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The experimental charge density ρ(r) of the non-standard amino acid sarcosine has been determined based on an extensive and complete data set measured at 100 K to high resolution (sin θ/λ = 1.18 Å−1) by single-crystal X-ray diffraction. Anisotropic thermal motion of the H atoms, obtained from TLS + ONIOM cluster methods, was included in the structural model. Based on the multipole-model geometry, the theoretical Hartree–Fock interaction density of a molecule in the crystal has been calculated with CRYSTAL98. It manifests itself in local rearrangements of ρ(r) and can be reproduced with a multipole projection via simulated structure factors. An attempt has also been made to obtain the interaction density from a combination of experimental and theoretical charge densities using either a whole-molecular calculation or the invariom database. Agreement with the periodic Hartree–Fock interaction density is qualitative. It is shown that invarioms reproduce the features of the theoretical multipole-projected whole-molecular electron density, and can be used to approximate it.
Supporting information
 | Crystallographic Information File (CIF) https://doi.org/10.1107/S0108767307039116/sh5061sup1.cif |
 | Structure factor file (CIF format) https://doi.org/10.1107/S0108767307039116/sh5061sup2.hkl |
 | Portable Document Format (PDF) file https://doi.org/10.1107/S0108767307039116/sh5061sup3.pdf |
CCDC reference: 660888
Computing details top
Program(s) used to refine structure: Koritsanszky et al., (2003); molecular graphics: Koritsanszky et al., (2003); software used to prepare material for publication: Koritsanszky et al., (2003).
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![[Figure 4]](http://journals.iucr.org/a/issues/2007/05/00/sh5061/sh5061fig4thm.gif)
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![[Figure 7]](http://journals.iucr.org/a/issues/2007/05/00/sh5061/sh5061fig7thm.gif)
![[Figure 8]](http://journals.iucr.org/a/issues/2007/05/00/sh5061/sh5061fig8thm.gif)
(sarcosine) top
Crystal data top
| C3H7NO2 | F(000) = 192.0 |
| Mr = 89.10 | Dx = 1.309 Mg m−3 |
| Orthorhombic, P212121 | ? radiation, λ = 0.71073 Å |
| Hall symbol: P 2ac 2ab | Cell parameters from 48765 reflections |
| a = 6.6558 (1) Å | θ = 3.1–57.2° |
| b = 7.8903 (1) Å | µ = 0.11 mm−1 |
| c = 8.6069 (1) Å | T = 100 K |
| V = 452.01 (1) Å3 | Tetrahedron, colorless |
| Z = 4.0 | 0.48 × 0.39 × 0.32 mm |
Data collection top
| Oxford Diffraction Xcalibur S diffractometer | 2927 reflections with F > 2.5u(σ)F |
| ω scans | Rint = 0.027 |
| Absorption correction: analytical CrysAlis RED, Oxford Diffraction Ltd., Version 1.171.31.7 (release 18-10-2006 CrysAlis171 .NET) Analytical numeric absorption correction using a multifaceted crystal model based on expressions derived by R.C. Clark & J.S. Reid. (Clark, R. C. & Reid, J. S. (1995). Acta Cryst. A51, 887-897) | θmax = 57.8°, θmin = 3.1° |
