Supporting information
Crystallographic Information File (CIF) https://doi.org/10.1107/S0108270113010299/fa3314sup1.cif | |
Structure factor file (CIF format) https://doi.org/10.1107/S0108270113010299/fa3314Isup2.hkl | |
Portable Document Format (PDF) file https://doi.org/10.1107/S0108270113010299/fa3314sup3.pdf | |
Chemical Markup Language (CML) file https://doi.org/10.1107/S0108270113010299/fa3314Isup4.cml |
CCDC reference: 950380
The title compound was prepared by solution-phase reaction processes described in the Supplementary materials. About 1 mg of (I) was dissolved in 40 µl of water in a 30 × 6 mm test tube. To this solution, 10 µl of tetramethoxysilane was added, and after 1 min of vigorous stirring the mixture was sealed with parafilm and left for 1 h to polymerize. A small hole was then pricked in the parafilm and the tube was placed inside a larger sealed test tube containing 1 ml of acetonitrile. The system was ultimately capped and left for one week at 293 K. Small crystals were formed as the organic solvent diffused into the gel.
Positional parameters of water and hydroxy H atoms, which had been located in a difference map, were refined with their respective O—H distances restrained to 0.85 (2) Å. N—H and C—H distances were fixed to 0.92 (NH2+), 0.88 (>N—H), 0.99 (CH2) or 1.00 (CH) Å, respectively. Uiso(H) values were set at 1.5Ueq of the carrier atom for H(—O) and at 1.2Ueq for H(—C/N). In the absence of significant anomalous scattering effects, 1950 Friedel pairs were merged.
Data collection: APEX2 (Bruker, 2007); cell refinement: SAINT-Plus (Bruker, 2007); data reduction: SAINT-Plus (Bruker, 2007); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL97 (Sheldrick, 2008); molecular graphics: SHELXTL (Sheldrick, 2008); software used to prepare material for publication: SHELXTL (Sheldrick, 2008).
C8H14N2O4·H2O | F(000) = 472 |
Mr = 220.23 | Dx = 1.419 Mg m−3 |
Monoclinic, P21 | Mo Kα radiation, λ = 0.71073 Å |
Hall symbol: P 2yb | Cell parameters from 1767 reflections |
a = 5.3101 (12) Å | θ = 2.8–22.4° |
b = 29.081 (7) Å | µ = 0.12 mm−1 |
c = 6.6757 (15) Å | T = 105 K |
β = 90.829 (3)° | Needle, colourless |
V = 1030.8 (4) Å3 | 0.31 × 0.09 × 0.06 mm |
Z = 4 |
Bruker APEXII CCD diffractometer | 2165 independent reflections |
Radiation source: fine-focus sealed tube | 1768 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.047 |
Detector resolution: 8.3 pixels mm-1 | θmax = 26.5°, θmin = 2.8° |
Sets of exposures each taken over 0.5° ω rotation scans | h = −6→6 |
Absorption correction: multi-scan (SADABS; Bruker, 2007) | k = −36→35 |
Tmin = 0.838, Tmax = 0.993 | l = −8→8 |
8313 measured reflections |
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)] = 0.044 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.110 | H atoms treated by a mixture of independent and constrained refinement |
