The influence of metal alkali binding on the properties of
hydrogen bonds in AantiGanti mispair
The O6 of guanine and N1 of adenine in the
AantiGanti mispair are blocked by the
hydrogen bonding. One can expect that N3 and N7 of guanine and adenine
to be principal acceptors of cations. The G(3), G(7), A(3) and A(7)
symbols are used to display these positions, respectively. The schematic
representation of optimized structure of
AantiGanti mispair in the presence of
cations are presented in Figure 2. In agreement with previous studies
[11. Sÿponer, J., Burda,
J.V., Sabat, M., Leszczynski, J., Hobza, P. J. Phys. Chem. A,1998 , 102, 5951-5957.,34], calculations indicate
that there is simultaneous coordination of the cation to both the N7 and
O6 sites of guanine.
The binding energy has been evaluated using the following equation
∆E =Emispair ˗ ∑ Emon
Where Emispair and Emon are the energies
of AantiGanti mispair and monomers in
their optimized geometries (DNA bases, metal-adenine or metal-guanine),
respectively (see Table 1). Unlike A(3) position, the cations binding to
A(7), G(7) and G(3)-positions amplified the absolute values of binding
energy ( ∆E ). For each ion type, the G(3) tautomer is the most stable
among all. Contrary to A(7) position, the ∆Evalues in A(3), G(7) and
G(3)-positions are in agreement with the charge/radius (q/rad) ratio of
cations.
Also, the interaction (ΔEint) and deformation
(ΔEdef) energies of the considered systems were
calculated. The interaction energies were evaluated as the difference
between the energy of the mispair and the sum of the energies of the
separated monomers, by the same geometries as they have in the complex.
The difference between the binding energy and the interaction energy is
the deformation energy of the monomers (see Table 1). Unlike
ΔEdef, the value of ΔEint is negative
and makes a positive contribution to the ΔE. As evident from Table 1,
the interaction energy is the most dominant contribution to the binding
energy in all studied systems. The good relationship is found between
∆Eint and ∆E values with coefficient of determination
R2= 0.9929 in studied systems.
The NH…O and NH…N hydrogen bonding (HB1 and HB2,
respectively) intermolecular energies were calculated based on the
Espinosa–Molins–Lecomte (EML) empirical criteria based on the obtained
electron density distribution at the BCPs of the hydrogen bonds
EEML,HB = 0.5V(r)
Where V(r) is the value of a local potential energy at the BCPs (see
Table 1). Contrary to G(7) and G(3)-positions, the absolute value of
EEML,HB1 ( EEML,HB1) in A(7) and
A(3)-positions upon interactions with alkali ions increases. An opposite
behavior is found for EEML,HB2. The results indicate
that unlike G(7) and G(3)-positions, increase in ion charge density in
A(7) and A(3)-positions is accompanied by increasing in
EEML,HB1and decreasing in the
EEML,HB2values. For each ion, the
EEML,HB1 and EEML,HB2 orders in
AantiGanti mismatch are respectively as
following:
A(7) > A(3) > G(3) > G(7)
G(7) > G(3) > A(7) > A(3)
The NH…O and NH…N hydrogen bond lengths
(dHB1 and dHB2, respectively) in
AantiGanti mismatch have been changed
after interaction with cations. These distances are often treated as a
rough measure of the strength of hydrogen bonds. As reported in Table 2,
dHB1 in A(7) and A(3)-positions decreases, whereas
dHB2 increases upon interactions with alkali ions. A
reverse behavior is found for G(7) and G(3)-positions. The highest
contraction in the HB1 and HB2 bond lengths correspond to
Li+ cation in A(7) 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. Contrary to A(3) and A(7) positions, the
dHB1 values in G(7) and G(3)-positions are in agreement
with the charge/radius (q/rad) ratio of cations. An opposite behavior is
found for dHB2 values. Also, the results indicate that
the shortest hydrogen bond length is related to highest absolute value
of corresponding EEML,HB and vice versa.
For each individual NH…X (X=O, N) hydrogen bond, the combinations
of dN–H and dX···H have been shown to
be very useful for studying hydrogen bonding phenomenon [22.
