Archive for the ‘Tips and tricks’ Category

Tips and tricks: generating machine-readable structural data from a structure

08 Nov 2019

Interested in making your article more discoverable and usable? As a reader, you have probably spent a lot of time re-drawing structures from an image in a PDF, or have struggled to find all relevant articles because your compound of interest is called by different names in different articles (IUPAC name, trivial name, registry number, drug development ID, generic name, brand name, revised trivial name etc etc etc…).

If you’re already drawing a structure for an article you are preparing to submit, it only takes a few seconds to generate machine-readable mol files or structure identifiers like SMILES or InChI. Including these files or identifiers in your article or supplementary information helps make your article indexable and structure-searchable, and is a great way to make your article stand out.

Save as MOL fileSave as mol file

 

All major structure drawing packages can save structures as MOL files. They generally follow the same steps:

Choose File > Save As from the top menu OR press Ctrl+Shift+S.

Select “MDL Molfile”, “MDL SDFile”, or “.mol” or “.sdf” in the dropdown.

Please note: There may be more than one molfile format listed in the dropdown. If there is more than one option, please be aware that V2000 mol format is more common and is supported by all cheminformatics software packages. The V3000 mol file has some extra features, but is not universally supported, so it is advised that you use V2000 mol format to ensure maximum interoperability.

Copy as SMILES or InChI

Start by selecting the structure you would like to copy as SMILES or InChI.

Avogadro

Copy as - Avogadro

From the top menu, choose Edit > Copy As > SMILES or InChI

ChemDoodle

Copy as - chemdoodle

From the top menu, choose Edit > Copy As > Daylight SMILES or IUPAC InChI

OR

To copy as SMILES, press Ctrl+Alt+C

ChemDraw

Copy as InChI

From the top menu, choose Edit > Copy As > SMILES or InChI

OR

Right click, and choose Molecule > Copy As > SMILES or InChI

OR

To copy as SMILES, press Alt+Ctrl+C

ChemSketch

machine readable copy as - chemsketch

From the top menu, choose Tools > Generate > SMILES Notation or InChI for Structure

MarvinSketch

Copy as - Marvin

Press Ctrl+K, then select SMILES or InChI from the Copy As pop-up

OR

From the top menu, choose Edit > Copy As and select SMILES or InChI from the pop-up

OR

To copy as SMILES, press Ctrl+L

Finally, paste your SMILES or InChI into your document or spreadsheet.

The less time we have to spend re-drawing structures from pdfs, the more time we can devote to doing science. Luckily, it really couldn’t be quicker or easier to improve the discoverability and reusability of your article by including machine-readable structure files or identifiers. Let’s work together to make chemistry articles easier to find and use.

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Recent Improvements to ChemSpider Search (part 3)

21 Jun 2013

In part one of this series we talked about searching by molecular formula ranges, and combining substructure searches with other types of searches. Part two covered how to search by supplementary information like bioactivity, appearance or melting point. This time we will demonstrate how you can use a search combining these new features to help answer a question you might encounter in the lab.

After performing a bromination reaction on phenol you isolate a product with a melting point of 90-93°C. If you start a search with just three pieces of information – your product is a derivative of phenol, it should contain at least one bromine, and your melting point is 90-93°C – you can construct a search on the Advanced Search page to help you get started in identifying your product.

Since you can now combine substructure searches with other searches, you start by looking for a compound containing phenol (Search by SubStructure). To restrict your results to brominated phenols, you add a molecular formula range search for C6H(1-5)O1Br(1-5) (Search by Properties). Lastly, you search for compounds with a melting point of 90-93°C (Search by Supplementary Information).

Your search turns up one result – 2,4,6-Tribromophenol. Although you need more information to conclusively confirm the identification, this gives you a lead in your analysis/elucidation.

Taking a look at the record, you may notice it has an interactive IR spectrum from NIST. If you check the Data Sources section, you will find that there are a lot data sources for the record.

To make it simpler to identify useful information you can browse the tabs to look for specific types of information: for instance the “Spectral Data” tab provides links to data in the MassBank and NMRShiftDB databases, which will hopefully aid you confirming/determining whether the product is 2,4,6-Tribromophenol.

This is just one example of how you can combine different searches on the Advanced Search page. Advanced searches are a great way to narrow down your results to help you find exactly what you are looking for, and there are many options we haven’t covered here, so have a look around and see what combinations might work for you.

