research communications
Redetermination of cytosinium hydrogen maleate–cytosine (1/1) from the original data
aInst. of Physics of the Czech Academy of Sciences, Na Slovance 2, 182 21 Praha 8, Czech Republic
*Correspondence e-mail: fabry@fzu.cz
The title salt, C4H6N3O+·C4H3O4−·C4H5N3O, has been redetermined from the data published by Benali-Cherif, Falek & Direm [Acta Cryst. (2009), E65, o3058–o3059]. The improvement of the present redetermination consists in the discovery of the splitting of one of the H atoms into two disordered positions, the occupancies of which are equal to 0.55 (2) and 0.45 (2). These H atoms are involved in an N⋯N hydrogen bond and are shifted towards its centre. The disorder of these H atoms is in agreement with a similar environment of the two independent, but chemically equivalent, cytosinium/cytosine molecules.
Keywords: crystal structure; redetermination; hydrogen bonding; refinement constraints; refinement restraints; Cambridge Structural Database.
CCDC reference: 1459296
1. Chemical context
Structures which contain hydroxyl, secondary and primary amine groups are often determined incorrectly because of an assumed geometry of these groups and the subsequent applied constraints or restraints. In such cases, the correct geometry is missed as it is not verified by inspection of the difference electron-density maps. Thus a considerable number of structures could have been determined more correctly – cf. Figs. 1 and 2 in Fábry et al. (2014). The inclusion of such structures causes bias in the crystallographic databases.
In the course of recalculation of suspect structures which were retrieved from the Cambridge Crystallographic Database (Groom & Allen, 2014), a defect in the of 2-amino-4,6-dimethoxypyrimidine–4-aminobenzoic acid (1/1) by Benali-Cherif et al. (2009) has been found; the CSD refcode is DUJCAN. The aim of the present article is to demonstrate how the original can be improved.
2. Structural commentary
The structure of the title compound has been described by Benali-Cherif et al. (2009). In that article, the hydrogen atom H3b was attached to atom N3b and refined with a distance constraint of N3b—H3b = 0.86 Å with Uiso(H3b) = 1.2Ueq(N3b). This hydrogen is involved in the hydrogen bond N3b—H3b⋯N3a (Fig. 1).
However, inspection of the difference b is disordered over two positions (Fig. 2), between atoms N3a and N3b. Thus, atom H3b was split into two atoms, labelled as H1n3b and H1n3a, with respective occupancies 0.52 (2) and 0.48 (2). These hydrogen atoms remain involved in the N3a⋯N3b hydrogen bond (Table 1), as shown in Fig. 3.
of the recalculated structure has shown that hydrogen atom H3The observed disorder of the secondary amine hydrogen atoms is probably due to the chemical equality of two symmetry-independent cytosinium/cytosine molecules and their quite similar environments. Otherwise, the description of the hydrogen-bond pattern by Benali-Cherif et al. (2009) remains intact because locally one of the nitrogen atoms, N3a or N3b, acts as a donor while the other acts as an acceptor of the hydrogen bond.
The hydrogen atom H3, which was situated about the centre of the hydrogen bond O3—H3⋯O1 has also been checked (Fig. 4). It turns out that the build-up of the electron density is not split into two positions and the original position determined by Benali-Cherif et al. (2009) is correct.
In a broader sense, the present redetermination emphasizes how important it is to carefully examine the difference electron-density maps during structure determinations.
3. Supramolecular features
The graph set analysis (Etter et al., 1990) of the title compound has been described by Benali-Cherif et al. (2009).
4. Database survey
The et al. (2009) has been included in the Cambridge Crystallographic Database (Groom & Allen, 2014) under the refcode DUJCAN.
file of the article by Benali-Cherif5. Synthesis and crystallization
The preparation of the title compound has been described by Benali-Cherif et al. (2009).
