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In the last decade three different data bank approaches have been developed that are intended to make electron-density examinations of large biologically important molecules possible. They rely on Bader's concept of transferability of submolecular fragments with retention of their electronic properties. Therefore, elaborate studies on the quantification of transferability in experiment and theory are still very important. Tripeptides of the type L-alanyl-X-L-alanine (X being any of the 20 naturally encoded amino acids) serve as a model case between amino acids and proteins. The two experimental electron-density determinations (L-alanyl-L-histidinyl-L-alanine and L-alanyl-L-phenylalanyl-L-alanine, highly resolved synchrotron X-ray diffraction data sets) performed in this study and theoretical calculations on all 20 different L-alanyl-X-L-alanine molecules contribute to a better estimation of transferability in the peptide case. As a measure of reproducibility and transferability, standard deviations from averaging over bond-topological and atomic properties of atoms or bonds that are considered equal in their chemical environments were calculated. This way, transferability and reproducibility indices were introduced. It can be shown that experimental transferability indices generally slightly exceed experimental reproducibility indices and that these larger deviations can be attributed to chemical effects such as changes in the geometry (bond lengths and angles), the polarization pattern and the neighboring sphere due to crystal packing. These effects can partly be separated from each other and quantified with the help of gas-phase calculations at optimized and experimental geometries. Thus, the degree of transferability can be quantified in very narrow limits taking into account experimental errors and chemical effects.
Supporting information
CCDC references: 746158; 746159
For both compounds, data collection: XDS Kabsch, W. J. Appl. Cryst. 26, 795 (1993); cell refinement: XDS Kabsch, W. J. Appl. Cryst. 26, 795 (1993); data reduction: XDS Kabsch, W. J. Appl. Cryst. 26, 795 (1993); program(s) used to solve structure: SHELXS97 (Sheldrick, 1990); program(s) used to refine structure: Volkov et al., (2006); molecular graphics: Volkov et al., (2006); software used to prepare material for publication: Volkov et al., (2006).
Crystal data top
C12H19N5O4·C3H8O·H2O | F(000) = 404 |
Mr = 375.43 | Dx = 1.269 Mg m−3 |
Monoclinic, P21 | Synchrotron radiation, λ = 0.56000 Å |
Hall symbol: P 2yb | Cell parameters from 43348 reflections |
a = 8.7410 (17) Å | θ = 2.2–40.6° |
b = 9.4200 (19) Å | µ = 0.06 mm−1 |
c = 11.989 (2) Å | T = 100 K |
β = 95.49 (3)° | Block, colourless |
V = 982.7 (3) Å3 | 0.4 × 0.35 × 0.25 mm |
Z = 2 | |
Data collection top
MarCCD 165 detector diffractometer | Rint = 0.027 |
phi scans | θmax = 40.6°, θmin = 2.2° |
152583 measured reflections | h = −20→20 |
13235 independent reflections | k = 0→21 |
11918 reflections with > 3σ(I) | l = 0→27 |
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)] = 0.020 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.035 | Only H-atom displacement parameters refined |
S = 1.96 | w2 = 1/[s2(Fo2)] |
11918 reflections | (Δ/σ)max < 0.001 |
783 parameters | Δρmax = 0.14 e Å−3 |
0 restraints | Δρmin = −0.22 e Å−3 |
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top | x | y | z | Uiso*/Ueq | |
O1 | 0.93272 (6) | −0.19177 (5) | 0.50612 (3) | 0.018 | |
