water-water interactions). The main objective of calculating these adducts was that
of enabling comparison of the binding strengths of individual sites. Neglecting
BSSE corrections does not appear to greatly affect comparisons among analogous
molecular systems when the correction is sufficiently small [31] (all the adducts
with one water molecule consist of one ARZ molecule and one water molecule, so,
they are analogous molecular systems). It was thus assumed that the comparisons
among these adducts remain reliable also without BSSE correction. Neglecting the
correction proved expedient also in view of the high number of calculated adducts
of this type.
All the calculations were performed with GAUSSIAN 03, Revision D 01 [32].
All the energy values reported are in kcal/mol and all the distances are in Å. For
conciseness sake, the calculation methods will be denoted simply as HF for HF/
6-31G(d,p) and DFT for DFT/B3LYP/6-31+G(d,p) in the text.
Detailed information, including tables with all energy values and H-bond
parameters for the calculated adducts, and figures showing the geometries of the
calculated adducts, is provided in the Supplementary Information.
3 Results
3.1 Naming of Conformers and Adducts
Following a practice introduced since the initial studies of ACPLs [6–10], the
conformers are denoted by acronyms which provide information about their
characteristics, to enable easy tracking of geometric characteristics and energyinfluencing features. The acronyms for the ARZ conformers start with the number
denoting the mutual orientation of the moieties. The other geometry features are
denoted by letters, whose meanings are listed in Table 1 [5]. The two lowest energy
conformers and their acronyms are shown in Fig. 3.
In order to identify them in a straightforward way, the adducts are denoted by the
acronym of the ARZ conformer at their centre, followed by information about the
water molecules. For the adducts with one water molecule, the name of the conformer is followed by ‘1aq’ and by the position to which the water molecule is
attached. Thus, 1-d-r-ξ-αδ-1aq-O14 denotes the adduct of the 1-d-r-ξ-αδ conformer
in which one water molecule is attached to O14; 1-d-r-αδ-1aq-H17-π1 denotes the
adduct of 1-d-r-αδ in which a water molecule is attached to H17 and is also
interacting with the π bond of the prenyl chain; and so on. The adducts containing
more than one water molecule are denoted with the name of the conformer followed
by the number of molecules in the adduct. For instance, 1-d-r-ξ-αδ-5aq denotes an
adduct of conformer 1-d-r-ξ-αδ with 5 water molecules. Since different arrangements of the water molecules are possible for adducts of the same conformer and
with the same number of water molecules, letters are added at the end of the
acronym to distinguish them from one another. However, the information on the
site to which each water molecule is attached would be too bulky to summarise it in
an acronym, and 3D models showing the arrangements of the water molecules are
288
L. Mammino
of enabling comparison of the binding strengths of individual sites. Neglecting
BSSE corrections does not appear to greatly affect comparisons among analogous
molecular systems when the correction is sufficiently small [31] (all the adducts
with one water molecule consist of one ARZ molecule and one water molecule, so,
they are analogous molecular systems). It was thus assumed that the comparisons
among these adducts remain reliable also without BSSE correction. Neglecting the
correction proved expedient also in view of the high number of calculated adducts
of this type.
All the calculations were performed with GAUSSIAN 03, Revision D 01 [32].
All the energy values reported are in kcal/mol and all the distances are in Å. For
conciseness sake, the calculation methods will be denoted simply as HF for HF/
6-31G(d,p) and DFT for DFT/B3LYP/6-31+G(d,p) in the text.
Detailed information, including tables with all energy values and H-bond
parameters for the calculated adducts, and figures showing the geometries of the
calculated adducts, is provided in the Supplementary Information.
3 Results
3.1 Naming of Conformers and Adducts
Following a practice introduced since the initial studies of ACPLs [6–10], the
conformers are denoted by acronyms which provide information about their
characteristics, to enable easy tracking of geometric characteristics and energyinfluencing features. The acronyms for the ARZ conformers start with the number
denoting the mutual orientation of the moieties. The other geometry features are
denoted by letters, whose meanings are listed in Table 1 [5]. The two lowest energy
conformers and their acronyms are shown in Fig. 3.
In order to identify them in a straightforward way, the adducts are denoted by the
acronym of the ARZ conformer at their centre, followed by information about the
water molecules. For the adducts with one water molecule, the name of the conformer is followed by ‘1aq’ and by the position to which the water molecule is
attached. Thus, 1-d-r-ξ-αδ-1aq-O14 denotes the adduct of the 1-d-r-ξ-αδ conformer
in which one water molecule is attached to O14; 1-d-r-αδ-1aq-H17-π1 denotes the
adduct of 1-d-r-αδ in which a water molecule is attached to H17 and is also
interacting with the π bond of the prenyl chain; and so on. The adducts containing
more than one water molecule are denoted with the name of the conformer followed
by the number of molecules in the adduct. For instance, 1-d-r-ξ-αδ-5aq denotes an
adduct of conformer 1-d-r-ξ-αδ with 5 water molecules. Since different arrangements of the water molecules are possible for adducts of the same conformer and
with the same number of water molecules, letters are added at the end of the
acronym to distinguish them from one another. However, the information on the
site to which each water molecule is attached would be too bulky to summarise it in
an acronym, and 3D models showing the arrangements of the water molecules are
288
L. Mammino