Key indicators
- Single-crystal X-ray study
- T = 88 K
- Mean (C-C) = 0.016 Å
- Disorder in solvent or counterion
- R factor = 0.053
- wR factor = 0.127
- Data-to-parameter ratio = 9.3
checkCIF/PLATON results
No syntax errors found
Alert level A
RINTA01_ALERT_3_A The value of Rint is greater than 0.20
Rint given 0.328
| Author Response: ...
Reflections were affected by surface powder diffraction. Subsequent
downweighting was applied by the processing program.
|
PLAT020_ALERT_3_A The value of Rint is greater than 0.10 ......... 0.33
| Author Response: ...
Reflections were affected by surface powder diffraction. Subsequent
downweighting was applied by the processing program.
|
PLAT026_ALERT_3_A Ratio Observed / Unique Reflections too Low .... 22 Perc.
| Author Response: ...
The best crystals that could be obtained diffracted weakly, consistent
with maximum size and occluded partial disordered solvent.
|
PLAT093_ALERT_1_A No su's on H-atoms, but refinement reported as . mixed
PLAT432_ALERT_2_A Short Inter X...Y Contact C33 .. C61 .. 2.65 Ang.
| Author Response: ...
These atoms are part of the model for coping with the disordered
diethyl solvent; no physical significance should be attached to
their relative positions.
|
PLAT432_ALERT_2_A Short Inter X...Y Contact C34 .. C61 .. 2.65 Ang.
| Author Response: ...
These atoms are part of the model for coping with the disordered
diethyl solvent; no physical significance should be attached to
their relative positions.
|
PLAT432_ALERT_2_A Short Inter X...Y Contact C55 .. C61 .. 2.15 Ang.
| Author Response: ...
These atoms are part of the model for coping with the disordered
diethyl solvent; no physical significance should be attached to
their relative positions.
|
PLAT432_ALERT_2_A Short Inter X...Y Contact C57 .. C61 .. 2.14 Ang.
| Author Response: ...
These atoms are part of the model for coping with the disordered
diethyl solvent; no physical significance should be attached to
their relative positions.
|
Alert level B
ABSTM02_ALERT_3_B The ratio of expected to reported Tmax/Tmin(RR') is < 0.75
Tmin and Tmax reported: 0.597 0.986
Tmin(prime) and Tmax expected: 0.960 0.986
RR(prime) = 0.622
Please check that your absorption correction is appropriate.
PLAT061_ALERT_3_B Tmax/Tmin Range Test RR' too Large ............. 0.62
PLAT201_ALERT_2_B Isotropic non-H Atoms in Main Residue(s) ....... 2
PLAT241_ALERT_2_B Check High Ueq as Compared to Neighbors for C30
PLAT241_ALERT_2_B Check High Ueq as Compared to Neighbors for C40
PLAT340_ALERT_3_B Low Bond Precision on C-C bonds (x 1000) Ang ... 16
PLAT432_ALERT_2_B Short Inter X...Y Contact C25 .. C61 .. 2.97 Ang.
| Author Response: ...
These atoms are part of the model for coping with the disordered
diethyl solvent; no physical significance should be attached to
their relative positions.
|
PLAT432_ALERT_2_B Short Inter X...Y Contact C51 .. C61 .. 2.95 Ang.
| Author Response: ...
These atoms are part of the model for coping with the disordered
diethyl solvent; no physical significance should be attached to
their relative positions.
|
PLAT432_ALERT_2_B Short Inter X...Y Contact C52 .. C61 .. 3.08 Ang.
| Author Response: ...
These atoms are part of the model for coping with the disordered
diethyl solvent; no physical significance should be attached to
their relative positions.
|
Alert level C
ABSMU01_ALERT_1_C The ratio of given/expected absorption coefficient lies
outside the range 0.99 <> 1.01
Calculated value of mu = 0.082
Value of mu given = 0.081
GOODF01_ALERT_2_C The least squares goodness of fit parameter lies
outside the range 0.80 <> 2.00
Goodness of fit given = 0.770
PLAT041_ALERT_1_C Calc. and Rep. SumFormula Strings Differ .... ?
PLAT042_ALERT_1_C Calc. and Rep. MoietyFormula Strings Differ .... ?
PLAT068_ALERT_1_C Reported F000 Differs from Calcd (or Missing)... ?
PLAT202_ALERT_3_C Isotropic non-H Atoms in Anion/Solvent ......... 5
PLAT220_ALERT_2_C Large Non-Solvent C Ueq(max)/Ueq(min) ... 2.52 Ratio
PLAT241_ALERT_2_C Check High Ueq as Compared to Neighbors for C20
PLAT241_ALERT_2_C Check High Ueq as Compared to Neighbors for C33
PLAT242_ALERT_2_C Check Low Ueq as Compared to Neighbors for O2
PLAT242_ALERT_2_C Check Low Ueq as Compared to Neighbors for O3
PLAT242_ALERT_2_C Check Low Ueq as Compared to Neighbors for O4
PLAT242_ALERT_2_C Check Low Ueq as Compared to Neighbors for C31
PLAT242_ALERT_2_C Check Low Ueq as Compared to Neighbors for C41
PLAT302_ALERT_4_C Anion/Solvent Disorder ......................... 51.00 Perc.
PLAT432_ALERT_2_C Short Inter X...Y Contact C26 .. C60 .. 3.17 Ang.
| Author Response: ...
These atoms are part of the model for coping with the disordered
diethyl solvent; no physical significance should be attached to
their relative positions.
|
PLAT480_ALERT_4_C Long H...A H-Bond Reported H14 .. N3 .. 2.70 Ang.
PLAT480_ALERT_4_C Long H...A H-Bond Reported H20B .. N3 .. 2.65 Ang.
PLAT764_ALERT_4_C Overcomplete CIF Bond List Detected (Rep/Expd) . 1.24 Ratio
Alert level G
REFLT03_ALERT_4_G Please check that the estimate of the number of Friedel pairs is
correct. If it is not, please give the correct count in the
_publ_section_exptl_refinement section of the submitted CIF.
