Literature DB >> 22412675

Bis[(2,2-dimethyl-propano-yloxy)meth-yl] {[2-(6-amino-9H-purin-9-yl)eth-oxy]meth-yl}phospho-nate-succinic acid (2/1).

Sungyup Jung, Jeong-Myeong Ha, Il Won Kim.   

Abstract

The title compound, C(20)H(32)N(5)O(8)P·0.5C(4)H(6)O(4), is composed of two 9-{2-[bis-(pivaloyloxymeth-oxy)phosphinylmeth-oxy]eth-yl}adenine, commonly known as adefovir dipivoxil (AD), mol-ecules linked to the carb-oxy-lic acid groups of succinic acid (SA). The asymmetric unit contains one mol-ecule of AD and half a mol-ecule of SA, which sits on an inversion center. Both adenine units in the two AD mol-ecules make AD-SA N-H⋯O and SA-AD O-H⋯N hydrogen bonds to SA. In addition, the inter-molecular AD-AD N-H⋯O-P hydrogen bond serves to stabilize the cocrystal. There is also a π-π stacking inter-action [inter-planar spacing 3.34 (19) Å] between adjacent inversion-related adenine groups.

Entities:  

Year:  2012        PMID: 22412675      PMCID: PMC3297872          DOI: 10.1107/S1600536812006873

Source DB:  PubMed          Journal:  Acta Crystallogr Sect E Struct Rep Online        ISSN: 1600-5368


Related literature

For the synthesis and process optimization of 9-{2-[bis(pivaloyloxymeth­oxy)phosphinylmeth­oxy]eth­yl}adenine, see: Starrett et al. (1992 ▶); Yu et al. (1999 ▶). For the biological and pharmacological relevance of 9-{2-[bis­(pivaloyloxymeth­oxy)phosphinylmeth­oxy]eth­yl}adenine, see: Qaqish et al. (2003 ▶); Julander et al. (2002 ▶). For the structure of a hydrate of the title compound, see: Chang et al. (2007 ▶).

Experimental

Crystal data

C20H32N5O8P·0.5C4H6O4 M = 560.52 Triclinic, a = 7.7122 (12) Å b = 10.1577 (15) Å c = 19.185 (3) Å α = 80.409 (8)° β = 79.718 (9)° γ = 80.407 (8)° V = 1443.5 (4) Å3 Z = 2 Mo Kα radiation μ = 0.15 mm−1 T = 296 K 0.11 × 0.10 × 0.08 mm

Data collection

Bruker SMART CCD diffractometer Absorption correction: multi-scan (SADABS; Bruker, 2002 ▶) T min = 0.982, T max = 0.987 49737 measured reflections 7222 independent reflections 4593 reflections with I > 2σ(I) R int = 0.053

