Imperial College London

Henry Rzepa

Following on from my re-investigation of close hydrogen bonding contacts
to the [π-face of
alkenes](http://www.ch.imperial.ac.uk/rzepa/blog/?p=18165), here now is
an updated scan for H-bonds to alkynes. The search query (dataDOI:
[10.14469/hpc/2478](http://doi.org/10.14469/hpc/2478)) is similar to the
previous one:

1.  QA is any of N,O,F,Cl.
2.  X is any atom, including metals and non-metals.
3.  The carbon atoms are both specified as 2-coordinate, and the C-C
    bond type as **any**.
4.  The distance is from the hydrogen (normalised) to the C-C centroid,
    restricted to \< 2.5Å to capture just the shortest examples.
5.  The mean of the sines of the two angles subtended at the centroid is
    calculated to indicate whether the approach is orthogonal.
6.  The mean of the absolute value of the sines of the two angles
    subtended at each carbon is calculated to indicate how non-linear
    the  X-C-C angle is.
7.  Other constraints are no disorder, no errors and R \< 0.05.

![](http://www.ch.ic.ac.uk/rzepa/blog/wp-content/uploads/2017/04/SQ-triple.jpg){.aligncenter
.size-full .wp-image-18219 decoding="async" width="450"
srcset="https://www.ch.ic.ac.uk/rzepa/blog/wp-content/uploads/2017/04/SQ-triple.jpg 838w, https://www.ch.ic.ac.uk/rzepa/blog/wp-content/uploads/2017/04/SQ-triple-300x213.jpg 300w, https://www.ch.ic.ac.uk/rzepa/blog/wp-content/uploads/2017/04/SQ-triple-768x544.jpg 768w"
sizes="(max-width: 838px) 100vw, 838px"}

First the intermolecular hits (38). Prominent short examples include:

|                                                                                                                                                                                                |                                            |                                                       |                     |
|------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|--------------------------------------------|-------------------------------------------------------|---------------------|
| Entry                                                                                                                                                                                          | Article DOI                                | DataDOI                                               | H-centroid distance |
| NOXHAJ                                                                                                                                                                                         | \[cite\]10.1021/om970538m\[/cite\]         | ^‡^                                                   | 2.16Å               |
| KESDAO                                                                                                                                                                                         | \[cite\]10.1002/chem.200600139\[/cite\]^†^ | [10.5517/CC9YHJ7](https://doi.org/10.5517/CC9YHJ7)^†^ | 2.11Å               |
| ICUTAC                                                                                                                                                                                         | \[cite\]10.1021/cg050598s\[/cite\]         | [10.5517/CC9PNSD](https://doi.org/10.5517/CC9PNSD)    | 2.19Å               |
| ![](http://www.ch.ic.ac.uk/rzepa/blog/wp-content/uploads/2017/04/triple-inter-1024x672.jpg){.aligncenter .size-large .wp-image-18216 loading="lazy" decoding="async" width="450" height="295"} |                                            |                                                       |                     |

In most of the stronger examples (blue), the approach of the hydrogen is
perpendicular to the C-C bond centroid (X-axis of plot
above). Many however exhibit significant bending (Y-axis of plot
above) from linearity at the two carbons (\~173°), mostly away from the
H but in some examples towards the H!

Selected entries from the intra-molecular search (34 hits) are shown
below. Perhaps due to the intra-molecular nature, the angle of approach
of the H is more variable than the intermolecular examples and the
bending of the erstwhile X-C-C angle is again prominent. 

|                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               |                                         |                     |     |
|-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|-----------------------------------------|---------------------|-----|
| Entry                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         | Article DOI                             | H-centroid distance |     |
| [KIXFOO](https://doi.org/10.5517/CC1209V7)                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                    | \[cite\]10.1021/om4004225\[/cite\]      | 2.11Å               |     |
| [KEMVOP](https://doi.org/10.5517/CCZSZZP)                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     | \[cite\]10.1021/cs300544w\[/cite\]      | 2.16Å               |     |
| [BEMPUF](https://doi.org/10.5517/CC79LLP)                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     | \[cite\]10.1002/anie.200352693\[/cite\] | 2.14Å               |     |
| [VEWMIV](https://doi.org/10.5517/CCY1ZNL)                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     | \[cite\]10.1021/om3001179\[/cite\]      | 2.14Å               |     |
| ![](http://www.ch.ic.ac.uk/rzepa/blog/wp-content/uploads/2017/04/triple-intra-1024x690.jpg){.aligncenter .size-large .wp-image-18217 loading="lazy" decoding="async" width="450" height="303" srcset="https://www.ch.ic.ac.uk/rzepa/blog/wp-content/uploads/2017/04/triple-intra-1024x690.jpg 1024w, https://www.ch.ic.ac.uk/rzepa/blog/wp-content/uploads/2017/04/triple-intra-300x202.jpg 300w, https://www.ch.ic.ac.uk/rzepa/blog/wp-content/uploads/2017/04/triple-intra-768x518.jpg 768w, https://www.ch.ic.ac.uk/rzepa/blog/wp-content/uploads/2017/04/triple-intra.jpg 1920w" sizes="(max-width: 450px) 100vw, 450px"} |                                         |                     |     |

