Buy article online - an online subscription or single-article purchase is required to access this article.
The structure of deca-dodecasil 3
R (DD-3
R), Si
120O
240, a very well suited material for the synthesis of inorganic/organic composites structured on a nanometer level, has been investigated in detail. So far, a highly complicated twinning has hampered its structure description at a desirable level of accuracy. This twinning has now been resolved and a new structure determination is presented. Structure refinement in the
R space group revealed a large, unusually shaped atomic displacement ellipsoid for oxygen-bridging units (tetrahedra), bridging Si-O bonds shorter than expected and the linear Si-O-Si' bond angle dictated by special positions at a threefold axis. A structure model based on a statistically disordered bridging O atom improved the accuracy of the Si-O bonds of interest, but provided unacceptable O-O contacts. To solve this dilemma,
ab initio NVT molecular dynamics calculations were performed to study the possible configurations. Wavelet analysis of the time variations of selected Si-O distances pointed to a synchronous shift of the whole building units (tetrahedra). Low-frequency features of the calculated phonon density of states agree well with the published INS (inelastic neutron scattering) spectra of several silica polymorphs, indicating that the nature of the disorder in DD-3
R is dynamic rather than static.
Supporting information
Data collection: SMART(Siemens, 1995); cell refinement: SAINT (Siemens, 1995); data reduction: SAINT (Siemens, 1995)& SADABS (Sheldrick, 2001); program(s) used to solve structure: SHELXTL (Bruker, 2001); program(s) used to refine structure: SHELXTL (Bruker, 2001); molecular graphics: DIAMOND (Brandenburg, 2005); software used to prepare material for publication: SHELXTL (Bruker, 2001).
Crystal data top
O120Si60 | Dx = 1.754 Mg m−3 |
Mr = 3605.40 | Mo Kα radiation, λ = 0.71073 Å |
Trigonal, R3 | Cell parameters from 7657 reflections |
Hall symbol: -R 3 | θ = 2.6–28.3° |
a = 13.7761 (1) Å | µ = 0.66 mm−1 |
c = 41.5456 (6) Å | T = 183 K |
V = 6828.23 (12) Å3 | Hexagonal plate, colourless |
Z = 2 | 0.26 × 0.22 × 0.08 mm |
F(000) = 3600 | |
Data collection top
CCD area detector diffractometer | 3622 independent reflections |
Radiation source: fine-focus sealed tube | 3556 reflections with I > 2σI |
Graphite monochromator | Rint = 0.031 |
ω scans | θmax = 28.3°, θmin = 2.6° |
Absorption correction: multi-scan SADABS (Sheldrick, 2001) | h = −18→18 |
Tmin = 0.880, Tmax = 0.949 | k = −18→18 |
