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The structure of deca-dodecasil 3R (DD-3R), Si120O240, 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\bar 3 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-3R is dynamic rather than static.

Supporting information

cif

Crystallographic Information File (CIF) https://doi.org/10.1107/S0108768105026698/lc5031sup1.cif
Contains datablock dd3r

fcf

Structure factor file (CIF format) https://doi.org/10.1107/S0108768105026698/lc5031sup2.fcf
Contains datablock dd3r

Computing details top

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).

Figures top
[Figure 1]
[Figure 2]
[Figure 3]
[Figure 4]
[Figure 5]
[Figure 6]
(dd3r) top
Crystal data top
O120Si60Dx = 1.754 Mg m3
Mr = 3605.40Mo Kα radiation, λ = 0.71073 Å
Trigonal, R3Cell parameters from 7657 reflections
Hall symbol: -R 3θ = 2.6–28.3°
a = 13.7761 (1) ŵ = 0.66 mm1
c = 41.5456 (6) ÅT = 183 K
V = 6828.23 (12) Å3Hexagonal plate, colourless
Z = 20.26 × 0.22 × 0.08 mm
F(000) = 3600
Data collection top
CCD area detector
diffractometer
3622 independent reflections
Radiation source: fine-focus sealed tube3556 reflections with I > 2σI
Graphite monochromatorRint = 0.031
ω scansθmax = 28.3°, θmin = 2.6°
Absorption correction: multi-scan
SADABS (Sheldrick, 2001)
h = 1818
Tmin = 0.880, Tmax = 0.949k = 1818
44259 measured reflectionsl = 054
Refinement top
Refinement on F20 restraints
Least-squares matrix: fullPrimary atom site location: structure-invariant direct methods
R[F2 > 2σ(F2)] = 0.024Secondary 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 reflectionsΔρmax = 1.13 e Å3
184 parametersΔρmin = 0.34 e Å3
Crystal data top
O120Si60Z = 2
Mr = 3605.40Mo Kα radiation
Trigonal, R3µ = 0.66 mm1
a = 13.7761 (1) ÅT = 183 K
c = 41.5456 (6) Å0.26 × 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 = 0.949Rint = 0.031
44259 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.024184 parameters
wR(F2) = 0.0820 restraints
S = 0.95Δρmax = 1.13 e Å3
3622 reflectionsΔρmin = 0.34 e Å3
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
xyzUiso*/Ueq
Si10.00000.00000.13722 (2)0.0123 (2)
Si20.00000.00000.21342 (2)0.00817 (18)
Si30.13827 (5)0.25814 (5)0.232250 (13)0.00771 (12)
Si40.18478 (5)0.40151 (5)0.167658 (13)0.00843 (12)
Si50.03853 (5)0.29578 (5)0.265664 (14)0.00883 (12)
