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The structure of L-ornithine hydrochloride, C5H13N2O_2^+Cl-, has been redetermined at 100 K by single-crystal X-ray diffraction within a project that aims to generate accurate bond-distance restraints for the invariom refinement of proteins. The high-resolution data were subject to an invariom and a multipole refinement, and the resulting electron densities on a grid were compared. Improvements in the conventional R factor obtained by multipole modelling were smaller than in other structures containing solely the elements CHNO owing to Cl core scattering. Cruickshank's diffraction-component precision index and Stevens & Coppens suitability factor are discussed.

Supporting information

cif

Crystallographic Information File (CIF) https://doi.org/10.1107/S0108768107014838/sn5050sup1.cif
Contains datablock ORNIT

hkl

Structure factor file (CIF format) https://doi.org/10.1107/S0108768107014838/sn5050sup2.hkl
Contains datablock ORNIT

pdf

Portable Document Format (PDF) file https://doi.org/10.1107/S0108768107014838/sn5050sup3.pdf
Static deformation density plots

CCDC reference: 650667

Computing details top

Data collection: CrysAlis CCD, Oxford Diffraction Ltd., Version 1.171.31.5; cell refinement: CrysAlis RED, Oxford Diffraction Ltd., Version 1.171.31.5; data reduction: CrysAlis RED, Oxford Diffraction Ltd., Version 1.171.31.5; program(s) used to refine structure: Koritsanszky et al., (2003); molecular graphics: PLATON, (Spek, 2003); software used to prepare material for publication: publCIF (Westrip, 2006).

Figures top
[Figure 1] Fig. 1.  
(ORNIT) top
Crystal data top
C5H13N2O2·ClF(000) = 180.0
Mr = 168.62Dx = 1.429 Mg m3
Monoclinic, P21Mo Kα radiation, λ = 0.7107 Å
Hall symbol: P2ybCell parameters from 24585 reflections
a = 9.9480 (2) Åθ = 3.3–52.7°
b = 7.9637 (2) ŵ = 0.43 mm1
c = 4.9826 (1) ÅT = 100 K
β = 83.13 (1)°Rectangle, colourless
V = 391.91 (2) Å30.71 × 0.63 × 0.24 mm
Z = 2
Data collection top
Oxford Diffraction Xcalibur S
diffractometer
8892 independent reflections
Radiation source: Enhance (Mo) X-ray Source8123 reflections with F > 3σ (F)
Graphite monochromatorRint = 0.020
Detector resolution: 16.0009 pixels mm-1θmax = 52.7°, θmin = 3.3°
ω scansh = 2222
Absorption correction: analytical
CrysAlis RED, Oxford Diffraction Ltd., Version 1.171.31.5, (Clark, R. C. & Reid, J. S. (1995). Acta Cryst. A51, 887-897)
k = 1717
Tmin = 0.790, Tmax = 0.914l = 1111
34435 measured reflections
Refinement top
Refinement on FAll H-atom parameters refined
Least-squares matrix: full w1 = 1/[s2(Fo)]
R[F2 > 2σ(F2)] = 0.014(Δ/σ)max < 0.001
wR(F2) = 0.009Δρmax = 0.33 e Å3
S = 1.80Δρmin = 0.45 e Å3
8123 reflectionsAbsolute structure: (Dittrich et al., 2006c)
103 parametersAbsolute structure parameter: 0.00 (7)
0 restraints
Crystal data top
C5H13N2O2·ClV = 391.91 (2) Å3
Mr = 168.62Z = 2
Monoclinic, P21Mo Kα radiation
a = 9.9480 (2) ŵ = 0.43 mm1
b = 7.9637 (2) ÅT = 100 K
c = 4.9826 (1) Å0.71 × 0.63 × 0.24 mm
β = 83.13 (1)°
Data collection top
Oxford Diffraction Xcalibur S
diffractometer
8892 independent reflections
Absorption correction: analytical
CrysAlis RED, Oxford Diffraction Ltd., Version 1.171.31.5, (Clark, R. C. & Reid, J. S. (1995). Acta Cryst. A51, 887-897)
8123 reflections with F > 3σ (F)
Tmin = 0.790, Tmax = 0.914Rint = 0.020
34435 measured reflections
Refinement top
R[F2 > 2σ(F2)] = 0.014All H-atom parameters refined
wR(F2) = 0.009Δρmax = 0.33 e Å3
S = 1.80Δρmin = 0.45 e Å3
8123 reflectionsAbsolute structure: (Dittrich et al., 2006c)
103 parametersAbsolute structure parameter: 0.00 (7)
0 restraints
Special details top

Experimental. A nitrogen gas-flow low temperature device was used. A face indexed analytical absorption correction was performed.

Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
xyzUiso*/Ueq
CL10.420733 (4)0.2206130.401602 (9)0.011
O10.00485 (2)0.06033 (2)0.17400 (3)0.011
O20.095930 (10)0.06593 (2)0.25880 (3)0.012
N10.10999 (2)0.14325 (2)0.39039 (3)0.009
N20.35613 (2)0.53068 (2)0.07902 (3)0.011
C10.00159 (2)0.03766 (2)0.07543 (4)0.008
C20.13384 (2)0.02295 (2)0.16088 (4)0.008
C30.21365 (2)0.12686 (3)0.25227 (4)0.01
C40.25894 (2)0.24816 (2)0.02337 (4)0.01
C50.32130 (2)0.40292 (3)0.13674 (4)0.011
H10.0647 (5)0.2507 (8)0.3347 (9)0.0280 (10)
H20.2017 (5)0.1780 (6)0.4382 (9)0.0230 (10)
H30.0551 (5)0.0849 (7)0.5542 (11)0.0250 (10)
H40.1908 (4)0.0873 (5)0.0031 (9)0.0200 (9)
H50.3001 (5)0.0776 (6)0.3379 (9)0.0240 (10)
H60.1495 (5)0.1922 (6)0.4114 (10)0.0260 (10)
H70.3315 (5)0.1891 (6)0.1273 (10)0.0290 (10)
H80.1734 (4)0.2873 (8)0.0786 (8)0.0274 (9)
H90.4125 (5)0.3773 (7)0.2154 (9)0.0290 (10)
H100.2505 (5)0.4607 (6)0.2924 (10)0.0290 (10)
H110.3937 (5)0.6356 (7)0.0088 (10)0.0250 (10)
H120.4292 (5)0.4850 (7)0.2211 (11)0.0280 (10)
H130.2716 (5)0.5613 (7)0.1646 (10)0.0290 (10)
Atomic displacement parameters (Å2) top
U11U22U33U12U13U23
CL10.009330 (10)0.01104 (2)0.01374 (2)0.00076 (2)0.002140 (10)0.00067 (2)
O10.01336 (6)0.01290 (6)0.00732 (5)0.00236 (5)0.00265 (4)0.00088 (4)
O20.00875 (5)0.01801 (7)0.00915 (5)0.00275 (5)0.00125 (4)0.00268 (5)
N10.00948 (6)0.00832 (6)0.00897 (5)0.00040 (5)0.00162 (4)0.00189 (5)
N20.01110 (6)0.00929 (6)0.01227 (6)0.00205 (5)0.00182 (5)0.00204 (5)
C10.00839 (6)0.00860 (6)0.00662 (5)0.00060 (5)0.00163 (5)0.00032 (5)
C20.00796 (6)0.00784 (6)0.00775 (6)0.00013 (5)0.00105 (5)0.00103 (5)
C30.00957 (6)0.00888 (7)0.01015 (6)0.00177 (5)0.00235 (5)0.00163 (5)
C40.01163 (6)0.00907 (8)0.01030 (6)0.00229 (5)0.00127 (5)0.00120 (5)
C50.01183 (7)0.00898 (7)0.01071 (7)0.00187 (5)0.00278 (5)0.00148 (5)
Geometric parameters (Å, º) top
O1—C11.2601 (2)C2—H41.068 (4)
O2—C11.2495 (2)C3—C41.5212 (3)
N1—H11.020 (6)C3—H51.079 (5)
N1—H21.008 (5)C3—H61.089 (5)
N1—H31.036 (5)C4—C51.5187 (3)
N2—H111.034 (6)C4—H71.085 (5)
N2—H121.019 (6)C4—H81.087 (4)
N2—H131.017 (5)C5—H91.051 (5)
C1—C21.5383 (2)C5—H101.086 (5)
C2—C31.5321 (3)
H1—N1—H2106.0 (4)C2—C3—H6108.0 (2)
H1—N1—H3112.5 (4)C4—C3—H5110.4 (2)
H2—N1—H3110.1 (4)C4—C3—H6109.7 (3)
H11—N2—H12108.6 (4)H5—C3—H6108.1 (3)
H11—N2—H13110.0 (4)C3—C4—C5109.511 (15)
H12—N2—H13110.6 (4)C3—C4—H7110.9 (3)
O1—C1—O2126.138 (18)C3—C4—H8110.7 (3)
O1—C1—C2116.395 (15)C5—C4—H7110.0 (3)
O2—C1—C2117.405 (16)C5—C4—H8108.5 (3)
C1—C2—C3109.876 (15)H7—C4—H8107.1 (3)
C1—C2—H4109.9 (2)C4—C5—H9113.0 (3)
C3—C2—H4110.8 (2)C4—C5—H10110.5 (3)
C2—C3—C4112.905 (15)H9—C5—H10109.4 (3)
C2—C3—H5107.5 (3)