S = 1.05 | w = 1/[σ2(Fo2) + (0.0625P)2 + 0.1448P] where P = (Fo2 + 2Fc2)/3 |
2165 reflections | (Δ/σ)max < 0.001 |
291 parameters | Δρmax = 0.26 e Å−3 |
7 restraints | Δρmin = −0.25 e Å−3 |
C8H14N2O4·H2O | V = 1030.8 (4) Å3 |
Mr = 220.23 | Z = 4 |
Monoclinic, P21 | Mo Kα radiation |
a = 5.3101 (12) Å | µ = 0.12 mm−1 |
b = 29.081 (7) Å | T = 105 K |
c = 6.6757 (15) Å | 0.31 × 0.09 × 0.06 mm |
β = 90.829 (3)° |
Bruker APEXII CCD diffractometer | 2165 independent reflections |
Absorption correction: multi-scan (SADABS; Bruker, 2007) | 1768 reflections with I > 2σ(I) |
Tmin = 0.838, Tmax = 0.993 | Rint = 0.047 |
8313 measured reflections |
R[F2 > 2σ(F2)] = 0.044 | 7 restraints |
wR(F2) = 0.110 | H atoms treated by a mixture of independent and constrained refinement |
S = 1.05 | Δρmax = 0.26 e Å−3 |
2165 reflections | Δρmin = −0.25 e Å−3 |
291 parameters |
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 | ||
O1A | 0.9100 (5) | 0.64715 (11) | 0.1962 (4) | 0.0288 (7) | |
O2A | 0.9929 (6) | 0.76776 (10) | −0.2147 (5) | 0.0331 (7) | |
H4A | 1.142 (5) | 0.766 (2) | −0.172 (7) | 0.047 (16)* | |
O3A | 0.8843 (5) | 0.61158 (9) | −0.3430 (4) | 0.0230 (6) | |
O4A | 0.5391 (5) | 0.65596 (9) | −0.3468 (4) | 0.0237 (6) | |
N1A | 1.2941 (6) | 0.60745 (11) | 0.3792 (4) | 0.0196 (7) | |
H1A | 1.3985 | 0.6222 | 0.4695 | 0.024* | |
H2A | 1.1299 | 0.6135 | 0.4127 | 0.024* | |
N2A | 1.1228 (6) | 0.67033 (11) | −0.0773 (5) | 0.0195 (7) | |
H3A | 1.2722 | 0.6750 | −0.1289 | 0.023* | |
C1A | 1.3436 (7) | 0.62424 (14) | 0.1712 (6) | 0.0193 (8) | |
H11A | 1.4898 | 0.6459 | 0.1718 | 0.023* | |
C2A | 1.4047 (8) | 0.58105 (14) | 0.0493 (6) | 0.0256 (9) | |
H21A | 1.3276 | 0.5827 | −0.0864 | 0.031* | |
H22A | 1.5890 | 0.5770 | 0.0370 | 0.031* | |
C3A | 1.2900 (9) | 0.54221 (15) | 0.1709 (6) | 0.0283 (9) | |
H31A | 1.1068 | 0.5395 | 0.1437 | 0.034* | |
H32A | 1.3720 | 0.5125 | 0.1411 | 0.034* | |
C4A | 1.3420 (8) | 0.55686 (14) | 0.3847 (6) | 0.0262 (9) | |
H41A | 1.2271 | 0.5412 | 0.4783 | 0.031* | |
H42A | 1.5184 | 0.5502 | 0.4250 | 0.031* | |
C5A | 1.1038 (7) | 0.64878 (13) | 0.0974 (6) | 0.0203 (8) | |
C6A | 0.8974 (7) | 0.68629 (13) | −0.1845 (6) | 0.0183 (8) | |
H61A | 0.7768 | 0.6978 | −0.0823 | 0.022* | |
C7A | 0.9600 (8) | 0.72644 (14) | −0.3213 (6) | 0.0236 (9) | |
H71A | 1.1162 | 0.7194 | −0.3943 | 0.028* | |
H72A | 0.8224 | 0.7304 | −0.4214 | 0.028* | |
C8A | 0.7663 (7) | 0.64746 (13) | −0.3006 (5) | 0.0189 (8) | |
O1B | 0.5901 (5) | 0.85064 (11) | 0.6766 (4) | 0.0297 (7) | |
O2B | 0.4713 (6) | 0.77900 (10) | −0.0200 (5) | 0.0321 (7) | |
H4B | 0.616 (5) | 0.7856 (17) | −0.072 (7) | 0.040 (14)* | |
O3B | 0.6174 (5) | 0.88334 (9) | 0.1501 (4) | 0.0238 (6) | |
O4B | 0.9599 (5) | 0.83898 (10) | 0.1422 (4) | 0.0243 (6) | |
N1B | 0.2005 (6) | 0.88486 (11) | 0.8591 (5) | 0.0201 (7) | |
