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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
CCDC reference: 223330
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).
Crystal data top
C5H12O5 | Dx = 1.540 Mg m−3 |
Mr = 152.15 | Melting point = 93–94.9 K |
Orthorhombic, P212121 | Neutron radiation, λ = 0.83950 Å |
Hall symbol: P 2ac 2ab | Cell parameters from 2917 reflections |
a = 8.2660 (4) Å | θ = 3.8–45.3° |
b = 8.8977 (4) Å | µ = 0.27 mm−1 |
c = 8.9116 (4) Å | T = 122 K |
V = 655.43 (5) Å3 | Prism, colourless |
Z = 4 | 2.5 × 2.0 × 0.9 mm |
F(000) = 328 | |
Data collection top
Four-circle diffractometer | Rint = 0.041 |
Cu 220 transmission geometry monochromator | θmax = 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 = −13→3 |
Absorption correction: integration datap | k = −3→15 |
Tmin = 0.132, Tmax = 0.223 | l = −15→10 |
2917 measured reflections | 2 standard reflections every 100 reflections |
1911 independent reflections | intensity decay: none |
1831 reflections with I > 2σ(I) | |
Refinement top
Refinement on F2 | Hydrogen site location: structure-invariant direct methods |
Least-squares matrix: full | All H-atom parameters refined |
wR(F2) = 0.054 | Weighting scheme based on measured s.u.'s w = 1/σ2(Fo2) |
S = 1.47 | (Δ/σ)max < 0.001 |
1911 reflections | Δρmax = 1.81 e Å−3 |
200 parameters | Δρmin = −1.23 e Å−3 |
0 restraints | Extinction correction: Becker-Coppens type 1 isotropic Lorentzian., Spackman, M. A.. (1987), Journal of Applied Crystallography, 20:256-258 |
0 constraints | Extinction coefficient: 12892 (154) |
Primary atom site location: structure-invariant direct methods | |
Crystal data top
C5H12O5 | V = 655.43 (5) Å3 |
Mr = 152.15 | Z = 4 |
Orthorhombic, P212121 | Neutron radiation, λ = 0.83950 Å |
a = 8.2660 (4) Å | µ = 0.27 mm−1 |
b = 8.8977 (4) Å | T = 122 K |
c = 8.9116 (4) Å | 2.5 × 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 = 0.223 | 2 standard reflections every 100 reflections |
2917 measured reflections | intensity decay: none |
1911 independent reflections | |
Refinement top
wR(F2) = 0.054 | 0 restraints |
S = 1.47 | All H-atom parameters refined |
1911 reflections | Δρmax = 1.81 e Å−3 |
200 parameters | Δρmin = −1.23 e Å−3 |
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 | x | y | z | Uiso*/Ueq | |
O1 | 0.67826 (10) | 0.22884 (10) | 0.42178 (9) | 0.0099 (2) | |
O2 | 0.61461 (10) | 0.43594 (10) | 0.18273 (10) | 0.0100 (2) | |
O3 | 0.31823 (11) | 0.43108 (10) | 0.04011 (10) | 0.0096 (2) | |
O4 | 0.22887 (10) | 0.12960 (10) | 0.10839 (10) | 0.0096 (2) | |
O5 | −0.08866 (10) | 0.20517 (11) | 0.21646 (10) | 0.0114 (2) | |
C1 | 0.52470 (9) | 0.29389 (9) | 0.39045 (8) | 0.0092 (1) | |