Si60.09872 (5)0.34502 (5)0.333414 (15)0.00889 (12)
Si70.01778 (5)0.39330 (5)0.402585 (13)0.00847 (12)
Si80.09487 (5)0.45115 (5)0.224061 (13)0.01007 (12)
O10.09544 (15)0.12081 (16)0.12437 (4)0.0209 (4)
O20.00000.00000.17547 (8)0.0495 (12)
O30.07050 (17)0.12578 (15)0.22611 (5)0.0282 (4)
O40.15270 (17)0.32494 (16)0.19927 (3)0.0206 (4)
O50.07297 (15)0.29034 (15)0.25830 (4)0.0162 (3)
O60.03693 (15)0.33004 (16)0.30274 (4)0.0182 (3)
O70.02068 (14)0.36753 (15)0.36467 (4)0.0167 (4)
O80.03934 (17)0.38815 (16)0.24238 (5)0.0220 (4)
O90.12607 (15)0.32187 (16)0.13710 (4)0.0176 (3)
O100.31761 (14)0.47062 (15)0.16245 (4)0.0201 (4)
O110.25985 (14)0.29461 (14)0.24666 (4)0.0143 (3)
O120.14638 (15)0.17497 (15)0.25858 (4)0.0208 (4)
O130.11907 (17)0.44852 (16)0.32776 (4)0.0241 (4)
O140.11701 (14)0.52702 (14)0.24908 (4)0.0169 (3)
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
Si10.0136 (3)0.0136 (3)0.0098 (4)0.00681 (15)0.0000.000
Si20.0074 (3)0.0074 (3)0.0098 (4)0.00368 (13)0.0000.000
Si30.0068 (2)0.0074 (3)0.0089 (2)0.0036 (2)0.0001 (2)0.00036 (19)
Si40.0085 (3)0.0106 (3)0.0079 (2)0.0060 (2)0.0008 (2)0.0000 (2)
Si50.0082 (3)0.0098 (3)0.0086 (2)0.0045 (2)0.0012 (2)0.0007 (2)
Si60.0097 (3)0.0084 (3)0.0079 (2)0.0040 (2)0.0002 (2)0.00097 (19)
Si70.0088 (3)0.0097 (3)0.0078 (2)0.0053 (2)0.0007 (2)0.0006 (2)
Si80.0111 (3)0.0087 (3)0.0104 (2)0.0049 (2)0.0009 (2)0.0006 (2)
O10.0148 (8)0.0133 (8)0.0331 (9)0.0059 (7)0.0055 (7)0.0050 (7)
O20.0698 (19)0.0698 (19)0.0088 (13)0.0349 (10)0.0000.000
O30.0231 (10)0.0099 (8)0.0480 (11)0.0055 (8)0.0048 (9)0.0067 (8)
O40.0223 (9)0.0296 (10)0.0109 (7)0.0137 (8)0.0011 (7)0.0091 (7)
O50.0127 (8)0.0265 (9)0.0129 (8)0.0125 (7)0.0022 (6)0.0009 (7)
O60.0167 (8)0.0262 (9)0.0128 (7)0.0115 (7)0.0008 (6)0.0049 (7)
O70.0158 (8)0.0276 (9)0.0076 (7)0.0115 (7)0.0024 (6)0.0023 (6)
O80.0241 (9)0.0222 (9)0.0235 (9)0.0145 (8)0.0014 (7)0.0091 (7)
O90.0185 (8)0.0220 (9)0.0135 (7)0.0109 (7)0.0028 (6)0.0069 (7)
O100.0082 (8)0.0250 (9)0.0243 (9)0.0063 (7)0.0004 (6)0.0059 (7)
O110.0102 (7)0.0192 (8)0.0155 (7)0.0087 (6)0.0026 (6)0.0012 (6)
O120.0133 (8)0.0149 (8)0.0250 (8)0.0002 (7)0.0025 (7)0.0042 (7)
O130.0374 (11)0.0183 (9)0.0244 (8)0.0198 (9)0.0032 (8)0.0019 (7)
O140.0185 (8)0.0107 (8)0.0161 (8)0.0032 (7)0.0072 (7)0.0018 (6)
Geometric parameters (Å, º) top
