[(1H-Benzimidazol-2-ylmeth­yl)iminodimethyl­ene]diphospho­nic acid dihydrate

Tong, J.-W.; Ma, L.-F.; Cao, D.-K.; Li, Y.-Z.; Zheng, L.-M.

doi:10.1107/S1600536806019763

[(1H-Benzimidazol-2-ylmethyl)iminodimethylene]diphosphonic acid dihydrate

J.-W. Tong, L.-F. Ma, D.-K. Cao, Y.-Z. Li and L.-M. Zheng

The title compound, C₉H₁₅O₆N₃P₂·2H₂O, contains two phosphonic acid groups and one benzimidazole group connected by an N(CH₂–)₃ group. One of the benzimidazole N atoms and two phosphonic acid O atoms of each PO₃ group are protonated. Extensive hydrogen-bonding interactions, as well as π–π stacking interactions, are found between the molecules, leading to a three-dimensional supramolecular network structure.

Read article Similar articles

Supporting information

	Crystallographic Information File (CIF) https://doi.org/10.1107/S1600536806019763/gh2009sup1.cif Contains datablocks global, I
	Structure factor file (CIF format) https://doi.org/10.1107/S1600536806019763/gh2009Isup2.hkl Contains datablock I

CCDC reference: 613684

checkCIF report

Key indicators

Single-crystal X-ray study
T = 298 K
Mean (C-C) = 0.005 Å
R factor = 0.061
wR factor = 0.161
Data-to-parameter ratio = 13.4

checkCIF/PLATON results

No syntax errors found



Alert level C
PLAT042_ALERT_1_C Calc. and Rep. MoietyFormula Strings Differ ....          ?
PLAT340_ALERT_3_C Low Bond Precision on C-C bonds (x 1000) Ang ...          5
PLAT720_ALERT_4_C Number of Unusual/Non-Standard Label(s) ........          4

   0 ALERT level A = In general: serious problem
   0 ALERT level B = Potentially serious problem
   3 ALERT level C = Check and explain
   0 ALERT level G = General alerts; check

   1 ALERT type 1 CIF construction/syntax error, inconsistent or missing data
   0 ALERT type 2 Indicator that the structure model may be wrong or deficient
   1 ALERT type 3 Indicator that the structure quality may be low
   1 ALERT type 4 Improvement, methodology, query or suggestion

Computing details top

Data collection: SMART (Bruker, 2000); cell refinement: SMART; data reduction: SAINT (Bruker, 2000); program(s) used to solve structure: SHELXTL (Bruker, 2000); program(s) used to refine structure: SHELXTL; molecular graphics: SHELXTL; software used to prepare material for publication: SHELXTL.

[(1H-Benzimidazol-2-ylmethyl)iminodimethylene]diphosphonic acid dihydrate top

Crystal data top

C₁₀H₁₅N₃O₆P₂·2H₂O	F(000) = 776
M_r = 371.22	D_x = 1.599 Mg m⁻³
Monoclinic, P2₁/c	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: -P 2ybc	Cell parameters from 1325 reflections
a = 7.0336 (8) Å	θ = 2.1–25.8°
b = 11.5822 (13) Å	µ = 0.33 mm⁻¹
c = 18.935 (2) Å	T = 298 K
β = 91.252 (2)°	Block, colourless
V = 1542.2 (3) Å³	0.32 × 0.28 × 0.26 mm
Z = 4

Data collection top

Bruker SMART APEX CCD area-detector diffractometer	3025 independent reflections
Radiation source: sealed tube	2151 reflections with I > 2σ(I)
Graphite monochromator	R_int = 0.052
φ and ω scans	θ_max = 26.0°, θ_min = 2.1°
Absorption correction: multi-scan (SADABS; Bruker, 2000)	h = −8→8
T_min = 0.91, T_max = 0.92	k = −13→14
8348 measured reflections	l = −17→23

Refinement top

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)] = 0.061	Hydrogen site location: inferred from neighbouring sites
wR(F²) = 0.161	H-atom parameters constrained
S = 0.95	w = 1/[σ²(F_o²) + (0.1074P)²] where P = (F_o² + 2F_c²)/3
3025 reflections	(Δ/σ)_max < 0.001
226 parameters	Δρ_max = 0.66 e Å⁻³
0 restraints	Δρ_min = −0.64 e Å⁻³

Special details top

Experimental. IR (KBr, ν, cm^-1): 3061 (s, br), 2935 (s, br), 2876 (s, br), 1628 (w), 1577 (w), 1523 (w), 1460 (m), 1399 (w), 1276 (w), 1177 (m), 1146 (w), 1057 (s, br), 957 (s, br), 930 (s, br), 853 (w), 836 (w), 809 (m), 753 (m), 730 (m), 645 (w), 622 (w), 575 (m), 555 (w), 462 (m).

