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The title compound [systematic name: 6-(1,3-dimethyl-2,6-dioxo-2,3,6,7-tetra­hydro-1H-purin-7-yl)hexa­noic acid monohydrate, CAS 61444-23-3], C13H18N4O4·H2O, was synthesized and crystallized from ethyl acetate. Hydrogen bonds between xanthine and water mol­ecules contribute to the formation of layers parallel to (10\overline{2}).

Supporting information

cif

Crystallographic Information File (CIF) https://doi.org/10.1107/S1600536807037257/bt2438sup1.cif
Contains datablocks I, global

hkl

Structure factor file (CIF format) https://doi.org/10.1107/S1600536807037257/bt2438Isup2.hkl
Contains datablock I

CCDC reference: 660218

Key indicators

  • Single-crystal X-ray study
  • T = 291 K
  • R factor = 0.048
  • wR factor = 0.158
  • Data-to-parameter ratio = 17.3

checkCIF/PLATON results

No syntax errors found


No errors found in this datablock

Comment top

7-(5-Carboxypentyl)-1,3-dimethylxanthine (Fig. 1) is a carboxylic acid derivative of caffeine and can be used to couple the xanthine moiety to labels (fluorescent, luminescent, colorimetric, radioactive, etc.), biomolecules (immunoassay tracer enzymes, immunogenic carrier proteins, coating proteins, etc.) or solid phases (microtitre plates, chip surfaces, affinity supports etc.) to construct assays and methods for the determination of caffeine.

Caffeine (1,3,7-trimethylxanthine) is a stimulant alkaloid whose annual world consumption exceeds 22 million tons (Fenske, 2007). Caffeine is an important analyte in pharmacology and pharmacokinetics serving as a metabolic probe for hepatic biotransformation (Wahlländer et al., 1990) and for renal clearance (Birkett and Miners, 1991), analyzed in blood, saliva and urine. Radioimmunoassay (Cook et al., 1976) and ELISA (Fickling et al., 1990) has been used in the past being replaced by Enzyme Multiplied Immunoassay Technique (EMIT) as the most common format (McDonagh et al., 1991).

About 1.8% of unmetabolized caffeine is excreted via urine (Newton et al., 1981) but daily intake is about 4 mg kg-1 body weight for US consumers (Barone et al., 1996) giving rise to high loads discharged into the waste water system. Kolpin et al. (2002) found caffeine in more than 70% of surface water samples taken all over the US in concentrations ranging from 0.1 µg L-1 to 5.7 µg L-1.

The title compound has been synthesized before (Cook et al., 1976), but the three-dimensional-crystal structure has not been reported so far while necessary for the understanding of the cross-reactivity of caffeine monoclonal antibodies against related xanthines.

The average C—N, C—C and C—O distances in the title compound (Fig. 1) are in good agreement with those in the caffeine molecule (Edwards et al., 1997; Derollez et al., 2005) and comparable compounds in the CSD (Version 5.27; Allen, 2002, for example Sutor, 1958). Analysis of the crystal packing shows that the molecules are linked via hydrogen bonds to result in a layer structure. The relevant hydrogen-bonding geometries and the symmetry codes are listed in Table 2. As illustrated in Fig. 2, intermolecular O—H··· N and O—H···O hydrogen bonds, involving the O atoms of aqua ligands and the N atoms of imidazole and a carboxylic O atom contribute to the hydrogen bonding. The center-to-center (DC) and center-to-plane (DP) distances between two neighboring almost parallel (interplanar angle α=0.62°) imidazole and adjacent pyrimidine rings are 3.545 (4) Å (DC) and 3.341 and 3.336 Å (DP), revealing the existence of π-π stacking interactions, which further stabilize the structure.

Related literature top

For related literature, see: Allen (2002); Barone & Roberts (1996); Birkett & Miners (1991); Cook et al. (1976); Derollez et al. (2005); Edwards et al. (1997); Fenske (2007); Fickling et al. (1990); Kolpin et al. (2002); Leyland-Jones & Wong (2000); McDonagh (1991); Newton et al. (1981); Sutor (1958); Wahlländer et al. (1990).

