164
L. Mammino
medium, thus making the consideration of those three solvents significant also in
view of the possible distribution of FNGB molecules in the different media in an
organism.
All the calculations were performed on desktop PCs using Gaussian 03, Revision
D 01 [51]. Visualization utilised GaussView [53] and Chem3D [52].
All the reported energy values are in kcal/mol and all the distances are in Å.
3 Results
3.1 Naming of Conformers and Complexes
The study of ACPLs [26–28, 32, 33] has shown the importance of keeping track of
the relevant features characterising the conformers, in a way that enables quick comparisons of specific characteristics. This is done through acronyms in which different
letters are utilised to denote individual characteristics. For what could be called the
“canonical structure” of ACPLs (the pattern shown in Fig. 1), the acronym system
remains basically the same [e.g., 6, 7, 26–28, 32, 33]. For ACPLs with more complex
structures, the symbols to be used in the acronyms are adapted to the characteristics
of the given structure. In the case of FNGB, the main characterising features and
stabilising factors are the IHBs present in a conformer; therefore, each of the possible IHBs is denoted by a symbol, with the letter d denoting the H15···O14 first IHB
as in all previous works, and Greek letters denoting the other IHBs (H219···O10,
H19···O8, H30···O16, H30···O25, H31···O25, H15···O19 and the O–H···π IHBs). All
the symbols are listed in Table 1. Figure 3 shows the possible IHBs through selected
conformers, thus also illustrating the meaning of the corresponding symbols. Since
the orientation of the prenyl chain has been found to be energy-influencing in some
prenylated ACPLs, it is also assigned symbols, in the same way as for hyperguinones
[7]. Thus, for instance, d-β-γ-ε-b denotes a conformer having the H15···O14 IHB (d),
the H19···O8 IHB (β), the H16···O18 IHB (γ), and the H31···O25 IHB (ε), and the
prenyl chain oriented ‘upwards’ and bending towards the benzene ring (b); d-α-ε-ηe denotes a conformer having the H15···O14 IHB (d), the H19···O25 IHB (α), the
H31···O25 IHB (ε), the H16···π1 IHB (η) and the prenyl chain oriented ‘downwards’
and bending towards the benzene ring (e); and so on.
The complexes are also denoted by acronyms, specifying both the type of conformer and the binding site/s of the Cu
2+ ion (by writing “Cu” followed by the binding
sites). For instance, d*-β-γ-a-Cu-O25-O30 denotes a complex where the H15···O14
IHB is present (d) and H15 has transferred to O14 on complexation (*), the H19···O8
and H16···O18 IHBs are also present (β and γ), the prenyl chain is oriented “upwards”
(a) and the Cu
2+ ion binds simultaneously to O25 and O30.
While the IHBs present in the conformers of the isolated molecule are always easily recognisable as such, because their bond length is shorter than the sum of the van
der Waals radii of the O and H atoms (2.7 Å) and their directionality is sufficiently
L. Mammino
medium, thus making the consideration of those three solvents significant also in
view of the possible distribution of FNGB molecules in the different media in an
organism.
All the calculations were performed on desktop PCs using Gaussian 03, Revision
D 01 [51]. Visualization utilised GaussView [53] and Chem3D [52].
All the reported energy values are in kcal/mol and all the distances are in Å.
3 Results
3.1 Naming of Conformers and Complexes
The study of ACPLs [26–28, 32, 33] has shown the importance of keeping track of
the relevant features characterising the conformers, in a way that enables quick comparisons of specific characteristics. This is done through acronyms in which different
letters are utilised to denote individual characteristics. For what could be called the
“canonical structure” of ACPLs (the pattern shown in Fig. 1), the acronym system
remains basically the same [e.g., 6, 7, 26–28, 32, 33]. For ACPLs with more complex
structures, the symbols to be used in the acronyms are adapted to the characteristics
of the given structure. In the case of FNGB, the main characterising features and
stabilising factors are the IHBs present in a conformer; therefore, each of the possible IHBs is denoted by a symbol, with the letter d denoting the H15···O14 first IHB
as in all previous works, and Greek letters denoting the other IHBs (H219···O10,
H19···O8, H30···O16, H30···O25, H31···O25, H15···O19 and the O–H···π IHBs). All
the symbols are listed in Table 1. Figure 3 shows the possible IHBs through selected
conformers, thus also illustrating the meaning of the corresponding symbols. Since
the orientation of the prenyl chain has been found to be energy-influencing in some
prenylated ACPLs, it is also assigned symbols, in the same way as for hyperguinones
[7]. Thus, for instance, d-β-γ-ε-b denotes a conformer having the H15···O14 IHB (d),
the H19···O8 IHB (β), the H16···O18 IHB (γ), and the H31···O25 IHB (ε), and the
prenyl chain oriented ‘upwards’ and bending towards the benzene ring (b); d-α-ε-ηe denotes a conformer having the H15···O14 IHB (d), the H19···O25 IHB (α), the
H31···O25 IHB (ε), the H16···π1 IHB (η) and the prenyl chain oriented ‘downwards’
and bending towards the benzene ring (e); and so on.
The complexes are also denoted by acronyms, specifying both the type of conformer and the binding site/s of the Cu
2+ ion (by writing “Cu” followed by the binding
sites). For instance, d*-β-γ-a-Cu-O25-O30 denotes a complex where the H15···O14
IHB is present (d) and H15 has transferred to O14 on complexation (*), the H19···O8
and H16···O18 IHBs are also present (β and γ), the prenyl chain is oriented “upwards”
(a) and the Cu
2+ ion binds simultaneously to O25 and O30.
While the IHBs present in the conformers of the isolated molecule are always easily recognisable as such, because their bond length is shorter than the sum of the van
der Waals radii of the O and H atoms (2.7 Å) and their directionality is sufficiently