H1B | 0.0940 | 0.8694 | 0.9432 | 0.024* | |
H2B | 0.3638 | 0.8785 | 0.8978 | 0.024* | |
N2B | 0.3786 (6) | 0.82456 (12) | 0.4015 (5) | 0.0215 (7) | |
H3B | 0.2313 | 0.8190 | 0.3443 | 0.026* | |
C1B | 0.1553 (7) | 0.86953 (14) | 0.6450 (5) | 0.0197 (8) | |
H11B | 0.0103 | 0.8477 | 0.6361 | 0.024* | |
C2B | 0.0944 (8) | 0.91468 (14) | 0.5320 (6) | 0.0248 (9) | |
H21B | 0.1714 | 0.9147 | 0.3978 | 0.030* | |
H22B | −0.0899 | 0.9188 | 0.5161 | 0.030* | |
C3B | 0.2073 (8) | 0.95224 (13) | 0.6627 (6) | 0.0249 (9) | |
H31B | 0.3908 | 0.9551 | 0.6418 | 0.030* | |
H32B | 0.1262 | 0.9823 | 0.6350 | 0.030* | |
C4B | 0.1526 (8) | 0.93601 (14) | 0.8721 (6) | 0.0261 (9) | |
H41B | −0.0241 | 0.9425 | 0.9082 | 0.031* | |
H42B | 0.2668 | 0.9507 | 0.9716 | 0.031* | |
C5B | 0.3937 (7) | 0.84702 (14) | 0.5745 (6) | 0.0208 (8) | |
C6B | 0.6101 (7) | 0.80928 (13) | 0.3083 (6) | 0.0197 (8) | |
H61B | 0.7290 | 0.8000 | 0.4186 | 0.024* | |
C7B | 0.5713 (8) | 0.76720 (14) | 0.1728 (6) | 0.0254 (9) | |
H71B | 0.7347 | 0.7514 | 0.1562 | 0.031* | |
H72B | 0.4550 | 0.7455 | 0.2385 | 0.031* | |
C8B | 0.7374 (7) | 0.84796 (13) | 0.1909 (5) | 0.0182 (8) | |
O1W | 0.8723 (5) | 0.51850 (10) | −0.2377 (5) | 0.0286 (7) | |
H11W | 0.862 (10) | 0.5474 (8) | −0.263 (8) | 0.043* | |
H12W | 0.717 (5) | 0.5105 (19) | −0.251 (8) | 0.043* | |
O2W | 0.6245 (6) | 0.97668 (10) | 0.2452 (5) | 0.0292 (7) | |
H21W | 0.637 (9) | 0.9494 (9) | 0.200 (7) | 0.044* | |
H22W | 0.776 (5) | 0.9870 (17) | 0.235 (8) | 0.044* |
U11 | U22 | U33 | U12 | U13 | U23 | |
O1A | 0.0192 (14) | 0.0429 (18) | 0.0245 (15) | 0.0014 (13) | 0.0017 (11) | 0.0077 (14) |
O2A | 0.0347 (18) | 0.0225 (15) | 0.0419 (19) | −0.0031 (14) | −0.0049 (14) | −0.0008 (13) |
O3A | 0.0251 (14) | 0.0185 (15) | 0.0254 (15) | 0.0001 (11) | 0.0036 (11) | −0.0013 (11) |
O4A | 0.0192 (14) | 0.0280 (16) | 0.0240 (15) | 0.0004 (11) | −0.0013 (11) | −0.0043 (12) |
N1A | 0.0207 (16) | 0.0221 (17) | 0.0160 (16) | 0.0019 (13) | −0.0011 (12) | 0.0001 (13) |
N2A | 0.0159 (15) | 0.0220 (17) | 0.0206 (17) | 0.0004 (13) | 0.0000 (12) | 0.0029 (14) |
C1A | 0.0171 (18) | 0.022 (2) | 0.019 (2) | −0.0009 (15) | −0.0009 (14) | 0.0017 (16) |
C2A | 0.031 (2) | 0.025 (2) | 0.020 (2) | 0.0083 (18) | −0.0007 (16) | −0.0031 (17) |
C3A | 0.040 (2) | 0.023 (2) | 0.022 (2) | −0.0003 (18) | −0.0015 (17) | −0.0019 (17) |
C4A | 0.038 (2) | 0.020 (2) | 0.020 (2) | 0.0016 (18) | −0.0049 (17) | −0.0004 (17) |
C5A | 0.0219 (19) | 0.0180 (19) | 0.021 (2) | −0.0005 (15) | −0.0038 (15) | −0.0039 (16) |
C6A | 0.0184 (18) | 0.020 (2) | 0.016 (2) | 0.0004 (14) | −0.0037 (14) | 0.0017 (15) |
C7A | 0.029 (2) | 0.021 (2) | 0.021 (2) | 0.0007 (16) | −0.0026 (16) | 0.0005 (16) |
C8A | 0.024 (2) | 0.021 (2) | 0.0117 (18) | −0.0009 (16) | 0.0028 (14) | −0.0021 (15) |
O1B | 0.0190 (14) | 0.0434 (19) | 0.0267 (16) | 0.0036 (13) | −0.0022 (11) | −0.0078 (13) |