Experimental top

The title compound was synthesized starting from theophylline. Briefly theophylline was reacted with 6-bromohexanoic acid ethyl ester in a solvent system consisting of potassium carbonate (21 mM) in anhydrous dimethylformamide (DMF). The mixture was kept at 60°C under reflux conditions for 14 h. The cleavage of the ethyl ester was achieved by 10% sodium hydroxide in DMF at 110°C under reflux for 30 min. The solvent was evaporated and the residue dissolved in water. 6 N hydrochloric acid was added to protonate the carboxylic acid group. Sodium chloride was added and the compound extracted by liquid-liquid extraction with ethyl acetate. Yields were 89% and 92% for the both reaction steps, respectively.

Colourless, needleshaped crystals of the compound were grown by solvent evaporation from ethyl acetate at room temperature. M.p. 124°C (DSC, onset, 0.75 mg; loss of crystal water at 106°C). NMR data: 1H NMR (400 MHz, DMSO), δ(p.p.m.): 8.07 (s,1H), 4.22 (t,2H), 3.41 (s,3H), 3.22 (s,3H), 2.19 (t,2H), 1.50 (m,2H), 1.22 (m,2H); the carboxylic acid proton exchanges. 13C NMR (400 MHz, DMSO) δ(p.p.m.): 174.3 (COOH), 154.3 (C-6'), 151.0 (C-2'), 148.4 (C-4'), 142.4 (CH), 105.9 (C-5'), 46.0 (CH2), 33.4 (CH2), 29.9 (CH3), 29.4 (CH2), 27.6 (CH3), 25.1 (CH2), 23.8 (CH2); Mass spectrum: 295.0 ([M+H]+, 100%), 317.1 ([M+Na]+, 34%. 277.4 (32%), 229.3 (18%), 181.0 ([theophylline+H]+, 14%).

Refinement top

The hydrogen atoms were located in difference maps but positioned with idealized geometry and refined using the riding model, with C—H = 0.93–0.97 Å, and Uiso(H) = 1.2Ueq(parent atom).

Structure description top

7-(5-Carboxypentyl)-1,3-dimethylxanthine (Fig. 1) is a carboxylic acid derivative of caffeine and can be used to couple the xanthine moiety to labels (fluorescent, luminescent, colorimetric, radioactive, etc.), biomolecules (immunoassay tracer enzymes, immunogenic carrier proteins, coating proteins, etc.) or solid phases (microtitre plates, chip surfaces, affinity supports etc.) to construct assays and methods for the determination of caffeine.

Caffeine (1,3,7-trimethylxanthine) is a stimulant alkaloid whose annual world consumption exceeds 22 million tons (Fenske, 2007). Caffeine is an important analyte in pharmacology and pharmacokinetics serving as a metabolic probe for hepatic biotransformation (Wahlländer et al., 1990) and for renal clearance (Birkett and Miners, 1991), analyzed in blood, saliva and urine. Radioimmunoassay (Cook et al., 1976) and ELISA (Fickling et al., 1990) has been used in the past being replaced by Enzyme Multiplied Immunoassay Technique (EMIT) as the most common format (McDonagh et al., 1991).

About 1.8% of unmetabolized caffeine is excreted via urine (Newton et al., 1981) but daily intake is about 4 mg kg-1 body weight for US consumers (Barone et al., 1996) giving rise to high loads discharged into the waste water system. Kolpin et al. (2002) found caffeine in more than 70% of surface water samples taken all over the US in concentrations ranging from 0.1 µg L-1 to 5.7 µg L-1.

The title compound has been synthesized before (Cook et al., 1976), but the three-dimensional-crystal structure has not been reported so far while necessary for the understanding of the cross-reactivity of caffeine monoclonal antibodies against related xanthines.