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Recent Improvements to ChemSpider Search (part 2)

21 Jun 2013

Last time we told you about a number of improvements we have added to ChemSpider in the recent site updates, including combined substructure and properties search and searching by molecular formula ranges. As promised, this time we will cover how to search by properties like melting point or appearance.

Searching by Supplementary Information

Until now, although you could view properties when you were already on a record, there was no way to search by melting point, refractive index, appearance or bioactivity. This update has implemented a new search interface which allows you to search this data. You can now find compounds that are reported as being isolated from yeast, or compounds with a melting point of 32-35 °C.

There are 2 main parts to our Supplementary search interface.

Text Properties Search

Text properties include appearance, chemical class, drug status, or safety data. You can search any of these properties by using key words. When you start typing, a number of suggested search terms will appear, which can help you narrow down what search term to use.

You can also use wild cards by entering *, which can give you a little more flexibility in your search term – so if your unknown is a blue, crystalline material a search for “Blue crystal*” will turn up all records which mention the word “blue”, as well as any word beginning with “crystal” (such as crystals or crystalline).

 

Numeric Properties Search

Numeric properties include physical properties like experimental or predicted boiling point, optical rotation, or LogP. Since we draw data from a wide range of data sources, not all of this information is sent to us in the same format or with the units depicted the same way. In order to make it possible for you to search across all the properties in our database no matter how it was supplied to us, we have done a lot of background work on tidying up and standardizing this data.

All numeric properties can be searched using min/max or with a +/- range and the search term can be entered in a variety of units – eg. Fahrenheit or Celsius for temperature, or psi or mmHg for pressure. Because the boiling point of a material is dependent at the pressure at which the measurement is made and not all boiling points are measured at atmospheric pressure we have created a feature that attempts to compensate for this. It uses the Clausius-Clapeyron equation to create estimated (standardised) boiling points for searching, please remember this when looking at your results.

 

As you can see, you are able to search on a wide variety of experimental properties, including boiling point, LogP, melting point, specific gravity and solubility. Please note that although many of the more common compounds have some properties, these properties are only available on a subset of our records – so if you do not get a result on a property search, it might be that we haven’t added that information yet.

Hopefully this gives you a good idea of the improvements we’ve made to ChemSpider search, and how these new features make it easier than ever to find what you are looking for. See the following post for a case study that showcases several of the new features covered in these posts.

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Recent Improvements to ChemSpider Search (part 1)

13 Jun 2013

We recently published an update to the ChemSpider website which, in addition to fixing a number of bugs, has added some useful new features. Three of these features are highlighted in this post – one which you might have noticed already, and two which you may not have discovered yet.

Auto-Complete

We have reinstated the auto-complete feature on the ChemSpider homepage. Now, when you begin typing in the search box, ChemSpider makes suggestions based on what you have typed. This makes it easier than ever to find what you are looking for – even if you aren’t quite sure how to spell it.

Autocomplete on the ChemSpider homepage

 

Combined Structure/Property Searches

People frequently ask if there is a way to search substructure and other properties like molecular weight or molecular formula at the same time. This update now makes it possible to perform this kind of combined search from our improved Advanced Search page.

E.g. If you are interested in finding compounds which are structurally similar to Valium, you can enter a benzodiazepinone substructure and restrict it to compounds with a molecular weight of 275-325.


This search then returns Valium along with other similar drugs like clonazepam, nitrazepam and lorazepam.

There are many other search options that can be combined with a substructure/similarity search so look at the Advanced Search page and have a play.

Molecular Formula Range Searching

You can also search a range of molecular formulae at once. To specify the range for a given element, put the range in parentheses after the element. E.g. C7H(10-12)O(0-1) would return all compounds containing exactly 7 carbons and between 10 to 12 hydrogens and which may or may not contain an oxygen. This type of search can be performed from the Simple Search page, as part of an Advanced Search or from the ChemSpider homepage.

Best of all, this can be combined with any of the other search parameters on the Advanced Search page including the substructure search. For example, if you wanted to find polychlorinated biphenyls containing at least three Chlorines you could perform a substructure search for a biphenyl with a molecular formula of C12H(0-7)Cl(3-10).


In our next post, we will cover some new ways you can search by properties that are stored in our records such as melting point, density, etc.

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