Fluorine substitutions on the furanose ring of nucleosides are known to strongly influence the conformational properties of oligonucleotides. In order to assess the effect of fluorine on the conformation of 3′-deoxy-3′-fluoro-5-methyluridine (
RT
F), C
10H
13FN
2O
5, we studied its stereochemistry in the crystalline state using X-ray crystallography. The compound crystallizes in the chiral orthorhombic space group
P2
12
12
1 and contains two symmetry-independent molecules (
A and
B) in the asymmetric unit. The furanose ring in molecules
A and
B adopts conformations between envelope (
2E, 2′-
endo,
P = 162°) and twisted (
2T
3, 2′-
endo and 3′
exo,
P = 180°), with pseudorotation phase angles (
P) of 164.3 and 170.2°, respectively. The maximum puckering amplitudes, ν
max, for molecules
A and
B are 38.8 and 36.1°, respectively. In contrast, for 5-methyluridine (
RT
OH), the value of
P is 21.2°, which is between the
3E (3′-
endo,
P = 18.0°) and
3T
4 (3′-
endo and 4′-
exo,
P = 36°) conformations. The value of ν
max for
RT
OH is 41.29°. Molecules
A and
B of
RT
F generate respective helical assemblies across the crystallographic 2
1-screw axis through classical N—H
O aand O—H
O hydrogen bonds supplemented by C—H
O contacts. Adjacent parallel helices of both molecules are linked to each other
via O—H
O and O
π interactions.
Supporting information
CCDC reference: 1988181
Data collection: APEX2 (Bruker, 2006); cell refinement: SAINT (Bruker, 2006); data reduction: SAINT (Bruker, 2006); program(s) used to solve structure: SHELXS97 (Sheldrick, 2008); program(s) used to refine structure: SHELXL2013 (Sheldrick, 2015); molecular graphics: ORTEP-3 (Farrugia, 2012) and Mercury (Macrae et al.,
2020); software used to prepare material for publication: SHELXTL (Bruker, 2006), PLATON (Spek, 2020) and publCIF
(Westrip, 2010).
3'-Fluoro-3'-deoxy-5-methyluridine
top
Crystal data top
C10H13FN2O5 | Dx = 1.520 Mg m−3 |
Mr = 260.22 | Mo Kα radiation, λ = 0.71073 Å |
Orthorhombic, P212121 | Cell parameters from 9902 reflections |
a = 7.0301 (3) Å | θ = 2.5–30.9° |
b = 17.1705 (8) Å | µ = 0.13 mm−1 |
c = 18.8369 (9) Å | T = 296 K |
V = 2273.81 (18) Å3 | Plate, colourless |
Z = 8 | 0.40 × 0.30 × 0.22 mm |
F(000) = 1088 | |
Data collection top
Bruker APEXII CCD diffractometer | 4002 independent reflections |
Radiation source: Fine focus sealed tube | 3837 reflections with I > 2σ(I) |
