The influence of metal alkali binding on the properties of
hydrogen bonds in AsynGanti mispair
The O6 of guanine and N7 atom of adenine in the
AsynGanti mispair directly contributes
in the formation of hydrogen bonds. Thus, N3 and N7 of guanine and N1
and N3 adenine to be principal acceptors of cations. The G(3), G(7),
A(1) and A(3) symbols are used to display these sites, respectively. The
schematic representation of optimized structures are shown in Figure 5.
In agreement with previous investigations [49,34], a simultaneous
coordination of the cation to both the N7 and O6 sites of guanine is
observed.
The values of ∆E, ∆Eint and ∆Edef are
reported in Table 5. The results indicate the cations binding to A(1),
A(3) and G(3)-positions amplified the absolute values of binding energy.
Unlike Li+ cation, the ∆E values diminished in the
presence of Na+ and K+ cations in N7
site of guanine. For each ion type, the A(1) tautomer is the most stable
among all. Contrary to ΔEdef values,
ΔEint makes a positive contribution to the ΔE. The
contribution of ΔEint is dominant in all considered
systems. The results in Table 5 indicate that a direct correlation
exists between ∆Eint and ∆E values with coefficient of
determination R2= 0.9967 in
AsynGanti systems involving cations. It
is observed that the reduction in ion charge density is associated with
decreasing the absolute values of ∆Eint and ∆E values.
Also, hydrogen bonding energies are calculated by the EML formula (see
Table 5). Unlike G(7) and G(3)-sites, the EEML,HB1 in
A(1) and A(3)-sites upon interactions with alkali ions increases. A
reverse behavior is observed for EEML,HB2. Contrary to
G(7) and G(3)-positions, the EEML,HB1values in A(1)
and A(3)-positions are in agreement with the charge/radius (q/rad) ratio
of cations. This opposite order is reversed for EEML,HB2values. For each ion, the EEML,HB1 and
EEML,HB2 values in
AsynGanti mismatch increase respectively
as following:
A(1) > A(3) > G(3) > G(7)
G(7) > G(3) > A(1) > A(3)
As evident from Tables 1 and 5, the
AantiGanti configuration is higher in
the absolute values of binding energy than the
AsynGanti configuration, indicating that
AantiGanti configuration is more stable
than AsynGanti one. Also, the absolute
values of hydrogen bonding intermolecular energies
(EEML,HB ) in AantiGantimismatch are higher than AsynGanti ones.
The most geometrical parameters of the considered systems are given in
Table 6. The results indicat that the length of HB1 and HB2 in
AsynGanti are greater than corresponding
in AantiGanti mispair. One can see that
dHB1 in A(1) and A(3)-sites decreases, whereas
dHB2 increases upon interactions with alkali ions. An
opposite behavior is observed in G(7) and G(3)-sites. The highest
contraction in the HB1 and HB2 bond lengths correspond to
Li+ cation in A(1) and G(7)- positions, respectively.
Also, the highest expansion in the HB1 and HB2 bond lengths correspond
to Li+ cation in G(7) and A(3)- positions,
respectively. The results indicate that unlike A(1) and A(3)- positions,
increase in ion charge density in G(7) and G(3)-positions is accompanied
by increasing in HB1 bond lengths. A reverse order are found for HB2
bond lengths. The results indicate that the increasing in
dHB is accompanied by decreasing of corresponding
EEML,HB values and vice versa.
Unlike A(1) and A(3)-sites, the interaction of cations
with G(7) and G(3)-sites leads to increases q1and q2 values
corresponding HB1. A reverse order are found for q1and q2 values
corresponding HB2. Contrary to A(1) and A(3)- positions, the q1and q2
values corresponding HB1 in G(7) and G(3)-positions are in agreement
with the charge/radius (q/rad) ratio of cations. This behavior is
reversed for HB2. There are good relationships between
|q1|, q2 and
corresponding bond length values. The maximum value of
dHB is accompanied by the highest
|q1 | and q2 values
for any type of hydrogen bond and vice versa. Figure 6 shows that there
are second order polynomial relationships between the absolute values of
q1 and q2 and corresponding
EEML for each hydrogen bond in considered systems.
The results of NBO analysis are gathered in Table 7. The results
indicate that the cation binding to N3 and N1 atoms of isolated adenine
increases positive charge of H atom participating in HB1and decreases negative charge of N atom participating in
HB2. One can expected that the strength of
HB1 increases due to interaction cations with adenine in
these positions. An opposite behavior is expected for HB2. The changes
in atomic charge on N3 and N7 atoms in isolated guanine in the presence
of cations are discussed in previous section. The most important
donor–acceptor interactions connected to HB1 and
HB2 are LpO →σ *N–H and LpN →σ *N–H, respectively. The results indicate that
the E(2) values of HB1 and HB2 in
AantiGanti are greater than
corresponding in AsynGanti mispair.
Unlike G(3) and G(7)-sites, interaction of cations with A(1) and
A(3)-sites increase the E(2) values of
HB1. This behavior is reversed for
E(2) values of HB2. Contrary to G(7) and
G(3)-positions, increase in ion charge density in A(1) and A(3)-
positions is accompanied by increasing in E(2) values
corresponding HB1. An opposite behavior are found for HB2. The results
indicate that second order polynomial relationship exists between the
E(2) values and corresponding dHB with
coefficient of determination R2=0.9992 and
R2=0.9982 respectively for HB1 and
HB2 in studied systems. For each hydrogen bonds, there
is a good linear relationship between EEML values and
corresponding E(2) values of these interaction. These
correlations are shown in Figure 7(a).
As given in Table 8, the ρHB1 and ρHB2values obtained using AIM analysis show that cations binding to N3 and
N1 atoms of adenine strengthens HB1 and weakens
HB2 in AsynGantimispair. Contrary to HB2, the strength of
HB1 decreases in the presence of cations in G(7) and
G(3)- sites. Unlike G(7) and G(3)- positions, the ρHB1values in A(1) and A(3)-positions are in agreement with the
charge/radius (q/rad) ratio of cations. This behavior is reversed for
ρHB2 values. The results indicate that the
ρHB1 and ρHB2 values in
AantiGanti are greater than
corresponding in AsynGanti mispair.
The nature of hydrogen bonds in
AsynGanti mispair involving cation is
dependent on position of ions. In the presence of cations in N1 and N3
atoms of adenine, HB1 has medium strength while HB2 of weak strength is
observed. Also, AsynGanti mispair
involving cations in G(7) and G(3)- positions are characterized by the
positive values of ∇2ρ(r) and H(r) in the BCP of the
HB1 showing that this interaction may be classified as weak bonds.
Although ∇2ρ(r) at the BCP of the HB2 in systems
involving cations in N3 and N7 atoms of guanine is positive, H(r) is
negative, indicating that HB2 has medium strength. There are good linear
relationships between E(2) values and corresponding
ρ(r) at the BCP of hydrogen bonds of considered systems.
The linear coefficients of determination between ρHB1,
ρHB2 and E(2) values are equal to
0.9994 and 0.9981, respectively. Also, there are good linear
correlations between ρ(r) and corresponding
EEML values in studied systems. This correlation is
displayed in Figure 7(b).