6. Refinement
Crystal data, data collection and structure . All the hydrogen atoms were discernible in the difference electron density maps. The aryl hydrogen atoms were refined as constrained with Caryl—Haryl = 0.93 Å and Uiso(Haryl) = 1.2Ueq(Caryl). The displacement parameter of the hydroxyl hydrogen atom H3 was constrained by Uiso(H3) = 1.5Ueq(O3). The hydrogen atoms of the primary and secondary amine groups were constrained by Uiso(Hamine) = 1.2Ueq(Namine). In addition, the distances of the disordered amine hydrogen atoms, H1n36 and H1n3b, were refined with the distance restraint N—H = 0.87 (1) Å, and their occupational parameters constrained to fulfill the condition that their sum = 1 [viz. 0.55 (2) (H1n3b) and 0.45 (2) (H1n3a)].
details are summarized in Table 2
|
Nine reflections [5 1 0; −9 1 1;-1 1 1; −8 2 1; 4 2 1; −2 0 2; 0 0 2;-3 1 2; −20 0 8; 22 2 8] for which ||Fo| − |Fc|| >10σ(F) were omitted from the final cycles of refinement.
Supporting information
CCDC reference: 1459296
https://doi.org/10.1107/S2056989016003923/su5280sup1.cif
contains datablocks global, I. DOI:Structure factors: contains datablock I. DOI: https://doi.org/10.1107/S2056989016003923/su5280Isup2.hkl
Supporting information file. DOI: https://doi.org/10.1107/S2056989016003923/su5280Isup3.smi
Data collection: KappaCCD Server Software (Nonius, 1998); cell
DENZO and SCALEPACK (Otwinowski & Minor, 1997); data reduction: DENZO and SCALEPACK (Otwinowski & Minor, 1997); program(s) used to solve structure: SIR2004 (Burla et al., 2005); program(s) used to refine structure: JANA2006 (Petříček et al., 2014); molecular graphics: PLATON (Spek, 2009) and JANA2006 (Petříček et al., 2014); software used to prepare material for publication: JANA2006 (Petříček et al., 2014).C4H6N3O+·C4H3O4−·C4H5N3O | F(000) = 1408 |
Mr = 338.29 | Dx = 1.526 Mg m−3 |
Monoclinic, C2/c | Mo Kα radiation, λ = 0.71073 Å |
Hall symbol: -C 2yc | Cell parameters from 3490 reflections |
a = 27.3226 (5) Å | θ = 2.8–28.0° |
b = 7.3618 (2) Å | µ = 0.13 mm−1 |
c = 14.6742 (4) Å | T = 298 K |
β = 93.905 (1)° | Prism, colourless |
V = 2944.77 (13) Å3 | 0.3 × 0.15 × 0.1 mm |
Z = 8 |
Nonius KappaCCD diffractometer | 2367 reflections with I > 3σ(I) |
Radiation source: fine-focus sealed tube | Rint = 0.043 |
Graphite monochromator | θmax = 28.0°, θmin = 2.8° |
ω–θ scans | h = 0→35 |
3490 measured reflections | k = 0→9 |
3474 independent reflections | l = −19→19 |
Refinement on F2 | H atoms treated by a mixture of independent and constrained refinement |