The average C—N, C—C and C—O distances in the title compound (Fig. 1) are in good agreement with those in the caffeine molecule (Edwards et al., 1997; Derollez et al., 2005) and comparable compounds in the CSD (Version 5.27; Allen, 2002, for example Sutor, 1958). Analysis of the crystal packing shows that the molecules are linked via hydrogen bonds to result in a layer structure. The relevant hydrogen-bonding geometries and the symmetry codes are listed in Table 2. As illustrated in Fig. 2, intermolecular O—H··· N and O—H···O hydrogen bonds, involving the O atoms of aqua ligands and the N atoms of imidazole and a carboxylic O atom contribute to the hydrogen bonding. The center-to-center (DC) and center-to-plane (DP) distances between two neighboring almost parallel (interplanar angle α=0.62°) imidazole and adjacent pyrimidine rings are 3.545 (4) Å (DC) and 3.341 and 3.336 Å (DP), revealing the existence of π-π stacking interactions, which further stabilize the structure.

For related literature, see: Allen (2002); Barone & Roberts (1996); Birkett & Miners (1991); Cook et al. (1976); Derollez et al. (2005); Edwards et al. (1997); Fenske (2007); Fickling et al. (1990); Kolpin et al. (2002); Leyland-Jones & Wong (2000); McDonagh (1991); Newton et al. (1981); Sutor (1958); Wahlländer et al. (1990).

Computing details top

Data collection: SMART (Bruker, 2001); cell refinement: SAINT (Bruker, 2001); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 1997); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: ORTEPIII (Burnett & Johnson, 1996) and SHELXTL (Sheldrick, 2001); software used to prepare material for publication: SHELXTL.

Figures top
[Figure 1] Fig. 1. ORTEP-3 representation of (I) with the atomic labeling of the asymmetric unit and coordination sphere, shown with 50% probability displacement ellipsoids.
[Figure 2] Fig. 2. View of the layers array of (I), formed via strong hydrogen-bonding interactions (indicated by green lines).
6-(1,3-dimethyl-2,6-dioxo-2,3,6,7-tetrahydro-1H-purin-7-yl)hexanoic acid monohydrate top
Crystal data top
C13H18N4O4·H2OF(000) = 664
Mr = 312.33Dx = 1.382 Mg m3
Monoclinic, P21/cMo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybcCell parameters from 128 reflections
a = 4.370 (4) Åθ = 3.5–29.6°
b = 34.55 (2) ŵ = 0.11 mm1
c = 9.960 (9) ÅT = 291 K
β = 93.21 (3)°Needle, colourless
V = 1501 (2) Å30.25 × 0.1 × 0.08 mm
Z = 4
Data collection top
Bruker APEX CCD area-detector
diffractometer
3520 independent reflections
Radiation source: fine-focus sealed tube1861 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.096
ω scansθmax = 27.9°, θmin = 1.2°
Absorption correction: multi-scan
(SADABS; Bruker, 2001)
h = 55
Tmin = 0.97, Tmax = 0.99k = 3544
10307 measured reflectionsl = 1211
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)] = 0.048Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.158H atoms treated by a mixture of independent and constrained refinement
S = 0.86 w = 1/[σ2(Fo2) + (0.0723P)2]
where P = (Fo2 + 2Fc2)/3
3520 reflections(Δ/σ)max = 0.031
203 parametersΔρmax = 0.19 e Å3
0 restraintsΔρmin = 0.20 e Å3
Crystal data top
C13H18N4O4·H2OV = 1501 (2) Å3
Mr = 312.33Z = 4
Monoclinic, P21/cMo Kα radiation
a = 4.370 (4) ŵ = 0.11 mm1
b = 34.55 (2) ÅT = 291 K
c = 9.960 (9) Å0.25 × 0.1 × 0.08 mm
β = 93.21 (3)°
Data collection top
Bruker APEX CCD area-detector
diffractometer
3520 independent reflections
Absorption correction: multi-scan
(SADABS; Bruker, 2001)
1861 reflections with I > 2σ(I)
Tmin = 0.97, Tmax = 0.99Rint = 0.096
10307 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.0480 restraints
wR(F2) = 0.158H atoms treated by a mixture of independent and constrained refinement
S = 0.86Δρmax = 0.19 e Å3
3520 reflectionsΔρmin = 0.20 e Å3
203 parameters
Special details top

