General
The report from the individual research project will be written up in the format of an actual scientific research article. We will assume that you are writing up an article to be submitted to the journal PCCP: Physical Chemistry Chemical Physics
Guidelines on preparting an article to PCCP can be found here: Prepare your article
Templates for writing an article in the PCCP format can be be found here: Word & Latex templates
Stick to the format that PCCP uses for tables, figures, references, citations, chapters etc.
Instead of reading boring article preparation information it is usually easiest to look at old PCCP articles to see how things are. A collection of open-access articles can be found on this page. Also the open-access journal Chemical Science uses the same format as PCCP and all of their articles can be downloaded for free.
Journal articles typically contain Electron Supplementary Information, ESI, (also called Supplementary Information). This is usually a document without any formatting that contains additional information that could not fit into the journal article or contains raw data that is not appropriate in the actual article. In a computational chemistry article, typically the ESI contains the Cartesian coordinates of the calculated molecules at least. You should write a simple ESI where you include the Cartesian coordinates of the molecules you calculated in this project and other information if relevant.
Article outline
Your article will obviously be a lot shorter than a real scientific article and it depends on how interesting your results are, but do your best.
The article should contain at least:
- Title
whatever you think an appropriate title is
- Abstract
should contain info about what the study was about and what the main results were. Look at example papers to see what people do.
- Introduction
In a scientific article the introduction section typically contains an overview of the relevant research field with appropriate references and then a paragraph that outlines what the present study is about. This is obviously tricky for you to do since this was a small project and you have not read many articles in this field. Hence the introduction can be a lot shorter than in an actual paper. But should include info about what the point of the study was and what you did in a few sentences.
Results and discussion
This could be one big chapter or you can divide it up into subchapters if appropriate. Should be most of the paper.
Paper should contain tables and figures as appropriate. Figures are always nice, show at least a picture of the molecule/molecules of the paper.
Computational details
This should contain technical details about how the calculations were run. What program, what method, what basis set etc. How were the geometries optimized and whether single-point calculations were done etc.
Conclusions
What did you find out in this study? Make suggestions for future studies of this topic. Try to avoid saying the same thing you did in the Abstract/Intro/Results&Discussion .
Supplementary Information
Free format but wise to look at example articles.
Include relevant Cartesian coordinates for your molecules (optimized geometries only) and perhaps an example ORCA inputfile for your calculations if your calculations used complicated non-obvious input.
Can be a separate document or as part of the main article file.
Note on figures/scheme:
If you want to use a scheme or figure from another article (e.g. in the introduction section) you can do this if you make sure to cite appropriately where the figure/scheme comes from.
Upload the final report as PDF.
Handling references
If you go into research it is recommended to start using an academic reference manager and it will probably be necessary for this project if you want to write a good report.
Many programs exist: Endnote, Papers, Sente, Zotero, Mendeley, Bookends and more.
A recommended option for Mac is Sente (what I use). You can download a free version that handles 100 references (suitable for this project).
To handle citations to references in a Word document, one can use the built-in footnote/endnote system in Word, using the Endnote-Word integration etc. LaTeX can use the built-in citation feature in combination with e.g. Bookends.
Example computational scientific articles
To be used for guidance regarding formatting (PCCP and Chemical Science papers), computational details or how to present computational data in papers.
All these articles should be accessible when on UI campus.
Photosystem II papers:
http://pubs.rsc.org/en/content/articlelanding/2016/sc/c5sc03124a#!divAbstract
http://pubs.rsc.org/en/content/articlehtml/2015/sc/c4sc03720k
Embedded cluster modelling of solids:
http://pubs.acs.org/doi/abs/10.1021/ic500197v
http://pubs.acs.org/doi/abs/10.1021/ct200824r
A benchmarking study using ORCA and other codes:
http://pubs.acs.org/doi/abs/10.1021/acs.jctc.5b00359
http://www.sciencedirect.com/science/article/pii/S0009261413000237
Computational reaction path studies using ORCA:
http://pubs.acs.org/doi/abs/10.1021/acs.inorgchem.5b00787
http://pubs.acs.org/doi/abs/10.1021/ic500829p
An experimental/computational study of electronic structure of a complicated system:
http://pubs.rsc.org/en/content/articlehtml/2014/sc/c4sc00337c