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Crystals 2012, 2(3), 974-983; doi:10.3390/cryst2030974
Abstract: The crystal structures of two zincophosphate networks prepared in the presence of 1,5-diaminopentane (dap) are described. In Zn3(PO4)2(C5H14N2)2·3H2O (1) the dap forms Zn–N coordinate bonds to generate an unusual three-dimensional “hybrid” framework constructed from ZnO3N, ZnO2N2 and PO4 tetrahedra with three different types of elongated channels occupied by water molecules. In C5H16N2·Zn3(PO4)2(HPO4)·H2O; (2) the doubly-protonated H2dap acts in a more typical way to template double layers of vertex-sharing ZnO4, PO4 and HPO4 tetrahedra incorporating 10-rings and interacts with the inorganic component via N–H O hydrogen bonds. Crystal data: 1 (C10H34N4O11P2Zn3), Mr = 644.46, monoclinic, C2 (No. 4), Z = 4, a = 25.302 (7) Å, b = 4.9327 (13) Å, c = 19.808 (6) Å, β = 107.377 (8)°, V = 2359.4 (12) Å3, R(F) = 0.054, wR(F2) = 0.139. 2 (C5H19N2O13P3Zn3), Mr = 604.24, monoclinic, P21/c (No. 14), Z = 4, a = 11.3275 (15) Å, b = 8.3235 (11) Å, c = 18.588 (2) Å, β = 96.979 (3)°, V = 1739.6 (4) Å3, R(F) = 0.056, wR(F2) = 0.119.
Linear-chain alkyl diamines of formula H2N(CH2)nNH2 are versatile and effective templates for a wide variety of porous inorganic networks incorporating many different metal ions [1,2,3,4]. As might be expected, the chain length n of the methylene groups of the diamine plays an important role in defining the resulting crystal structure: this is demonstrated with diamine-templated zinc phosphates (ZnPOs) and varied structures with n = 2 (i.e., ethylenediamine) , n = 3 , n = 4  and n = 6  have been described.
As an extension of these studies we now describe the structures of two zincophosphate networks incorporating the n = 5 member of this series, 1,5-diaminopentane [H2N(CH2)5NH2; C5H14N2; dap], as the structure-directing agent. In Zn3(PO4)2(C5H14N2)2·3H2O (1) the neutral dap molecule bonds directly to the zinc ions as a bridging ligand to generate an unusual structure containing elongated “hybrid” channels containing water molecules, whereas in C5H16N2·Zn3(PO4)2(HPO4)·H2O; (2) doubly-protonated H2dap dications help to template a layered ZnPO network via N-H O hydrogen bonds. So far as we are aware, there are no other known dap-ZnPO structures, although H2dap dications have been shown to template zinc phosphite (containing HPO32− groups)  and zinc diphosphonate  materials.
2. Results and Discussion
2.1. Crystal Structure of Zn3(PO4)2(C5H14N2)2·3H2O (1)
The asymmetric unit of compound 1 contains four Zn atoms, two P atoms, 11 O atoms (three of which belong to water molecules) and two C5H14N2 (dap) molecules (Figure 1).
|Zn1-O5||1.964 (9)||Zn1-N3||2.037 (13)|
|Zn2-O3||1.914 (9)||Zn2-N2#1||2.027 (11)|
|Zn3-O8#2||1.914 (10)||Zn3-O1||1.933 (7)|
|Zn3-O6||1.943 (11)||Zn3-N1||2.032 (10)|
|Zn4-O2||1.939 (10)||Zn4-O7||1.942 (7)|
|Zn4-O4#3||1.949 (9)||Zn4-N4#4||2.055 (10)|
|P1-O4||1.516 (12)||P1-O2||1.542 (8)|
|P1-O3||1.543 (8)||P1-O1||1.550 (8)|
|P2-O5||1.526 (8)||P2-O8||1.537 (13)|
|P2-O7||1.549 (8)||P2-O6||1.551 (8)|
|P1-O1-Zn3||130.4 (5)||P1-O2-Zn4||115.3 (5)|
|P1-O3-Zn2||125.2 (7)||P1-O4-Zn4#2||128.2 (6)|
|P2-O5-Zn1||121.7 (7)||P2-O6-Zn3||114.3 (5)|
|P2-O7-Zn4||132.6 (6)||P2-O8-Zn3#3||128.5 (6)|
Symmetry codes: (#1) ½−x, y−½, 1−z; (#2) x, y−1, z; (#3) x, y+1, z; (#4) x−½, y−½, z.
