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A neutron diffraction study of xylitol (C5O5H12) is presented. The nuclear anisotropic displacement parameters have been analysed showing that the carbon-oxygen skeleton conforms to a rigid-body (TLS) description. Applying this TLS model to the xylitol H atoms allows characterization of the internal molecular displacements of the H nuclei, assuming that the observed H nuclear mean-square displacements are a sum of the internal displacements and rigid-body displacements. These internal molecular displacements are very similar for chemically equivalent H atoms and in good agreement with the values obtained by other methods. In all cases the smallest eigenvector of the residual mean-square displacement tensor is almost parallel to the X-H bond. The use of ab initio calculations to obtain the internal vibrations in xylitol is discouraging. Another 12 structures extracted from the literature which have been investigated by neutron diffraction were subjected to a similar analysis. The results for the nine compounds investigated at low temperature conform to the results from xylitol and provide estimates of the internal vibrations of H atoms in a range of chemical environments.

Supporting information

cif

Crystallographic Information File (CIF) https://doi.org/10.1107/S010876810301557X/bs5000sup1.cif
Contains datablocks global, anders

pdf

Portable Document Format (PDF) file https://doi.org/10.1107/S010876810301557X/bs5000sup2.pdf
Supplementary material

hkl

Structure factor file (CIF format) https://doi.org/10.1107/S010876810301557X/bs5000sup3.hkl
Contains datablock anders

CCDC reference: 223330

Computing details top

Cell refinement: rafd9; data reduction: racer; program(s) used to solve structure: SHELXL; program(s) used to refine structure: VALRAY (Stewart et al., 2000); molecular graphics: ORTEP; software used to prepare material for publication: PLATON (Spek, 1990).

Figures top
[Figure 1]
[Figure 2]
[Figure 3]
[Figure 4]
[Figure 5]
[Figure 6]
(anders) top
Crystal data top
C5H12O5Dx = 1.540 Mg m3
Mr = 152.15Melting point = 93–94.9 K
Orthorhombic, P212121Neutron radiation, λ = 0.83950 Å
Hall symbol: P 2ac 2abCell parameters from 2917 reflections
a = 8.2660 (4) Åθ = 3.8–45.3°
b = 8.8977 (4) ŵ = 0.27 mm1
c = 8.9116 (4) ÅT = 122 K
V = 655.43 (5) Å3Prism, colourless
Z = 42.5 × 2.0 × 0.9 mm
F(000) = 328
Data collection top
Four-circle
diffractometer
Rint = 0.041
Cu 220 transmission geometry monochromatorθmax = 45.3°, θmin = 3.8°
%T Coupled ${\w}–x\q$–scans with scan width between 1.2 and 4.5${χirc}$ and $1 λeq x λeq 2$.h = 133
Absorption correction: integration
datap
k = 315
Tmin = 0.132, Tmax = 0.223l = 1510
2917 measured reflections2 standard reflections every 100 reflections
1911 independent reflections intensity decay: none
1831 reflections with I > 2σ(I)
Refinement top
Refinement on F2Hydrogen site location: structure-invariant direct methods
Least-squares matrix: fullAll H-atom parameters refined
wR(F2) = 0.054Weighting scheme based on measured s.u.'s w = 1/σ2(Fo2)
S = 1.47(Δ/σ)max < 0.001
1911 reflectionsΔρmax = 1.81 e Å3
200 parametersΔρmin = 1.23 e Å3
0 restraintsExtinction correction: Becker-Coppens type 1 isotropic Lorentzian., Spackman, M. A.. (1987), Journal of Applied Crystallography, 20:256-258
0 constraintsExtinction coefficient: 12892 (154)
Primary atom site location: structure-invariant direct methods
Crystal data top
C5H12O5V = 655.43 (5) Å3
Mr = 152.15Z = 4
Orthorhombic, P212121Neutron radiation, λ = 0.83950 Å
a = 8.2660 (4) ŵ = 0.27 mm1
b = 8.8977 (4) ÅT = 122 K
c = 8.9116 (4) Å2.5 × 2.0 × 0.9 mm
Data collection top
Four-circle
diffractometer
1831 reflections with I > 2σ(I)
Absorption correction: integration
datap
Rint = 0.041
Tmin = 0.132, Tmax = 0.2232 standard reflections every 100 reflections
2917 measured reflections intensity decay: none
1911 independent reflections
Refinement top
wR(F2) = 0.0540 restraints
S = 1.47All H-atom parameters refined
1911 reflectionsΔρmax = 1.81 e Å3
200 parametersΔρmin = 1.23 e Å3
Special details top

