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A high-resolution dataset of the tripeptide L-alanyl-L-prolyl-L-alanine hydrate was measured at 100 K using synchrotron radiation and CCD area detection. Electron densities were obtained from a full multipole refinement of the X-ray experimental data, from an invariom transfer and from a theoretical calculation. Topological and atomic properties were derived via an AIM analysis [Atoms in Molecules; see Bader (1990). Atoms in Molecules: A Quantum Theory, No. 22 in International Series of Monographs on Chemistry, 1st ed. Oxford: Clarendon Press] of these densities and compared with each other, as well as with results from the literature of other oligopeptides and amino acids. By application of the invariom formalism to a dataset of limited resolution, its performance was compared with a conventional spherical refinement, highlighting the possibility of aspherically modelling routine structure-determination experiments. The hydrogen-bonding scheme was subject to a detailed analysis according to the criteria of Koch & Popelier [(1995), J. Phys. Chem. 99, 9747-9754] as well as to the characterization of Espinosa et al. [(1998), Chem. Phys. Lett. 285, 170-173; (1999), Acta Cryst. B55, 563-572; (2002), J. Chem. Phys. 117, 5529-5542] using the results from the refined and invariom multipole densities as well as the spherical-density model, which are critically compared.
Keywords: charge density; topological properties; CCD area detection; invariom transfer; amino acids; oligopeptides; hydrogen bonding; spherical-density model.
Supporting information
 | Crystallographic Information File (CIF) https://doi.org/10.1107/S0108768107030388/sn5053sup1.cif |
 | Structure factor file (CIF format) https://doi.org/10.1107/S0108768107030388/sn5053APAsup2.hkl |
 | Portable Document Format (PDF) file https://doi.org/10.1107/S0108768107030388/sn5053sup3.pdf |
CCDC reference: 665696
Computing details top
Data collection: XDS (Kabsch, (1993)); cell refinement: XDS (Kabsch, (1993)); data reduction: XDS (Kabsch, (1993)); program(s) used to solve structure: SHELXS97 (Sheldrick, (1997)); program(s) used to refine structure: XD (Koritsanszky et al., (2003)); molecular graphics: XD (Koritsanszky et al., (2003)); software used to prepare material for publication: XD (Koritsanszky et al., (2003)).
(APA) top
Crystal data top
| C11H19N3O4·OH2 | F(000) = 592 |
| Mr = 275.30 | Dx = 1.364 (1) Mg m−3 |
| Orthorhombic, P212121 | Synchrotron radiation, λ = 0.56000 Å |
| Hall symbol: P 2ac 2ab | Cell parameters from 186017 reflections |
| a = 6.8250 (14) Å | θ = 3.2–49.8° |
| b = 9.0420 (18) Å | µ = 0.06 mm−1 |
| c = 21.728 (4) Å | T = 100 K |
| V = 1340.9 (5) Å3 | Needle, colorless |
| Z = 4 | 0.57 × 0.22 × 0.13 mm |