O2B | 0.0306 (16) | 0.0343 (18) | 0.0313 (17) | −0.0035 (14) | 0.0022 (13) | −0.0050 (14) |
O3B | 0.0296 (15) | 0.0201 (15) | 0.0217 (15) | −0.0005 (12) | −0.0032 (11) | 0.0015 (12) |
O4B | 0.0199 (14) | 0.0314 (16) | 0.0218 (15) | −0.0006 (11) | 0.0013 (11) | 0.0025 (12) |
N1B | 0.0199 (16) | 0.0200 (18) | 0.0203 (18) | −0.0007 (13) | 0.0014 (12) | 0.0022 (13) |
N2B | 0.0207 (16) | 0.0265 (18) | 0.0173 (16) | −0.0017 (13) | 0.0005 (12) | −0.0003 (14) |
C1B | 0.0184 (19) | 0.023 (2) | 0.017 (2) | 0.0013 (15) | −0.0005 (14) | 0.0013 (16) |
C2B | 0.030 (2) | 0.022 (2) | 0.022 (2) | 0.0034 (17) | 0.0008 (16) | 0.0012 (17) |
C3B | 0.033 (2) | 0.016 (2) | 0.026 (2) | −0.0016 (17) | 0.0004 (17) | 0.0032 (16) |
C4B | 0.033 (2) | 0.023 (2) | 0.023 (2) | 0.0042 (17) | 0.0013 (16) | −0.0035 (17) |
C5B | 0.0196 (19) | 0.019 (2) | 0.023 (2) | −0.0001 (15) | 0.0033 (15) | 0.0036 (16) |
C6B | 0.0200 (18) | 0.019 (2) | 0.020 (2) | 0.0015 (15) | 0.0011 (15) | −0.0022 (15) |
C7B | 0.031 (2) | 0.020 (2) | 0.026 (2) | −0.0038 (17) | 0.0045 (16) | −0.0030 (17) |
C8B | 0.0195 (19) | 0.023 (2) | 0.0122 (18) | 0.0000 (16) | −0.0027 (13) | −0.0045 (15) |
O1W | 0.0277 (15) | 0.0217 (15) | 0.0362 (18) | 0.0014 (13) | −0.0027 (13) | 0.0047 (13) |
O2W | 0.0284 (16) | 0.0214 (15) | 0.0379 (19) | 0.0021 (13) | 0.0003 (13) | −0.0049 (14) |
O1A—C5A | 1.231 (5) | O2B—H4B | 0.87 (2) |
O2A—C7A | 1.406 (5) | O3B—C8B | 1.239 (5) |
O2A—H4A | 0.84 (2) | O4B—C8B | 1.257 (4) |
O3A—C8A | 1.252 (5) | N1B—C4B | 1.512 (5) |
O4A—C8A | 1.265 (5) | N1B—C1B | 1.513 (5) |
N1A—C4A | 1.494 (5) | N1B—H1B | 0.9200 |
N1A—C1A | 1.498 (5) | N1B—H2B | 0.9200 |
N1A—H1A | 0.9200 | N2B—C5B | 1.329 (5) |
N1A—H2A | 0.9200 | N2B—C6B | 1.455 (5) |
N2A—C5A | 1.330 (5) | N2B—H3B | 0.8800 |
N2A—C6A | 1.461 (5) | C1B—C5B | 1.506 (5) |
N2A—H3A | 0.8800 | C1B—C2B | 1.546 (5) |
C1A—C2A | 1.534 (5) | C1B—H11B | 1.0000 |
C1A—C5A | 1.534 (5) | C2B—C3B | 1.517 (6) |
C1A—H11A | 1.0000 | C2B—H21B | 0.9900 |
C2A—C3A | 1.523 (6) | C2B—H22B | 0.9900 |
C2A—H21A | 0.9900 | C3B—C4B | 1.508 (6) |
C2A—H22A | 0.9900 | C3B—H31B | 0.9900 |
C3A—C4A | 1.511 (6) | C3B—H32B | 0.9900 |
C3A—H31A | 0.9900 | C4B—H41B | 0.9900 |
C3A—H32A | 0.9900 | C4B—H42B | 0.9900 |
C4A—H41A | 0.9900 | C6B—C8B | 1.534 (5) |
C4A—H42A | 0.9900 | C6B—C7B | 1.534 (5) |
C6A—C7A | 1.522 (5) | C6B—H61B | 1.0000 |
C6A—C8A | 1.531 (5) | C7B—H71B | 0.9900 |
C6A—H61A | 1.0000 | C7B—H72B | 0.9900 |
C7A—H71A | 0.9900 | O1W—H11W | 0.86 (2) |
C7A—H72A | 0.9900 | O1W—H12W | 0.86 (2) |
O1B—C5B | 1.242 (5) | O2W—H21W | 0.85 (2) |
O2B—C7B | 1.426 (5) | O2W—H22W | 0.86 (2) |
C7A—O2A—H4A | 103 (4) | C4B—N1B—C1B | 108.6 (3) |
C4A—N1A—C1A | 108.2 (3) | C4B—N1B—H1B | 110.0 |
C4A—N1A—H1A | 110.1 | C1B—N1B—H1B | 110.0 |
C1A—N1A—H1A | 110.1 | C4B—N1B—H2B | 110.0 |
