Is the fluorenyl cation 1 antiaromatic or non-aromatic? This is still an open question. But the recent paper by Costa, et al. provides a new path towards potentially answering this question; they have finally synthesized this molecule.¹

By photolizing 2 in low-density amorphous ice (LDA ice) and in deuterated ice at 8 K, they have identified a new IR spectrum.

To identify the origin of these spectra, they optimized the geometry of the fluorenyl cation 1 at B3LYP-D3/def2-TZVP (see Figure 1) and computed its IR spectra. These computed IR frequencies were then scaled by 0.97. The agreement between the computed and experimental frequencies is quite reasonable, and the isotopic shifts are also reasonably well reproduced. The agreement is not perfect, as seen in Table 1. Hopefully, further experiments will now be carried out to try to answer the lead question of this post.

Figure 1. B3LYP-D3/def2-TZVP optimized geometry of 1.

Table 1. Experimental and computed IR frequencies (cm^-1)
and isotopic shift (in parentheses) of 1.

Calc.	Exp.
1008.8	986
1106.8 (+2.1)	1076.8 (+1.7)
1152.8	1117.2
1198.6	1163.5
1267.0	1235.1
1373.4 (-16.4)	1343.7
1510.8(-8.3)	1469.0 (-7.3)
1530.7 (-3.2)	1490.5 (-1.0)
1616.8(-6.4)	1575.7(-4.4)
1640.9 (0.0)	1601.2 (-4.0)

References

(1) Costa, P.; Trosien, I.; Fernandez-Oliva, M.; Sanchez-Garcia, E.; Sander, W. "The Fluorenyl Cation," Angew. Chem. Int. Ed. 2015, 54, 2656-2660, DOI: 10.1002/anie.201411234.

InChIs

1: InChI=1S/C13H9/c1-3-7-12-10(5-1)9-11-6-2-4-8-13(11)12/h1-9H/q+1
InChIKey=KZCNYQVQQBONEY-UHFFFAOYSA-N

To advance our understanding of why ribose takes on the furanose form, rather than the pyranose form, in RNA, Alonso and co-workers have examined the structure of uridine 1 in the gas phase.¹

1

Uridine is sensitive to temperature, and so the laser-ablation method long used by the Alonso group is ideal for examining uridine. The microwave spectrum is quite complicated due to the presence of many photofragments. Careful analysis lead to the identification of a number of lines and hyperfine structure that could be definitively assigned to uridine, leading to experimental values of the rotational constants and the diagonal elements of the ¹⁴N nuclear quadrupole coupling tensor for each nitrogen. These values are listed in Table 1.

Table 1. Experimental and calculated rotational constants (MHz), quadrupole coupling constants (MHz) and relative energy (kcal mol^-1).

		calculated
	Expt.	anti/C2’-endo-g+	syn/C2’-endo-g+	anti/C3’-endo-g+	anti/C2’-endo-t	syn/C3’-endo-g+
A	885.98961	901.2	935.8	790.0	799.7	925.5
B	335.59622	340.6	308.4	352.6	330.6	300.4
C	270.11210	276.6	266.6	261.4	262.9	264.0
14N1 χxx	1.540	1.50	1.82	1.48	1.46	1.82
14N1 χyy	1.456	1.43	0.73	1.71	1.81	-0.72
14N1 χzz	-2.996	-2.93	-2.56	-3.19	-3.27	-1.11
14N3 χxx	1.719	1.74	2.03	1.78	1.62	1.98
14N3 χyy	1.261	1.11	0.47	1.34	1.51	-0.75
14N3 χzz	-2.979	-2.85	-2.50	-3.12	-3.13	-1.23
Rel E		0.0	1.10	1.90	2.00	2.15

In order to assign a 3-D structure to these experimental values, they examined the PES of uridine with molecular mechanics and semi-empirical methods, before reoptimizing the structure of the lowest 5 energy structures at MP2/6-311++G(d,p). Then, comparison of the resulting rotational constants and ¹⁴N nuclear quadrupole coupling constants of these computed structures (see Table 1) led to identification of the lowest energy structure (anti/C2’-endo-g+, see Figure 1) in best agreement with the experiment. Once again, the Alonso group has demonstrated the value of the synergy between experiment and computation in structure identification.

Figure 1. MP2/6-311++G(d,p) optimized structure of 1 (anti/C2’-endo-g+).

References

(1) Peña, I.; Cabezas, C.; Alonso, J. L. "The Nucleoside Uridine Isolated in the Gas Phase," Angew. Chem. Int. Ed. 2015, 54, 2991-2994, DOI: 10.1002/anie.201412460.

Inchis:

1: Inchi=1S/C9H12N2O6/c12-3-4-6(14)7(15)8(17-4)11-2-1-5(13)10-9(11)16/h1-2,4,6-8,12,14-15H,3H2,(H,10,13,16)/t4-,6-,7-,8-/m1/s1
InChiKey=DRTQHJPVMGBUCF-XVFCMESISA-N