The zinc ions in 1 adopt two coordination modes: Zn1 and Zn2 (which both lie on crystallographic twofold axes) are coordinated by two O and two N atoms and Zn3 and Zn4 are bonded to three O and one N atom in tetrahedral geometries (Table 1). The global mean Zn-O and Zn-N separations are 1.937 Å and 2.038 Å, respectively, which are very similar to the equivalent geometrical data for related compounds . The XO4 tetrahedral angular variances, defined as where ϑ is the O-X-O bond angle (°) , indicate that all the Zn-centred tetrahedra in 1 are significantly distorted: values of 98.4°2, 79.8°2, 81.2°2 and 85.9°2 arise for Zn1, Zn2, Zn3 and Zn4, respectively. All the O atoms also link to an adjacent P atom (mean Zn-O-P = 124.5°) and the N atoms are all parts of neutral dap molecules. Both PO4 groups in 1 are close to regular tetrahedra (mean P1-O = 1.538 Å, angular variance = 2.7°2; mean P2-O = 1.541 Å, angular variance = 1.4°2) and all the O atoms link to an adjacent Zn atom, thus there are no terminal or “dangling” P=O or P-OH bonds  in 1. The geometrical parameters for the two unique dap molecules are unexceptional , and both molecules are in essentially extended conformations (mean absolute values of the N-C-C-C and C-C-C-C torsion angles = 177.6° and 174.7°, respectively).
The polyhedral connectivity of the Zn- and P-centred moieties leads to (100) sheets of vertex-sharing tetrahedra (Figure 2), in which there is prefect alternation of the Zn and P nodes (i.e., no Zn-O-Zn or P-O-P links). These sheets can be decomposed into four-ring ladders  propagating in  built up from the Zn3- and Zn4-centred species and the phosphate groups, with Zn1 and Zn2 (i.e., the ZnN2O2 species) providing inter-chain links, as parts of polyhedral 8-rings. For any  stack of 8-rings, all the Zn1 (or Zn2) tetrahedra point in the same direction.
The dap molecules form bridges (via both their N atoms) to the adjacent (100) polyhedral sheets to generate a distinctive porous network (Figure 3), in which elongated  channels are bounded by the methylene groups of the dap molecules on their “long” sides and by the ZnPO framework on their “short” sides. Measured atom-to-atom, their dimensions are about 4.5 Å × 11.3 Å. It remarkable that there are three distinct types of channel in this structure: one contains four water molecules per b unit-cell repeat distance (type-A), one contains two water molecules (type-B) and the third (type-C) is empty. It is apparent from Figure 3 that the type-A channels “bulge out” to accommodate the water molecules and the type-C channels are consequently compressed inwards and are empty.
Within the type-A channel, the water molecules interact via O-H∙∙∙O hydrogen bonds (Table 2), such that a C(2) chain of O12-H6W∙∙∙O12 bonds propagates up the central region of the channel. The other H atom attached to O12 forms a link to O11, which in turn forms two hydrogen bonds to framework O atoms. The -NH2 groups of the dap molecules form N-H∙∙∙O hydrogen bonds to framework O atoms as well as the water molecules to reinforce this rather intricate network, which occurs in a largely hydrophobic environment.
Symmetry codes as Table 1; additionally: (#5) ½+x, y−½, z; (#6) −x, y+1, −z; (#7) ½−x, ½+y, −z; (#8) −x, y, −z; (#9) ½−x, ½+y, 1−z.
2.2. Crystal Structure of C5H16N2·Zn3(PO4)2(HPO4)·H2O (2)
The asymmetric unit of 2 contains three Zn atoms, two PO4 groups, one HPO4 group, a water molecule and a doubly-protonated H2dap dication (Figure 4).
The three Zn atoms form the centers of ZnO4 tetrahedra (mean Zn1-O =1.943 Å, mean Zn2-O = 1.939 Å, mean Zn3-O = 1.939 Å). These are somewhat less distorted than the zinc polyhedra in 1 as indicated by the angular variances of 32.2°2, 37.4°2, and 47.2°2, for Zn1, Zn2 and Zn3, respectively. Atoms P1 and P2 (mean P-O = 1.534 Å and 1.536 Å, respectively; angular variances = 2.9°2 and 2.4°2, respectively) are the central atoms of essentially regular phosphate groups and all their O atoms link to nearby zinc atoms. Atom P3 (mean P-O = 1.534 Å, angular variance = 14.9°2) forms three links to Zn but also possesses a terminal bond to O12. Its length of 1.587 (4) Å indicates that it must by protonated (i.e., a P-OH species) and the corresponding H atom could indeed be located in a difference map. Geometrical data for 2 are summarized in Table 3.
