| Literature DB >> 36072142 |
Emma L Markun1, Drew A Jensen1, Joshua D Vegetabile1, James A Kaduk1.
Abstract
The crystal structure of poly[di-hydroxido(μ6-terepthalato)dizinc], [Zn2(C8H4O4)(OH)2] n , was solved and refined using synchrotron powder data, and the structures of the isostructural Co and Ni analogues were refined using laboratory powder X-ray data. The structure of [Co2(C8H4O4)(OH)2] n has been reported previously in space group C2/m, which yields disordered terephthalate anions. Doubling the c-axis of that cell results in an ordered model in space group C2/c. The octa-hedral MO6 coordination polyhedra of the metal cations share edges, forming chains running parallel to the b-axis direction. These chains share corners (hydroxyl groups), forming layers lying perpendicular to the a-axis direction. © Markun et al. 2022.Entities:
Keywords: cobalt; density functional theory; hydroxide; nickel; powder diffraction; terephthalate; zinc
Year: 2022 PMID: 36072142 PMCID: PMC9431782 DOI: 10.1107/S2056989022005023
Source DB: PubMed Journal: Acta Crystallogr E Crystallogr Commun
Figure 1The X-ray powder diffraction patterns of Co2(C8H4O4)(OH)2 (black), Ni2(C8H4O4)(OH)2 (green), and Zn2(C8H4O4)(OH)2 (red). The Zn pattern (measured using Co radiation) and the Zn pattern (measured using synchrotron radiation) were converted to the Mo wavelength used to measure the Co pattern using JADE Pro (MDI, 2021 ▸).
Figure 2Comparison of the Rietveld-refined (red) and VASP-optimized (blue) structures of Co2(C8H4O4)(OH)2. The r.m.s. Cartesian displacement is 0.125 Å.
Figure 3Comparison of the Rietveld-refined (red) and VASP-optimized (blue) structures of Ni2(C8H4O4)(OH)2. The r.m.s. Cartesian displacement is 0.143 Å.
Figure 4Comparison of the Rietveld-refined (red) and VASP-optimized (blue) structures of Zn2(C8H4O4)(OH)2. The r.m.s. Cartesian displacement is 0.339 Å.
Figure 5The asymmetric unit of Co2(C8H4O4)(OH)2, with the atom numbering. The atoms are represented by 50% probability spheroids.
Figure 6The crystal structure of Co2(C8H4O4)(OH)2, viewed down the b-axis direction.
Figure 7The crystal structure of Co2(C8H4O4)(OH)2, viewed down the c-axis direction.
Figure 8The layers in the crystal structure of Co2(C8H4O4)(OH)2, viewed down the a-axis direction.
Experimental details
| [Co2(C8H4O4)(OH)2] | [Ni2(C8H4O4)(OH)2] | [Zn2(C8H4O4)(OH)2] | |
|---|---|---|---|
| Crystal data | |||
|
| 316 | 315.53 | 328.89 |
| Crystal system, space group | Monoclinic, | Monoclinic, | Monoclinic, |
| Temperature (K) | 300 | 300 | 300 |
|
| 19.9554 (10), 3.2883 (2), 12.6139 (8) | 20.35 (5), 3.364 (6), 12.19 (4) | 20.165 (2), 3.3273 (5), 12.5956 (16) |
| β (°) | 96.059 (5) | 98.9 (2) | 97.431 (10) |
|
| 823.08 (6) | 824.6 (15) | 837.99 (14) |
|
| 4 | 4 | 4 |
| Radiation type | Mo | Co | Synchrotron, λ = 1.15008 Å |
| Specimen shape, size (mm) | Cylinder, 12 × 0.7 | Flat sheet, 16 × 16 | Cylinder, ? × ? |
| Data collection | |||
| Diffractometer | PANalytical Empyrean | PANalytical X’Pert | NSLS beamline X3B1 |
| Specimen mounting | Glass capillary | Si zero-background plate with well | Kapton capillary |
| Data collection mode | Transmission | Reflection | Transmission |
| Scan method | Step | Step | Step |
| 2θ values (°) | 2θmin = 1.002, 2θmax = 49.991, 2θstep = 0.008 | 2θmin = 4.007, 2θmax = 69.983, 2θstep = 0.017 | 2θmin = 6.0, 2θmax = 60.0, 2θstep = 0.01 |
| Refinement | |||
|
|
|
|
|
| No. of parameters | 42 | 12 | 57 |
| No. of restraints | 15 | 0 | 14 |
| (Δ/σ)max | 0.025 | 97.398 | 1.459 |
The same symmetry and lattice parameters were used for the DFT calculations as for each powder diffraction study. Computer programs: GSAS-II (Toby & Von Dreele, 2013 ▸), Mercury (Macrae et al., 2020 ▸), DIAMOND (Crystal Impact, 2015 ▸), and publCIF (Westrip, 2010 ▸).
