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Jan Jensen edited subsection_Hydrogen_bond_scans_label__.tex
almost 9 years ago
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\subsection{Hydrogen bond scans} \label{subsec:HBscan}
$\Delta \sigma_{HB}$ and $\Delta \sigma_{H\alpha B}$ (cf. Eq \ref{eqn:procs})
is are parameterized using the model systems shown in Figures \ref{fig:HB} and \ref{fig:HAB}. For $\Delta \sigma_{HB}$ the
scan scans are done by scanning over the hydrogen bond length $r_{OH}$, the bond angle $\theta_{\mathrm{H}}$ defined by H..O=C or H..O-C and the dihedral angle $\rho_{mathrm{H}}$ defined by H..O=C-N, H..O=C-C or H..O-C(..)H^{O}. The bond length scan was scanned from 1.5 to 4.0 Å in 0.125 Å steps. $\theta_{\mathrm{H}}$ was scanned from 180.0 to 90.0$^\circ$ in 10.0$^\circ$ steps and $\rho_\mathrm{H}$ was done in the entire range -180$^\circ$ to 180$^\circ$.
The \HA hydrogen bonding Similarly, for $\Delta \sigma_{H\alpha B}$ the
scan was done equivalently. The $r_{OH\alpha}$ bond length
$r_{OH\alpha}$ was is scanned from
$1.8$ 1.8 to
$4.0$ \AA\xspace 4.0 Å in steps of
$0.2$ \AA. 0.2 Å. The bond angle
$\theta$ $\theta_{\mathrm{H}\alpha}$ defined by
H\(\alpha\)..O=C H$\alpha$..O=C or
H\(\alpha\)..O-C was H$\alpha$..O-C is scanned from
$180$ 180$^\circ$ to
$90^\circ$ 90$^\circ$ with
$10^\circ$ steps a 10$^\circ$ step size. The
$\rho$ $\rho_{\mathrm{H}\alpha}$ dihedral
H\(\alpha\)..O=C-N, H\(\alpha\)..O=C-C H$\alpha$..O=C-N, H$\alpha$..O=C-C and
H\(\alpha\)..O-C(..)H\textsuperscript{O} H$\alpha\$..O-C(..)H^{O} was scanned in steps of
$15^\circ$ 15$^\circ$ over the entire range. To get the change in chemical shift caused by the hydrogen bonding the
OPBE/6-31G(d,p)//xx chemical
shift shielding of systems without hydrogen bonding
were are subtracted from the scans. The result of the scan is interpolated and saved in another set of .npy files.
The monomer geometries are optimized at the xx level of theory and kept fixed during the scan.