Geometry. Bond distances, angles etc. have been calculated using the rounded fractional coordinates. All e.s.d.'s are estimated from the variances of the (full) variance-covariance matrix. The cell e.s.d.'s are taken into account in the estimation of distances, angles and torsion angles

Refinement. Refinement on F2 for ALL reflections. Weighted R-factors wR and all goodnesses of fit S are based on F2, conventional R-factors R are based on F, with F set to zero for negative F2.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
O10.67826 (10)0.22884 (10)0.42178 (9)0.0099 (2)
O20.61461 (10)0.43594 (10)0.18273 (10)0.0100 (2)
O30.31823 (11)0.43108 (10)0.04011 (10)0.0096 (2)
O40.22887 (10)0.12960 (10)0.10839 (10)0.0096 (2)
O50.08866 (10)0.20517 (11)0.21646 (10)0.0114 (2)
C10.52470 (9)0.29389 (9)0.39045 (8)0.0092 (1)
C20.50050 (8)0.32283 (8)0.22439 (7)0.0074 (1)
C30.32774 (8)0.37534 (8)0.18980 (8)0.0078 (1)
C40.20081 (8)0.25179 (8)0.20983 (8)0.0075 (1)
C50.03186 (8)0.31486 (9)0.18585 (9)0.0101 (2)
H1A0.5127 (3)0.4016 (2)0.4520 (2)0.0271 (5)
H1B0.4318 (2)0.2168 (3)0.4333 (2)0.0275 (5)
H20.5262 (2)0.2190 (2)0.1611 (2)0.0205 (4)
H30.2979 (2)0.46794 (19)0.26822 (19)0.0201 (4)
H40.2073 (2)0.2095 (2)0.32600 (18)0.0212 (4)
H5A0.0131 (3)0.4103 (2)0.2618 (3)0.0314 (5)
H5B0.0197 (2)0.3565 (2)0.0695 (2)0.0265 (5)
H110.7560 (2)0.2432 (2)0.3376 (2)0.0216 (4)
H120.6521 (2)0.4163 (2)0.0805 (2)0.0249 (5)
H130.3268 (2)0.54153 (19)0.0450 (2)0.0220 (4)
H140.2766 (2)0.0490 (2)0.1667 (2)0.0248 (4)
H150.1183 (2)0.1567 (2)0.1209 (2)0.0240 (4)
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
O10.0086 (3)0.0138 (4)0.0073 (3)0.0010 (3)0.0003 (3)0.0003 (3)
O20.0097 (3)0.0118 (3)0.0086 (3)0.0032 (3)0.0003 (3)0.0007 (3)
O30.0119 (3)0.0103 (3)0.0065 (3)0.0004 (3)0.0001 (3)0.0006 (3)
O40.0101 (3)0.0091 (3)0.0097 (3)0.0016 (3)0.0020 (3)0.0015 (3)
O50.0080 (3)0.0154 (4)0.0108 (3)0.0015 (3)0.0016 (3)0.0016 (3)
C10.0079 (2)0.0128 (3)0.0068 (2)0.0002 (2)0.0004 (2)0.0000 (2)
C20.0077 (2)0.0083 (2)0.0062 (2)0.0001 (2)0.0001 (2)0.0012 (2)
C30.0072 (2)0.0085 (2)0.0076 (2)0.0004 (2)0.0002 (2)0.0009 (2)
C40.0068 (2)0.0097 (3)0.0060 (2)0.0001 (2)0.0006 (2)0.0008 (2)
C50.0073 (2)0.0105 (3)0.0125 (3)0.0010 (2)0.0001 (2)0.0013 (2)
H1A0.0316 (8)0.0253 (8)0.0243 (8)0.0081 (7)0.0024 (8)0.0112 (7)
H1B0.0184 (7)0.0379 (10)0.0262 (8)0.0070 (7)0.0017 (6)0.0123 (8)
H20.0190 (6)0.0181 (6)0.0244 (7)0.0013 (6)0.0011 (6)0.0072 (6)
H30.0226 (7)0.0175 (6)0.0203 (7)0.0023 (6)0.0004 (6)0.0066 (6)
H40.0230 (7)0.0266 (8)0.0139 (6)0.0004 (6)0.0008 (6)0.0048 (6)