Data collection top
| MAR165 CCD detector
at HASYLAB/DESY beamline F1
on kappa-axis diffractometer | Rint = 0.038 |
| φ scans | θmax = 49.8° |
| 186017 measured reflections | h = 0→15 |
| 13992 independent reflections | k = 0→24 |
| 11358 reflections with I > 3 σ(I) | l = 0→54 |
Refinement top
| Refinement on F | 0 restraints |
| Least-squares matrix: full | All H-atom parameters refined |
| R[F2 > 2σ(F2)] = 0.021 | w1 = 1/[s2(Fo)] |
| wR(F2) = 0.013 | (Δ/σ)max < 0.001 |
| S = 1.54 | Δρmax = 0.15 e Å−3 |
| 11358 reflections | Δρmin = −0.15 e Å−3 |
| 566 parameters |
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top
| x | y | z | Uiso*/Ueq | ||
| O(4) | 0.14466 (4) | 0.21813 (3) | 0.571840 (10) | 0.016 | |
| O(3) | 0.41116 (4) | 0.34809 (3) | 0.598780 (10) | 0.016 | |
| O(2) | 0.25774 (5) | 0.21501 (4) | 0.807190 (10) | 0.018 | |
| O(1) | 0.28546 (5) | 0.56496 (3) | 0.838520 (10) | 0.017 | |
| O(100) | 0.29419 (6) | 0.07305 (4) | 0.92558 (2) | 0.024 | |
| N(3) | 0.35409 (4) | 0.32352 (2) | 0.717270 (10) | 0.014 | |
| N(2) | 0.53711 (3) | 0.41380 (2) | 0.867740 (10) | 0.012 | |
| N(1) | 0.26215 (3) | 0.70103 (2) | 0.950290 (10) | 0.013 | |
| C(6) | 0.25446 (4) | 0.27975 (2) | 0.611520 (10) | 0.012 | |
| C(5) | 0.18950 (4) | 0.27374 (3) | 0.679510 (10) | 0.012 | |
| C(8) | 0.00733 (4) | 0.37258 (3) | 0.689320 (10) | 0.017 | |
| C(4) | 0.37528 (3) | 0.29193 (2) | 0.777440 (10) | 0.013 | |
| C(3) | 0.56637 (4) | 0.35149 (3) | 0.805670 (10) | 0.012 | |
| C(20) | 0.71400 (4) | 0.22478 (3) | 0.817490 (10) | 0.015 | |
| C(21) | 0.83734 (4) | 0.28450 (3) | 0.871400 (10) | 0.016 | |
| C(22) | 0.68157 (4) | 0.35631 (3) | 0.912870 (10) | 0.015 | |
| C(2) | 0.39329 (3) | 0.51327 (2) | 0.879090 (10) | 0.012 | |
| C(1) | 0.36268 (4) | 0.55431 (3) | 0.947050 (10) | 0.012 | |
| C(7) | 0.23823 (4) | 0.43650 (3) | 0.979500 (10) | 0.018 | |
| H(5) | 0.15617 | 0.15827 | 0.69122 | 0.038 (2) | |
| H(8A) | −0.11913 | 0.32118 | 0.67092 | 0.047 (2) | |
| H(8C) | 0.02852 | 0.47805 | 0.66925 | 0.050 (2) | |
| H(8B) | −0.01488 | 0.38690 | 0.73718 | 0.049 (2) | |
| H(13) | 0.46016 | 0.37978 | 0.69498 | 0.029 (3) | |
| H(3) | 0.63200 | 0.43487 | 0.77523 | 0.036 (2) | |
| H(20A) | 0.63233 | 0.12817 | 0.83330 | 0.039 (2) | |
| H(20B) | 0.79691 | 0.19420 | 0.77646 | 0.039 (2) | |
| H(21A) | 0.91994 | 0.19829 | 0.89514 | 0.046 (2) | |
| H(21B) | 0.93935 | 0.36821 | 0.85457 | 0.044 (2) | |
| H(22A) | 0.61258 | 0.27419 | 0.94265 | 0.038 (2) | |
| H(22B) | 0.73897 | 0.44562 | 0.94145 | 0.039 (2) | |
| H(1) | 0.50441 | 0.56726 | 0.97037 | 0.031 (2) | |
| H(7B) | 0.30515 | 0.33133 | 0.97540 | 0.048 (2) | |
| H(7C) | 0.22214 | 0.46498 | 1.02650 | 0.048 (2) | |
| H(7A) | 0.09806 | 0.43283 | 0.95872 | 0.051 (2) | |
| H(11C) | 0.26610 | 0.73553 | 0.99559 | 0.028 (2) | |
