Crystals of L-leucylglycine (L-Leu–Gly) 0.67-hydrate, C8H16N2O3·0.67H2O, (I), were obtained from an aqueous solution. There are three symmetrically independent dipeptide zwitterionic molecules in (I) and they are parallel to one another. The hydrogen-bond network composed of carboxylate and amino groups and water molecules extends parallel to the ab plane. Hydrophilic regions composed of main chains and hydrophobic regions composed of the isobutyl groups of the leucyl residues are aligned alternately along the c axis. An imidazolidinone derivative was obtained from L-Leu–Gly and acetone, viz. [(4S)-2,2-dimethyl-4-(2-methylpropyl)-5-oxoimidazolidin-3-ium-1-yl]acetate, C11H20N2O3, (II), and was crystallized from a methanol–acetone solution of L-Leu–Gly. The unit-cell parameters coincide with those reported previously for L-Leu–Gly dihydrate revealing that the previously reported values should be assigned to the structure of (II). One of the imidazolidine N atoms is protonated and the ring is nearly planar, except for the protonated N atom. Protonated N atoms and deprotonated carboxy groups of neighbouring molecules form hydrogen-bonded chains. The ring carbonyl group is not involved in hydrogen bonding.
Supporting information
CCDC references: 915103; 915104
L-Leu–Gly was purchased from Peptide Institute Inc. Crystals of (I)
were obtained from an aqueous solution and crystals of (II) were obtained from
a water–acetone solution according to the literature method of Leonard &
Pasternak (1952). The cell parameters coincided with the reported values.
However, the quality of the crystals was insufficient for structure analysis.
After employing several organic solvents, we obtained crystals of (II)
suitable for single-crystal X-ray analysis by the slow vapor diffusion method
using methanol as solvent and acetone as precipitant.
H atoms were initially located on a difference Fourier map and then placed at
calculated positions, with C—H = 0.96 (CH3), 0.97 (CH2) or 0.98 Å
(CH), O—H = 0.82 Å and N—H = 0.87 (NH3, NH) or N—H = 0.90 Å
(NH2), and were allowed to ride on the atom to which they were attached,
with Uiso(H) = 1.2Ueq(C,N,O) except for methyl groups in (I)
with Uiso(H) = 1.5Ueq(C). The absolute configuration was
known for the purchased material.
For both compounds, data collection: CrystalClear (Rigaku/MSC, 2006); cell refinement: CrystalClear (Rigaku/MSC, 2006); data reduction: CrystalClear (Rigaku/MSC, 2006); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: Mercury (Macrae et al., 2006); software used to prepare material for publication: Yadokari-XG 2009 (Kabuto et al., 2009).
(I)
L-Leucylglycine 0.67-hydrate
top
Crystal data top
3C8H16N2O3·2H2O | F(000) = 1304 |
Mr = 600.72 | Dx = 1.213 Mg m−3 |
Orthorhombic, P212121 | Mo Kα radiation, λ = 0.71070 Å |
Hall symbol: P 2ac 2ab | Cell parameters from 1539 reflections |
a = 8.735 (5) Å | θ = 10.0–15.0° |
b = 15.54 (1) Å | µ = 0.10 mm−1 |
c = 24.238 (15) Å | T = 299 K |
V = 3290 (4) Å3 | Needle, colorless |
Z = 4 | 0.49 × 0.07 × 0.02 mm |
Data collection top
Rigaku Mercury CCD area-detector diffractometer | 4707 reflections with I > 2σ(I) |
Radiation source: rotating anode | Rint = 0.064 |
Graphite monochromator | θmax = 25.0°, θmin = 2.6° |
ω scans | h = −10→10 |
21778 measured reflections | k = −16→18 |
5794 independent reflections | l = −28→28 |
Refinement top
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)] = 0.060 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.161 | H-atom parameters constrained |
S = 1.09 | w = 1/[σ2(Fo2) + (0.0719P)2 + 0.4708P] where P = (Fo2 + 2Fc2)/3 |
5794 reflections | (Δ/σ)max < 0.001 |
370 parameters | Δρmax = 0.26 e Å−3 |
0 restraints | Δρmin = −0.19 e Å−3 |
Crystal data top
3C8H16N2O3·2H2O | V = 3290 (4) Å3 |
Mr = 600.72 | Z = 4 |
Orthorhombic, P212121 | Mo Kα radiation |
a = 8.735 (5) Å | µ = 0.10 mm−1 |
b = 15.54 (1) Å | T = 299 K |
c = 24.238 (15) Å | 0.49 × 0.07 × 0.02 mm |
Data collection top
Rigaku Mercury CCD area-detector diffractometer | 4707 reflections with I > 2σ(I) |
21778 measured reflections | Rint = 0.064 |
5794 independent reflections | |
Refinement top
R[F2 > 2σ(F2)] = 0.060 | 0 restraints |
wR(F2) = 0.161 | H-atom parameters constrained |
S = 1.09 | Δρmax = 0.26 e Å−3 |
5794 reflections | Δρmin = −0.19 e Å−3 |
370 parameters | |
Special details top
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. |
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top | x | y | z | Uiso*/Ueq | |
N1A | 1.0573 (3) | 0.08948 (17) | 0.22525 (11) | 0.0431 (6) | |
H1A | 1.1185 | 0.0461 | 0.2306 | 0.052* | |
H2A | 1.0187 | 0.1057 | 0.2567 | 0.052* | |
H3A | 1.1081 | 0.1319 | 0.2107 | 0.052* | |
C1A | 0.9316 (3) | 0.06326 (19) | 0.18740 (13) | 0.0417 (7) | |
H4A | 0.8723 | 0.1139 | 0.1762 | 0.050* | |
C2A | 0.8291 (3) | 0.0000 (2) | 0.21743 (15) | 0.0433 (8) | |
O1A | 0.8828 (3) | −0.06594 (14) | 0.23804 (11) | 0.0560 (6) | |