H5A0.0240 (8)0.0246 (8)0.0457 (11)0.0024 (7)0.0037 (8)0.0181 (8)
H5B0.0228 (7)0.0304 (9)0.0264 (8)0.0001 (7)0.0053 (7)0.0112 (7)
H110.0160 (6)0.0297 (8)0.0192 (7)0.0012 (6)0.0045 (6)0.0034 (7)
H120.0265 (8)0.0282 (8)0.0199 (8)0.0047 (7)0.0071 (6)0.0019 (7)
H130.0297 (8)0.0155 (6)0.0207 (7)0.0010 (6)0.0010 (7)0.0023 (6)
H140.0313 (8)0.0174 (7)0.0258 (8)0.0086 (7)0.0030 (7)0.0014 (6)
H150.0255 (8)0.0258 (8)0.0206 (7)0.0064 (7)0.0002 (6)0.0070 (7)
Geometric parameters (Å, º) top
O1—C11.4227 (11)C2—C31.5338 (9)
O2—C21.4284 (11)C3—C41.5301 (10)
O3—C31.4254 (11)C4—C51.5202 (10)
O4—C41.4328 (11)C1—H1A1.109 (2)
O5—C51.4211 (12)C1—H1B1.098 (2)
O1—H110.9960 (19)C2—H21.1031 (19)
O2—H120.978 (2)C3—H31.1082 (18)
O3—H130.9863 (19)C4—H41.1028 (18)
O4—H140.970 (2)C5—H5A1.097 (2)
O5—H150.986 (2)C5—H5B1.106 (2)
C1—C21.5154 (10)
O1···O22.8654 (12)H1A···H14v2.423 (3)
O1···O5i2.6654 (12)H1B···C42.7764 (19)
O1···C1ii3.3229 (11)H1B···H42.089 (2)
O1···C4ii3.2927 (11)H1B···O1x2.5088 (19)
O1···C3iii3.2991 (11)H1B···H11x2.531 (2)
O1···O3iii2.6712 (13)H1B···O2iii2.732 (3)
O2···O5i3.2129 (12)H1B···H13iii2.540 (3)
O2···O32.7603 (12)H2···O42.6256 (19)
O2···O4iv2.8218 (13)H2···H112.476 (2)
O2···O4v2.8475 (12)H2···H142.559 (2)
O2···O12.8654 (12)H2···H5Biv2.163 (3)
O2···C4v3.3381 (11)H3···H1A2.487 (3)
O3···O5iv2.7000 (13)H3···H5A2.410 (3)
O3···O1v2.6712 (13)H3···O3xi2.7567 (19)
O3···O22.7603 (12)H3···O1v2.8801 (19)
O3···O42.8481 (13)H3···O5xii2.7323 (19)
O4···O52.8755 (12)H3···H15xii2.450 (2)
O4···O2vi2.8218 (13)H4···C12.7887 (18)
O4···O32.8481 (13)H4···H1B2.089 (2)
O4···O2iii2.8475 (12)H4···O1x2.3261 (18)
O5···O3vi2.7000 (13)H4···C1x2.9435 (18)
O5···O1vii2.6654 (12)H4···O2iii2.846 (2)
O5···O42.8755 (12)H5A···H32.410 (3)
O5···O2vii3.2129 (12)H5A···O5xii2.704 (2)
O1···H1Bii2.5088 (19)H5A···H15xii2.580 (3)
O1···H13iii1.6932 (19)H5B···O32.5687 (19)
O1···H4ii2.3261 (18)H5B···H1Aviii2.408 (3)
O1···H3iii2.8801 (19)H5B···O4vi2.8823 (19)
O2···H112.492 (2)H5B···C2vi3.0709 (19)
O2···H4v2.846 (2)H5B···H2vi2.163 (3)
O2···H14v1.903 (2)H11···O22.492 (2)
O2···H1Bv2.732 (3)H11···O5i1.7113 (19)
O2···H132.8371 (19)H11···C5i2.7267 (18)
O3···H3viii2.7567 (19)H11···H22.476 (2)
O3···H122.7862 (19)H11···H15i2.324 (2)
O3···H5B2.5687 (19)H11···H1Bii2.531 (2)
O3···H15iv1.716 (2)H11···H13iii2.187 (2)
O4···H12vi1.845 (2)H12···O32.7862 (19)
O4···H22.6256 (19)H12···O4iv1.845 (2)
O4···H152.8820 (19)H12···C4iv3.0155 (19)
O4···H5Biv2.8823 (19)H12···H14iv2.451 (2)
O5···H11vii1.7113 (19)H13···O22.8371 (19)
O5···H3ix2.7323 (19)H13···H15iv2.346 (2)
