The structure of N-isopropyl-D-glycero-D-gulo-heptonamide, C10H21NO7, shows a bent C chain conformation in the glucoheptonic acid moiety. The crystal packing comprises a two-dimensional arrangement of intermolecular hydrogen bonds involving all O atoms. A feature of the crystal packing is a hydrogen-bonded (OH)4 ring, which might be responsible for the observed conformation.
Supporting information
CCDC reference: 242343
Key indicators
- Single-crystal X-ray study
- T = 293 K
- Mean (C-C) = 0.005 Å
- R factor = 0.044
- wR factor = 0.113
- Data-to-parameter ratio = 9.1
checkCIF/PLATON results
No syntax errors found
Alert level C
PLAT152_ALERT_1_C Supplied and Calc Volume s.u. Inconsistent ..... ?
PLAT220_ALERT_2_C Large Non-Solvent C Ueq(max)/Ueq(min) ... 2.60 Ratio
PLAT340_ALERT_3_C Low Bond Precision on C-C bonds (x 1000) Ang ... 5
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 27.30
From the CIF: _reflns_number_total 1504
Count of symmetry unique reflns 1520
Completeness (_total/calc) 98.95%
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
0 ALERT level A = In general: serious problem
0 ALERT level B = Potentially serious problem
3 ALERT level C = Check and explain
1 ALERT level G = General alerts; check
1 ALERT type 1 CIF construction/syntax error, inconsistent or missing data
1 ALERT type 2 Indicator that the structure model may be wrong or deficient
1 ALERT type 3 Indicator that the structure quality may be low
1 ALERT type 4 Improvement, methodology, query or suggestion
Data collection: SMART (Bruker 2000a); cell refinement: SMART; data reduction: SAINT (Bruker 2000b); program(s) used to solve structure: SHELXS97 (Sheldrick, 1990); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: SHELXTL (Bruker 2000c); software used to prepare material for publication: SHELXTL and enCIFer v1.1 (Allen et al. 2004).
N-isopropyl-
D-
glycero-
D-
gulo-heptonamide
top
Crystal data top
C10H21NO7 | F(000) = 288 |
Mr = 267.28 | Dx = 1.346 Mg m−3 |
Monoclinic, P21 | Melting point: 534 K |
Hall symbol: P 2yb | Mo Kα radiation, λ = 0.71073 Å |
a = 4.866 (2) Å | Cell parameters from 1024 reflections |
b = 22.435 (9) Å | θ = 3.5–27.3° |
c = 6.040 (2) Å | µ = 0.11 mm−1 |
β = 90.664 (7)° | T = 293 K |
V = 659.3 (5) Å3 | Trigonal prismatic, colorless |
Z = 2 | 0.40 × 0.20 × 0.05 mm |
Data collection top
Bruker SMART CCD area-detector diffractometer | 1361 reflections with I > 2σ(I) |
Radiation source: fine-focus sealed tube | Rint = 0.037 |
Graphite monochromator | θmax = 27.3°, θmin = 1.8° |
φ and ω scans | h = −6→6 |
3915 measured reflections | k = −28→24 |
1504 independent reflections | l = −7→6 |
