organic compounds
(2S,3R)-2-[(4-Ethyl-2,3-dioxopiperazin-1-yl)carbonylamino]-3-hydroxybutyric acid monohydrate
aDepartment of Applied Chemistry, College of Science, Nanjing University of Technolgy, Xinmofan Road No. 5, Nanjing 210009, People's Republic of China, and bNanjing FroChem Tech Co. Ltd., Xinmofan Road No. 36 Nanjing, Nanjing 210009, People's Republic of China
*Correspondence e-mail: guocheng@njut.edu.cn
In the title compound, C11H17N3O6·H2O, an important building block of the medicine cefbuperazone sodium, the piperazine ring adopts a screw-boat conformation. Intermolecular O—H⋯O and intramolecular N—H⋯O hydrogen bonds are observed. The water molecule participates as both donor and acceptor in this framework.
Related literature
For related literature, see: Anger et al. (2001); Özcan et al. (2003); Rondu et al. (1997); Saikawa et al. (1981).
Experimental
Crystal data
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Refinement
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Data collection: CAD-4 Software (Enraf–Nonius, 1989); cell CAD-4 Software; data reduction: XCAD4 (Harms & Wocadlo, 1995); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: SHELXTL (Sheldrick, 2008); software used to prepare material for publication: PLATON (Spek, 2003).
Supporting information
10.1107/S1600536808017832/bh2173sup1.cif
contains datablocks global, I. DOI:Structure factors: contains datablock I. DOI: 10.1107/S1600536808017832/bh2173Isup2.hkl
To a suspension of 2.0 g of L-threonine [(2S,3R)-2-amino-3-hydroxybutanoic acid] in methylene chloride (50 ml), 6.6 ml of trimethylchlorosilane were added, after which 7.1 ml of triethylamine were added dropwise at 273 K. The mixture was heated to 293 K for 2 h, and then a mixture of 4-ethyl-2,3-dioxo-1-piperazinecarbonyl chloride and triethylamine was added to the reaction mixture. After stirring for 1 h, the solvent was removed under reduced pressure. To the residue, 30 ml of water was added, and the pH was adjusted to 8 with NaHCO3, after which the solution was washed with 50 ml of ethyl acetate. Acetonitrile (50 ml) was added to the solution. The pH of the mixture was adjusted to 1 with HCl. The mixture was then saturated with NaCl, and the acetonitrile layer was thereafter separated. The aqueous layer was extracted with acetonitrile (3 × 50 ml), the combined acetonitrile layers were washed with saturated NaCl, and then distilled in vacuo to remove the solvent. The residue was recrystallized from ethanol to obtain 3.2 g of (I). Crystals of (I) suitable for X-ray diffraction were obtained by slow evaporation of an ethanol solution. 1H NMR (DMSO): δ 3.78–4.30 (m, 4H), 3.28–3.75 (m, 4H), 1.13 (d, 3H), 1.11 (t, 3H).