O5···H5Aix2.704 (2)H13···O1v1.6932 (19)
C1···O1x3.3229 (11)H13···C1v2.6229 (19)
C3···O1v3.2991 (11)H13···H1Bv2.540 (3)
C4···O1x3.2927 (11)H13···H11v2.187 (2)
C4···O2iii3.3381 (11)H14···H22.559 (2)
C1···H42.7887 (18)H14···H12vi2.451 (2)
C1···H14v2.8477 (19)H14···O2iii1.903 (2)
C1···H13iii2.6229 (19)H14···C1iii2.8477 (19)
C1···H4ii2.9435 (18)H14···C2iii2.8959 (19)
C2···H14v2.8959 (19)H14···H1Aiii2.423 (3)
C2···H5Biv3.0709 (19)H15···O42.8820 (19)
C3···H15iv2.8190 (19)H15···H11vii2.324 (2)
C4···H12vi3.0155 (19)H15···O3vi1.716 (2)
C4···H1B2.7764 (19)H15···C3vi2.8190 (19)
C5···H11vii2.7267 (18)H15···H13vi2.346 (2)
H1A···H32.487 (3)H15···H3ix2.450 (2)
H1A···H5Bxi2.408 (3)H15···H5Aix2.580 (3)
C1—O1—H11112.06 (12)C2—C1—H1A108.93 (11)
C2—O2—H12108.99 (13)C2—C1—H1B110.70 (11)
C3—O3—H13107.54 (13)H1A—C1—H1B107.78 (18)
C4—O4—H14106.80 (13)O2—C2—H2109.27 (11)
C5—O5—H15108.00 (13)C1—C2—H2109.37 (11)
O1—C1—C2112.24 (6)C3—C2—H2109.37 (10)
O2—C2—C3110.36 (6)O3—C3—H3108.62 (11)
C1—C2—C3111.77 (6)C2—C3—H3107.88 (10)
O2—C2—C1106.64 (6)C4—C3—H3107.94 (10)
O3—C3—C4108.74 (6)O4—C4—H4109.00 (11)
C2—C3—C4113.34 (6)C3—C4—H4108.74 (11)
O3—C3—C2110.21 (6)C5—C4—H4107.61 (10)
C3—C4—C5110.38 (6)O5—C5—H5A108.31 (14)
O4—C4—C3111.13 (6)O5—C5—H5B110.27 (11)
O4—C4—C5109.88 (6)C4—C5—H5A109.20 (14)
O5—C5—C4111.32 (7)C4—C5—H5B109.82 (10)
O1—C1—H1A109.54 (14)H5A—C5—H5B107.84 (17)
O1—C1—H1B107.55 (13)
O1—C1—C2—O266.06 (8)O3—C3—C4—O460.62 (8)
O1—C1—C2—C3173.25 (7)O3—C3—C4—C561.57 (8)
O2—C2—C3—O349.43 (8)C2—C3—C4—O462.32 (8)
O2—C2—C3—C4171.56 (6)C2—C3—C4—C5175.50 (6)
C1—C2—C3—O3167.93 (7)O4—C4—C5—O562.08 (9)
C1—C2—C3—C469.94 (8)C3—C4—C5—O5175.00 (7)
Symmetry codes: (i) x+1, y, z; (ii) x+1/2, y+1/2, z+1; (iii) x+1, y1/2, z+1/2; (iv) x+1/2, y+1/2, z; (v) x+1, y+1/2, z+1/2; (vi) x1/2, y+1/2, z; (vii) x1, y, z; (viii) x+1/2, y+1, z1/2; (ix) x, y1/2, z+1/2; (x) x1/2, y+1/2, z+1; (xi) x+1/2, y+1, z+1/2; (xii) x, y+1/2, z+1/2.
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
O1—H11···O20.9960 (19)2.492 (2)2.8654 (12)101.70 (12)
O1—H11···O5i0.9960 (19)1.7113 (19)2.6654 (12)159.04 (17)
O2—H12···O4iv0.978 (2)1.845 (2)2.8218 (13)176.90 (17)
O3—H13···O1v0.9863 (19)1.6932 (19)2.6712 (13)170.66 (17)
O4—H14···O2iii0.970 (2)1.903 (2)2.8475 (12)164.00 (17)
O5—H15···O3vi0.986 (2)1.716 (2)2.7000 (13)176.22 (17)
C1—H1B···O1x1.098 (2)2.5088 (19)3.3229 (11)129.99 (18)
C4—H4···O1x1.1028 (18)2.3261 (18)3.2927 (11)145.24 (14)
Symmetry codes: (i) x+1, y, z; (iii) x+1, y1/2, z+1/2; (iv) x+1/2, y+1/2, z; (v) x+1, y+1/2, z+1/2; (vi) x1/2, y+1/2, z; (x) x1/2, y+1/2, z+1.

