191
6 Quantum Chemical Approaches in Modeling the Structure of DNA …
base pairs with two hydrogen bonds between two neighbour bases was found to be
−66.07 kcal/mol at the B3LYP/6-311G(d, p) level of theory. Complexes of metal ions
with G-quartets can be classified into different structure types. The one with Ca
2+
in the central cavity adopts a C 4h -symmetric structure with coplanar bases, whereas
the energies of the planar and nonplanar Na
+
complexes are almost identical. Metal
cations with small radii (Li
+
, Be
2+
, Cu
+
, and Zn
2+
) and a high charge enforce a
nonplanarity of the base quartets and may thus prevent a stacking of G-quartet, unlike Na
+
and K
+
cations. The electrostatic potential of G-quartets provides probably
favourable binding sites for metal ions between the stacked quartet planes, whereas
isolated quartets have the region of most negative electrostatic potential in the central cavity. Uracil quartets in the orientation with N3–H3…O4 H-bond are probably
also capable of binding cations at the centre.
The complexes of metal cations Fe
2+
, Co
2+
, Ni
2+
, Cu
2+
and Zn
2+
with guanine
tetrads (G 4 ) of C 4h , C 4 and S 4 symmetry) were studied in [100]. The system contained two water molecules above and under the G 4 -cation plane, with six-coordinated metal ion. G 4 –Co
2+
and G 4 –Cu
2+
being open shell species were treated using
unrestricted method UB3LYP and 6-31G(d) basis set. BSSE (Basis Set Superposition Error) correction was evaluated according to the counterpoise method of Boys
and Bernardi [101]. Bader’s AIM (atoms in molecules) theory [102] was applied to
determine a strong hydrogen bond [103]. The main conclusions were as follows:
(a) the stability sequence is Ni
2+
> Cu
2+
> Co
2+
> Fe
2+
> Zn
2+
when including BSSE
correction, and Ni
2+
> Fe
2+
> Co
2+
> Cu
2+
> Zn
2+
after hydration energy correction;
(b) the sequence for G 4 –M–water complexes is Co
2+
> Fe
2+
> Ni
2+
> Cu
2+
> Zn
2+
with
BSSE correction; (c) electron density and its Laplacian at the bond critical points
well correlate with the hydrogen bond length in the tetrads.
Structural properties and the effect of interaction of alkali (Li
+
, Na
+
, K
+
) and
alkaline earth (Be
2+
, Mg
2+
, Ca
2+
) metal cations with guanine and thioguanine (SG)
tetrads were studied [104]. Complex formation was investigated using ab initio
and DFT methods. In some cases MP2/6-311G** single point energy calculation
was performed for the geometries optimized by B3LYP/6-311G** level of theory.
Single point energy calculations were carried out to study the solute–solvent interaction using the self-consistent reaction field theory (SCRF) [95] at B3LYP/6311G** level of theory. This method is based on Tomasi’s polarized continuum
model (PCM), which defines the cavity as the union of a series of interlocking
atomic spheres. The calculations revealed that cation-G and SG-tetrad complexes
adopt normal four-stranded Hoogsteen bonded structures. The substitution of cations on guanine and SG-tetrads affects their geometries and charge distributions.
The gas phase binding sequence for cation-G and SG-tetrads follows the interaction
energy and metal ion affinity order Li
+
> Na
+
> K
+
, Be
2+
> Mg
2+
> Ca
2+
. The smaller
ions are tightly bonded to the quartets suggesting the domination of electrostatic
interaction in the cation–tetraplexes systems. The solvent interaction with the molecular systems has increased the stability of both guanine and thioguanine quartets
and their complexes. The two and three-body interaction energies have been used to
analyze the influence of a metal cation on the stability of tetrads. AIM theory was
also used to study the hydrogen bonds in the metal interacting complexes.
6 Quantum Chemical Approaches in Modeling the Structure of DNA …
base pairs with two hydrogen bonds between two neighbour bases was found to be
−66.07 kcal/mol at the B3LYP/6-311G(d, p) level of theory. Complexes of metal ions
with G-quartets can be classified into different structure types. The one with Ca
2+
in the central cavity adopts a C 4h -symmetric structure with coplanar bases, whereas
the energies of the planar and nonplanar Na
+
complexes are almost identical. Metal
cations with small radii (Li
+
, Be
2+
, Cu
+
, and Zn
2+
) and a high charge enforce a
nonplanarity of the base quartets and may thus prevent a stacking of G-quartet, unlike Na
+
and K
+
cations. The electrostatic potential of G-quartets provides probably
favourable binding sites for metal ions between the stacked quartet planes, whereas
isolated quartets have the region of most negative electrostatic potential in the central cavity. Uracil quartets in the orientation with N3–H3…O4 H-bond are probably
also capable of binding cations at the centre.
The complexes of metal cations Fe
2+
, Co
2+
, Ni
2+
, Cu
2+
and Zn
2+
with guanine
tetrads (G 4 ) of C 4h , C 4 and S 4 symmetry) were studied in [100]. The system contained two water molecules above and under the G 4 -cation plane, with six-coordinated metal ion. G 4 –Co
2+
and G 4 –Cu
2+
being open shell species were treated using
unrestricted method UB3LYP and 6-31G(d) basis set. BSSE (Basis Set Superposition Error) correction was evaluated according to the counterpoise method of Boys
and Bernardi [101]. Bader’s AIM (atoms in molecules) theory [102] was applied to
determine a strong hydrogen bond [103]. The main conclusions were as follows:
(a) the stability sequence is Ni
2+
> Cu
2+
> Co
2+
> Fe
2+
> Zn
2+
when including BSSE
correction, and Ni
2+
> Fe
2+
> Co
2+
> Cu
2+
> Zn
2+
after hydration energy correction;
(b) the sequence for G 4 –M–water complexes is Co
2+
> Fe
2+
> Ni
2+
> Cu
2+
> Zn
2+
with
BSSE correction; (c) electron density and its Laplacian at the bond critical points
well correlate with the hydrogen bond length in the tetrads.
Structural properties and the effect of interaction of alkali (Li
+
, Na
+
, K
+
) and
alkaline earth (Be
2+
, Mg
2+
, Ca
2+
) metal cations with guanine and thioguanine (SG)
tetrads were studied [104]. Complex formation was investigated using ab initio
and DFT methods. In some cases MP2/6-311G** single point energy calculation
was performed for the geometries optimized by B3LYP/6-311G** level of theory.
Single point energy calculations were carried out to study the solute–solvent interaction using the self-consistent reaction field theory (SCRF) [95] at B3LYP/6311G** level of theory. This method is based on Tomasi’s polarized continuum
model (PCM), which defines the cavity as the union of a series of interlocking
atomic spheres. The calculations revealed that cation-G and SG-tetrad complexes
adopt normal four-stranded Hoogsteen bonded structures. The substitution of cations on guanine and SG-tetrads affects their geometries and charge distributions.
The gas phase binding sequence for cation-G and SG-tetrads follows the interaction
energy and metal ion affinity order Li
+
> Na
+
> K
+
, Be
2+
> Mg
2+
> Ca
2+
. The smaller
ions are tightly bonded to the quartets suggesting the domination of electrostatic
interaction in the cation–tetraplexes systems. The solvent interaction with the molecular systems has increased the stability of both guanine and thioguanine quartets
and their complexes. The two and three-body interaction energies have been used to
analyze the influence of a metal cation on the stability of tetrads. AIM theory was
also used to study the hydrogen bonds in the metal interacting complexes.