Figure 9The Rietveld plot for the refinement of Co2(C8H4O4)(OH)2. The blue crosses represent the observed data points, and the green line is the calculated pattern. The cyan curve is the normalized error plot. The row of tick marks indicates the calculated reflection positions. The vertical scale has been multiplied by a factor of 4× for 2θ > 5.0°, and by a factor of 20× for 2θ > 27.0°.
Figure 10The Rietveld plot for the refinement of Ni2(C8H4O4)(OH)2. The blue crosses represent the observed data points, and the green line is the calculated pattern. The cyan curve is the normalized error plot. The row of tick marks indicates the calculated reflection positions.
Figure 11The Rietveld plot for the refinement of Zn2(C8H4O4)(OH)2. The blue crosses represent the observed data points, and the green line is the calculated pattern. The cyan curve is the normalized error plot. The row of tick marks indicates the calculated reflection positions. The vertical scale has been multiplied by a factor of 5× for 2θ > 10.0°, and by a factor of 15× for 2θ > 18.0°.
| [Co2(C8H4O4)(OH)2] | |
| Monoclinic, | |
| Mo | |
| pink | |
| β = 96.059 (5)° | cylinder, 12 × 0.7 mm |
| PANalytical Empyrean diffractometer | Scan method: step |
| Specimen mounting: glass capillary | 2θmin = 1.002°, 2θmax = 49.991°, 2θstep = 0.008° |
| Data collection mode: transmission |
| Least-squares matrix: full | 42 parameters |
| 15 restraints | |
| H-atom parameters not defined? | |
| Weighting scheme based on measured s.u.'s | |
| (Δ/σ)max = 0.025 | |
| 5864 data points | Background function: Background function: "chebyschev-1" function with 4 terms: 1063(5), -577(6), 95(4), -25(3), Background peak parameters: pos, int, sig, gam: 11.866, 3892.401, 44425.907, 0.100, |
| Profile function: Finger-Cox-Jephcoat function parameters U, V, W, X, Y, SH/L: peak variance(Gauss) = Utan(Th)2+Vtan(Th)+W: peak HW(Lorentz) = X/cos(Th)+Ytan(Th); SH/L = S/L+H/L U, V, W in (centideg)2, X & Y in centideg 30.816, 10.768, 0.000, 1.935, 0.000, 0.033, Crystallite size in microns with "isotropic" model: parameters: Size, G/L mix 1.000, 1.000, Microstrain, "generalized" model (106 * delta Q/Q) parameters: S400, S040, S004, S220, S202, S022, S301, S103, S121, G/L mix 2180.060, 4.385767395e6, 5373.300, 103711.383, 724.789, 689333.161, -2196.502, 2609.389, 91248.973, 0.800, | Preferred orientation correction: Simple spherical harmonic correction Order = 2 Coefficients: 0:0:C(2,-2) = -0.0542; 0:0:C(2,0) = -0.1055; 0:0:C(2,2) = -0.0207 |
| C1 | 0.3140 (2) | 0.106 (3) | 0.0412 (4) | 0.018 (3)* | |
| C2 | 0.2695 (3) | 0.269 (3) | 0.1093 (3) | 0.0184* | |
| C3 | 0.2024 (3) | 0.368 (4) | 0.0686 (4) | 0.0184* | |
| H4 | 0.28873 | 0.24618 | 0.19840 | 0.0220* | |
| H5 | 0.17120 | 0.48125 | 0.13117 | 0.0220* | |