Hydroxyl H atoms were located in a difference map and refined freely. Water H atoms were found in a difference map and refined with a restrained geometry, O—H = 0.84 (2) Å. Other H atoms were positioned geometrically and refined using a riding model, with C—H = 0.96-0.98 Å, N—H = 0.86 Å and Uiso(H) = 1.2 or 1.5 Ueq of the
Friedel pairs were merged and the was assigned from starting materials.Data collection: CAD–4 Software (Enraf–Nonius, 1989); cell
CAD–4 Software (Enraf–Nonius, 1989); data reduction: XCAD4 (Harms & Wocadlo, 1995); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: SHELXTL (Sheldrick, 2008); software used to prepare material for publication: PLATON (Spek, 2003).C11H17N3O6·H2O | F(000) = 648 |
Mr = 305.29 | Dx = 1.382 Mg m−3 |
Orthorhombic, P212121 | Mo Kα radiation, λ = 0.71073 Å |
Hall symbol: P 2ac 2ab | Cell parameters from 25 reflections |
a = 9.4640 (19) Å | θ = 10–13° |
b = 11.389 (2) Å | µ = 0.12 mm−1 |
c = 13.611 (3) Å | T = 293 K |
V = 1467.1 (5) Å3 | Block, colourless |
Z = 4 | 0.40 × 0.30 × 0.20 mm |
Enraf–Nonius CAD-4 diffractometer | 1287 reflections with I > 2σ(I) |
Radiation source: fine-focus sealed tube | Rint = 0.000 |
Graphite monochromator | θmax = 25.1°, θmin = 2.3° |
ω/2θ scans | h = 0→11 |
Absorption correction: ψ scan (North et al., 1968) | k = 0→13 |
Tmin = 0.955, Tmax = 0.977 | l = 0→16 |
1519 measured reflections | 3 standard reflections every 200 reflections |
1519 independent reflections | intensity decay: <1% |
Refinement on F2 | Secondary atom site location: difference Fourier map |
Least-squares matrix: full | Hydrogen site location: inferred from neighbouring sites |
R[F2 > 2σ(F2)] = 0.041 | H atoms treated by a mixture of independent and constrained refinement |
wR(F2) = 0.105 | w = 1/[σ2(Fo2) + (0.0652P)2 + 0.1558P] where P = (Fo2 + 2Fc2)/3 |
S = 1.04 | (Δ/σ)max < 0.001 |
1519 reflections | Δρmax = 0.16 e Å−3 |
205 parameters | Δρmin = −0.16 e Å−3 |
2 restraints | Extinction correction: SHELXL97 (Sheldrick, 2008), Fc*=kFc[1+0.001xFc2λ3/sin(2θ)]-1/4 |
Primary atom site location: structure-invariant direct methods | Extinction coefficient: 0.037 (4) |
C11H17N3O6·H2O | V = 1467.1 (5) Å3 |
Mr = 305.29 | Z = 4 |
Orthorhombic, P212121 | Mo Kα radiation |
a = 9.4640 (19) Å | µ = 0.12 mm−1 |
b = 11.389 (2) Å | T = 293 K |
c = 13.611 (3) Å | 0.40 × 0.30 × 0.20 mm |
Enraf–Nonius CAD-4 diffractometer | 1287 reflections with I > 2σ(I) |
Absorption correction: ψ scan (North et al., 1968) | Rint = 0.000 |
Tmin = 0.955, Tmax = 0.977 | 3 standard reflections every 200 reflections |
1519 measured reflections | intensity decay: <1% |