C4A—N1A—H2A | 110.1 | C1B—N1B—H2B | 110.0 |
C1A—N1A—H2A | 110.1 | H1B—N1B—H2B | 108.3 |
H1A—N1A—H2A | 108.4 | C5B—N2B—C6B | 118.7 (3) |
C5A—N2A—C6A | 120.5 (3) | C5B—N2B—H3B | 120.6 |
C5A—N2A—H3A | 119.7 | C6B—N2B—H3B | 120.6 |
C6A—N2A—H3A | 119.7 | C5B—C1B—N1B | 107.5 (3) |
N1A—C1A—C2A | 105.4 (3) | C5B—C1B—C2B | 112.8 (3) |
N1A—C1A—C5A | 107.0 (3) | N1B—C1B—C2B | 103.9 (3) |
C2A—C1A—C5A | 113.1 (3) | C5B—C1B—H11B | 110.8 |
N1A—C1A—H11A | 110.4 | N1B—C1B—H11B | 110.8 |
C2A—C1A—H11A | 110.4 | C2B—C1B—H11B | 110.8 |
C5A—C1A—H11A | 110.4 | C3B—C2B—C1B | 104.6 (3) |
C3A—C2A—C1A | 103.6 (3) | C3B—C2B—H21B | 110.8 |
C3A—C2A—H21A | 111.0 | C1B—C2B—H21B | 110.8 |
C1A—C2A—H21A | 111.0 | C3B—C2B—H22B | 110.8 |
C3A—C2A—H22A | 111.0 | C1B—C2B—H22B | 110.8 |
C1A—C2A—H22A | 111.0 | H21B—C2B—H22B | 108.9 |
H21A—C2A—H22A | 109.0 | C4B—C3B—C2B | 103.2 (3) |
C4A—C3A—C2A | 103.0 (3) | C4B—C3B—H31B | 111.1 |
C4A—C3A—H31A | 111.2 | C2B—C3B—H31B | 111.1 |
C2A—C3A—H31A | 111.2 | C4B—C3B—H32B | 111.1 |
C4A—C3A—H32A | 111.2 | C2B—C3B—H32B | 111.1 |
C2A—C3A—H32A | 111.2 | H31B—C3B—H32B | 109.1 |
H31A—C3A—H32A | 109.1 | C3B—C4B—N1B | 102.7 (3) |
N1A—C4A—C3A | 103.0 (3) | C3B—C4B—H41B | 111.2 |
N1A—C4A—H41A | 111.2 | N1B—C4B—H41B | 111.2 |
C3A—C4A—H41A | 111.2 | C3B—C4B—H42B | 111.2 |
N1A—C4A—H42A | 111.2 | N1B—C4B—H42B | 111.2 |
C3A—C4A—H42A | 111.2 | H41B—C4B—H42B | 109.1 |
H41A—C4A—H42A | 109.1 | O1B—C5B—N2B | 124.0 (4) |
O1A—C5A—N2A | 124.2 (3) | O1B—C5B—C1B | 119.6 (3) |
O1A—C5A—C1A | 120.4 (3) | N2B—C5B—C1B | 116.4 (3) |
N2A—C5A—C1A | 115.3 (3) | N2B—C6B—C8B | 112.1 (3) |
N2A—C6A—C7A | 110.7 (3) | N2B—C6B—C7B | 112.9 (3) |
N2A—C6A—C8A | 112.1 (3) | C8B—C6B—C7B | 109.9 (3) |
C7A—C6A—C8A | 111.3 (3) | N2B—C6B—H61B | 107.2 |
N2A—C6A—H61A | 107.5 | C8B—C6B—H61B | 107.2 |
C7A—C6A—H61A | 107.5 | C7B—C6B—H61B | 107.2 |
C8A—C6A—H61A | 107.5 | O2B—C7B—C6B | 112.7 (3) |
O2A—C7A—C6A | 112.2 (3) | O2B—C7B—H71B | 109.1 |
O2A—C7A—H71A | 109.2 | C6B—C7B—H71B | 109.1 |
C6A—C7A—H71A | 109.2 | O2B—C7B—H72B | 109.1 |
O2A—C7A—H72A | 109.2 | C6B—C7B—H72B | 109.1 |
C6A—C7A—H72A | 109.2 | H71B—C7B—H72B | 107.8 |
H71A—C7A—H72A | 107.9 | O3B—C8B—O4B | 126.7 (4) |
O3A—C8A—O4A | 125.9 (4) | O3B—C8B—C6B | 119.5 (3) |
O3A—C8A—C6A | 120.2 (3) | O4B—C8B—C6B | 113.7 (3) |
O4A—C8A—C6A | 113.8 (3) | H11W—O1W—H12W | 101 (5) |
C7B—O2B—H4B | 95 (3) | H21W—O2W—H22W | 103 (5) |
N1A—C1A—C5A—N2A | 173.0 (3) | N1B—C1B—C5B—N2B | 169.3 (3) |
C1A—C5A—N2A—C6A | 166.6 (3) | C1B—C5B—N2B—C6B | 169.1 (3) |
C5A—N2A—C6A—C8A | −80.3 (4) | C5B—N2B—C6B—C8B | −81.6 (4) |
N2A—C6A—C8A—O3A | −19.8 (5) | N2B—C6B—C8B—O3B | −14.7 (5) |
N1A—C1A—C2A—C3A | 21.0 (4) | N1B—C1B—C2B—C3B | 21.7 (4) |
C1A—C2A—C3A—C4A | −37.9 (4) | C1B—C2B—C3B—C4B | −38.8 (4) |
C2A—C3A—C4A—N1A | 40.2 (4) | C2B—C3B—C4B—N1B | 40.1 (4) |
C3A—C4A—N1A—C1A | −27.5 (4) | C3B—C4B—N1B—C1B | −27.0 (4) |