ωB97XD/Def2-TZVPP calculations of one intermolecular example, ICUTAC
(two molecules, dataDOI:
[10.14469/hpc/2482](https://doi.org/10.14469/hpc/2482)) and one
intramolecular case, KIXFOO (dataDOI:
[10.14469/hpc/2481](http://doi.org/10.14469/hpc/2481)). For the former,
crystal packing compressions perhaps provide some shortening of the
hydrogen bond and the molecule also includes an example of a short C-H
to π interaction (obs\[cite\]10.1021/cg050598s\[/cite\] 2.63Å).

![](http://www.ch.ic.ac.uk/rzepa/blog/wp-content/uploads/2017/04/090-1024x694.jpg){.aligncenter
.size-large .wp-image-18239 loading="lazy" decoding="async" width="450"
height="305"
srcset="https://www.ch.ic.ac.uk/rzepa/blog/wp-content/uploads/2017/04/090-1024x694.jpg 1024w, https://www.ch.ic.ac.uk/rzepa/blog/wp-content/uploads/2017/04/090-300x203.jpg 300w, https://www.ch.ic.ac.uk/rzepa/blog/wp-content/uploads/2017/04/090-768x520.jpg 768w, https://www.ch.ic.ac.uk/rzepa/blog/wp-content/uploads/2017/04/090.jpg 1098w"
sizes="(max-width: 450px) 100vw, 450px"}
![](http://www.ch.ic.ac.uk/rzepa/blog/wp-content/uploads/2017/04/095.jpg){.aligncenter
.size-large .wp-image-18240 decoding="async" width="400"
srcset="https://www.ch.ic.ac.uk/rzepa/blog/wp-content/uploads/2017/04/095.jpg 895w, https://www.ch.ic.ac.uk/rzepa/blog/wp-content/uploads/2017/04/095-264x300.jpg 264w, https://www.ch.ic.ac.uk/rzepa/blog/wp-content/uploads/2017/04/095-768x872.jpg 768w"
sizes="(max-width: 895px) 100vw, 895px"}

What is noticeable from reading the abstracts of the articles cited
above is that these hydrogen bonds are rarely commented upon by the
authors and it does seem that most of these close contacts are
serendipitous (they were not designed). All are somewhat longer than the
shortest distances encountered for alkenes and it would be interesting
to establish if this is an intrinsic property of the triple bond or
whether less effort has hitherto been expended on designing
closer approaches.

------------------------------------------------------------------------

^‡^ Not all entries have an assigned dataDOI at CCDC.

^†^CrossRef DOIs here are collected as a citation at the bottom of the
post using the WordPress [KCite](http://knowledgeblog.org/kcite-plugin)
plugin. Unfortunately for a few months now, this plugin has stopped
recognising DataCite DOIs, which is why here they are treated
differently from CrossRef DOIs. This is purely a current attribute of
the KCite plugin and does not imply any fundamental difference in the
two types of DOI, other than one tends to be used as persistent
identifiers of journal articles and the other of datasets.

::: {.wp_orcid_field}
[https://orcid.org/0000-0002-8635-8390](https://orcid.org/0000-0002-8635-8390){target="_blank"
rel="author"}
:::


Following on from my re-investigation of close hydrogen bonding contacts to the π-face of alkenes, here now is an updated scan for H-bonds to alkynes. The search query (dataDOI: 10.14469/hpc/2478) is similar to the previous one: QA is any of N,O,F,Cl. X is any atom, including metals and non-metals.

Messaggi di Rogue Scholar

π-Facial hydrogen bonds to alkynes (revisited): how close can an acidic hydrogen approach?