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Jan Jensen edited subsection_Hydrogen_bond_scans__.tex
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\subsection{Hydrogen bond scans}
Three systems with an N-methylacetamide and a hydrogen bond acceptor were the basis of the \HN hydrogen bond parameterization. The hydrogen bonding system for the negatively charged aspartic and glutamic acids side chains were modeled with an acetate anion. The system for bonding with the alcohol groups of threonine and serine was done with a methanol molecule. The system for bond with another backbone segment was modeled with an additional N-methylacetamide. The \HA scans used a methyl capped alanine peptide to model the donor residue backbone and the same three molecules to model the acceptors. See {\bf \ref{supinfo} Supplementary Information} \fref{fig:hbondscans}{\bf-\ref{fig:ALAscans}} for schematics of the model system used.
For \HN the scan was done by scanning over the hydrogen bond length $r_{OH}$, the bond angle $\theta$ defined by H..O=C or H..O-C and the dihedral angle $\rho$ defined by H..O=C-N, H..O=C-C or H..O-C(..)H\textsuperscript{O}. The bond length scan was scanned from $1.5$ \AA\xspace to $4.0$ \AA\xspace in $0.125$ Å steps. $\theta$ was scanned from $180$ to $90\deg$ in $10\deg$ steps and $\rho$ was done in the entire range $-180$ to $180$.
The \HA hydrogen bonding the scan was done equivalently. The bond length $r_{OH\alpha}$ was scanned from $1.8$ to $4.0$ \AA\xspace in steps of $0.2$ \AA. The bond angle $\theta$ defined by H\(\alpha\)..O=C or H\(\alpha\)..O-C was scanned from $180$ to $90^\circ$ with $10\deg$ steps size. The $\rho$ dihedral H\(\alpha\)..O=C-N, H\(\alpha\)..O=C-C and H\(\alpha\)..O-C(..)H\textsuperscript{O} was scanned in steps of $15^\circ$ over the entire range.
To get the change in chemical shift caused by the hydrogen bonding the chemical shift of systems without hydrogen bonding were subtracted from the scans. The result of the scan is interpolated and saved in another set of .npy files.