| H(11A) | 0.34286 | 0.77650 | 0.92517 | 0.027 (2) | |
| H(11B) | 0.11912 | 0.69741 | 0.93486 | 0.029 (2) | |
| H(101) | 0.27505 | 0.12117 | 0.88628 | 0.036 (3) | |
| H(102) | 0.41051 | 0.01538 | 0.91719 | 0.039 (3) |
Atomic displacement parameters (Å2) top
| U11 | U22 | U33 | U12 | U13 | U23 | |
| O(4) | 0.01541 (9) | 0.02094 (10) | 0.01066 (5) | −0.00217 (7) | −0.00088 (5) | −0.00137 (6) |
| O(3) | 0.01398 (9) | 0.01982 (9) | 0.01325 (6) | −0.00237 (7) | 0.00176 (6) | 0.00117 (6) |
| O(2) | 0.01680 (10) | 0.02370 (10) | 0.01320 (10) | −0.00550 (10) | −0.00060 (10) | 0.00350 (10) |
| O(1) | 0.01960 (10) | 0.02030 (10) | 0.01180 (10) | 0.00790 (10) | −0.00330 (10) | −0.00110 (10) |
| O(100) | 0.02630 (10) | 0.02610 (10) | 0.02030 (10) | 0.00540 (10) | 0.00070 (10) | 0.00210 (10) |
| N(3) | 0.01422 (7) | 0.01767 (7) | 0.00958 (5) | −0.00195 (6) | −0.00075 (5) | 0.00043 (5) |
| N(2) | 0.01239 (7) | 0.01457 (6) | 0.01009 (5) | 0.00298 (5) | −0.00113 (4) | −0.00141 (4) |
| N(1) | 0.01383 (7) | 0.01359 (6) | 0.01171 (5) | 0.00116 (5) | 0.00064 (4) | −0.00109 (4) |
| C(6) | 0.01231 (7) | 0.01431 (7) | 0.00974 (5) | 0.00016 (6) | 0.00008 (5) | 0.00019 (4) |
| C(5) | 0.01340 (8) | 0.01405 (8) | 0.00991 (5) | −0.00087 (6) | 0.00011 (5) | 0.00007 (5) |
| C(8) | 0.01397 (8) | 0.01963 (9) | 0.01655 (7) | 0.00055 (6) | 0.00183 (6) | −0.00225 (6) |
| C(4) | 0.01313 (8) | 0.01481 (7) | 0.00971 (5) | −0.00048 (6) | −0.00004 (5) | −0.00003 (5) |
| C(3) | 0.01238 (8) | 0.01401 (7) | 0.01039 (5) | 0.00060 (6) | 0.00011 (5) | −0.00088 (5) |
| C(20) | 0.01474 (8) | 0.01588 (8) | 0.01475 (6) | 0.00299 (6) | 0.00043 (6) | −0.00234 (6) |
| C(21) | 0.01248 (9) | 0.01989 (9) | 0.01619 (7) | 0.00352 (6) | −0.00104 (5) | −0.00178 (7) |
| C(22) | 0.01425 (8) | 0.01903 (9) | 0.01190 (6) | 0.00429 (7) | −0.00195 (5) | −0.00097 (5) |
| C(2) | 0.01242 (7) | 0.01352 (7) | 0.00983 (5) | 0.00218 (6) | −0.00052 (5) | −0.00067 (5) |
| C(1) | 0.01264 (8) | 0.01336 (7) | 0.01027 (5) | 0.00080 (5) | 0.00017 (5) | −0.00071 (5) |
| C(7) | 0.02270 (10) | 0.01520 (10) | 0.01690 (10) | −0.00120 (10) | 0.00640 (10) | 0.00050 (10) |
Geometric parameters (Å, º) top
| O(4)—C(6) | 1.2710 (3) | C(8)—H(8C) | 1.0585 (2) |
| O(3)—C(6) | 1.2658 (4) | C(8)—H(8B) | 1.0588 (2) |
| O(2)—C(4) | 1.2430 (3) | C(4)—C(3) | 1.5386 (3) |
| O(1)—C(2) | 1.2398 (3) | C(3)—C(20) | 1.5472 (3) |
| O(100)—H(101) | 0.9671 (4) | C(3)—H(3) | 1.0984 (2) |
| O(100)—H(102) | 0.9671 (5) | C(20)—C(21) | 1.5401 (3) |
| N(3)—C(5) | 1.4620 (3) | C(20)—H(20A) | 1.0917 (2) |
| N(3)—C(4) | 1.3461 (3) | C(20)—H(20B) | 1.0916 (2) |
| N(3)—H(13) | 1.0086 (3) | C(21)—C(22) | 1.5374 (3) |
| N(2)—C(3) | 1.4751 (3) | C(21)—H(21A) | 1.0916 (2) |
| N(2)—C(22) | 1.4845 (3) | C(21)—H(21B) | 1.0914 (3) |
| N(2)—C(2) | 1.3539 (3) | C(22)—H(22A) | 1.0917 (2) |