O2 | 1.04547 (7) | 0.16971 (6) | 0.23879 (3) | 0.021 | |
O3 | 0.91839 (5) | 0.05960 (6) | −0.08500 (3) | 0.018 | |
O4 | 1.11847 (6) | 0.20542 (5) | −0.09695 (3) | 0.018 | |
O5 | 0.62491 (3) | 0.06583 (5) | 0.58438 (3) | 0.017 | |
O6 | 0.68186 (6) | −0.11637 (6) | −0.03402 (4) | 0.020 | |
N1 | 0.89037 (4) | −0.04533 (4) | 0.69941 (2) | 0.013 | |
N2 | 0.96416 (3) | 0.01900 (5) | 0.41694 (2) | 0.012 | |
N3 | 1.04651 (4) | −0.02934 (5) | 0.13043 (2) | 0.013 | |
N4 | 0.61009 (4) | 0.13679 (5) | 0.35754 (3) | 0.016 | |
N5 | 0.50568 (4) | 0.24206 (6) | 0.20176 (3) | 0.019 | |
C1 | 0.99961 (4) | 0.01262 (5) | 0.62189 (2) | 0.013 | |
C2 | 0.96204 (3) | −0.06221 (5) | 0.50893 (2) | 0.012 | |
C3 | 0.93079 (4) | −0.04494 (1) | 0.30621 (2) | 0.011 | |
C4 | 1.01201 (3) | 0.04299 (4) | 0.22128 (2) | 0.012 | |
C5 | 1.14237 (4) | 0.03211 (5) | 0.04935 (2) | 0.014 | |
C6 | 1.05053 (4) | 0.10631 (5) | −0.05039 (2) | 0.013 | |
C7 | 1.16624 (4) | −0.01533 (6) | 0.66851 (3) | 0.022 | |
C8 | 1.24118 (5) | −0.08525 (6) | 0.00243 (3) | 0.027 | |
C9 | 0.75553 (4) | −0.06534 (5) | 0.27437 (2) | 0.013 | |
C10 | 0.65792 (4) | 0.06595 (5) | 0.26470 (2) | 0.014 | |
C11 | 0.51869 (4) | 0.24150 (5) | 0.31573 (3) | 0.019 | |
C12 | 0.59320 (4) | 0.13039 (5) | 0.16797 (3) | 0.018 | |
C13 | 0.54317 (5) | 0.14881 (7) | 0.75869 (3) | 0.022 | |
C14 | 0.55861 (4) | 0.18693 (5) | 0.63619 (3) | 0.016 | |
C15 | 0.65668 (7) | 0.31977 (7) | 0.62597 (5) | 0.028 | |
H1 | 0.976938 | 0.127002 | 0.612904 | 0.025 | |
H3 | 0.982426 | −0.151328 | 0.306389 | 0.027 | |
H5 | 1.215996 | 0.112432 | 0.094048 | 0.032 | |
H7A | 1.190659 | 0.041462 | 0.744358 | 0.044 | |
H7B | 1.241447 | 0.018591 | 0.609624 | 0.045 | |
H7C | 1.18175 | −0.125315 | 0.68389 | 0.041 | |
H8A | 1.311567 | −0.13261 | 0.069051 | 0.058 | |
H8B | 1.311165 | −0.040358 | −0.055775 | 0.046 | |
H8C | 1.16844 | −0.16324 | −0.038072 | 0.049 | |
H9A | 0.714423 | −0.134593 | 0.338169 | 0.029 | |
H9B | 0.743389 | −0.114375 | 0.206685 | 0.038 | |
H11 | 0.465693 | 0.320938 | 0.363956 | 0.039 | |
H12 | 0.601981 | 0.104345 | 0.081346 | 0.038 | |
H1NA | 0.906127 | −0.153624 | 0.707812 | 0.026 | |
H1NB | 0.778768 | −0.02497 | 0.666967 | 0.022 | |
H1NC | 0.910707 | 0.002481 | 0.776953 | 0.024 | |
H2N | 0.990045 | 0.123321 | 0.422018 | 0.019 | |
H3N | 1.008132 | −0.130195 | 0.122447 | 0.022 | |
H5N | 0.438201 | 0.302693 | 0.147906 | 0.039 | |
H13A | 0.480651 | 0.052884 | 0.762236 | 0.040 | |
H13B | 0.483984 | 0.23104 | 0.796789 | 0.042 | |
H13C | 0.653792 | 0.135897 | 0.801795 | 0.042 | |
H14 | 0.444371 | 0.203449 | 0.591343 | 0.032 | |
H15A | 0.762501 | 0.307875 | 0.675982 | 0.064 | |
H15B | 0.597583 | 0.409304 | 0.653698 | 0.056 | |
H15C | 0.677793 | 0.334468 | 0.541228 | 0.061 | |
H5O | 0.625723 | 0.087045 | 0.505525 | 0.022 | |
H6OA | 0.738167 | −0.187592 | 0.0097 | 0.041 | |
H6OB | 0.76287 | −0.052805 | −0.049176 | 0.025 | |
Atomic displacement parameters (Å2) top | U11 | U22 | U33 | U12 | U13 | U23 |
O1 | 0.03078 (17) | 0.00989 (10) | 0.01166 (9) | −0.00084 (12) | 0.00057 (10) | 0.00064 (8) |
O2 | 0.0356 (2) | 0.01159 (11) | 0.01757 (12) | −0.00638 (14) | 0.00966 (13) | −0.00345 (10) |
O3 | 0.01833 (14) | 0.02400 (16) | 0.01254 (10) | −0.00260 (14) | −0.00074 (9) | 0.00078 (10) |
O4 | 0.02296 (16) | 0.01458 (12) | 0.01618 (11) | −0.00018 (13) | 0.00242 (11) | 0.00542 (9) |
O5 | 0.01968 (12) | 0.01824 (11) | 0.01398 (10) | 0.00465 (10) | 0.00020 (7) | −0.00019 (9) |
O6 | 0.01970 (15) | 0.02045 (15) | 0.01999 (13) | −0.00232 (14) | −0.00244 (12) | −0.00213 (12) |