| C6 | 0.3837 (3) | −0.024 (5) | 0.0845 (5) | 0.0200* | |
| O7 | 0.3988 (3) | −0.007 (7) | 0.1799 (5) | 0.020000* | |
| O8 | 0.4268 (3) | −0.031 (5) | 0.0168 (5) | 0.020000* | |
| Co9 | 0.50000 | 0.50000 | 0.50000 | 0.0020 (5)* | |
| Co10 | 0.00000 | 0.495 (3) | −0.25000 | 0.0020* | |
| O11 | 0.0287 (3) | 0.030 (7) | 0.1569 (7) | 0.0200* | |
| H12 | 0.06922 | −0.03114 | 0.16621 | 0.0260* |
| C1—C2 | 1.406 (6) | O8—C6 | 1.274 (4) |
| C1—C3i | 1.391 (3) | O8—Co9ii | 2.151 (12) |
| C1—C6 | 1.501 (5) | Co9—O8iii | 2.151 (12) |
| C2—C1 | 1.406 (6) | Co9—O8iv | 2.151 (12) |
| C2—C3 | 1.421 (4) | Co9—O11v | 2.004 (8) |
| C3—C1i | 1.391 (3) | Co9—O11vi | 2.004 (8) |
| C3—C2 | 1.421 (4) | Co10—O7i | 2.119 (5) |
| C6—C1 | 1.501 (5) | Co10—O7vii | 2.119 (5) |
| C6—O7 | 1.211 (5) | Co10—O11viii | 2.072 (16) |
| C6—O8 | 1.274 (4) | Co10—O11ix | 2.072 (16) |
| O7—C6 | 1.211 (5) | O11—Co9x | 2.004 (8) |
| O7—Co10i | 2.119 (5) | O11—Co10viii | 2.072 (16) |
| C2—C1—C3i | 119.1 (3) | C1i—C3—C2 | 119.2 (3) |
| C2—C1—C6 | 120.4 (2) | C1—C6—O7 | 118.2 (4) |
| C3i—C1—C6 | 119.5 (3) | C1—C6—O8 | 115.2 (5) |
| C1—C2—C3 | 119.9 (3) | O7—C6—O8 | 123.5 (6) |
| C8H6Co2O6 | |
| β = 96.33° | |
| Monoclinic, | |
| C1 | 0.31569 | 0.14758 | 0.04012 | 0.0184 | |
| C2 | 0.26806 | 0.23812 | 0.11006 | 0.0184 | |
| C3 | 0.20287 | 0.33955 | 0.07035 | 0.0184 | |
| H4 | 0.28329 | 0.23013 | 0.19578 | 0.022 | |
| H5 | 0.16565 | 0.41266 | 0.12436 | 0.022 | |
| C6 | 0.38562 | 0.03773 | 0.08352 | 0.020 | |
| O7 | 0.39861 | 0.98679 | 0.18301 | 0.020 | |
| O8 | 0.42960 | 0.00198 | 0.01583 | 0.020 | |
| Co9 | 0.00000 | 0.00000 | 0.00000 | 0.002 | |
| Co10 | 0.50000 | 0.97237 | 0.25000 | 0.002 | |
| O11 | 0.02838 | 0.97997 | 0.15714 | 0.020 | |
| H12 | 0.07726 | 0.97414 | 0.17088 | 0.026 |
| [Ni2(C8H4O4)(OH)2] | |
| Monoclinic, | |
| Co | |
| pale green | |
| β = 98.9 (2)° | flat_sheet, 16 × 16 mm |
| PANalytical X'Pert diffractometer | Scan method: step |
| Specimen mounting: Si zero-background plate with well | 2θmin = 4.007°, 2θmax = 69.983°, 2θstep = 0.017° |
| Data collection mode: reflection |
| Least-squares matrix: full | 12 parameters |
| 0 restraints | |
| H-atom parameters not defined? | |
| (Δ/σ)max = 97.398 | |
| Background function: Background function: "chebyschev-1" function with 3 terms: 139.3(6), -71.0(8), 7.7(7), | |
| 3949 data points | Preferred orientation correction: Simple spherical harmonic correction Order = 2 Coefficients: 0:0:C(2,-2) = -0.91(8); 0:0:C(2,0) = 0.63(8); 0:0:C(2,2) = 0.93(13) |
| Profile function: Finger-Cox-Jephcoat function parameters U, V, W, X, Y, SH/L: peak variance(Gauss) = Utan(Th)2+Vtan(Th)+W: peak HW(Lorentz) = X/cos(Th)+Ytan(Th); SH/L = S/L+H/L U, V, W in (centideg)2, X & Y in centideg 2.761, 0.000, 1.090, 3.610, 0.000, 0.047, |