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

	x	y	z	U_iso*/U_eq
C1	0.7696 (5)	0.9507 (3)	0.51721 (19)	0.0298 (8)
C2	0.7534 (5)	0.9668 (4)	0.4460 (2)	0.0392 (9)
H2	0.7621	0.9053	0.4147	0.047*
C3	0.7239 (6)	1.0769 (4)	0.4226 (2)	0.0476 (11)
H3	0.7147	1.0909	0.3743	0.057*
C4	0.7072 (6)	1.1701 (4)	0.4701 (2)	0.0489 (11)
H4	0.6872	1.2440	0.4523	0.059*
C5	0.7196 (6)	1.1545 (3)	0.5419 (2)	0.0388 (9)
H5	0.7092	1.2156	0.5734	0.047*
C6	0.7486 (5)	1.0421 (3)	0.56446 (19)	0.0283 (8)
C7	0.8113 (5)	0.8845 (3)	0.62784 (18)	0.0263 (7)
C8	0.8639 (5)	0.8076 (3)	0.68795 (19)	0.0269 (7)
H8A	0.8319	0.7284	0.6760	0.032*
H8B	0.9999	0.8118	0.6972	0.032*
C9	0.5586 (5)	0.8124 (3)	0.75073 (18)	0.0240 (7)
H9A	0.4945	0.8590	0.7150	0.029*
H9B	0.5087	0.8351	0.7960	0.029*
C10	0.8675 (5)	0.8190 (3)	0.81772 (19)	0.0301 (8)
H10A	0.9382	0.7475	0.8136	0.036*
H10B	0.7785	0.8105	0.8558	0.036*
N1	0.8048 (4)	0.8525 (2)	0.55911 (15)	0.0274 (6)
N2	0.7766 (4)	0.9962 (2)	0.63158 (15)	0.0249 (6)
H2C	0.7718	1.0350	0.6702	0.030*
N3	0.7623 (4)	0.8426 (2)	0.75080 (15)	0.0223 (6)
O1	0.2897 (4)	0.6433 (2)	0.75629 (14)	0.0315 (6)
O2	0.6394 (4)	0.5864 (2)	0.77705 (14)	0.0332 (6)
H2A	0.720 (7)	0.555 (4)	0.748 (2)	0.040*
O3	0.5176 (4)	0.6481 (2)	0.65486 (13)	0.0358 (6)
H3B	0.5863	0.5904	0.6492	0.043*
O4	1.1280 (4)	0.9154 (2)	0.90771 (14)	0.0381 (7)
O5	0.9074 (4)	1.0486 (2)	0.84597 (15)	0.0364 (6)
H5A	0.817 (7)	1.034 (4)	0.871 (3)	0.044*
O6	1.1570 (4)	0.9483 (3)	0.77288 (15)	0.0426 (7)
H6B	1.2189	1.0095	0.7763	0.051*
O1W	0.8437 (5)	0.6297 (3)	0.50700 (17)	0.0463 (8)
H1WA	0.934 (8)	0.621 (5)	0.479 (3)	0.056*
H1WB	0.881 (8)	0.576 (5)	0.530 (3)	0.056*
O2W	0.4904 (5)	0.4542 (3)	0.5848 (2)	0.0587 (10)
H2WA	0.606 (9)	0.433 (5)	0.577 (3)	0.070*
H2WB	0.413 (10)	0.442 (5)	0.554 (3)	0.070*
P1	0.49279 (13)	0.66327 (7)	0.73527 (5)	0.0248 (2)
P2	1.02950 (13)	0.93654 (8)	0.83741 (5)	0.0288 (3)