N2A | 0.6805 (3) | 0.01804 (17) | 0.21830 (12) | 0.0446 (7) | |
H5A | 0.6493 | 0.0670 | 0.2051 | 0.054* | |
C3A | 0.5684 (3) | −0.0416 (2) | 0.24070 (16) | 0.0508 (9) | |
H6A | 0.6014 | −0.0606 | 0.2769 | 0.061* | |
H7A | 0.5619 | −0.0918 | 0.2170 | 0.061* | |
C4A | 0.4114 (3) | 0.0000 (2) | 0.24524 (13) | 0.0429 (7) | |
O2A | 0.4058 (3) | 0.07911 (15) | 0.24817 (11) | 0.0551 (6) | |
O3A | 0.2970 (2) | −0.04994 (16) | 0.24721 (11) | 0.0555 (6) | |
C5A | 1.0049 (4) | 0.0211 (2) | 0.13664 (14) | 0.0527 (8) | |
H8A | 1.0700 | 0.0631 | 0.1186 | 0.063* | |
H9A | 1.0698 | −0.0258 | 0.1490 | 0.063* | |
C6A | 0.8914 (5) | −0.0141 (2) | 0.09418 (16) | 0.0632 (10) | |
H10A | 0.8223 | −0.0540 | 0.1132 | 0.076* | |
C7A | 0.9768 (7) | −0.0644 (4) | 0.0503 (2) | 0.1026 (18) | |
H11A | 1.0332 | −0.0253 | 0.0273 | 0.154* | |
H12A | 0.9049 | −0.0959 | 0.0281 | 0.154* | |
H13A | 1.0463 | −0.1039 | 0.0676 | 0.154* | |
C8A | 0.7938 (7) | 0.0571 (4) | 0.0682 (2) | 0.1041 (19) | |
H14A | 0.8579 | 0.0938 | 0.0462 | 0.156* | |
H15A | 0.7461 | 0.0903 | 0.0968 | 0.156* | |
H16A | 0.7165 | 0.0317 | 0.0452 | 0.156* | |
N1B | 0.8991 (3) | 0.36914 (16) | 0.16818 (12) | 0.0446 (6) | |
H1B | 0.9568 | 0.3238 | 0.1714 | 0.053* | |
H2B | 0.8635 | 0.3835 | 0.2004 | 0.053* | |
H3B | 0.9527 | 0.4115 | 0.1548 | 0.053* | |
C1B | 0.7695 (3) | 0.3498 (2) | 0.13038 (13) | 0.0396 (7) | |
H4B | 0.7166 | 0.4033 | 0.1205 | 0.048* | |
C2B | 0.6590 (3) | 0.2893 (2) | 0.15932 (14) | 0.0412 (7) | |
O1B | 0.7080 (2) | 0.23040 (15) | 0.18869 (11) | 0.0539 (6) | |
N2B | 0.5129 (3) | 0.30142 (18) | 0.14888 (12) | 0.0495 (7) | |
H5B | 0.4868 | 0.3445 | 0.1280 | 0.059* | |
C3B | 0.3929 (4) | 0.2463 (2) | 0.17050 (17) | 0.0570 (10) | |
H6B | 0.4035 | 0.2415 | 0.2102 | 0.068* | |
H7B | 0.4028 | 0.1891 | 0.1548 | 0.068* | |
C4B | 0.2370 (4) | 0.2825 (2) | 0.15667 (16) | 0.0479 (8) | |
O2B | 0.2294 (3) | 0.34832 (16) | 0.12942 (13) | 0.0676 (8) | |
O3B | 0.1240 (3) | 0.23989 (14) | 0.17583 (12) | 0.0581 (7) | |
C5B | 0.8285 (4) | 0.3060 (2) | 0.07844 (14) | 0.0499 (8) | |
H8B | 0.8944 | 0.2589 | 0.0897 | 0.060* | |
H9B | 0.7415 | 0.2810 | 0.0594 | 0.060* | |
C6B | 0.9157 (5) | 0.3603 (2) | 0.03750 (16) | 0.0615 (10) | |
H10B | 1.0000 | 0.3889 | 0.0569 | 0.074* | |
C7B | 0.9838 (7) | 0.3005 (4) | −0.0066 (2) | 0.111 (2) | |
H11B | 0.9029 | 0.2693 | −0.0244 | 0.167* | |
H12B | 1.0530 | 0.2606 | 0.0106 | 0.167* | |
H13B | 1.0382 | 0.3341 | −0.0334 | 0.167* | |
C8B | 0.8168 (7) | 0.4282 (3) | 0.0112 (2) | 0.0965 (17) | |
H14B | 0.7305 | 0.4014 | −0.0062 | 0.145* | |
H15B | 0.8754 | 0.4590 | −0.0159 | 0.145* | |
H16B | 0.7815 | 0.4675 | 0.0390 | 0.145* | |
N1C | 0.7393 (3) | 0.64922 (17) | 0.16174 (12) | 0.0475 (7) | |
H1C | 0.7876 | 0.6093 | 0.1435 | 0.057* | |
H2C | 0.7083 | 0.6286 | 0.1932 | 0.057* | |
H3C | 0.8006 | 0.6924 | 0.1676 | 0.057* | |
C1C | 0.6045 (3) | 0.6789 (2) | 0.12904 (14) | 0.0452 (8) | |
H4C | 0.5480 | 0.7220 | 0.1504 | 0.054* | |
C2C | 0.5012 (4) | 0.6013 (2) | 0.11892 (14) | 0.0433 (7) | |
O1C | 0.5564 (3) | 0.53145 (16) | 0.10786 (12) | 0.0644 (7) | |
N2C | 0.3524 (3) | 0.61679 (17) | 0.12288 (12) | 0.0470 (7) | |
H5C | 0.3228 | 0.6685 | 0.1317 | 0.056* | |
C3C | 0.2364 (3) | 0.5514 (2) | 0.11324 (15) | 0.0444 (8) | |
H6C | 0.2748 | 0.4959 | 0.1253 | 0.053* | |
H7C | 0.2151 | 0.5478 | 0.0740 | 0.053* | |
C4C | 0.0904 (3) | 0.57185 (19) | 0.14379 (14) | 0.0427 (7) | |
O2C | 0.0972 (3) | 0.62780 (15) | 0.18099 (11) | 0.0597 (7) | |
O3C | −0.0279 (2) | 0.53187 (15) | 0.12990 (11) | 0.0573 (7) | |
C5C | 0.6583 (4) | 0.7193 (3) | 0.07484 (16) | 0.0566 (9) | |
H8C | 0.7407 | 0.7592 | 0.0829 | 0.068* | |
H9C | 0.6999 | 0.6742 | 0.0516 | 0.068* | |
C6C | 0.5353 (4) | 0.7667 (3) | 0.04268 (17) | 0.0648 (11) | |
H10C | 0.4505 | 0.7266 | 0.0363 | 0.078* | |
C7C | 0.5985 (6) | 0.7938 (4) | −0.0138 (2) | 0.0931 (16) | |
H11C | 0.5214 | 0.8252 | −0.0336 | 0.140* | |
H12C | 0.6267 | 0.7435 | −0.0344 | 0.140* | |
H13C | 0.6869 | 0.8297 | −0.0087 | 0.140* | |
C8C | 0.4728 (6) | 0.8435 (3) | 0.0731 (2) | 0.0927 (16) | |
H14C | 0.4098 | 0.8243 | 0.1031 | 0.139* | |
H15C | 0.4128 | 0.8779 | 0.0483 | 0.139* | |
H16C | 0.5561 | 0.8772 | 0.0872 | 0.139* | |
O1W | 0.2869 (5) | 0.7849 (2) | 0.19550 (13) | 0.0965 (12) | |
H1W | 0.2917 | 0.8329 | 0.2094 | 0.116* | |
H2W | 0.2874 | 0.7519 | 0.2219 | 0.116* | |
O2W | −0.0671 (4) | 0.78829 (18) | 0.17455 (15) | 0.0847 (10) | |
H3W | −0.0780 | 0.8323 | 0.1928 | 0.102* | |
H4W | 0.0247 | 0.7790 | 0.1707 | 0.102* | |
Atomic displacement parameters (Å2) top | U11 | U22 | U33 | U12 | U13 | U23 |
N1A | 0.0290 (12) | 0.0434 (14) | 0.0570 (16) | −0.0021 (11) | 0.0062 (12) | 0.0015 (12) |
C1A | 0.0288 (14) | 0.0379 (16) | 0.0585 (19) | −0.0060 (13) | 0.0041 (14) | 0.0018 (14) |
C2A | 0.0283 (15) | 0.0380 (18) | 0.063 (2) | −0.0034 (13) | 0.0034 (15) | −0.0016 (15) |
