone & Colapietro, 2007a,b,c,d) we became interested in guanamine (I), as a good candidate to be associated in the crystal with pyrimidinic nucleobases.
The asymmetric unit of (I) comprises a planar molecule and is shown in Fig. 1. With regard to the aromatic ring, the bond lengths and angles are normal and conform within experimental error to C2v symmetry (Table 1). The H-bonding scheme involves all H atoms of the NH2 groups (Fig. 2) and consists entirely of N—H··· N intermolecular interactions (Table 2). These interactions delineate patterns in which rings are the most prominent features. Besides the intermolecular N—H··· N hydrogen bonds, two small rings of descriptor R22(8) are formed by centrosymmetric molecules. Infinite C22(6) chains are then generated by the 21 screw axis running along the b direction,