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.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
O10.6656 (6)0.26684 (7)0.4862 (3)0.0647 (8)
O20.6266 (6)0.39794 (7)0.5376 (2)0.0538 (7)
O30.3153 (7)0.63559 (7)0.1447 (3)0.0803 (10)
H30.40730.64890.08750.120*
O40.4681 (7)0.58849 (7)0.0088 (3)0.0773 (9)
O1W0.3703 (10)0.68701 (8)0.0072 (4)0.1010 (12)
H1A0.395 (14)0.7096 (6)0.003 (6)0.152*
H1B0.263 (12)0.6786 (16)0.054 (4)0.152*
N10.6354 (6)0.33202 (8)0.5114 (3)0.0446 (7)
N30.3446 (7)0.29961 (7)0.3420 (3)0.0469 (8)
N70.1420 (6)0.39731 (7)0.3044 (3)0.0437 (7)
N90.0103 (7)0.34122 (8)0.2042 (3)0.0519 (8)
C20.5525 (8)0.29755 (10)0.4475 (4)0.0486 (9)
C40.2218 (8)0.33503 (9)0.3049 (3)0.0434 (9)
C50.3098 (8)0.36827 (9)0.3684 (3)0.0415 (8)
C60.5302 (8)0.36947 (9)0.4767 (3)0.0418 (8)
C80.0300 (9)0.37944 (10)0.2077 (4)0.0524 (10)
H80.16540.39250.14830.063*
C90.8520 (9)0.32890 (10)0.6276 (3)0.0577 (10)
H9A0.74280.32340.70640.087*
H9B0.96100.35290.63990.087*
H9C0.99480.30840.61310.087*
C100.2521 (9)0.26402 (10)0.2716 (4)0.0657 (12)
H10A0.42810.25220.23510.099*
H10B0.10340.27000.19990.099*
H10C0.16390.24650.33340.099*
C110.1366 (9)0.43804 (9)0.3433 (3)0.0508 (10)
H11A0.34390.44640.36860.061*
H11B0.01570.44080.42150.061*
C120.0055 (9)0.46391 (9)0.2332 (3)0.0557 (10)
H12A0.19760.45480.20450.067*
H12B0.13290.46230.15670.067*
C130.0156 (9)0.50577 (9)0.2763 (3)0.0544 (10)
H13A0.14300.50740.35280.065*
H13B0.18760.51490.30520.065*
C140.1457 (9)0.53182 (9)0.1672 (3)0.0565 (10)
H14A0.34670.52230.13690.068*
H14B0.01550.53060.09150.068*
C150.1745 (9)0.57328 (9)0.2096 (4)0.0572 (10)
H15A0.28340.57410.29170.069*
H15B0.02940.58350.23000.069*
C160.3345 (8)0.59884 (10)0.1092 (4)0.0506 (9)
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
O10.080 (2)0.0363 (14)0.0758 (18)0.0091 (14)0.0110 (15)0.0073 (13)
O20.0639 (17)0.0407 (14)0.0550 (15)0.0025 (12)0.0125 (12)0.0065 (12)
O30.120 (3)0.0362 (15)0.0799 (19)0.0077 (15)0.0402 (17)0.0002 (14)
O40.110 (2)0.0457 (15)0.0710 (18)0.0130 (16)0.0422 (17)0.0064 (14)
O1W0.141 (3)0.0350 (15)0.118 (3)0.0056 (19)0.072 (2)0.0037 (18)
N10.0492 (18)0.0375 (16)0.0460 (17)0.0010 (14)0.0081 (14)0.0035 (13)
N30.059 (2)0.0297 (16)0.0505 (18)0.0010 (14)0.0058 (15)0.0040 (13)
N70.0563 (19)0.0301 (15)0.0431 (16)0.0024 (14)0.0106 (14)0.0009 (13)
N90.061 (2)0.0421 (18)0.0514 (18)0.0004 (15)0.0099 (16)0.0029 (14)
C20.052 (2)0.038 (2)0.056 (2)0.0040 (18)0.0028 (19)0.0017 (18)
C40.049 (2)0.0362 (19)0.045 (2)0.0010 (17)0.0018 (18)0.0005 (17)
C50.052 (2)0.0315 (18)0.0404 (19)0.0006 (16)0.0031 (17)0.0017 (15)
C60.044 (2)0.039 (2)0.041 (2)0.0016 (17)0.0008 (17)0.0016 (16)
C80.061 (3)0.042 (2)0.053 (2)0.0048 (19)0.0106 (19)0.0013 (18)