R[F > 3σ(F)] = 0.038 | Weighting scheme based on measured s.u.'s w = 1/(σ2(I) + 0.0004I2) |
wR(F) = 0.093 | (Δ/σ)max = 0.022 |
S = 1.85 | Δρmax = 0.20 e Å−3 |
3474 reflections | Δρmin = −0.20 e Å−3 |
246 parameters | Extinction correction: B–C type 1 Lorentzian isotropic (Becker & Coppens, 1974) |
2 restraints | Extinction coefficient: 21000 (5000) |
33 constraints |
Refinement. This part differs from the original article by Benali-Cherif et al. (2009). In the refinement, F2 > 3σ(F2) has been used as a criterion for observed diffractions. The diffractions for which ||Fo|-|Fc||>10σ(F) were discarded from the refinement. This refers to the diffractions 5 1 0; -9 1 1; -1 1 1; -8 2 1; 4 2 1; -2 0 2; 0 0 2; -3 1 2; -20 0 8; 22 2 8. |
x | y | z | Uiso*/Ueq | Occ. (<1) | |
O7b | 0.33926 (3) | 1.06385 (11) | 0.29287 (6) | 0.0445 (3) | |
N1b | 0.40065 (3) | 0.90018 (14) | 0.23744 (7) | 0.0400 (3) | |
H1b | 0.4157 (5) | 1.011 (2) | 0.2197 (9) | 0.048* | |
N3b | 0.33591 (3) | 0.75686 (12) | 0.30318 (7) | 0.0368 (3) | |
N8b | 0.33297 (5) | 0.44786 (15) | 0.31476 (9) | 0.0506 (4) | |
H8b1 | 0.3454 (5) | 0.338 (2) | 0.3026 (9) | 0.0607* | |
H8b2 | 0.3002 (6) | 0.458 (2) | 0.3394 (9) | 0.0607* | |
C2b | 0.35770 (4) | 0.91429 (16) | 0.27860 (8) | 0.0352 (4) | |
C4b | 0.35664 (4) | 0.59317 (16) | 0.28928 (8) | 0.0386 (4) | |
C5b | 0.40187 (4) | 0.58331 (18) | 0.24835 (9) | 0.0443 (4) | |
H5b | 0.416945 | 0.472174 | 0.23913 | 0.0531* | |
C6b | 0.42233 (5) | 0.73892 (18) | 0.22326 (9) | 0.0443 (4) | |
H6b | 0.451959 | 0.735942 | 0.195619 | 0.0531* | |
O7a | 0.23772 (3) | 0.47438 (12) | 0.38018 (7) | 0.0481 (3) | |
N1a | 0.17576 (3) | 0.63613 (15) | 0.43512 (7) | 0.0413 (3) | |
H1a | 0.1595 (4) | 0.528 (2) | 0.4518 (9) | 0.0496* | |
N3a | 0.24303 (3) | 0.78185 (13) | 0.37815 (7) | 0.0375 (3) | |
N8a | 0.24808 (5) | 1.09110 (16) | 0.37611 (9) | 0.0522 (4) | |
H8a1 | 0.2767 (6) | 1.0812 (19) | 0.3501 (10) | 0.0627* | |
H8a2 | 0.2363 (5) | 1.200 (2) | 0.3886 (10) | 0.0627* | |
C2a | 0.21958 (4) | 0.62341 (16) | 0.39695 (8) | 0.0364 (4) | |
C4a | 0.22340 (4) | 0.94481 (16) | 0.39665 (8) | 0.0388 (4) | |
C5a | 0.17788 (4) | 0.95478 (18) | 0.43679 (9) | 0.0439 (4) | |
H5a | 0.164021 | 1.066081 | 0.450387 | 0.0527* | |
C6a | 0.15539 (5) | 0.79794 (18) | 0.45457 (9) | 0.0447 (4) | |
H6a | 0.125322 | 0.800462 | 0.480683 | 0.0536* | |
O1 | 0.00024 (3) | 0.51326 (12) | 0.62974 (6) | 0.0463 (3) | |
O2 | −0.05067 (3) | 0.30108 (13) | 0.67262 (7) | 0.0560 (3) | |
O3 | 0.07413 (3) | 0.53082 (11) | 0.54869 (6) | 0.0433 (3) | |
H3 | 0.0368 (5) | 0.535 (2) | 0.5874 (9) | 0.0649* | |