Graphite monochromator | Rint = 0.030 |
φ and ω scans | θmax = 25.0°, θmin = 1.6° |
Absorption correction: multi-scan (SADABS; Bruker, 2006) | h = −7→8 |
Tmin = 0.949, Tmax = 0.972 | k = −20→20 |
31022 measured reflections | l = −22→22 |
Refinement top
Refinement on F2 | Hydrogen site location: mixed |
Least-squares matrix: full | H atoms treated by a mixture of independent and constrained refinement |
R[F2 > 2σ(F2)] = 0.029 | w = 1/[σ2(Fo2) + (0.0307P)2 + 0.4954P] where P = (Fo2 + 2Fc2)/3 |
wR(F2) = 0.067 | (Δ/σ)max = 0.001 |
S = 1.10 | Δρmax = 0.13 e Å−3 |
4002 reflections | Δρmin = −0.14 e Å−3 |
351 parameters | Absolute structure: Flack x determined using 1541 quotients [(I+)-(I-)]/[(I+)+(I-)]
(Parsons et al., 2013) |
0 restraints | Absolute structure parameter: 0.0 (2) |
Special details top
Geometry. All esds (except the esd in the dihedral angle between two l.s. planes)
are estimated using the full covariance matrix. The cell esds are taken
into account individually in the estimation of esds in distances, angles
and torsion angles; correlations between esds in cell parameters are only
used when they are defined by crystal symmetry. An approximate (isotropic)
treatment of cell esds is used for estimating esds involving l.s. planes. |
Fractional atomic coordinates and isotropic or equivalent isotropic displacement parameters (Å2) top | x | y | z | Uiso*/Ueq | |
F3' | −0.0060 (2) | 0.65373 (10) | 0.70579 (7) | 0.0464 (4) | |
F3'' | 0.2654 (2) | 0.32166 (9) | 1.06606 (7) | 0.0422 (4) | |
O2A | −0.0021 (3) | 0.54059 (10) | 0.95157 (9) | 0.0391 (4) | |
O4A | 0.4226 (3) | 0.63184 (11) | 1.11204 (8) | 0.0374 (4) | |
O2' | −0.0442 (3) | 0.71961 (13) | 0.83490 (10) | 0.0401 (5) | |
O4' | 0.3141 (3) | 0.58196 (9) | 0.79074 (8) | 0.0346 (4) | |
O5' | 0.5620 (3) | 0.71432 (13) | 0.77067 (12) | 0.0520 (6) | |
O2'' | 0.3545 (3) | 0.24214 (10) | 0.94469 (9) | 0.0363 (4) | |
O4'' | 0.4260 (3) | 0.44496 (9) | 0.96731 (8) | 0.0336 (4) | |
O5'' | 0.8193 (3) | 0.40864 (11) | 1.00190 (11) | 0.0455 (5) | |
O2B | 0.1154 (3) | 0.34758 (13) | 0.81722 (10) | 0.0484 (5) | |
O4B | 0.5120 (3) | 0.44644 (13) | 0.65023 (9) | 0.0514 (5) | |
N1A | 0.2535 (3) | 0.60931 (11) | 0.91032 (9) | 0.0260 (4) | |
N3A | 0.2127 (3) | 0.58861 (11) | 1.03050 (10) | 0.0273 (4) | |
N1B | 0.4065 (3) | 0.39216 (11) | 0.85359 (9) | 0.0286 (4) | |
N3B | 0.3184 (3) | 0.39792 (12) | 0.73551 (11) | 0.0333 (5) | |