From the CIF: _diffrn_reflns_theta_max 26.40
From the CIF: _reflns_number_total 4038
Count of symmetry unique reflns 4050
Completeness (_total/calc) 99.70%
TEST3: Check Friedels for noncentro structure
Estimate of Friedel pairs measured 0
Fraction of Friedel pairs measured 0.000
Are heavy atom types Z>Si present no
8 ALERT level A = In general: serious problem
9 ALERT level B = Potentially serious problem
19 ALERT level C = Check and explain
1 ALERT level G = General alerts; check
5 ALERT type 1 CIF construction/syntax error, inconsistent or missing data
20 ALERT type 2 Indicator that the structure model may be wrong or deficient
7 ALERT type 3 Indicator that the structure quality may be low
5 ALERT type 4 Improvement, methodology, query or suggestion
1D-3,4,5,6-Tetra-O-benzy-myo-inositol was treated with methanesulfonyl chloride in pyridine overnight at room temperature to give the 1,2-dimesylate, which was then subjected to a displacement reaction using sodium azide in dimethylformamide overnight at 383 K. [Please give brief details of quantities] Crystals of the title compound were isolated from diethyl ether.
All non-H atoms except C23 and C24 were refined with anisotropic displacement parameters. Friedel-related reflections were merged. The H atoms of the amino (N1) and hydroxyl (O1) atoms were positionally refined. All C-bound H atoms were constrained to their expected geometries, with C—H(methyl) = 0.98 Å and the remaining C—H = 1.0 Å. For all H atoms, Uiso(H) = 1.2Ueq(parent atom). The disordered diethyl ether was modelled with density at 11 atomic sites using C atoms only and a common Uiso; no extra O or H atoms were included for the ether solvate. Models of diethyl ether in two main orientations fit on these positions, but no rational model could be constructed. On the basis of the total electron density, about 0.62 of a diethyl ether molecule per asymmetric unit was found.
Data collection: SMART (Siemens, 1996); cell refinement: SMART; data reduction: SAINT (Siemens, 1996); program(s) used to solve structure: SHELXS97 (Sheldrick, 1997); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: ORTEP-3 for Windows (Farrugia, 1997); software used to prepare material for publication: SHELXL97 and PLATON (Spek, 2003).
1D-1,2-diazido-1,2-dideoxy-3,4,5,6-tetra-
O-benzyl-myo-inositol diethyl ether 0.6-solvate
top
Crystal data top
C34H34N6O4·0.6C4H10O | F(000) = 1356 |
Mr = 655.53 | Dx = 1.241 Mg m−3 |
Orthorhombic, P212121 | Mo Kα radiation, λ = 0.71073 Å |
Hall symbol: P 2ac 2ab | Cell parameters from 895 reflections |
a = 9.006 (3) Å | θ = 2.6–14.6° |
b = 15.324 (6) Å | µ = 0.08 mm−1 |
c = 25.424 (11) Å | T = 88 K |
V = 3509 (2) Å3 | Needle, colourless |
Z = 4 | 0.50 × 0.22 × 0.18 mm |
Data collection top
Bruker SMART CCD area-detector diffractometer | 4038 independent reflections |
Radiation source: fine-focus sealed tube | 908 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.328 |
Detector resolution: 8.192 pixels mm-1 | θmax = 26.4°, θmin = 2.1° |
ϕ and ω scans | h = −10→11 |
Absorption correction: multi-scan (SADABS; Blessing, 1995; Sheldrick, 1996) | k = −19→19 |
Tmin = 0.597, Tmax = 0.986 | l = −31→28 |
19603 measured reflections | |
Refinement top
Refinement on F2 | Primary atom site location: structure-invariant direct methods |
Least-squares matrix: full | Secondary atom site location: difference Fourier map |
R[F2 > 2σ(F2)] = 0.053 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.127 | H atoms treated by a mixture of independent and constrained refinement |
S = 0.77 | w = 1/[σ2(Fo2) + (0.0367P)2] where P = (Fo2 + 2Fc2)/3 |
4038 reflections | (Δ/σ)max = 0.001 |
432 parameters | Δρmax = 0.16 e Å−3 |