C4A—N1A—C1A—C2A | 3.9 (4) | C4B—N1B—C1B—C2B | 3.2 (4) |
N2A—C6A—C7A—O2A | −76.3 (4) | N2B—C6B—C7B—O2B | 80.3 (4) |
C4A—N1A—C1A—C5A | 124.6 (3) | C4B—N1B—C1B—C5B | 123.0 (3) |
C5A—C1A—C2A—C3A | −95.6 (4) | C5B—C1B—C2B—C3B | −94.4 (4) |
C6A—N2A—C5A—O1A | −12.2 (6) | C6B—N2B—C5B—O1B | −10.0 (6) |
N1A—C1A—C5A—O1A | −8.1 (5) | N1B—C1B—C5B—O1B | −11.5 (5) |
C2A—C1A—C5A—O1A | 107.6 (4) | C2B—C1B—C5B—O1B | 102.4 (4) |
C2A—C1A—C5A—N2A | −71.3 (4) | C2B—C1B—C5B—N2B | −76.8 (4) |
C5A—N2A—C6A—C7A | 154.7 (3) | C5B—N2B—C6B—C7B | 153.7 (3) |
C8A—C6A—C7A—O2A | 158.2 (3) | C8B—C6B—C7B—O2B | −45.6 (4) |
C7A—C6A—C8A—O3A | 104.8 (4) | C7B—C6B—C8B—O3B | 111.6 (4) |
N2A—C6A—C8A—O4A | 160.9 (3) | N2B—C6B—C8B—O4B | 166.7 (3) |
C7A—C6A—C8A—O4A | −74.5 (4) | C7B—C6B—C8B—O4B | −67.0 (4) |
D—H···A | D—H | H···A | D···A | D—H···A |
O2A—H4A···O2Bi | 0.84 (2) | 2.05 (3) | 2.856 (4) | 162 (5) |
N1A—H1A···O4Aii | 0.92 | 1.73 | 2.638 (4) | 168 |
N1A—H2A···O3Aiii | 0.92 | 2.10 | 2.882 (4) | 142 |
N2A—H3A···O4Ai | 0.88 | 2.12 | 2.900 (4) | 148 |
C1A—H11A···O1Ai | 1.00 | 2.24 | 3.083 (5) | 142 |
O2B—H4B···O2A | 0.87 (2) | 2.29 (3) | 3.094 (4) | 154 (5) |
N1B—H1B···O4Biv | 0.92 | 1.76 | 2.656 (4) | 165 |
N1B—H2B···O3Biii | 0.92 | 2.15 | 2.924 (4) | 142 |
N2B—H3B···O4Bv | 0.88 | 2.04 | 2.829 (4) | 148 |
C1B—H11B···O1Bv | 1.00 | 2.25 | 3.062 (5) | 137 |
C1B—H11B···O2Aiv | 1.00 | 2.53 | 3.226 (5) | 126 |
O1W—H11W···O3A | 0.86 (2) | 1.95 (2) | 2.797 (4) | 171 (5) |
O1W—H12W···O2Wvi | 0.86 (2) | 2.07 (2) | 2.905 (4) | 166 (5) |
O2W—H21W···O3B | 0.85 (2) | 1.95 (2) | 2.788 (4) | 167 (5) |
O2W—H22W···O1Wvii | 0.86 (2) | 2.08 (2) | 2.937 (4) | 173 (5) |
Symmetry codes: (i) x+1, y, z; (ii) x+1, y, z+1; (iii) x, y, z+1; (iv) x−1, y, z+1; (v) x−1, y, z; (vi) −x+1, y−1/2, −z; (vii) −x+2, y+1/2, −z. |
Experimental details
Crystal data | |
Chemical formula | C8H14N2O4·H2O |
Mr | 220.23 |
Crystal system, space group | Monoclinic, P21 |
Temperature (K) | 105 |
a, b, c (Å) | 5.3101 (12), 29.081 (7), 6.6757 (15) |
β (°) | 90.829 (3) |
V (Å3) | 1030.8 (4) |
Z | 4 |
Radiation type | Mo Kα |
µ (mm−1) | 0.12 |
Crystal size (mm) | 0.31 × 0.09 × 0.06 |
Data collection | |
Diffractometer | Bruker APEXII CCD diffractometer |
Absorption correction | Multi-scan (SADABS; Bruker, 2007) |
Tmin, Tmax | 0.838, 0.993 |
No. of measured, independent and observed [I > 2σ(I)] reflections | 8313, 2165, 1768 |
Rint | 0.047 |
(sin θ/λ)max (Å−1) | 0.627 |
Refinement | |
R[F2 > 2σ(F2)], wR(F2), S | 0.044, 0.110, 1.05 |
No. of reflections | 2165 |
No. of parameters | 291 |
No. of restraints | 7 |
H-atom treatment | H atoms treated by a mixture of independent and constrained refinement |
Δρmax, Δρmin (e Å−3) | 0.26, −0.25 |
Computer programs: APEX2 (Bruker, 2007), SAINT-Plus (Bruker, 2007), SHELXS97 (Sheldrick, 2008), SHELXL97 (Sheldrick, 2008), SHELXTL (Sheldrick, 2008).