Refinement

R[F 2 > 2σ(F 2)] = 0.046 wR(F 2) = 0.143 S = 1.01 7222 reflections 417 parameters H atoms treated by a mixture of independent and constrained refinement Δρmax = 0.38 e Å−3 Δρmin = −0.29 e Å−3 Data collection: SMART (Bruker, 2002 ▶); cell refinement: SAINT (Bruker, 2002 ▶); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 2008 ▶); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008 ▶); molecular graphics: ORTEP-3 for Windows (Farrugia, 1997 ▶); software used to prepare material for publication: WinGX (Farrugia, 1999 ▶). Crystal structure: contains datablock(s) I, global. DOI: 10.1107/S1600536812006873/pk2386sup1.cif Structure factors: contains datablock(s) I. DOI: 10.1107/S1600536812006873/pk2386Isup2.hkl Supplementary material file. DOI: 10.1107/S1600536812006873/pk2386Isup3.cml Additional supplementary materials: crystallographic information; 3D view; checkCIF report
C20H32N5O8P·0.5C4H6O4Z = 2
Mr = 560.52F(000) = 594
Triclinic, P1Dx = 1.290 Mg m3
Hall symbol: -P 1Melting point: 410 K
a = 7.7122 (12) ÅMo Kα radiation, λ = 0.71073 Å
b = 10.1577 (15) ÅCell parameters from 9846 reflections
c = 19.185 (3) Åθ = 2.2–25.7°
α = 80.409 (8)°µ = 0.15 mm1
β = 79.718 (9)°T = 296 K
γ = 80.407 (8)°Block, colourless
V = 1443.5 (4) Å30.11 × 0.10 × 0.08 mm
Bruker SMART CCD diffractometer7222 independent reflections
Radiation source: fine-focus sealed tube4593 reflections with I > 2σ(I)
Graphite monochromatorRint = 0.053
φ and ω scansθmax = 28.4°, θmin = 1.1°
Absorption correction: multi-scan (SADABS; Bruker, 2002)h = −10→10
Tmin = 0.982, Tmax = 0.987k = −13→13
49737 measured reflectionsl = −25→25
Refinement on F2Primary atom site location: structure-invariant direct methods
Least-squares matrix: fullSecondary atom site location: difference Fourier map
R[F2 > 2σ(F2)] = 0.046Hydrogen site location: inferred from neighbouring sites
wR(F2) = 0.143H atoms treated by a mixture of independent and constrained refinement
S = 1.01w = 1/[σ2(Fo2) + (0.0783P)2] where P = (Fo2 + 2Fc2)/3
7222 reflections(Δ/σ)max < 0.001
417 parametersΔρmax = 0.38 e Å3
0 restraintsΔρmin = −0.29 e Å3
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.
xyzUiso*/Ueq
P10.85354 (6)0.35488 (4)0.23364 (3)0.04127 (14)
O21.16908 (15)0.27477 (11)0.16611 (7)0.0465 (3)
H22A0.869 (3)−0.400 (2)0.0252 (13)0.083 (8)*
O10.75924 (17)0.37739 (12)0.17242 (7)0.0520 (3)