Golubev, N. S., Shenderovich, I. G., Smirnov, S. N., Denisov, G. S.,
Limbach, H. H. Chem Eur J , 1999 , 5, 492–497.].
q1 = 0.5 (dN–H ˗
dX···H)
q2 = dN–H + dX···H
Whereas the proton in NH…X (X=O, N) hydrogen bond is located on
average closer to N, the q1 values is negative. On the
other hand, q2 value goes through a minimum that leads
to the strongly Nδ+···H···Xδ−hydrogen bond. The values of q1 and q2in studied systems are also gathered in Table 2. Contrary to A(7) and
A(3)-positions, the absolute values of q1(q1) and q2 associated with HB1
increase in G(7) and G(3)-positions. This behavior is reversed for
HB2. The results indicate that unlike A(7) and A(3)-
positions, increase in ion charge density in G(7) and G(3)-positions is
accompanied by increasing in q1and q2values corresponding HB1. A reverse order are found for
q1and q2 values corresponding HB2.
For two type of considered hydrogen bond, there are good relationships
between |q1|, q2 and
corresponding bond length values. As evident from Figure 3, second order
polynomial relationships are found between the absolute values of
q1 and q2 and corresponding
EEML for each hydrogen bond in considered systems.
Natural bond orbital (NBO) analysis stresses the role of intermolecular
orbital interaction in the complex. In NBO theory, atomic charge
assignments are based on natural population analysis, where each natural
atomic charge is simply determined from the summed natural atomic
orbitals populations on the atom [33. Reed, A. E., Weinstock,
R. B., Weinhold, F. J. Chem. Phys . 1985 , 83, 735−746.].
The atomic charge on atoms involved in hydrogen bond formation in
isolated adenine and guanine in the presence of cations have been
calculated by NBO approach. One can see from Table 3 that the cation
binding to N7 and N3 atoms of isolated adenine increases positive charge
of H atom participating in HB1 and 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. This behavior is reversed for
HB2. The interaction of cations with N3 atom of isolated
guanine leads to increases positive charge of H atom participating in
HB2 and decreases negative charge of O atom
participating in HB1. Thus, the strength of
HB1 and HB2 are expected to decrease and increase,
respectively.
The negative and positive atomic charge on O and H atoms participating
respectively in HB1 and HB2 increases
due to interaction of cations with N7 atom of isolated guanine. One can
expected that the strength of HB2 increases due to
interaction cations with guanine in N7 site. Although, the negative
atomic charge on O atom increased in this position, the strength of
HB1 decreases. This can be explained by the fact that a
second attractive side in guanine, i.e. not only nitrogen N7 but also
oxygen O6.
For each acceptor NBO (j) and donor NBO (i), the stabilization energy
E(2) associated with electron delocalization between
donor and acceptor is estimated as:
\begin{equation}
E^{2}=q_{i}\frac{\left(F_{i,j}\right)^{2}}{\varepsilon_{j}-\varepsilon_{i}}\nonumber \\
\end{equation}Where qi is the orbital occupancy, εiand εj are diagonal elements, and Fi,jis the off-diagonal NBO Fock matrix element [45]. In Table 3, we
analyze the main contributions to donor-acceptor second-order energies
(E2). The most important donor–acceptor interactions
connected to HB1 and HB2 are
LpO → σ *N–H and
LpN → σ *N–H, respectively. The
results indicated that interaction of cations with N3 and N7 sites of
adenine increase the E(2) values of
HB1. A reverse behavior is found for N3 and N7 sites of
guanine. The E(2) values of HB2amplified/diminished in the presence of cations in N3 and N7 positions
of guanine /adenine. Contrary to G(7) and G(3)-positions, increase in
ion charge density in A(7) and A(3)- positions is accompanied by
increasing in E(2) values corresponding HB1. An
opposite behavior are found for HB2. For HB1 and
HB2 interactions, there is a good linear relationship
between EEML values and corresponding
E(2) values of these interaction (see Figure 4(a)).