Atomic displacement parameters (Å²) top

	U¹¹	U²²	U³³	U¹²	U¹³	U²³
C1	0.0237 (18)	0.0376 (19)	0.0280 (18)	−0.0031 (14)	−0.0002 (13)	−0.0006 (15)
C2	0.0272 (19)	0.065 (3)	0.0254 (17)	−0.0067 (18)	−0.0044 (15)	−0.0088 (18)
C3	0.032 (2)	0.075 (3)	0.036 (2)	−0.007 (2)	−0.0047 (17)	0.018 (2)
C4	0.042 (2)	0.048 (3)	0.056 (3)	0.000 (2)	−0.001 (2)	0.025 (2)
C5	0.038 (2)	0.0295 (19)	0.049 (3)	−0.0092 (16)	−0.0015 (17)	0.0002 (17)
C6	0.0242 (17)	0.0320 (18)	0.0288 (18)	−0.0052 (14)	0.0041 (13)	0.0054 (14)
C7	0.0254 (17)	0.0252 (17)	0.0284 (18)	−0.0056 (13)	0.0029 (13)	−0.0067 (14)
C8	0.0234 (17)	0.0220 (16)	0.0355 (19)	0.0013 (13)	0.0035 (13)	0.0016 (14)
C9	0.0193 (16)	0.0261 (17)	0.0267 (17)	0.0000 (12)	0.0010 (12)	0.0024 (13)
C10	0.0285 (19)	0.0294 (18)	0.0322 (18)	−0.0042 (14)	−0.0030 (14)	0.0004 (15)
N1	0.0272 (15)	0.0308 (15)	0.0241 (15)	0.0009 (12)	0.0009 (11)	−0.0100 (12)
N2	0.0330 (15)	0.0214 (14)	0.0204 (13)	−0.0020 (11)	0.0030 (11)	−0.0059 (11)
N3	0.0153 (13)	0.0285 (14)	0.0231 (14)	0.0016 (11)	0.0010 (10)	0.0035 (11)
O1	0.0305 (13)	0.0299 (13)	0.0343 (14)	−0.0084 (10)	0.0046 (10)	0.0001 (11)
O2	0.0443 (16)	0.0247 (12)	0.0307 (14)	0.0080 (11)	−0.0001 (12)	−0.0007 (10)
O3	0.0450 (16)	0.0408 (15)	0.0217 (13)	−0.0049 (12)	0.0041 (11)	0.0011 (11)
O4	0.0319 (15)	0.0453 (16)	0.0363 (15)	−0.0073 (12)	−0.0155 (11)	0.0062 (12)
O5	0.0367 (16)	0.0315 (14)	0.0408 (16)	−0.0038 (11)	−0.0029 (12)	−0.0022 (11)
O6	0.0388 (16)	0.0484 (17)	0.0409 (16)	−0.0120 (13)	0.0098 (13)	−0.0005 (13)
O1W	0.063 (2)	0.0344 (16)	0.0423 (18)	0.0150 (15)	0.0086 (15)	0.0042 (13)
O2W	0.0416 (19)	0.061 (2)	0.073 (3)	0.0041 (17)	−0.0085 (17)	−0.0277 (18)
P1	0.0293 (5)	0.0215 (4)	0.0235 (5)	−0.0027 (3)	−0.0014 (3)	0.0016 (3)
P2	0.0222 (5)	0.0309 (5)	0.0331 (5)	−0.0041 (4)	−0.0029 (3)	0.0035 (4)

Geometric parameters (Å, º) top

C1—C2	1.363 (5)	C9—H9B	0.9700
C1—C6	1.396 (5)	C10—N3	1.479 (4)
C1—N1	1.406 (5)	C10—P2	1.809 (4)
C2—C3	1.365 (6)	C10—H10A	0.9700
C2—H2	0.9300	C10—H10B	0.9700
C3—C4	1.411 (7)	N2—H2C	0.8600
C3—H3	0.9300	O1—P1	1.509 (3)
C4—C5	1.372 (6)	O2—P1	1.564 (3)
C4—H4	0.9300	O2—H2A	0.88 (5)
C5—C6	1.383 (5)	O3—P1	1.546 (3)
C5—H5	0.9300	O3—H3B	0.8335
C6—N2	1.388 (4)	O4—P2	1.507 (3)
C7—N2	1.318 (4)	O5—P2	1.567 (3)
C7—N1	1.353 (4)	O5—H5A	0.82 (5)
C7—C8	1.486 (5)	O6—P2	1.537 (3)
C8—N3	1.459 (4)	O6—H6B	0.8340
C8—H8A	0.9700	O1W—H1WA	0.85 (6)
C8—H8B	0.9700	O1W—H1WB	0.80 (6)
C9—N3	1.474 (4)	O2W—H2WA	0.87 (6)
C9—P1	1.810 (3)	O2W—H2WB	0.80 (7)
C9—H9A	0.9700