0 restraints | Δρmin = −0.20 e Å−3 |
Crystal data top
C34H34N6O4·0.6C4H10O | V = 3509 (2) Å3 |
Mr = 655.53 | Z = 4 |
Orthorhombic, P212121 | Mo Kα radiation |
a = 9.006 (3) Å | µ = 0.08 mm−1 |
b = 15.324 (6) Å | T = 88 K |
c = 25.424 (11) Å | 0.50 × 0.22 × 0.18 mm |
Data collection top
Bruker SMART CCD area-detector diffractometer | 4038 independent reflections |
Absorption correction: multi-scan (SADABS; Blessing, 1995; Sheldrick, 1996) | 908 reflections with I > 2σ(I) |
Tmin = 0.597, Tmax = 0.986 | Rint = 0.328 |
19603 measured reflections | |
Refinement top
R[F2 > 2σ(F2)] = 0.053 | 0 restraints |
wR(F2) = 0.127 | H atoms treated by a mixture of independent and constrained refinement |
S = 0.77 | Δρmax = 0.16 e Å−3 |
4038 reflections | Δρmin = −0.20 e Å−3 |
432 parameters | |
Special details top
Experimental. Crystal decay was monitored by repeating the initial 10 frames at the end of the data collection and analyzing duplicate reflections. The standard 0.8 mm diameter collimator was used. |
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 | Occ. (<1) |
O1 | 0.7436 (6) | 0.3110 (4) | 0.1485 (2) | 0.0547 (17) | |
O2 | 0.7278 (6) | 0.1551 (4) | 0.0859 (2) | 0.0522 (17) | |
O3 | 0.8286 (5) | 0.1748 (4) | −0.0209 (2) | 0.0477 (16) | |
O4 | 0.7249 (6) | 0.3301 (3) | −0.0704 (2) | 0.0451 (15) | |
N1 | 0.7476 (11) | 0.4853 (7) | −0.0070 (3) | 0.076 (3) | |
N2 | 0.6674 (12) | 0.5128 (6) | −0.0405 (4) | 0.080 (3) | |
N3 | 0.5965 (14) | 0.5481 (7) | −0.0733 (4) | 0.105 (4) | |
N4 | 0.8966 (10) | 0.4188 (6) | 0.0776 (3) | 0.067 (3) | |
N5 | 0.9346 (8) | 0.4555 (7) | 0.1199 (4) | 0.076 (3) | |
N6 | 0.9805 (10) | 0.4868 (7) | 0.1563 (4) | 0.095 (4) | |
C1 | 0.6971 (9) | 0.3995 (6) | 0.0131 (3) | 0.045 (2) | |
H1 | 0.5874 | 0.3930 | 0.0082 | 0.054* | |
C2 | 0.7362 (10) | 0.3986 (6) | 0.0714 (3) | 0.049 (2) | |
H2 | 0.6763 | 0.4441 | 0.0900 | 0.058* | |
C3 | 0.7012 (9) | 0.3103 (6) | 0.0944 (4) | 0.050 (3) | |
H3 | 0.5916 | 0.3008 | 0.0922 | 0.060* | |
C4 | 0.7785 (9) | 0.2368 (6) | 0.0649 (3) | 0.049 (2) | |
H4 | 0.8883 | 0.2417 | 0.0700 | 0.058* | |
C5 | 0.7432 (9) | 0.2396 (5) | 0.0064 (3) | 0.044 (2) | |
H5 | 0.6351 | 0.2272 | 0.0012 | 0.053* | |
C6 | 0.7795 (9) | 0.3291 (6) | −0.0171 (3) | 0.046 (2) | |
H6 | 0.8889 | 0.3401 | −0.0163 | 0.056* | |
C10 | 0.6367 (10) | 0.2744 (6) | 0.1831 (3) | 0.060 (3) | |
H10A | 0.6218 | 0.2118 | 0.1751 | 0.073* | |
H10B | 0.5404 | 0.3049 | 0.1793 | 0.073* | |
C11 | 0.6970 (10) | 0.2856 (8) | 0.2388 (4) | 0.057 (3) | |
C12 | 0.7496 (10) | 0.3635 (7) | 0.2570 (4) | 0.061 (3) | |
H12 | 0.7446 | 0.4136 | 0.2351 | 0.073* | |
C13 | 0.8094 (11) | 0.3703 (7) | 0.3062 (4) | 0.072 (3) | |
H13 | 0.8445 | 0.4251 | 0.3185 | 0.086* | |
C14 | 0.8187 (11) | 0.2975 (8) | 0.3382 (4) | 0.074 (3) | |
H14 | 0.8598 | 0.3023 | 0.3725 | 0.089* | |
C15 | 0.7697 (12) | 0.2198 (7) | 0.3208 (4) | 0.082 (3) | |
H15 | 0.7764 | 0.1700 | 0.3430 | 0.098* | |
C16 | 0.7088 (9) | 0.2114 (7) | 0.2702 (4) | 0.067 (3) | |
H16 | 0.6762 | 0.1562 | 0.2577 | 0.080* | |
C20 | 0.8410 (11) | 0.1078 (7) | 0.1139 (4) | 0.096 (4) | |
H20A | 0.8894 | 0.1462 | 0.1401 | 0.115* | |
H20B | 0.9177 | 0.0864 | 0.0892 | 0.115* | |
C21 | 0.7654 (16) | 0.0311 (8) | 0.1413 (5) | 0.088 (4) | |
C22 | 0.8293 (11) | 0.0112 (7) | 0.1900 (5) | 0.090 (4) | |
H22 | 0.9091 | 0.0457 | 0.2029 | 0.108* | |
C23 | 0.7766 (14) | −0.0590 (7) | 0.2197 (5) | 0.106 (4)* | |
H23 | 0.8199 | −0.0742 | 0.2526 | 0.127* | |
C24 | 0.6635 (15) | −0.1032 (7) | 0.1999 (5) | 0.107 (5)* | |
H24 | 0.6271 | −0.1507 | 0.2201 | 0.129* | |
C25 | 0.5942 (13) | −0.0871 (9) | 0.1531 (6) | 0.111 (4) | |
H25 | 0.5120 | −0.1208 | 0.1415 | 0.133* | |
C26 | 0.6519 (14) | −0.0166 (9) | 0.1225 (6) | 0.106 (5) | |
