Supporting information
Crystallographic Information File (CIF) https://doi.org/10.1107/S0108270100010325/bm1417sup1.cif | |
Structure factor file (CIF format) https://doi.org/10.1107/S0108270100010325/bm1417Isup2.hkl |
CCDC reference: 152635
Crystals of (I) were grown by slow diffusion of ethanol into a saturated aqueous solution of the amino acid. This yielded crystals suitable for the collection of a low-temperature dataset.
All hydrogen atoms were found in the difference Fourier maps. Five types of hydrogen atoms were refined with a common isotropic displacement parameters for each.
## AUTHOR: Were H atoms restrained? If so, please give distances used. ## If refined freely, please state this clearly. The CIF states: ## _atom_sites_solution_hydrogens GEOM ## _refine_ls_hydrogen_treatment mixed
Data collection: COLLECT (Hooft, 1998); cell refinement: DENZO (Otwinowski & Minor, 1997); data reduction: DENZO and SORTAV (Blessing, 1995); program(s) used to solve structure: SHELXS97 (Sheldrick, 1997); program(s) used to refine structure: SHELXL97 (Sheldrick, 1997); molecular graphics: ORTEPIII (Burnett & Johnson, 1996) and SCHAKAL (Keller, 1997); software used to prepare material for publication: SHELXL97 and PLATON (Spek, 1990).
C6H14N4O2·H2O | Dx = 1.394 Mg m−3 |
Mr = 192.23 | Melting point: 230 K |
Orthorhombic, Pbca | Mo Kα radiation, λ = 0.71073 Å |
Hall symbol: -P 2ac 2ab | Cell parameters from 15774 reflections |
a = 11.470 (3) Å | θ = 2.5–26.4° |
b = 9.966 (6) Å | µ = 0.11 mm−1 |
c = 16.023 (1) Å | T = 100 K |
V = 1832 (1) Å3 | Plate, colourless |
Z = 8 | 0.60 × 0.50 × 0.20 mm |
F(000) = 832 |
Nonius kappaCCD area detector diffractometer | 1870 independent reflections |
Radiation source: rotating anode | 1862 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.032 |
ω and ϕ scans | θmax = 26.4°, θmin = 2.5° |
Absorption correction: empirical (using intensity measurements) (SORTAV; Blessing, 1995) | h = −14→14 |
Tmin = 0.936, Tmax = 0.978 | k = −12→12 |
41487 measured reflections | l = −20→20 |
Refinement on F2 | Primary atom site location: structure-invariant direct methods |
Least-squares matrix: full | Secondary atom site location: difference Fourier map |
R[F2 > 2σ(F2)] = 0.034 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.080 | H atoms treated by a mixture of independent and constrained refinement |
S = 1.12 | w = 1/[σ2(Fo2) + (0.0335P)2 + 1.2913P] where P = (Fo2 + 2Fc2)/3 |
1870 reflections | (Δ/σ)max = 0.001 |
172 parameters | Δρmax = 0.33 e Å−3 |
