224
N. Tshilande and L. Mammino
living organism. A similar quick evaluation of the octanol/water partition coefficient
for MODL yields 3.54563, confirming the greater affinity for water of the OH-rich
ABDE ring system, and the solubility-decreasing effect of the bulky hydrocarbon R
in MYRA, c-DBPO and t-DBPO.
3.4.2 Adducts with Explicit Water Molecules
Adducts with explicit water molecules were calculated for low energy conformers
of MYRA. Four types of adducts were considered: adducts with only one water
molecule binding to one of the donor or acceptor sites of MYRA; adducts with
two water molecules binding to the two atoms of an OH; adducts with two water
molecules binding to the two atoms of an OH and a third water molecule bridging
them; and adducts with several explicit water molecules. The first type of adducts
is meant to provide indications about the H-bonding strength of individual sites (or
binding-site preferences for the water molecules, [14, 39]); the second type indicates
whether the two water molecules binding to a given OH bind also to each other; the
third type provides indications about the preference for the presence of a bridging
water molecule and about the preferred arrangements of three water molecules in the
vicinity of an OH; and the last type is meant to approximate possible arrangements
in the first solvation layer (which comprises the water molecules attached to MYRA
and those bridging them). Figure 7 shows the geometries of representative adducts
and fig. S16 shows the geometries of all the calculated adducts.
The adducts are denoted with acronyms providing information on the conformer
of MYRA, on the number of water molecules and on their binding sites. Each binding
site is denoted by an uppercase letter, as listed in Table 4. The acronym contains the
symbols denoting the conformer of MYRA, the list of the binding sites to which the
water molecules are H-bonded and the total number of water molecules (which may
be greater than the number of binding sites, when water molecules bridging those
attached to sites of MYRA are present). For example, d-r-η-p-a-e-j-L-1aq denotes
an adduct of conformer d-r-η-p-a-e-j with one water molecule (1aq) attached to O10
(L); d-r-η-p-a-e-j-LG-2aq denotes an adduct of conformer d-r-η-p-a-e-j with two
water molecules (2aq), attached to O10 (L) and H16 (G) respectively; d-r-η-p-a-ej-LG-3aq denotes an adduct of conformer d-r-η-p-a-e-j with three water molecules
(3aq), two of which are attached to O10 (L) and H16 (G) respectively, while the third
one bridges them.
Table S81 reports the relative energies of the calculated adducts and the MYRAwater interaction energy (E interaction ), calculated as explained in Sect. 2. Since relative energies have a meaning only for adducts with the same number of water
molecules, the adducts are grouped according to the number of water molecules.
Table S82 reports the distances between the water molecules and the atoms of MYRA
to which they are attached (bond lengths of the intermolecular H-bonds).
For the adducts with one water molecule H-bonded to different donor or acceptor
sites of the MYRA molecule, the MYRA-water interaction energy corresponds to
the energy of the MYRA-water intermolecular H-bond. Similarly to other findings
N. Tshilande and L. Mammino
living organism. A similar quick evaluation of the octanol/water partition coefficient
for MODL yields 3.54563, confirming the greater affinity for water of the OH-rich
ABDE ring system, and the solubility-decreasing effect of the bulky hydrocarbon R
in MYRA, c-DBPO and t-DBPO.
3.4.2 Adducts with Explicit Water Molecules
Adducts with explicit water molecules were calculated for low energy conformers
of MYRA. Four types of adducts were considered: adducts with only one water
molecule binding to one of the donor or acceptor sites of MYRA; adducts with
two water molecules binding to the two atoms of an OH; adducts with two water
molecules binding to the two atoms of an OH and a third water molecule bridging
them; and adducts with several explicit water molecules. The first type of adducts
is meant to provide indications about the H-bonding strength of individual sites (or
binding-site preferences for the water molecules, [14, 39]); the second type indicates
whether the two water molecules binding to a given OH bind also to each other; the
third type provides indications about the preference for the presence of a bridging
water molecule and about the preferred arrangements of three water molecules in the
vicinity of an OH; and the last type is meant to approximate possible arrangements
in the first solvation layer (which comprises the water molecules attached to MYRA
and those bridging them). Figure 7 shows the geometries of representative adducts
and fig. S16 shows the geometries of all the calculated adducts.
The adducts are denoted with acronyms providing information on the conformer
of MYRA, on the number of water molecules and on their binding sites. Each binding
site is denoted by an uppercase letter, as listed in Table 4. The acronym contains the
symbols denoting the conformer of MYRA, the list of the binding sites to which the
water molecules are H-bonded and the total number of water molecules (which may
be greater than the number of binding sites, when water molecules bridging those
attached to sites of MYRA are present). For example, d-r-η-p-a-e-j-L-1aq denotes
an adduct of conformer d-r-η-p-a-e-j with one water molecule (1aq) attached to O10
(L); d-r-η-p-a-e-j-LG-2aq denotes an adduct of conformer d-r-η-p-a-e-j with two
water molecules (2aq), attached to O10 (L) and H16 (G) respectively; d-r-η-p-a-ej-LG-3aq denotes an adduct of conformer d-r-η-p-a-e-j with three water molecules
(3aq), two of which are attached to O10 (L) and H16 (G) respectively, while the third
one bridges them.
Table S81 reports the relative energies of the calculated adducts and the MYRAwater interaction energy (E interaction ), calculated as explained in Sect. 2. Since relative energies have a meaning only for adducts with the same number of water
molecules, the adducts are grouped according to the number of water molecules.
Table S82 reports the distances between the water molecules and the atoms of MYRA
to which they are attached (bond lengths of the intermolecular H-bonds).
For the adducts with one water molecule H-bonded to different donor or acceptor
sites of the MYRA molecule, the MYRA-water interaction energy corresponds to
the energy of the MYRA-water intermolecular H-bond. Similarly to other findings