O1A | 0.0377 (12) | 0.0393 (12) | 0.0910 (19) | 0.0023 (10) | 0.0034 (12) | 0.0178 (12) |
N2A | 0.0246 (12) | 0.0390 (15) | 0.0703 (18) | −0.0015 (10) | 0.0073 (12) | 0.0041 (13) |
C3A | 0.0269 (15) | 0.0441 (18) | 0.081 (2) | −0.0075 (14) | 0.0099 (16) | −0.0007 (17) |
C4A | 0.0266 (15) | 0.051 (2) | 0.0509 (18) | 0.0000 (13) | 0.0055 (14) | 0.0033 (15) |
O2A | 0.0434 (13) | 0.0446 (14) | 0.0774 (16) | 0.0035 (11) | 0.0092 (13) | 0.0047 (12) |
O3A | 0.0305 (12) | 0.0581 (15) | 0.0780 (16) | −0.0094 (10) | 0.0065 (11) | 0.0012 (13) |
C5A | 0.0448 (19) | 0.053 (2) | 0.060 (2) | −0.0053 (16) | 0.0107 (17) | −0.0062 (16) |
C6A | 0.066 (3) | 0.058 (2) | 0.065 (2) | −0.0145 (19) | 0.002 (2) | −0.0105 (18) |
C7A | 0.113 (4) | 0.107 (4) | 0.088 (3) | −0.020 (3) | 0.017 (3) | −0.040 (3) |
C8A | 0.131 (5) | 0.088 (4) | 0.094 (4) | 0.009 (3) | −0.048 (4) | −0.007 (3) |
N1B | 0.0290 (13) | 0.0397 (14) | 0.0651 (17) | −0.0066 (11) | 0.0015 (12) | −0.0047 (12) |
C1B | 0.0269 (14) | 0.0348 (16) | 0.0572 (19) | 0.0010 (12) | 0.0054 (14) | 0.0004 (14) |
C2B | 0.0293 (15) | 0.0368 (17) | 0.0574 (19) | 0.0002 (12) | 0.0029 (14) | 0.0013 (15) |
O1B | 0.0343 (12) | 0.0479 (14) | 0.0794 (17) | 0.0032 (10) | 0.0015 (12) | 0.0158 (12) |
N2B | 0.0280 (13) | 0.0490 (16) | 0.0716 (19) | −0.0017 (12) | 0.0005 (13) | 0.0186 (14) |
C3B | 0.0275 (16) | 0.056 (2) | 0.088 (3) | −0.0059 (15) | 0.0034 (17) | 0.0253 (19) |
C4B | 0.0277 (16) | 0.0400 (18) | 0.076 (2) | −0.0030 (13) | 0.0011 (16) | 0.0032 (17) |
O2B | 0.0377 (13) | 0.0530 (15) | 0.112 (2) | 0.0001 (11) | −0.0033 (14) | 0.0335 (15) |
O3B | 0.0288 (11) | 0.0460 (13) | 0.0995 (19) | −0.0047 (10) | 0.0057 (12) | 0.0145 (13) |
C5B | 0.0448 (19) | 0.0465 (19) | 0.058 (2) | −0.0029 (15) | 0.0078 (16) | −0.0036 (16) |
C6B | 0.055 (2) | 0.058 (2) | 0.072 (2) | −0.0055 (19) | 0.016 (2) | −0.0012 (18) |
C7B | 0.137 (5) | 0.093 (4) | 0.104 (4) | 0.011 (3) | 0.068 (4) | −0.001 (3) |
C8B | 0.119 (4) | 0.095 (4) | 0.075 (3) | 0.021 (3) | 0.022 (3) | 0.020 (3) |
N1C | 0.0323 (14) | 0.0434 (15) | 0.0667 (18) | 0.0008 (12) | −0.0013 (13) | 0.0030 (13) |
C1C | 0.0276 (15) | 0.0418 (17) | 0.066 (2) | −0.0003 (13) | 0.0047 (15) | 0.0043 (15) |
C2C | 0.0260 (15) | 0.0425 (19) | 0.061 (2) | −0.0023 (13) | 0.0022 (15) | 0.0043 (15) |
O1C | 0.0395 (13) | 0.0491 (14) | 0.105 (2) | 0.0063 (12) | 0.0022 (13) | −0.0177 (14) |
N2C | 0.0302 (13) | 0.0367 (14) | 0.0740 (19) | −0.0026 (11) | 0.0070 (13) | 0.0015 (13) |
C3C | 0.0334 (16) | 0.0369 (17) | 0.063 (2) | −0.0034 (13) | 0.0022 (15) | −0.0006 (14) |
C4C | 0.0303 (15) | 0.0369 (16) | 0.061 (2) | −0.0028 (13) | 0.0021 (14) | 0.0089 (15) |
O2C | 0.0493 (14) | 0.0533 (15) | 0.0767 (17) | −0.0097 (12) | 0.0191 (13) | −0.0120 (13) |
O3C | 0.0317 (12) | 0.0440 (13) | 0.0961 (19) | −0.0040 (10) | 0.0020 (12) | −0.0019 (13) |
C5C | 0.0375 (18) | 0.064 (2) | 0.068 (2) | −0.0065 (17) | 0.0053 (17) | 0.0160 (18) |
C6C | 0.047 (2) | 0.071 (3) | 0.077 (3) | −0.0085 (18) | −0.0033 (18) | 0.024 (2) |
C7C | 0.077 (3) | 0.119 (4) | 0.083 (3) | −0.018 (3) | 0.000 (3) | 0.041 (3) |
C8C | 0.090 (4) | 0.081 (3) | 0.107 (4) | 0.016 (3) | 0.004 (3) | 0.034 (3) |
O1W | 0.146 (3) | 0.0593 (18) | 0.085 (2) | −0.022 (2) | 0.024 (2) | −0.0098 (16) |
O2W | 0.0697 (19) | 0.0504 (15) | 0.134 (3) | −0.0020 (14) | −0.023 (2) | −0.0157 (16) |
Geometric parameters (Å, º) top
N1A—C1A | 1.487 (4) | C5B—C6B | 1.509 (5) |
N1A—H1A | 0.8700 | C5B—H8B | 0.9700 |
N1A—H2A | 0.8700 | C5B—H9B | 0.9700 |
N1A—H3A | 0.8700 | C6B—C8B | 1.505 (6) |
C1A—C2A | 1.516 (4) | C6B—C7B | 1.536 (6) |
C1A—C5A | 1.534 (5) | C6B—H10B | 0.9800 |
C1A—H4A | 0.9800 | C7B—H11B | 0.9600 |
C2A—O1A | 1.232 (4) | C7B—H12B | 0.9600 |
C2A—N2A | 1.329 (4) | C7B—H13B | 0.9600 |
N2A—C3A | 1.453 (4) | C8B—H14B | 0.9600 |
N2A—H5A | 0.8700 | C8B—H15B | 0.9600 |
C3A—C4A | 1.521 (4) | C8B—H16B | 0.9600 |
C3A—H6A | 0.9700 | N1C—C1C | 1.493 (4) |
C3A—H7A | 0.9700 | N1C—H1C | 0.8700 |
C4A—O2A | 1.232 (4) | N1C—H2C | 0.8700 |
C4A—O3A | 1.266 (4) | N1C—H3C | 0.8700 |
C5A—C6A | 1.530 (5) | C1C—C2C | 1.525 (4) |
C5A—H8A | 0.9700 | C1C—C5C | 1.530 (5) |
C5A—H9A | 0.9700 | C1C—H4C | 0.9800 |
C6A—C7A | 1.516 (6) | C2C—O1C | 1.218 (4) |
C6A—C8A | 1.532 (6) | C2C—N2C | 1.325 (4) |
C6A—H10A | 0.9800 | N2C—C3C | 1.454 (4) |
C7A—H11A | 0.9600 | N2C—H5C | 0.8700 |
C7A—H12A | 0.9600 | C3C—C4C | 1.508 (4) |
C7A—H13A | 0.9600 | C3C—H6C | 0.9700 |
C8A—H14A | 0.9600 | C3C—H7C | 0.9700 |
C8A—H15A | 0.9600 | C4C—O3C | 1.252 (4) |
C8A—H16A | 0.9600 | C4C—O2C | 1.254 (4) |
N1B—C1B | 1.487 (4) | C5C—C6C | 1.518 (5) |
N1B—H1B | 0.8700 | C5C—H8C | 0.9700 |
N1B—H2B | 0.8700 | C5C—H9C | 0.9700 |
N1B—H3B | 0.8700 | C6C—C8C | 1.504 (7) |
C1B—C2B | 1.519 (4) | C6C—C7C | 1.534 (6) |
C1B—C5B | 1.521 (5) | C6C—H10C | 0.9800 |
C1B—H4B | 0.9800 | C7C—H11C | 0.9600 |
C2B—O1B | 1.237 (4) | C7C—H12C | 0.9600 |
C2B—N2B | 1.314 (4) | C7C—H13C | 0.9600 |
N2B—C3B | 1.452 (4) | C8C—H14C | 0.9600 |