44259 measured reflections | l = 0→54 |
Refinement top
Refinement on F2 | 0 restraints |
Least-squares matrix: full | Primary atom site location: structure-invariant direct methods |
R[F2 > 2σ(F2)] = 0.024 | Secondary atom site location: difference Fourier map |
wR(F2) = 0.082 | w = 1/[σ2(Fo2) + (0.0757P)2 + 2.4398P] where P = (Fo2 + 2Fc2)/3 |
S = 0.95 | (Δ/σ)max = 0.001 |
3622 reflections | Δρmax = 1.13 e Å−3 |
184 parameters | Δρmin = −0.34 e Å−3 |
Crystal data top
O120Si60 | Z = 2 |
Mr = 3605.40 | Mo Kα radiation |
Trigonal, R3 | µ = 0.66 mm−1 |
a = 13.7761 (1) Å | T = 183 K |
c = 41.5456 (6) Å | 0.26 × 0.22 × 0.08 mm |
V = 6828.23 (12) Å3 | |
Data collection top
CCD area detector diffractometer | 3622 independent reflections |
Absorption correction: multi-scan SADABS (Sheldrick, 2001) | 3556 reflections with I > 2σI |
Tmin = 0.880, Tmax = 0.949 | Rint = 0.031 |
44259 measured reflections | |
Refinement top
R[F2 > 2σ(F2)] = 0.024 | 184 parameters |
wR(F2) = 0.082 | 0 restraints |
S = 0.95 | Δρmax = 1.13 e Å−3 |
3622 reflections | Δρmin = −0.34 e Å−3 |
Special details top
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 | Uiso*/Ueq | |
Si1 | 0.0000 | 0.0000 | 0.13722 (2) | 0.0123 (2) | |
Si2 | 0.0000 | 0.0000 | 0.21342 (2) | 0.00817 (18) | |
Si3 | 0.13827 (5) | 0.25814 (5) | 0.232250 (13) | 0.00771 (12) | |
Si4 | 0.18478 (5) | 0.40151 (5) | 0.167658 (13) | 0.00843 (12) | |
Si5 | −0.03853 (5) | 0.29578 (5) | 0.265664 (14) | 0.00883 (12) | |
Si6 | −0.09872 (5) | 0.34502 (5) | 0.333414 (15) | 0.00889 (12) | |
Si7 | −0.01778 (5) | 0.39330 (5) | 0.402585 (13) | 0.00847 (12) | |
Si8 | −0.09487 (5) | 0.45115 (5) | 0.224061 (13) | 0.01007 (12) | |
O1 | 0.09544 (15) | 0.12081 (16) | 0.12437 (4) | 0.0209 (4) | |
O2 | 0.0000 | 0.0000 | 0.17547 (8) | 0.0495 (12) | |
O3 | 0.07050 (17) | 0.12578 (15) | 0.22611 (5) | 0.0282 (4) | |
O4 | 0.15270 (17) | 0.32494 (16) | 0.19927 (3) | 0.0206 (4) | |
O5 | 0.07297 (15) | 0.29034 (15) | 0.25830 (4) | 0.0162 (3) | |
O6 | −0.03693 (15) | 0.33004 (16) | 0.30274 (4) | 0.0182 (3) | |
O7 | −0.02068 (14) | 0.36753 (15) | 0.36467 (4) | 0.0167 (4) | |
O8 | −0.03934 (17) | 0.38815 (16) | 0.24238 (5) | 0.0220 (4) | |
O9 | 0.12607 (15) | 0.32187 (16) | 0.13710 (4) | 0.0176 (3) | |
O10 | 0.31761 (14) | 0.47062 (15) | 0.16245 (4) | 0.0201 (4) | |
O11 | 0.25985 (14) | 0.29461 (14) | 0.24666 (4) | 0.0143 (3) | |
O12 | −0.14638 (15) | 0.17497 (15) | 0.25858 (4) | 0.0208 (4) | |
O13 | −0.11907 (17) | 0.44852 (16) | 0.32776 (4) | 0.0241 (4) | |
O14 | −0.11701 (14) | 0.52702 (14) | 0.24908 (4) | 0.0169 (3) | |