H7A1.410 (3)0.2107 (19)0.1924 (10)0.052 (5)*
N41.30471 (18)−0.10694 (13)0.07213 (8)0.0408 (3)
H6A1.364 (3)0.2683 (19)0.0495 (10)0.050 (5)*
N51.40907 (18)0.07897 (12)0.08442 (7)0.0376 (3)
H8A1.137 (3)0.353 (2)0.2554 (13)0.077 (7)*
O101.08166 (19)−0.23084 (12)0.01701 (8)0.0561 (4)
H1C1.590 (3)−0.454 (2)0.1269 (10)0.047 (5)*
N11.5210 (2)−0.38651 (15)0.11658 (10)0.0497 (4)
H51.177 (3)0.0849 (19)0.0460 (10)0.054 (5)*
O60.79832 (17)0.45855 (12)0.28933 (7)0.0545 (3)
H7B1.377 (3)0.371 (2)0.1459 (10)0.057 (5)*
O30.83198 (18)0.21639 (11)0.28310 (7)0.0526 (3)
H6B1.549 (3)0.2239 (18)0.0706 (10)0.054 (6)*
C31.4627 (2)−0.14293 (15)0.09965 (9)0.0350 (4)
H1A1.870 (3)−0.1491 (19)0.1681 (11)0.059 (6)*
N21.7135 (2)−0.26489 (14)0.14725 (9)0.0508 (4)
H15B0.551 (3)0.523 (2)0.2714 (12)0.071 (7)*
N31.6779 (2)−0.02193 (14)0.13207 (9)0.0513 (4)
H15A0.633 (3)0.619 (2)0.3206 (12)0.078 (7)*
C41.5280 (2)−0.02841 (15)0.10754 (9)0.0372 (4)
H22B0.974 (3)−0.383 (2)−0.0530 (12)0.065 (6)*
O40.9500 (2)0.00392 (13)0.25970 (8)0.0628 (4)
H8B1.104 (3)0.456 (2)0.1946 (12)0.073 (7)*
O70.5407 (2)0.45750 (14)0.37225 (8)0.0645 (4)
C51.2792 (2)0.02556 (16)0.06432 (10)0.0415 (4)
C21.5646 (2)−0.26729 (15)0.12075 (9)0.0383 (4)
H9B0.689 (4)0.071 (3)0.2924 (16)0.112 (10)*
C61.4277 (3)0.22069 (16)0.08249 (11)0.0438 (4)
H1B1.438 (3)−0.3928 (19)0.0988 (10)0.044 (6)*
C71.3572 (2)0.27262 (18)0.15218 (11)0.0450 (4)
H9A0.792 (3)0.126 (2)0.2055 (14)0.088 (8)*
C220.9785 (3)−0.42444 (17)−0.00200 (12)0.0436 (4)
H101.161 (3)−0.206 (2)0.0348 (13)0.081 (8)*
C211.1118 (2)−0.36274 (17)0.02458 (10)0.0445 (4)
C81.0864 (3)0.3663 (2)0.21406 (13)0.0505 (5)
C11.7603 (3)−0.14515 (19)0.15018 (13)0.0577 (5)
O91.2352 (2)−0.42677 (14)0.05093 (11)0.0873 (6)
O50.8495 (3)−0.0752 (3)0.37084 (13)0.1501 (12)
C90.7978 (3)0.10227 (19)0.25713 (16)0.0618 (6)
C111.1398 (3)−0.1700 (2)0.31830 (12)0.0678 (6)
C150.6237 (3)0.5252 (2)0.30718 (14)0.0625 (6)
O80.4230 (3)0.3366 (2)0.31153 (9)0.0959 (6)
C160.4436 (3)0.3614 (2)0.36752 (12)0.0608 (5)
C100.9642 (3)−0.0782 (2)0.32119 (13)0.0696 (6)
C180.2912 (6)0.3830 (4)0.4914 (2)0.1566 (19)
H18A0.18430.43370.47640.235*
H18B0.37260.44360.49360.235*
H18C0.26270.33240.53790.235*
C141.2937 (4)−0.0882 (3)0.28699 (18)0.1026 (10)
H14A1.2850−0.05230.23800.154*
H14B1.4052−0.14580.28940.154*
H14C1.2870−0.01550.31400.154*
C121.1638 (5)−0.2356 (4)0.39287 (18)0.1525 (18)
H12A1.1480−0.16750.42350.229*