N1 | 0.01603 (9) | 0.01282 (8) | 0.01063 (6) | 0.00125 (8) | 0.00158 (7) | 0.00025 (6) |
N2 | 0.01724 (11) | 0.01000 (8) | 0.00880 (7) | −0.00075 (7) | 0.00120 (6) | −0.00001 (6) |
N3 | 0.01985 (11) | 0.01200 (9) | 0.00884 (6) | −0.00195 (9) | 0.00305 (7) | −0.00064 (6) |
N4 | 0.01846 (11) | 0.01795 (10) | 0.01269 (9) | 0.00440 (12) | 0.00126 (8) | −0.00042 (8) |
N5 | 0.01873 (12) | 0.02024 (12) | 0.01737 (12) | 0.00426 (13) | −0.00204 (9) | 0.00257 (10) |
C1 | 0.01745 (12) | 0.01211 (10) | 0.00959 (7) | −0.00080 (9) | 0.00121 (7) | −0.00058 (7) |
C2 | 0.01792 (11) | 0.00967 (9) | 0.00908 (7) | 0.00020 (8) | 0.00086 (6) | 0.00010 (6) |
C3 | 0.01499 (10) | 0.00998 (9) | 0.00926 (7) | −0.00023 (9) | 0.00169 (7) | −0.00011 (6) |
C4 | 0.01696 (10) | 0.01007 (9) | 0.00945 (7) | −0.00112 (8) | 0.00213 (7) | −0.00030 (6) |
C5 | 0.01612 (11) | 0.01556 (11) | 0.01018 (8) | 0.00040 (10) | 0.00202 (8) | 0.00221 (8) |
C6 | 0.01704 (12) | 0.01223 (10) | 0.00946 (8) | 0.00067 (10) | 0.00145 (8) | 0.00080 (7) |
C7 | 0.01564 (12) | 0.03430 (18) | 0.01520 (10) | −0.00253 (12) | 0.00064 (8) | −0.00392 (10) |
C8 | 0.03115 (17) | 0.02823 (17) | 0.02364 (14) | 0.01538 (15) | 0.01357 (13) | 0.01074 (12) |
C9 | 0.01541 (11) | 0.01222 (10) | 0.01279 (9) | −0.00100 (9) | 0.00119 (7) | −0.00146 (7) |
C10 | 0.01486 (10) | 0.01476 (10) | 0.01151 (9) | 0.00066 (10) | 0.00048 (7) | −0.00022 (7) |
C11 | 0.01872 (13) | 0.01963 (13) | 0.01752 (12) | 0.00556 (13) | 0.00065 (9) | −0.00034 (10) |
C12 | 0.01988 (12) | 0.02049 (13) | 0.01269 (10) | 0.00302 (13) | −0.00082 (8) | 0.00101 (9) |
C13 | 0.02067 (15) | 0.02831 (18) | 0.01582 (12) | 0.00543 (15) | 0.00182 (11) | −0.00132 (12) |
C14 | 0.01461 (11) | 0.01798 (12) | 0.01618 (10) | 0.00250 (10) | 0.00023 (9) | −0.00092 (9) |
C15 | 0.0293 (2) | 0.02092 (18) | 0.0335 (2) | −0.00416 (18) | 0.00597 (18) | −0.00419 (16) |
Geometric parameters (Å, º) top
O1—C2 | 1.2468 (5) | C3—C9 | 1.5549 (5) |
O2—C4 | 1.2421 (5) | C3—H3 | 1.0989 |
O3—C6 | 1.2682 (5) | C5—C6 | 1.5425 (4) |
O4—C6 | 1.2646 (5) | C5—C8 | 1.5419 (6) |
O5—C14 | 1.4463 (6) | C5—H5 | 1.0990 |
O5—H5O | 0.9670 | C7—H7A | 1.0590 |
O6—H6OA | 0.9580 | C7—H7B | 1.0589 |
O6—H6OB | 0.9579 | C7—H7C | 1.0588 |
N1—C1 | 1.4978 (5) | C8—H8A | 1.0591 |
N1—H1NA | 1.0330 | C8—H8B | 1.0591 |
N1—H1NB | 1.0330 | C8—H8C | 1.0587 |
N1—H1NC | 1.0330 | C9—C10 | 1.5007 (5) |
N2—C2 | 1.3438 (4) | C9—H9A | 1.0919 |
N2—C3 | 1.4615 (4) | C9—H9B | 0.9309 |
N2—H2N | 1.0090 | C10—C12 | 1.3813 (5) |
N3—C4 | 1.3432 (3) | C11—H11 | 1.0770 |
N3—C5 | 1.4622 (5) | C12—H12 | 1.0770 |
N3—H3N | 1.0090 | C13—C14 | 1.5304 (5) |
N4—C10 | 1.3957 (5) | C13—H13A | 1.0590 |
N4—C11 | 1.3364 (5) | C13—H13B | 1.0590 |
N5—C11 | 1.3603 (6) | C13—H13C | 1.0590 |
N5—C12 | 1.3839 (6) | C14—C15 | 1.5284 (6) |
N5—H5N | 1.0090 | C14—H14 | 1.0990 |
C1—C2 | 1.5343 (4) | C15—H15A | 1.0591 |
C1—C7 | 1.5322 (5) | C15—H15B | 1.0590 |
C1—H1 | 1.0989 | C15—H15C | 1.0589 |
C3—C4 | 1.5380 (3) | | |
| | | |
C14—O5—H5O | 107.31 | C1—C7—H7A | 109.44 |
H6OA—O6—H6OB | 101.02 | C1—C7—H7B | 109.52 |
C1—N1—H1NA | 109.48 | C1—C7—H7C | 109.46 |
C1—N1—H1NB | 109.50 | H7A—C7—H7B | 109.45 |
C1—N1—H1NC | 109.54 | H7A—C7—H7C | 109.44 |
H1NA—N1—H1NB | 109.42 | H7B—C7—H7C | 109.52 |
H1NA—N1—H1NC | 109.45 | C5—C8—H8A | 109.40 |
H1NB—N1—H1NC | 109.45 | C5—C8—H8B | 109.46 |
C2—N2—C3 | 119.58 (3) | C5—C8—H8C | 109.40 |
C2—N2—H2N | 121.71 | H8A—C8—H8B | 109.55 |
C3—N2—H2N | 118.71 | H8A—C8—H8C | 109.49 |
C4—N3—C5 | 121.71 (5) | H8B—C8—H8C | 109.53 |
C4—N3—H3N | 117.14 | C3—C9—C10 | 117.17 (3) |
