194
M. Ilchenko and I. Dubey
gas-phase experimental results. The gas-phase binding sequence between the monovalent cations and the xanthine quartet follows the order Li
+
> Na
+
> K
+
, which is
consistent with that obtained for the guanine quartet in the literature. The smallest stabilization energy of K
+
and its position versus the other alkali metal ions in
guanine and xanthine quartets is consistent with the fact that the potassium cation
can be located between two guanine or xanthine quartets, for providing a [(G or
Xan) 8 + K]
+
octamer adduct. While an octamer adduct with K
+
for xanthine was detected by ESI-MS, it was not the case for guanine. The formation of tetrameric and
octameric aggregates of guanine analog 3-methylxanthine with NH 4
+
, Na
+
and K
+
ions has been also observed in the gas phase in ESI-MS spectra to confirm the results of computational studies performed at the BLYP-D/TZ2P level of theory [113].
Nucleic acid tetraplexes and lipophilic self-assembling G-quadruplexes contain
stacked base tetrads with intercalated metal ions as basic building blocks. In [114]
quantum-chemical methods were also used to systematically explore the geometric
and energetic properties of base tetrads with and without metal ions. The structures
were optimized with the B3LYP hybrid density functional method and the DZVP
basis sets. Sandwiched G-, C-, U-, and T-tetrads with Na
+
and K
+
ions at different
symmetries were studied. The detailed information on total energies as well as on
metal ion tetrad and base– base interaction energies was obtained. The geometrical
parameters of the sandwiched metal ion complexes were compared to both experimental structures and to calculated geometries of complexes of single tetrads with
metal ions. A microsolvation model was successfully applied to explain the ion
selectivity preference of K
+
over Na
+
in a qualitative sense.
A systematic DFT study of sandwiched isoguanine (iG) complexes with intercalating alkali metal ions was carried out in [115]. The study of sandwiched isoguanine tetrad and pentad complexes consisting of two polyads with Na
+
, K
+
and Rb
+
ions was performed at the B3LYP level. In iG sandwich structures, the ion-base
interaction energy is slightly larger than in the corresponding guanine sandwich
complexes. Because the base–base interaction energy is even more increased in
passing from guanine to isoguanine, the iG sandwiches are thus far the only examples where the base–base interaction energy is larger than that of the base–metal ion
interaction. Stacking interactions have been studied in smaller models consisting of
two bases, retaining the geometry from the complete complex structures. From the
data obtained at the B3LYP and BH&H levels and with Møller-Plesset perturbation
theory, one can conclude that the B3LYP method overestimates the repulsion in
stacked base dimers. For the complexes studied in this work, this is only of minor
importance because the direct inter-tetrad or inter-pentad interaction is supplemented by a strong metal ion-base interaction. Using a microsolvation model, the metal
ion preference K
+
≈ Rb
+
> Na
+
was found for tetrad complexes. On the other hand,
for pentads the corresponding ordering is Rb
+
> K
+
> Na
+
. In the latter case experimental data are available that agree with this theoretical prediction.
DFT calculations at the M052X/6-31G(d) level and PCM/TD-PBE0/6-31G(d)
level were performed in [116] to get insights into the effect of metal ions on the
excited states of guanine nanostructures, short d(TG 4 T) 4 quadruplexes and long G 4 -
wires. As a first step, the ground state geometry of short d(TG 4 T) 4 quadruplexes
M. Ilchenko and I. Dubey
gas-phase experimental results. The gas-phase binding sequence between the monovalent cations and the xanthine quartet follows the order Li
+
> Na
+
> K
+
, which is
consistent with that obtained for the guanine quartet in the literature. The smallest stabilization energy of K
+
and its position versus the other alkali metal ions in
guanine and xanthine quartets is consistent with the fact that the potassium cation
can be located between two guanine or xanthine quartets, for providing a [(G or
Xan) 8 + K]
+
octamer adduct. While an octamer adduct with K
+
for xanthine was detected by ESI-MS, it was not the case for guanine. The formation of tetrameric and
octameric aggregates of guanine analog 3-methylxanthine with NH 4
+
, Na
+
and K
+
ions has been also observed in the gas phase in ESI-MS spectra to confirm the results of computational studies performed at the BLYP-D/TZ2P level of theory [113].
Nucleic acid tetraplexes and lipophilic self-assembling G-quadruplexes contain
stacked base tetrads with intercalated metal ions as basic building blocks. In [114]
quantum-chemical methods were also used to systematically explore the geometric
and energetic properties of base tetrads with and without metal ions. The structures
were optimized with the B3LYP hybrid density functional method and the DZVP
basis sets. Sandwiched G-, C-, U-, and T-tetrads with Na
+
and K
+
ions at different
symmetries were studied. The detailed information on total energies as well as on
metal ion tetrad and base– base interaction energies was obtained. The geometrical
parameters of the sandwiched metal ion complexes were compared to both experimental structures and to calculated geometries of complexes of single tetrads with
metal ions. A microsolvation model was successfully applied to explain the ion
selectivity preference of K
+
over Na
+
in a qualitative sense.
A systematic DFT study of sandwiched isoguanine (iG) complexes with intercalating alkali metal ions was carried out in [115]. The study of sandwiched isoguanine tetrad and pentad complexes consisting of two polyads with Na
+
, K
+
and Rb
+
ions was performed at the B3LYP level. In iG sandwich structures, the ion-base
interaction energy is slightly larger than in the corresponding guanine sandwich
complexes. Because the base–base interaction energy is even more increased in
passing from guanine to isoguanine, the iG sandwiches are thus far the only examples where the base–base interaction energy is larger than that of the base–metal ion
interaction. Stacking interactions have been studied in smaller models consisting of
two bases, retaining the geometry from the complete complex structures. From the
data obtained at the B3LYP and BH&H levels and with Møller-Plesset perturbation
theory, one can conclude that the B3LYP method overestimates the repulsion in
stacked base dimers. For the complexes studied in this work, this is only of minor
importance because the direct inter-tetrad or inter-pentad interaction is supplemented by a strong metal ion-base interaction. Using a microsolvation model, the metal
ion preference K
+
≈ Rb
+
> Na
+
was found for tetrad complexes. On the other hand,
for pentads the corresponding ordering is Rb
+
> K
+
> Na
+
. In the latter case experimental data are available that agree with this theoretical prediction.
DFT calculations at the M052X/6-31G(d) level and PCM/TD-PBE0/6-31G(d)
level were performed in [116] to get insights into the effect of metal ions on the
excited states of guanine nanostructures, short d(TG 4 T) 4 quadruplexes and long G 4 -
wires. As a first step, the ground state geometry of short d(TG 4 T) 4 quadruplexes