Redetermination of α-D-glucosa­mine hydro­chloride: elucidation of the hydrogen-bonding scheme

The previously reported crystal structures [Chu & Jeffery (1965). Proc. R. Soc. London Ser. A, 285, 470–479; Chandrasekharan & Mallikarjunan (1969). Z. Kristallogr. 129, 29] of the title compound, C₆H₁₄NO₅⁺·Cl⁻, have been confirmed to higher precision, and the H atoms located, allowing the elucidaton of the hydrogen-bonding network. A combination of O—H...O, N—H...O, O—H...Cl and N—H...Cl links results in a three-dimensional network. Considered by them­selves, the inter-cation O—H...O and N—H...O hydrogen bonds result in undulating (001) layers. The configurations of the chiral C atoms are: C1 S, C2 R, C3 R, C4 S and C5 R.

Key indicators

• Single-crystal X-ray study
• T = 295 K
• Mean [sigma](C-C) = 0.002 Å
• R factor = 0.029
• wR factor = 0.075
• Data-to-parameter ratio = 18.5

checkCIF/PLATON results

No syntax errors found



Alert level C
PLAT180_ALERT_3_C Check Cell Rounding: # of Values Ending with 0 =          3

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           30.04
           From the CIF: _reflns_number_total               2217
           Count of symmetry unique reflns         1456
           Completeness (_total/calc)            152.27%
           TEST3: Check Friedels for noncentro structure
           Estimate of Friedel pairs measured       761
           Fraction of Friedel pairs measured     0.523
           Are heavy atom types Z>Si present        yes
PLAT791_ALERT_1_G Confirm the Absolute Configuration of C1     = .          S
PLAT791_ALERT_1_G Confirm the Absolute Configuration of C2     = .          R
PLAT791_ALERT_1_G Confirm the Absolute Configuration of C3     = .          R
PLAT791_ALERT_1_G Confirm the Absolute Configuration of C4     = .          S
PLAT791_ALERT_1_G Confirm the Absolute Configuration of C5     = .          R
PLAT860_ALERT_3_G Note: Number of Least-Squares Restraints .......          1

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

   5 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
   2 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

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S1. Comment

The present study confirms the previous structure determinations (Chu & Jeffery, 1965; Chandrasekharan & Mallikarjunan, 1969) of the title compound, (I), to modern standards of precision. All the geometrical values for (I) (Fig. 1) fall within their expected ranges (Allen et al., 1995) and the six-membered ring is well described as a chair: for atoms C1, C2, C4 and C5, the r.m.s. deviation from their mean plane is 0.021 Å: C3 and O1 deviate from the plane by -0.652 (2)Å and 0.6477 (19) Å, respectively.

Here, the H atoms have been located, allowing the hydrogen-bonding scheme, involving a combination of O—H···O, N—H···O, O—H···Cl and N—H···Cl links, to be elucidated (Table 1). The inter-cation N—H···O and O—H···O bonds result in undulating (001) sheets (Fig. 2).

Related literature

For the earlier structure determinations of the title compound in which the H atoms were not located, and background literature, see: Chu & Jeffery (1965); Chandrasekharan & Mallikarjunan (1969).

For related literature, see: Allen et al. (1995).

S2. Experimental

A sample of glucosamine hydrochloride was obtained from Strides Arco labs, Mangalore, India and recrystallized from water to yield colourless chunks of (I). m.p.: 449–451 K.

S3. Refinement

The O-bound hydrogen atoms were located in a difference map and refined as riding in their as-found relative positions with U_iso(H) = 1.2U_eq(O). The other hydrogen atoms were geometrically placed (C—H = 0.97–0.98 Å, N—H = 0.89 Å) and refined as riding with U_iso(H) = 1.2U_eq(carrier). The –NH₃⁺ group was allowed to rotate, but not to tip, to best fit the electron density.

Computing details

Data collection: SMART (Bruker, 1999); cell refinement: SAINT (Bruker, 1999); data reduction: SAINT; program(s) used to solve structure: SHELXS97 (Sheldrick, 1997); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: ORTEP-3 (Farrugia, 1997); software used to prepare material for publication: SHELXL97.

Figures

	Fig. 1. View of the molecular structure of (I) showing 50% displacement ellipsoids (arbitrary spheres for the H atoms). The hydrogen bond is shown as a double dashed line.
	Fig. 2. Part of an (001) sheet of cations in (I) linked by O—H···O and N—H···O hydrogen bonds. Symmetry codes as in Table 1.