C1' | 0.1779 (4) | 0.61286 (13) | 0.83765 (11) | 0.0273 (5) | |
H1' | 0.0609 | 0.5820 | 0.8348 | 0.033* | |
C2' | 0.1380 (3) | 0.69566 (14) | 0.81246 (12) | 0.0270 (5) | |
H2'1 | 0.2348 | 0.7312 | 0.8311 | 0.032* | |
C3' | 0.1608 (4) | 0.68712 (15) | 0.73269 (12) | 0.0314 (5) | |
H3' | 0.1914 | 0.7367 | 0.7096 | 0.038* | |
C4' | 0.3208 (4) | 0.62813 (15) | 0.72601 (12) | 0.0348 (6) | |
H4' | 0.2923 | 0.5938 | 0.6858 | 0.042* | |
C5' | 0.5168 (4) | 0.66062 (19) | 0.71579 (15) | 0.0471 (7) | |
H5'1 | 0.6087 | 0.6185 | 0.7159 | 0.057* | |
H5'2 | 0.5241 | 0.6866 | 0.6702 | 0.057* | |
C1'' | 0.3606 (4) | 0.37925 (13) | 0.92824 (11) | 0.0283 (5) | |
H1'' | 0.2224 | 0.3747 | 0.9336 | 0.034* | |
C2'' | 0.4553 (3) | 0.30963 (13) | 0.96250 (12) | 0.0264 (5) | |
H2'2 | 0.5871 | 0.3053 | 0.9461 | 0.032* | |
C3'' | 0.4514 (3) | 0.33313 (14) | 1.03996 (12) | 0.0281 (5) | |
H3'' | 0.5469 | 0.3053 | 1.0681 | 0.034* | |
C4'' | 0.4890 (4) | 0.41983 (14) | 1.03721 (12) | 0.0300 (5) | |
H4'' | 0.4081 | 0.4451 | 1.0728 | 0.036* | |
C5'' | 0.6911 (4) | 0.44507 (15) | 1.04993 (14) | 0.0400 (6) | |
H5'3 | 0.7000 | 0.5011 | 1.0446 | 0.048* | |
H5'4 | 0.7272 | 0.4321 | 1.0982 | 0.048* | |
C2A | 0.1451 (3) | 0.57611 (12) | 0.96287 (12) | 0.0262 (5) | |
C4A | 0.3810 (3) | 0.62377 (13) | 1.04851 (11) | 0.0269 (5) | |
C5A | 0.4990 (4) | 0.64899 (13) | 0.99056 (12) | 0.0270 (5) | |
C6A | 0.4285 (3) | 0.64152 (13) | 0.92457 (12) | 0.0261 (5) | |
H6A | 0.5017 | 0.6590 | 0.8867 | 0.031* | |
C7A | 0.6878 (4) | 0.68522 (17) | 1.00607 (14) | 0.0397 (6) | |
H7A1 | 0.6690 | 0.7355 | 1.0272 | 0.060* | |
H7A2 | 0.7582 | 0.6908 | 0.9627 | 0.060* | |
H7A3 | 0.7574 | 0.6526 | 1.0383 | 0.060* | |
C2B | 0.2677 (4) | 0.37686 (14) | 0.80336 (12) | 0.0324 (6) | |
C4B | 0.4890 (4) | 0.42850 (14) | 0.71324 (12) | 0.0342 (6) | |
C5B | 0.6317 (4) | 0.43750 (14) | 0.76744 (12) | 0.0306 (5) | |
C6B | 0.5841 (4) | 0.41923 (14) | 0.83428 (12) | 0.0302 (5) | |
H6B | 0.6756 | 0.4251 | 0.8695 | 0.036* | |
C7B | 0.8240 (4) | 0.46819 (19) | 0.74696 (14) | 0.0449 (7) | |
H7B1 | 0.9086 | 0.4645 | 0.7868 | 0.067* | |
H7B2 | 0.8128 | 0.5217 | 0.7327 | 0.067* | |
H7B3 | 0.8737 | 0.4380 | 0.7083 | 0.067* | |
H2' | −0.032 (6) | 0.766 (3) | 0.846 (2) | 0.086 (15)* | |
H5' | 0.683 (6) | 0.718 (2) | 0.7765 (19) | 0.072 (12)* | |
H5" | 0.886 (6) | 0.447 (2) | 0.9857 (19) | 0.072 (11)* | |
H2" | 0.394 (5) | 0.2046 (18) | 0.9643 (17) | 0.051 (10)* | |