C2 | 0.50050 (8) | 0.32283 (8) | 0.22439 (7) | 0.0074 (1) | |
C3 | 0.32774 (8) | 0.37534 (8) | 0.18980 (8) | 0.0078 (1) | |
C4 | 0.20081 (8) | 0.25179 (8) | 0.20983 (8) | 0.0075 (1) | |
C5 | 0.03186 (8) | 0.31486 (9) | 0.18585 (9) | 0.0101 (2) | |
H1A | 0.5127 (3) | 0.4016 (2) | 0.4520 (2) | 0.0271 (5) | |
H1B | 0.4318 (2) | 0.2168 (3) | 0.4333 (2) | 0.0275 (5) | |
H2 | 0.5262 (2) | 0.2190 (2) | 0.1611 (2) | 0.0205 (4) | |
H3 | 0.2979 (2) | 0.46794 (19) | 0.26822 (19) | 0.0201 (4) | |
H4 | 0.2073 (2) | 0.2095 (2) | 0.32600 (18) | 0.0212 (4) | |
H5A | 0.0131 (3) | 0.4103 (2) | 0.2618 (3) | 0.0314 (5) | |
H5B | 0.0197 (2) | 0.3565 (2) | 0.0695 (2) | 0.0265 (5) | |
H11 | 0.7560 (2) | 0.2432 (2) | 0.3376 (2) | 0.0216 (4) | |
H12 | 0.6521 (2) | 0.4163 (2) | 0.0805 (2) | 0.0249 (5) | |
H13 | 0.3268 (2) | 0.54153 (19) | 0.0450 (2) | 0.0220 (4) | |
H14 | 0.2766 (2) | 0.0490 (2) | 0.1667 (2) | 0.0248 (4) | |
H15 | −0.1183 (2) | 0.1567 (2) | 0.1209 (2) | 0.0240 (4) | |
Atomic displacement parameters (Å2) top | U11 | U22 | U33 | U12 | U13 | U23 |
O1 | 0.0086 (3) | 0.0138 (4) | 0.0073 (3) | 0.0010 (3) | −0.0003 (3) | 0.0003 (3) |
O2 | 0.0097 (3) | 0.0118 (3) | 0.0086 (3) | −0.0032 (3) | −0.0003 (3) | −0.0007 (3) |
O3 | 0.0119 (3) | 0.0103 (3) | 0.0065 (3) | 0.0004 (3) | −0.0001 (3) | 0.0006 (3) |
O4 | 0.0101 (3) | 0.0091 (3) | 0.0097 (3) | 0.0016 (3) | −0.0020 (3) | −0.0015 (3) |
O5 | 0.0080 (3) | 0.0154 (4) | 0.0108 (3) | −0.0015 (3) | 0.0016 (3) | −0.0016 (3) |
C1 | 0.0079 (2) | 0.0128 (3) | 0.0068 (2) | 0.0002 (2) | 0.0004 (2) | 0.0000 (2) |
C2 | 0.0077 (2) | 0.0083 (2) | 0.0062 (2) | −0.0001 (2) | −0.0001 (2) | −0.0012 (2) |
C3 | 0.0072 (2) | 0.0085 (2) | 0.0076 (2) | 0.0004 (2) | −0.0002 (2) | −0.0009 (2) |
C4 | 0.0068 (2) | 0.0097 (3) | 0.0060 (2) | 0.0001 (2) | −0.0006 (2) | −0.0008 (2) |
C5 | 0.0073 (2) | 0.0105 (3) | 0.0125 (3) | 0.0010 (2) | −0.0001 (2) | −0.0013 (2) |
H1A | 0.0316 (8) | 0.0253 (8) | 0.0243 (8) | 0.0081 (7) | −0.0024 (8) | −0.0112 (7) |
H1B | 0.0184 (7) | 0.0379 (10) | 0.0262 (8) | −0.0070 (7) | 0.0017 (6) | 0.0123 (8) |
H2 | 0.0190 (6) | 0.0181 (6) | 0.0244 (7) | 0.0013 (6) | 0.0011 (6) | −0.0072 (6) |
H3 | 0.0226 (7) | 0.0175 (6) | 0.0203 (7) | 0.0023 (6) | −0.0004 (6) | −0.0066 (6) |
H4 | 0.0230 (7) | 0.0266 (8) | 0.0139 (6) | −0.0004 (6) | −0.0008 (6) | 0.0048 (6) |
H5A | 0.0240 (8) | 0.0246 (8) | 0.0457 (11) | 0.0024 (7) | 0.0037 (8) | −0.0181 (8) |
H5B | 0.0228 (7) | 0.0304 (9) | 0.0264 (8) | −0.0001 (7) | −0.0053 (7) | 0.0112 (7) |
H11 | 0.0160 (6) | 0.0297 (8) | 0.0192 (7) | −0.0012 (6) | 0.0045 (6) | 0.0034 (7) |
H12 | 0.0265 (8) | 0.0282 (8) | 0.0199 (8) | −0.0047 (7) | 0.0071 (6) | −0.0019 (7) |