α-D-glucosamine hydrochloride

Crystal data

C6H14NO5^+·Cl^−	F(000) = 228
Mr = 215.63	Dx = 1.520 Mg m^−3
Monoclinic, P21	Mo Kα radiation, λ = 0.71073 Å
Hall symbol: P 2yb	Cell parameters from 2993 reflections
a = 7.1474 (5) Å	θ = 5.0–30.0°
b = 9.2140 (6) Å	µ = 0.40 mm^−1
c = 7.7650 (5) Å	T = 295 K
β = 112.884 (1)°	Chunk, colourless
V = 471.12 (5) Å^3	0.42 × 0.30 × 0.15 mm
Z = 2

Data collection

Bruker SMART1000 CCD diffractometer	2217 independent reflections
Radiation source: fine-focus sealed tube	2124 reflections with I > 2σ(I)
Graphite monochromator	Rint = 0.020
ω scans	θmax = 30.0°, θmin = 5.0°
Absorption correction: multi-scan SADABS (Bruker, 1999)	h = −10→10
Tmin = 0.851, Tmax = 0.944	k = −9→12
3941 measured reflections	l = −10→9

Refinement

Refinement on F^2	Hydrogen site location: difmap (O-H) and geom (others)
Least-squares matrix: full	H-atom parameters constrained
R[F^2 > 2σ(F^2)] = 0.029	w = 1/[σ^2(Fo^2) + (0.0452P)^2 + 0.0391P] where P = (Fo^2 + 2Fc^2)/3
wR(F^2) = 0.075	(Δ/σ)max < 0.001
S = 1.07	Δρmax = 0.27 e Å^−3
2217 reflections	Δρmin = −0.21 e Å^−3
120 parameters	Extinction correction: SHELXL, Fc^*=kFc[1+0.001xFc^2λ^3/sin(2θ)]^-1/4
1 restraint	Extinction coefficient: 0.042 (7)
Primary atom site location: structure-invariant direct methods	Absolute structure: Flack (1983), 761 Friedel pairs
Secondary atom site location: difference Fourier map	Absolute structure parameter: 0.07 (5)

Special details

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
C1	0.0118 (2)	0.23568 (18)	0.9307 (2)	0.0254 (3)
H1A	−0.0990	0.2269	0.9748	0.030*
C2	0.2141 (2)	0.22407 (17)	1.09837 (19)	0.0224 (3)
H2A	0.2115	0.1363	1.1687	0.027*
C3	0.3952 (2)	0.21459 (18)	1.0412 (2)	0.0234 (3)
H3A	0.4058	0.3070	0.9830	0.028*
C4	0.3592 (2)	0.09447 (18)	0.89614 (19)	0.0233 (3)
H4A	0.3528	0.0017	0.9553	0.028*
C5	0.1553 (2)	0.11884 (19)	0.7337 (2)	0.0248 (3)
H5A	0.1577	0.2125	0.6748	0.030*
C6	0.1010 (3)	0.0004 (2)	0.5870 (2)	0.0332 (4)
H6A	−0.0254	0.0255	0.4850	0.040*
H6B	0.2059	−0.0051	0.5371	0.040*
N1	0.23946 (19)	0.35206 (15)	1.22281 (17)	0.0266 (3)
H1B	0.1307	0.3608	1.2511	0.032*
H1C	0.2535	0.4319	1.1644	0.032*
H1D	0.3494	0.3400	1.3272	0.032*
O1	−0.00356 (15)	0.12014 (13)	0.80456 (15)	0.0261 (2)
O2	0.00134 (17)	0.37174 (15)	0.85023 (15)	0.0348 (3)
H2	−0.1164	0.3899	0.7813	0.042*
O3	0.57819 (17)	0.19429 (15)	1.20313 (17)	0.0332 (3)
H3	0.5477	0.1193	1.2483	0.040*
O4	0.52073 (18)	0.08680 (15)	0.83229 (17)	0.0325 (3)
H4	0.5190	0.1640	0.7788	0.039*
O5	0.07990 (17)	−0.13730 (14)	0.65823 (17)	0.0354 (3)
H5	0.1895	−0.1737	0.7165	0.042*
Cl1	0.52602 (6)	0.39359 (5)	0.65041 (5)	0.03359 (11)

Atomic displacement parameters (Ų)

	U^11	U^22	U^33	U^12	U^13	U^23
C1	0.0204 (6)	0.0265 (8)	0.0268 (6)	0.0012 (5)	0.0064 (5)	−0.0039 (6)
C2	0.0207 (6)	0.0209 (7)	0.0242 (6)	0.0001 (5)	0.0074 (5)	0.0000 (5)
C3	0.0193 (6)	0.0222 (8)	0.0269 (6)	−0.0004 (5)	0.0068 (5)	−0.0002 (5)
C4	0.0230 (6)	0.0210 (8)	0.0271 (6)	0.0000 (5)	0.0111 (5)	0.0003 (5)
C5	0.0255 (6)	0.0244 (8)	0.0252 (6)	−0.0004 (5)	0.0106 (5)	0.0007 (6)
C6	0.0328 (8)	0.0396 (10)	0.0280 (7)	−0.0020 (7)	0.0127 (6)	−0.0073 (7)
N1	0.0261 (6)	0.0271 (7)	0.0252 (5)	0.0003 (5)	0.0085 (4)	−0.0036 (5)
O1	0.0217 (5)	0.0266 (6)	0.0293 (5)	−0.0030 (4)	0.0092 (4)	−0.0067 (4)
O2	0.0322 (5)	0.0282 (8)	0.0344 (5)	0.0054 (5)	0.0025 (4)	0.0018 (5)
O3	0.0213 (5)	0.0321 (7)	0.0366 (6)	−0.0031 (5)	0.0009 (4)	−0.0014 (5)
O4	0.0308 (5)	0.0306 (7)	0.0429 (7)	0.0047 (5)	0.0217 (5)	0.0018 (5)
O5	0.0264 (5)	0.0293 (8)	0.0496 (7)	−0.0001 (5)	0.0137 (5)	−0.0106 (5)
Cl1	0.03269 (18)	0.0357 (2)	0.02785 (16)	−0.00225 (17)	0.00684 (12)	−0.00076 (17)