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)] = 0.044 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.113 | H atoms treated by a mixture of independent and constrained refinement |
S = 1.00 | w = 1/[σ2(Fo2) + (0.0755P)2] where P = (Fo2 + 2Fc2)/3 |
1504 reflections | (Δ/σ)max < 0.001 |
165 parameters | Δρmax = 0.24 e Å−3 |
1 restraint | Δρmin = −0.18 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 | |
C1 | 0.1920 (6) | 0.37616 (12) | 0.1509 (4) | 0.0347 (6) | |
C2 | 0.0042 (6) | 0.40484 (13) | −0.0215 (5) | 0.0351 (6) | |
C3 | 0.1732 (6) | 0.44277 (13) | −0.1800 (4) | 0.0312 (6) | |
C4 | 0.3208 (6) | 0.49653 (12) | −0.0772 (4) | 0.0306 (6) | |
C5 | 0.1398 (5) | 0.53999 (11) | 0.0456 (4) | 0.0284 (5) | |
C6 | 0.3119 (6) | 0.58734 (12) | 0.1655 (4) | 0.0322 (6) | |
C7 | 0.1397 (6) | 0.63217 (13) | 0.2891 (5) | 0.0393 (7) | |
C8 | 0.3943 (8) | 0.28165 (14) | 0.2836 (6) | 0.0473 (8) | |
C9 | 0.4991 (11) | 0.2294 (2) | 0.1520 (7) | 0.0738 (13) | |
H9A | 0.6325 | 0.2079 | 0.2388 | 0.089* | |
H9B | 0.5829 | 0.2437 | 0.0189 | 0.089* | |
H9C | 0.3487 | 0.2035 | 0.1144 | 0.089* | |
C10 | 0.2483 (11) | 0.26276 (18) | 0.4913 (7) | 0.0716 (12) | |
H10A | 0.1703 | 0.2971 | 0.5614 | 0.086* | |
H10B | 0.3771 | 0.2441 | 0.5909 | 0.086* | |
H10C | 0.1047 | 0.2351 | 0.4538 | 0.086* | |
N1 | 0.2133 (6) | 0.31719 (12) | 0.1412 (4) | 0.0420 (6) | |
O1 | 0.3181 (6) | 0.40739 (10) | 0.2843 (3) | 0.0533 (6) | |
O2 | −0.1400 (4) | 0.35979 (10) | −0.1387 (4) | 0.0479 (6) | |
O3 | 0.3726 (4) | 0.40529 (10) | −0.2765 (3) | 0.0418 (5) | |
O4 | 0.4498 (4) | 0.52732 (10) | −0.2547 (3) | 0.0384 (5) | |
O5 | −0.0524 (4) | 0.56883 (8) | −0.1012 (3) | 0.0331 (4) | |
O6 | 0.5062 (4) | 0.55920 (10) | 0.3101 (3) | 0.0387 (5) | |
O7 | −0.0088 (4) | 0.60602 (10) | 0.4627 (3) | 0.0399 (5) | |
H2 | −0.1280 | 0.4300 | 0.0415 | 0.048* | |
H3 | 0.0504 | 0.4562 | −0.2844 | 0.048* | |
H4 | 0.4601 | 0.4844 | 0.0130 | 0.048* | |
H5 | 0.0329 | 0.5188 | 0.1492 | 0.048* | |
H6 | 0.4209 | 0.6069 | 0.0450 | 0.048* | |
H7A | −0.0093 | 0.6513 | 0.1858 | 0.048* | |
H7B | 0.2584 | 0.6574 | 0.3478 | 0.048* | |
H8 | 0.5441 | 0.3064 | 0.3160 | 0.048* | |
H1N | 0.1381 | 0.3018 | 0.0446 | 0.060* | |
H2O | −0.2894 | 0.3733 | −0.1674 | 0.060* | |
H3O | 0.3644 | 0.4107 | −0.3932 | 0.060* | |
H4O | 0.6034 | 0.5377 | −0.2123 | 0.060* | |
H5O | 0.0172 | 0.5767 | −0.2111 | 0.060* | |
H6O | 0.4309 | 0.5462 | 0.4059 | 0.060* | |
H7O | −0.1650 | 0.5970 | 0.4242 | 0.060* | |
Atomic displacement parameters (Å2) top | U11 | U22 | U33 | U12 | U13 | U23 |
C1 | 0.0489 (16) | 0.0329 (14) | 0.0224 (12) | 0.0018 (12) | 0.0059 (10) | −0.0004 (10) |
C2 | 0.0340 (14) | 0.0325 (13) | 0.0387 (14) | 0.0058 (12) | 0.0006 (10) | −0.0052 (12) |