Atomic displacement parameters (Å2) top | U11 | U22 | U33 | U12 | U13 | U23 |
Si1 | 0.0136 (3) | 0.0136 (3) | 0.0098 (4) | 0.00681 (15) | 0.000 | 0.000 |
Si2 | 0.0074 (3) | 0.0074 (3) | 0.0098 (4) | 0.00368 (13) | 0.000 | 0.000 |
Si3 | 0.0068 (2) | 0.0074 (3) | 0.0089 (2) | 0.0036 (2) | −0.0001 (2) | 0.00036 (19) |
Si4 | 0.0085 (3) | 0.0106 (3) | 0.0079 (2) | 0.0060 (2) | −0.0008 (2) | 0.0000 (2) |
Si5 | 0.0082 (3) | 0.0098 (3) | 0.0086 (2) | 0.0045 (2) | 0.0012 (2) | 0.0007 (2) |
Si6 | 0.0097 (3) | 0.0084 (3) | 0.0079 (2) | 0.0040 (2) | 0.0002 (2) | −0.00097 (19) |
Si7 | 0.0088 (3) | 0.0097 (3) | 0.0078 (2) | 0.0053 (2) | −0.0007 (2) | 0.0006 (2) |
Si8 | 0.0111 (3) | 0.0087 (3) | 0.0104 (2) | 0.0049 (2) | 0.0009 (2) | 0.0006 (2) |
O1 | 0.0148 (8) | 0.0133 (8) | 0.0331 (9) | 0.0059 (7) | −0.0055 (7) | 0.0050 (7) |
O2 | 0.0698 (19) | 0.0698 (19) | 0.0088 (13) | 0.0349 (10) | 0.000 | 0.000 |
O3 | 0.0231 (10) | 0.0099 (8) | 0.0480 (11) | 0.0055 (8) | −0.0048 (9) | −0.0067 (8) |
O4 | 0.0223 (9) | 0.0296 (10) | 0.0109 (7) | 0.0137 (8) | 0.0011 (7) | 0.0091 (7) |
O5 | 0.0127 (8) | 0.0265 (9) | 0.0129 (8) | 0.0125 (7) | 0.0022 (6) | −0.0009 (7) |
O6 | 0.0167 (8) | 0.0262 (9) | 0.0128 (7) | 0.0115 (7) | 0.0008 (6) | −0.0049 (7) |
O7 | 0.0158 (8) | 0.0276 (9) | 0.0076 (7) | 0.0115 (7) | −0.0024 (6) | −0.0023 (6) |
O8 | 0.0241 (9) | 0.0222 (9) | 0.0235 (9) | 0.0145 (8) | 0.0014 (7) | 0.0091 (7) |
O9 | 0.0185 (8) | 0.0220 (9) | 0.0135 (7) | 0.0109 (7) | −0.0028 (6) | −0.0069 (7) |
O10 | 0.0082 (8) | 0.0250 (9) | 0.0243 (9) | 0.0063 (7) | 0.0004 (6) | 0.0059 (7) |
O11 | 0.0102 (7) | 0.0192 (8) | 0.0155 (7) | 0.0087 (6) | −0.0026 (6) | 0.0012 (6) |
O12 | 0.0133 (8) | 0.0149 (8) | 0.0250 (8) | 0.0002 (7) | 0.0025 (7) | −0.0042 (7) |
O13 | 0.0374 (11) | 0.0183 (9) | 0.0244 (8) | 0.0198 (9) | −0.0032 (8) | −0.0019 (7) |
O14 | 0.0185 (8) | 0.0107 (8) | 0.0161 (8) | 0.0032 (7) | 0.0072 (7) | −0.0018 (6) |
Geometric parameters (Å, º) top
Si1—O2i | 1.589 (3) | Si5—O12 | 1.6098 (18) |
Si1—O2 | 1.589 (3) | Si6—O13 | 1.6020 (19) |
Si1—O1ii | 1.6111 (19) | Si6—O6 | 1.6020 (18) |
Si1—O1 | 1.6111 (19) | Si6—O13iv | 1.6052 (19) |
Si1—O1i | 1.6111 (19) | Si6—O7 | 1.6138 (17) |
Si2—O2i | 1.577 (3) | Si7—O11v | 1.5995 (16) |
Si2—O2 | 1.577 (3) | Si7—O12vi | 1.6011 (18) |
Si2—O3 | 1.5939 (18) | Si7—O14iv | 1.6098 (17) |
Si2—O3ii | 1.5939 (18) | Si7—O7 | 1.6108 (16) |
Si2—O3i | 1.5939 (18) | Si8—O9iii | 1.6051 (17) |
Si3—O3 | 1.5998 (19) | Si8—O1iii | 1.606 (2) |
Si3—O11 | 1.6046 (17) | Si8—O8 | 1.6069 (18) |
Si3—O5 | 1.6051 (16) | Si8—O14 | 1.6076 (17) |