| Tmin = 0.969, Tmax = 0.977 | h = −15→15 |
| 78770 measured reflections | k = −18→18 |
| 3555 independent reflections | l = −20→20 |
Refinement top
| Refinement on F | 0 restraints |
| Least-squares matrix: full | All H-atom parameters refined |
| R[F2 > 2σ(F2)] = 0.017 | w1 = 1/[s2(Fo)] |
| wR(F2) = 0.010 | (Δ/σ)max < 0.001 |
| S = 1.71 | Δρmax = 0.17 e Å−3 |
| 2927 reflections | Δρmin = −0.16 e Å−3 |
| 156 parameters |
Crystal data top
| C3H7NO2 | V = 452.01 (1) Å3 |
| Mr = 89.10 | Z = 4.0 |
| Orthorhombic, P212121 | ? radiation, λ = 0.71073 Å |
| a = 6.6558 (1) Å | µ = 0.11 mm−1 |
| b = 7.8903 (1) Å | T = 100 K |
| c = 8.6069 (1) Å | 0.48 × 0.39 × 0.32 mm |
Data collection top
| Oxford Diffraction Xcalibur S diffractometer | 3555 independent reflections |
| Absorption correction: analytical CrysAlis RED, Oxford Diffraction Ltd., Version 1.171.31.7 (release 18-10-2006 CrysAlis171 .NET) Analytical numeric absorption correction using a multifaceted crystal model based on expressions derived by R.C. Clark & J.S. Reid. (Clark, R. C. & Reid, J. S. (1995). Acta Cryst. A51, 887-897) | 2927 reflections with F > 2.5u(σ)F |
| Tmin = 0.969, Tmax = 0.977 | Rint = 0.027 |
| 78770 measured reflections |
Refinement top
| R[F2 > 2σ(F2)] = 0.017 | 0 restraints |
| wR(F2) = 0.010 | All H-atom parameters refined |
| S = 1.71 | Δρmax = 0.17 e Å−3 |
| 2927 reflections | Δρmin = −0.16 e Å−3 |
| 156 parameters |
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
| x | y | z | Uiso*/Ueq | Occ. (<1) | |
| O(1) | 0.77985 (3) | 0.18119 (2) | 0.17238 (2) | 0.014 | |
| O(2) | 0.76653 (3) | −0.09296 (2) | 0.23721 (2) | 0.018 | |
| N(1) | 1.01610 (3) | −0.06195 (2) | 0.47965 (2) | 0.01 | |
| C(1) | 0.82272 (3) | 0.05492 (3) | 0.25761 (2) | 0.011 | |
| C(2) | 0.95498 (3) | 0.09441 (3) | 0.39760 (2) | 0.011 | |
| C(3) | 1.18181 (4) | −0.03359 (3) | 0.59155 (3) | 0.017 | |
| H(1) | 1.0576 (7) | −0.1511 (6) | 0.4049 (6) | 0.024 | |
| H(2) | 0.8981 (8) | −0.1059 (6) | 0.5387 (6) | 0.033 | |
| H(3) | 1.0843 (8) | 0.1638 (6) | 0.3583 (6) | 0.032 | |
| H(4) | 0.8722 (8) | 0.1719 (6) | 0.4761 (6) | 0.031 | |
| H(5) | 1.3186 (8) | 0.0054 (7) | 0.5326 (7) | 0.042 | |
| H(6) | 1.2092 (8) | −0.1506 (7) | 0.6522 (6) | 0.037 | |
| H(7) | 1.1388 (8) | 0.0621 (8) | 0.6749 (7) | 0.045 | |
| DUM1 | 1.08006 | 0.05094 | 0.49785 | 0 | 0 |
Atomic displacement parameters (Å2) top
| U11 | U22 | U33 | U12 | U13 | U23 | |
| O(1) | 0.01736 (7) | 0.01148 (6) | 0.01315 (6) | −0.00181 (6) | −0.00362 (6) | 0.00387 (5) |
| O(2) | 0.02510 (9) | 0.00983 (5) | 0.01828 (8) | −0.00150 (6) | −0.00887 (7) | 0.00061 (6) |
| N(1) | 0.01281 (7) | 0.00894 (6) | 0.00962 (6) | 0.00028 (5) | −0.00115 (5) | 0.00007 (5) |
| C(1) | 0.01345 (7) | 0.00932 (6) | 0.01003 (7) | 0.00016 (6) | −0.00089 (6) | 0.00104 (6) |
| C(2) | 0.01473 (8) | 0.00944 (7) | 0.00987 (7) | −0.00042 (6) | −0.00099 (6) | 0.00017 (6) |