N1A—C1A—C5A—N2A | 173.0 (3) | N1B—C1B—C5B—N2B | 169.3 (3) |
C1A—C5A—N2A—C6A | 166.6 (3) | C1B—C5B—N2B—C6B | 169.1 (3) |
C5A—N2A—C6A—C8A | −80.3 (4) | C5B—N2B—C6B—C8B | −81.6 (4) |
N2A—C6A—C8A—O3A | −19.8 (5) | N2B—C6B—C8B—O3B | −14.7 (5) |
N1A—C1A—C2A—C3A | 21.0 (4) | N1B—C1B—C2B—C3B | 21.7 (4) |
C1A—C2A—C3A—C4A | −37.9 (4) | C1B—C2B—C3B—C4B | −38.8 (4) |
C2A—C3A—C4A—N1A | 40.2 (4) | C2B—C3B—C4B—N1B | 40.1 (4) |
C3A—C4A—N1A—C1A | −27.5 (4) | C3B—C4B—N1B—C1B | −27.0 (4) |
C4A—N1A—C1A—C2A | 3.9 (4) | C4B—N1B—C1B—C2B | 3.2 (4) |
N2A—C6A—C7A—O2A | −76.3 (4) | N2B—C6B—C7B—O2B | 80.3 (4) |
D—H···A | D—H | H···A | D···A | D—H···A |
O2A—H4A···O2Bi | 0.84 (2) | 2.05 (3) | 2.856 (4) | 162 (5) |
N1A—H1A···O4Aii | 0.92 | 1.73 | 2.638 (4) | 168.2 |
N1A—H2A···O3Aiii | 0.92 | 2.10 | 2.882 (4) | 141.6 |
N2A—H3A···O4Ai | 0.88 | 2.12 | 2.900 (4) | 147.5 |
C1A—H11A···O1Ai | 1.00 | 2.24 | 3.083 (5) | 141.7 |
O2B—H4B···O2A | 0.87 (2) | 2.29 (3) | 3.094 (4) | 154 (5) |
N1B—H1B···O4Biv | 0.92 | 1.76 | 2.656 (4) | 165.4 |
N1B—H2B···O3Biii | 0.92 | 2.15 | 2.924 (4) | 141.7 |
N2B—H3B···O4Bv | 0.88 | 2.04 | 2.829 (4) | 148.0 |
C1B—H11B···O1Bv | 1.00 | 2.25 | 3.062 (5) | 137.0 |
C1B—H11B···O2Aiv | 1.00 | 2.53 | 3.226 (5) | 126.4 |
O1W—H11W···O3A | 0.86 (2) | 1.95 (2) | 2.797 (4) | 171 (5) |
O1W—H12W···O2Wvi | 0.86 (2) | 2.07 (2) | 2.905 (4) | 166 (5) |
O2W—H21W···O3B | 0.85 (2) | 1.95 (2) | 2.788 (4) | 167 (5) |
O2W—H22W···O1Wvii | 0.86 (2) | 2.08 (2) | 2.937 (4) | 173 (5) |
Symmetry codes: (i) x+1, y, z; (ii) x+1, y, z+1; (iii) x, y, z+1; (iv) x−1, y, z+1; (v) x−1, y, z; (vi) −x+1, y−1/2, −z; (vii) −x+2, y+1/2, −z. |
Group/refcode | Sequence | Hydration | Space group | x (Å)* | y (Å)* |
Pro–Npo | |||||
BAPBEZ10 | Pro–Met | hydrate | P21 | 5.472 (4) | 6.411 (5) |
BIBVOX | Pro–Val | hydrate | P212121 | 5.436 (2) | 6.549 (2) |
BUHGIU | Pro–Gly | hydrate | P21 | 5.417 (2) | 6.553 (2) |
LPRLAL | Pro–Ala | hydrate | P21 | 5.52 (2) | 6.58 (2) |
SEYWEY | Pro–Ile | hydrate | P21 | 5.413 (3) | 6.601 (3) |
SOJPAI | Pro–Tyr | hydrate | P1 | 5.524 (3) | 6.621 (2) |
Pol–Npo | |||||
EYIVAJ | Ser–Val | P21 | 5.383 (4) | 6.315 (4) | |
GUKVUD | Ser–Leu | P21 | 5.3288 (3) | 6.3696 (6) | |
JUKMOR | His–Leu | P21 | 5.451 (1) | 6.559 (1) | |
PAJFIQ | Ser–Phe | P212121 | 5.3382 (13) | 6.3827 (16) | |
RAVZAQ | His–Met | P21 | 5.4676 (11) | 6.5893 (13) | |
TIPTUH | Glu–Val | P21 | 5.505 (2) | 6.487 (2) | |
Gly–Npo | |||||
GLYLEU10 | Gly–Leu | P21 | 5.565 (5) | 6.369 (5) | |
QQQEVJ01 | Gly–Phe | P21 | 5.4926 (17) | 6.433 (2) | |
WEVWOK | Gly–Val | P212121 | 5.5238 (7) | 6.299 (1) | |
Other | |||||
DEZQOO | Ala–Leu | hemihydrate | C2 | 5.5592 (8) | 6.3349 (7) |
BELCUQ | Glu–Glu | P21 | 5.524 (3) | 6.621 (2) | |
(I) | Pro–Ser | hydrate | P21 | 5.3101 (12) | 6.6757 (15) |
Note: (*) see Fig. 2. |
Dipeptides are known to form nanoporous structures belonging to three different classes (Görbitz, 2007). A large number of compounds belong to the Val–Ala class, with hydrophobic pores, while seven structures belong to the Phe–Phe class, with hydrophilic pores (all amino acids discussed here are of the L-configuration, stereochemical indicators are thus not included). The third class has but a single member, Leu–Ser (Görbitz et al., 2005; Cambridge Structural Database refcode JAZBOC; Allen 2002). In a search for additional Leu–Ser class structures with hydrophobic pores, Pro–Ser.H2O, (I), was synthesized and investigated by single-crystal X-ray diffraction methods.