H3A | 0.145 (4) | 0.5732 (15) | 1.0667 (14) | 0.033 (7)* | |
H3B | 0.238 (4) | 0.3889 (16) | 0.7024 (15) | 0.037 (7)* | |
Atomic displacement parameters (Å2) top | U11 | U22 | U33 | U12 | U13 | U23 |
F3' | 0.0397 (9) | 0.0693 (11) | 0.0304 (8) | −0.0070 (8) | −0.0089 (7) | −0.0016 (7) |
F3'' | 0.0366 (8) | 0.0567 (9) | 0.0334 (8) | −0.0118 (8) | 0.0116 (7) | −0.0027 (7) |
O2A | 0.0385 (10) | 0.0487 (11) | 0.0303 (9) | −0.0193 (9) | −0.0006 (8) | 0.0059 (7) |
O4A | 0.0423 (11) | 0.0502 (11) | 0.0197 (8) | −0.0066 (9) | −0.0031 (7) | −0.0024 (7) |
O2' | 0.0327 (11) | 0.0468 (12) | 0.0408 (10) | 0.0055 (9) | 0.0057 (8) | −0.0037 (9) |
O4' | 0.0489 (11) | 0.0326 (9) | 0.0225 (8) | 0.0082 (8) | 0.0030 (8) | −0.0011 (7) |
O5' | 0.0356 (13) | 0.0657 (14) | 0.0545 (13) | −0.0093 (11) | 0.0059 (10) | 0.0002 (10) |
O2'' | 0.0455 (11) | 0.0275 (9) | 0.0358 (10) | −0.0050 (8) | −0.0042 (9) | 0.0004 (8) |
O4'' | 0.0496 (11) | 0.0264 (8) | 0.0248 (8) | 0.0038 (8) | −0.0029 (8) | −0.0003 (6) |
O5'' | 0.0379 (11) | 0.0356 (10) | 0.0632 (13) | −0.0074 (9) | 0.0081 (10) | 0.0077 (9) |
O2B | 0.0380 (11) | 0.0674 (13) | 0.0396 (10) | −0.0161 (10) | −0.0076 (9) | 0.0118 (9) |
O4B | 0.0554 (13) | 0.0769 (14) | 0.0220 (9) | −0.0188 (11) | −0.0056 (9) | 0.0083 (9) |
N1A | 0.0277 (11) | 0.0294 (10) | 0.0209 (9) | −0.0052 (9) | −0.0015 (8) | 0.0017 (7) |
N3A | 0.0314 (11) | 0.0328 (10) | 0.0178 (9) | −0.0054 (9) | 0.0048 (9) | 0.0022 (8) |
N1B | 0.0298 (11) | 0.0348 (11) | 0.0212 (9) | −0.0007 (9) | −0.0031 (8) | 0.0039 (8) |
N3B | 0.0375 (13) | 0.0390 (12) | 0.0235 (10) | −0.0067 (10) | −0.0100 (10) | 0.0010 (9) |
C1' | 0.0313 (13) | 0.0312 (12) | 0.0195 (10) | −0.0054 (10) | −0.0020 (10) | −0.0006 (9) |
C2' | 0.0246 (12) | 0.0322 (12) | 0.0242 (11) | 0.0012 (10) | 0.0001 (10) | −0.0001 (9) |
C3' | 0.0321 (13) | 0.0384 (13) | 0.0238 (12) | −0.0048 (11) | −0.0041 (10) | 0.0033 (10) |
C4' | 0.0440 (15) | 0.0427 (14) | 0.0178 (11) | 0.0011 (12) | 0.0019 (11) | −0.0011 (10) |
C5' | 0.0422 (17) | 0.0657 (19) | 0.0335 (14) | 0.0066 (15) | 0.0118 (13) | 0.0064 (13) |
C1'' | 0.0291 (13) | 0.0318 (12) | 0.0241 (11) | 0.0018 (11) | 0.0023 (10) | 0.0015 (9) |
C2'' | 0.0275 (13) | 0.0263 (11) | 0.0253 (11) | 0.0002 (10) | 0.0019 (10) | −0.0001 (9) |
C3'' | 0.0240 (12) | 0.0374 (13) | 0.0228 (11) | −0.0027 (10) | 0.0016 (10) | 0.0045 (10) |
C4'' | 0.0366 (14) | 0.0332 (13) | 0.0203 (11) | 0.0032 (11) | 0.0032 (11) | −0.0013 (9) |