H12B1.2813−0.28520.39220.229*
H12C1.0774−0.29600.41050.229*
C170.3749 (4)0.2886 (3)0.43929 (13)0.0794 (7)
C200.5398 (7)0.2122 (6)0.4705 (3)0.213 (3)
H20A0.50300.16450.51700.320*
H20B0.61620.27520.47460.320*
H20C0.60300.14910.43950.320*
C190.2625 (9)0.1901 (6)0.4313 (2)0.227 (3)
H19A0.24330.13000.47540.341*
H19B0.32070.13920.39370.341*
H19C0.15010.23670.41980.341*
C131.1420 (4)−0.2716 (3)0.2684 (2)0.1238 (13)
H13A1.2543−0.32940.26510.186*
H13B1.1254−0.22490.22170.186*
H13C1.0477−0.32490.28660.186*
U11U22U33U12U13U23
P10.0401 (3)0.0328 (2)0.0502 (3)0.00576 (17)−0.0116 (2)−0.01014 (19)
O20.0360 (7)0.0422 (6)0.0663 (8)−0.0040 (5)−0.0069 (6)−0.0242 (6)
O10.0506 (8)0.0463 (7)0.0587 (8)0.0086 (6)−0.0214 (6)−0.0078 (6)
N40.0401 (8)0.0326 (7)0.0523 (9)−0.0019 (6)−0.0169 (7)−0.0061 (6)
N50.0391 (8)0.0280 (6)0.0449 (8)−0.0019 (5)−0.0073 (6)−0.0046 (6)
O100.0544 (9)0.0388 (7)0.0831 (10)−0.0083 (6)−0.0301 (8)−0.0090 (6)
N10.0500 (10)0.0280 (7)0.0766 (12)−0.0011 (7)−0.0322 (9)−0.0034 (7)
O60.0524 (8)0.0457 (7)0.0661 (9)0.0058 (6)−0.0065 (7)−0.0249 (6)
O30.0654 (9)0.0379 (6)0.0564 (8)−0.0030 (6)−0.0194 (7)−0.0062 (6)
C30.0367 (9)0.0315 (8)0.0377 (9)−0.0033 (6)−0.0095 (7)−0.0054 (6)
N20.0493 (9)0.0369 (8)0.0724 (11)0.0008 (6)−0.0288 (8)−0.0117 (7)
N30.0483 (9)0.0385 (8)0.0751 (11)−0.0039 (7)−0.0245 (8)−0.0172 (7)
C40.0382 (9)0.0317 (8)0.0426 (9)−0.0018 (6)−0.0082 (7)−0.0087 (7)
O40.0758 (10)0.0428 (7)0.0635 (9)0.0123 (6)−0.0158 (8)−0.0050 (6)
O70.0757 (10)0.0612 (9)0.0554 (9)−0.0103 (7)0.0005 (8)−0.0159 (7)
C50.0416 (10)0.0335 (8)0.0498 (10)−0.0018 (7)−0.0131 (8)−0.0042 (7)
C20.0400 (9)0.0340 (8)0.0420 (9)−0.0027 (7)−0.0111 (8)−0.0058 (7)
C60.0421 (11)0.0283 (8)0.0588 (12)−0.0039 (7)−0.0047 (9)−0.0038 (8)
C70.0353 (10)0.0356 (9)0.0676 (13)−0.0042 (7)−0.0089 (9)−0.0167 (9)
C220.0392 (10)0.0415 (9)0.0544 (12)−0.0054 (8)−0.0170 (9)−0.0090 (8)
C210.0420 (10)0.0397 (9)0.0553 (11)−0.0078 (7)−0.0155 (9)−0.0066 (8)
C80.0455 (11)0.0486 (11)0.0624 (13)−0.0021 (9)−0.0105 (10)−0.0245 (10)
C10.0504 (12)0.0462 (10)0.0869 (16)0.0009 (9)−0.0357 (11)−0.0201 (10)
O90.0812 (11)0.0438 (8)0.1585 (17)−0.0067 (7)−0.0839 (12)−0.0076 (9)
O50.1080 (17)0.147 (2)0.1177 (18)0.0577 (15)0.0455 (14)0.0593 (15)
C90.0713 (15)0.0328 (9)0.0861 (17)0.0026 (9)−0.0317 (14)−0.0108 (10)
C110.0641 (14)0.0598 (13)0.0673 (14)0.0139 (11)−0.0086 (11)0.0018 (11)
C150.0613 (14)0.0448 (11)0.0703 (15)0.0110 (10)0.0058 (12)−0.0123 (10)