N2B—H5B | 0.8700 | C8C—H15C | 0.9600 |
C3B—C4B | 1.512 (4) | C8C—H16C | 0.9600 |
C3B—H6B | 0.9700 | O1W—H1W | 0.8198 |
C3B—H7B | 0.9700 | O1W—H2W | 0.8200 |
C4B—O2B | 1.219 (4) | O2W—H3W | 0.8200 |
C4B—O3B | 1.277 (4) | O2W—H4W | 0.8202 |
| | | |
C1A—N1A—H1A | 109.5 | C6B—C5B—C1B | 117.7 (3) |
C1A—N1A—H2A | 109.5 | C6B—C5B—H8B | 107.9 |
H1A—N1A—H2A | 109.5 | C1B—C5B—H8B | 107.9 |
C1A—N1A—H3A | 109.5 | C6B—C5B—H9B | 107.9 |
H1A—N1A—H3A | 109.5 | C1B—C5B—H9B | 107.9 |
H2A—N1A—H3A | 109.5 | H8B—C5B—H9B | 107.2 |
N1A—C1A—C2A | 108.5 (3) | C8B—C6B—C5B | 112.4 (4) |
N1A—C1A—C5A | 107.7 (3) | C8B—C6B—C7B | 110.6 (4) |
C2A—C1A—C5A | 110.7 (3) | C5B—C6B—C7B | 108.3 (3) |
N1A—C1A—H4A | 110.0 | C8B—C6B—H10B | 108.5 |
C2A—C1A—H4A | 110.0 | C5B—C6B—H10B | 108.5 |
C5A—C1A—H4A | 110.0 | C7B—C6B—H10B | 108.5 |
O1A—C2A—N2A | 122.7 (3) | C6B—C7B—H11B | 109.5 |
O1A—C2A—C1A | 120.6 (3) | C6B—C7B—H12B | 109.5 |
N2A—C2A—C1A | 116.6 (3) | H11B—C7B—H12B | 109.5 |
C2A—N2A—C3A | 122.0 (3) | C6B—C7B—H13B | 109.5 |
C2A—N2A—H5A | 119.0 | H11B—C7B—H13B | 109.5 |
C3A—N2A—H5A | 119.0 | H12B—C7B—H13B | 109.5 |
N2A—C3A—C4A | 111.3 (3) | C6B—C8B—H14B | 109.5 |
N2A—C3A—H6A | 109.4 | C6B—C8B—H15B | 109.5 |
C4A—C3A—H6A | 109.4 | H14B—C8B—H15B | 109.5 |
N2A—C3A—H7A | 109.4 | C6B—C8B—H16B | 109.5 |
C4A—C3A—H7A | 109.4 | H14B—C8B—H16B | 109.5 |
H6A—C3A—H7A | 108.0 | H15B—C8B—H16B | 109.5 |
O2A—C4A—O3A | 125.3 (3) | C1C—N1C—H1C | 109.5 |
O2A—C4A—C3A | 117.7 (3) | C1C—N1C—H2C | 109.5 |
O3A—C4A—C3A | 117.0 (3) | H1C—N1C—H2C | 109.5 |
C6A—C5A—C1A | 115.0 (3) | C1C—N1C—H3C | 109.5 |
C6A—C5A—H8A | 108.5 | H1C—N1C—H3C | 109.5 |
C1A—C5A—H8A | 108.5 | H2C—N1C—H3C | 109.5 |
C6A—C5A—H9A | 108.5 | N1C—C1C—C2C | 107.9 (2) |
C1A—C5A—H9A | 108.5 | N1C—C1C—C5C | 109.9 (3) |
H8A—C5A—H9A | 107.5 | C2C—C1C—C5C | 111.6 (3) |
C7A—C6A—C5A | 109.7 (4) | N1C—C1C—H4C | 109.1 |
C7A—C6A—C8A | 110.9 (4) | C2C—C1C—H4C | 109.1 |
C5A—C6A—C8A | 112.3 (3) | C5C—C1C—H4C | 109.1 |
C7A—C6A—H10A | 107.9 | O1C—C2C—N2C | 124.5 (3) |
C5A—C6A—H10A | 107.9 | O1C—C2C—C1C | 120.4 (3) |
C8A—C6A—H10A | 107.9 | N2C—C2C—C1C | 115.2 (3) |
C6A—C7A—H11A | 109.5 | C2C—N2C—C3C | 123.1 (3) |
C6A—C7A—H12A | 109.5 | C2C—N2C—H5C | 118.5 |
H11A—C7A—H12A | 109.5 | C3C—N2C—H5C | 118.5 |
C6A—C7A—H13A | 109.5 | N2C—C3C—C4C | 111.3 (3) |
H11A—C7A—H13A | 109.5 | N2C—C3C—H6C | 109.4 |
H12A—C7A—H13A | 109.5 | C4C—C3C—H6C | 109.4 |
C6A—C8A—H14A | 109.5 | N2C—C3C—H7C | 109.4 |
C6A—C8A—H15A | 109.5 | C4C—C3C—H7C | 109.4 |
H14A—C8A—H15A | 109.5 | H6C—C3C—H7C | 108.0 |
C6A—C8A—H16A | 109.5 | O3C—C4C—O2C | 125.2 (3) |
H14A—C8A—H16A | 109.5 | O3C—C4C—C3C | 117.5 (3) |
H15A—C8A—H16A | 109.5 | O2C—C4C—C3C | 117.3 (3) |
C1B—N1B—H1B | 109.5 | C6C—C5C—C1C | 115.0 (3) |
C1B—N1B—H2B | 109.5 | C6C—C5C—H8C | 108.5 |
H1B—N1B—H2B | 109.5 | C1C—C5C—H8C | 108.5 |
C1B—N1B—H3B | 109.5 | C6C—C5C—H9C | 108.5 |
H1B—N1B—H3B | 109.5 | C1C—C5C—H9C | 108.5 |
H2B—N1B—H3B | 109.5 | H8C—C5C—H9C | 107.5 |
N1B—C1B—C2B | 108.9 (3) | C8C—C6C—C5C | 113.0 (4) |
N1B—C1B—C5B | 110.0 (3) | C8C—C6C—C7C | 110.5 (4) |
C2B—C1B—C5B | 108.7 (3) | C5C—C6C—C7C | 109.7 (4) |
N1B—C1B—H4B | 109.7 | C8C—C6C—H10C | 107.8 |
C2B—C1B—H4B | 109.7 | C5C—C6C—H10C | 107.8 |
C5B—C1B—H4B | 109.7 | C7C—C6C—H10C | 107.8 |
O1B—C2B—N2B | 123.6 (3) | C6C—C7C—H11C | 109.5 |
O1B—C2B—C1B | 120.3 (3) | C6C—C7C—H12C | 109.5 |
N2B—C2B—C1B | 116.1 (3) | H11C—C7C—H12C | 109.5 |
C2B—N2B—C3B | 123.2 (3) | C6C—C7C—H13C | 109.5 |
C2B—N2B—H5B | 118.4 | H11C—C7C—H13C | 109.5 |
C3B—N2B—H5B | 118.4 | H12C—C7C—H13C | 109.5 |
N2B—C3B—C4B | 110.5 (3) | C6C—C8C—H14C | 109.5 |
N2B—C3B—H6B | 109.5 | C6C—C8C—H15C | 109.5 |
C4B—C3B—H6B | 109.5 | H14C—C8C—H15C | 109.5 |
N2B—C3B—H7B | 109.5 | C6C—C8C—H16C | 109.5 |
C4B—C3B—H7B | 109.5 | H14C—C8C—H16C | 109.5 |
H6B—C3B—H7B | 108.1 | H15C—C8C—H16C | 109.5 |
O2B—C4B—O3B | 126.2 (3) | H1W—O1W—H2W | 104.4 |
O2B—C4B—C3B | 118.8 (3) | H3W—O2W—H4W | 108.7 |
O3B—C4B—C3B | 115.0 (3) | | |
| | | |
N1A—C1A—C2A—O1A | −55.3 (4) | N2B—C3B—C4B—O2B | 1.9 (5) |
C5A—C1A—C2A—O1A | 62.7 (4) | N2B—C3B—C4B—O3B | −177.5 (3) |
N1A—C1A—C2A—N2A | 127.1 (3) | N1B—C1B—C5B—C6B | −72.4 (4) |
C5A—C1A—C2A—N2A | −114.9 (3) | C2B—C1B—C5B—C6B | 168.4 (3) |
O1A—C2A—N2A—C3A | −4.0 (5) | C1B—C5B—C6B—C8B | −65.9 (5) |
C1A—C2A—N2A—C3A | 173.6 (3) | C1B—C5B—C6B—C7B | 171.6 (4) |
C2A—N2A—C3A—C4A | 170.8 (3) | N1C—C1C—C2C—O1C | −40.2 (4) |
N2A—C3A—C4A—O2A | −23.5 (5) | C5C—C1C—C2C—O1C | 80.6 (4) |
N2A—C3A—C4A—O3A | 158.4 (3) | N1C—C1C—C2C—N2C | 140.1 (3) |
N1A—C1A—C5A—C6A | 177.2 (3) | C5C—C1C—C2C—N2C | −99.1 (4) |
C2A—C1A—C5A—C6A | 58.7 (4) | O1C—C2C—N2C—C3C | −1.3 (6) |
C1A—C5A—C6A—C7A | −172.4 (4) | C1C—C2C—N2C—C3C | 178.4 (3) |
C1A—C5A—C6A—C8A | 63.8 (5) | C2C—N2C—C3C—C4C | 154.5 (3) |
N1B—C1B—C2B—O1B | −39.3 (4) | N2C—C3C—C4C—O3C | 164.8 (3) |
C5B—C1B—C2B—O1B | 80.6 (4) | N2C—C3C—C4C—O2C | −14.9 (4) |
N1B—C1B—C2B—N2B | 143.9 (3) | N1C—C1C—C5C—C6C | −169.2 (3) |