C5'' | 0.0481 (17) | 0.0346 (13) | 0.0372 (14) | −0.0100 (12) | −0.0050 (13) | 0.0004 (11) |
C2A | 0.0294 (13) | 0.0246 (11) | 0.0246 (11) | −0.0031 (10) | 0.0026 (10) | 0.0036 (9) |
C4A | 0.0325 (13) | 0.0257 (11) | 0.0224 (11) | 0.0030 (10) | 0.0003 (10) | 0.0000 (9) |
C5A | 0.0290 (12) | 0.0271 (12) | 0.0250 (11) | −0.0010 (10) | 0.0000 (10) | −0.0018 (9) |
C6A | 0.0277 (13) | 0.0273 (11) | 0.0234 (11) | −0.0036 (10) | 0.0045 (10) | 0.0028 (9) |
C7A | 0.0335 (15) | 0.0507 (15) | 0.0350 (14) | −0.0094 (12) | −0.0002 (12) | −0.0019 (12) |
C2B | 0.0361 (15) | 0.0319 (12) | 0.0293 (12) | −0.0002 (12) | −0.0080 (11) | 0.0040 (10) |
C4B | 0.0406 (15) | 0.0356 (13) | 0.0265 (12) | −0.0022 (12) | −0.0038 (11) | −0.0007 (10) |
C5B | 0.0311 (13) | 0.0334 (12) | 0.0273 (12) | 0.0016 (11) | −0.0029 (11) | 0.0004 (10) |
C6B | 0.0299 (13) | 0.0352 (13) | 0.0256 (12) | 0.0021 (11) | −0.0066 (10) | 0.0012 (10) |
C7B | 0.0360 (16) | 0.0607 (18) | 0.0378 (15) | −0.0011 (14) | −0.0020 (12) | 0.0085 (13) |
Geometric parameters (Å, º) top
F3'—C3' | 1.400 (3) | C2'—C3' | 1.518 (3) |
F3''—C3'' | 1.411 (3) | C2'—H2'1 | 0.9800 |
O2A—C2A | 1.220 (3) | C3'—C4' | 1.519 (4) |
O4A—C4A | 1.240 (3) | C3'—H3' | 0.9800 |
O2'—C2' | 1.410 (3) | C4'—C5' | 1.499 (4) |
O2'—H2' | 0.83 (4) | C4'—H4' | 0.9800 |
O4'—C1' | 1.407 (3) | C5'—H5'1 | 0.9700 |
O4'—C4' | 1.455 (3) | C5'—H5'2 | 0.9700 |
O5'—C5' | 1.421 (4) | C1''—C2'' | 1.513 (3) |
O5'—H5' | 0.86 (4) | C1''—H1'' | 0.9800 |
O2''—C2'' | 1.399 (3) | C2''—C3'' | 1.514 (3) |
O2''—H2" | 0.79 (3) | C2''—H2'2 | 0.9800 |
O4''—C1'' | 1.423 (3) | C3''—C4'' | 1.513 (3) |
O4''—C4'' | 1.455 (3) | C3''—H3'' | 0.9800 |
O5''—C5'' | 1.422 (3) | C4''—C5'' | 1.505 (4) |
O5''—H5" | 0.87 (4) | C4''—H4'' | 0.9800 |
O2B—C2B | 1.212 (3) | C5''—H5'3 | 0.9700 |
O4B—C4B | 1.237 (3) | C5''—H5'4 | 0.9700 |
N1A—C2A | 1.373 (3) | C4A—C5A | 1.438 (3) |
N1A—C6A | 1.376 (3) | C5A—C6A | 1.344 (3) |
N1A—C1' | 1.470 (3) | C5A—C7A | 1.494 (4) |
N3A—C4A | 1.371 (3) | C6A—H6A | 0.9300 |
N3A—C2A | 1.376 (3) | C7A—H7A1 | 0.9600 |
N3A—H3A | 0.87 (3) | C7A—H7A2 | 0.9600 |
N1B—C6B | 1.381 (3) | C7A—H7A3 | 0.9600 |
N1B—C2B | 1.384 (3) | C4B—C5B | 1.440 (3) |
N1B—C1'' | 1.460 (3) | C5B—C6B | 1.340 (3) |
N3B—C4B | 1.374 (3) | C5B—C7B | 1.502 (4) |
N3B—C2B | 1.375 (3) | C6B—H6B | 0.9300 |
N3B—H3B | 0.85 (3) | C7B—H7B1 | 0.9600 |
C1'—C2' | 1.525 (3) | C7B—H7B2 | 0.9600 |
C1'—H1' | 0.9800 | C7B—H7B3 | 0.9600 |