0 restraints | Δρmin = −0.20 e Å−3 |
C6H14N4O2·H2O | V = 1832 (1) Å3 |
Mr = 192.23 | Z = 8 |
Orthorhombic, Pbca | Mo Kα radiation |
a = 11.470 (3) Å | µ = 0.11 mm−1 |
b = 9.966 (6) Å | T = 100 K |
c = 16.023 (1) Å | 0.60 × 0.50 × 0.20 mm |
Nonius kappaCCD area detector diffractometer | 1870 independent reflections |
Absorption correction: empirical (using intensity measurements) (SORTAV; Blessing, 1995) | 1862 reflections with I > 2σ(I) |
Tmin = 0.936, Tmax = 0.978 | Rint = 0.032 |
41487 measured reflections |
R[F2 > 2σ(F2)] = 0.034 | 0 restraints |
wR(F2) = 0.080 | H atoms treated by a mixture of independent and constrained refinement |
S = 1.12 | Δρmax = 0.33 e Å−3 |
1870 reflections | Δρmin = −0.20 e Å−3 |
172 parameters |
Experimental. An Oxford Cryosystems low temperature device was used. Reciprocal space was explored by ω and ϕ-scans. No intensity decay was observed. All non-hydrogen atoms were refined anisotropically. |
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. |
x | y | z | Uiso*/Ueq | ||
O1 | 0.09635 (7) | 0.64767 (8) | 0.62401 (5) | 0.0146 (2) | |
O2 | 0.18322 (8) | 0.49433 (8) | 0.54327 (5) | 0.0169 (2) | |
N1 | 0.00031 (9) | 0.77965 (11) | 0.48646 (6) | 0.0164 (2) | |
H2 | 0.0240 (15) | 0.8350 (17) | 0.5293 (11) | 0.026 (3)* | |
H3 | −0.0658 (15) | 0.7393 (18) | 0.5006 (11) | 0.026 (3)* | |
N2 | 0.38611 (8) | 0.76189 (10) | 0.30292 (6) | 0.0126 (2) | |
H10 | 0.4497 (14) | 0.7655 (16) | 0.3321 (10) | 0.022 (4)* | |
N3 | 0.46176 (9) | 0.57487 (10) | 0.23697 (7) | 0.0143 (2) | |
H71 | 0.4476 (14) | 0.5069 (16) | 0.2017 (10) | 0.023 (2)* | |
H72 | 0.5031 (15) | 0.5588 (16) | 0.2792 (10) | 0.023 (2)* | |
N4 | 0.29681 (9) | 0.67581 (11) | 0.18398 (6) | 0.0149 (2) | |
H81 | 0.3010 (14) | 0.6160 (17) | 0.1403 (10) | 0.023 (2)* | |
H82 | 0.2491 (14) | 0.7433 (17) | 0.1808 (10) | 0.023 (2)* | |
C1 | 0.12472 (9) | 0.60032 (12) | 0.55352 (7) | 0.0117 (2) | |
C2 | 0.09004 (10) | 0.67665 (12) | 0.47352 (7) | 0.0132 (2) | |
H1 | 0.0572 (12) | 0.6089 (15) | 0.4331 (9) | 0.015 (3)* | |
C3 | 0.20162 (10) | 0.73814 (12) | 0.43668 (7) | 0.0132 (2) | |
H4 | 0.2333 (13) | 0.8049 (15) | 0.4789 (9) | 0.0171 (15)* | |
H5 | 0.2587 (13) | 0.6624 (15) | 0.4304 (9) | 0.0171 (15)* | |
C4 | 0.18335 (10) | 0.80988 (12) | 0.35324 (8) | 0.0151 (3) | |
H6 | 0.1299 (13) | 0.8854 (16) | 0.3610 (9) | 0.0171 (15)* | |
H7 | 0.1454 (13) | 0.7508 (16) | 0.3150 (9) | 0.0171 (15)* | |
C5 | 0.29742 (10) | 0.86543 (12) | 0.31729 (7) | 0.0140 (2) | |
