Ab Initio and DFT Computational Study …
209
Calculations in solution used the Conductor-like Polarizable Continuum Model
(CPCM) [32]. They were performed with fully relaxed geometry, because reoptimization is important to identify conformational changes induced by the solvent [33]. They were performed only at the HF/6-31G(d,p) level and only for the
lower energy conformers of each of the three molecules, because of the high computational demands for molecules of this size (DFT calculations in solution proved
computationally too expensive). Three solvents with different polarities and different
hydrogen bonding abilities were selected: chloroform, acetonitrile and water; their
dielectric constants are 4.81, 36.64 and 78.54 respectively.
Representative adducts with explicit water molecules were calculated for the
lower-energy conformers of MYRA, because they are important for a better understanding of the solute-solvent interactions when the solute can form H-bonds with the
solvent molecules (as continuum solvation models do not take into explicit account
directional interactions such as H-bonds). The three molecules contain five OH
groups, each of which can be H-bond donor or H-bond acceptor to a water molecule,
and the sp
2 O of CRO can also be H-bond acceptor; this gives rise to a high variety
of possible adducts. The selection of the adducts to calculate utilised the information
in [14] and pursued objectives such as the comparison of the H-bonding ability of
the different sites of MYRA and the investigation of possible arrangements of water
molecules around the MYRA molecule. The general equation for the calculation of
the energy of the interaction between the MYRA molecule and the water molecules
attached to it (E interaction ) is [34]:
E interaction = E adduct −
E MYRA + n E aq
− E aq-aq
where E adduct is the energy of the adduct, E MYRA is the energy of the isolated conformer of the MYRA molecule, E aq is the energy of an isolated water molecule, n is
the number of water molecules in the adduct, and E aq-aq is the energy of the interactions among the water molecules in the adduct. E aq-aq needs to be considered when
the water molecules are also interacting with each other, and is evaluated through
a single-point calculation on the water molecules arranged in the same way as in
the adduct, but without the solute molecule [34]; if the energy of this arrangement
of water molecules is denoted as E aq-cluster , then E aq-aq = E aq-cluster − n E aq , and the
equation for the calculation of E interaction becomes
E interaction = E adduct −E MYRA − E aq-cluster
Both E adduct and E aq-cluster were corrected for Basis Set Superposition Error (BSSE)
using the counterpoise method [35]. The adducts were calculated at the HF/631G(d,p) level because of the costly computational demands of the supermolecular
structures.
All the calculations were performed with Gaussian 09, revision E.0.1 [36]. The
visualisation of results utilised GaussView 4.1 [37] and Chem3D [38]. All the energy
values reported in this work are in kcal/mol and all the distances are in angstroms (Å).
For the sake of conciseness, the calculation methods and the media will be denoted
209
Calculations in solution used the Conductor-like Polarizable Continuum Model
(CPCM) [32]. They were performed with fully relaxed geometry, because reoptimization is important to identify conformational changes induced by the solvent [33]. They were performed only at the HF/6-31G(d,p) level and only for the
lower energy conformers of each of the three molecules, because of the high computational demands for molecules of this size (DFT calculations in solution proved
computationally too expensive). Three solvents with different polarities and different
hydrogen bonding abilities were selected: chloroform, acetonitrile and water; their
dielectric constants are 4.81, 36.64 and 78.54 respectively.
Representative adducts with explicit water molecules were calculated for the
lower-energy conformers of MYRA, because they are important for a better understanding of the solute-solvent interactions when the solute can form H-bonds with the
solvent molecules (as continuum solvation models do not take into explicit account
directional interactions such as H-bonds). The three molecules contain five OH
groups, each of which can be H-bond donor or H-bond acceptor to a water molecule,
and the sp
2 O of CRO can also be H-bond acceptor; this gives rise to a high variety
of possible adducts. The selection of the adducts to calculate utilised the information
in [14] and pursued objectives such as the comparison of the H-bonding ability of
the different sites of MYRA and the investigation of possible arrangements of water
molecules around the MYRA molecule. The general equation for the calculation of
the energy of the interaction between the MYRA molecule and the water molecules
attached to it (E interaction ) is [34]:
E interaction = E adduct −
E MYRA + n E aq
− E aq-aq
where E adduct is the energy of the adduct, E MYRA is the energy of the isolated conformer of the MYRA molecule, E aq is the energy of an isolated water molecule, n is
the number of water molecules in the adduct, and E aq-aq is the energy of the interactions among the water molecules in the adduct. E aq-aq needs to be considered when
the water molecules are also interacting with each other, and is evaluated through
a single-point calculation on the water molecules arranged in the same way as in
the adduct, but without the solute molecule [34]; if the energy of this arrangement
of water molecules is denoted as E aq-cluster , then E aq-aq = E aq-cluster − n E aq , and the
equation for the calculation of E interaction becomes
E interaction = E adduct −E MYRA − E aq-cluster
Both E adduct and E aq-cluster were corrected for Basis Set Superposition Error (BSSE)
using the counterpoise method [35]. The adducts were calculated at the HF/631G(d,p) level because of the costly computational demands of the supermolecular
structures.
All the calculations were performed with Gaussian 09, revision E.0.1 [36]. The
visualisation of results utilised GaussView 4.1 [37] and Chem3D [38]. All the energy
values reported in this work are in kcal/mol and all the distances are in angstroms (Å).
For the sake of conciseness, the calculation methods and the media will be denoted