H13 | 0.0297 (8) | 0.0155 (6) | 0.0207 (7) | −0.0010 (6) | 0.0010 (7) | 0.0023 (6) |
H14 | 0.0313 (8) | 0.0174 (7) | 0.0258 (8) | 0.0086 (7) | −0.0030 (7) | 0.0014 (6) |
H15 | 0.0255 (8) | 0.0258 (8) | 0.0206 (7) | −0.0064 (7) | 0.0002 (6) | −0.0070 (7) |
Geometric parameters (Å, º) top
O1—C1 | 1.4227 (11) | C2—C3 | 1.5338 (9) |
O2—C2 | 1.4284 (11) | C3—C4 | 1.5301 (10) |
O3—C3 | 1.4254 (11) | C4—C5 | 1.5202 (10) |
O4—C4 | 1.4328 (11) | C1—H1A | 1.109 (2) |
O5—C5 | 1.4211 (12) | C1—H1B | 1.098 (2) |
O1—H11 | 0.9960 (19) | C2—H2 | 1.1031 (19) |
O2—H12 | 0.978 (2) | C3—H3 | 1.1082 (18) |
O3—H13 | 0.9863 (19) | C4—H4 | 1.1028 (18) |
O4—H14 | 0.970 (2) | C5—H5A | 1.097 (2) |
O5—H15 | 0.986 (2) | C5—H5B | 1.106 (2) |
C1—C2 | 1.5154 (10) | | |
| | | |
O1···O2 | 2.8654 (12) | H1A···H14v | 2.423 (3) |
O1···O5i | 2.6654 (12) | H1B···C4 | 2.7764 (19) |
O1···C1ii | 3.3229 (11) | H1B···H4 | 2.089 (2) |
O1···C4ii | 3.2927 (11) | H1B···O1x | 2.5088 (19) |
O1···C3iii | 3.2991 (11) | H1B···H11x | 2.531 (2) |
O1···O3iii | 2.6712 (13) | H1B···O2iii | 2.732 (3) |
O2···O5i | 3.2129 (12) | H1B···H13iii | 2.540 (3) |
O2···O3 | 2.7603 (12) | H2···O4 | 2.6256 (19) |
O2···O4iv | 2.8218 (13) | H2···H11 | 2.476 (2) |
O2···O4v | 2.8475 (12) | H2···H14 | 2.559 (2) |
O2···O1 | 2.8654 (12) | H2···H5Biv | 2.163 (3) |
O2···C4v | 3.3381 (11) | H3···H1A | 2.487 (3) |
O3···O5iv | 2.7000 (13) | H3···H5A | 2.410 (3) |
O3···O1v | 2.6712 (13) | H3···O3xi | 2.7567 (19) |
O3···O2 | 2.7603 (12) | H3···O1v | 2.8801 (19) |
O3···O4 | 2.8481 (13) | H3···O5xii | 2.7323 (19) |
O4···O5 | 2.8755 (12) | H3···H15xii | 2.450 (2) |
O4···O2vi | 2.8218 (13) | H4···C1 | 2.7887 (18) |
O4···O3 | 2.8481 (13) | H4···H1B | 2.089 (2) |
O4···O2iii | 2.8475 (12) | H4···O1x | 2.3261 (18) |
O5···O3vi | 2.7000 (13) | H4···C1x | 2.9435 (18) |
O5···O1vii | 2.6654 (12) | H4···O2iii | 2.846 (2) |
O5···O4 | 2.8755 (12) | H5A···H3 | 2.410 (3) |
O5···O2vii | 3.2129 (12) | H5A···O5xii | 2.704 (2) |
O1···H1Bii | 2.5088 (19) | H5A···H15xii | 2.580 (3) |
O1···H13iii | 1.6932 (19) | H5B···O3 | 2.5687 (19) |
O1···H4ii | 2.3261 (18) | H5B···H1Aviii | 2.408 (3) |
O1···H3iii | 2.8801 (19) | H5B···O4vi | 2.8823 (19) |
O2···H11 | 2.492 (2) | H5B···C2vi | 3.0709 (19) |
O2···H4v | 2.846 (2) | H5B···H2vi | 2.163 (3) |
O2···H14v | 1.903 (2) | H11···O2 | 2.492 (2) |
O2···H1Bv | 2.732 (3) | H11···O5i | 1.7113 (19) |
O2···H13 | 2.8371 (19) | H11···C5i | 2.7267 (18) |
O3···H3viii | 2.7567 (19) | H11···H2 | 2.476 (2) |
O3···H12 | 2.7862 (19) | H11···H15i | 2.324 (2) |
O3···H5B | 2.5687 (19) | H11···H1Bii | 2.531 (2) |
O3···H15iv | 1.716 (2) | H11···H13iii | 2.187 (2) |