C5—N3—H3N | 121.07 | C3—C9—H9A | 106.52 |
C10—N4—C11 | 105.53 (3) | C3—C9—H9B | 107.63 |
C11—N5—C12 | 107.19 (4) | C10—C9—H9A | 108.89 |
C11—N5—H5N | 129.24 | C10—C9—H9B | 108.96 |
C12—N5—H5N | 123.27 | H9A—C9—H9B | 107.24 |
N1—C1—C2 | 106.55 (2) | N4—C10—C9 | 122.95 (3) |
N1—C1—C7 | 110.57 (2) | N4—C10—C12 | 109.24 (3) |
N1—C1—H1 | 107.37 | C9—C10—C12 | 127.68 (3) |
C2—C1—C7 | 111.03 (3) | N4—C11—N5 | 111.67 (4) |
C2—C1—H1 | 110.03 | N4—C11—H11 | 125.72 |
C7—C1—H1 | 111.13 | N5—C11—H11 | 122.52 |
O1—C2—N2 | 123.64 (3) | N5—C12—C10 | 106.37 (3) |
O1—C2—C1 | 119.98 (3) | N5—C12—H12 | 123.22 |
N2—C2—C1 | 116.38 (3) | C10—C12—H12 | 130.41 |
N2—C3—C4 | 108.34 (2) | C14—C13—H13A | 109.39 |
N2—C3—C9 | 112.35 (2) | C14—C13—H13B | 109.51 |
N2—C3—H3 | 109.14 | C14—C13—H13C | 109.58 |
C4—C3—C9 | 114.22 (2) | H13A—C13—H13B | 109.37 |
C4—C3—H3 | 106.08 | H13A—C13—H13C | 109.45 |
C9—C3—H3 | 106.42 | H13B—C13—H13C | 109.54 |
O2—C4—N3 | 123.85 (3) | O5—C14—C13 | 107.62 (3) |
O2—C4—C3 | 121.46 (3) | O5—C14—C15 | 111.13 (3) |
N3—C4—C3 | 114.66 (3) | O5—C14—H14 | 106.51 |
N3—C5—C6 | 113.95 (3) | C13—C14—C15 | 111.76 (4) |
N3—C5—C8 | 109.59 (3) | C13—C14—H14 | 110.08 |
N3—C5—H5 | 107.13 | C15—C14—H14 | 109.59 |
C6—C5—C8 | 108.07 (3) | C14—C15—H15A | 109.52 |
C6—C5—H5 | 107.65 | C14—C15—H15B | 109.43 |
C8—C5—H5 | 110.44 | C14—C15—H15C | 109.54 |
O3—C6—O4 | 124.28 (4) | H15A—C15—H15B | 109.41 |
O3—C6—C5 | 119.12 (4) | H15A—C15—H15C | 109.52 |
O4—C6—C5 | 116.43 (4) | H15B—C15—H15C | 109.39 |
| | | |
H5O—O5—C14—C13 | 174.85 | N2—C3—C4—O2 | −24.43 (4) |
H5O—O5—C14—C15 | −62.48 | N2—C3—C4—N3 | 153.72 (4) |
H5O—O5—C14—H14 | 56.82 | N2—C3—C9—C10 | 62.45 (3) |
H1NA—N1—C1—C2 | 60.33 | N2—C3—C9—H9A | −59.68 |
H1NA—N1—C1—C7 | −60.42 | N2—C3—C9—H9B | −174.43 |
H1NA—N1—C1—H1 | 178.19 | C9—C3—C4—O2 | 101.62 (4) |
H1NB—N1—C1—C2 | −59.63 | C9—C3—C4—N3 | −80.23 (3) |
H1NB—N1—C1—C7 | 179.62 | C4—C3—C9—C10 | −61.48 (3) |
H1NB—N1—C1—H1 | 58.24 | C4—C3—C9—H9A | 176.40 |
H1NC—N1—C1—C2 | −179.66 | C4—C3—C9—H9B | 61.65 |
H1NC—N1—C1—C7 | 59.59 | H3—C3—C4—O2 | −141.50 |
H1NC—N1—C1—H1 | −61.79 | H3—C3—C4—N3 | 36.66 |
C3—N2—C2—O1 | −0.03 (4) | H3—C3—C9—C10 | −178.17 |
C3—N2—C2—C1 | 179.50 (5) | H3—C3—C9—H9A | 59.71 |
C2—N2—C3—C4 | −153.40 (4) | H3—C3—C9—H9B | −55.04 |
C2—N2—C3—C9 | 79.46 (3) | N3—C5—C6—O3 | −31.70 (4) |
C2—N2—C3—H3 | −38.32 | N3—C5—C6—O4 | 152.85 (5) |
H2N—N2—C2—O1 | −178.98 | N3—C5—C8—H8A | −59.50 |
H2N—N2—C2—C1 | 0.55 | N3—C5—C8—H8B | −179.54 |
H2N—N2—C3—C4 | 25.58 | N3—C5—C8—H8C | 60.44 |
H2N—N2—C3—C9 | −101.55 | C8—C5—C6—O3 | 90.36 (5) |
H2N—N2—C3—H3 | 140.66 | C8—C5—C6—O4 | −85.09 (4) |
C5—N3—C4—O2 | 6.80 (4) | C6—C5—C8—H8A | 175.80 |
C5—N3—C4—C3 | −171.31 (5) | C6—C5—C8—H8B | 55.75 |
C4—N3—C5—C6 | −93.31 (4) | C6—C5—C8—H8C | −64.26 |
C4—N3—C5—C8 | 145.47 (5) | H5—C5—C6—O3 | −150.35 |
C4—N3—C5—H5 | 25.64 | H5—C5—C6—O4 | 34.20 |
H3N—N3—C4—O2 | −176.38 | H5—C5—C8—H8A | 58.29 |
H3N—N3—C4—C3 | 5.51 | H5—C5—C8—H8B | −61.76 |
H3N—N3—C5—C6 | 90.00 | H5—C5—C8—H8C | 178.23 |
H3N—N3—C5—C8 | −31.23 | C3—C9—C10—N4 | −79.19 (4) |
H3N—N3—C5—H5 | −151.06 | C3—C9—C10—C12 | 105.45 (5) |
C10—N4—C11—N5 | −0.19 (4) | H9A—C9—C10—N4 | 41.70 |
C11—N4—C10—C9 | −176.20 (5) | H9A—C9—C10—C12 | −133.66 |
C11—N4—C10—C12 | −0.09 (4) | H9B—C9—C10—N4 | 158.37 |
C10—N4—C11—H11 | −176.77 | H9B—C9—C10—C12 | −16.99 |
C12—N5—C11—N4 | 0.39 (4) | N4—C10—C12—N5 | 0.32 (3) |
C11—N5—C12—C10 | −0.43 (4) | N4—C10—C12—H12 | −178.71 |
C12—N5—C11—H11 | 177.10 | C9—C10—C12—N5 | 176.20 (6) |
C11—N5—C12—H12 | 178.69 | C9—C10—C12—H12 | −2.83 |