| C(3) | 0.01940 (10) | 0.01370 (10) | 0.01760 (10) | 0.00030 (10) | −0.00720 (10) | −0.00010 (10) |
| H(1) | 0.028 (2) | 0.02 | 0.025 | 0.007 | 0 | −0.006 |
| H(2) | 0.040 (3) | 0.02 | 0.039 | −0.003 | 0.008 | 0.005 |
| H(3) | 0.035 (3) | 0.029 | 0.032 | −0.007 | −0.004 | 0.013 |
| H(4) | 0.048 (3) | 0.022 | 0.023 | 0.011 | 0 | −0.004 |
| H(5) | 0.021 (3) | 0.051 | 0.054 | −0.016 | −0.003 | −0.001 |
| H(6) | 0.037 (3) | 0.033 | 0.04 | 0.007 | −0.018 | 0.012 |
| H(7) | 0.051 (3) | 0.046 | 0.038 | 0.015 | −0.018 | −0.025 |
Geometric parameters (Å, º) top
| O(1)—C(1) | 1.2697 (3) | C(2)—H(3) | 1.075 (5) |
| O(2)—C(1) | 1.2378 (3) | C(2)—H(4) | 1.065 (5) |
| N(1)—H(1) | 0.993 (5) | C(3)—H(5) | 1.087 (5) |
| N(1)—H(2) | 0.997 (5) | C(3)—H(6) | 1.077 (5) |
| C(1)—C(2) | 1.5244 (3) | C(3)—H(7) | 1.080 (6) |
| H(1)—N(1)—H(2) | 107.6 (4) | C(1)—C(2)—H(4) | 108.7 (3) |
| O(1)—C(1)—O(2) | 126.14 (2) | H(3)—C(2)—H(4) | 108.8 (4) |
| O(1)—C(1)—C(2) | 115.215 (18) | H(5)—C(3)—H(6) | 109.1 (4) |
| O(2)—C(1)—C(2) | 118.640 (19) | H(5)—C(3)—H(7) | 109.5 (4) |
| C(1)—C(2)—H(3) | 108.5 (3) | H(6)—C(3)—H(7) | 108.8 (4) |
Experimental details
| Crystal data | |
| Chemical formula | C3H7NO2 |
| Mr | 89.10 |
| Crystal system, space group | Orthorhombic, P212121 |
| Temperature (K) | 100 |
| a, b, c (Å) | 6.6558 (1), 7.8903 (1), 8.6069 (1) |
| V (Å3) | 452.01 (1) |
| Z | 4.0 |
| Radiation type | ?, λ = 0.71073 Å |
| µ (mm−1) | 0.11 |
| Crystal size (mm) | 0.48 × 0.39 × 0.32 |
| Data collection | |
| Diffractometer | Oxford Diffraction Xcalibur S diffractometer |
| Absorption correction | Analytical CrysAlis RED, Oxford Diffraction Ltd., Version 1.171.31.7 (release 18-10-2006 CrysAlis171 .NET) Analytical numeric absorption correction using a multifaceted crystal model based on expressions derived by R.C. Clark & J.S. Reid. (Clark, R. C. & Reid, J. S. (1995). Acta Cryst. A51, 887-897) |
| Tmin, Tmax | 0.969, 0.977 |
| No. of measured, independent and observed [F > 2.5u(σ)F] reflections | 78770, 3555, 2927 |
| Rint | 0.027 |
| (sin θ/λ)max (Å−1) | 1.190 |
| Refinement | |
| R[F2 > 2σ(F2)], wR(F2), S | 0.017, 0.010, 1.71 |
| No. of reflections | 2927 |
| No. of parameters | 156 |
| H-atom treatment | All H-atom parameters refined |
| Δρmax, Δρmin (e Å−3) | 0.17, −0.16 |
Computer programs: Koritsanszky et al., (2003).
Selected geometric parameters (Å, º) top
| O(1)—C(1) | 1.2697 (3) | C(2)—H(3) | 1.075 (5) |
| O(2)—C(1) | 1.2378 (3) | C(2)—H(4) | 1.065 (5) |
| N(1)—H(1) | 0.993 (5) | C(3)—H(5) | 1.087 (5) |
| N(1)—H(2) | 0.997 (5) | C(3)—H(6) | 1.077 (5) |
| C(1)—C(2) | 1.5244 (3) | C(3)—H(7) | 1.080 (6) |
| H(1)—N(1)—H(2) | 107.6 (4) | C(1)—C(2)—H(4) | 108.7 (3) |
| O(1)—C(1)—O(2) | 126.14 (2) | H(3)—C(2)—H(4) | 108.8 (4) |
| O(1)—C(1)—C(2) | 115.215 (18) | H(5)—C(3)—H(6) | 109.1 (4) |
| O(2)—C(1)—C(2) | 118.640 (19) | H(5)—C(3)—H(7) | 109.5 (4) |
| C(1)—C(2)—H(3) | 108.5 (3) | H(6)—C(3)—H(7) | 108.8 (4) |