H8 | 0.2832 (12) | 0.9146 (15) | 0.2655 (9) | 0.0171 (15)* | |
H9 | 0.3331 (13) | 0.9287 (15) | 0.3577 (9) | 0.0171 (15)* | |
C6 | 0.38086 (10) | 0.67190 (11) | 0.24145 (7) | 0.0115 (2) | |
O1W | 0.41679 (8) | 0.51029 (10) | 0.61367 (6) | 0.0209 (2) | |
H1W | 0.3454 (19) | 0.506 (2) | 0.5954 (12) | 0.046 (4)* | |
H2W | 0.4469 (17) | 0.584 (2) | 0.5869 (12) | 0.046 (4)* |
U11 | U22 | U33 | U12 | U13 | U23 | |
O1 | 0.0160 (4) | 0.0147 (4) | 0.0129 (4) | 0.0021 (3) | 0.0019 (3) | 0.0005 (3) |
O2 | 0.0199 (4) | 0.0149 (4) | 0.0158 (4) | 0.0056 (3) | 0.0025 (3) | 0.0014 (3) |
N1 | 0.0129 (5) | 0.0199 (6) | 0.0165 (5) | 0.0043 (4) | 0.0025 (4) | 0.0043 (4) |
N2 | 0.0099 (5) | 0.0154 (5) | 0.0126 (5) | −0.0012 (4) | −0.0010 (4) | −0.0020 (4) |
N3 | 0.0154 (5) | 0.0149 (5) | 0.0125 (5) | 0.0014 (4) | −0.0019 (4) | −0.0004 (4) |
N4 | 0.0159 (5) | 0.0144 (5) | 0.0145 (5) | 0.0022 (4) | −0.0034 (4) | −0.0024 (4) |
C1 | 0.0087 (5) | 0.0130 (5) | 0.0134 (5) | −0.0015 (4) | 0.0009 (4) | 0.0014 (4) |
C2 | 0.0124 (5) | 0.0148 (6) | 0.0123 (5) | 0.0010 (5) | 0.0004 (4) | 0.0003 (4) |
C3 | 0.0118 (5) | 0.0144 (5) | 0.0135 (6) | 0.0004 (5) | 0.0005 (4) | 0.0007 (5) |
C4 | 0.0129 (6) | 0.0174 (6) | 0.0149 (6) | 0.0018 (5) | 0.0015 (5) | 0.0028 (5) |
C5 | 0.0159 (6) | 0.0123 (5) | 0.0140 (6) | −0.0001 (4) | 0.0020 (5) | 0.0000 (5) |
C6 | 0.0107 (5) | 0.0126 (5) | 0.0111 (5) | −0.0039 (4) | 0.0025 (4) | 0.0023 (4) |
O1W | 0.0179 (5) | 0.0225 (5) | 0.0223 (5) | −0.0050 (4) | −0.0035 (4) | 0.0087 (4) |
O1—C1 | 1.2666 (14) | C1—C2 | 1.5427 (16) |
O2—C1 | 1.2622 (15) | C2—C3 | 1.5369 (16) |
N1—C2 | 1.4683 (16) | C2—H1 | 1.009 (15) |
N1—H2 | 0.922 (18) | C3—C4 | 1.5305 (16) |
N1—H3 | 0.888 (18) | C3—H4 | 1.016 (15) |
N2—C6 | 1.3333 (15) | C3—H5 | 1.005 (15) |
N2—C5 | 1.4672 (16) | C4—C5 | 1.5331 (16) |
N2—H10 | 0.867 (16) | C4—H6 | 0.978 (15) |
N3—C6 | 1.3422 (16) | C4—H7 | 0.955 (16) |
N3—H71 | 0.898 (17) | C5—H8 | 0.977 (15) |
N3—H72 | 0.842 (17) | C5—H9 | 0.992 (15) |
N4—C6 | 1.3339 (15) | O1W—H1W | 0.87 (2) |
N4—H81 | 0.920 (17) | O1W—H2W | 0.92 (2) |
N4—H82 | 0.868 (17) | ||
C2—N1—H2 | 108.5 (10) | C4—C3—H4 | 109.0 (8) |
C2—N1—H3 | 108.6 (11) | C2—C3—H4 | 107.7 (8) |
H2—N1—H3 | 109.4 (15) | C4—C3—H5 | 110.7 (8) |
C6—N2—C5 | 123.90 (10) | C2—C3—H5 | 106.4 (8) |
C6—N2—H10 | 117.7 (11) | H4—C3—H5 | 108.9 (11) |
C5—N2—H10 | 118.0 (11) | C3—C4—C5 | 112.34 (10) |
C6—N3—H71 | 116.9 (10) | C3—C4—H6 | 109.5 (9) |
C6—N3—H72 | 118.9 (11) | C5—C4—H6 | 107.7 (9) |
H71—N3—H72 | 117.7 (15) | C3—C4—H7 | 109.6 (9) |