C5B—C1B—C2B—N2B | −96.3 (4) | C2C—C1C—C5C—C6C | 71.1 (4) |
O1B—C2B—N2B—C3B | −0.4 (6) | C1C—C5C—C6C—C8C | 63.5 (5) |
C1B—C2B—N2B—C3B | 176.3 (3) | C1C—C5C—C6C—C7C | −172.7 (4) |
C2B—N2B—C3B—C4B | 173.5 (3) | | |
Hydrogen-bond geometry (Å, º) top
D—H···A | D—H | H···A | D···A | D—H···A |
N1A—H1A···O3Ai | 0.87 | 2.20 | 3.060 (4) | 172 |
N1A—H2A···O2Cii | 0.87 | 1.85 | 2.709 (4) | 169 |
N1A—H3A···O3Bi | 0.87 | 1.88 | 2.690 (4) | 154 |
N1B—H1B···O3Bi | 0.87 | 1.96 | 2.816 (4) | 167 |
N1B—H2B···O3Aiii | 0.87 | 2.16 | 2.953 (4) | 152 |
N1B—H3B···O3Ci | 0.87 | 1.97 | 2.768 (4) | 151 |
N1C—H1C···O3Ci | 0.87 | 2.04 | 2.838 (4) | 152 |
N1C—H2C···O2Aiii | 0.87 | 1.90 | 2.750 (4) | 166 |
N1C—H3C···O2Wi | 0.87 | 1.89 | 2.762 (5) | 176 |
N2C—H5C···O1W | 0.87 | 2.40 | 3.202 (5) | 153 |
O1W—H1W···O3Aiv | 0.82 | 2.04 | 2.857 (5) | 177 |
O1W—H2W···O1Biii | 0.82 | 2.19 | 2.933 (5) | 150 |
O2W—H3W···O1Av | 0.82 | 1.96 | 2.773 (5) | 176 |
O2W—H4W···O1W | 0.82 | 2.37 | 3.134 (5) | 156 |
O2W—H4W···O2C | 0.82 | 2.45 | 2.882 (5) | 114 |
C1A—H4A···O1B | 0.98 | 2.33 | 3.250 (4) | 156 |
C1B—H4B···O1C | 0.98 | 2.45 | 3.425 (4) | 171 |
C3C—H6C···O2B | 0.97 | 2.33 | 3.181 (5) | 146 |
Symmetry codes: (i) x+1, y, z; (ii) −x+1, y−1/2, −z+1/2; (iii) −x+1, y+1/2, −z+1/2; (iv) x, y+1, z; (v) x−1, y+1, z. |
(II) [(4
S)-2,2-dimethyl-4-(2-methylpropyl)-
5-oxoimidazolidin-3-ium-1-yl]acetate
top
Crystal data top
C11H20N2O3 | Z = 1 |
Mr = 228.29 | F(000) = 124 |
Triclinic, P1 | Dx = 1.219 Mg m−3 |
Hall symbol: P 1 | Mo Kα radiation, λ = 0.71070 Å |
a = 6.0060 (14) Å | Cell parameters from 871 reflections |
b = 6.8782 (18) Å | θ = 5.4–25.0° |
c = 7.9717 (18) Å | µ = 0.09 mm−1 |
α = 90.202 (11)° | T = 298 K |
β = 98.272 (8)° | Plate, colorless |
γ = 107.193 (11)° | 0.60 × 0.55 × 0.04 mm |
V = 310.96 (13) Å3 | |
Data collection top
Rigaku Mercury CCD area-detector diffractometer | 2526 independent reflections |
Radiation source: rotating anode | 2501 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.013 |
Detector resolution: 14.2959 pixels mm-1 | θmax = 27.5°, θmin = 3.1° |
ω scans | h = −7→7 |
Absorption correction: multi-scan (CrystalClear; Rigaku/MSC, 2006) | k = −8→8 |
Tmin = 0.661, Tmax = 1.000 | l = −10→10 |
3600 measured reflections | |
Refinement top
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) = 0.093 | H-atom parameters constrained |
S = 1.04 | w = 1/[σ2(Fo2) + (0.0586P)2 + 0.0404P] where P = (Fo2 + 2Fc2)/3 |
2526 reflections | (Δ/σ)max < 0.001 |
149 parameters | Δρmax = 0.17 e Å−3 |
3 restraints | Δρmin = −0.15 e Å−3 |
Crystal data top
C11H20N2O3 | γ = 107.193 (11)° |
Mr = 228.29 | V = 310.96 (13) Å3 |
Triclinic, P1 | Z = 1 |
a = 6.0060 (14) Å | Mo Kα radiation |
b = 6.8782 (18) Å | µ = 0.09 mm−1 |
c = 7.9717 (18) Å | T = 298 K |
α = 90.202 (11)° | 0.60 × 0.55 × 0.04 mm |
β = 98.272 (8)° | |
Data collection top
Rigaku Mercury CCD area-detector diffractometer | 2526 independent reflections |
Absorption correction: multi-scan (CrystalClear; Rigaku/MSC, 2006) | 2501 reflections with I > 2σ(I) |
Tmin = 0.661, Tmax = 1.000 | Rint = 0.013 |
3600 measured reflections | |
Refinement top
R[F2 > 2σ(F2)] = 0.034 | 3 restraints |
wR(F2) = 0.093 | H-atom parameters constrained |
S = 1.04 | Δρmax = 0.17 e Å−3 |
2526 reflections | Δρmin = −0.15 e Å−3 |
149 parameters | |
Special details top
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. |
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top | x | y | z | Uiso*/Ueq | |
N1 | 0.89234 (19) | 0.34603 (16) | 0.50248 (15) | 0.0294 (2) | |
C2 | 1.0403 (2) | 0.48160 (19) | 0.39433 (17) | 0.0289 (3) | |
N3 | 1.16888 (18) | 0.65959 (15) | 0.51877 (14) | 0.0259 (2) | |
H3A | 1.3170 | 0.7153 | 0.4974 | 0.031* | |
H3B | 1.0942 | 0.7557 | 0.5091 | 0.031* | |
C4 | 1.1729 (2) | 0.5814 (2) | 0.69338 (17) | 0.0319 (3) | |
H4 | 1.3162 | 0.5409 | 0.7245 | 0.038* | |
C5 | 0.9605 (3) | 0.3930 (2) | 0.67005 (19) | 0.0355 (3) | |
O5 | 0.8677 (3) | 0.2983 (2) | 0.78350 (17) | 0.0605 (4) | |
C6 | 0.7115 (2) | 0.1578 (2) | 0.4436 (2) | 0.0351 (3) | |
H6A | 0.6636 | 0.1627 | 0.3226 | 0.042* | |
H6B | 0.5752 | 0.1484 | 0.4988 | 0.042* | |
C7 | 0.7863 (2) | −0.0356 (2) | 0.47641 (18) | 0.0308 (3) | |
O7A | 1.00096 (18) | −0.01889 (16) | 0.49825 (17) | 0.0444 (3) | |
O7B | 0.62318 (19) | −0.19790 (16) | 0.47462 (18) | 0.0469 (3) | |
C8 | 1.1626 (3) | 0.7353 (3) | 0.82590 (19) | 0.0382 (3) | |
H8A | 1.1323 | 0.6662 | 0.9299 | 0.046* | |
H8B | 1.0302 | 0.7858 | 0.7874 | 0.046* | |
C9 | 1.3845 (3) | 0.9170 (2) | 0.86607 (19) | 0.0392 (3) | |
H9 | 1.4286 | 0.9730 | 0.7586 | 0.047* | |
C10 | 1.5902 (4) | 0.8572 (4) | 0.9603 (3) | 0.0627 (5) | |
H10A | 1.7268 | 0.9747 | 0.9799 | 0.075* | |
H10B | 1.6225 | 0.7550 | 0.8936 | 0.075* | |
H10C | 1.5515 | 0.8039 | 1.0671 | 0.075* | |
C11 | 1.3345 (4) | 1.0817 (4) | 0.9684 (3) | 0.0659 (6) | |
H11A | 1.3015 | 1.0330 | 1.0776 | 0.079* | |
H11B | 1.2008 | 1.1154 | 0.9095 | 0.079* | |