1519 independent reflections |
R[F2 > 2σ(F2)] = 0.041 | 2 restraints |
wR(F2) = 0.105 | H atoms treated by a mixture of independent and constrained refinement |
S = 1.04 | Δρmax = 0.16 e Å−3 |
1519 reflections | Δρmin = −0.16 e Å−3 |
205 parameters |
x | y | z | Uiso*/Ueq | ||
C1 | 0.2982 (5) | 0.8688 (4) | 0.3149 (3) | 0.0802 (14) | |
H1A | 0.2231 | 0.9061 | 0.2793 | 0.120* | |
H1B | 0.3779 | 0.9207 | 0.3183 | 0.120* | |
H1C | 0.2666 | 0.8505 | 0.3802 | 0.120* | |
C2 | 0.3399 (4) | 0.7585 (3) | 0.2637 (3) | 0.0517 (9) | |
H2A | 0.2588 | 0.7066 | 0.2601 | 0.062* | |
H2B | 0.3683 | 0.7771 | 0.1970 | 0.062* | |
C3 | 0.5900 (3) | 0.7122 (3) | 0.2851 (2) | 0.0401 (7) | |
C4 | 0.7064 (3) | 0.6501 (3) | 0.3450 (2) | 0.0385 (7) | |
C5 | 0.5156 (3) | 0.5303 (3) | 0.4161 (3) | 0.0549 (10) | |
H5A | 0.4893 | 0.4738 | 0.3659 | 0.066* | |
H5B | 0.4997 | 0.4945 | 0.4798 | 0.066* | |
C6 | 0.4272 (3) | 0.6364 (3) | 0.4065 (3) | 0.0544 (9) | |
H6B | 0.3282 | 0.6145 | 0.4091 | 0.065* | |
H6C | 0.4461 | 0.6891 | 0.4609 | 0.065* | |
C7 | 0.7632 (3) | 0.4841 (3) | 0.4570 (2) | 0.0403 (7) | |
C8 | 1.0033 (3) | 0.4380 (3) | 0.5054 (2) | 0.0373 (7) | |
H8A | 0.9525 | 0.4006 | 0.5598 | 0.045* | |
C9 | 1.1128 (3) | 0.5210 (3) | 0.5489 (2) | 0.0390 (7) | |
C10 | 1.0768 (3) | 0.3423 (3) | 0.4465 (2) | 0.0425 (7) | |
H10A | 1.1384 | 0.2984 | 0.4913 | 0.051* | |
C11 | 0.9774 (4) | 0.2570 (3) | 0.3990 (3) | 0.0570 (9) | |
H11A | 1.0306 | 0.1992 | 0.3633 | 0.085* | |
H11B | 0.9161 | 0.2982 | 0.3547 | 0.085* | |
H11C | 0.9219 | 0.2188 | 0.4487 | 0.085* | |
N1 | 0.4564 (2) | 0.6970 (2) | 0.31326 (19) | 0.0416 (7) | |
N2 | 0.6683 (3) | 0.5610 (2) | 0.4054 (2) | 0.0397 (6) | |
N3 | 0.9022 (2) | 0.5055 (2) | 0.44847 (19) | 0.0383 (6) | |
H3A | 0.9314 | 0.5594 | 0.4091 | 0.046* | |
O1 | 0.6257 (2) | 0.7700 (3) | 0.21398 (19) | 0.0635 (8) | |
O2 | 0.8292 (2) | 0.6821 (2) | 0.33274 (19) | 0.0534 (7) | |
O3 | 0.7145 (3) | 0.4047 (2) | 0.5047 (2) | 0.0648 (8) | |
O4 | 1.1991 (3) | 0.4638 (2) | 0.6080 (2) | 0.0654 (8) | |
H4 | 1.254 (6) | 0.501 (4) | 0.632 (3) | 0.072 (15)* | |
O5 | 1.1208 (2) | 0.6236 (2) | 0.53094 (18) | 0.0506 (6) | |
O6 | 1.1642 (3) | 0.4009 (2) | 0.3763 (2) | 0.0600 (7) | |
H6 | 1.217 (5) | 0.354 (4) | 0.347 (3) | 0.064 (12)* | |
O7 | 0.9118 (3) | 0.9195 (3) | 0.3221 (2) | 0.0663 (8) | |
H7A | 0.894 (5) | 0.847 (2) | 0.332 (3) | 0.080* | |
H7B | 0.909 (5) | 0.937 (4) | 0.2641 (17) | 0.080* |
U11 | U22 | U33 | U12 | U13 | U23 | |
C1 | 0.071 (3) | 0.088 (3) | 0.081 (3) | 0.038 (3) | −0.034 (3) | −0.023 (3) |
C2 | 0.0347 (16) | 0.063 (2) | 0.057 (2) | 0.0056 (17) | −0.0130 (16) | −0.0023 (18) |