Experimental details

Crystal data
Chemical formulaC5H13N2O2·Cl
Mr168.62
Crystal system, space groupMonoclinic, P21
Temperature (K)100
a, b, c (Å)9.9480 (2), 7.9637 (2), 4.9826 (1)
β (°) 83.13 (1)
V3)391.91 (2)
Z2
Radiation typeMo Kα
µ (mm1)0.43
Crystal size (mm)0.71 × 0.63 × 0.24
Data collection
DiffractometerOxford Diffraction Xcalibur S
diffractometer
Absorption correctionAnalytical
CrysAlis RED, Oxford Diffraction Ltd., Version 1.171.31.5, (Clark, R. C. & Reid, J. S. (1995). Acta Cryst. A51, 887-897)
Tmin, Tmax0.790, 0.914
No. of measured, independent and
observed [F > 3σ (F)] reflections
34435, 8892, 8123
Rint0.020
(sin θ/λ)max1)1.119
Refinement
R[F2 > 2σ(F2)], wR(F2), S 0.014, 0.009, 1.80
No. of reflections8123
No. of parameters103
H-atom treatmentAll H-atom parameters refined
Δρmax, Δρmin (e Å3)0.33, 0.45
Absolute structure(Dittrich et al., 2006c)
Absolute structure parameter0.00 (7)

Computer programs: CrysAlis CCD, Oxford Diffraction Ltd., Version 1.171.31.5, CrysAlis RED, Oxford Diffraction Ltd., Version 1.171.31.5, Koritsanszky et al., (2003), PLATON, (Spek, 2003), publCIF (Westrip, 2006).

Table 1. Comparison of geometries for IAM, invariom and multipole refinement. In invariom refinement bond distances, especially to H, improve. Invariom model and multipole refinement results are almost identical. top
BondIAMInvariomMultipole
O1—C11.2614 (4)1.2601 (2)1.2599 (3)
O(2) - C(1)1.2513 (4)1.2495 (2)1.2503 (3)
N(1) - H(1)0.836 (9)1.020 (6)
N(1) - H(2)0.857 (7)1.008 (5)
N(1) - H(3)0.864 (8)1.036 (5)
N(2) - H(11)0.869 (8)1.034 (6)
N(2) - H(12)0.886 (8)1.019 (6)
N(2) - H(13)0.879 (8)1.017 (5)
C(1) - C(2)1.5391 (4)1.5383 (2)1.5396 (3)
C(2) - C(3)1.5310 (5)1.5321 (3)1.5323 (3)
C(2) - H(4)0.932 (7)1.068 (4)
C(3) - C(4)1.5217 (5)1.5212 (3)1.5214 (3)
C(3) - H(5)0.991 (7)1.079 (5)
C(3) - H(6)0.950 (7)1.089 (5)
C(4) - C(5)1.5187 (5)1.5187 (3)1.5193 (3)
C(4) - H(7)0.981 (7)1.085 (5)
C(4) - H(8)0.984 (7)1.087 (4)
C(5) - H(9)0.963 (7)1.051 (5)
C(5) - H(10)0.921 (7)1.086 (5)
Table 2. H bond pattern in L-ornithine hydrochloride top
DonorHAcceptorSymmetryD···HH···AD···AAngle DHA
N1H1O1-x,1/2 + y,-z1.021 (6)1.837 (6)2.8458 (2)169.1 (4)
N1H2Clintra1.009 (5)2.191 (5)3.1591 (2)160.3 (4)
N1H3O1x,y,1 + z1.036 (5)1.826 (5)2.8376 (2)164.3 (5)
N2H11Clx,-1 + y,z1.034 (5)2.311 (5)3.2309 (2)147.5 (4)
N2H12Cl1 − x,-1/2 + y,-z1.019 (5)2.323 (5)3.2654 (2)153.2 (4)
N2H13O2-x,-1/2 + y,-z1.017 (5)1.863 (5)2.8523 (2)163.3 (5)
C3H5Clintra1.079 (5)2.697 (5)3.5807 (2)138.9 (3)
C4H7Cl1 − x,-1/2 + y,-z1.085 (5)2.767 (5)3.6176 (2)135.2 (3)
C4H8O2-x,-1/2 + y,-z1.088 (4)2.547 (6)3.3993 (2)134.5 (4)
C5H9Cl1 − x,-1/2 + y,1 − z1.050 (5)2.786 (5)3.7757 (2)157.2 (3)
Table 3. Suitability factor for five chosen structures mentioned in the text top
CompoundV/ZΣn2coreS
L-ornithine hydrochloride196.01361.44
L-valinol160.2285.72
4-O-methylalpinumisoflavone419.41044.03
O,O-dimethylalpinumisoflavone447.51084.14
5-O-methyl-4-O-(3-methylbut-2-en-1-yl)alpinumisoflavone1111.82484.48
 

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