C6—N4—H81 | 117.9 (10) | C5—C4—H7 | 111.8 (9) |
C6—N4—H82 | 121.2 (10) | H6—C4—H7 | 105.6 (12) |
H81—N4—H82 | 119.4 (14) | N2—C5—C4 | 113.37 (10) |
O2—C1—O1 | 124.37 (11) | N2—C5—H8 | 109.6 (8) |
O2—C1—C2 | 116.21 (10) | C4—C5—H8 | 111.0 (8) |
O1—C1—C2 | 119.40 (10) | N2—C5—H9 | 105.3 (9) |
N1—C2—C3 | 111.05 (10) | C4—C5—H9 | 109.6 (9) |
N1—C2—C1 | 114.09 (10) | H8—C5—H9 | 107.7 (12) |
C3—C2—C1 | 107.52 (9) | N2—C6—N4 | 121.53 (11) |
N1—C2—H1 | 107.3 (8) | N2—C6—N3 | 119.54 (11) |
C3—C2—H1 | 109.3 (8) | N4—C6—N3 | 118.94 (11) |
C1—C2—H1 | 107.5 (8) | H1W—O1W—H2W | 103.6 (17) |
C4—C3—C2 | 114.06 (10) |
D—H···A | D—H | H···A | D···A | D—H···A |
N1—H2···O1Wi | 0.92 (2) | 2.31 (2) | 3.216 (2) | 167 (2) |
N2—H10···O1ii | 0.87 (2) | 2.02 (2) | 2.828 (2) | 155 (2) |
N3—H71···O1iii | 0.90 (2) | 2.04 (2) | 2.939 (2) | 176 (2) |
N3—H72···O1Wiv | 0.84 (2) | 2.07 (2) | 2.896 (2) | 169 (2) |
N4—H81···O2iii | 0.92 (2) | 1.91 (2) | 2.830 (2) | 174 (2) |
N4—H82···O1v | 0.87 (2) | 2.25 (2) | 3.050 (2) | 152 (2) |
O1W—H1W···O2 | 0.87 (2) | 2.04 (2) | 2.911 (2) | 175 (2) |
O1W—H2W···N1ii | 0.92 (2) | 1.90 (2) | 2.806 (2) | 169 (2) |
C3—H4···O2i | 1.02 (2) | 2.36 (2) | 3.344 (2) | 164 (1) |
Symmetry codes: (i) −x+1/2, y+1/2, z; (ii) x+1/2, −y+3/2, −z+1; (iii) −x+1/2, −y+1, z−1/2; (iv) −x+1, −y+1, −z+1; (v) x, −y+3/2, z−1/2. |
Experimental details
Crystal data | |
Chemical formula | C6H14N4O2·H2O |
Mr | 192.23 |
Crystal system, space group | Orthorhombic, Pbca |
Temperature (K) | 100 |
a, b, c (Å) | 11.470 (3), 9.966 (6), 16.023 (1) |
V (Å3) | 1832 (1) |
Z | 8 |
Radiation type | Mo Kα |
µ (mm−1) | 0.11 |
Crystal size (mm) | 0.60 × 0.50 × 0.20 |
Data collection | |
Diffractometer | Nonius kappaCCD area detector diffractometer |
Absorption correction | Empirical (using intensity measurements) (SORTAV; Blessing, 1995) |
Tmin, Tmax | 0.936, 0.978 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 41487, 1870, 1862 |
Rint | 0.032 |
(sin θ/λ)max (Å−1) | 0.625 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.034, 0.080, 1.12 |
No. of reflections | 1870 |
No. of parameters | 172 |
H-atom treatment | H atoms treated by a mixture of independent and constrained refinement |
Δρmax, Δρmin (e Å−3) | 0.33, −0.20 |
Computer programs: COLLECT (Hooft, 1998), DENZO (Otwinowski & Minor, 1997), DENZO and SORTAV (Blessing, 1995), SHELXS97 (Sheldrick, 1997), SHELXL97 (Sheldrick, 1997), ORTEPIII (Burnett & Johnson, 1996) and SCHAKAL (Keller, 1997), SHELXL97 and PLATON (Spek, 1990).
