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Chemical bonding in the pentaerythritol crystal based on the experimental electron density at 15 (1) K, and theoretical calculations at the experimental molecular geometries obtained at room and low (15 K) temperatures have been analyzed and compared in terms of the topological analysis. Topological electron-density features corresponding to the high-pressure (1.15 GPa) geometry are also reported. In addition to the bond critical points (CPs) within the molecular layers, CPs between the atoms of different molecular layers have been located and the bonding character of these relatively weak interactions discussed. Atomic charges and energies have been integrated over the atomic basins delimited by the zero-flux surfaces, and the intermolecular interaction energies have been calculated. The interaction between molecular layers in the crystal becomes stronger both at very low temperature and high pressure, as demonstrated by the more negative intermolecular interaction energies, higher electron density and energy density values at the CPs, and sharper electronic-energy density profiles.
Supporting information
CCDC reference: 612214
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Data collection: CrystalClear,(2005); cell refinement: Otwinowski & Minor (1997); data reduction: Zhurov et al.,(2005); program(s) used to solve structure: Sheldrick (1997); program(s) used to refine structure: Koritsanszky et al., (2003); molecular graphics: Koritsanszky et al., (2003); software used to prepare material for publication: Koritsanszky et al., (2003).
Crystal data top
C5H12O4 | Mo Kα radiation, λ = 0.71073 Å |
Mr = 135.15 | Cell parameters from 29440 reflections |
Tetragonal, I4 | θ = 0–70° |
a = 6.0867 (1) Å | µ = 0.12 mm−1 |
c = 8.4958 (4) Å | T = 15 K |
V = 314.75 Å3 | Tetragonal bipyramid, colorless |
Z = 2 | 0.30 × 0.30 × 0.25 mm |
Dx = 1.434 Mg m−3 | |
Data collection top
Rigaku R-axis Rapid diffractometer | Rint = 0.018 |
w scans | θmax = 70.1° |
29440 measured reflections | h = 0→16 |
29440 independent reflections | k = 0→16 |
27057 reflections with I > 4σ | l = −22→22 |
Refinement top
Refinement on F2 | All H-atom parameters refined |
R[F2 > 2σ(F2)] = 0.012 | w = 1/[s2(Fsqd)] |
wR(F2) = 0.012 | (Δ/σ)max < 0.001 |
S = 1.51 | Δρmax = 0.06 e Å−3 |
2378 reflections | Δρmin = −0.06 e Å−3 |
125 parameters | |
Crystal data top
C5H12O4 | Z = 2 |
Mr = 135.15 | Mo Kα radiation |
Tetragonal, I4 | µ = 0.12 mm−1 |
a = 6.0867 (1) Å | T = 15 K |
c = 8.4958 (4) Å | 0.30 × 0.30 × 0.25 mm |
V = 314.75 Å3 | |
Data collection top
Rigaku R-axis Rapid diffractometer | 27057 reflections with I > 4σ |
29440 measured reflections | Rint = 0.018 |
29440 independent reflections | |
Refinement top
R[F2 > 2σ(F2)] = 0.012 | 125 parameters |
wR(F2) = 0.012 | All H-atom parameters refined |
S = 1.51 | Δρmax = 0.06 e Å−3 |
2378 reflections | Δρmin = −0.06 e Å−3 |
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top | x | y | z | Uiso*/Ueq | Occ. (<1) |
O(1) | −0.31978 (2) | −0.24540 (2) | 0.01876 (2) | 0.008 | |
C(1) | 0.00000 | 0.00000 | 0.00000 | 0.005 | |
C(2) | −0.16021 (2) | −0.12529 (2) | 0.10680 (1) | 0.007 | |
H(1) | −0.06946 | −0.23630 | 0.18188 | 0.024 (2) | |
H(2) | −0.24692 | −0.01404 | 0.18196 | 0.025 (2) | |
H(3) | −0.26608 | −0.38641 | −0.00055 | 0.021 (2) | |
DUM0 | 1.00000 | 0.00000 | 0.00000 | 0.000 | 0.0000 |