C3 | 0.0329 (15) | 0.0434 (17) | 0.0441 (17) | 0.0010 (14) | 0.0026 (14) | 0.0032 (15) |
C4 | 0.0277 (15) | 0.0402 (16) | 0.0476 (17) | −0.0004 (13) | 0.0058 (14) | 0.0067 (15) |
C5 | 0.0280 (15) | 0.056 (2) | 0.081 (3) | −0.0076 (15) | 0.0075 (17) | 0.017 (2) |
C6 | 0.0271 (15) | 0.067 (2) | 0.069 (2) | −0.0013 (16) | 0.0102 (17) | 0.016 (2) |
C7 | 0.0325 (15) | 0.0342 (15) | 0.0541 (18) | −0.0024 (13) | 0.0063 (15) | 0.0054 (16) |
C8 | 0.0310 (14) | 0.0399 (15) | 0.0410 (15) | −0.0004 (14) | −0.0004 (13) | 0.0091 (15) |
C9 | 0.0337 (15) | 0.0446 (17) | 0.0389 (16) | 0.0053 (14) | 0.0036 (14) | −0.0016 (14) |
C10 | 0.0366 (15) | 0.0394 (16) | 0.0515 (17) | 0.0076 (15) | −0.0094 (16) | −0.0010 (15) |
C11 | 0.051 (2) | 0.0486 (18) | 0.071 (2) | 0.0071 (17) | −0.016 (2) | −0.0059 (19) |
N1 | 0.0261 (12) | 0.0516 (16) | 0.0471 (15) | 0.0005 (11) | 0.0009 (12) | 0.0043 (13) |
N2 | 0.0228 (11) | 0.0387 (13) | 0.0577 (15) | −0.0007 (11) | 0.0055 (12) | 0.0078 (13) |
N3 | 0.0283 (12) | 0.0399 (14) | 0.0468 (14) | 0.0006 (11) | 0.0037 (12) | 0.0092 (12) |
O1 | 0.0382 (13) | 0.0902 (19) | 0.0622 (14) | 0.0059 (13) | 0.0057 (12) | 0.0350 (15) |
O2 | 0.0280 (11) | 0.0555 (14) | 0.0765 (16) | 0.0003 (11) | 0.0077 (12) | 0.0252 (13) |
O3 | 0.0400 (13) | 0.0541 (15) | 0.100 (2) | −0.0055 (12) | 0.0030 (14) | 0.0349 (15) |
O4 | 0.0657 (18) | 0.0583 (16) | 0.0722 (18) | −0.0039 (15) | −0.0344 (16) | 0.0042 (14) |
O5 | 0.0444 (13) | 0.0402 (12) | 0.0672 (15) | −0.0013 (11) | 0.0009 (12) | −0.0009 (12) |
O6 | 0.0441 (13) | 0.0687 (17) | 0.0672 (16) | 0.0033 (14) | 0.0184 (13) | −0.0123 (14) |
O7 | 0.0633 (16) | 0.0645 (16) | 0.0710 (16) | −0.0032 (15) | 0.0206 (16) | −0.0012 (16) |
C1—C2 | 1.491 (5) | C7—N3 | 1.343 (4) |
C1—H1A | 0.9600 | C7—N2 | 1.438 (4) |
C1—H1B | 0.9600 | C8—N3 | 1.451 (4) |
C1—H1C | 0.9600 | C8—C10 | 1.521 (4) |
C2—N1 | 1.470 (4) | C8—C9 | 1.522 (4) |
C2—H2A | 0.9700 | C8—H8A | 0.9800 |
C2—H2B | 0.9700 | C9—O5 | 1.196 (4) |
C3—O1 | 1.218 (4) | C9—O4 | 1.319 (4) |
C3—N1 | 1.333 (4) | C10—O6 | 1.430 (4) |
C3—C4 | 1.542 (4) | C10—C11 | 1.499 (5) |
C4—O2 | 1.229 (3) | C10—H10A | 0.9800 |
C4—N2 | 1.354 (4) | C11—H11A | 0.9600 |
C5—C6 | 1.476 (5) | C11—H11B | 0.9600 |
C5—N2 | 1.495 (4) | C11—H11C | 0.9600 |
C5—H5A | 0.9700 | N3—H3A | 0.8600 |
C5—H5B | 0.9700 | O4—H4 | 0.75 (5) |
C6—N1 | 1.470 (4) | O6—H6 | 0.83 (4) |
C6—H6B | 0.9700 | O7—H7A | 0.85 (2) |
C6—H6C | 0.9700 | O7—H7B | 0.815 (19) |
C7—O3 | 1.205 (4) | ||
C2—C1—H1A | 109.5 | N3—C8—C10 | 113.6 (2) |
C2—C1—H1B | 109.5 | N3—C8—C9 | 109.1 (2) |
H1A—C1—H1B | 109.5 | C10—C8—C9 | 109.8 (2) |
C2—C1—H1C | 109.5 | N3—C8—H8A | 108.1 |
H1A—C1—H1C | 109.5 | C10—C8—H8A | 108.1 |