O1—C1 | 1.2666 (14) | N4—C6 | 1.3339 (15) |
O2—C1 | 1.2622 (15) | C1—C2 | 1.5427 (16) |
N1—C2 | 1.4683 (16) | C2—C3 | 1.5369 (16) |
N2—C6 | 1.3333 (15) | C3—C4 | 1.5305 (16) |
N2—C5 | 1.4672 (16) | C4—C5 | 1.5331 (16) |
C6—N2—C5 | 123.90 (10) | C4—C3—C2 | 114.06 (10) |
O2—C1—O1 | 124.37 (11) | C3—C4—C5 | 112.34 (10) |
O2—C1—C2 | 116.21 (10) | N2—C5—C4 | 113.37 (10) |
O1—C1—C2 | 119.40 (10) | N2—C6—N4 | 121.53 (11) |
N1—C2—C3 | 111.05 (10) | N2—C6—N3 | 119.54 (11) |
N1—C2—C1 | 114.09 (10) | N4—C6—N3 | 118.94 (11) |
C3—C2—C1 | 107.52 (9) |
D—H···A | D—H | H···A | D···A | D—H···A |
N1—H2···O1Wi | 0.92 (2) | 2.31 (2) | 3.216 (2) | 167 (2) |
N2—H10···O1ii | 0.87 (2) | 2.02 (2) | 2.828 (2) | 155 (2) |
N3—H71···O1iii | 0.90 (2) | 2.04 (2) | 2.939 (2) | 176 (2) |
N3—H72···O1Wiv | 0.84 (2) | 2.07 (2) | 2.896 (2) | 169 (2) |
N4—H81···O2iii | 0.92 (2) | 1.91 (2) | 2.830 (2) | 174 (2) |
N4—H82···O1v | 0.87 (2) | 2.25 (2) | 3.050 (2) | 152 (2) |
O1W—H1W···O2 | 0.87 (2) | 2.04 (2) | 2.911 (2) | 175 (2) |
O1W—H2W···N1ii | 0.92 (2) | 1.90 (2) | 2.806 (2) | 169 (2) |
C3—H4···O2i | 1.02 (2) | 2.36 (2) | 3.344 (2) | 164 (1) |
Symmetry codes: (i) −x+1/2, y+1/2, z; (ii) x+1/2, −y+3/2, −z+1; (iii) −x+1/2, −y+1, z−1/2; (iv) −x+1, −y+1, −z+1; (v) x, −y+3/2, z−1/2. |
DL-Arg monohydrate | L-Arg dihydrate | DL-Arg dihydrate | ||
O2-C1-C2-N1 | 166.33 (10) | |||
O1-C1-C2-N1 | ϕ1 | -15.37 (15) | -13.0 (2) | -11.5 (3) |
O2-C1-C2-C3 | -70.05 (13) | |||
O1-C1-C2-C3 | 108.25 (12) | |||
N1-C2-C3-C4 | χ1 | -58.47 (13) | 63.9 (2) | -54.1 (3) |
C1-C2-C3-C4 | 176.08 (10) | |||
C2-C3-C4-C5 | χ2 | -178.02 (10) | 150.5 (2) | -179.8 (2) |
C6-N2-C5-C4 | χ4 | 72.81 (14) | 163.2 (2) | -92.2 (3) |
C3-C4-C5-N2 | χ3 | 59.02 (13) | 175.1 (2) | -163.0 (2) |
C5-N2-C6-N4 | χ5 | 4.86 (17) | -10.1 (2) | 7.4 (4) |
C5-N2-C6-N3 | -175.13 (10) |
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In conjunction with our work of comparative charge-density studies on different amino acids at low temperature by X-ray diffraction methods (Flaig et al., 1999), we crystallized DL-arginine monohydrate, (I), whose structure had not yet been investigated. Arginine is one of the 20 naturally occurring amino acids. It is found in large amounts in protamines and histones. High concentrations of free arginine are also found in many plants including red algae, curcurbitaceae and conifers, where it serves as a nitrogen storage and transport form. For this reason, it is found in particularly high concentrations in seedlings and reserve organs like rat liver. Young rats and chicks require the amino acid and show stunted growth when fed arginine-free diets because they cannot synthesize it in adequate amounts (Scott & Brewer, 1983). \sch
Various complexes involving arginine have been investigated by X-ray and neutron techniques, with the Cambridge Structural Database (Allen & Kennard, 1993) containing over 50 entries. Only two crystalline forms involving hydrated free arginine are known: L-arginine dihydrate at room temperature from both X-ray (Karle & Karle, 1964) and neutron diffraction (Lehmann et al., 1973), and DL-arginine dihydrate (Suresh et al., 1994).