O80.0926 (14)0.1482 (18)0.0600 (11)−0.0470 (12)−0.0158 (10)−0.0182 (11)
C160.0598 (13)0.0672 (13)0.0557 (13)−0.0030 (10)−0.0095 (11)−0.0147 (11)
C100.0685 (15)0.0583 (13)0.0648 (15)0.0093 (11)0.0023 (12)0.0085 (11)
C180.227 (5)0.119 (3)0.102 (3)−0.060 (3)0.081 (3)−0.034 (2)
C140.0750 (19)0.108 (2)0.119 (2)−0.0001 (16)−0.0038 (17)−0.0247 (19)
C120.117 (3)0.192 (4)0.094 (2)0.056 (3)−0.010 (2)0.051 (2)
C170.107 (2)0.0736 (15)0.0561 (14)−0.0243 (15)0.0029 (14)−0.0100 (12)
C200.201 (5)0.230 (5)0.145 (4)0.024 (4)−0.028 (4)0.104 (4)
C190.361 (8)0.261 (6)0.110 (3)−0.248 (6)0.027 (4)−0.034 (3)
C130.095 (2)0.0793 (19)0.201 (4)0.0341 (16)−0.047 (2)−0.053 (2)
P1—O11.4562 (13)C22—H22B1.00 (2)
P1—O31.5760 (13)C21—O91.200 (2)
P1—O61.5794 (13)C8—H8A0.93 (2)
P1—C81.787 (2)C8—H8B0.95 (2)
O2—C81.413 (2)C1—H1A0.96 (2)
O2—C71.424 (2)O5—C101.179 (3)
N4—C51.314 (2)C9—H9B1.04 (3)
N4—C31.383 (2)C9—H9A0.99 (3)
N5—C51.354 (2)C11—C121.504 (4)
N5—C41.3707 (19)C11—C101.508 (3)
N5—C61.464 (2)C11—C131.518 (4)
O10—C211.309 (2)C11—C141.538 (4)
O10—H100.84 (3)C15—H15B0.96 (2)
N1—C21.328 (2)C15—H15A1.05 (2)
N1—H1C0.81 (2)O8—C161.186 (3)
N1—H1B0.79 (2)C16—C171.501 (3)
O6—C151.413 (2)C18—C171.490 (4)
O3—C91.415 (2)C18—H18A0.9600
C3—C41.383 (2)C18—H18B0.9600
C3—C21.411 (2)C18—H18C0.9600
N2—C11.337 (2)C14—H14A0.9600
N2—C21.341 (2)C14—H14B0.9600
N3—C11.327 (2)C14—H14C0.9600
N3—C41.338 (2)C12—H12A0.9600
O4—C101.337 (2)C12—H12B0.9600
O4—C91.411 (2)C12—H12C0.9600
O7—C161.349 (3)C17—C191.471 (5)
O7—C151.420 (3)C17—C201.539 (5)
C5—H50.990 (19)C20—H20A0.9600
C6—C71.497 (3)C20—H20B0.9600
C6—H6A0.90 (2)C20—H20C0.9600
C6—H6B0.93 (2)C19—H19A0.9600
C7—H7A1.012 (19)C19—H19B0.9600
C7—H7B1.02 (2)C19—H19C0.9600
C22—C211.490 (2)C13—H13A0.9600
C22—C22i1.507 (3)C13—H13B0.9600
C22—H22A0.93 (3)C13—H13C0.9600
O1—P1—O3113.85 (8)O3—C9—H9B104.5 (16)
O1—P1—O6117.52 (7)O4—C9—H9A103.8 (15)
O3—P1—O6101.92 (8)O3—C9—H9A108.4 (14)
O1—P1—C8116.19 (10)H9B—C9—H9A120 (2)
O3—P1—C8106.95 (9)C12—C11—C10109.1 (2)
O6—P1—C898.37 (8)C12—C11—C13112.7 (3)
C8—O2—C7111.57 (13)C10—C11—C13108.6 (2)
C5—N4—C3104.30 (13)C12—C11—C14109.0 (3)
C5—N5—C4105.98 (13)C10—C11—C14110.11 (19)
C5—N5—C6129.31 (15)C13—C11—C14107.4 (2)
C4—N5—C6124.70 (15)O6—C15—O7109.46 (17)
C21—O10—H10106.4 (17)O6—C15—H15B111.4 (14)
C2—N1—H1C118.2 (13)O7—C15—H15B106.6 (14)
C2—N1—H1B121.6 (14)O6—C15—H15A108.1 (13)
H1C—N1—H1B119.5 (19)O7—C15—H15A103.0 (13)