H5N—N5—C11—N4 | 174.25 | H13A—C13—C14—O5 | −54.13 |
H5N—N5—C11—H11 | −9.04 | H13A—C13—C14—C15 | −176.41 |
H5N—N5—C12—C10 | −174.74 | H13A—C13—C14—H14 | 61.58 |
H5N—N5—C12—H12 | 4.38 | H13B—C13—C14—O5 | −173.97 |
N1—C1—C2—O1 | −41.28 (4) | H13B—C13—C14—C15 | 63.75 |
N1—C1—C2—N2 | 139.17 (4) | H13B—C13—C14—H14 | −58.27 |
N1—C1—C7—H7A | −64.68 | H13C—C13—C14—O5 | 65.86 |
N1—C1—C7—H7B | 175.33 | H13C—C13—C14—C15 | −56.42 |
N1—C1—C7—H7C | 55.25 | H13C—C13—C14—H14 | −178.44 |
C7—C1—C2—O1 | 79.18 (4) | O5—C14—C15—H15A | −68.31 |
C7—C1—C2—N2 | −100.37 (4) | O5—C14—C15—H15B | 171.76 |
C2—C1—C7—H7A | 177.27 | O5—C14—C15—H15C | 51.83 |
C2—C1—C7—H7B | 57.28 | C13—C14—C15—H15A | 51.94 |
C2—C1—C7—H7C | −62.80 | C13—C14—C15—H15B | −68.00 |
H1—C1—C2—O1 | −157.37 | C13—C14—C15—H15C | 172.08 |
H1—C1—C2—N2 | 23.08 | H14—C14—C15—H15A | 174.24 |
H1—C1—C7—H7A | 54.45 | H14—C14—C15—H15B | 54.30 |
H1—C1—C7—H7B | −65.54 | H14—C14—C15—H15C | −65.62 |
H1—C1—C7—H7C | 174.38 | | |
Crystal data top
C15H21N3O4·C3H7NO | F(000) = 408 |
Mr = 380.44 | Dx = 1.278 Mg m−3 |
Monoclinic, P21 | Synchrotron radiation, λ = 0.56000 Å |
Hall symbol: P 2yb | Cell parameters from 53159 reflections |
a = 9.598 (2) Å | θ = 1.4–40.6° |
b = 8.9390 (5) Å | µ = 0.06 mm−1 |
c = 12.170 (1) Å | T = 100 K |
β = 108.754 (13)° | Block, colourless |
V = 988.7 (2) Å3 | 0.45 × 0.25 × 0.15 mm |
Z = 2 | |
Data collection top
MarCCD 165 detector diffractometer | Rint = 0.059 |
phi scans | θmax = 40.6°, θmin = 1.4° |
180324 measured reflections | h = −22→21 |
13499 independent reflections | k = 0→20 |
12060 reflections with > 3σ(I) | l = 0→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)] = 0.022 | Hydrogen site location: inferred from neighbouring sites |
wR(F2) = 0.033 | Only H-atom displacement parameters refined |
S = 1.95 | w2 = 1/[s2(Fo2)] |
12060 reflections | (Δ/σ)max < 0.001 |
733 parameters | Δρmax = 0.32 e Å−3 |
0 restraints | Δρmin = −0.34 e Å−3 |
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top | x | y | z | Uiso*/Ueq | |
O1 | 0.41602 (4) | 0.03249 (5) | 0.98625 (3) | 0.013 | |
O2 | 0.49704 (6) | 0.42296 (5) | 0.73918 (4) | 0.018 | |
O3 | 0.34281 (5) | 0.22011 (6) | 0.40702 (4) | 0.018 | |
O4 | 0.46376 (5) | 0.40284 (5) | 0.35069 (3) | 0.015 | |
O5 | 1.09598 (6) | 0.14282 (9) | 1.03306 (5) | 0.024 | |
N1 | 0.38701 (3) | 0.19428 (4) | 1.17191 (2) | 0.012 | |
N2 | 0.44902 (3) | 0.24831 (4) | 0.89919 (2) | 0.010 | |
N3 | 0.52174 (3) | 0.22564 (4) | 0.62873 (2) | 0.011 | |
N4 | 0.95075 (5) | 0.01790 (5) | 0.87476 (4) | 0.021 | |
C1 | 0.47977 (4) | 0.25263 (4) | 1.10496 (2) | 0.011 | |
C2 | 0.44431 (3) | 0.16793 (4) | 0.99066 (2) | 0.009 | |
C3 | 0.42384 (3) | 0.181506 | 0.78548 (2) | 0.009 | |
C4 | 0.48717 (3) | 0.28776 (4) | 0.71546 (2) | 0.010 | |
C5 | 0.56755 (4) | 0.31186 (5) | 0.54473 (2) | 0.012 | |
C6 | 0.44539 (4) | 0.31227 (5) | 0.42592 (2) | 0.011 | |
C7 | 0.64202 (4) | 0.23458 (5) | 1.17559 (2) | 0.017 | |
C8 | 0.70678 (4) | 0.24311 (6) | 0.53019 (3) | 0.021 | |
C9 | 0.25852 (4) | 0.15243 (5) | 0.71995 (2) | 0.012 | |
C10 | 0.16414 (3) | 0.29129 (4) | 0.69258 (2) | 0.012 | |
C11 | 0.10073 (3) | 0.34890 (5) | 0.77238 (3) | 0.017 | |
C12 | 0.01112 (4) | 0.47565 (5) | 0.74611 (3) | 0.021 | |
C13 | −0.01604 (4) | 0.54699 (5) | 0.63941 (3) | 0.022 | |
C14 | 0.04886 (4) | 0.49203 (5) | 0.56023 (3) | 0.019 | |
C15 | 0.13818 (3) | 0.36516 (5) | 0.58644 (3) | 0.015 | |
C16 | 0.82369 (6) | 0.10904 (11) | 0.86693 (7) | 0.040 | |
C17 | 0.94126 (6) | −0.08887 (8) | 0.78187 (5) | 0.030 | |