Experimental details

Crystal data
Chemical formulaC5H12O5
Mr152.15
Crystal system, space groupOrthorhombic, P212121
Temperature (K)122
a, b, c (Å)8.2660 (4), 8.8977 (4), 8.9116 (4)
V3)655.43 (5)
Z4
Radiation typeNeutron, λ = 0.83950 Å
µ (mm1)0.27
Crystal size (mm)2.5 × 2.0 × 0.9
Data collection
DiffractometerFour-circle
diffractometer
Absorption correctionIntegration
datap
Tmin, Tmax0.132, 0.223
No. of measured, independent and
observed [I > 2σ(I)] reflections
2917, 1911, 1831
Rint0.041
(sin θ/λ)max1)0.847
Refinement
R[F2 > 2σ(F2)], wR(F2), S ?, 0.054, 1.47
No. of reflections1911
No. of parameters200
H-atom treatmentAll H-atom parameters refined
Δρmax, Δρmin (e Å3)1.81, 1.23

Computer programs: rafd9, racer, SHELXL, VALRAY (Stewart et al., 2000), ORTEP, PLATON (Spek, 1990).

Selected geometric parameters (Å, º) top
O1—C11.4227 (11)O4—C41.4328 (11)
O2—C21.4284 (11)O5—C51.4211 (12)
O3—C31.4254 (11)
O1—C1—C2112.24 (6)O3—C3—C2110.21 (6)
O2—C2—C3110.36 (6)O4—C4—C3111.13 (6)
O2—C2—C1106.64 (6)O4—C4—C5109.88 (6)
O3—C3—C4108.74 (6)O5—C5—C4111.32 (7)
Hydrogen-bond geometry (Å, º) top
D—H···AD—HH···AD···AD—H···A
O1—H11···O20.9960 (19)2.492 (2)2.8654 (12)101.70 (12)
O1—H11···O5i0.9960 (19)1.7113 (19)2.6654 (12)159.04 (17)
O2—H12···O4ii0.978 (2)1.845 (2)2.8218 (13)176.90 (17)
O3—H13···O1iii0.9863 (19)1.6932 (19)2.6712 (13)170.66 (17)
O4—H14···O2iv0.970 (2)1.903 (2)2.8475 (12)164.00 (17)
O5—H15···O3v0.986 (2)1.716 (2)2.7000 (13)176.22 (17)
C1—H1B···O1vi1.098 (2)2.5088 (19)3.3229 (11)129.99 (18)
C4—H4···O1vi1.1028 (18)2.3261 (18)3.2927 (11)145.24 (14)
Symmetry codes: (i) x+1, y, z; (ii) x+1/2, y+1/2, z; (iii) x+1, y+1/2, z+1/2; (iv) x+1, y1/2, z+1/2; (v) x1/2, y+1/2, z; (vi) x1/2, y+1/2, z+1.
 

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