| | | |
C2'—O2'—H2' | 105 (3) | O2''—C2''—H2'2 | 109.9 |
C1'—O4'—C4' | 110.06 (18) | C1''—C2''—H2'2 | 109.9 |
C5'—O5'—H5' | 111 (3) | C3''—C2''—H2'2 | 109.9 |
C2''—O2''—H2" | 113 (2) | F3''—C3''—C4'' | 108.12 (19) |
C1''—O4''—C4'' | 109.33 (17) | F3''—C3''—C2'' | 108.37 (19) |
C5''—O5''—H5" | 103 (2) | C4''—C3''—C2'' | 103.07 (18) |
C2A—N1A—C6A | 121.50 (19) | F3''—C3''—H3'' | 112.3 |
C2A—N1A—C1' | 119.22 (19) | C4''—C3''—H3'' | 112.3 |
C6A—N1A—C1' | 119.24 (18) | C2''—C3''—H3'' | 112.3 |
C4A—N3A—C2A | 126.6 (2) | O4''—C4''—C5'' | 110.2 (2) |
C4A—N3A—H3A | 114.2 (18) | O4''—C4''—C3'' | 105.65 (18) |
C2A—N3A—H3A | 119.2 (18) | C5''—C4''—C3'' | 116.3 (2) |
C6B—N1B—C2B | 121.41 (19) | O4''—C4''—H4'' | 108.1 |
C6B—N1B—C1'' | 120.32 (19) | C5''—C4''—H4'' | 108.1 |
C2B—N1B—C1'' | 118.3 (2) | C3''—C4''—H4'' | 108.1 |
C4B—N3B—C2B | 127.6 (2) | O5''—C5''—C4'' | 111.7 (2) |
C4B—N3B—H3B | 114.9 (18) | O5''—C5''—H5'3 | 109.3 |
C2B—N3B—H3B | 117.4 (19) | C4''—C5''—H5'3 | 109.3 |
O4'—C1'—N1A | 108.87 (19) | O5''—C5''—H5'4 | 109.3 |
O4'—C1'—C2' | 106.35 (18) | C4''—C5''—H5'4 | 109.3 |
N1A—C1'—C2' | 113.26 (18) | H5'3—C5''—H5'4 | 107.9 |
O4'—C1'—H1' | 109.4 | O2A—C2A—N1A | 123.5 (2) |
N1A—C1'—H1' | 109.4 | O2A—C2A—N3A | 122.2 (2) |
C2'—C1'—H1' | 109.4 | N1A—C2A—N3A | 114.3 (2) |
O2'—C2'—C3' | 114.9 (2) | O4A—C4A—N3A | 119.5 (2) |
O2'—C2'—C1' | 110.2 (2) | O4A—C4A—C5A | 124.3 (2) |
C3'—C2'—C1' | 101.45 (18) | N3A—C4A—C5A | 116.27 (19) |
O2'—C2'—H2'1 | 110.0 | C6A—C5A—C4A | 117.4 (2) |
C3'—C2'—H2'1 | 110.0 | C6A—C5A—C7A | 123.2 (2) |
C1'—C2'—H2'1 | 110.0 | C4A—C5A—C7A | 119.3 (2) |
F3'—C3'—C2' | 108.0 (2) | C5A—C6A—N1A | 123.3 (2) |
F3'—C3'—C4' | 108.5 (2) | C5A—C6A—H6A | 118.4 |
C2'—C3'—C4' | 102.97 (19) | N1A—C6A—H6A | 118.4 |
F3'—C3'—H3' | 112.3 | C5A—C7A—H7A1 | 109.5 |
C2'—C3'—H3' | 112.3 | C5A—C7A—H7A2 | 109.5 |
C4'—C3'—H3' | 112.3 | H7A1—C7A—H7A2 | 109.5 |
O4'—C4'—C5' | 109.9 (2) | C5A—C7A—H7A3 | 109.5 |
O4'—C4'—C3' | 105.65 (19) | H7A1—C7A—H7A3 | 109.5 |
C5'—C4'—C3' | 116.3 (2) | H7A2—C7A—H7A3 | 109.5 |
O4'—C4'—H4' | 108.2 | O2B—C2B—N3B | 122.6 (2) |
C5'—C4'—H4' | 108.2 | O2B—C2B—N1B | 123.7 (2) |
C3'—C4'—H4' | 108.2 | N3B—C2B—N1B | 113.7 (2) |
O5'—C5'—C4' | 110.7 (2) | O4B—C4B—N3B | 120.1 (2) |
O5'—C5'—H5'1 | 109.5 | O4B—C4B—C5B | 124.3 (3) |
C4'—C5'—H5'1 | 109.5 | N3B—C4B—C5B | 115.6 (2) |
O5'—C5'—H5'2 | 109.5 | C6B—C5B—C4B | 117.9 (2) |
C4'—C5'—H5'2 | 109.5 | C6B—C5B—C7B | 123.2 (2) |