O4 | 0.12217 (3) | 0.33900 (14) | 0.48088 (7) | 0.0555 (3) | |
C1 | 0.08603 (4) | 0.37076 (18) | 0.52453 (8) | 0.0394 (4) | |
C2 | 0.05595 (5) | 0.21144 (19) | 0.54864 (10) | 0.0512 (5) | |
H1 | 0.067397 | 0.100138 | 0.528962 | 0.0614* | |
C3 | 0.01546 (5) | 0.20204 (19) | 0.59362 (10) | 0.0523 (5) | |
H2 | 0.003281 | 0.085236 | 0.600501 | 0.0628* | |
C4 | −0.01355 (4) | 0.34770 (18) | 0.63476 (8) | 0.0415 (4) | |
H1n3b | 0.3079 (5) | 0.763 (3) | 0.3267 (14) | 0.0442* | 0.554 (16) |
H1n3a | 0.2718 (6) | 0.783 (4) | 0.3556 (18) | 0.045* | 0.446 (16) |
U11 | U22 | U33 | U12 | U13 | U23 | |
O7b | 0.0462 (5) | 0.0256 (5) | 0.0628 (6) | 0.0015 (3) | 0.0110 (4) | −0.0015 (4) |
N1b | 0.0413 (6) | 0.0342 (6) | 0.0454 (6) | −0.0014 (4) | 0.0100 (5) | −0.0016 (5) |
N3b | 0.0375 (5) | 0.0249 (6) | 0.0486 (6) | 0.0009 (4) | 0.0073 (4) | −0.0018 (4) |
N8b | 0.0551 (7) | 0.0278 (6) | 0.0705 (8) | 0.0025 (5) | 0.0171 (6) | 0.0000 (5) |
C2b | 0.0374 (6) | 0.0291 (7) | 0.0388 (7) | 0.0009 (5) | 0.0007 (5) | −0.0022 (5) |
C4b | 0.0450 (6) | 0.0285 (7) | 0.0420 (7) | 0.0019 (5) | 0.0002 (5) | −0.0021 (5) |
C5b | 0.0452 (7) | 0.0368 (8) | 0.0516 (8) | 0.0105 (5) | 0.0093 (6) | −0.0029 (6) |
C6b | 0.0425 (6) | 0.0435 (8) | 0.0476 (8) | 0.0062 (5) | 0.0093 (6) | −0.0040 (6) |
O7a | 0.0468 (5) | 0.0246 (5) | 0.0740 (6) | 0.0004 (4) | 0.0134 (4) | −0.0008 (4) |
N1a | 0.0382 (5) | 0.0335 (6) | 0.0532 (6) | −0.0044 (4) | 0.0100 (5) | −0.0018 (5) |
N3a | 0.0354 (5) | 0.0246 (5) | 0.0531 (6) | 0.0008 (4) | 0.0079 (4) | −0.0001 (4) |
N8a | 0.0515 (6) | 0.0263 (6) | 0.0806 (9) | 0.0013 (5) | 0.0171 (6) | 0.0004 (6) |
C2a | 0.0374 (6) | 0.0269 (7) | 0.0448 (7) | 0.0008 (5) | 0.0024 (5) | 0.0000 (5) |
C4a | 0.0400 (6) | 0.0296 (7) | 0.0467 (7) | 0.0024 (5) | 0.0009 (5) | −0.0017 (5) |
C5a | 0.0421 (7) | 0.0341 (7) | 0.0560 (8) | 0.0085 (5) | 0.0059 (6) | −0.0059 (6) |
C6a | 0.0375 (6) | 0.0457 (8) | 0.0514 (8) | 0.0032 (5) | 0.0073 (6) | −0.0065 (6) |
O1 | 0.0411 (5) | 0.0411 (6) | 0.0582 (6) | −0.0016 (4) | 0.0155 (4) | −0.0041 (4) |
O2 | 0.0471 (5) | 0.0532 (6) | 0.0703 (7) | −0.0059 (4) | 0.0234 (5) | 0.0033 (5) |
O3 | 0.0426 (5) | 0.0365 (5) | 0.0521 (5) | −0.0035 (4) | 0.0137 (4) | −0.0025 (4) |
O4 | 0.0547 (5) | 0.0476 (6) | 0.0677 (6) | −0.0001 (4) | 0.0288 (5) | −0.0052 (5) |
C1 | 0.0402 (6) | 0.0388 (7) | 0.0398 (7) | 0.0003 (5) | 0.0070 (5) | −0.0002 (6) |
C2 | 0.0545 (8) | 0.0338 (8) | 0.0675 (9) | 0.0020 (6) | 0.0202 (7) | −0.0028 (6) |
C3 | 0.0544 (8) | 0.0332 (8) | 0.0714 (10) | −0.0045 (6) | 0.0185 (7) | 0.0033 (7) |