O4···H12vi | 1.845 (2) | H12···O3 | 2.7862 (19) |
O4···H2 | 2.6256 (19) | H12···O4iv | 1.845 (2) |
O4···H15 | 2.8820 (19) | H12···C4iv | 3.0155 (19) |
O4···H5Biv | 2.8823 (19) | H12···H14iv | 2.451 (2) |
O5···H11vii | 1.7113 (19) | H13···O2 | 2.8371 (19) |
O5···H3ix | 2.7323 (19) | H13···H15iv | 2.346 (2) |
O5···H5Aix | 2.704 (2) | H13···O1v | 1.6932 (19) |
C1···O1x | 3.3229 (11) | H13···C1v | 2.6229 (19) |
C3···O1v | 3.2991 (11) | H13···H1Bv | 2.540 (3) |
C4···O1x | 3.2927 (11) | H13···H11v | 2.187 (2) |
C4···O2iii | 3.3381 (11) | H14···H2 | 2.559 (2) |
C1···H4 | 2.7887 (18) | H14···H12vi | 2.451 (2) |
C1···H14v | 2.8477 (19) | H14···O2iii | 1.903 (2) |
C1···H13iii | 2.6229 (19) | H14···C1iii | 2.8477 (19) |
C1···H4ii | 2.9435 (18) | H14···C2iii | 2.8959 (19) |
C2···H14v | 2.8959 (19) | H14···H1Aiii | 2.423 (3) |
C2···H5Biv | 3.0709 (19) | H15···O4 | 2.8820 (19) |
C3···H15iv | 2.8190 (19) | H15···H11vii | 2.324 (2) |
C4···H12vi | 3.0155 (19) | H15···O3vi | 1.716 (2) |
C4···H1B | 2.7764 (19) | H15···C3vi | 2.8190 (19) |
C5···H11vii | 2.7267 (18) | H15···H13vi | 2.346 (2) |
H1A···H3 | 2.487 (3) | H15···H3ix | 2.450 (2) |
H1A···H5Bxi | 2.408 (3) | H15···H5Aix | 2.580 (3) |
| | | |
C1—O1—H11 | 112.06 (12) | C2—C1—H1A | 108.93 (11) |
C2—O2—H12 | 108.99 (13) | C2—C1—H1B | 110.70 (11) |
C3—O3—H13 | 107.54 (13) | H1A—C1—H1B | 107.78 (18) |
C4—O4—H14 | 106.80 (13) | O2—C2—H2 | 109.27 (11) |
C5—O5—H15 | 108.00 (13) | C1—C2—H2 | 109.37 (11) |
O1—C1—C2 | 112.24 (6) | C3—C2—H2 | 109.37 (10) |
O2—C2—C3 | 110.36 (6) | O3—C3—H3 | 108.62 (11) |
C1—C2—C3 | 111.77 (6) | C2—C3—H3 | 107.88 (10) |
O2—C2—C1 | 106.64 (6) | C4—C3—H3 | 107.94 (10) |
O3—C3—C4 | 108.74 (6) | O4—C4—H4 | 109.00 (11) |
C2—C3—C4 | 113.34 (6) | C3—C4—H4 | 108.74 (11) |
O3—C3—C2 | 110.21 (6) | C5—C4—H4 | 107.61 (10) |
C3—C4—C5 | 110.38 (6) | O5—C5—H5A | 108.31 (14) |
O4—C4—C3 | 111.13 (6) | O5—C5—H5B | 110.27 (11) |
O4—C4—C5 | 109.88 (6) | C4—C5—H5A | 109.20 (14) |
O5—C5—C4 | 111.32 (7) | C4—C5—H5B | 109.82 (10) |
O1—C1—H1A | 109.54 (14) | H5A—C5—H5B | 107.84 (17) |
O1—C1—H1B | 107.55 (13) | | |
| | | |
O1—C1—C2—O2 | −66.06 (8) | O3—C3—C4—O4 | 60.62 (8) |
O1—C1—C2—C3 | 173.25 (7) | O3—C3—C4—C5 | −61.57 (8) |
O2—C2—C3—O3 | 49.43 (8) | C2—C3—C4—O4 | −62.32 (8) |
O2—C2—C3—C4 | 171.56 (6) | C2—C3—C4—C5 | 175.50 (6) |
C1—C2—C3—O3 | 167.93 (7) | O4—C4—C5—O5 | 62.08 (9) |
C1—C2—C3—C4 | −69.94 (8) | C3—C4—C5—O5 | −175.00 (7) |
Symmetry codes: (i) x+1, y, z; (ii) x+1/2, −y+1/2, −z+1; (iii) −x+1, y−1/2, −z+1/2; (iv) x+1/2, −y+1/2, −z; (v) −x+1, y+1/2, −z+1/2; (vi) x−1/2, −y+1/2, −z; (vii) x−1, y, z; (viii) −x+1/2, −y+1, z−1/2; (ix) −x, y−1/2, −z+1/2; (x) x−1/2, −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···A | D—H | H···A | D···A | D—H···A |