C90.061 (3)0.055 (2)0.055 (2)0.0041 (19)0.013 (2)0.0067 (19)
C100.078 (3)0.043 (2)0.075 (3)0.000 (2)0.003 (2)0.017 (2)
C110.063 (3)0.0321 (18)0.056 (2)0.0027 (17)0.0093 (19)0.0007 (17)
C120.072 (3)0.039 (2)0.055 (2)0.0112 (19)0.011 (2)0.0015 (17)
C130.068 (3)0.040 (2)0.054 (2)0.0110 (19)0.0054 (19)0.0030 (17)
C140.077 (3)0.039 (2)0.051 (2)0.0072 (19)0.014 (2)0.0013 (17)
C150.073 (3)0.038 (2)0.058 (2)0.0100 (19)0.021 (2)0.0008 (17)
C160.058 (3)0.037 (2)0.055 (2)0.0026 (18)0.005 (2)0.0003 (18)
Geometric parameters (Å, º) top
O1—C21.224 (4)C9—H9A0.9600
O2—C61.218 (4)C9—H9B0.9600
O3—C161.320 (4)C9—H9C0.9600
O3—H30.8200C10—H10A0.9600
O4—C161.185 (4)C10—H10B0.9600
O1W—H1A0.789 (19)C10—H10C0.9600
O1W—H1B0.80 (2)C11—C121.503 (4)
N1—C21.389 (4)C11—H11A0.9700
N1—C61.410 (4)C11—H11B0.9700
N1—C91.457 (4)C12—C131.513 (5)
N3—C21.352 (4)C12—H12A0.9700
N3—C41.379 (4)C12—H12B0.9700
N3—C101.462 (4)C13—C141.498 (4)
N7—C81.339 (4)C13—H13A0.9700
N7—C51.378 (4)C13—H13B0.9700
N7—C111.460 (4)C14—C151.501 (5)
N9—C81.333 (4)C14—H14A0.9700
N9—C41.343 (4)C14—H14B0.9700
C4—C51.356 (4)C15—C161.480 (5)
C5—C61.406 (5)C15—H15A0.9700
C8—H80.9300C15—H15B0.9700
C16—O3—H3109.5N3—C10—H10C109.5
H1A—O1W—H1B113 (6)H10A—C10—H10C109.5
C2—N1—C6127.0 (3)H10B—C10—H10C109.5
C2—N1—C9116.2 (3)N7—C11—C12113.0 (3)
C6—N1—C9116.8 (3)N7—C11—H11A109.0
C2—N3—C4119.3 (3)C12—C11—H11A109.0
C2—N3—C10119.0 (3)N7—C11—H11B109.0
C4—N3—C10121.7 (3)C12—C11—H11B109.0
C8—N7—C5105.1 (3)H11A—C11—H11B107.8
C8—N7—C11128.2 (3)C11—C12—C13112.8 (3)
C5—N7—C11126.5 (3)C11—C12—H12A109.0
C8—N9—C4103.0 (3)C13—C12—H12A109.0
O1—C2—N3122.2 (3)C11—C12—H12B109.0
O1—C2—N1120.6 (3)C13—C12—H12B109.0
N3—C2—N1117.2 (3)H12A—C12—H12B107.8
N9—C4—C5112.3 (3)C14—C13—C12113.2 (3)
N9—C4—N3125.7 (3)C14—C13—H13A108.9
C5—C4—N3122.1 (3)C12—C13—H13A108.9
C4—C5—N7105.7 (3)C14—C13—H13B108.9
C4—C5—C6123.2 (3)C12—C13—H13B108.9
N7—C5—C6131.1 (3)H13A—C13—H13B107.7
O2—C6—C5127.5 (3)C13—C14—C15113.8 (3)
O2—C6—N1121.4 (3)C13—C14—H14A108.8
C5—C6—N1111.1 (3)C15—C14—H14A108.8
N9—C8—N7114.0 (3)C13—C14—H14B108.8
N9—C8—H8123.0C15—C14—H14B108.8
N7—C8—H8123.0H14A—C14—H14B107.7
N1—C9—H9A109.5C16—C15—C14115.1 (3)
N1—C9—H9B109.5C16—C15—H15A108.5
H9A—C9—H9B109.5C14—C15—H15A108.5
N1—C9—H9C109.5C16—C15—H15B108.5
H9A—C9—H9C109.5C14—C15—H15B108.5
H9B—C9—H9C109.5H15A—C15—H15B107.5
N3—C10—H10A109.5O4—C16—O3122.5 (3)
N3—C10—H10B109.5O4—C16—C15125.6 (3)
H10A—C10—H10B109.5O3—C16—C15111.9 (3)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
O1W—H1A···O1i0.79 (2)2.00 (2)2.764 (4)163 (6)
O1W—H1B···N9ii0.80 (4)1.98 (5)2.786 (6)179 (7)
O3—H3···O1Wiii0.821.802.590 (5)162
Symmetry codes: (i) x+1, y+1/2, z+1/2; (ii) x, y+1, z; (iii) x1, y, z.