The asymmetric unit of (I) (Fig. 1) contains two peptide molecules (A and B), as well as two water molecules. As reflected by the torsion angles listed in Table 1, the peptide backbones occur in very similar semiextended conformations with ϕ2 (C5—N2—C6—C8) close to -80°. The Pro pyrrolidinium rings exhibit envelope conformations with C4—N1—C1—C2 torsion angles close to 0° and endo puckering for C3 (see Supplementary materials). Molecules A and B are interconnected by hydrogen bonds between the L-Ser side chains, but the strong amino–carboxylate interactions in Table 2 connect only identical molecules within two independent hydrogen-bonded sheets in a structure that is clearly layered and nonporous (Fig. 2a). A recent review of the crystal structures of dipeptides (Görbitz, 2010a) showed that most structures in fact incorporate two-dimensional sheets with two coexisting C(8) head-to-tail hydrogen-bonded chains. Neighbouring molecules along such chains were found to be related either by just translation (T) or by a screw (S) operation, while a third hydrogen-bonded chain, involving the amide >N—H donor, is of type C(4) or C(5). This leads to four basic patterns called T4, T5, S4 and S5. The structure of (I) belongs to the T5 group, as can be seen from the hydrogen-bonded sheet depicted in Fig. 3, which is derived solely from A molecules. A total of 17 other structures with similar sheets are listed in Table 3. The geometric parameters given in the table display small variations among the structures, but x reaches the smallest value for (I) (crystallographic a axis) while y has the largest value (c axis).
Table 3 furthermore shows that crystals with T5 sheets occur mainly for dipeptides with the sequences Pro–Nop, Gly–Nop and Pol–Nop, where Nop is a nonpolar residue and Pol is a polar (but uncharged) residue. The title compound belongs to none of these groups and is only the second T5 structure after Glu–Glu (CSD refcode BELCUQ; Eggleston & Hodgson, 1982) with a polar C-terminal residue. Compared to e.g. Pro–Val (BIBVOX; Narasimhan et al., 1982), (I) introduces an extra side-chain hydrogen-bond donor that needs to find a suitable acceptor atom. Fig. 2(a) reveals how this has been achieved: the symmetry of the orthorhombic P212121 space group of Pro–Val in Fig. 2(b) has been retained for peptide main chains, Pro side chains and water molecules, but is broken locally as consecutive peptide molecules along the a-axis shift between two different Ser side chain conformations (gauche– for molecule A, gauche+ for molecule B, Table 1) to form a hydrogen-bonded co-operative chain of hydroxy groups (Fig. 4). Consequently, the r.m.s. deviation for the best overlay between molecules A and B is 0.554 Å when all heavy atoms are included, but only 0.066 Å when the O—H group is excluded from the calculation (illustrations available as Supplementary materials). The resulting pseudo-orthorhombic [β = 90.829 (3)°] structure of (I) is the only entry in Table 3 with Z' = 2. Fig. 4 also highlights the water wires running parallel to the hydroxy chains. Investigations of small molecule crystal structures with water wires (Prohens et al., 2013; Le Duc et al., 2011; Görbitz, 2010b; Raghavender et al., 2010) has attracted considerable attention recently as models for single lane water channels in proteins such as aquaporin, a biologically important transmembrane protein that carries water molecules in a single line into a cell from its extracellular environment (Yu et al., 2011; Agre, 2004; Kozono et al., 2002), and also for their suspected roles in a series of disorders and diseases, including amyloid formation (Thirumalai et al. 2012).
Finally, the reason why Pol-Nop peptides in Table 3 can pack in the same manner as Pro–Nop peptides as well as (I) is evident from a comparison of Pro–Val (BIBVOX; Narasimhan et al., 1982) in Fig. 2(b) and Ser–Val (EYIVAJ; Moen et al., 2004) in Fig. 2(c): the extra amino N—H donor of Ser compared to Pro needs an additional hydrogen-bond acceptor, which is provided by the side chain of the polar, N-terminal residue. At the same time, the side chain fuctional group, in this case –OH, saturates the hydrogen-bond accepting capacity of the C-terminal carboxylate group, a role taken by the solvent water molecules in the structures with N-terminal Pro such as (I).