Si3—O4 | 1.6063 (16) | O1—Si8vii | 1.6057 (19) |
Si4—O10 | 1.5998 (17) | O2—O2i | 0.000 (6) |
Si4—O4 | 1.6022 (16) | O9—Si8vii | 1.6050 (17) |
Si4—O10iii | 1.6053 (16) | O10—Si4vii | 1.6052 (16) |
Si4—O9 | 1.6070 (17) | O11—Si7v | 1.5996 (16) |
Si5—O8 | 1.6029 (18) | O12—Si7iv | 1.6011 (18) |
Si5—O5 | 1.6042 (17) | O13—Si6vi | 1.6052 (19) |
Si5—O6 | 1.6081 (18) | O14—Si7vi | 1.6098 (17) |
| | | |
O2i—Si1—O1ii | 109.36 (7) | O5—Si5—O12 | 109.10 (10) |
O2—Si1—O1ii | 109.36 (7) | O6—Si5—O12 | 110.41 (9) |
O2i—Si1—O1 | 109.36 (7) | O13—Si6—O6 | 109.80 (10) |
O2—Si1—O1 | 109.36 (7) | O13—Si6—O13iv | 108.34 (15) |
O1ii—Si1—O1 | 109.58 (7) | O6—Si6—O13iv | 110.40 (10) |
O2i—Si1—O1i | 109.36 (7) | O13—Si6—O7 | 110.07 (10) |
O2—Si1—O1i | 109.36 (7) | O6—Si6—O7 | 108.60 (9) |
O1ii—Si1—O1i | 109.58 (7) | O13iv—Si6—O7 | 109.63 (10) |
O1—Si1—O1i | 109.58 (7) | O11v—Si7—O12vi | 109.87 (10) |
O2i—Si2—O3 | 109.31 (8) | O11v—Si7—O14iv | 109.44 (9) |
O2—Si2—O3 | 109.31 (8) | O12vi—Si7—O14iv | 108.90 (10) |
O2i—Si2—O3ii | 109.31 (8) | O11v—Si7—O7 | 109.71 (9) |
O2—Si2—O3ii | 109.31 (8) | O12vi—Si7—O7 | 110.18 (10) |
O3—Si2—O3ii | 109.63 (8) | O14iv—Si7—O7 | 108.71 (10) |
O2i—Si2—O3i | 109.31 (8) | O9iii—Si8—O1iii | 110.52 (10) |
O2—Si2—O3i | 109.31 (8) | O9iii—Si8—O8 | 109.13 (10) |
O3—Si2—O3i | 109.63 (8) | O1iii—Si8—O8 | 108.72 (11) |
O3ii—Si2—O3i | 109.63 (8) | O9iii—Si8—O14 | 109.60 (9) |
O3—Si3—O11 | 109.83 (10) | O1iii—Si8—O14 | 108.89 (10) |
O3—Si3—O5 | 109.52 (11) | O8—Si8—O14 | 109.95 (10) |
O11—Si3—O5 | 107.66 (9) | Si8vii—O1—Si1 | 145.60 (12) |
O3—Si3—O4 | 110.58 (10) | Si2—O2—Si1 | 180.0 |
O11—Si3—O4 | 109.15 (10) | Si2—O3—Si3 | 169.40 (15) |
O5—Si3—O4 | 110.04 (10) | Si4—O4—Si3 | 172.19 (14) |
O10—Si4—O4 | 111.08 (10) | Si5—O5—Si3 | 145.43 (12) |
O10—Si4—O10iii | 109.83 (14) | Si6—O6—Si5 | 150.41 (13) |
O4—Si4—O10iii | 109.40 (11) | Si7—O7—Si6 | 140.35 (12) |
O10—Si4—O9 | 109.57 (10) | Si5—O8—Si8 | 155.35 (14) |
O4—Si4—O9 | 108.62 (10) | Si8vii—O9—Si4 | 152.27 (12) |
O10iii—Si4—O9 | 108.29 (9) | Si4—O10—Si4vii | 163.57 (12) |
O8—Si5—O5 | 107.99 (10) | Si7v—O11—Si3 | 154.76 (12) |
O8—Si5—O6 | 110.46 (11) | Si7iv—O12—Si5 | 153.67 (12) |
O5—Si5—O6 | 108.87 (9) | Si6—O13—Si6vi | 159.21 (13) |
O8—Si5—O12 | 109.95 (10) | Si8—O14—Si7vi | 148.69 (11) |
| | | |
O2i—Si1—O1—Si8vii | −102.7 (2) | O6—Si6—O7—Si7 | 177.87 (17) |
O2—Si1—O1—Si8vii | −102.7 (2) | O13iv—Si6—O7—Si7 | −61.4 (2) |
O1ii—Si1—O1—Si8vii | 17.2 (3) | O5—Si5—O8—Si8 | 163.2 (3) |
O1i—Si1—O1—Si8vii | 137.45 (14) | O6—Si5—O8—Si8 | −77.9 (3) |
O2i—Si2—O3—Si3 | 17.4 (8) | O12—Si5—O8—Si8 | 44.2 (4) |