|Zn1-O5#1||1.908 (4)||Zn1-O3#2||1.929 (4)|
|Zn1-O11#2||1.930 (4)||Zn1-O4||2.005 (4)|
|Zn2-O10||1.909 (4)||Zn2-O7#3||1.929 (4)|
|Zn2-O2#2||1.952 (4)||Zn2-O4||1.966 (4)|
|Zn3-O1||1.923 (4)||Zn3-O9#2||1.929 (4)|
|Zn3-O6||1.944 (4)||Zn3-O8#3||1.959 (4)|
|P1-O1||1.514 (4)||P1-O2||1.519 (4)|
|P1-O3||1.530 (4)||P1-O4||1.570 (4)|
|P2-O5||1.532 (4)||P2-O6||1.537 (4)|
|P2-O8||1.537 (4)||P2-O7||1.539 (4)|
|P3-O9||1.509 (4)||P3-O10||1.517 (4)|
|P3-O11||1.522 (4)||P3-O12||1.588 (4)|
|P1-O1-Zn3||139.8 (2)||P1-O2-Zn2#4||131.5 (2)|
|P1-O3-Zn1#4||131.2 (2)||P1-O4-Zn2||119.0 (2)|
|P1-O4-Zn1||120.1 (2)||Zn2-O4-Zn1||118.50 (18)|
|P2-O5-Zn1#5||129.7 (2)||P2-O6-Zn3||132.9 (2)|
|P2-O7-Zn2#3||130.5 (2)||P2-O8-Zn3#3||132.1 (2)|
|P3-O9-Zn3#4||136.2 (3)||P3-O10-Zn2||134.4 (3)|
Symmetry codes: (#1) x, 3/2−y, z−½; (#2) 1–x, y−½, ½−z; (#3) 1−x, 1−y, 1−z; (#4) 1−x, ½+y, ½−z; (#5) x, 3/2−y, ½+z.
In the extended structure of 2, atom O4 plays an important role in the linking of the tetrahedra, as it forms bonds to Zn1, Zn2 and P1 (bond-angle sum = 357.6°). This results in “dimers” of the zinc species (Figure 4), but the Zn-O-Zn connectivity does not extend any further than this . The mean value of the Zn-O-P bond angle for the other O atoms is 133.7°, almost 10 degrees larger than the corresponding value in 1.
In the extended structure of 2, the inorganic layers form infinite (100) sheets containing 4- and 10-rings (Figure 5). The sheets sandwich the H2dap cations and the extra-layer water molecule (O13) (Figure 6). The water molecule accepts an O-H∙∙∙O hydrogen bond from the hydrogen phosphate group and also probably forms O-H∙∙∙O links to framework oxygen atoms. The protonated -NH3+ groups of the H2dap cation form three N-H∙∙∙O hydrogen bonds each (Table 4), which is a thoroughly typical bonding mode for a protonated amine in a ZnPO . The conformation of the carbon chain of the H2dap species is somewhat uncertain, but its contorted geometry is clearly different to the extended conformation found for the bridging dap molecules in 1.
Symmetry codes as in Table 3; additionally: (#6) 1+x, y–1, z; (#7) 2−x, y−½, ½−z; (#8) x, ½−y, z−½.
3. Experimental Section
Compound 1 was prepared from0.798 g ZnO, 4.9 mL 85% H3PO4, 1.00 g dap and 10 mL water (Zn:PO4:dap ratio = 2:1:2). The components were placed in a 60-mL HDPE bottle and sealed (starting pH ≈ 6.0). The bottle was shaken for five minutes and placed in an 80 °C oven for four days. The bottle was removed from the oven and cooled to room temperature over 30 minutes and the solid product, consisting of colorless plates of 1 accompanied by white and brownish powders was recovered by vacuum filtration and rinsing with water and acetone. Compound 2 was prepared from 0.794 g ZnO, 9.8 mL 85% H3PO4, 0.51 g dap and 10 mL water (Zn:PO4:dap ratio = 2:2:1; starting pH ≈ 2.0) and subjected to the same heating and product recovery protocol. Pale brown blocks of 2 were recovered, accompanied by some white powder.
3.2. Single-Crystal Data Collection and Analysis
The single-crystal data for 1 (colorless slab, 0.10 × 0.10 × 0.02 mm) were collected using a Rigaku Saturn CCD diffractometer at 93 K (Mo Kα radiation, λ = 0.71073 Å); the data for 2 (pale brown block, 0.40 × 0.30 × 0.24 mm) were collected using a Bruker Kappa APEX II CCD diffractometer (Mo Kα radiation, λ = 0.71073 Å) at room temperature. After data reduction, the structures were solved by direct methods with SHELXS and the resulting atomic models were developed and refined against |F|2 with SHELXL . The “observed data” threshold for calculating the R(F) residuals was set as I > 2σ(I).