DUM1 | 0.00000 | 1.00000 | 0.00000 | 0.000 | 0.0000 |
DUM2 | 0.14270 | 0.01660 | −0.10640 | 0.000 | 0.0000 |
DUM3 | −0.01800 | 0.14110 | −0.10740 | 0.000 | 0.0000 |
Atomic displacement parameters (Å2) top | U11 | U22 | U33 | U12 | U13 | U23 |
O(1) | 0.00565 (3) | 0.00622 (3) | 0.01263 (4) | −0.00103 (2) | −0.00037 (3) | −0.00075 (3) |
C(1) | 0.00455 (3) | 0.00455 (3) | 0.00549 (6) | 0.00000 | 0.00000 | 0.00000 |
C(2) | 0.00639 (3) | 0.00626 (3) | 0.00688 (3) | −0.00093 (2) | 0.00079 (3) | 0.00032 (3) |
Geometric parameters (Å, º) top
O(1)—C(2) | 1.4273 (2) | C(1)—C(2)ii | 1.5348 (1) |
O(1)—H(3) | 0.9330 (1) | C(1)—C(2)iii | 1.5348 (1) |
C(1)—C(2) | 1.5348 (1) | C(2)—H(1) | 1.0810 (1) |
C(1)—C(2)i | 1.5348 (1) | C(2)—H(2) | 1.0700 (1) |
| | | |
C(2)—O(1)—H(3) | 108.960 (13) | O(1)—C(2)—H(1) | 109.681 (11) |
C(2)—C(1)—C(2)i | 107.522 (9) | O(1)—C(2)—H(2) | 107.530 (10) |
C(2)—C(1)—C(2)ii | 110.454 (5) | C(1)—C(2)—H(1) | 109.560 (8) |
C(2)—C(1)—C(2)iii | 110.454 (5) | C(1)—C(2)—H(2) | 110.596 (8) |
C(2)i—C(1)—C(2)ii | 110.454 (5) | C(1)i—C(2)—H(1) | 109.560 (8) |
C(2)i—C(1)—C(2)iii | 110.454 (5) | C(1)i—C(2)—H(2) | 110.596 (8) |
C(2)ii—C(1)—C(2)iii | 107.522 (9) | C(1)ii—C(2)—H(1) | 109.560 (8) |
O(1)—C(2)—C(1) | 112.152 (10) | C(1)ii—C(2)—H(2) | 110.596 (8) |
O(1)—C(2)—C(1)i | 112.152 (10) | C(1)iii—C(2)—H(1) | 109.560 (8) |
O(1)—C(2)—C(1)ii | 112.152 (10) | C(1)iii—C(2)—H(2) | 110.596 (8) |
O(1)—C(2)—C(1)iii | 112.152 (10) | H(1)—C(2)—H(2) | 107.180 (11) |
Symmetry codes: (i) −x, −y, z; (ii) y, −x, −z; (iii) −y, x, −z. |
Experimental details
Crystal data |
Chemical formula | C5H12O4 |
Mr | 135.15 |
Crystal system, space group | Tetragonal, I4 |
Temperature (K) | 15 |
a, c (Å) | 6.0867 (1), 8.4958 (4) |
V (Å3) | 314.75 |
Z | 2 |
Radiation type | Mo Kα |
µ (mm−1) | 0.12 |
Crystal size (mm) | 0.30 × 0.30 × 0.25 |
|
Data collection |
Diffractometer | Rigaku R-axis Rapid diffractometer |
Absorption correction | – |
No. of measured, independent and observed (I > 4σ) reflections | 29440, 29440, 27057 |
Rint | 0.018 |
(sin θ/λ)max (Å−1) | 1.323 |
|
Refinement |
R[F2 > 2σ(F2)], wR(F2), S | 0.012, 0.012, 1.51 |
No. of reflections | 2378 |
No. of parameters | 125 |
No. of restraints | ? |
H-atom treatment | All H-atom parameters refined |
Δρmax, Δρmin (e Å−3) | 0.06, −0.06 |
Selected geometric parameters (Å, º) topO(1)—C(2) | 1.4273 (2) | C(1)—C(2)ii | 1.5348 (1) |
O(1)—H(3) | 0.9330 (1) | C(1)—C(2)iii | 1.5348 (1) |
C(1)—C(2) | 1.5348 (1) | C(2)—H(1) | 1.0810 (1) |
C(1)—C(2)i | 1.5348 (1) | C(2)—H(2) | 1.0700 (1) |
| | | |
C(2)—O(1)—H(3) | 108.960 (13) | O(1)—C(2)—H(1) | 109.681 (11) |
C(2)—C(1)—C(2)i | 107.522 (9) | O(1)—C(2)—H(2) | 107.530 (10) |
C(2)—C(1)—C(2)ii | 110.454 (5) | C(1)—C(2)—H(1) | 109.560 (8) |
C(2)—C(1)—C(2)iii | 110.454 (5) | C(1)—C(2)—H(2) | 110.596 (8) |
C(2)i—C(1)—C(2)ii | 110.454 (5) | C(1)i—C(2)—H(1) | 109.560 (8) |
C(2)i—C(1)—C(2)iii | 110.454 (5) | C(1)i—C(2)—H(2) | 110.596 (8) |
C(2)ii—C(1)—C(2)iii | 107.522 (9) | C(1)ii—C(2)—H(1) | 109.560 (8) |
O(1)—C(2)—C(1) | 112.152 (10) | C(1)ii—C(2)—H(2) | 110.596 (8) |
O(1)—C(2)—C(1)i | 112.152 (10) | C(1)iii—C(2)—H(1) | 109.560 (8) |
O(1)—C(2)—C(1)ii | 112.152 (10) | C(1)iii—C(2)—H(2) | 110.596 (8) |
O(1)—C(2)—C(1)iii | 112.152 (10) | H(1)—C(2)—H(2) | 107.180 (11) |
Symmetry codes: (i) −x, −y, z; (ii) y, −x, −z; (iii) −y, x, −z. |
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