C18 | 1.07712 (4) | 0.04380 (6) | 0.95823 (4) | 0.019 | |
H1 | 0.452959 | 0.37054 | 1.082231 | 0.021 (2) | |
H3 | 0.480838 | 0.073433 | 0.793462 | 0.018 (2) | |
H5 | 0.591231 | 0.426197 | 0.578813 | 0.019 (2) | |
H7A | 0.666899 | 0.119557 | 1.191324 | 0.0311 (18) | |
H7B | 0.664089 | 0.291744 | 1.255595 | 0.0316 (18) | |
H7C | 0.707709 | 0.280285 | 1.12869 | 0.039 (2) | |
H8A | 0.686163 | 0.130175 | 0.503673 | 0.040 (2) | |
H8B | 0.793497 | 0.247293 | 0.610224 | 0.045 (2) | |
H8C | 0.737254 | 0.30325 | 0.466481 | 0.042 (2) | |
H9A | 0.214557 | 0.078771 | 0.772422 | 0.028 (2) | |
H9B | 0.25127 | 0.094828 | 0.652297 | 0.034 (2) | |
H11 | 0.121137 | 0.302586 | 0.858364 | 0.037 (2) | |
H12 | −0.043392 | 0.512746 | 0.806581 | 0.038 (2) | |
H13 | −0.094529 | 0.638143 | 0.61937 | 0.043 (3) | |
H14 | 0.035583 | 0.548639 | 0.478815 | 0.038 (2) | |
H15 | 0.185068 | 0.318684 | 0.523982 | 0.0296 (19) | |
H1NA | 0.27998 | 0.182269 | 1.117592 | 0.019 (3) | |
H1NB | 0.389296 | 0.268259 | 1.237675 | 0.019 (3) | |
H1NC | 0.426805 | 0.091666 | 1.207301 | 0.017 (2) | |
H2N | 0.47864 | 0.357075 | 0.908311 | 0.016 (2) | |
H3N | 0.511838 | 0.113214 | 0.626138 | 0.013 (2) | |
H16A | 0.83443 | 0.215781 | 0.831436 | 0.058 (4) | |
H16B | 0.816037 | 0.123994 | 0.951706 | 0.070 (4) | |
H16C | 0.726345 | 0.054677 | 0.814076 | 0.069 (4) | |
H17A | 1.037629 | −0.156827 | 0.804914 | 0.064 (4) | |
H17B | 0.932241 | −0.029396 | 0.703958 | 0.070 (4) | |
H17C | 0.846573 | −0.157727 | 0.768547 | 0.068 (4) | |
H18 | 1.16673 | −0.031806 | 0.956612 | 0.041 (3) | |
Atomic displacement parameters (Å2) top | U11 | U22 | U33 | U12 | U13 | U23 |
O1 | 0.02140 (13) | 0.00771 (9) | 0.00891 (9) | −0.00070 (9) | 0.00525 (9) | −0.00034 (8) |
O2 | 0.03392 (19) | 0.00955 (11) | 0.01571 (13) | −0.00490 (12) | 0.01437 (14) | −0.00369 (10) |
O3 | 0.01592 (14) | 0.02323 (15) | 0.01313 (12) | −0.00700 (13) | 0.00124 (11) | 0.00187 (12) |
O4 | 0.02457 (15) | 0.01287 (11) | 0.00828 (10) | −0.00061 (11) | 0.00650 (11) | 0.00141 (8) |
O5 | 0.01969 (18) | 0.0336 (2) | 0.01581 (15) | −0.00202 (18) | 0.00293 (14) | −0.00233 (17) |
N1 | 0.01707 (9) | 0.01300 (8) | 0.00733 (7) | 0.00220 (7) | 0.00504 (7) | 0.00032 (6) |
N2 | 0.01698 (11) | 0.00854 (8) | 0.00611 (7) | −0.00077 (6) | 0.00440 (6) | −0.00030 (7) |
N3 | 0.01752 (11) | 0.00980 (9) | 0.00709 (7) | −0.00075 (6) | 0.00592 (8) | −0.00081 (6) |
N4 | 0.01352 (12) | 0.02946 (16) | 0.01740 (11) | −0.00334 (12) | 0.00086 (12) | 0.00169 (12) |
C1 | 0.01738 (11) | 0.00881 (8) | 0.00659 (8) | −0.00051 (8) | 0.00357 (8) | −0.00048 (7) |
C2 | 0.01399 (10) | 0.00794 (8) | 0.00592 (8) | 0.00042 (6) | 0.00333 (6) | −0.00001 (7) |
C3 | 0.01290 (10) | 0.00854 (8) | 0.00644 (8) | 0.00011 (8) | 0.00348 (7) | −0.00034 (7) |
C4 | 0.01423 (10) | 0.00855 (8) | 0.00623 (7) | −0.00081 (7) | 0.00396 (7) | −0.00085 (6) |
C5 | 0.01535 (11) | 0.01335 (10) | 0.00683 (8) | −0.00302 (9) | 0.00414 (8) | −0.00079 (8) |
C6 | 0.01457 (11) | 0.01122 (9) | 0.00703 (9) | 0.00056 (9) | 0.00381 (8) | −0.00004 (7) |
C7 | 0.01654 (12) | 0.02048 (12) | 0.01141 (9) | −0.00407 (9) | 0.00138 (8) | 0.00012 (8) |
C8 | 0.01347 (10) | 0.03531 (17) | 0.01513 (11) | 0.00102 (11) | 0.00583 (8) | 0.00309 (11) |
C9 | 0.01292 (10) | 0.01116 (9) | 0.01108 (9) | −0.00087 (8) | 0.00302 (8) | −0.00132 (7) |
C10 | 0.01263 (9) | 0.01371 (9) | 0.01036 (9) | 0.00099 (9) | 0.00389 (7) | 0.00039 (7) |
C11 | 0.01937 (12) | 0.01883 (11) | 0.01439 (11) | 0.00418 (10) | 0.00894 (9) | 0.00142 (9) |