C15—O6—P1124.52 (15)H15B—C15—H15A117.8 (18)
C9—O3—P1122.53 (14)O8—C16—O7121.8 (2)
C4—C3—N4109.79 (13)O8—C16—C17125.3 (2)
C4—C3—C2116.20 (15)O7—C16—C17112.77 (19)
N4—C3—C2134.00 (15)O5—C10—O4121.8 (2)
C1—N2—C2118.43 (15)O5—C10—C11125.9 (2)
C1—N3—C4110.16 (15)O4—C10—C11112.3 (2)
N3—C4—N5126.26 (14)C17—C18—H18A109.5
N3—C4—C3127.50 (14)C17—C18—H18B109.5
N5—C4—C3106.24 (14)H18A—C18—H18B109.5
C10—O4—C9117.94 (19)C17—C18—H18C109.5
C16—O7—C15117.27 (18)H18A—C18—H18C109.5
N4—C5—N5113.69 (15)H18B—C18—H18C109.5
N4—C5—H5125.8 (11)C11—C14—H14A109.5
N5—C5—H5120.5 (11)C11—C14—H14B109.5
N1—C2—N2118.11 (15)H14A—C14—H14B109.5
N1—C2—C3123.89 (16)C11—C14—H14C109.5
N2—C2—C3118.00 (14)H14A—C14—H14C109.5
N5—C6—C7113.36 (15)H14B—C14—H14C109.5
N5—C6—H6A106.7 (12)C11—C12—H12A109.5
C7—C6—H6A108.1 (12)C11—C12—H12B109.5
N5—C6—H6B104.9 (12)H12A—C12—H12B109.5
C7—C6—H6B110.5 (12)C11—C12—H12C109.5
H6A—C6—H6B113.5 (17)H12A—C12—H12C109.5
O2—C7—C6108.72 (15)H12B—C12—H12C109.5
O2—C7—H7A108.3 (11)C19—C17—C18114.6 (3)
C6—C7—H7A110.1 (10)C19—C17—C16110.5 (3)
O2—C7—H7B105.4 (11)C18—C17—C16112.3 (2)
C6—C7—H7B107.8 (11)C19—C17—C20108.7 (4)
H7A—C7—H7B116.2 (15)C18—C17—C20104.0 (4)
C21—C22—C22i113.30 (19)C16—C17—C20106.1 (3)
C21—C22—H22A106.6 (15)C17—C20—H20A109.5
C22i—C22—H22A111.2 (15)C17—C20—H20B109.5
C21—C22—H22B107.6 (12)H20A—C20—H20B109.5
C22i—C22—H22B109.4 (12)C17—C20—H20C109.5
H22A—C22—H22B108.6 (18)H20A—C20—H20C109.5
O9—C21—O10122.58 (16)H20B—C20—H20C109.5
O9—C21—C22123.77 (16)C17—C19—H19A109.5
O10—C21—C22113.65 (15)C17—C19—H19B109.5
O2—C8—P1108.92 (13)H19A—C19—H19B109.5
O2—C8—H8A112.5 (14)C17—C19—H19C109.5
P1—C8—H8A111.6 (15)H19A—C19—H19C109.5
O2—C8—H8B111.4 (14)H19B—C19—H19C109.5
P1—C8—H8B109.8 (14)C11—C13—H13A109.5
H8A—C8—H8B102.5 (19)C11—C13—H13B109.5
N3—C1—N2129.67 (18)H13A—C13—H13B109.5
N3—C1—H1A115.2 (12)C11—C13—H13C109.5
N2—C1—H1A115.1 (12)H13A—C13—H13C109.5
O4—C9—O3107.72 (17)H13B—C13—H13C109.5
O4—C9—H9B111.6 (16)
D—H···AD—HH···AD···AD—H···A
N1—H1C···O1ii0.812 (19)2.14 (2)2.941 (2)170.16 (18)
N1—H1B···O90.79 (2)2.05 (2)2.842 (2)175 (2)
O10—H10···N40.84 (2)1.91 (2)2.734 (2)166 (2)
Table 1

Hydrogen-bond geometry (Å, °)

D—H⋯AD—HH⋯ADAD—H⋯A
N1—H1C⋯O1i0.812 (19)2.14 (2)2.941 (2)170.16 (18)
N1—H1B⋯O90.79 (2)2.05 (2)2.842 (2)175 (2)
O10—H10⋯N40.84 (2)1.91 (2)2.734 (2)166 (2)

Symmetry code: (i) .

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