Si1—O2i1.589 (3)Si5—O121.6098 (18)
Si1—O21.589 (3)Si6—O131.6020 (19)
Si1—O1ii1.6111 (19)Si6—O61.6020 (18)
Si1—O11.6111 (19)Si6—O13iv1.6052 (19)
Si1—O1i1.6111 (19)Si6—O71.6138 (17)
Si2—O2i1.577 (3)Si7—O11v1.5995 (16)
Si2—O21.577 (3)Si7—O12vi1.6011 (18)
Si2—O31.5939 (18)Si7—O14iv1.6098 (17)
Si2—O3ii1.5939 (18)Si7—O71.6108 (16)
Si2—O3i1.5939 (18)Si8—O9iii1.6051 (17)
Si3—O31.5998 (19)Si8—O1iii1.606 (2)
Si3—O111.6046 (17)Si8—O81.6069 (18)
Si3—O51.6051 (16)Si8—O141.6076 (17)
Si3—O41.6063 (16)O1—Si8vii1.6057 (19)
Si4—O101.5998 (17)O2—O2i0.000 (6)
Si4—O41.6022 (16)O9—Si8vii1.6050 (17)
Si4—O10iii1.6053 (16)O10—Si4vii1.6052 (16)
Si4—O91.6070 (17)O11—Si7v1.5996 (16)
Si5—O81.6029 (18)O12—Si7iv1.6011 (18)
Si5—O51.6042 (17)O13—Si6vi1.6052 (19)
Si5—O61.6081 (18)O14—Si7vi1.6098 (17)
O2i—Si1—O1ii109.36 (7)O5—Si5—O12109.10 (10)
O2—Si1—O1ii109.36 (7)O6—Si5—O12110.41 (9)
O2i—Si1—O1109.36 (7)O13—Si6—O6109.80 (10)
O2—Si1—O1109.36 (7)O13—Si6—O13iv108.34 (15)
O1ii—Si1—O1109.58 (7)O6—Si6—O13iv110.40 (10)
O2i—Si1—O1i109.36 (7)O13—Si6—O7110.07 (10)
O2—Si1—O1i109.36 (7)O6—Si6—O7108.60 (9)
O1ii—Si1—O1i109.58 (7)O13iv—Si6—O7109.63 (10)
O1—Si1—O1i109.58 (7)O11v—Si7—O12vi109.87 (10)
O2i—Si2—O3109.31 (8)O11v—Si7—O14iv109.44 (9)
O2—Si2—O3109.31 (8)O12vi—Si7—O14iv108.90 (10)
O2i—Si2—O3ii109.31 (8)O11v—Si7—O7109.71 (9)
O2—Si2—O3ii109.31 (8)O12vi—Si7—O7110.18 (10)
O3—Si2—O3ii109.63 (8)O14iv—Si7—O7108.71 (10)
O2i—Si2—O3i109.31 (8)O9iii—Si8—O1iii110.52 (10)
O2—Si2—O3i109.31 (8)O9iii—Si8—O8109.13 (10)
O3—Si2—O3i109.63 (8)O1iii—Si8—O8108.72 (11)
O3ii—Si2—O3i109.63 (8)O9iii—Si8—O14109.60 (9)
O3—Si3—O11109.83 (10)O1iii—Si8—O14108.89 (10)
O3—Si3—O5109.52 (11)O8—Si8—O14109.95 (10)
O11—Si3—O5107.66 (9)Si8vii—O1—Si1145.60 (12)
O3—Si3—O4110.58 (10)Si2—O2—Si1180.0
O11—Si3—O4109.15 (10)Si2—O3—Si3169.40 (15)
O5—Si3—O4110.04 (10)Si4—O4—Si3172.19 (14)
O10—Si4—O4111.08 (10)Si5—O5—Si3145.43 (12)
O10—Si4—O10iii109.83 (14)Si6—O6—Si5150.41 (13)
O4—Si4—O10iii109.40 (11)Si7—O7—Si6140.35 (12)
O10—Si4—O9109.57 (10)Si5—O8—Si8155.35 (14)
O4—Si4—O9108.62 (10)Si8vii—O9—Si4152.27 (12)
O10iii—Si4—O9108.29 (9)Si4—O10—Si4vii163.57 (12)
O8—Si5—O5107.99 (10)Si7v—O11—Si3154.76 (12)
O8—Si5—O6110.46 (11)Si7iv—O12—Si5153.67 (12)
O5—Si5—O6108.87 (9)Si6—O13—Si6vi159.21 (13)
O8—Si5—O12109.95 (10)Si8—O14—Si7vi148.69 (11)