Experimental details

Crystal data
Chemical formulaC13H18N4O4·H2O
Mr312.33
Crystal system, space groupMonoclinic, P21/c
Temperature (K)291
a, b, c (Å)4.370 (4), 34.55 (2), 9.960 (9)
β (°) 93.21 (3)
V3)1501 (2)
Z4
Radiation typeMo Kα
µ (mm1)0.11
Crystal size (mm)0.25 × 0.1 × 0.08
Data collection
DiffractometerBruker APEX CCD area-detector
Absorption correctionMulti-scan
(SADABS; Bruker, 2001)
Tmin, Tmax0.97, 0.99
No. of measured, independent and
observed [I > 2σ(I)] reflections
10307, 3520, 1861
Rint0.096
(sin θ/λ)max1)0.659
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.048, 0.158, 0.86
No. of reflections3520
No. of parameters203
H-atom treatmentH atoms treated by a mixture of independent and constrained refinement
Δρmax, Δρmin (e Å3)0.19, 0.20

Computer programs: SMART (Bruker, 2001), SAINT (Bruker, 2001), SAINT, SHELXS97 (Sheldrick, 1997), SHELXL97 (Sheldrick, 1997), ORTEPIII (Burnett & Johnson, 1996) and SHELXTL (Sheldrick, 2001), SHELXTL.

Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
O1W—H1A···O1i0.79 (2)2.00 (2)2.764 (4)163 (6)
O1W—H1B···N9ii0.80 (4)1.98 (5)2.786 (6)179 (7)
O3—H3···O1Wiii0.821.802.590 (5)162
Symmetry codes: (i) x+1, y+1/2, z+1/2; (ii) x, y+1, z; (iii) x1, y, z.
 

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