Imperial College London

Henry Rzepa

The title of this post summarises the contents of a new molecular
database: [www.molecularspace.org](http://www.molecularspace.org/){target="_blank"}\[cite\]10.1021/jz200866s\[/cite\]
and I picked up on it by following [the post by Jan
Jensen](http://www.compchemhighlights.org/2013/06/molecularspaceorg.html){target="_blank"}
at [www.compchemhighlights.org](http://www.compchemhighlights.org){target="_blank"}
(a wonderful overlay journal that tracks recent interesting articles).
The molecularspace project more formally is called "*The Harvard Clean
Energy Project: Large-scale computational screening and design of
organic photovoltaics on the world community grid*". It reminds of a
2005 project by Peter Murray-Rust *et al* at the same sort of
concept\[cite\]10.1007/s00894-005-0278-1\[/cite\] (the
World-Wide-Molecular-Matrix, or
**WWMM**\[cite\]10.1186/1758-2946-3-42\[/cite\]), although the new scale
is certainly impressive. Here I report my initial experiences looking
through molecularspace.org

The 150,000,000 calculations are released under the the CC-BY license,
which is an encouraging (open) start. One does need however to login to
the site, which I was able to do using my Google credentials. Shown
below is a screenshot of a typical result in a search (of Power
conversion efficiency in my case).

![CEPDB1](http://www.ch.imperial.ac.uk/rzepa/blog/wp-content/uploads/2013/07/CEPDB1.jpeg){.aligncenter
.wp-image-10827 decoding="async" width="480"}

It comes in two parts, the first being the structure (given as a SMILES
and 2D layout) with the principle predicted energy levels and predicted
photovoltaic performance listed below that. This is then followed by
what might be called an annotation with further computed/predicted
properties using the algorithms applied by Chemicalize.org. This idea
that a data set could accrete via semantically powerful annotations
using other tools was also very much part of the concept of the WWMM
(the matrix had at its heart a molecule in one dimension and a property,
measured or computed in the other. The matrix is of course very sparse,
which is why it needs annotation!).

It was at this point however that I started to wonder how I might add
other annotations, based perhaps on other types of calculations. But
thus far at least, I have not found any trace of something which I could
immediately use for my own calculation; 3D coordinates specifically.
Thus, the HOMO-LUMO energy gap is the key property which makes
**molecularspace** unique and valuable (to someone working in the field
of photovoltaics). But HOMO/LUMO gaps can be calculated in many
different ways, and it can always be valuable to calibrate/validate the
reported values against other methods. Perhaps if I continue to look, I
might find these 3D coordinates (which, for 2,300,000 molecules would be
a very valuable resource).  Certainly for example, should  I wish to do
so, I could not at the moment readily replicate the calculation for any
specific entry on the **molecularspace** site (which can be regarded as
an essential component of scientific validation). When I use the first
person, I mean of course either myself as a human or a software agent
acting on my behalf (the latter having the endurance to repeat its
procedures millions of times if necessary). 

The reader of this blog may have noticed that whenever I report a
calculation here, I like to cite its doi (more formally its **handle**),
which links to a digital repository. In my case, the repository
certainly carries the 3D coordinates, and also the full wavefunction
provided if the reader wishes other properties to be derived from it.^‡^
Now if **molecularspace** is able to provide that in the fullness of
time, it truly would be an impressive resource.

But the important take-home message from **molecularspace** is that
archiving (under a CC-BY license) the "big" data from any given research
in a manner which makes it readily re-usable by others (perhaps from
quite different fields of science) is now an essential requisite of
doing science. And it is really nice to see good examples of this in
practice!

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

^‡^ Generally, the calculations I perform for this blog are published in
a DSpace repository (the [original
one,](https://spectradspace.lib.imperial.ac.uk:8443/dspace/handle/10042/13){target="_blank"}
started in 2006\[cite\]10.1021/ci7004737\[/cite\]), and more recently in
[Chempound](http://chempound.ch.ic.ac.uk:8090){target="_blank"} (a
[project by Peter Murray-Rust and
colleagues](http://journals.tdl.org/jodi/index.php/jodi/article/view/5873/5879){target="_blank"}
which emerged out of the WWMM experiments) as well as
Figshare\[cite\]10.6084/m9.figshare.739310\[/cite\]. The first and the
third assign [unique
handles](http://www.ch.imperial.ac.uk/rzepa/blog/?p=10736 "Research data and the “h-index”."){target="_blank"}
(*i.e.* a **doi**) to the data; chempound does not (and neither does
molecularspace).

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


The title of this post summarises the contents of a new molecular database: www.molecularspace.org[cite]10.1021/jz200866s[/cite] and I picked up on it by following the post by Jan Jensen at www.compchemhighlights.org (a wonderful overlay journal that tracks recent interesting articles). The molecularspace project more formally is called “
<em>
 The Harvard Clean Energy Project: Large-scale computational screening and design of organic
</em>

Messaggi di Rogue Scholar

150,000,000 DFT calculations on 2,300,000 compounds!