Geometric parameters (Å, º)

C1—O2	1.390 (2)	C5—O1	1.4413 (17)
C1—O1	1.4219 (19)	C5—C6	1.515 (2)
C1—C2	1.5273 (18)	C5—H5A	0.9800
C1—H1A	0.9800	C6—O5	1.415 (2)
C2—N1	1.4902 (19)	C6—H6A	0.9700
C2—C3	1.5260 (19)	C6—H6B	0.9700
C2—H2A	0.9800	N1—H1B	0.8900
C3—O3	1.4311 (17)	N1—H1C	0.8900
C3—C4	1.528 (2)	N1—H1D	0.8900
C3—H3A	0.9800	O2—H2	0.8199
C4—O4	1.4243 (16)	O3—H3	0.8407
C4—C5	1.5286 (19)	O4—H4	0.8213
C4—H4A	0.9800	O5—H5	0.8094
O2—C1—O1	112.90 (12)	O1—C5—C6	106.48 (12)
O2—C1—C2	108.30 (13)	O1—C5—C4	109.03 (11)
O1—C1—C2	109.18 (12)	C6—C5—C4	113.42 (14)
O2—C1—H1A	108.8	O1—C5—H5A	109.3
O1—C1—H1A	108.8	C6—C5—H5A	109.3
C2—C1—H1A	108.8	C4—C5—H5A	109.3
N1—C2—C3	109.32 (12)	O5—C6—C5	112.77 (12)
N1—C2—C1	109.48 (12)	O5—C6—H6A	109.0
C3—C2—C1	112.65 (11)	C5—C6—H6A	109.0
N1—C2—H2A	108.4	O5—C6—H6B	109.0
C3—C2—H2A	108.4	C5—C6—H6B	109.0
C1—C2—H2A	108.4	H6A—C6—H6B	107.8
O3—C3—C2	109.91 (12)	C2—N1—H1B	109.5
O3—C3—C4	112.80 (13)	C2—N1—H1C	109.5
C2—C3—C4	109.71 (12)	H1B—N1—H1C	109.5
O3—C3—H3A	108.1	C2—N1—H1D	109.5
C2—C3—H3A	108.1	H1B—N1—H1D	109.5
C4—C3—H3A	108.1	H1C—N1—H1D	109.5
O4—C4—C3	111.44 (12)	C1—O1—C5	114.09 (11)
O4—C4—C5	111.22 (11)	C1—O2—H2	109.8
C3—C4—C5	109.58 (12)	C3—O3—H3	100.2
O4—C4—H4A	108.2	C4—O4—H4	106.1
C3—C4—H4A	108.2	C6—O5—H5	111.2
C5—C4—H4A	108.2
O2—C1—C2—N1	51.67 (15)	C2—C3—C4—C5	53.63 (15)
O1—C1—C2—N1	174.97 (12)	O4—C4—C5—O1	177.79 (13)
O2—C1—C2—C3	−70.19 (16)	C3—C4—C5—O1	−58.55 (16)
O1—C1—C2—C3	53.11 (18)	O4—C4—C5—C6	59.34 (18)
N1—C2—C3—O3	61.87 (16)	C3—C4—C5—C6	−177.00 (13)
C1—C2—C3—O3	−176.18 (13)	O1—C5—C6—O5	−57.79 (16)
N1—C2—C3—C4	−173.55 (11)	C4—C5—C6—O5	62.12 (17)
C1—C2—C3—C4	−51.60 (17)	O2—C1—O1—C5	60.77 (16)
O3—C3—C4—O4	−59.95 (16)	C2—C1—O1—C5	−59.75 (16)
C2—C3—C4—O4	177.16 (12)	C6—C5—O1—C1	−173.77 (13)
O3—C3—C4—C5	176.52 (12)	C4—C5—O1—C1	63.51 (16)

Hydrogen-bond geometry (Å, º)

D—H···A	D—H	H···A	D···A	D—H···A
N1—H1B···O5^i	0.89	1.89	2.7772 (17)	172
N1—H1C···O4^ii	0.89	2.15	2.8930 (19)	141
N1—H1D···Cl1^iii	0.89	2.38	3.1744 (13)	149
O2—H2···Cl1^iv	0.82	2.35	3.1448 (12)	162
O3—H3···Cl1^v	0.84	2.35	3.1911 (14)	173
O4—H4···Cl1	0.82	2.35	3.1667 (14)	175
O5—H5···O3^v	0.81	1.95	2.7373 (17)	163

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