C4 | 0.0383 (6) | 0.0417 (8) | 0.0449 (7) | −0.0028 (5) | 0.0059 (5) | 0.0025 (6) |
O7b—C2b | 1.2345 (14) | N3a—H1n3a | 0.873 (18) |
N1b—H1b | 0.956 (15) | N8a—H8a1 | 0.897 (16) |
N1b—C2b | 1.3600 (15) | N8a—H8a2 | 0.885 (17) |
N1b—C6b | 1.3492 (17) | N8a—C4a | 1.3165 (17) |
N3b—C2b | 1.3627 (15) | H8a1—H8a2 | 1.54 (2) |
N3b—C4b | 1.3528 (15) | C4a—C5a | 1.4137 (17) |
N3b—H1n3b | 0.861 (16) | C5a—H5a | 0.93 |
N8b—H8b1 | 0.900 (17) | C5a—C6a | 1.3420 (19) |
N8b—H8b2 | 0.992 (15) | C6a—H6a | 0.93 |
N8b—C4b | 1.3174 (17) | O1—H3 | 1.223 (14) |
H8b1—H8b2 | 1.64 (2) | O1—C4 | 1.2793 (16) |
C4b—C5b | 1.4123 (17) | O2—C4 | 1.2376 (15) |
C5b—H5b | 0.93 | O3—H3 | 1.201 (14) |
C5b—C6b | 1.3373 (18) | O3—C1 | 1.2789 (15) |
C6b—H6b | 0.93 | O4—C1 | 1.2354 (15) |
O7a—C2a | 1.2356 (14) | C1—C2 | 1.4886 (19) |
N1a—H1a | 0.952 (14) | C2—H1 | 0.93 |
N1a—C2a | 1.3591 (15) | C2—C3 | 1.328 (2) |
N1a—C6a | 1.3535 (17) | C3—H2 | 0.93 |
N3a—C2a | 1.3679 (15) | C3—C4 | 1.4859 (19) |
N3a—C4a | 1.3493 (15) | H1n3b—H1n3a | 1.11 (2) |
H1b—N1b—C2b | 117.2 (8) | H8a2—N8a—C4a | 119.4 (10) |
H1b—N1b—C6b | 120.3 (8) | O7a—C2a—N1a | 121.32 (11) |
C2b—N1b—C6b | 122.48 (11) | O7a—C2a—N3a | 121.14 (10) |
C2b—N3b—C4b | 121.52 (10) | N1a—C2a—N3a | 117.53 (10) |
C2b—N3b—H1n3b | 118.7 (15) | N3a—C4a—N8a | 117.68 (11) |
C4b—N3b—H1n3b | 119.8 (15) | N3a—C4a—C5a | 120.20 (11) |
H8b1—N8b—H8b2 | 120.1 (13) | N8a—C4a—C5a | 122.12 (12) |
H8b1—N8b—C4b | 118.2 (9) | C4a—C5a—H5a | 121.18 |
H8b2—N8b—C4b | 121.2 (9) | C4a—C5a—C6a | 117.64 (12) |
O7b—C2b—N1b | 121.19 (11) | H5a—C5a—C6a | 121.18 |
O7b—C2b—N3b | 121.54 (10) | N1a—C6a—C5a | 121.06 (12) |
N1b—C2b—N3b | 117.28 (10) | N1a—C6a—H6a | 119.47 |
N3b—C4b—N8b | 117.51 (11) | C5a—C6a—H6a | 119.47 |
N3b—C4b—C5b | 119.83 (11) | H3—O1—C4 | 114.1 (8) |
N8b—C4b—C5b | 122.67 (11) | H3—O3—C1 | 113.3 (8) |
C4b—C5b—H5b | 121.07 | O1—H3—O3 | 170.6 (15) |
C4b—C5b—C6b | 117.86 (12) | O3—C1—O4 | 123.05 (12) |
H5b—C5b—C6b | 121.07 | O3—C1—C2 | 120.35 (11) |
N1b—C6b—C5b | 121.00 (12) | O4—C1—C2 | 116.60 (12) |
N1b—C6b—H6b | 119.5 | C1—C2—H1 | 114.68 |
C5b—C6b—H6b | 119.5 | C1—C2—C3 | 130.64 (13) |
H1a—N1a—C2a | 119.2 (8) | H1—C2—C3 | 114.68 |
H1a—N1a—C6a | 118.4 (8) | C2—C3—H2 | 114.74 |
C2a—N1a—C6a | 122.28 (11) | C2—C3—C4 | 130.53 (13) |
C2a—N3a—C4a | 121.30 (10) | H2—C3—C4 | 114.74 |
C2a—N3a—H1n3a | 121.9 (18) | O1—C4—O2 | 122.93 (12) |
C4a—N3a—H1n3a | 116.8 (18) | O1—C4—C3 | 119.78 (11) |
H8a1—N8a—H8a2 | 120.2 (14) | O2—C4—C3 | 117.28 (12) |
H8a1—N8a—C4a | 120.4 (9) |
D—H···A | D—H | H···A | D···A | D—H···A |
N1b—H1b···O2i | 0.956 (15) | 1.824 (15) | 2.7718 (14) | 170.8 (13) |