H26 | 0.6105 | −0.0035 | 0.0890 | 0.127* | |
C30 | 0.7428 (11) | 0.1059 (7) | −0.0402 (4) | 0.094 (4) | |
H30A | 0.6617 | 0.1298 | −0.0622 | 0.113* | |
H30B | 0.6969 | 0.0746 | −0.0102 | 0.113* | |
C31 | 0.8306 (11) | 0.0438 (8) | −0.0716 (6) | 0.068 (4) | |
C32 | 0.8859 (13) | −0.0288 (10) | −0.0474 (5) | 0.082 (4) | |
H32 | 0.8670 | −0.0383 | −0.0111 | 0.099* | |
C33 | 0.9672 (17) | −0.0869 (10) | −0.0747 (7) | 0.109 (5) | |
H33 | 1.0062 | −0.1359 | −0.0563 | 0.131* | |
C34 | 0.9964 (12) | −0.0800 (9) | −0.1260 (7) | 0.092 (4) | |
H34 | 1.0544 | −0.1229 | −0.1435 | 0.110* | |
C35 | 0.9387 (13) | −0.0068 (11) | −0.1541 (4) | 0.078 (3) | |
H35 | 0.9548 | −0.0002 | −0.1908 | 0.093* | |
C36 | 0.8576 (13) | 0.0548 (8) | −0.1254 (6) | 0.079 (4) | |
H36 | 0.8202 | 0.1051 | −0.1428 | 0.094* | |
C40 | 0.8304 (10) | 0.3439 (7) | −0.1094 (3) | 0.089 (4) | |
H40A | 0.9110 | 0.3004 | −0.1057 | 0.107* | |
H40B | 0.8743 | 0.4027 | −0.1051 | 0.107* | |
C41 | 0.7624 (11) | 0.3364 (7) | −0.1631 (3) | 0.050 (3) | |
C42 | 0.6582 (11) | 0.2761 (6) | −0.1741 (4) | 0.053 (3) | |
H42 | 0.6249 | 0.2376 | −0.1473 | 0.064* | |
C43 | 0.5992 (11) | 0.2697 (6) | −0.2243 (5) | 0.068 (3) | |
H43 | 0.5252 | 0.2272 | −0.2316 | 0.081* | |
C44 | 0.6467 (12) | 0.3238 (8) | −0.2628 (4) | 0.074 (3) | |
H44 | 0.6069 | 0.3188 | −0.2973 | 0.089* | |
C45 | 0.7535 (13) | 0.3865 (6) | −0.2520 (4) | 0.073 (3) | |
H45 | 0.7852 | 0.4255 | −0.2788 | 0.088* | |
C46 | 0.8135 (11) | 0.3919 (6) | −0.2021 (4) | 0.064 (3) | |
H46 | 0.8890 | 0.4333 | −0.1946 | 0.076* | |
C51 | 0.541 (5) | −0.171 (4) | −0.001 (2) | 0.205 (6)* | 0.65 (5) |
C52 | 0.387 (4) | −0.170 (2) | −0.0678 (14) | 0.205 (6)* | 0.73 (4) |
C53 | 0.389 (4) | −0.220 (3) | −0.036 (2) | 0.205 (6)* | 0.63 (4) |
C54 | 0.508 (4) | −0.1490 (19) | −0.0428 (19) | 0.205 (6)* | 0.71 (4) |
C55 | 0.305 (4) | −0.254 (2) | −0.0731 (15) | 0.205 (6)* | 0.63 (3) |
C56 | 0.657 (7) | −0.230 (3) | −0.009 (2) | 0.205 (6)* | 0.45 (3) |
C57 | 0.218 (5) | −0.285 (2) | −0.038 (2) | 0.205 (6)* | 0.50 (3) |
C58 | 0.304 (7) | −0.223 (3) | 0.0128 (17) | 0.205 (6)* | 0.44 (3) |
C59 | 0.438 (7) | −0.163 (4) | 0.042 (3) | 0.205 (6)* | 0.32 (3) |
C60 | 0.578 (9) | −0.102 (8) | 0.012 (3) | 0.205 (6)* | 0.22 (3) |
C61 | 0.081 (13) | −0.240 (8) | −0.101 (5) | 0.205 (6)* | 0.132 (18) |
Atomic displacement parameters (Å2) top | U11 | U22 | U33 | U12 | U13 | U23 |
O1 | 0.046 (4) | 0.083 (5) | 0.035 (4) | 0.002 (4) | 0.010 (3) | 0.009 (4) |
O2 | 0.036 (4) | 0.060 (5) | 0.061 (4) | −0.002 (3) | 0.001 (3) | 0.019 (4) |
O3 | 0.031 (4) | 0.057 (4) | 0.055 (4) | −0.011 (4) | −0.005 (3) | 0.000 (4) |
O4 | 0.035 (4) | 0.061 (4) | 0.040 (4) | 0.002 (3) | 0.003 (3) | −0.004 (4) |
N1 | 0.094 (8) | 0.083 (8) | 0.050 (7) | 0.011 (6) | −0.004 (6) | 0.002 (6) |
N2 | 0.097 (11) | 0.059 (9) | 0.084 (11) | −0.024 (7) | 0.039 (8) | −0.013 (8) |
N3 | 0.151 (11) | 0.084 (9) | 0.079 (10) | −0.024 (7) | 0.013 (7) | 0.002 (6) |
N4 | 0.069 (7) | 0.085 (7) | 0.046 (6) | 0.000 (5) | 0.013 (5) | 0.003 (5) |
N5 | 0.032 (6) | 0.134 (11) | 0.061 (8) | −0.002 (6) | 0.012 (6) | 0.000 (8) |
N6 | 0.064 (7) | 0.147 (10) | 0.073 (8) | −0.011 (6) | 0.012 (5) | −0.042 (7) |
C1 | 0.038 (6) | 0.037 (6) | 0.059 (7) | −0.003 (5) | 0.001 (5) | 0.008 (6) |
C2 | 0.022 (6) | 0.073 (8) | 0.051 (7) | 0.003 (5) | 0.006 (5) | −0.005 (6) |
C3 | 0.042 (7) | 0.056 (7) | 0.052 (7) | −0.007 (5) | 0.002 (5) | 0.020 (6) |
C4 | 0.029 (6) | 0.065 (8) | 0.053 (7) | −0.001 (5) | −0.007 (5) | 0.007 (6) |
C5 | 0.029 (6) | 0.054 (7) | 0.049 (7) | 0.010 (5) | −0.005 (5) | −0.009 (6) |
C6 | 0.039 (6) | 0.045 (6) | 0.055 (7) | −0.001 (5) | 0.011 (5) | −0.003 (6) |