| C1 | 0.31564 | 0.11999 | 0.03425 | 0.0100* | |
| C2 | 0.27426 | 0.26556 | 0.10759 | 0.0100* | |
| C3 | 0.20930 | 0.40008 | 0.07333 | 0.0100* | |
| H4 | 0.28873 | 0.24618 | 0.19840 | 0.0130* | |
| H5 | 0.17120 | 0.48125 | 0.13117 | 0.0130* | |
| C6 | 0.38661 | −0.01497 | 0.07632 | 0.0100* | |
| O7 | 0.39933 | −0.00110 | 0.17831 | 0.0100* | |
| O8 | 0.43321 | −0.00173 | 0.01302 | 0.0100* | |
| Ni9 | 0.50000 | 0.50000 | 0.50000 | 0.0387* | |
| Ni10 | 0.00000 | 0.50145 | −0.25000 | 0.0387* | |
| O11 | 0.02771 | 0.0007 | 0.15823 | 0.0063* | |
| H12 | 0.06922 | −0.03114 | 0.16621 | 0.0082* |
| C1—C2 | 1.4074 | O8—C6 | 1.3123 |
| C1—C3i | 1.3331 | Ni9—O11ii | 1.9246 |
| C1—C6 | 1.5251 | Ni9—O11iii | 1.9246 |
| C2—C1 | 1.4074 | Ni10—O7i | 2.0995 |
| C2—C3 | 1.3985 | Ni10—O7iv | 2.0995 |
| C3—C1i | 1.3331 | Ni10—O11v | 2.149 |
| C3—C2 | 1.3985 | Ni10—O11vi | 2.1377 |
| H5—C3 | 1.1584 | Ni10—O11vii | 2.149 |
| C6—C1 | 1.5251 | Ni10—O11viii | 2.1377 |
| C6—O7 | 1.2313 | O11—Ni9ix | 1.9246 |
| C6—O8 | 1.3123 | O11—Ni10v | 2.149 |
| O7—C6 | 1.2313 | O11—Ni10vi | 2.1377 |
| O7—Ni10i | 2.0995 | ||
| C2—C1—C3i | 117.925 | C1i—C3—C2 | 118.448 |
| C2—C1—C6 | 121.216 | C1—C6—O7 | 111.649 |
| C3i—C1—C6 | 120.856 | C1—C6—O8 | 121.645 |
| C1—C2—C3 | 123.601 | O7—C6—O8 | 122.291 |
| C8H6Ni2O6 | |
| β = 99.20° | |
| Monoclinic, | |
| C1 | 0.31659 | 0.14671 | 0.03597 | 0.010 | |
| C2 | 0.27424 | 0.23178 | 0.11288 | 0.010 | |
| C3 | 0.20831 | 0.33316 | 0.07742 | 0.010 | |
| H4 | 0.29416 | 0.22005 | 0.20095 | 0.013 | |
| H5 | 0.17519 | 0.40045 | 0.13678 | 0.013 | |
| C6 | 0.38690 | 0.03143 | 0.07591 | 0.010 | |
| O7 | 0.90294 | 0.45891 | 0.17836 | 0.010 | |
| O8 | 0.42774 | 0.00936 | 0.00489 | 0.010 | |
| Ni9 | 0.00000 | 0.00000 | 0.00000 | 0.03866 | |
| Ni10 | 0.00000 | 0.45204 | 0.25000 | 0.03866 | |
| O11 | 0.52764 | 0.45960 | 0.16035 | 0.00631 | |
| H12 | 0.57607 | 0.45471 | 0.17494 | 0.00821 |
| [Zn2(C8H4O4)(OH)2] | |
| Monoclinic, | |
| Synchrotron radiation, λ = 1.15008 Å | |
| white | |
| β = 97.431 (10)° |
| NSLS beamline X3B1 diffractometer | Scan method: step |
| Specimen mounting: Kapton capillary | 2θmin = 6.0°, 2θmax = 60.0°, 2θstep = 0.01° |
| Data collection mode: transmission |
| Least-squares matrix: full | 57 parameters |
| 14 restraints | |
| H-atom parameters not defined? | |
| (Δ/σ)max = 1.459 | |
| Background function: Background function: "chebyschev-1" function with 12 terms: 28.78(11), -16.88(18), 8.18(16), 0.45(16), -2.60(15), -1.04(14), 3.60(13), -1.88(13), 0.46(12), 1.97(12), -1.94(11), 1.26(10), | |
| 5400 data points | Preferred orientation correction: Simple spherical harmonic correction Order = 2 Coefficients: 0:0:C(2,-2) = -0.05(4); 0:0:C(2,0) = -0.18(6); 0:0:C(2,2) = -0.21(4) |