H5'1—C5'—H5'2 | 108.1 | C4B—C5B—C7B | 118.9 (2) |
O4''—C1''—N1B | 107.83 (18) | C5B—C6B—N1B | 123.5 (2) |
O4''—C1''—C2'' | 105.30 (18) | C5B—C6B—H6B | 118.3 |
N1B—C1''—C2'' | 115.69 (19) | N1B—C6B—H6B | 118.3 |
O4''—C1''—H1'' | 109.3 | C5B—C7B—H7B1 | 109.5 |
N1B—C1''—H1'' | 109.3 | C5B—C7B—H7B2 | 109.5 |
C2''—C1''—H1'' | 109.3 | H7B1—C7B—H7B2 | 109.5 |
O2''—C2''—C1'' | 109.23 (19) | C5B—C7B—H7B3 | 109.5 |
O2''—C2''—C3'' | 116.28 (19) | H7B1—C7B—H7B3 | 109.5 |
C1''—C2''—C3'' | 101.10 (18) | H7B2—C7B—H7B3 | 109.5 |
| | | |
C4'—O4'—C1'—N1A | −139.95 (19) | F3''—C3''—C4''—O4'' | −89.4 (2) |
C4'—O4'—C1'—C2' | −17.6 (2) | C2''—C3''—C4''—O4'' | 25.2 (2) |
C2A—N1A—C1'—O4' | −128.7 (2) | F3''—C3''—C4''—C5'' | 148.0 (2) |
C6A—N1A—C1'—O4' | 53.4 (3) | C2''—C3''—C4''—C5'' | −97.4 (2) |
C2A—N1A—C1'—C2' | 113.2 (2) | O4''—C4''—C5''—O5'' | −64.1 (3) |
C6A—N1A—C1'—C2' | −64.7 (3) | C3''—C4''—C5''—O5'' | 56.1 (3) |
O4'—C1'—C2'—O2' | 155.48 (18) | C6A—N1A—C2A—O2A | −172.9 (2) |
N1A—C1'—C2'—O2' | −85.0 (2) | C1'—N1A—C2A—O2A | 9.2 (3) |
O4'—C1'—C2'—C3' | 33.3 (2) | C6A—N1A—C2A—N3A | 9.4 (3) |
N1A—C1'—C2'—C3' | 152.9 (2) | C1'—N1A—C2A—N3A | −168.5 (2) |
O2'—C2'—C3'—F3' | −39.8 (3) | C4A—N3A—C2A—O2A | 176.0 (2) |
C1'—C2'—C3'—F3' | 79.1 (2) | C4A—N3A—C2A—N1A | −6.2 (3) |
O2'—C2'—C3'—C4' | −154.5 (2) | C2A—N3A—C4A—O4A | 179.2 (2) |
C1'—C2'—C3'—C4' | −35.6 (2) | C2A—N3A—C4A—C5A | −0.9 (3) |
C1'—O4'—C4'—C5' | 120.6 (2) | O4A—C4A—C5A—C6A | −175.1 (2) |
C1'—O4'—C4'—C3' | −5.7 (3) | N3A—C4A—C5A—C6A | 5.0 (3) |
F3'—C3'—C4'—O4' | −87.9 (2) | O4A—C4A—C5A—C7A | 2.0 (4) |
C2'—C3'—C4'—O4' | 26.4 (2) | N3A—C4A—C5A—C7A | −177.8 (2) |
F3'—C3'—C4'—C5' | 149.9 (2) | C4A—C5A—C6A—N1A | −1.9 (3) |
C2'—C3'—C4'—C5' | −95.8 (2) | C7A—C5A—C6A—N1A | −178.9 (2) |
O4'—C4'—C5'—O5' | −65.2 (3) | C2A—N1A—C6A—C5A | −5.8 (3) |
C3'—C4'—C5'—O5' | 54.8 (3) | C1'—N1A—C6A—C5A | 172.1 (2) |
C4''—O4''—C1''—N1B | −146.43 (18) | C4B—N3B—C2B—O2B | −177.2 (3) |
C4''—O4''—C1''—C2'' | −22.4 (2) | C4B—N3B—C2B—N1B | 2.7 (4) |
C6B—N1B—C1''—O4'' | 45.4 (3) | C6B—N1B—C2B—O2B | 174.2 (2) |
C2B—N1B—C1''—O4'' | −134.4 (2) | C1''—N1B—C2B—O2B | −6.1 (4) |
C6B—N1B—C1''—C2'' | −72.2 (3) | C6B—N1B—C2B—N3B | −5.7 (3) |
C2B—N1B—C1''—C2'' | 108.1 (2) | C1''—N1B—C2B—N3B | 174.0 (2) |
O4''—C1''—C2''—O2'' | 160.26 (19) | C2B—N3B—C4B—O4B | −178.2 (3) |
N1B—C1''—C2''—O2'' | −80.8 (2) | C2B—N3B—C4B—C5B | 1.6 (4) |
O4''—C1''—C2''—C3'' | 37.2 (2) | O4B—C4B—C5B—C6B | 176.8 (3) |
