1L-1-Amino-1-de­oxy-2,3,4,5-tetra-O-methyl-scyllo-inositol

In the crystal structure of the title compound, C₁₀H₂₁NO₅, mol­ecules are linked by strong N—H...O and O—H...N hydrogen bonds into infinite zigzag chains.

Key indicators

• Single-crystal X-ray study
• T = 88 K
• Mean [sigma](C-C) = 0.004 Å
• R factor = 0.033
• wR factor = 0.065
• Data-to-parameter ratio = 9.1

checkCIF/PLATON results

No syntax errors found



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               1471
           Count of symmetry unique reflns         1476
           Completeness (_total/calc)             99.66%
           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
PLAT791_ALERT_1_G Confirm the Absolute Configuration of C1     = .          R
PLAT791_ALERT_1_G Confirm the Absolute Configuration of C2     = .          S
PLAT791_ALERT_1_G Confirm the Absolute Configuration of C3     = .          R
PLAT791_ALERT_1_G Confirm the Absolute Configuration of C4     = .          R
PLAT791_ALERT_1_G Confirm the Absolute Configuration of C5     = .          S
PLAT791_ALERT_1_G Confirm the Absolute Configuration of C6     = .          R

   0 ALERT level A = In general: serious problem
   0 ALERT level B = Potentially serious problem
   0 ALERT level C = Check and explain
   7 ALERT level G = General alerts; check

   6 ALERT type 1 CIF construction/syntax error, inconsistent or missing data
   0 ALERT type 2 Indicator that the structure model may be wrong or deficient
   0 ALERT type 3 Indicator that the structure quality may be low
   1 ALERT type 4 Improvement, methodology, query or suggestion
   0 ALERT type 5 Informative message, check

---

Computing details

Data collection: SMART (Siemens, 1996); cell refinement: SAINT (Siemens, 1996); data reduction: SAINT and SADABS (Sheldrick, 1996); program(s) used to solve structure: SHELXS97 (Sheldrick, 1997); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: ORTEP-3 in WinGX (Farrugia, 1997) and PLATON (Spek, 2003); software used to prepare material for publication: SHELXL97.

1L-1-Amino-1-deoxy-2,3,4,5-tetra-O-methyl-scyllo-inositol

Crystal data

C10H21NO5	F(000) = 512
Mr = 235.28	Dx = 1.276 Mg m^−3
Orthorhombic, P212121	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: P 2ac 2ab	Cell parameters from 1993 reflections
a = 6.7256 (14) Å	θ = 2.9–21.0°
b = 12.920 (3) Å	µ = 0.10 mm^−1
c = 14.091 (3) Å	T = 88 K
V = 1224.4 (5) Å^3	Needle, colourless
Z = 4	0.50 × 0.10 × 0.05 mm

Data collection

Bruker–Nonius APEX2 CCD area-detector diffractometer	1471 independent reflections
Radiation source: fine-focus sealed tube	913 reflections with I > 2σ(I)
Graphite monochromator	Rint = 0.064
Detector resolution: 8.192 pixels mm^-1	θmax = 26.4°, θmin = 2.1°
φ and ω scans	h = −8→8
Absorption correction: multi-scan (Blessing, 1995)	k = −16→16
Tmin = 0.888, Tmax = 1.0	l = −17→15
10832 measured reflections

Refinement

Refinement on F^2	Primary atom site location: structure-invariant direct methods
Least-squares matrix: full	Secondary atom site location: difference Fourier map
R[F^2 > 2σ(F^2)] = 0.033	Hydrogen site location: inferred from neighbouring sites
wR(F^2) = 0.065	H atoms treated by a mixture of independent and constrained refinement
S = 0.83	w = 1/[σ^2(Fo^2) + (0.0338P)^2] where P = (Fo^2 + 2Fc^2)/3
1471 reflections	(Δ/σ)max = 0.001
161 parameters	Δρmax = 0.15 e Å^−3
0 restraints	Δρmin = −0.18 e Å^−3