| Profile function: Finger-Cox-Jephcoat function parameters U, V, W, X, Y, SH/L: peak variance(Gauss) = Utan(Th)2+Vtan(Th)+W: peak HW(Lorentz) = X/cos(Th)+Ytan(Th); SH/L = S/L+H/L U, V, W in (centideg)2, X & Y in centideg 6.427, -1.067, 0.000, 0.000, 0.000, 0.022, Crystallite size in microns with "isotropic" model: parameters: Size, G/L mix 1.000, 1.000, Microstrain, "generalized" model (106 * delta Q/Q) parameters: S400, S040, S004, S220, S202, S022, S301, S103, S121, G/L mix 807.414, 6.074702219e6, 12850.425, 116093.843, 1080.871, 214564.056, 1450.184, -4276.159, -164837.348, 0.600, |
| C1 | 0.3153 (9) | 0.132 (11) | 0.038 (2) | 0.148 (18)* | |
| C2 | 0.2801 (13) | 0.369 (13) | 0.1020 (17) | 0.148* | |
| C3 | 0.2145 (14) | 0.477 (16) | 0.067 (2) | 0.148* | |
| H7 | 0.29840 | 0.55800 | 0.17260 | 0.192* | |
| H8 | 0.18320 | 0.73700 | 0.09150 | 0.192* | |
| C11 | 0.3863 (5) | 0.016 (8) | 0.0750 (18) | 0.0500* | |
| O12 | 0.4045 (9) | 0.025 (16) | 0.1743 (18) | 0.050000* | |
| O13 | 0.4201 (7) | −0.156 (9) | 0.008 (2) | 0.050000* | |
| Zn14 | 0.50000 | 0.50000 | 0.50000 | 0.078 (4)* | |
| Zn15 | 0.00000 | 0.54200 | −0.25000 | 0.078* | |
| O16 | 0.0318 (13) | 0.072 (14) | 0.161 (3) | 0.0500* | |
| H17 | 0.06922 | −0.03114 | 0.16621 | 0.065000* |
| C1—C2 | 1.3877 (16) | O13—C11 | 1.284 (2) |
| C1—C3i | 1.43 (4) | O13—Zn14ii | 1.989 (13) |
| C1—C11 | 1.498 (3) | Zn14—O13iii | 1.989 (13) |
| C2—C1 | 1.3877 (16) | Zn14—O13iv | 1.989 (13) |
| C2—C3 | 1.385 (2) | Zn14—O16v | 2.06 (3) |
| C3—C1i | 1.43 (4) | Zn14—O16vi | 2.06 (3) |
| C3—C2 | 1.385 (2) | Zn15—O12i | 2.048 (17) |
| C11—C1 | 1.498 (3) | Zn15—O12vii | 2.048 (17) |
| C11—O12 | 1.2573 (14) | Zn15—O16viii | 1.87 (4) |
| C11—O13 | 1.284 (2) | Zn15—O16ix | 1.87 (4) |
| O12—C11 | 1.2573 (14) | O16—Zn14x | 2.06 (3) |
| O12—Zn15i | 2.048 (17) | O16—Zn15viii | 1.87 (4) |
| C2—C1—C3i | 119.81 (12) | C1—C11—O12 | 116.6 (2) |
| C2—C1—C11 | 120.4 (2) | C1—C11—O13 | 118.59 (19) |
| C3i—C1—C11 | 119.6 (4) | O12—C11—O13 | 123.42 (15) |
| C1—C2—C3 | 120.20 (17) | O16viii—Zn15—O16xi | 93 (2) |
| C1i—C3—C2 | 119.83 (12) |
| C8H6O6Zn2 | |
| β = 97.52° | |
| Monoclinic, | |
| C1 | 0.31537 | 0.14052 | 0.03973 | 0.14798 | |
| C2 | 0.26900 | 0.22410 | 0.11036 | 0.14798 | |
| C3 | 0.20398 | 0.33320 | 0.07087 | 0.14798 | |
| H7 | 0.28504 | 0.20470 | 0.19624 | 0.19231 | |
| H8 | 0.16745 | 0.40076 | 0.12504 | 0.19231 | |
| C11 | 0.38529 | 0.02740 | 0.08247 | 0.050 | |
| O12 | 0.39938 | 0.97473 | 0.18247 | 0.050 | |
| O13 | 0.42745 | 0.99381 | 0.01434 | 0.050 | |
| O16 | 0.02778 | 0.97322 | 0.15570 | 0.050 | |
| H17 | 0.07652 | 0.96489 | 0.16886 | 0.065 | |
| Zn14 | 0.00000 | 0.00000 | 0.00000 | 0.07842 | |
| Zn15 | 0.50000 | 0.96690 | 0.25000 | 0.07842 |