An ORTEPIII (Johnson & Burnett, 1996) representation of the molecular structure of the title compound with the atomic numbering scheme is shown in Fig 1. The molecule exists as a zwitterion in the crystal structure, the α-carboxylic group is deprotonated and the proton resides in one of the two amino groups of the mesomeric guanidinium fragment. This arrangement permits the formation of two direct N–H···O hydrogen bonds [N3–H71···O1iii and N4–H81···O2iii] (for numbering and symmetry codes of hydrogen bonds see Table 2) between the polar guanidinium and carboxylate groups. This results in a dimeric unit formed by the reference molecule and one generated by the symmetry operation iii. Each dimer is further linked to other dimeric units by their polar ends, forming an infinite chain of molecules of the same chirality. On the other hand, dimers are interconnected by N4–H82···O1v and C3–H4···O2i. Finally a pair of these chains is bonded directly by N2–H10···O1ii and indirectly via water molecules leading to an infinite three-dimensional lattice.
This arrangement permits the formation of two direct N—H···O hydrogen bonds [N3—H71···O1iii and N4—H81···O2iii] (see Fig. 2 and Table 2) between these polar groups. Similar hydrogen bonding schemes have been observed in L-arginine dihydrate (Karle & Karle, 1964; Lehmann et al., 1973) and DL-arginine dihydrate (Suresh et al., 1994) which also have a neutral α-amino group. This pattern differs from that previously observed for some arginine complexes [L-arginine phosphate monohydrate (Espinosa et al., 1996), DL-arginine formate dihydrate and L-arginine formate (Suresh et al., 1994), DL-arginine DL-glutamate monohydrate and DL-arginine DL-aspartate (Soman et al., 1990)] and crystalline complexes of some peptides [L-arginine L-glutamate (Bhat & Vijayan, 1977)] and α-helical peptides (Karle & Balaram, 1990), where the carboxylate group bonds to the protonated α-amino group and not to the guanidinium group. The former sequence is described as having head-to-tail hydrogen bonding (Karle & Balaram, 1990). Unlike L-arginine dihydrate and DL-arginine dihydrate, where the α-amino group does not contribute to N—H···O hydrogen bonding, in (I) one of the H atoms of the α-amino group is donor to an O atom of a solvent water molecule (N1—H2···O1Wii). The observed lack of hydrogen-bond acceptor atoms for H3 of the α-amino group is not surprising. In L-arginine dihydrate (Karle & Karle, 1964; Lehmann et al., 1973) and DL-arginine dihydrate (Suresh et al., 1994) neither α-amino H atom forms a hydrogen bond. Another difference between (I) and the dihydrates is the hydrogen-bonding environment around the guanidinium atom N2. Here, the N—H···N interactions involving these atoms in L-arginine dihydrate and DL-arginine dihydrate (Lehmann et al., 1973; Suresh et al., 1994) are replaced by N—H···O hydrogen bonding: [N2—H10···O1i].
This substitution of an N–H···O in lieu of an N–H···N hydrogen bond seems to have a conformational significance for the title compound. The backbone in DL-arginine monohydrate shows a less extended conformation than its close analogues cited in the discussion. The carbon chain C1···C5 is in a fully extended conformation, which holds also for the molecule in the DL-arginine dihydrate structure but not for the L-dihydrate. However, the torsion angles (IUPAC-IUB, 1970) C3–C4–C5–N2 [χ3 = 59.0 (1)°] and C4–C5–N2–C6 [χ4= 72.8 (1)°] on the other hand describe a more bent conformation in the nitrogen-rich region. This results in a near gauche-gauche conformation. This is different from the trans-trans and trans-perpendicular conformation observed for the L-arginine dihydrate and DL-arginine dihydrate. The underlying factor for this less extended backbone conformation in the title compound might be the N2–H10···O1ii hydrogen bond shown by the title compound.