Also, the results indicate that second order polynomial correlation
exists between the E(2) values and corresponding
hydrogen bond lengths with coefficient of determination
R2=0.9985 and in R2=0.9980
respectively for HB1 and HB2 in studied
systems.
The QTAIM is useful to analyze various intra and intermolecular
interactions. The results indicate that the bond critical points of the
hydrogen bonds was found. The electron density at the BCP of the
hydrogen bond may be treated as a measure of the hydrogen bond strength
[44. Galvez, O., Gomez, P. C., Pacio, L. F. J. Chem.
Phys . 2003 , 118, 4878‒4895.,55. Domagala, M.,
Grabowski, S. J. J. Phys. Chem. A. 2005 , 109,
5683‒5688.]. Rozas et al. have introduced a classification of
hydrogen bonds according to their strength [66. Rozas, I.,
Alkorta, I., Elguero, J. J. Am. Chem. Soc . 2000 , 122,
11154‒11161.
Figure1. Electrostatic potentials mapped on the molecular surfaces of
isolated (a) guanine, (b) adenine bases with VMD software.
Figure 2. The Schematic representation of optimized structure of
AantiGanti mispair in the presence of
cations (M= Li+, Na+ and
K+ ) in (a) N3 (b) N7 sites of adenine and (c) N3
(d) N7 sites of guanine, respectively.
Figure 3. Relationships between EEML values and (a)
q1 and (b) q2 for each hydrogen bond
in AantiGanti systems involving
cations. The (●) and (▲) symbols correspond to HB1 and
HB2, respectively.
Figure 4. Relationships between EEML and corresponding
(a) E(2) and (b) ρ(r) values for each hydrogen bond
in AantiGanti systems involving
cations. The (●) and (▲) symbols correspond to HB1 and
HB2, respectively.
Figure 5. The Schematic representation of optimized structure of
AsynGanti mispair in the presence of
cations (M= Li+, Na+ and
K+ ) in (a) N1 (b) N3 sites of adenine and (c) N3
(d) N7 sites of guanine, respectively.
Figure 6. Relationships between EEML values and (a)
q1 and (b) q2 for each hydrogen bond
in AsynGanti systems involving
cations. The (●) and (▲) symbols correspond to HB1 and
HB2, respectively.
Figure 7. Relationships between EEML and corresponding
(a) E(2) and (b) ρ(r) values for each hydrogen bond
in AsynGanti systems involving
cations. The (●) and (▲) symbols correspond to HB1 and
HB2, respectively]. Weak H-bonds show both
∇2ρ(r) and H(r) values positive; for medium H-bonds
∇2ρ(r)> 0 and H(r)< 0 and also
for strong H-bonds the ∇2ρ(r) as well as H(r) are
negative. The results of AIM analysis are gathered in Table 4. Unlike
G(3) and G(7)-positions, the ρ(r) values at the BCP of the HB1
(ρHB1) in the presence of cations in N7 and N3-positions
of adenine increase. The ρ(r) values at the BCP of HB2(ρHB2) amplified/diminished in the presence of cations
in N3 and N7 positions of guanine /adenine. Contrary to G(7) and G(3)-
positions, the ρHB1 values in A(3) and A(7) positions
are in agreement with the charge/radius (q/rad) ratio of cations. An
opposite behavior is found for ρHB2 values. The nature
of hydrogen bonds in considered complexes is dependent on position of
cations. In the presence of cations in N3 and N7 sites of adenine, HB1
has medium strength while HB2 of weak strength is observed. Here,
AantiGanti mispair involving cations in
N3 and N7 positions of guanine 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 positions of guanine is positive, H(r) is negative,
indicating that HB2 has medium strength. The results indicate that 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 (and ρHB2) and
E(2) values are equal to 0.9993 (and 0.9968). The
ρ(r) values and corresponding distance of interactions
also show good reverse relationships. Figure 4(b) shows that there are
good linear relationships between ρ(r) values and
corresponding EEML in studied systems. One can see that
the maximum value of the ρ(r) is related to highest
absolute value of corresponding EEML for both types of
hydrogen bond and vice versa.