Special details

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 (Ų)

	x	y	z	Uiso*/Ueq	Occ. (<1)
O1	0.5884 (3)	0.79701 (15)	0.55668 (14)	0.0230 (5)
H1O	0.634 (4)	0.738 (2)	0.565 (2)	0.042 (11)*
O2	0.0327 (2)	1.02666 (13)	0.55995 (12)	0.0206 (5)
O3	−0.0655 (2)	0.95532 (13)	0.75192 (13)	0.0243 (5)
O4	0.2668 (2)	0.88160 (13)	0.85230 (13)	0.0195 (4)
O5	0.4936 (2)	0.73086 (12)	0.74610 (14)	0.0210 (4)
N1	0.2901 (3)	0.89387 (19)	0.45393 (16)	0.0201 (6)
H1N	0.260 (4)	0.955 (2)	0.4238 (18)	0.030 (9)*
H2N	0.417 (4)	0.8732 (18)	0.4342 (18)	0.024 (8)*
C1	0.3101 (3)	0.90941 (19)	0.55718 (18)	0.0169 (6)
H1	0.4012	0.9692	0.5690	0.020*
C2	0.1082 (4)	0.9329 (2)	0.60104 (18)	0.0178 (6)
H2	0.0145	0.8747	0.5871	0.021*
C3	0.1251 (4)	0.9470 (2)	0.70797 (18)	0.0167 (6)
H3	0.2025	1.0115	0.7212	0.020*
C4	0.2282 (4)	0.85637 (18)	0.75510 (19)	0.0166 (6)
H4	0.1370	0.7953	0.7531	0.020*
C5	0.4233 (4)	0.82663 (19)	0.70784 (19)	0.0164 (6)
H5	0.5241	0.8819	0.7201	0.020*
C6	0.3999 (4)	0.8123 (2)	0.60163 (18)	0.0172 (7)
H6	0.3118	0.7515	0.5888	0.021*
C7	−0.1342 (4)	1.0133 (2)	0.49823 (19)	0.0306 (8)
H7A	−0.0935	0.9736	0.4422	0.046*	0.79 (3)
H7B	−0.1838	1.0813	0.4783	0.046*	0.79 (3)
H7C	−0.2397	0.9760	0.5318	0.046*	0.79 (3)
H7D	−0.2512	1.0469	0.5260	0.046*	0.21 (3)
H7E	−0.1608	0.9393	0.4899	0.046*	0.21 (3)
H7F	−0.1050	1.0446	0.4364	0.046*	0.21 (3)
C8	−0.1531 (4)	1.0560 (2)	0.7529 (2)	0.0304 (7)
H8A	−0.0549	1.1066	0.7749	0.046*
H8B	−0.2678	1.0562	0.7958	0.046*
H8C	−0.1967	1.0742	0.6887	0.046*
C9	0.1640 (4)	0.8206 (2)	0.92037 (19)	0.0349 (8)
H9A	0.0205	0.8319	0.9138	0.052*
H9B	0.2064	0.8406	0.9843	0.052*
H9C	0.1941	0.7473	0.9099	0.052*
C10	0.6464 (4)	0.7407 (2)	0.8146 (2)	0.0375 (9)
H10A	0.7546	0.7828	0.7885	0.056*
H10B	0.6971	0.6720	0.8312	0.056*
H10C	0.5931	0.7743	0.8716	0.056*