C12 | 0.02342 (14) | 0.02278 (13) | 0.02170 (13) | 0.00833 (12) | 0.01204 (12) | 0.00085 (11) |
C13 | 0.02037 (14) | 0.02050 (13) | 0.02414 (16) | 0.00843 (12) | 0.00781 (11) | 0.00389 (11) |
C14 | 0.01806 (12) | 0.02210 (13) | 0.01720 (12) | 0.00612 (11) | 0.00495 (10) | 0.00641 (10) |
C15 | 0.01528 (10) | 0.01933 (11) | 0.01110 (9) | 0.00369 (9) | 0.00420 (8) | 0.00269 (8) |
C16 | 0.0173 (2) | 0.0551 (4) | 0.0392 (3) | 0.0075 (2) | −0.0016 (2) | −0.0060 (3) |
C17 | 0.0236 (2) | 0.0389 (2) | 0.0246 (2) | −0.01205 (19) | 0.00533 (16) | −0.0076 (2) |
C18 | 0.01327 (13) | 0.02680 (15) | 0.01575 (12) | −0.00188 (12) | 0.00116 (11) | 0.00165 (13) |
Geometric parameters (Å, º) top
O1—C2 | 1.2382 (4) | C7—H7A | 1.0590 |
O2—C4 | 1.2391 (4) | C7—H7B | 1.0590 |
O3—C6 | 1.2471 (5) | C7—H7C | 1.0590 |
O4—C6 | 1.2762 (4) | C8—H8A | 1.0590 |
O5—C18 | 1.2407 (7) | C8—H8B | 1.0590 |
N1—C1 | 1.4815 (4) | C8—H8C | 1.0590 |
N1—H1NA | 1.0330 | C9—C10 | 1.5094 (4) |
N1—H1NB | 1.0330 | C9—H9A | 1.0920 |
N1—H1NC | 1.0330 | C9—H9B | 0.9545 |
N2—C2 | 1.3378 (4) | C10—C11 | 1.3996 (4) |
N2—C3 | 1.4543 (4) | C10—C15 | 1.3999 (4) |
N2—H2N | 1.0090 | C11—C12 | 1.3961 (5) |
N3—C4 | 1.3258 (4) | C11—H11 | 1.0830 |
N3—C5 | 1.4565 (4) | C12—C13 | 1.3940 (5) |
N3—H3N | 1.0090 | C12—H12 | 1.0830 |
N4—C16 | 1.4441 (8) | C13—C14 | 1.3941 (5) |
N4—C17 | 1.4598 (7) | C13—H13 | 1.0830 |
N4—C18 | 1.3284 (6) | C14—C15 | 1.3954 (4) |
C1—C2 | 1.5231 (4) | C14—H14 | 1.0830 |
C1—C7 | 1.5262 (5) | C15—H15 | 1.0830 |
C1—H1 | 1.0990 | C16—H16A | 1.0660 |
C3—C4 | 1.5267 (4) | C16—H16B | 1.0660 |
C3—C9 | 1.5517 (4) | C16—H16C | 1.0660 |
C3—H3 | 1.0990 | C17—H17A | 1.0660 |
C5—C6 | 1.5412 (4) | C17—H17B | 1.0660 |
C5—C8 | 1.5320 (5) | C17—H17C | 1.0660 |
C5—H5 | 1.0990 | C18—H18 | 1.0990 |
| | | |
C1—N1—H1NA | 109.54 | H7B—C7—H7C | 109.37 |
C1—N1—H1NB | 109.51 | C5—C8—H8A | 109.46 |
C1—N1—H1NC | 109.57 | C5—C8—H8B | 109.66 |
H1NA—N1—H1NB | 109.35 | C5—C8—H8C | 109.72 |
H1NA—N1—H1NC | 109.44 | H8A—C8—H8B | 109.18 |
H1NB—N1—H1NC | 109.42 | H8A—C8—H8C | 109.23 |
C2—N2—C3 | 122.10 (3) | H8B—C8—H8C | 109.58 |
C2—N2—H2N | 120.64 | C3—C9—C10 | 114.68 (2) |
C3—N2—H2N | 117.07 | C3—C9—H9A | 108.91 |
C4—N3—C5 | 123.13 (3) | C3—C9—H9B | 108.21 |
C4—N3—H3N | 113.38 | C10—C9—H9A | 107.92 |
C5—N3—H3N | 123.49 | C10—C9—H9B | 112.40 |
C16—N4—C17 | 118.47 (5) | H9A—C9—H9B | 104.15 |
C16—N4—C18 | 119.75 (5) | C9—C10—C11 | 120.89 (3) |
C17—N4—C18 | 121.36 (4) | C9—C10—C15 | 120.51 (2) |
N1—C1—C2 | 109.27 (2) | C11—C10—C15 | 118.60 (3) |
N1—C1—C7 | 109.75 (2) | C10—C11—C12 | 120.86 (3) |
N1—C1—H1 | 110.04 | C10—C11—H11 | 123.09 |
C2—C1—C7 | 110.47 (2) | C12—C11—H11 | 115.99 |
C2—C1—H1 | 106.34 | C11—C12—C13 | 120.10 (3) |
C7—C1—H1 | 110.92 | C11—C12—H12 | 119.31 |
O1—C2—N2 | 123.69 (3) | C13—C12—H12 | 120.43 |
O1—C2—C1 | 120.48 (3) | C12—C13—C14 | 119.43 (4) |
N2—C2—C1 | 115.82 (2) | C12—C13—H13 | 117.52 |
N2—C3—C4 | 107.55 (2) | C14—C13—H13 | 122.85 |
N2—C3—C9 | 112.80 (2) | C13—C14—C15 | 120.44 (3) |
N2—C3—H3 | 110.56 | C13—C14—H14 | 121.36 |
C4—C3—C9 | 110.01 (2) | C15—C14—H14 | 118.15 |
C4—C3—H3 | 108.66 | C10—C15—C14 | 120.55 (3) |
C9—C3—H3 | 107.21 | C10—C15—H15 | 118.41 |
O2—C4—N3 | 125.03 (3) | C14—C15—H15 | 120.98 |
O2—C4—C3 | 119.41 (3) | N4—C16—H16A | 110.00 |
N3—C4—C3 | 115.49 (3) | N4—C16—H16B | 109.05 |
N3—C5—C6 | 110.45 (3) | N4—C16—H16C | 109.90 |
N3—C5—C8 | 109.89 (3) | H16A—C16—H16B | 109.01 |
N3—C5—H5 | 107.44 | H16A—C16—H16C | 110.10 |
C6—C5—C8 | 108.75 (2) | H16B—C16—H16C | 108.75 |
C6—C5—H5 | 110.77 | N4—C17—H17A | 109.63 |
