| Literature DB >> 21888640 |
Abstract
BACKGROUND: Cytosine is a biologically important compound owing to its natural occurrence as a component of nucleic acids. Cytosine plays a crucial role in DNA/RNA base pairing, through several hydrogen-bonding patterns, and controls the essential features of life as it is involved in genetic codon of 17 amino acids. The molecular recognition among cytosines, and the molecular heterosynthons of molecular salts fabricated through proton-transfer reactions, might be used to investigate the theoretical sites of cytosine-specific DNA-binding proteins and the design for molecular imprint.Entities:
Year: 2011 PMID: 21888640 PMCID: PMC3182958 DOI: 10.1186/1752-153X-5-51
Source DB: PubMed Journal: Chem Cent J ISSN: 1752-153X Impact factor: 4.215
Figure 1The asymmetric unit of CytNit, showing the atom-labeling scheme and hydrogen bonding (double dashed lines). Displacements ellipsoids are drawn at 50% probability level and H atoms as small spheres of arbitrary size.
Figure 2The schematic diagram for CytNit, (I), and 5FcytNit, (II), respectively.
Selected bond lengths (Å) and angles (°) for CytNit and 5FcytNit
| a = nil | a = a | a = nil | |
|---|---|---|---|
| O2a--C8a | 1.217 (4) | 1.211 (4) | 1.221 (8) |
| O3a--C10a | 1.235 (4) | 1.225 (4) | 1.201 (8) |
| O4a--N4a | 1.211 (3) | 1.218 (4) | 1.208 (7) |
| O5a--N4a | 1.241 (4) | 1.220 (3) | 1.219 (7) |
| N4a--C7a | 1.418 (4) | 1.437 (4) | 1.430 (8) |
| C7a--C12a | 1.371 (4) | 1.361 (4) | 1.371 (8) |
| C7a--C8a | 1.452 (5) | 1.462 (4) | 1.448 (8) |
| C8a--N9a | 1.390 (4) | 1.387 (4) | 1.369 (8) |
| N9a--C10a | 1.364 (4) | 1.362 (4) | 1.371 (9) |
| C10a--N11a | 1.373 (4) | 1.383 (4) | 1.382 (9) |
| N11a--C12a | 1.324 (4) | 1.324 (4) | 1.314 (9) |
| C10a --N11a--C12a | 118.7 (3) | 121.7 (3) | 123.1 (5) |
| F1--C5 | 1.347 (7) | ||
| O1a--C2a | 1.232 (4) | 1.241 (4) | 1.252 (8) |
| N2a--C4a | 1.320 (4) | 1.317 (4) | 1.314 (9) |
| N1a--C6a | 1.356 (4) | 1.362 (4) | 1.362 (8) |
| N1a--C2a | 1.357 (4) | 1.375 (4) | 1.358 (8) |
| C2a--N3a | 1.367 (4) | 1.357 (4) | 1.340 (9) |
| N3a--C4a | 1.355 (4) | 1.350 (4) | 1.343 (8) |
| C4a--C5a | 1.417 (4) | 1.427 (5) | 1.421 (9) |
| C5a--C6a | 1.336 (5) | 1.328 (5) | 1.319 (9) |
| C2a --N3a--C4a | 122.5 (3) | 121.1 (3) | 120.6 (5) |
Hydrogen bonding geometry for CytNit and 5FcytNit
| H··· | ||||
|---|---|---|---|---|
| N1--H1···O3ai | 0.94 (5) | 1.88 (5) | 2.780 (4) | 161 (4) |
| N2--H2a···O1a | 0.95 (4) | 1.89 (4) | 2.830 (4) | 172 (3) |
| N2--H2b···O2a | 0.96 (3) | 1.92 (3) | 2.848 (3) | 164 (3) |
| N2--H2b···O4a | 0.96 (3) | 2.29 (3) | 2.829 (4) | 115 (3) |
| N3--H3+···N3a | 0.99 (5) | 1.85 (5) | 2.837 (3) | 175 (2) |
| N9--H9···O6w | 0.84 (3) | 1.96 (3) | 2.795 (4) | 175 (3) |
| N1a--H1a···O3ii | 0.95 (4) | 1.88 (5) | 2.790 (4) | 157 (4) |
| N2a--H21a···O1 | 0.93 (4) | 1.96 (4) | 2.876 (4) | 171 (3) |