O1—H11···O2 | 0.9960 (19) | 2.492 (2) | 2.8654 (12) | 101.70 (12) |
O1—H11···O5i | 0.9960 (19) | 1.7113 (19) | 2.6654 (12) | 159.04 (17) |
O2—H12···O4iv | 0.978 (2) | 1.845 (2) | 2.8218 (13) | 176.90 (17) |
O3—H13···O1v | 0.9863 (19) | 1.6932 (19) | 2.6712 (13) | 170.66 (17) |
O4—H14···O2iii | 0.970 (2) | 1.903 (2) | 2.8475 (12) | 164.00 (17) |
O5—H15···O3vi | 0.986 (2) | 1.716 (2) | 2.7000 (13) | 176.22 (17) |
C1—H1B···O1x | 1.098 (2) | 2.5088 (19) | 3.3229 (11) | 129.99 (18) |
C4—H4···O1x | 1.1028 (18) | 2.3261 (18) | 3.2927 (11) | 145.24 (14) |
Symmetry codes: (i) x+1, y, z; (iii) −x+1, y−1/2, −z+1/2; (iv) x+1/2, −y+1/2, −z; (v) −x+1, y+1/2, −z+1/2; (vi) x−1/2, −y+1/2, −z; (x) x−1/2, −y+1/2, −z+1. |
Experimental details
Crystal data |
Chemical formula | C5H12O5 |
Mr | 152.15 |
Crystal system, space group | Orthorhombic, P212121 |
Temperature (K) | 122 |
a, b, c (Å) | 8.2660 (4), 8.8977 (4), 8.9116 (4) |
V (Å3) | 655.43 (5) |
Z | 4 |
Radiation type | Neutron, λ = 0.83950 Å |
µ (mm−1) | 0.27 |
Crystal size (mm) | 2.5 × 2.0 × 0.9 |
|
Data collection |
Diffractometer | Four-circle diffractometer |
Absorption correction | Integration datap |
Tmin, Tmax | 0.132, 0.223 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 2917, 1911, 1831 |
Rint | 0.041 |
(sin θ/λ)max (Å−1) | 0.847 |
|
Refinement |
R[F2 > 2σ(F2)], wR(F2), S | ?, 0.054, 1.47 |
No. of reflections | 1911 |
No. of parameters | 200 |
H-atom treatment | All H-atom parameters refined |
Δρmax, Δρmin (e Å−3) | 1.81, −1.23 |
Selected geometric parameters (Å, º) topO1—C1 | 1.4227 (11) | O4—C4 | 1.4328 (11) |
O2—C2 | 1.4284 (11) | O5—C5 | 1.4211 (12) |
O3—C3 | 1.4254 (11) | | |
| | | |
O1—C1—C2 | 112.24 (6) | O3—C3—C2 | 110.21 (6) |
O2—C2—C3 | 110.36 (6) | O4—C4—C3 | 111.13 (6) |
O2—C2—C1 | 106.64 (6) | O4—C4—C5 | 109.88 (6) |
O3—C3—C4 | 108.74 (6) | O5—C5—C4 | 111.32 (7) |
Hydrogen-bond geometry (Å, º) top
D—H···A | D—H | H···A | D···A | D—H···A |
O1—H11···O2 | 0.9960 (19) | 2.492 (2) | 2.8654 (12) | 101.70 (12) |
O1—H11···O5i | 0.9960 (19) | 1.7113 (19) | 2.6654 (12) | 159.04 (17) |
O2—H12···O4ii | 0.978 (2) | 1.845 (2) | 2.8218 (13) | 176.90 (17) |
O3—H13···O1iii | 0.9863 (19) | 1.6932 (19) | 2.6712 (13) | 170.66 (17) |
O4—H14···O2iv | 0.970 (2) | 1.903 (2) | 2.8475 (12) | 164.00 (17) |
O5—H15···O3v | 0.986 (2) | 1.716 (2) | 2.7000 (13) | 176.22 (17) |
C1—H1B···O1vi | 1.098 (2) | 2.5088 (19) | 3.3229 (11) | 129.99 (18) |
C4—H4···O1vi | 1.1028 (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, y−1/2, −z+1/2; (v) x−1/2, −y+1/2, −z; (vi) x−1/2, −y+1/2, −z+1. |
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