Biomedical Engineering Reference
In-Depth Information
and principally from that labeled N
1
in the standard ring numbering (the nitrogen
that is
not
in between the keto carbons). The most prominent feature in the
(U
H)
production cross section is a sharp peak at 1.0 eV. Neither this feature
nor a weaker one at 0.69 eV appears to correlate with any of the measured or
calculated elastic resonance positions just mentioned; rather, these are thought
[
16
,
70
] to be vibrational Feshbach resonances associated with temporary trapping
of the projectile electron in the potential well created by the stong dipole moment
of uracil. Because the electronic wavefunction of such a dipole-bound state is
diffuse, it unclear whether such a resonance mechanism is relevant to nucleic acids
in the condensed phase. However, there is also a broader peak near 1.8 eV in the
dissociative attachment signal that may plausibly be associated with the resonance
observed in transmission at 1.58 eV. As described in the preceding paragraph, that
resonance has been variously assigned as
1
2
, both of which are compact
valence states; without clarity on the correct assignment, though, it is difficult to be
confident in any model of the dissociation mechanism.
In applying the SMC method to uracil, therefore, we employed different one-
electron basis sets and levels of approximation in order to develop confidence in the
consistency and convergence of our calculations [
71
]. The final results included an
extensive treatment of polarization effects, represented as virtual excitations of the
target molecule, and placed the three
and
shape resonances at 0.32, 1.91, and 5.08 eV.
For comparison, with polarization omitted (thus treating the target charge density as
frozen, the so-called static-exchange approximation), these energies shift upward
to 2.1, 4.2, and 8.2 eV, reflecting the attractive nature of the polarization effect. The
principal conclusion to be drawn from our results is that they strongly support the
original assignment of the resonances observed in transmission [
16
,
65
] by placing
1
2
3
near 0.3 eV rather than at 2.2 eV, while also placing
and
reasonably close
to the second and third transmission features.
In computations, unlike gas-phase experiments, it is easy to take advantage of
the symmetry properties of the molecule, both to speed the calculations and to assist
in the analysis of results. In the case of uracil, we carried out separate scattering
calculations for wavefunctions of
A
00
symmetry, that is, even and odd,
respectively, with respect to the molecular plane. The
A
0
and
resonances just discussed
A
0
, there is a broad peak near 8.5 eV
similar to that seen in the 7-10 eV range in many other molecules that is likely
associated with overlapping, short-lived
A
00
of course occur in the
component. In
resonances. However, there is also a
sharp resonance peak at 1.45 eV, which in our experience is unusually low for a
resonance. As discussed immediately below, this peak may be artifactual.
Subsequent studies of the
resonances of uracil have tended to confirm the
picture outlined above and therefore to support the original resonance assignments
[
16
,
65
]. An expanded calculation by the group that originally placed
1
at 2.2 eV
was interpreted as indicating a fourth
resonance (one more than expected on
1
chemical grounds), now assigned as
,at0.33eV[
72
]. That interpretation was
questioned [
73
], and the low-energy feature was subsequently found to be a com-
putational artifact [
74
], leaving
1
at 1.7 eV, near the original position calculated
by the same group. In contrast, a recent, extensive
R
-matrix calculation [
75
] places