| N2a--H21b···O2 | 0.89 (3) | 1.96 (3) | 2.830 (4) | 165 (3) |
| N2a--H21b···O4 | 0.89 (3) | 2.36 (3) | 2.869 (4) | 117 (2) |
| N9a--H9a···O7w | 1.00 (4) | 1.75 (4) | 2.744 (4) | 176 (4) |
| N11a--H11a···N11iii | 0.99 (3) | 1.70 (4) | 2.686 (3) | 176 (3) |
| O6w--H61···O1aiv | 0.84 (5) | 2.02 (5) | 2.858 (4) | 171 (5) |
| O6w--H62···O5aiv | 0.85 (5) | 2.43 (5) | 3.271 (4) | 170 (5) |
| O7w--H71···O1v | 0.86 (5) | 2.02 (5) | 2.878 (4) | 175 (5) |
| O7w--H72···O5v | 0.80 (5) | 2.41 (5) | 3.199 (4) | 168 (6) |
| N11--H11···N3 | 1.00 (6) | 1.80 (6) | 2.763 (7) | 162 (5) |
| N9--H9···O1vi | 0.88 (8) | 1.80 (8) | 2.670 (7) | 174 (7) |
| N2--H2a···O3 | 0.87 (8) | 2.27 (8) | 3.104 (7) | 161 (8) |
| N2--H2b···O7w | 0.71 (9) | 2.27 (9) | 2.964 (9) | 167 (10) |
| N1--H1···O2vii | 0.86 (7) | 2.03 (7) | 2.881 (7) | 171 (5) |
| O6w--H6a···O2 | 0.89 (2) | 1.93 (4) | 2.801 (7) | 167 (14) |
| O6w--H6b···O6wviii | 0.89 (2) | 1.92 (8) | 2.723 (5) | 151 (14) |
| O7w--H7a···O7wix | 0.89 (2) | 2.07 (4) | 2.935 (9) | 164 (12) |
| O7w--H7b···O6wx | 0.88 (2) | 2.33 (4) | 3.189 (12) | 166 (12) |
Symmetry code(s): (i) x, -y-1/2, z-1/2; (ii) x, -y+1/2, z+1/2; (iii) x, y, z+1; (iv) x, -y+1/2, z-1/2; (v) x, -y-1/2, z+1/2; (vi) x-1/2, -y+1/2, z-3/2; (vii) x+1/2, -y+1/2, z+3/2; (viii) x, -y, z+1/2; (ix) x, -y+1, z-1/2; (x) x-1/2, -y+1/2, z-1/2.
Figure 3Part of the crystal structure of CytNit, viewed perpendicular to the (100) plane. Displacements ellipsoids are drawn at 50% probability level and H atoms as small spheres of arbitrary size. Hydrogen bonds are indicated by double dashed lines.
Figure 4The asymmetric unit of 5FcytNit, showing the atom-labeling scheme and hydrogen bonding (double dashed lines). Displacements ellipsoids are drawn at 50% probability level and H atoms as small spheres of arbitrary size.
Figure 5Part of the crystal structure of 5FcytNit, viewed perpendicular to the (001) plane. Displacements ellipsoids are drawn at 50% probability level and H atoms as small spheres of arbitrary size. Hydrogen bonds are indicated by double dashed lines.
Experimental details for CytNit and 5FcytNit
| Chemical formula | C4H5N3O·C4H3N3O4· | C4H4FN3O· C4H3N3O4· |
| 572.44 | 322.23 | |
| Crystal system | Orthorhombic | Monoclinic |
| Space group | ||
| 12.7424 (9) | 10.2066 (6) | |
| 17.4112 (7) | 28.2758 (11) | |
| 21.0833 (10) | 4.7187 (3) | |
| 90 | 90 | |
| 90 | 111.293 (6) | |
| 90 | 90 | |
| 4677.6 (4) | 1268.85 (12) | |
| 8 | 4 | |
| 0.71069 | 0.71069 | |
| 298 (2) | 298(2) | |
| 0.14 | 0.16 | |
| Crystal size (mm) | 0.15 × 0.12 × 0.12 | 0.15 × 0.12 × 0.03 |
| No. of measured | 13436 | 39739 |
| independent | 4177 | 1246 |
| observed [ | 2589 | 1230 |
| 0.041 | 0.050 | |
| 0.080 | 0.067 | |
| 0.139 | 0.154 | |
| 1.16 | 1.47 | |
| No. of parameters | 416 | 229 |
| 0.24, -0.19 | 0.25, -0.28 |