For 1, the C- and N-bound bound H atoms were placed in idealised locations (C-H = 0.99 Å, N-H = 0.92 Å) and refined as riding atoms. The O-bound (water) H atoms were located in difference maps and refined as riding atoms in their as-found relative locations. The constraint Uiso(H) = 1.2Ueq(carrier) was applied in all cases. The structural model was analysed and validated with PLATON  and full refinement details are given in the deposited cif. PLATON indicated considerable pseudo-symmetry corresponding to space group C2/c. Trial refinements in this space group, which revealed a number of systematic absence violations, led to essentially the same structure for the framework (albeit with dubious anisotropic displacement parameters) but un-resolvable disorder of the water molecules in the channels. Thus it appears that the symmetry lowering is due to ordering of the water molecules in the channels.
The methylene chain in the H2dap species in 2 was found to be severely disordered although the terminal -NH3+ groupings were well defined. The application of C-C bond distance restraints led to a geometrically plausible conformation but this cannot be regarded as certain. The H atoms of the water molecule could not be located from difference maps and may be disordered. The C- and N-bound bound H atoms in 2 were placed in idealised locations (C-H = 0.97 Å, N-H = 0.89 Å) and refined as riding atoms. The P-OH H atom was located in a difference map and refined as riding in its as-found relative location. The constraint Uiso(H) = 1.2Ueq(carrier) was applied in all cases. Further refinement details are given in the deposited cif.
Crystal data for 1: C10H34N4O11P2Zn3, Mr = 644.46, monoclinic, C2 (No. 4), Z = 4, a = 25.302 (7) Å, b = 4.9327 (13) Å, c = 19.808 (6) Å, β = 107.377 (8)°, V = 2359.4 (12) Å3, F(000) = 1320, T = 93 (2) K, ρcalc = 1.814 g cm−3, µ = 3.216 mm−1, 7612 reflections recorded (3.4° ≤ 2θ ≤ 50.7°; −30 ≤ h ≤ 30, −5 ≤ k ≤ 3, −23 ≤ l ≤ 18), RInt = 0.047, 3310 merged reflections, 2728 with I > 2σ(I), 273 variable parameters, Flack absolute structure parameter = 0.46 (5), R(F) = 0.054, wR(F2) = 0.139, min./max. Δρ = –1.23, +1.01 e Å−3. Cambridge Structural Database deposition number: CCDC-883458.
Crystal data for 2: C5H19N2O13P3Zn3, Mr = 604.24, monoclinic, P21/c (No. 14), Z = 4, a = 11.3275 (15) Å, b = 8.3235 (11) Å, c = 18.588 (2) Å, β = 96.979 (3)°, V = 1739.6 (4) Å3, F(000) = 1208, T = 293 (2) K, ρcalc = 2.307 g cm−3, μ = 4.447 mm−1, 10734 reflections recorded (8.7° ≤ 2θ ≤ 60.0°; −14 ≤ h ≤ 15, −11 ≤ k ≤ 11, −20 ≤ l ≤ 26), RInt = 0.076, 4954 merged reflections, 3105 with I > 2σ(I), 237 variable parameters, R(F) = 0.056, wR(F2) = 0.119, min./max. Δρ = −0.85, +1.97 eÅ–3. Cambridge Structural Database deposition number: CCDC-883459.
The crystal structures of Zn3(PO4)2(C5H14N2)2·3H2O (1) and C5H16N2·Zn3(PO4)2(HPO4)·H2O (2) have been described. The structure of 1 displays some unusual features for ZnPOs including ZnO2N2 and ZnO3N polyhedra and un-protonated (neutral) template molecules bonding as bridging ligands. This appears to correlate with the relatively high starting pH for the synthesis of 1, which would presumably favor the presence of un-protonated organic molecules in solution. The structure of [Zn4(HPO4)4(C18H18N4)3]·4H2O (C18H18N4 = 1,4-bis(N-benzimidazolyl)butane)  shares these features, but its overall structure, which features ZnPO chains cross-linked by the ligands, and no obvious channel system, is quite different to that of 1. The structure of 2, prepared from a reaction with a lower initial pH, is much more commonplace, and the “multipoint” N–H∙∙∙O hydrogen bonds from the protonated template to the anionic ZnPO sheets have been seen in many other structures . The triply-bridging O atom in the framework of 2 is also a known feature of porous  and dense (i.e., non-templated)  ZnPOs.
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