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
O1	0.0244 (11)	0.0199 (13)	0.0247 (13)	0.0049 (9)	0.0085 (9)	0.0011 (10)
O2	0.0216 (10)	0.0187 (11)	0.0214 (12)	0.0015 (8)	−0.0044 (8)	0.0047 (9)
O3	0.0272 (10)	0.0208 (11)	0.0248 (11)	0.0083 (8)	0.0110 (9)	0.0045 (10)
O4	0.0277 (11)	0.0198 (10)	0.0109 (11)	−0.0028 (8)	−0.0003 (8)	−0.0003 (9)
O5	0.0261 (10)	0.0162 (10)	0.0208 (12)	0.0026 (8)	−0.0066 (9)	0.0029 (9)
N1	0.0289 (14)	0.0182 (15)	0.0132 (15)	−0.0003 (11)	0.0021 (11)	0.0028 (12)
C1	0.0209 (14)	0.0159 (16)	0.0140 (17)	−0.0055 (11)	0.0000 (12)	−0.0016 (13)
C2	0.0184 (15)	0.0159 (16)	0.0191 (17)	−0.0012 (11)	−0.0017 (11)	0.0006 (12)
C3	0.0218 (15)	0.0118 (16)	0.0166 (17)	−0.0033 (11)	0.0013 (12)	−0.0003 (13)
C4	0.0242 (14)	0.0110 (14)	0.0146 (16)	−0.0036 (11)	−0.0012 (13)	−0.0006 (13)
C5	0.0195 (14)	0.0133 (15)	0.0163 (17)	−0.0022 (11)	−0.0002 (12)	0.0024 (12)
C6	0.0209 (15)	0.0146 (16)	0.0160 (17)	−0.0005 (11)	0.0006 (12)	−0.0005 (13)
C7	0.0283 (17)	0.033 (2)	0.031 (2)	−0.0011 (14)	−0.0065 (13)	0.0087 (15)
C8	0.0387 (17)	0.0262 (18)	0.0264 (17)	0.0170 (13)	0.0090 (15)	0.0018 (16)
C9	0.052 (2)	0.0359 (19)	0.0164 (19)	−0.0161 (15)	0.0022 (15)	0.0025 (15)
C10	0.0384 (19)	0.034 (2)	0.040 (2)	0.0076 (15)	−0.0189 (15)	0.0037 (15)

Geometric parameters (Å, º)