H1B—C1—H1C | 109.5 | C9—C8—H8A | 108.1 |
N1—C2—C1 | 112.7 (3) | O5—C9—O4 | 124.6 (3) |
N1—C2—H2A | 109.1 | O5—C9—C8 | 124.8 (3) |
C1—C2—H2A | 109.1 | O4—C9—C8 | 110.6 (3) |
N1—C2—H2B | 109.1 | O6—C10—C11 | 112.2 (3) |
C1—C2—H2B | 109.1 | O6—C10—C8 | 106.4 (3) |
H2A—C2—H2B | 107.8 | C11—C10—C8 | 113.9 (3) |
O1—C3—N1 | 124.2 (3) | O6—C10—H10A | 108.1 |
O1—C3—C4 | 118.0 (3) | C11—C10—H10A | 108.1 |
N1—C3—C4 | 117.8 (3) | C8—C10—H10A | 108.1 |
O2—C4—N2 | 123.8 (3) | C10—C11—H11A | 109.5 |
O2—C4—C3 | 117.8 (3) | C10—C11—H11B | 109.5 |
N2—C4—C3 | 118.3 (2) | H11A—C11—H11B | 109.5 |
C6—C5—N2 | 110.3 (3) | C10—C11—H11C | 109.5 |
C6—C5—H5A | 109.6 | H11A—C11—H11C | 109.5 |
N2—C5—H5A | 109.6 | H11B—C11—H11C | 109.5 |
C6—C5—H5B | 109.6 | C3—N1—C2 | 121.2 (3) |
N2—C5—H5B | 109.6 | C3—N1—C6 | 119.2 (3) |
H5A—C5—H5B | 108.1 | C2—N1—C6 | 118.6 (2) |
N1—C6—C5 | 110.7 (3) | C4—N2—C7 | 125.9 (2) |
N1—C6—H6B | 109.5 | C4—N2—C5 | 119.5 (3) |
C5—C6—H6B | 109.5 | C7—N2—C5 | 114.4 (2) |
N1—C6—H6C | 109.5 | C7—N3—C8 | 120.2 (3) |
C5—C6—H6C | 109.5 | C7—N3—H3A | 119.9 |
H6B—C6—H6C | 108.1 | C8—N3—H3A | 119.9 |
O3—C7—N3 | 123.9 (3) | C9—O4—H4 | 115 (4) |
O3—C7—N2 | 118.8 (3) | C10—O6—H6 | 111 (3) |
N3—C7—N2 | 117.3 (3) | H7A—O7—H7B | 113 (5) |
O1—C3—C4—O2 | 16.1 (5) | C1—C2—N1—C6 | 72.6 (4) |
N1—C3—C4—O2 | −165.3 (3) | C5—C6—N1—C3 | −44.8 (4) |
O1—C3—C4—N2 | −161.7 (3) | C5—C6—N1—C2 | 146.7 (3) |
N1—C3—C4—N2 | 16.9 (4) | O2—C4—N2—C7 | −6.0 (5) |
N2—C5—C6—N1 | 55.3 (4) | C3—C4—N2—C7 | 171.7 (3) |
N3—C8—C9—O5 | −6.4 (4) | O2—C4—N2—C5 | 179.1 (3) |
C10—C8—C9—O5 | 118.6 (3) | C3—C4—N2—C5 | −3.2 (4) |
N3—C8—C9—O4 | 174.5 (3) | O3—C7—N2—C4 | −176.4 (3) |
C10—C8—C9—O4 | −60.4 (3) | N3—C7—N2—C4 | 3.4 (5) |
N3—C8—C10—O6 | 67.5 (3) | O3—C7—N2—C5 | −1.3 (5) |
C9—C8—C10—O6 | −54.9 (3) | N3—C7—N2—C5 | 178.5 (3) |
N3—C8—C10—C11 | −56.5 (4) | C6—C5—N2—C4 | −32.7 (5) |
C9—C8—C10—C11 | −179.0 (3) | C6—C5—N2—C7 | 151.8 (3) |
O1—C3—N1—C2 | −5.0 (5) | O3—C7—N3—C8 | −5.7 (5) |
C4—C3—N1—C2 | 176.5 (3) | N2—C7—N3—C8 | 174.5 (2) |
O1—C3—N1—C6 | −173.2 (3) | C10—C8—N3—C7 | 101.8 (3) |
C4—C3—N1—C6 | 8.3 (4) | C9—C8—N3—C7 | −135.4 (3) |
C1—C2—N1—C3 | −95.7 (4) |
D—H···A | D—H | H···A | D···A | D—H···A |
N3—H3A···O2 | 0.86 | 1.99 | 2.647 (3) | 132 |
O7—H7A···O2 | 0.85 (2) | 1.98 (2) | 2.817 (4) | 169 (5) |
O4—H4···O7i | 0.75 (5) | 1.85 (5) | 2.593 (4) | 170 (5) |
O6—H6···O1ii | 0.83 (4) | 1.95 (4) | 2.772 (3) | 167 (4) |
O7—H7B···O6iii | 0.82 (2) | 2.07 (3) | 2.803 (4) | 149 (4) |
Symmetry codes: (i) x+1/2, −y+3/2, −z+1; (ii) −x+2, y−1/2, −z+1/2; (iii) −x+2, y+1/2, −z+1/2. |
Experimental details
Crystal data | |
Chemical formula | C11H17N3O6·H2O |