C3 | 0.0346 (14) | 0.0375 (13) | 0.0213 (12) | 0.0100 (11) | −0.0050 (9) | −0.0015 (10) |
C4 | 0.0297 (13) | 0.0410 (15) | 0.0210 (12) | 0.0024 (11) | −0.0009 (9) | 0.0032 (10) |
C5 | 0.0292 (13) | 0.0348 (13) | 0.0210 (12) | −0.0016 (11) | 0.0020 (9) | 0.0048 (10) |
C6 | 0.0349 (14) | 0.0381 (14) | 0.0235 (12) | −0.0090 (11) | 0.0021 (10) | 0.0060 (10) |
C7 | 0.0483 (18) | 0.0347 (14) | 0.0349 (15) | −0.0082 (13) | 0.0015 (12) | −0.0037 (12) |
C8 | 0.057 (2) | 0.0353 (15) | 0.0492 (18) | 0.0072 (14) | −0.0118 (15) | 0.0019 (14) |
C9 | 0.090 (3) | 0.064 (2) | 0.067 (3) | 0.035 (2) | −0.009 (2) | −0.005 (2) |
C10 | 0.115 (4) | 0.051 (2) | 0.050 (2) | 0.012 (2) | 0.003 (2) | 0.0111 (17) |
N1 | 0.0528 (15) | 0.0330 (12) | 0.0400 (13) | 0.0044 (12) | −0.0085 (11) | −0.0018 (11) |
O1 | 0.0947 (18) | 0.0392 (11) | 0.0256 (10) | −0.0024 (12) | −0.0121 (10) | 0.0013 (10) |
O2 | 0.0382 (12) | 0.0380 (11) | 0.0672 (16) | 0.0066 (9) | −0.0160 (10) | −0.0073 (10) |
O3 | 0.0482 (11) | 0.0568 (13) | 0.0203 (8) | 0.0204 (10) | −0.0020 (7) | −0.0044 (9) |
O4 | 0.0341 (10) | 0.0594 (13) | 0.0216 (9) | −0.0052 (9) | 0.0015 (7) | 0.0068 (8) |
O5 | 0.0311 (9) | 0.0422 (10) | 0.0262 (9) | 0.0018 (8) | −0.0005 (7) | 0.0052 (8) |
O6 | 0.0335 (10) | 0.0591 (12) | 0.0233 (10) | −0.0070 (9) | −0.0001 (7) | 0.0042 (8) |
O7 | 0.0359 (11) | 0.0569 (13) | 0.0270 (10) | −0.0029 (9) | 0.0014 (8) | −0.0022 (9) |
Geometric parameters (Å, º) top
C1—O1 | 1.227 (3) | C7—H7A | 1.0434 |
C1—N1 | 1.328 (4) | C7—H7B | 0.8795 |
C1—C2 | 1.521 (4) | C8—N1 | 1.461 (4) |
C2—O2 | 1.415 (3) | C8—C9 | 1.508 (5) |
C2—C3 | 1.528 (4) | C8—C10 | 1.510 (6) |
C2—H2 | 0.9393 | C8—H8 | 0.9348 |
C3—O3 | 1.414 (3) | C9—H9A | 0.9600 |
C3—C4 | 1.532 (4) | C9—H9B | 0.9600 |
C3—H3 | 0.9148 | C9—H9C | 0.9600 |
C4—O4 | 1.427 (3) | C10—H10A | 0.9600 |
C4—C5 | 1.514 (4) | C10—H10B | 0.9600 |
C4—H4 | 0.9061 | C10—H10C | 0.9600 |
C5—O5 | 1.435 (3) | N1—H1N | 0.7671 |
C5—C6 | 1.530 (4) | O2—H2O | 0.8044 |
C5—H5 | 0.9468 | O3—H3O | 0.7159 |
C6—O6 | 1.427 (3) | O4—H4O | 0.8214 |
C6—C7 | 1.512 (4) | O5—H5O | 0.7687 |
C6—H6 | 1.0056 | O6—H6O | 0.7471 |
C7—O7 | 1.408 (4) | O7—H7O | 0.8180 |
| | | |
O1—C1—N1 | 124.0 (3) | O7—C7—C6 | 112.5 (2) |
O1—C1—C2 | 120.0 (2) | O7—C7—H7A | 104.9 |
N1—C1—C2 | 116.0 (2) | C6—C7—H7A | 111.3 |
O2—C2—C1 | 109.3 (2) | O7—C7—H7B | 107.9 |
O2—C2—C3 | 110.6 (2) | C6—C7—H7B | 105.2 |
C1—C2—C3 | 109.9 (2) | H7A—C7—H7B | 115.2 |
O2—C2—H2 | 107.1 | N1—C8—C9 | 108.6 (3) |
C1—C2—H2 | 112.6 | N1—C8—C10 | 110.9 (3) |
C3—C2—H2 | 107.2 | C9—C8—C10 | 112.7 (3) |
O3—C3—C2 | 107.7 (2) | N1—C8—H8 | 105.2 |
O3—C3—C4 | 108.3 (2) | C9—C8—H8 | 107.6 |