C8—C5—H5 | 109.53 | N4—C17—H17B | 109.25 |
O3—C6—O4 | 124.73 (4) | N4—C17—H17C | 109.46 |
O3—C6—C5 | 119.26 (3) | H17A—C17—H17B | 109.49 |
O4—C6—C5 | 115.83 (3) | H17A—C17—H17C | 109.64 |
C1—C7—H7A | 109.54 | H17B—C17—H17C | 109.34 |
C1—C7—H7B | 109.45 | O5—C18—N4 | 124.58 (5) |
C1—C7—H7C | 109.40 | O5—C18—H18 | 121.43 |
H7A—C7—H7B | 109.59 | N4—C18—H18 | 113.99 |
H7A—C7—H7C | 109.47 | | |
| | | |
H1NA—N1—C1—C2 | −44.85 | N2—C3—C4—O2 | −25.91 (3) |
H1NA—N1—C1—C7 | −166.12 | N2—C3—C4—N3 | 157.00 (3) |
H1NA—N1—C1—H1 | 71.55 | N2—C3—C9—C10 | 62.63 (3) |
H1NB—N1—C1—C2 | −164.77 | N2—C3—C9—H9A | −58.39 |
H1NB—N1—C1—C7 | 73.96 | N2—C3—C9—H9B | −171.02 |
H1NB—N1—C1—H1 | −48.37 | C9—C3—C4—O2 | 97.30 (4) |
H1NC—N1—C1—C2 | 75.21 | C9—C3—C4—N3 | −79.79 (3) |
H1NC—N1—C1—C7 | −46.05 | C4—C3—C9—C10 | −57.45 (3) |
H1NC—N1—C1—H1 | −168.38 | C4—C3—C9—H9A | −178.47 |
C3—N2—C2—O1 | −1.32 (3) | C4—C3—C9—H9B | 68.90 |
C3—N2—C2—C1 | 177.37 (4) | H3—C3—C4—O2 | −145.61 |
C2—N2—C3—C4 | −161.15 (4) | H3—C3—C4—N3 | 37.30 |
C2—N2—C3—C9 | 77.37 (3) | H3—C3—C9—C10 | −175.44 |
C2—N2—C3—H3 | −42.66 | H3—C3—C9—H9A | 63.54 |
H2N—N2—C2—O1 | −176.26 | H3—C3—C9—H9B | −49.09 |
H2N—N2—C2—C1 | 2.42 | N3—C5—C6—O3 | −15.02 (4) |
H2N—N2—C3—C4 | 13.97 | N3—C5—C6—O4 | 169.61 (5) |
H2N—N2—C3—C9 | −107.51 | N3—C5—C8—H8A | 57.77 |
H2N—N2—C3—H3 | 132.46 | N3—C5—C8—H8B | −61.98 |
C5—N3—C4—O2 | −4.10 (4) | N3—C5—C8—H8C | 177.62 |
C5—N3—C4—C3 | 172.80 (4) | C8—C5—C6—O3 | 105.65 (5) |
C4—N3—C5—C6 | −108.22 (4) | C8—C5—C6—O4 | −69.73 (4) |
C4—N3—C5—C8 | 131.80 (4) | C6—C5—C8—H8A | −63.24 |
C4—N3—C5—H5 | 12.70 | C6—C5—C8—H8B | 177.01 |
H3N—N3—C4—O2 | 176.67 | C6—C5—C8—H8C | 56.60 |
H3N—N3—C4—C3 | −6.42 | H5—C5—C6—O3 | −133.93 |
H3N—N3—C5—C6 | 70.93 | H5—C5—C6—O4 | 50.69 |
H3N—N3—C5—C8 | −49.06 | H5—C5—C8—H8A | 175.58 |
H3N—N3—C5—H5 | −168.16 | H5—C5—C8—H8B | 55.83 |
C17—N4—C16—H16A | −96.84 | H5—C5—C8—H8C | −64.58 |
C17—N4—C16—H16B | 143.66 | C3—C9—C10—C11 | −87.67 (4) |
C17—N4—C16—H16C | 24.54 | C3—C9—C10—C15 | 92.37 (4) |
C16—N4—C17—H17A | −172.88 | H9A—C9—C10—C11 | 33.89 |
C16—N4—C17—H17B | 67.12 | H9A—C9—C10—C15 | −146.07 |
C16—N4—C17—H17C | −52.58 | H9B—C9—C10—C11 | 148.17 |
C16—N4—C18—O5 | 0.28 (6) | H9B—C9—C10—C15 | −31.79 |
C18—N4—C16—H16A | 75.85 | C9—C10—C11—C12 | −178.74 (5) |
C18—N4—C16—H16B | −43.64 | C9—C10—C11—H11 | 4.09 |
C18—N4—C16—H16C | −162.76 | C9—C10—C15—C14 | 178.87 (5) |
C16—N4—C18—H18 | 179.89 | C9—C10—C15—H15 | 1.52 |
C17—N4—C18—O5 | 172.76 (8) | C15—C10—C11—C12 | 1.22 (3) |
C18—N4—C17—H17A | 14.55 | C11—C10—C15—C14 | −1.09 (3) |
C18—N4—C17—H17B | −105.45 | C15—C10—C11—H11 | −175.95 |
C18—N4—C17—H17C | 134.85 | C11—C10—C15—H15 | −178.44 |
C17—N4—C18—H18 | −7.63 | C10—C11—C12—C13 | −0.18 (4) |
N1—C1—C2—O1 | −36.98 (3) | C10—C11—C12—H12 | 175.24 |
N1—C1—C2—N2 | 144.29 (4) | H11—C11—C12—C13 | 177.18 |
N1—C1—C7—H7A | 62.19 | H11—C11—C12—H12 | −7.40 |
N1—C1—C7—H7B | −57.99 | C11—C12—C13—C14 | −1.00 (4) |
N1—C1—C7—H7C | −177.81 | C11—C12—C13—H13 | 174.14 |
C7—C1—C2—O1 | 83.85 (4) | H12—C12—C13—C14 | −176.37 |
C7—C1—C2—N2 | −94.88 (3) | H12—C12—C13—H13 | −1.23 |
C2—C1—C7—H7A | −58.35 | C12—C13—C14—C15 | 1.13 (4) |
C2—C1—C7—H7B | −178.53 | C12—C13—C14—H14 | −176.18 |
C2—C1—C7—H7C | 61.65 | H13—C13—C14—C15 | −173.74 |
H1—C1—C2—O1 | −155.71 | H13—C13—C14—H14 | 8.95 |
H1—C1—C2—N2 | 25.56 | C13—C14—C15—C10 | −0.08 (3) |
H1—C1—C7—H7A | −176.02 | C13—C14—C15—H15 | 177.20 |
H1—C1—C7—H7B | 63.80 | H14—C14—C15—C10 | 177.32 |
H1—C1—C7—H7C | −56.02 | H14—C14—C15—H15 | −5.40 |
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