H11C | 1.4695 | 1.2007 | 0.9829 | 0.079* | |
C21 | 1.2178 (3) | 0.3901 (3) | 0.3314 (3) | 0.0460 (4) | |
H21A | 1.3131 | 0.3550 | 0.4267 | 0.055* | |
H21B | 1.3168 | 0.4878 | 0.2671 | 0.055* | |
H21C | 1.1349 | 0.2699 | 0.2606 | 0.055* | |
C22 | 0.8964 (3) | 0.5542 (3) | 0.24924 (19) | 0.0404 (3) | |
H22A | 0.8297 | 0.4466 | 0.1631 | 0.048* | |
H22B | 0.9964 | 0.6700 | 0.2020 | 0.048* | |
H22C | 0.7720 | 0.5920 | 0.2909 | 0.048* | |
Atomic displacement parameters (Å2) top | U11 | U22 | U33 | U12 | U13 | U23 |
N1 | 0.0284 (5) | 0.0175 (5) | 0.0422 (6) | 0.0051 (4) | 0.0084 (4) | 0.0028 (4) |
C2 | 0.0286 (6) | 0.0200 (6) | 0.0393 (7) | 0.0066 (5) | 0.0110 (5) | −0.0003 (5) |
N3 | 0.0240 (5) | 0.0191 (5) | 0.0364 (5) | 0.0071 (4) | 0.0090 (4) | 0.0029 (4) |
C4 | 0.0298 (6) | 0.0287 (7) | 0.0372 (7) | 0.0081 (5) | 0.0063 (5) | 0.0059 (5) |
C5 | 0.0378 (7) | 0.0261 (7) | 0.0423 (7) | 0.0069 (6) | 0.0107 (6) | 0.0094 (5) |
O5 | 0.0680 (8) | 0.0503 (8) | 0.0520 (7) | −0.0041 (6) | 0.0191 (6) | 0.0172 (6) |
C6 | 0.0254 (6) | 0.0203 (6) | 0.0578 (8) | 0.0062 (5) | 0.0024 (6) | 0.0039 (6) |
C7 | 0.0280 (6) | 0.0189 (6) | 0.0458 (7) | 0.0059 (5) | 0.0091 (5) | 0.0009 (5) |
O7A | 0.0281 (5) | 0.0238 (5) | 0.0819 (8) | 0.0104 (4) | 0.0048 (5) | 0.0047 (5) |
O7B | 0.0343 (6) | 0.0211 (5) | 0.0859 (9) | 0.0026 (4) | 0.0238 (6) | −0.0004 (5) |
C8 | 0.0367 (7) | 0.0425 (8) | 0.0341 (6) | 0.0076 (6) | 0.0100 (6) | −0.0004 (6) |
C9 | 0.0392 (7) | 0.0384 (8) | 0.0350 (6) | 0.0054 (6) | 0.0034 (6) | −0.0005 (6) |
C10 | 0.0426 (9) | 0.0673 (14) | 0.0731 (13) | 0.0155 (9) | −0.0057 (9) | −0.0028 (10) |
C11 | 0.0676 (13) | 0.0549 (12) | 0.0697 (12) | 0.0181 (10) | −0.0065 (10) | −0.0214 (10) |
C21 | 0.0414 (8) | 0.0323 (8) | 0.0697 (10) | 0.0114 (6) | 0.0255 (8) | −0.0075 (7) |
C22 | 0.0463 (9) | 0.0368 (8) | 0.0352 (7) | 0.0089 (6) | 0.0047 (6) | 0.0028 (6) |
Geometric parameters (Å, º) top
N1—C5 | 1.3482 (19) | C8—C9 | 1.527 (2) |
N1—C6 | 1.4469 (17) | C8—H8A | 0.9700 |
N1—C2 | 1.4624 (17) | C8—H8B | 0.9700 |
C2—N3 | 1.5137 (17) | C9—C10 | 1.515 (2) |
C2—C22 | 1.5186 (19) | C9—C11 | 1.518 (3) |
C2—C21 | 1.5275 (19) | C9—H9 | 0.9800 |
N3—C4 | 1.4935 (17) | C10—H10A | 0.9600 |
N3—H3A | 0.9000 | C10—H10B | 0.9600 |
N3—H3B | 0.9000 | C10—H10C | 0.9600 |
C4—C8 | 1.513 (2) | C11—H11A | 0.9600 |
C4—C5 | 1.515 (2) | C11—H11B | 0.9600 |
C4—H4 | 0.9800 | C11—H11C | 0.9600 |
C5—O5 | 1.2194 (19) | C21—H21A | 0.9600 |
C6—C7 | 1.5363 (17) | C21—H21B | 0.9600 |
C6—H6A | 0.9700 | C21—H21C | 0.9600 |
C6—H6B | 0.9700 | C22—H22A | 0.9600 |
C7—O7A | 1.2467 (17) | C22—H22B | 0.9600 |
C7—O7B | 1.2472 (17) | C22—H22C | 0.9600 |
| | | |
C5—N1—C6 | 120.35 (12) | C9—C8—H8A | 108.5 |
C5—N1—C2 | 114.20 (11) | C4—C8—H8B | 108.5 |
C6—N1—C2 | 124.73 (12) | C9—C8—H8B | 108.5 |
N1—C2—N3 | 100.61 (10) | H8A—C8—H8B | 107.5 |
N1—C2—C22 | 112.45 (11) | C10—C9—C11 | 110.07 (15) |
N3—C2—C22 | 109.03 (10) | C10—C9—C8 | 112.21 (14) |
N1—C2—C21 | 112.66 (11) | C11—C9—C8 | 110.02 (15) |
N3—C2—C21 | 109.70 (12) | C10—C9—H9 | 108.1 |
C22—C2—C21 | 111.77 (13) | C11—C9—H9 | 108.1 |
C4—N3—C2 | 107.84 (10) | C8—C9—H9 | 108.1 |
C4—N3—H3A | 110.1 | C9—C10—H10A | 109.5 |
C2—N3—H3A | 110.1 | C9—C10—H10B | 109.5 |
C4—N3—H3B | 110.1 | H10A—C10—H10B | 109.5 |
C2—N3—H3B | 110.1 | C9—C10—H10C | 109.5 |
H3A—N3—H3B | 108.5 | H10A—C10—H10C | 109.5 |
N3—C4—C8 | 113.12 (11) | H10B—C10—H10C | 109.5 |
N3—C4—C5 | 102.15 (11) | C9—C11—H11A | 109.5 |
C8—C4—C5 | 113.55 (12) | C9—C11—H11B | 109.5 |
N3—C4—H4 | 109.3 | H11A—C11—H11B | 109.5 |
C8—C4—H4 | 109.3 | C9—C11—H11C | 109.5 |
C5—C4—H4 | 109.3 | H11A—C11—H11C | 109.5 |
O5—C5—N1 | 125.63 (15) | H11B—C11—H11C | 109.5 |
O5—C5—C4 | 125.88 (14) | C2—C21—H21A | 109.5 |
N1—C5—C4 | 108.49 (12) | C2—C21—H21B | 109.5 |
N1—C6—C7 | 114.65 (10) | H21A—C21—H21B | 109.5 |
N1—C6—H6A | 108.6 | C2—C21—H21C | 109.5 |
C7—C6—H6A | 108.6 | H21A—C21—H21C | 109.5 |
N1—C6—H6B | 108.6 | H21B—C21—H21C | 109.5 |
C7—C6—H6B | 108.6 | C2—C22—H22A | 109.5 |
H6A—C6—H6B | 107.6 | C2—C22—H22B | 109.5 |
O7A—C7—O7B | 125.68 (12) | H22A—C22—H22B | 109.5 |
O7A—C7—C6 | 118.18 (12) | C2—C22—H22C | 109.5 |
O7B—C7—C6 | 116.12 (11) | H22A—C22—H22C | 109.5 |
C4—C8—C9 | 115.07 (12) | H22B—C22—H22C | 109.5 |
C4—C8—H8A | 108.5 | | |
| | | |
C5—N1—C2—N3 | −16.44 (13) | C2—N1—C5—C4 | 1.44 (15) |
C6—N1—C2—N3 | 173.30 (10) | N3—C4—C5—O5 | −166.10 (15) |
C5—N1—C2—C22 | −132.31 (13) | C8—C4—C5—O5 | −44.0 (2) |
C6—N1—C2—C22 | 57.43 (15) | N3—C4—C5—N1 | 14.53 (13) |
C5—N1—C2—C21 | 100.30 (15) | C8—C4—C5—N1 | 136.67 (12) |
C6—N1—C2—C21 | −69.96 (16) | C5—N1—C6—C7 | −69.75 (17) |
N1—C2—N3—C4 | 25.14 (11) | C2—N1—C6—C7 | 99.95 (15) |
C22—C2—N3—C4 | 143.54 (11) | N1—C6—C7—O7A | −22.0 (2) |
C21—C2—N3—C4 | −93.76 (13) | N1—C6—C7—O7B | 159.69 (14) |
C2—N3—C4—C8 | −147.13 (11) | N3—C4—C8—C9 | −70.17 (15) |
C2—N3—C4—C5 | −24.70 (12) | C5—C4—C8—C9 | 174.00 (12) |