N1B—C1''—C2''—C3'' | 156.1 (2) | N3B—C4B—C5B—C6B | −3.1 (3) |
O2''—C2''—C3''—F3'' | −41.1 (3) | O4B—C4B—C5B—C7B | −2.0 (4) |
C1''—C2''—C3''—F3'' | 77.0 (2) | N3B—C4B—C5B—C7B | 178.1 (2) |
O2''—C2''—C3''—C4'' | −155.5 (2) | C4B—C5B—C6B—N1B | 0.2 (4) |
C1''—C2''—C3''—C4'' | −37.4 (2) | C7B—C5B—C6B—N1B | 178.9 (2) |
C1''—O4''—C4''—C5'' | 124.5 (2) | C2B—N1B—C6B—C5B | 4.5 (4) |
C1''—O4''—C4''—C3'' | −1.9 (2) | C1''—N1B—C6B—C5B | −175.2 (2) |
Hydrogen-bond geometry (Å, º) topCg2 is the centroid of the N1A/C2A/N3A/C4A–C6A ring. |
D—H···A | D—H | H···A | D···A | D—H···A |
N3A—H3A···O4Bi | 0.87 (3) | 1.95 (3) | 2.818 (3) | 172 (2) |
N3Bii—H3Bii···O4A | 0.85 (3) | 2.08 (3) | 2.923 (3) | 172 (3) |
O5′—H5′···O2′iii | 0.86 (4) | 2.21 (4) | 3.022 (3) | 157 (3) |
O2′—H2′···O4Aiv | 0.83 (4) | 1.95 (4) | 2.749 (3) | 161 (4) |
O2"—H2"···O5"v | 0.79 (3) | 2.11 (3) | 2.789 (3) | 143 (3) |
O5"—H5"···O2Aiii | 0.87 (4) | 1.90 (4) | 2.758 (3) | 172 (4) |
C7B—H7B3···O4Avi | 0.96 | 2.60 | 3.547 (3) | 168 |
C7B—H7B1···O2Biii | 0.96 | 2.54 | 3.199 (4) | 126 |
C3"—H3"···O2"vii | 0.98 | 2.32 | 3.128 (3) | 139 |
C2"—H2′2···F3"vii | 0.98 | 2.53 | 3.182 (3) | 124 |
C7A—H7A1···Cg2viii | 0.96 | 2.78 | 3.571 (3) | 140 |
Symmetry codes: (i) −x+1/2, −y+1, z+1/2; (ii) −x+1/2, −y+1, z−1/2; (iii) x+1, y, z; (iv) x−1/2, −y+3/2, −z+2; (v) x−1/2, −y+1/2, −z+2; (vi) −x+3/2, −y+1, z−1/2; (vii) x+1/2, −y+1/2, −z+2; (viii) x+1/2, −y+3/2, −z+2. |
Geometrical parameters of the torsion angles (°) and pseudorotation
parameters (°) of the furanose ring for molecules A and B
of RTF and 5-methyluridine (RTOH) topTorsion angle | Molecule A | Molecule B | RTOH |
C4'—O4'—C1'—C2' | -17.6 (2) | -22.3 (2) | 2.5 |
O4'—C1'—C2'—C3' | 33.3 (2) | 37.1 (2) | -25.5 |
C1'—C2'—C3'—C4' | -35.5 (2) | -37.4 (2) | 38.5 |
C1'—O4'—C4'—C3' | -5.6 (3) | -2.0 (2) | 22.5 |
C2'—C3'—C4'—O4' | 26.3 (2) | 25.2 (2) | -38.2 |
C2—N1—C1'—O4' | -128.7 (2) | -134.3 (2) | -154 |
χ | anti | anti | anti |
C3'—C4'—C5'—O5' | 54.8 (3) | 56.1 (3) | 49.3 |
γt / γ+ / γ- | γ+ | γ+ | γ+ |
Phase Angle (P) | 170.2 | 164.3 | 21.2 |
Puckering amplitude (νmax) | 36.1 | 38.8 | 41.29 |
S or N | S | S | N |
Notes: (a) for anti, χ = 180±90° and for syn,
χ = 0±90°; (b) γt = 180°, γ+ = 60° and γ- = -60°;
(c) for south S type, P = 180±90° and for north N type,
P = 0±90°; (d) data for 5-methyluridine (RTOH) has been retrieved
from the CSD (refcode MEURID). |