O2i—Si1—O1—Si8vii102.7 (2)O6—Si6—O7—Si7177.87 (17)
O2—Si1—O1—Si8vii102.7 (2)O13iv—Si6—O7—Si761.4 (2)
O1ii—Si1—O1—Si8vii17.2 (3)O5—Si5—O8—Si8163.2 (3)
O1i—Si1—O1—Si8vii137.45 (14)O6—Si5—O8—Si877.9 (3)
O2i—Si2—O3—Si317.4 (8)O12—Si5—O8—Si844.2 (4)
O2—Si2—O3—Si317.4 (8)O9iii—Si8—O8—Si5165.3 (3)
O3ii—Si2—O3—Si3102.4 (9)O1iii—Si8—O8—Si544.7 (4)
O3i—Si2—O3—Si3137.2 (8)O14—Si8—O8—Si574.4 (4)
O11—Si3—O3—Si2126.7 (8)O10—Si4—O9—Si8vii39.6 (3)
O5—Si3—O3—Si2115.2 (8)O4—Si4—O9—Si8vii81.9 (3)
O4—Si3—O3—Si26.2 (8)O10iii—Si4—O9—Si8vii159.4 (3)
O8—Si5—O5—Si366.6 (2)O4—Si4—O10—Si4vii6.9 (5)
O6—Si5—O5—Si3173.5 (2)O10iii—Si4—O10—Si4vii128.1 (5)
O12—Si5—O5—Si352.9 (2)O9—Si4—O10—Si4vii113.1 (5)
O3—Si3—O5—Si565.9 (2)O3—Si3—O11—Si7v19.1 (3)
O11—Si3—O5—Si5174.7 (2)O5—Si3—O11—Si7v100.1 (3)
O4—Si3—O5—Si555.9 (2)O4—Si3—O11—Si7v140.5 (3)
O13—Si6—O6—Si570.3 (3)O8—Si5—O12—Si7iv90.9 (3)
O13iv—Si6—O6—Si549.1 (3)O5—Si5—O12—Si7iv150.9 (3)
O7—Si6—O6—Si5169.3 (2)O6—Si5—O12—Si7iv31.3 (3)
O8—Si5—O6—Si672.2 (3)O6—Si6—O13—Si6vi117.9 (4)
O5—Si5—O6—Si6169.4 (3)O13iv—Si6—O13—Si6vi121.4 (4)
O12—Si5—O6—Si649.6 (3)O7—Si6—O13—Si6vi1.6 (4)
O11v—Si7—O7—Si6164.26 (18)O9iii—Si8—O14—Si7vi19.9 (3)
O12vi—Si7—O7—Si674.6 (2)O1iii—Si8—O14—Si7vi140.9 (2)
O14iv—Si7—O7—Si644.6 (2)O8—Si8—O14—Si7vi100.1 (2)
O13—Si6—O7—Si757.6 (2)
Symmetry codes: (i) x+y, x, z; (ii) y, xy, z; (iii) y1/3, x+y+1/3, z+1/3; (iv) y2/3, x+y1/3, z+2/3; (v) x+1/3, y+2/3, z+2/3; (vi) xy+1/3, x+2/3, z+2/3; (vii) xy+2/3, x+1/3, z+1/3.

Experimental details

Crystal data
Chemical formulaO120Si60
Mr3605.40
Crystal system, space groupTrigonal, R3
Temperature (K)183
a, c (Å)13.7761 (1), 41.5456 (6)
V3)6828.23 (12)
Z2
Radiation typeMo Kα
µ (mm1)0.66
Crystal size (mm)0.26 × 0.22 × 0.08
Data collection
DiffractometerCCD area detector
diffractometer
Absorption correctionMulti-scan
SADABS (Sheldrick, 2001)
Tmin, Tmax0.880, 0.949
No. of measured, independent and
observed (I > 2σI) reflections
44259, 3622, 3556
Rint0.031
(sin θ/λ)max1)0.667
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.024, 0.082, 0.95
No. of reflections3622
No. of parameters184
Δρmax, Δρmin (e Å3)1.13, 0.34

Computer programs: SMART(Siemens, 1995), SAINT (Siemens, 1995)& SADABS (Sheldrick, 2001), SHELXTL (Bruker, 2001), DIAMOND (Brandenburg, 2005).

 

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