C2—C1—C6	121.5 (4)	H9A—C9—H9B	107.1
C2—C1—N1	132.7 (4)	N3—C10—P2	109.8 (2)
C6—C1—N1	105.8 (3)	N3—C10—H10A	109.7
C1—C2—C3	117.3 (4)	P2—C10—H10A	109.7
C1—C2—H2	121.4	N3—C10—H10B	109.7
C3—C2—H2	121.4	P2—C10—H10B	109.7
C2—C3—C4	121.4 (4)	H10A—C10—H10B	108.2
C2—C3—H3	119.3	C7—N1—C1	108.8 (3)
C4—C3—H3	119.3	C7—N2—C6	110.5 (3)
C5—C4—C3	121.8 (4)	C7—N2—H2C	124.8
C5—C4—H4	119.1	C6—N2—H2C	124.8
C3—C4—H4	119.1	C8—N3—C9	115.3 (3)
C4—C5—C6	115.8 (4)	C8—N3—C10	113.8 (3)
C4—C5—H5	122.1	C9—N3—C10	115.2 (3)
C6—C5—H5	122.1	P1—O2—H2A	110 (3)
C5—C6—N2	131.3 (3)	P1—O3—H3B	107.2
C5—C6—C1	122.2 (3)	P2—O5—H5A	109 (3)
N2—C6—C1	106.3 (3)	P2—O6—H6B	109.0
N2—C7—N1	108.6 (3)	H1WA—O1W—H1WB	91 (5)
N2—C7—C8	126.2 (3)	H2WA—O2W—H2WB	117 (6)
N1—C7—C8	125.1 (3)	O1—P1—O3	111.72 (15)
N3—C8—C7	109.9 (3)	O1—P1—O2	113.38 (15)
N3—C8—H8A	109.7	O3—P1—O2	110.25 (15)
C7—C8—H8A	109.7	O1—P1—C9	110.09 (15)
N3—C8—H8B	109.7	O3—P1—C9	103.53 (15)
C7—C8—H8B	109.7	O2—P1—C9	107.33 (15)
H8A—C8—H8B	108.2	O4—P2—O6	116.84 (17)
N3—C9—P1	118.1 (2)	O4—P2—O5	106.59 (16)
N3—C9—H9A	107.8	O6—P2—O5	109.85 (17)
P1—C9—H9A	107.8	O4—P2—C10	109.60 (17)
N3—C9—H9B	107.8	O6—P2—C10	106.17 (17)
P1—C9—H9B	107.8	O5—P2—C10	107.48 (17)

Hydrogen-bond geometry (Å, º) top

D—H···A	D—H	H···A	D···A	D—H···A
O2W—H2WB···O1Wⁱ	0.80 (7)	2.28 (7)	3.051 (5)	163 (6)
O1W—H1WA···O4ⁱⁱ	0.85 (6)	1.98 (6)	2.823 (4)	173 (5)
O2W—H2WA···O4ⁱⁱⁱ	0.87 (6)	1.90 (7)	2.722 (5)	158 (6)
O1W—H1WB···O4ⁱⁱⁱ	0.80 (6)	2.20 (6)	2.965 (4)	159 (5)
O2—H2A···O6ⁱⁱⁱ	0.88 (5)	1.56 (5)	2.359 (4)	148 (4)
O5—H5A···O2W^iv	0.82 (5)	2.51 (5)	3.302 (5)	162 (5)
N2—H2C···O1^iv	0.86	1.93	2.770 (4)	165

Symmetry codes: (i) −x+1, −y+1, −z+1; (ii) x, −y+3/2, z−1/2; (iii) −x+2, y−1/2, −z+3/2; (iv) −x+1, y+1/2, −z+3/2.

Format		BIBTeX
		EndNote
		RefMan
		Refer
		Medline
		CIF
		SGML
		Text
		Plain Text

Format		BIBTeX
		EndNote
		RefMan
		Refer
		Medline
		CIF
		SGML
		Text
		Plain Text

Search IUCr Journals		doi		Advanced search
Author		volume	page

[(1H-Benzimidazol-2-ylmeth­yl)iminodimethyl­ene]diphospho­nic acid dihydrate

Supporting information

Key indicators

checkCIF/PLATON results

[(1H-Benzimidazol-2-ylmethyl)iminodimethylene]diphosphonic acid dihydrate