Mr | 305.29 |
Crystal system, space group | Orthorhombic, P212121 |
Temperature (K) | 293 |
a, b, c (Å) | 9.4640 (19), 11.389 (2), 13.611 (3) |
V (Å3) | 1467.1 (5) |
Z | 4 |
Radiation type | Mo Kα |
µ (mm−1) | 0.12 |
Crystal size (mm) | 0.40 × 0.30 × 0.20 |
Data collection | |
Diffractometer | Enraf–Nonius CAD-4 diffractometer |
Absorption correction | ψ scan (North et al., 1968) |
Tmin, Tmax | 0.955, 0.977 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 1519, 1519, 1287 |
Rint | 0.000 |
(sin θ/λ)max (Å−1) | 0.598 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.041, 0.105, 1.04 |
No. of reflections | 1519 |
No. of parameters | 205 |
No. of restraints | 2 |
H-atom treatment | H atoms treated by a mixture of independent and constrained refinement |
Δρmax, Δρmin (e Å−3) | 0.16, −0.16 |
Computer programs: CAD–4 Software (Enraf–Nonius, 1989), XCAD4 (Harms & Wocadlo, 1995), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), SHELXTL (Sheldrick, 2008), PLATON (Spek, 2003).
D—H···A | D—H | H···A | D···A | D—H···A |
N3—H3A···O2 | 0.86 | 1.99 | 2.647 (3) | 132.0 |
O7—H7A···O2 | 0.85 (2) | 1.98 (2) | 2.817 (4) | 169 (5) |
O4—H4···O7i | 0.75 (5) | 1.85 (5) | 2.593 (4) | 170 (5) |
O6—H6···O1ii | 0.83 (4) | 1.95 (4) | 2.772 (3) | 167 (4) |
O7—H7B···O6iii | 0.815 (19) | 2.07 (3) | 2.803 (4) | 149 (4) |
Symmetry codes: (i) x+1/2, −y+3/2, −z+1; (ii) −x+2, y−1/2, −z+1/2; (iii) −x+2, y+1/2, −z+1/2. |
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Some derivatives of piperazine are important chemical materials (Saikawa et al., 1981) with pharmaceutical properties (Rondu et al., 1997) for example against migraine, and are calcium channel antagonist (Anger et al., 2001). As part of our studies in this area, we report here the crystal structure of the title compound, (I).
The refined molecular structure of (I) is shown in Fig. 1. The title compound includes a piperzaine and a threonine moieties, and the asymmetric unit is completed by one lattice water molecule. The piperazine ring adopts a screw-boat conformation with atoms C4 and C6 displaced by 0.104 (8) and 0.596 (2) Å, respectively, from the mean plane through atoms N1, C3, N2 and C5. The dihedral angle between N1/C3/N2/C5 and N2/C7/N3/C8 planes is 4.1°.
The threonine molecular group has two chiral atoms, C8 and C10, and adopts a configuration in agreement with previous reports (e.g. Özcan et al., 2003). The separation O6···O1 suggests an interaction between the ketone and the carboxyl group (Table 1). The water molecule is linked to the main molecule via O—H···O hydrogen bonds. These hydrogen bonds are effective in the stabilization of the crystal structure.