C10 | 0.051 (7) | 0.079 (8) | 0.051 (7) | −0.001 (6) | 0.010 (6) | 0.002 (6) |
C11 | 0.053 (7) | 0.060 (8) | 0.058 (8) | −0.003 (6) | 0.006 (6) | 0.008 (7) |
C12 | 0.057 (8) | 0.074 (9) | 0.052 (8) | 0.012 (7) | 0.006 (6) | 0.008 (6) |
C13 | 0.084 (9) | 0.081 (10) | 0.050 (8) | 0.013 (7) | 0.019 (7) | −0.002 (7) |
C14 | 0.090 (9) | 0.082 (9) | 0.049 (7) | −0.024 (7) | −0.018 (6) | −0.005 (8) |
C15 | 0.110 (9) | 0.081 (9) | 0.054 (8) | −0.029 (8) | 0.008 (7) | 0.010 (6) |
C16 | 0.054 (7) | 0.093 (10) | 0.054 (7) | −0.019 (6) | −0.007 (5) | −0.019 (7) |
C20 | 0.054 (8) | 0.096 (9) | 0.138 (11) | 0.020 (7) | 0.012 (7) | 0.073 (8) |
C21 | 0.093 (12) | 0.083 (11) | 0.087 (10) | 0.057 (9) | 0.015 (9) | 0.030 (8) |
C22 | 0.085 (9) | 0.071 (9) | 0.113 (10) | −0.020 (8) | 0.034 (8) | −0.008 (8) |
C25 | 0.047 (9) | 0.120 (11) | 0.165 (15) | −0.003 (8) | 0.033 (9) | −0.009 (10) |
C26 | 0.048 (10) | 0.108 (12) | 0.162 (15) | 0.009 (8) | 0.017 (9) | −0.031 (11) |
C30 | 0.068 (9) | 0.072 (8) | 0.141 (11) | −0.006 (8) | 0.030 (8) | −0.019 (8) |
C31 | 0.048 (8) | 0.042 (9) | 0.114 (13) | −0.016 (7) | −0.017 (8) | 0.003 (9) |
C32 | 0.075 (10) | 0.081 (11) | 0.091 (11) | −0.032 (8) | 0.009 (8) | −0.026 (11) |
C33 | 0.145 (14) | 0.088 (12) | 0.094 (13) | −0.029 (11) | −0.026 (11) | 0.029 (11) |
C34 | 0.086 (10) | 0.068 (11) | 0.121 (14) | −0.014 (8) | −0.012 (10) | −0.024 (10) |
C35 | 0.066 (9) | 0.111 (12) | 0.057 (9) | −0.020 (8) | −0.003 (7) | 0.002 (10) |
C36 | 0.057 (9) | 0.092 (11) | 0.087 (11) | −0.012 (8) | −0.023 (7) | 0.004 (10) |
C40 | 0.058 (8) | 0.169 (11) | 0.039 (7) | −0.013 (8) | −0.001 (6) | 0.012 (7) |
C41 | 0.039 (7) | 0.075 (8) | 0.038 (6) | 0.003 (6) | 0.013 (5) | −0.001 (6) |
C42 | 0.042 (7) | 0.065 (8) | 0.053 (8) | 0.010 (6) | 0.000 (5) | 0.031 (6) |
C43 | 0.075 (8) | 0.042 (8) | 0.086 (9) | −0.015 (6) | 0.021 (7) | −0.006 (7) |
C44 | 0.086 (9) | 0.087 (10) | 0.049 (8) | −0.006 (8) | −0.011 (6) | −0.021 (8) |
C45 | 0.103 (10) | 0.067 (8) | 0.050 (8) | −0.004 (8) | 0.003 (7) | 0.013 (6) |
C46 | 0.070 (8) | 0.067 (8) | 0.053 (8) | −0.013 (6) | 0.002 (6) | −0.015 (6) |
Geometric parameters (Å, º) top
O1—C10 | 1.418 (8) | C23—H23 | 0.9500 |
O1—C3 | 1.429 (8) | C24—C25 | 1.367 (14) |
O2—C4 | 1.435 (8) | C24—H24 | 0.9500 |
O2—C20 | 1.440 (9) | C25—C26 | 1.430 (14) |
O3—C30 | 1.397 (9) | C25—H25 | 0.9500 |
O3—C5 | 1.435 (8) | C26—H26 | 0.9500 |
O4—C40 | 1.389 (8) | C30—C31 | 1.474 (13) |
O4—C6 | 1.442 (8) | C30—H30A | 0.9900 |
N1—N2 | 1.194 (11) | C30—H30B | 0.9900 |
N1—C1 | 1.482 (10) | C31—C32 | 1.365 (13) |
N2—N3 | 1.180 (11) | C31—C36 | 1.400 (12) |
N4—N5 | 1.261 (10) | C32—C33 | 1.345 (14) |
N4—C2 | 1.486 (10) | C32—H32 | 0.9500 |
N5—N6 | 1.122 (10) | C33—C34 | 1.335 (13) |
C1—C6 | 1.518 (9) | C33—H33 | 0.9500 |
C1—C2 | 1.522 (9) | C34—C35 | 1.427 (12) |
C1—H1 | 1.0000 | C34—H34 | 0.9500 |
C2—C3 | 1.507 (10) | C35—C36 | 1.399 (13) |
C2—H2 | 1.0000 | C35—H35 | 0.9500 |
C3—C4 | 1.522 (10) | C36—H36 | 0.9500 |
C3—H3 | 1.0000 | C40—C41 | 1.500 (10) |
C4—C5 | 1.520 (9) | C40—H40A | 0.9900 |
C4—H4 | 1.0000 | C40—H40B | 0.9900 |
C5—C6 | 1.532 (9) | C41—C42 | 1.347 (11) |
C5—H5 | 1.0000 | C41—C46 | 1.386 (10) |
C6—H6 | 1.0000 | C42—C43 | 1.385 (11) |
C10—C11 | 1.526 (11) | C42—H42 | 0.9500 |
C10—H10A | 0.9900 | C43—C44 | 1.353 (11) |
C10—H10B | 0.9900 | C43—H43 | 0.9500 |
C11—C12 | 1.364 (10) | C44—C45 | 1.387 (11) |
C11—C16 | 1.394 (10) | C44—H44 | 0.9500 |
C12—C13 | 1.367 (11) | C45—C46 | 1.381 (11) |
C12—H12 | 0.9500 | C45—H45 | 0.9500 |
C13—C14 | 1.383 (10) | C46—H46 | 0.9500 |
C13—H13 | 0.9500 | C51—C56 | 1.40 (6) |
C14—C15 | 1.344 (10) | C51—C59 | 1.44 (6) |
C14—H14 | 0.9500 | C52—C54 | 1.31 (4) |
C15—C16 | 1.404 (10) | C52—C55 | 1.49 (5) |
