H Capping

Simple Replacement

The simplest possible capping scheme. When a bond between an atom \(X\) and an atom \(Y\) is severed such that \(X\) is in the fragment \(F\), but \(Y\) is not. This capping scheme adds a hydrogen atom to \(F\) at the location of \(Y\).

Standard Distance

This capping scheme is a slight variation on Simple Replacement. Given a bond between an atom \(X\) and an atom \(Y\) which has been severed such that \(X\) is in the fragment \(F\), but \(Y\) is not, this capping scheme adds a hydrogen atom to \(F\) such that the \(X\)-H bond length corresponds to the length of a “typical \(X\)-H bond”. In general the location of the cap will NOT be the location of \(Y\).

In the context of MTA this capping scheme is first described by Babu and Gadre¹. A more detailed description is given later by Rahalkar et al.⁷⁷. To our knowledge, the exact values of the standard bond length is not given.

DCLC Capping Method

Li and Li⁵⁷ introduced a capping method which is a slight variation on the Standard Distance method. If we are breaking an \(X\)-\(Y\) bond, the \(X\)-H bond distance is set to the average of any existing \(X\)-H bonds (e.g., if we are capping a carbon which is part of a CH2 group, you average the two existing C-H bonds). If there are no other \(X\)-H bonds the DCLC capping method falls back to Standard Distance.

One of the somewhat unique features of DCLC is that it allows for severing non-standard bonds (e.g. multiple bonds, or bonds on charged species). To accomplish this, DCLC actually includes two more steps beyond placing the original H caps. First, one adds or removes additional hydrogens to \(X\) in order to satisfy the valency of \(X\) (adding is needed when severing a multiple bond, whereas removing is needed when \(X\) is positively charged). Second, a constrained geometry optimization is performed (only the caps can move) to obtain the final positions. N.B. the geometry optimizaton is only performed if the origninal \(X\)-H capping was insufficient.

Li and Li⁵⁷ provided the standard distances of 1.07, 1.00, and 0.96 \(\AA\) for C-H, N-H, and O-H bonds respectively.

Weighted Distance

As part of the SMF method Deev and Collins¹¹ introduced a capping method. Say we are breaking a bond \(X-Y\) and that \(X\) is in the fragment, then a hydrogen atom is placed at the point \(\mathbf{r}_H\) given by:

\[\mathbf{r}_H = \mathbf{r}_X + c\left(\mathbf{r}_Y - \mathbf{r}_X\right),\]

where \(\mathbf{r}_X\) is the position of \(X\), \(\mathbf{r}_Y\) is the position of \(Y\), and \(c\) is the ratio of a normal \(X-H\) bond to a normal \(X-Y\) bond.