Quantum theory of atoms in molecules (QTAIM) analysis
Quantum theory of atoms in molecules (QTAIM) analysis has been widely
used to interpret any chemical bonds including the nature of H-bond
interaction and confirmed to be a useful and successful tool for
interpreting charge density. We carried out AIM study of electron
density at the bond critical points (BCPs) by AIM2000 software to gain
information on variation of the geometrical parameters and the H-bond
strength in the conjugate bases of Deoxy-hexose sugars.
Topological parameters (calculated at the B3LYP/6-311++G(d,p) level)
such as electron density,, and its Laplacian,, kinetic energy density, ,
potential energy density, , and H-bond energy,, at the BCPs for the
conjugate bases of Deoxy-hexose sugars are listed in Tables 5 and 6.
According to Bader theory of atom in molecules [45], if hydrogen
bond exists, the range of electron density is 0.002 to 0.035 (a.u,) and
its Laplacian is 0.024-0.139 (e/au5). The value of
electron density and its Laplacian at BCPs for the conjugate bases of
CH3-pentose fall between 0.0233-0.0439 (a.u.) and
0.0877-0.1257 (e/au5), respectively (Table 5); and
those for the conjugate bases of aldo-pentose fall between 0.0177-0.0752
(a.u.) and 0.0847-0.1380 (e/au5), respectively (Table
6). Based on these ranges, the characteristic values and at BCPs imply
the presence of H-bond interaction in the conjugate bases of
Deoxy-hexose sugars. Laplacian of electron density is related to the
chemical bond interaction energy by a local expression of the virial
theorem [38]. Based on QTAIM, a positive value of Laplacian of
electron density at BCPs indicates closed-shell electrostatic
interactions such as ionic bonds, hydrogen bonds, and van der Waals
interactions; whereas a negative value of Laplacian of the electron
density shows shared-shell electron covalent interaction [38]. Thus,
a positive value of at BCPs of H-bonds in the conjugate bases of
Deoxy-hexose sugars indicates that these H-bonds are mostly closed-shell
electrostatic interactions.
The electronic energy densityat BCPs is defined as [47]; where
refers to the electronic kinetic energy density, which is always
positive, and refers to the electronic potential energy density and must
be negative [46] . The sign of depends on which contribution,
potential or kinetic, locally prevails at BCPs and it determines whether
the accumulation of charge at a given point of r is stabilizing;
or destabilizing. Popelier [39] proposed the following criteria of
strength: for weak H-bond both and ; for medium H-bond and ; and for
strong H-bond both and . This classification shows that weak H-bonds
eventually merge with van der Waals interaction; whereas strong H-bonds
merge with covalent and polar bonds.
Different types of H-bonds are seen in the conjugate bases of
Deoxy-hexose sugars. For example, the
O2…HO1-O1 and
O2…HO3-O3 H-bonds
(Figure 3h) in the conjugate base of L-xylose (formed from deprotonation
of L-xylose at C2-HO2); and
O3…HO1-O1 and
O3…HO4-O4 H-bonds
(Figure 3e) in the conjugate base of L-arabinose (formed from
deprotonation of L-arabinose at C3-HO3)
show one bifurcated H-bond. However, the
O3…HO2-O2 and
O3…HO4-O4 H-bonds
in the conjugate base of D-ribose (formed from deprotonation of D-ribose
at C3-HO3); and
O4…HO2-O2 and
O4…HO3-O3 H-bonds
in this conjugate base (formed from deprotonation of D-ribose at
C4-HO4) exhibit two bifurcated H-bonds
(Figures 3m and 3n). Moreover, the conjugate bases of D-xylose and
L-arabinose (formed from deprotonation at
C1-HO1) do not indicate any H-bonds.
The conjugate bases of L-fucose formed from deprotonation of L-fucose at
C2-HO2 and
C4-HO4 show the
O2….HO1-O1 and
O4….HO3-O3hydrogen bonds, respectively (Figure 2b, 2d); and the conjugate base of
L-rhamnose formed from deprotonation of L-rhamnose at
C2-HO2 (Figure 2f ) indicates the
O2….HO3-O3H-bond. These three H-bonds indicate medium and normal intramolecular
H-bonds due to positive and negative . Thus, these O-H…O bonds
are categorized as partially covalent-partially electrostatic
(Pc-Pe ). Whereas, the conjugate
bases of aldo-pentose sugars exhibit normal and bifurcated
intramolecular O-H…O bonds. The normal intramolecular H-bonds in
the conjugate base of D-xylose indicate van der Waals interaction due to
> 0 and > 0. The bifurcated intramolecular
H-bonds are identified in the conjugate base of D-ribose (formed from
deprotonation of D-ribose at C3-HO3 and
C4-HO4); and in the conjugate base of
L-lyxose (formed from deprotonation of L-lyxose at
C2-HO2); and in the conjugate base of
L-arabinose (formed from deprotonation of L-arabinose at
C3-HO3). These bifurcated intramolecular
H-bonds are categorized as medium H-bonds and partially
covalent-partially electrostatic
(Pc-Pe ) interaction in nature due
to and .
According to topological parameters discussed above and results given in
Tables 5 and 6, the conjugate bases of L-fucose, L-rhamnose and
L-D-xylose indicate conventional H-bonds; whereas conjugate bases of L-
lyxose, L-arabinose, and L- arabinose show both conventional and
unconventional H-bonds.