C6—N1—C5—O5 | −7.2 (2) | C4—C8—C9—C10 | −69.84 (18) |
C2—N1—C5—O5 | −177.93 (15) | C4—C8—C9—C11 | 167.25 (15) |
C6—N1—C5—C4 | 172.17 (11) | | |
Hydrogen-bond geometry (Å, º) top
D—H···A | D—H | H···A | D···A | D—H···A |
N3—H3A···O7Bi | 0.90 | 1.79 | 2.688 (2) | 172 |
N3—H3B···O7Aii | 0.90 | 1.80 | 2.685 (2) | 169 |
Symmetry codes: (i) x+1, y+1, z; (ii) x, y+1, z. |
Experimental details
| (I) | (II) |
Crystal data |
Chemical formula | 3C8H16N2O3·2H2O | C11H20N2O3 |
Mr | 600.72 | 228.29 |
Crystal system, space group | Orthorhombic, P212121 | Triclinic, P1 |
Temperature (K) | 299 | 298 |
a, b, c (Å) | 8.735 (5), 15.54 (1), 24.238 (15) | 6.0060 (14), 6.8782 (18), 7.9717 (18) |
α, β, γ (°) | 90, 90, 90 | 90.202 (11), 98.272 (8), 107.193 (11) |
V (Å3) | 3290 (4) | 310.96 (13) |
Z | 4 | 1 |
Radiation type | Mo Kα | Mo Kα |
µ (mm−1) | 0.10 | 0.09 |
Crystal size (mm) | 0.49 × 0.07 × 0.02 | 0.60 × 0.55 × 0.04 |
|
Data collection |
Diffractometer | Rigaku Mercury CCD area-detector diffractometer | Rigaku Mercury CCD area-detector diffractometer |
Absorption correction | – | Multi-scan (CrystalClear; Rigaku/MSC, 2006) |
Tmin, Tmax | – | 0.661, 1.000 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 21778, 5794, 4707 | 3600, 2526, 2501 |
Rint | 0.064 | 0.013 |
(sin θ/λ)max (Å−1) | 0.595 | 0.649 |
|
Refinement |
R[F2 > 2σ(F2)], wR(F2), S | 0.060, 0.161, 1.09 | 0.034, 0.093, 1.04 |
No. of reflections | 5794 | 2526 |
No. of parameters | 370 | 149 |
No. of restraints | 0 | 3 |
H-atom treatment | H-atom parameters constrained | H-atom parameters constrained |
Δρmax, Δρmin (e Å−3) | 0.26, −0.19 | 0.17, −0.15 |
Selected torsion angles (º) for (I) topN1A—C1A—C2A—N2A | 127.1 (3) | N1B—C1B—C5B—C6B | −72.4 (4) |
C1A—C2A—N2A—C3A | 173.6 (3) | C2B—C1B—C5B—C6B | 168.4 (3) |
C2A—N2A—C3A—C4A | 170.8 (3) | C1B—C5B—C6B—C8B | −65.9 (5) |
N2A—C3A—C4A—O2A | −23.5 (5) | C1B—C5B—C6B—C7B | 171.6 (4) |
N1A—C1A—C5A—C6A | 177.2 (3) | N1C—C1C—C2C—N2C | 140.1 (3) |
C2A—C1A—C5A—C6A | 58.7 (4) | C1C—C2C—N2C—C3C | 178.4 (3) |
C1A—C5A—C6A—C7A | −172.4 (4) | C2C—N2C—C3C—C4C | 154.5 (3) |
C1A—C5A—C6A—C8A | 63.8 (5) | N2C—C3C—C4C—O2C | −14.9 (4) |
N1B—C1B—C2B—N2B | 143.9 (3) | N1C—C1C—C5C—C6C | −169.2 (3) |
C1B—C2B—N2B—C3B | 176.3 (3) | C2C—C1C—C5C—C6C | 71.1 (4) |
C2B—N2B—C3B—C4B | 173.5 (3) | C1C—C5C—C6C—C8C | 63.5 (5) |
N2B—C3B—C4B—O2B | 1.9 (5) | C1C—C5C—C6C—C7C | −172.7 (4) |
Hydrogen-bond geometry (Å, º) for (I) top
D—H···A | D—H | H···A | D···A | D—H···A |
N1A—H1A···O3Ai | 0.87 | 2.20 | 3.060 (4) | 172.1 |
N1A—H2A···O2Cii | 0.87 | 1.85 | 2.709 (4) | 168.5 |
N1A—H3A···O3Bi | 0.87 | 1.88 | 2.690 (4) | 153.5 |
N1B—H1B···O3Bi | 0.87 | 1.96 | 2.816 (4) | 167.2 |
N1B—H2B···O3Aiii | 0.87 | 2.16 | 2.953 (4) | 152.1 |
N1B—H3B···O3Ci | 0.87 | 1.97 | 2.768 (4) | 151.2 |
N1C—H1C···O3Ci | 0.87 | 2.04 | 2.838 (4) | 152.4 |
N1C—H2C···O2Aiii | 0.87 | 1.90 | 2.750 (4) | 165.5 |
N1C—H3C···O2Wi | 0.87 | 1.89 | 2.762 (5) | 175.8 |
N2C—H5C···O1W | 0.87 | 2.40 | 3.202 (5) | 153.1 |
O1W—H1W···O3Aiv | 0.82 | 2.04 | 2.857 (5) | 177.1 |
O1W—H2W···O1Biii | 0.82 | 2.19 | 2.933 (5) | 149.9 |
O2W—H3W···O1Av | 0.82 | 1.96 | 2.773 (5) | 176.1 |
O2W—H4W···O1W | 0.82 | 2.37 | 3.134 (5) | 155.5 |
O2W—H4W···O2C | 0.82 | 2.45 | 2.882 (5) | 114.3 |
C1A—H4A···O1B | 0.98 | 2.33 | 3.250 (4) | 155.9 |
C1B—H4B···O1C | 0.98 | 2.45 | 3.425 (4) | 170.9 |
C3C—H6C···O2B | 0.97 | 2.33 | 3.181 (5) | 146.0 |
Symmetry codes: (i) x+1, y, z; (ii) −x+1, y−1/2, −z+1/2; (iii) −x+1, y+1/2, −z+1/2; (iv) x, y+1, z; (v) x−1, y+1, z. |
Selected torsion angles (º) for (II) topC5—N1—C2—N3 | −16.44 (13) | N3—C4—C5—N1 | 14.53 (13) |
N1—C2—N3—C4 | 25.14 (11) | C2—N1—C6—C7 | 99.95 (15) |
C2—N3—C4—C5 | −24.70 (12) | N1—C6—C7—O7A | −22.0 (2) |
C2—N1—C5—O5 | −177.93 (15) | N3—C4—C8—C9 | −70.17 (15) |
C6—N1—C5—C4 | 172.17 (11) | C4—C8—C9—C10 | −69.84 (18) |
C2—N1—C5—C4 | 1.44 (15) | C4—C8—C9—C11 | 167.25 (15) |
Hydrogen-bond geometry (Å, º) for (II) top
D—H···A | D—H | H···A | D···A | D—H···A |
N3—H3A···O7Bi | 0.90 | 1.79 | 2.688 (2) | 172.1 |
N3—H3B···O7Aii | 0.90 | 1.80 | 2.685 (2) | 169.1 |
Symmetry codes: (i) x+1, y+1, z; (ii) x, y+1, z. |
In living organisms, oligopeptides are produced from polypeptides by hydrolysis. A fair number of them are biologically active substances together with their derivatives. Among the dipeptides, the crystal structure of L-leucyl-glycine (L-Leu–Gly) has not been reported except for its cell parameters (Leonard & Pasternak, 1952). However, the cell parameters should be assigned to the crystal of the imidazolidinone derived from L-Leu–Gly (see below). We obtained crystals of L-Leu–Gly 0.67-hydrate, (I), from an aqueous solution. There are three L-Leu–Gly molecules (A, B and C) and two water molecules in an asymmetric unit (Fig. 1). The N-terminal and C-terminal groups of the three molecules are ionized. The backbones of molecules A, B and C are in extended forms parallel to the a