N8b—H8b1···O7bii | 0.900 (17) | 2.030 (18) | 2.8517 (14) | 151.2 (13) |
N8b—H8b2···O7a | 0.992 (15) | 1.850 (15) | 2.8411 (15) | 177.4 (12) |
C5b—H5b···O2iii | 0.93 | 2.43 | 3.3347 (16) | 164.60 |
N1a—H1a···O4 | 0.952 (14) | 1.793 (14) | 2.7411 (14) | 173.2 (12) |
N8a—H8a1···O7b | 0.897 (16) | 1.959 (16) | 2.8555 (15) | 179.0 (13) |
N8a—H8a2···O7aiv | 0.885 (17) | 2.028 (18) | 2.8368 (15) | 151.5 (14) |
C5a—H5a···O4iv | 0.93 | 2.37 | 3.2970 (16) | 175.15 |
O1—H3···O3 | 1.223 (14) | 1.201 (14) | 2.4155 (12) | 170.6 (15) |
O1—H3···C1 | 1.223 (14) | 2.071 (15) | 3.0775 (15) | 136.7 (11) |
O3—H3···O1 | 1.201 (14) | 1.223 (14) | 2.4155 (12) | 170.6 (15) |
O3—H3···C4 | 1.201 (14) | 2.100 (15) | 3.0927 (15) | 137.4 (12) |
N3b—H1n3b···N3a | 0.861 (16) | 1.979 (16) | 2.8398 (14) | 178 (2) |
N3a—H1n3a···N3b | 0.873 (18) | 1.970 (18) | 2.8398 (14) | 174 (3) |
Symmetry codes: (i) x+1/2, −y+3/2, z−1/2; (ii) x, y−1, z; (iii) x+1/2, −y+1/2, z−1/2; (iv) x, y+1, z. |
Acknowledgements
The author is grateful for the support of the Ministry of Education of the Czech Republic under Project NPU I-LO1603.
References
Becker, P. J. & Coppens, P. (1974). Acta Cryst. A30, 129–147. CrossRef IUCr Journals Web of Science Google Scholar
Benali-Cherif, N., Falek, W. & Direm, A. (2009). Acta Cryst. E65, o3058–o3059. Web of Science CSD CrossRef CAS IUCr Journals Google Scholar
Burla, M. C., Caliandro, R., Camalli, M., Carrozzini, B., Cascarano, G. L., De Caro, L., Giacovazzo, C., Polidori, G. & Spagna, R. (2005). J. Appl. Cryst. 38, 381–388. Web of Science CrossRef CAS IUCr Journals Google Scholar
Etter, M. C., MacDonald, J. C. & Bernstein, J. (1990). Acta Cryst. B46, 256–262. CrossRef CAS Web of Science IUCr Journals Google Scholar
Fábry, J., Dušek, M., Vaněk, P., Rafalovskyi, I., Hlinka, J. & Urban, J. (2014). Acta Cryst. C70, 1153–1160. Web of Science CSD CrossRef IUCr Journals Google Scholar
Groom, C. R. & Allen, F. H. (2014). Angew. Chem. Int. Ed. 53, 662–671. Web of Science CSD CrossRef CAS Google Scholar
Nonius (1998). KappaCCD Server Software. Nonius BV, Delft, The Netherlands. Google Scholar
Otwinowski, Z. & Minor, W. (1997). Methods in Enzymology, Vol. 276, Macromolecular Crystallography, Part A, edited by C. W. Carter Jr & R. M. Sweet, pp. 307–326. New York: Academic Press. Google Scholar
Petříček, V., Dušek, M. & Palatinus, L. (2014). Z. Kristallogr. 229, 345–352. Google Scholar
Spek, A. L. (2009). Acta Cryst. D65, 148–155. Web of Science CrossRef CAS IUCr Journals Google Scholar
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