C15—H15 | 0.9500 | C53—C55 | 1.31 (4) |
C16—H16 | 0.9500 | C53—C58 | 1.47 (5) |
C20—C21 | 1.528 (13) | C53—C54 | 1.54 (5) |
C20—H20A | 0.9900 | C54—C60 | 1.69 (11) |
C20—H20B | 0.9900 | C55—C57 | 1.27 (5) |
C21—C26 | 1.344 (14) | C56—C57i | 1.35 (5) |
C21—C22 | 1.397 (13) | C56—C58i | 1.50 (6) |
C22—C23 | 1.399 (12) | C57—C56ii | 1.35 (5) |
C22—H22 | 0.9500 | C58—C56ii | 1.50 (6) |
C23—C24 | 1.323 (13) | | |
| | | |
C10—O1—C3 | 114.4 (6) | C21—C20—H20A | 110.2 |
C4—O2—C20 | 113.5 (7) | O2—C20—H20B | 110.2 |
C30—O3—C5 | 113.3 (7) | C21—C20—H20B | 110.2 |
C40—O4—C6 | 116.1 (6) | H20A—C20—H20B | 108.5 |
N2—N1—C1 | 111.9 (10) | C26—C21—C22 | 120.8 (13) |
N3—N2—N1 | 172.9 (13) | C26—C21—C20 | 126.4 (14) |
N5—N4—C2 | 116.6 (8) | C22—C21—C20 | 112.8 (14) |
N6—N5—N4 | 174.1 (11) | C21—C22—C23 | 120.4 (12) |
N1—C1—C6 | 107.7 (7) | C21—C22—H22 | 119.8 |
N1—C1—C2 | 105.8 (8) | C23—C22—H22 | 119.8 |
C6—C1—C2 | 111.9 (7) | C24—C23—C22 | 116.7 (12) |
N1—C1—H1 | 110.4 | C24—C23—H23 | 121.7 |
C6—C1—H1 | 110.4 | C22—C23—H23 | 121.7 |
C2—C1—H1 | 110.4 | C23—C24—C25 | 126.2 (13) |
N4—C2—C3 | 110.4 (7) | C23—C24—H24 | 116.9 |
N4—C2—C1 | 109.1 (7) | C25—C24—H24 | 116.9 |
C3—C2—C1 | 109.7 (8) | C24—C25—C26 | 116.4 (13) |
N4—C2—H2 | 109.2 | C24—C25—H25 | 121.8 |
C3—C2—H2 | 109.2 | C26—C25—H25 | 121.8 |
C1—C2—H2 | 109.2 | C21—C26—C25 | 119.5 (14) |
O1—C3—C2 | 108.2 (7) | C21—C26—H26 | 120.3 |
O1—C3—C4 | 111.0 (7) | C25—C26—H26 | 120.3 |
C2—C3—C4 | 112.2 (7) | O3—C30—C31 | 112.5 (8) |
O1—C3—H3 | 108.5 | O3—C30—H30A | 109.1 |
C2—C3—H3 | 108.5 | C31—C30—H30A | 109.1 |
C4—C3—H3 | 108.5 | O3—C30—H30B | 109.1 |
O2—C4—C5 | 108.8 (7) | C31—C30—H30B | 109.1 |
O2—C4—C3 | 108.5 (7) | H30A—C30—H30B | 107.8 |
C5—C4—C3 | 111.4 (8) | C32—C31—C36 | 118.3 (12) |
O2—C4—H4 | 109.4 | C32—C31—C30 | 118.6 (15) |
C5—C4—H4 | 109.4 | C36—C31—C30 | 123.0 (14) |
C3—C4—H4 | 109.4 | C33—C32—C31 | 120.4 (14) |
O3—C5—C4 | 110.0 (7) | C33—C32—H32 | 119.8 |
O3—C5—C6 | 108.4 (7) | C31—C32—H32 | 119.8 |
C4—C5—C6 | 111.2 (7) | C34—C33—C32 | 123.9 (16) |
O3—C5—H5 | 109.1 | C34—C33—H33 | 118.1 |
C4—C5—H5 | 109.1 | C32—C33—H33 | 118.1 |
C6—C5—H5 | 109.1 | C33—C34—C35 | 118.7 (14) |
O4—C6—C1 | 107.6 (7) | C33—C34—H34 | 120.7 |
O4—C6—C5 | 107.6 (7) | C35—C34—H34 | 120.7 |
C1—C6—C5 | 109.5 (7) | C36—C35—C34 | 117.4 (11) |
O4—C6—H6 | 110.7 | C36—C35—H35 | 121.3 |
C1—C6—H6 | 110.7 | C34—C35—H35 | 121.3 |
C5—C6—H6 | 110.7 | C35—C36—C31 | 121.2 (12) |
O1—C10—C11 | 106.8 (7) | C35—C36—H36 | 119.4 |
O1—C10—H10A | 110.4 | C31—C36—H36 | 119.4 |
C11—C10—H10A | 110.4 | O4—C40—C41 | 111.0 (7) |
O1—C10—H10B | 110.4 | O4—C40—H40A | 109.4 |
C11—C10—H10B | 110.4 | C41—C40—H40A | 109.4 |
H10A—C10—H10B | 108.6 | O4—C40—H40B | 109.4 |
C12—C11—C16 | 119.5 (9) | C41—C40—H40B | 109.4 |
C12—C11—C10 | 122.4 (10) | H40A—C40—H40B | 108.0 |
C16—C11—C10 | 117.8 (10) | C42—C41—C46 | 120.2 (9) |
C11—C12—C13 | 120.9 (10) | C42—C41—C40 | 121.8 (10) |
C11—C12—H12 | 119.5 | C46—C41—C40 | 118.0 (10) |
C13—C12—H12 | 119.5 | C41—C42—C43 | 120.5 (9) |
C12—C13—C14 | 120.0 (10) | C41—C42—H42 | 119.8 |
C12—C13—H13 | 120.0 | C43—C42—H42 | 119.8 |
C14—C13—H13 | 120.0 | C44—C43—C42 | 120.2 (9) |
C15—C14—C13 | 120.1 (10) | C44—C43—H43 | 119.9 |
C15—C14—H14 | 120.0 | C42—C43—H43 | 119.9 |
C13—C14—H14 | 120.0 | C43—C44—C45 | 120.0 (9) |
C14—C15—C16 | 120.7 (10) | C43—C44—H44 | 120.0 |
C14—C15—H15 | 119.6 | C45—C44—H44 | 120.0 |
C16—C15—H15 | 119.6 | C46—C45—C44 | 119.7 (9) |
C11—C16—C15 | 118.7 (9) | C46—C45—H45 | 120.2 |
C11—C16—H16 | 120.7 | C44—C45—H45 | 120.2 |
C15—C16—H16 | 120.7 | C45—C46—C41 | 119.4 (9) |
O2—C20—C21 | 107.3 (9) | C45—C46—H46 | 120.3 |
O2—C20—H20A | 110.2 | C41—C46—H46 | 120.3 |
| | | |