C2—C3—C4 | 116.0 (2) | C10—C8—H8 | 111.5 |
O3—C3—H3 | 111.0 | C8—C9—H9A | 109.5 |
C2—C3—H3 | 105.3 | C8—C9—H9B | 109.5 |
C4—C3—H3 | 108.6 | H9A—C9—H9B | 109.5 |
O4—C4—C5 | 108.6 (2) | C8—C9—H9C | 109.5 |
O4—C4—C3 | 106.5 (2) | H9A—C9—H9C | 109.5 |
C5—C4—C3 | 115.7 (2) | H9B—C9—H9C | 109.5 |
O4—C4—H4 | 105.4 | C8—C10—H10A | 109.5 |
C5—C4—H4 | 109.6 | C8—C10—H10B | 109.5 |
C3—C4—H4 | 110.5 | H10A—C10—H10B | 109.5 |
O5—C5—C4 | 111.5 (2) | C8—C10—H10C | 109.5 |
O5—C5—C6 | 109.2 (2) | H10A—C10—H10C | 109.5 |
C4—C5—C6 | 111.1 (2) | H10B—C10—H10C | 109.5 |
O5—C5—H5 | 106.0 | C1—N1—C8 | 124.4 (3) |
C4—C5—H5 | 109.1 | C1—N1—H1N | 116.4 |
C6—C5—H5 | 109.8 | C8—N1—H1N | 118.8 |
O6—C6—C7 | 111.0 (2) | C2—O2—H2O | 106.2 |
O6—C6—C5 | 109.7 (2) | C3—O3—H3O | 106.0 |
C7—C6—C5 | 113.1 (2) | C4—O4—H4O | 108.0 |
O6—C6—H6 | 106.5 | C5—O5—H5O | 110.2 |
C7—C6—H6 | 111.6 | C6—O6—H6O | 108.6 |
C5—C6—H6 | 104.5 | C7—O7—H7O | 112.0 |
| | | |
O1—C1—C2—O2 | −173.6 (3) | C3—C4—C5—O5 | −65.1 (3) |
N1—C1—C2—O2 | 8.3 (3) | O4—C4—C5—C6 | −67.5 (2) |
O1—C1—C2—C3 | 64.8 (3) | C3—C4—C5—C6 | 172.9 (2) |
N1—C1—C2—C3 | −113.3 (3) | O5—C5—C6—O6 | −179.30 (19) |
O2—C2—C3—O3 | −63.4 (3) | C4—C5—C6—O6 | −55.9 (2) |
C1—C2—C3—O3 | 57.4 (3) | O5—C5—C6—C7 | 56.1 (3) |
O2—C2—C3—C4 | 175.1 (2) | C4—C5—C6—C7 | 179.5 (2) |
C1—C2—C3—C4 | −64.1 (3) | O6—C6—C7—O7 | −59.7 (3) |
O3—C3—C4—O4 | 62.4 (2) | C5—C6—C7—O7 | 64.2 (3) |
C2—C3—C4—O4 | −176.4 (2) | O1—C1—N1—C8 | −1.6 (5) |
O3—C3—C4—C5 | −176.7 (2) | C2—C1—N1—C8 | 176.5 (3) |
C2—C3—C4—C5 | −55.6 (3) | C9—C8—N1—C1 | −145.4 (4) |
O4—C4—C5—O5 | 54.6 (3) | C10—C8—N1—C1 | 90.3 (4) |
Hydrogen-bond geometry (Å, º) top
D—H···A | D—H | H···A | D···A | D—H···A |
N1—H1N···O2 | 0.77 | 2.17 | 2.581 (3) | 114 |
O5—H5O···O4 | 0.77 | 2.40 | 2.784 (3) | 113 |
O6—H6O···O7 | 0.75 | 2.55 | 2.878 (3) | 109 |
O2—H2O···O3i | 0.80 | 1.91 | 2.704 (3) | 172 |
O3—H3O···O1ii | 0.72 | 1.96 | 2.663 (3) | 168 |
O4—H4O···O5iii | 0.82 | 1.93 | 2.746 (3) | 175 |
O5—H5O···O7ii | 0.77 | 2.08 | 2.773 (3) | 150 |
O6—H6O···O4iv | 0.75 | 2.09 | 2.741 (3) | 145 |
O7—H7O···O6i | 0.82 | 1.93 | 2.734 (3) | 167 |
Symmetry codes: (i) x−1, y, z; (ii) x, y, z−1; (iii) x+1, y, z; (iv) x, y, z+1. |
Deviations from the plane 07-06i-05ii-04iii for the atoms present in the
(OH)4 ringa (Å) top07 | 0.0324 (11) | H7O | 0.1427 (13) | C7 | -0.004 (4) |
O6i | -0.0328 (11) | H6Oi | 0.0012 (28) | C6i | 0.749 (4) |
O5ii | -0.0323 (11) | H5Oii | -0.1727 (18) | C5ii | -0.820 (4) |
O4iii | 0.0327 (11) | H4Oiii | -0.0405 (28) | C4iii | -0.059 (4) |
Symmetry codes:
(i) x-1, y, z;
(ii) x, y, z+1;
(iii) x-1, y, z+1.
Note: (a) Rms deviation of fitted atoms = 0.033. |