O1—C6	1.431 (3)	C4—C5	1.521 (3)
O1—H1O	0.83 (3)	C4—H4	1.0000
O2—C7	1.430 (3)	C5—C6	1.516 (3)
O2—C2	1.436 (3)	C5—H5	1.0000
O3—C8	1.428 (3)	C6—H6	1.0000
O3—C3	1.428 (3)	C7—H7A	0.9800
O4—C9	1.421 (3)	C7—H7B	0.9800
O4—C4	1.432 (3)	C7—H7C	0.9800
O5—C10	1.415 (3)	C7—H7D	0.9800
O5—C5	1.430 (3)	C7—H7E	0.9800
N1—C1	1.475 (3)	C7—H7F	0.9800
N1—H1N	0.92 (3)	C8—H8A	0.9800
N1—H2N	0.94 (3)	C8—H8B	0.9800
C1—C2	1.523 (3)	C8—H8C	0.9800
C1—C6	1.527 (3)	C9—H9A	0.9800
C1—H1	1.0000	C9—H9B	0.9800
C2—C3	1.522 (3)	C9—H9C	0.9800
C2—H2	1.0000	C10—H10A	0.9800
C3—C4	1.515 (3)	C10—H10B	0.9800
C3—H3	1.0000	C10—H10C	0.9800
C6—O1—H1O	113 (2)	C5—C6—H6	109.7
C7—O2—C2	114.90 (19)	C1—C6—H6	109.7
C8—O3—C3	116.3 (2)	O2—C7—H7A	109.5
C9—O4—C4	115.56 (19)	O2—C7—H7B	109.5
C10—O5—C5	114.77 (19)	H7A—C7—H7B	109.5
C1—N1—H1N	111.0 (16)	O2—C7—H7C	109.5
C1—N1—H2N	104.4 (15)	H7A—C7—H7C	109.5
H1N—N1—H2N	108 (2)	H7B—C7—H7C	109.5
N1—C1—C2	110.2 (2)	O2—C7—H7D	109.5
N1—C1—C6	109.2 (2)	H7A—C7—H7D	141.1
C2—C1—C6	110.5 (2)	H7B—C7—H7D	56.3
N1—C1—H1	109.0	H7C—C7—H7D	56.3
C2—C1—H1	109.0	O2—C7—H7E	109.5
C6—C1—H1	109.0	H7A—C7—H7E	56.3
O2—C2—C3	108.9 (2)	H7B—C7—H7E	141.1
O2—C2—C1	108.7 (2)	H7C—C7—H7E	56.3
C3—C2—C1	111.0 (2)	H7D—C7—H7E	109.5
O2—C2—H2	109.4	O2—C7—H7F	109.5
C3—C2—H2	109.4	H7A—C7—H7F	56.3
C1—C2—H2	109.4	H7B—C7—H7F	56.3
O3—C3—C4	106.2 (2)	H7C—C7—H7F	141.1
O3—C3—C2	111.8 (2)	H7D—C7—H7F	109.5
C4—C3—C2	112.0 (2)	H7E—C7—H7F	109.5
O3—C3—H3	108.9	O3—C8—H8A	109.5
C4—C3—H3	108.9	O3—C8—H8B	109.5
C2—C3—H3	108.9	H8A—C8—H8B	109.5
O4—C4—C3	109.0 (2)	O3—C8—H8C	109.5
O4—C4—C5	108.66 (19)	H8A—C8—H8C	109.5
C3—C4—C5	113.5 (2)	H8B—C8—H8C	109.5
O4—C4—H4	108.5	O4—C9—H9A	109.5
C3—C4—H4	108.5	O4—C9—H9B	109.5
C5—C4—H4	108.5	H9A—C9—H9B	109.5
O5—C5—C6	107.5 (2)	O4—C9—H9C	109.5
O5—C5—C4	109.8 (2)	H9A—C9—H9C	109.5
C6—C5—C4	111.9 (2)	H9B—C9—H9C	109.5
O5—C5—H5	109.2	O5—C10—H10A	109.5
C6—C5—H5	109.2	O5—C10—H10B	109.5
C4—C5—H5	109.2	H10A—C10—H10B	109.5
O1—C6—C5	111.2 (2)	O5—C10—H10C	109.5
O1—C6—C1	106.4 (2)	H10A—C10—H10C	109.5
C5—C6—C1	110.2 (2)	H10B—C10—H10C	109.5
O1—C6—H6	109.7
C7—O2—C2—C3	−128.9 (2)	C2—C3—C4—C5	49.8 (3)
C7—O2—C2—C1	110.0 (2)	C10—O5—C5—C6	137.0 (2)
N1—C1—C2—O2	−61.4 (3)	C10—O5—C5—C4	−101.0 (3)
C6—C1—C2—O2	177.8 (2)	O4—C4—C5—O5	68.1 (2)
N1—C1—C2—C3	178.9 (2)	C3—C4—C5—O5	−170.4 (2)
C6—C1—C2—C3	58.1 (3)	O4—C4—C5—C6	−172.57 (19)
C8—O3—C3—C4	152.8 (2)	C3—C4—C5—C6	−51.1 (3)
C8—O3—C3—C2	−84.8 (3)	O5—C5—C6—O1	−66.5 (3)
O2—C2—C3—O3	68.2 (2)	C4—C5—C6—O1	172.81 (19)
C1—C2—C3—O3	−172.2 (2)	O5—C5—C6—C1	175.7 (2)
O2—C2—C3—C4	−172.73 (19)	C4—C5—C6—C1	55.1 (3)
C1—C2—C3—C4	−53.1 (3)	N1—C1—C6—O1	59.0 (3)
C9—O4—C4—C3	115.0 (2)	C2—C1—C6—O1	−179.6 (2)
C9—O4—C4—C5	−120.8 (2)	N1—C1—C6—C5	179.6 (2)
O3—C3—C4—O4	−66.6 (2)	C2—C1—C6—C5	−59.0 (3)
C2—C3—C4—O4	171.06 (19)	C8—O3—C3—H3	36
O3—C3—C4—C5	172.1 (2)

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1N···O4^i	0.92 (3)	2.35 (3)	3.258 (3)	171 (2)
O1—H1O···N1^ii	0.83 (3)	2.02 (3)	2.819 (3)	162 (3)
C10—H10A···O3^iii	0.98	2.59	3.496 (3)	154

Symmetry codes: (i) −x+1/2, −y+2, z−1/2; (ii) x+1/2, −y+3/2, −z+1; (iii) x+1, y, z.