N2—N1—C1—C6 | 94.6 (10) | C10—C11—C12—C13 | −176.9 (8) |
N2—N1—C1—C2 | −145.5 (9) | C11—C12—C13—C14 | 0.7 (14) |
N5—N4—C2—C3 | −88.0 (10) | C12—C13—C14—C15 | 0.3 (15) |
N5—N4—C2—C1 | 151.4 (8) | C13—C14—C15—C16 | 0.1 (16) |
N1—C1—C2—N4 | −53.9 (9) | C12—C11—C16—C15 | 2.4 (13) |
C6—C1—C2—N4 | 63.2 (9) | C10—C11—C16—C15 | 177.4 (8) |
N1—C1—C2—C3 | −175.0 (7) | C14—C15—C16—C11 | −1.4 (14) |
C6—C1—C2—C3 | −57.9 (9) | C4—O2—C20—C21 | 170.8 (8) |
C10—O1—C3—C2 | 134.6 (7) | O2—C20—C21—C26 | 36.3 (15) |
C10—O1—C3—C4 | −101.9 (8) | O2—C20—C21—C22 | −145.3 (9) |
N4—C2—C3—O1 | 58.0 (9) | C26—C21—C22—C23 | 0.4 (17) |
C1—C2—C3—O1 | 178.2 (6) | C20—C21—C22—C23 | −178.1 (9) |
N4—C2—C3—C4 | −64.8 (10) | C21—C22—C23—C24 | −1.3 (15) |
C1—C2—C3—C4 | 55.5 (9) | C22—C23—C24—C25 | 0.4 (17) |
C20—O2—C4—C5 | 126.6 (8) | C23—C24—C25—C26 | 1.3 (18) |
C20—O2—C4—C3 | −112.0 (8) | C22—C21—C26—C25 | 1.4 (18) |
O1—C3—C4—O2 | 64.5 (8) | C20—C21—C26—C25 | 179.6 (9) |
C2—C3—C4—O2 | −174.4 (7) | C24—C25—C26—C21 | −2.1 (17) |
O1—C3—C4—C5 | −175.8 (7) | C5—O3—C30—C31 | 175.5 (9) |
C2—C3—C4—C5 | −54.7 (10) | O3—C30—C31—C32 | 95.1 (11) |
C30—O3—C5—C4 | 110.5 (8) | O3—C30—C31—C36 | −86.1 (12) |
C30—O3—C5—C6 | −127.7 (8) | C36—C31—C32—C33 | 1.5 (15) |
O2—C4—C5—O3 | −66.0 (8) | C30—C31—C32—C33 | −179.7 (10) |
C3—C4—C5—O3 | 174.5 (7) | C31—C32—C33—C34 | −1.7 (19) |
O2—C4—C5—C6 | 173.9 (7) | C32—C33—C34—C35 | 0.0 (19) |
C3—C4—C5—C6 | 54.4 (9) | C33—C34—C35—C36 | 1.7 (16) |
C40—O4—C6—C1 | 122.1 (8) | C34—C35—C36—C31 | −1.8 (16) |
C40—O4—C6—C5 | −119.9 (8) | C32—C31—C36—C35 | 0.3 (15) |
N1—C1—C6—O4 | −69.3 (8) | C30—C31—C36—C35 | −178.5 (10) |
C2—C1—C6—O4 | 174.8 (7) | C6—O4—C40—C41 | 175.5 (7) |
N1—C1—C6—C5 | 174.0 (7) | O4—C40—C41—C42 | −38.5 (13) |
C2—C1—C6—C5 | 58.1 (9) | O4—C40—C41—C46 | 143.5 (9) |
O3—C5—C6—O4 | 66.5 (8) | C46—C41—C42—C43 | −1.0 (13) |
C4—C5—C6—O4 | −172.5 (6) | C40—C41—C42—C43 | −178.9 (9) |
O3—C5—C6—C1 | −176.9 (7) | C41—C42—C43—C44 | 0.5 (14) |
C4—C5—C6—C1 | −55.8 (9) | C42—C43—C44—C45 | −0.7 (15) |
C3—O1—C10—C11 | −176.8 (7) | C43—C44—C45—C46 | 1.6 (15) |
O1—C10—C11—C12 | 49.4 (11) | C44—C45—C46—C41 | −2.1 (14) |
O1—C10—C11—C16 | −125.5 (8) | C42—C41—C46—C45 | 1.8 (14) |
C16—C11—C12—C13 | −2.1 (14) | C40—C41—C46—C45 | 179.8 (9) |
Symmetry codes: (i) x+1/2, −y−1/2, −z; (ii) x−1/2, −y−1/2, −z. |
Hydrogen-bond geometry (Å, º) top
D—H···A | D—H | H···A | D···A | D—H···A |
C2—H2···Cg1iii | 1.0 | 2.64 | 3.510 (10) | 146 |
C43—H43···Cg2iii | 0.95 | 2.82 | 3.597 (11) | 140 |
C1—H1···O3iii | 1.00 | 2.57 | 3.514 (10) | 157 |
C30—H30A···N4iii | 0.99 | 2.53 | 3.282 (13) | 132 |
C14—H14···N3iv | 0.95 | 2.70 | 3.353 (16) | 126 |
C20—H20B···N3v | 0.99 | 2.65 | 3.474 (16) | 141 |
Symmetry codes: (iii) x−1/2, −y+1/2, −z; (iv) −x+3/2, −y+1, z+1/2; (v) x+1/2, −y+1/2, −z. |
Experimental details
Crystal data |
Chemical formula | C34H34N6O4·0.6C4H10O |
Mr | 655.53 |
Crystal system, space group | Orthorhombic, P212121 |
Temperature (K) | 88 |
a, b, c (Å) | 9.006 (3), 15.324 (6), 25.424 (11) |
V (Å3) | 3509 (2) |
Z | 4 |
Radiation type | Mo Kα |
µ (mm−1) | 0.08 |
Crystal size (mm) | 0.50 × 0.22 × 0.18 |
|
Data collection |
Diffractometer | Bruker SMART CCD area-detector diffractometer |
Absorption correction | Multi-scan (SADABS; Blessing, 1995; Sheldrick, 1996) |
Tmin, Tmax | 0.597, 0.986 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 19603, 4038, 908 |
Rint | 0.328 |
(sin θ/λ)max (Å−1) | 0.626 |
|
Refinement |
R[F2 > 2σ(F2)], wR(F2), S | 0.053, 0.127, 0.77 |
No. of reflections | 4038 |
No. of parameters | 432 |
H-atom treatment | H atoms treated by a mixture of independent and constrained refinement |
Δρmax, Δρmin (e Å−3) | 0.16, −0.20 |
Selected geometric parameters (Å, º) topO1—C3 | 1.429 (8) | N1—C1 | 1.482 (10) |