O2—Si2—O3—Si3 | 17.4 (8) | O9iii—Si8—O8—Si5 | −165.3 (3) |
O3ii—Si2—O3—Si3 | −102.4 (9) | O1iii—Si8—O8—Si5 | −44.7 (4) |
O3i—Si2—O3—Si3 | 137.2 (8) | O14—Si8—O8—Si5 | 74.4 (4) |
O11—Si3—O3—Si2 | −126.7 (8) | O10—Si4—O9—Si8vii | 39.6 (3) |
O5—Si3—O3—Si2 | 115.2 (8) | O4—Si4—O9—Si8vii | −81.9 (3) |
O4—Si3—O3—Si2 | −6.2 (8) | O10iii—Si4—O9—Si8vii | 159.4 (3) |
O8—Si5—O5—Si3 | −66.6 (2) | O4—Si4—O10—Si4vii | 6.9 (5) |
O6—Si5—O5—Si3 | 173.5 (2) | O10iii—Si4—O10—Si4vii | 128.1 (5) |
O12—Si5—O5—Si3 | 52.9 (2) | O9—Si4—O10—Si4vii | −113.1 (5) |
O3—Si3—O5—Si5 | −65.9 (2) | O3—Si3—O11—Si7v | −19.1 (3) |
O11—Si3—O5—Si5 | 174.7 (2) | O5—Si3—O11—Si7v | 100.1 (3) |
O4—Si3—O5—Si5 | 55.9 (2) | O4—Si3—O11—Si7v | −140.5 (3) |
O13—Si6—O6—Si5 | −70.3 (3) | O8—Si5—O12—Si7iv | −90.9 (3) |
O13iv—Si6—O6—Si5 | 49.1 (3) | O5—Si5—O12—Si7iv | 150.9 (3) |
O7—Si6—O6—Si5 | 169.3 (2) | O6—Si5—O12—Si7iv | 31.3 (3) |
O8—Si5—O6—Si6 | 72.2 (3) | O6—Si6—O13—Si6vi | −117.9 (4) |
O5—Si5—O6—Si6 | −169.4 (3) | O13iv—Si6—O13—Si6vi | 121.4 (4) |
O12—Si5—O6—Si6 | −49.6 (3) | O7—Si6—O13—Si6vi | 1.6 (4) |
O11v—Si7—O7—Si6 | 164.26 (18) | O9iii—Si8—O14—Si7vi | −19.9 (3) |
O12vi—Si7—O7—Si6 | −74.6 (2) | O1iii—Si8—O14—Si7vi | −140.9 (2) |
O14iv—Si7—O7—Si6 | 44.6 (2) | O8—Si8—O14—Si7vi | 100.1 (2) |
O13—Si6—O7—Si7 | 57.6 (2) | | |
Symmetry codes: (i) −x+y, −x, z; (ii) −y, x−y, z; (iii) y−1/3, −x+y+1/3, −z+1/3; (iv) y−2/3, −x+y−1/3, −z+2/3; (v) −x+1/3, −y+2/3, −z+2/3; (vi) x−y+1/3, x+2/3, −z+2/3; (vii) x−y+2/3, x+1/3, −z+1/3. |
Experimental details
Crystal data |
Chemical formula | O120Si60 |
Mr | 3605.40 |
Crystal system, space group | Trigonal, R3 |
Temperature (K) | 183 |
a, c (Å) | 13.7761 (1), 41.5456 (6) |
V (Å3) | 6828.23 (12) |
Z | 2 |
Radiation type | Mo Kα |
µ (mm−1) | 0.66 |
Crystal size (mm) | 0.26 × 0.22 × 0.08 |
|
Data collection |
Diffractometer | CCD area detector diffractometer |
Absorption correction | Multi-scan SADABS (Sheldrick, 2001) |
Tmin, Tmax | 0.880, 0.949 |
No. of measured, independent and observed (I > 2σI) reflections | 44259, 3622, 3556 |
Rint | 0.031 |
(sin θ/λ)max (Å−1) | 0.667 |
|
Refinement |
R[F2 > 2σ(F2)], wR(F2), S | 0.024, 0.082, 0.95 |
No. of reflections | 3622 |
No. of parameters | 184 |
Δρmax, Δρmin (e Å−3) | 1.13, −0.34 |
Subscribe to Acta Crystallographica Section B: Structural Science, Crystal Engineering and Materials
The full text of this article is available to subscribers to the journal.
If you have already registered and are using a computer listed in your registration details, please email
support@iucr.org for assistance.