axis. The conformation of the side chain of the leucyl group of molecule B is different from those of molecules A and C (Table 1). The conformation at N1—C1—C5—C6 of molecules A and C is trans, and that of molecule B is gauche-. The conformations at C1—C5—C6—C7 and C1—C5—C6—C8 of molecules A and C are trans and gauche+, respectively. On the other hand, the conformations of the corresponding parts of molecule B are trans and gauche-. The atomic displacement parameters of the side-chain atoms of leucyl residues are large. It is a general tendency that leucyl side-chain atoms, which are involved in van der Waals-type contacts and form hydrophobic regions in crystals, librate with large amplitude. Hydrogen-bonded chains between ionized carboxy and protonated amino groups extend parallel to the ab plane, partly intermediated by two water molecules, which exist every three L-Leu–Gly molecules (Fig. 2). One of the O—H bonds of the water molecules (O2W—H4W) forms a bifurcated hydrogen bond (Table 2). There are C—H···O interactions between the H atoms at the Cα positions of the leucyl residue and the carbonyl O atoms (C1A—H4A···O1B and C1B—H4B···O1C), and between the H atom at the Cα position of the glycyl residue and the carboxylate O atom (C3C—H6C···O2B). Two-dimensional sheets built from the hydrophilic parts of the main chains are paired by a twofold screw axis, which is parallel to the b axis (Fig. 3), and additional hydrogen bonds are formed between these sheets (Table 2). The paired sheets are isolated by hydrophobic regions composed of the isobutyl groups of the leucyl residues. As in the case of glycyl-L-leucine (Pattabhi et al., 1974), the hydrophobic and hydrophilic regions are aligned alternately along the c axis.
The crystal structure of D-leucylglycine hydrobromide (D-Leu–Gly.HBr) (Rao, 1969) is quite different from that of L-Leu–Gly 0.67-hydrate. In the case of D-Leu–Gly.HBr, the carboxyl groups are protonated and molecules related by a twofold screw axis form hydrogen-bonded chains involving protonated carboxy, carbonyl and protonated amino groups; one NH group and two NH3+ groups act as hydrogen-bond donors for Br-.
Topological analyses of hydrogen-bonding patterns in amino acids and oligopeptides in crystals have been reported based on searches of the Cambridge Structure Database (Allen, 2002). Görbitz (2010) classified dipeptides focusing on head-to-tail sequences connected by hydrogen bonds among the N-terminal amino and the C-terminal carboxyl groups. Glycyl-L-leucine belongs to the `T' group, where two peptides related by translational symmetry form a hydrogen bond between the N-terminal amino and the C-terminal carboxyl groups. L-Leu–Gly belongs to the same group. Görbitz also pays attention to the hydrogen-bonding arrangements of amide groups. In the case of L-Leu–Gly, however, there are no sequential hydrogen-bonding schemes among the amide groups, i.e. the N—H groups of molecules A and B form no hydrogen bonds, and that of molecule C acts as a hydrogen-bond donor for water atom O1W.
Imidazolidinones of oligopeptides are formed from compounds containing an α-aminoamide group, such as peptides with a free N-terminal amino group, and aldehydes or ketones. The parent peptides are released by hydrolysis in aqueous solution. Therefore, imidazolidinones of oligopeptides have been investigated as candidates for prodrugs (Sood & Panchagnula, 2001; Viso et al., 2005). One typical example is the imidazolidin-4-one of Leu-enkephalin (Rasmussen & Bundgaard, 1991). Although the synthesis and hydrolysis kinetics of the imidazolidinone derived from L-Leu–Gly and acetone, i.e. [(4S)-2,2-dimethyl-4-(2-methylpropyl)-5-oxoimidazolidin-1-yl] acetic acid, have already been investigated (Hardy & Samworth, 1977; Klixbüll & Bundgaard, 1984), the crystal structure of the compound has not been reported yet. By crystallizing L-Leu–Gly from a methanol–acetone solution, we obtained (II) (Fig. 4). The condensation reaction between L-Leu–Gly and acetone, which was used as the solvent, had proceeded, and the product crystallized. The cell parameters coincide with those reported for L-Leu–Gly dihydrate obtained from a water–acetone solution (Leonard & Pasternak, 1952). Therefore, Leonard & Pasternak had probably obtained (II).
The crystal system is triclinic and there is one molecule in the asymmetric unit. The carboxy group is deprotonated and the imidazolidine N atom at position 3 is protonated. The N1—C5 bond is a peptide bond and the atoms of the imidazolidinone ring (except for N3) are approximately on a plane together with oxo atom O5 (Table 3). As in the case of (I), the hydrophilic and hydrophobic regions are aligned alternately along the c axis. In the hydrophilic regions, carboxylate groups and protonated N atoms form hydrogen-bonded chains (Fig. 5). The carbonyl group is not involved hydrogen bonding.