N1—N2 | 1.194 (11) | N2—N3 | 1.180 (11) |
| | | |
C10—O1—C3 | 114.4 (6) | N3—N2—N1 | 172.9 (13) |
N2—N1—C1 | 111.9 (10) | N1—C1—C2 | 105.8 (8) |
Hydrogen-bond geometry (Å, º) top
D—H···A | D—H | H···A | D···A | D—H···A |
C2—H2···Cg1i | 1.0 | 2.64 | 3.510 (10) | 146 |
C43—H43···Cg2i | 0.95 | 2.82 | 3.597 (11) | 140 |
C1—H1···O3i | 1.00 | 2.57 | 3.514 (10) | 157 |
C30—H30A···N4i | 0.99 | 2.53 | 3.282 (13) | 132 |
C14—H14···N3ii | 0.95 | 2.70 | 3.353 (16) | 126 |
C20—H20B···N3iii | 0.99 | 2.65 | 3.474 (16) | 141 |
Symmetry codes: (i) x−1/2, −y+1/2, −z; (ii) −x+3/2, −y+1, z+1/2; (iii) x+1/2, −y+1/2, −z. |
The title compound, (I), was prepared as part of a programme aimed at generating new hydrogenation catalyst ligands from inositol molecules (Gainsford et al., 2000; Falshaw et al., 1999).
The asymmetric unit of (I) contains one independent molecule, as shown in Fig. 1. The absolute configuration shown is that determined from the chemical synthesis route. There are few cyclohexane structures in the Cambridge Structural Database (CSD, Version?; Allen, 2002) with adjacent azide and O substituents, namely CSD refcodes QAPSAB and QAPSEF (Akai, Nakamura et al., 1999; Akai, Sugita et al., 1999), AZUZAW (Busscher et al., 2004) and IXEVAI (Carballido et al., 2004). The azide angular geometries C1—N1—N2 and N1—N2—N3 in (I) fall within the previously observed ranges of 114–119° and 170–174°, respectively. The cyclohexane ring adopts a chair conformation, with puckering parameters (Cremer & Pople, 1975) Q = 0.573 (9) Å, θ = 2.6 (9)° and ϕ = 347 (20)°.
Normally, inositol derivatives are strongly hydrogen-bonded, utilizing all available bound groups, e.g. O—H···O (GEGWIY; Dietrich et al., 1999) and C—H···O═C (HADKIG; Steiner et al., 1993). Although the crystals of (I) were weakly diffracting, the crystal packing stability has again been assisted by definite, though weak, non-classical hydrogen bonding involving C—H···X (where X is O or Nazide) and C—H···π interactions, as detailed in Table 2. These forces are sufficient to stabilize a partial molecule of the crystallizing solvent diethyl ether in the lattice (estimated as 0.6 of a molecule).
There are two types of C—H···Nazide interactions in the structure of (I). One was unexpected, being to the inositol ring-bound atom N4, while the other two were to the terminal azide atom N3. The former have rarely been observed, according to a CSD search, with only one occurrence noted in SUMRAT (Goulaouic et al., 1993), with H···N = 2.67 Å and C—H···N = 131°. There are currently five instances of C—H···Nterminal interactions. Three examples are ZDGPLN (Schmidt et al., 1980), MIYKIO (Barnes et al., 2002) and YASBAW (Humphreys et al., 2005) with H···N values of 2.62, 2.59 and 2.47 Å, respectively, and C—H···N angles of 127, 146 and 161°, respectively. In the last of these structures, the interaction was apparently insufficient to reduce the disorder found in the azide group.
The C—H···π interactions listed in Table 2 fit within the normal applied H···Cg limit of 3 Å. From the interaction distances, it seems highly likely that there is also a C—H···O hydrogen bond to the disordered diethyl ether solvent, with C26—H26···O(C60) = 2.49 Å, C26···O = 3.17 (9) Å and C—H···O = 138°.
The combined weak interactions give three-dimensional stability to the crystal structure, although it is difficult to show this meaningfully in a packing diagram. Instead, Fig. 2 (Mercury; Bruno et al., 2002), shows the full interaction commitments of all the bound groups to the inositol as dotted bonds, with the disordered solvent molecules represented by one atom, O(C60) (see Experimental).