| N(1)—C(1) | 1.4952 (3) | C(22)—H(22B) | 1.0916 (2) |
| N(1)—H(11C) | 1.0330 (2) | C(2)—C(1) | 1.5369 (3) |
| N(1)—H(11A) | 1.0329 (2) | C(1)—C(7) | 1.5341 (3) |
| N(1)—H(11B) | 1.0326 (2) | C(1)—H(1) | 1.0982 (2) |
| C(6)—C(5) | 1.5434 (3) | C(7)—H(7B) | 1.0587 (2) |
| C(5)—C(8) | 1.5460 (4) | C(7)—H(7C) | 1.0589 (2) |
| C(5)—H(5) | 1.0984 (3) | C(7)—H(7A) | 1.0584 (3) |
| C(8)—H(8A) | 1.0587 (2) | H(101)—H(102) | 1.4902 |
| H(101)—O(100)—H(102) | 100.79 (4) | C(4)—C(3)—H(3) | 110.237 (18) |
| C(5)—N(3)—C(4) | 124.21 (2) | C(20)—C(3)—H(3) | 110.040 (19) |
| C(5)—N(3)—H(13) | 115.940 (19) | C(3)—C(20)—C(21) | 102.861 (19) |
| C(4)—N(3)—H(13) | 119.75 (2) | C(3)—C(20)—H(20A) | 108.20 (2) |
| C(3)—N(2)—C(22) | 112.34 (2) | C(3)—C(20)—H(20B) | 112.930 (19) |
| C(3)—N(2)—C(2) | 121.22 (2) | C(21)—C(20)—H(20A) | 108.691 (19) |
| C(22)—N(2)—C(2) | 126.43 (2) | C(21)—C(20)—H(20B) | 115.25 (2) |
| C(1)—N(1)—H(11C) | 107.503 (18) | H(20A)—C(20)—H(20B) | 108.59 (2) |
| C(1)—N(1)—H(11A) | 108.454 (19) | C(20)—C(21)—C(22) | 102.46 (2) |
| C(1)—N(1)—H(11B) | 112.974 (19) | C(20)—C(21)—H(21A) | 113.03 (2) |
| H(11C)—N(1)—H(11A) | 106.870 (18) | C(20)—C(21)—H(21B) | 109.698 (18) |
| H(11C)—N(1)—H(11B) | 110.096 (19) | C(22)—C(21)—H(21A) | 112.442 (18) |
| H(11A)—N(1)—H(11B) | 110.708 (18) | C(22)—C(21)—H(21B) | 110.16 (2) |
| O(4)—C(6)—O(3) | 124.32 (2) | H(21A)—C(21)—H(21B) | 108.91 (2) |
| O(4)—C(6)—C(5) | 117.67 (2) | N(2)—C(22)—C(21) | 102.713 (18) |
| O(3)—C(6)—C(5) | 117.99 (2) | N(2)—C(22)—H(22A) | 110.08 (2) |
| N(3)—C(5)—C(6) | 107.789 (19) | N(2)—C(22)—H(22B) | 110.80 (2) |
| N(3)—C(5)—C(8) | 111.260 (18) | C(21)—C(22)—H(22A) | 111.00 (2) |
| N(3)—C(5)—H(5) | 108.773 (19) | C(21)—C(22)—H(22B) | 113.44 (2) |
| C(6)—C(5)—C(8) | 110.035 (18) | H(22A)—C(22)—H(22B) | 108.70 (2) |
| C(6)—C(5)—H(5) | 108.340 (18) | O(1)—C(2)—N(2) | 123.46 (2) |
| C(8)—C(5)—H(5) | 110.55 (2) | O(1)—C(2)—C(1) | 120.76 (2) |
| C(5)—C(8)—H(8A) | 110.47 (2) | N(2)—C(2)—C(1) | 115.72 (2) |
| C(5)—C(8)—H(8C) | 110.75 (2) | N(1)—C(1)—C(2) | 108.773 (17) |
| C(5)—C(8)—H(8B) | 108.73 (2) | N(1)—C(1)—C(7) | 109.900 (19) |
| H(8A)—C(8)—H(8C) | 110.57 (2) | N(1)—C(1)—H(1) | 106.729 (18) |
| H(8A)—C(8)—H(8B) | 107.93 (2) | C(2)—C(1)—C(7) | 110.442 (18) |
| H(8C)—C(8)—H(8B) | 108.30 (2) | C(2)—C(1)—H(1) | 110.445 (19) |
| O(2)—C(4)—N(3) | 123.68 (3) | C(7)—C(1)—H(1) | 110.466 (19) |
| O(2)—C(4)—C(3) | 122.38 (2) | C(1)—C(7)—H(7B) | 110.25 (2) |
| N(3)—C(4)—C(3) | 113.83 (2) | C(1)—C(7)—H(7C) | 109.39 (2) |
| N(2)—C(3)—C(4) | 112.543 (18) | C(1)—C(7)—H(7A) | 109.03 (2) |
| N(2)—C(3)—C(20) | 102.664 (18) | H(7B)—C(7)—H(7C) | 110.14 (2) |
| N(2)—C(3)—H(3) | 110.09 (2) | H(7B)—C(7)—H(7A) | 109.02 (2) |
| C(4)—C(3)—C(20) | 111.040 (19) | H(7C)—C(7)—H(7A) | 108.99 (2) |
