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Searching for a Substance

Using the Find a Substance search in the PSDI Cross Data Search service you can build a search by customising the parameters of a variety of methods to narrow down the results that you are looking for:

  • All Substances
  • Elemental Composition
  • Periodicity and Symmetry
  • Crystal Cell Parameter
  • Molecule
  • Linked Publication Reference

You can change the parameters for each search type by selecting the appropriate tab at the top of the page, beneath the main navigation. The selections that you make are combined into a single query. You can choose to constrain your search by as many or as few criteria as required.

Changes that you make to the parameters may affect the data sources that are selected if the selections only apply to a subset of the data sources that can be searched.

Use the sections in this topic to find out how to configure parameters for each search type and how to choose the data sources to search.

Click All Substance, to open the All Substance search in the PSDI Cross Data Search Service in a new tab.

All Substances​

You can use the All Substances search tab to find a substance based on the chemical formula.

note

The chemical formula can be represented in a variety of ways. For example, Descriptive chemical formula, which can be searched on here, uses the chemical formula chosen by each data provider. If you need a specific definition of the chemical formula, the Advanced Search option, enables you to search using fields such Hill, reduced, or anonymous chemical formulas. Note that not all data sources offer these additional chemical formula fields.

Chemical formulas may contain properly capitalized element symbols followed by integers or decimal numbers, balanced parentheses, square, and curly brackets, commas, plus, minus, colon, and equal symbols. For example:

  • (H2O)2 Na
  • NaCl
  • CaCO3
  • CCaO3
  • (CH3)3N+ - [CH2]2-OH = Me3N+ - CH2 - CH2OH

You can choose a query that either exactly matches the formula you entered or instead performs a partial match to find any results that contain the formula entered.

To construct a query including the chemical formula:

  1. Enter the chemical formula that you would like to search in the Descriptive chemical formula field.
  2. Optional: To search only for results that match the entered formula, click the Exact match toggle to turn on the exact match option.

If you only want to search on the chemical formula, go to Selecting data sources to search for instructions on how to select the data sources before you perform this search. If you would like to add more constraints to your query, use the information in the following sections to help.

Elemental Composition​

The Elemental Composition enables you to constrain the number of elements in your substance and to select elements to include or exclude from your search by selecting them from a periodic table.

Number of elements​

  • To select a specific number of elements: Enter the number of elements in your substance in the Number of elements field.
  • To select a minimum number of elements:
    1. Click the Range toggle to turn on the range option.
    2. Enter the minimum number of elements in your substance in the Min number of elements field.
  • To select a range for the minimum number of elements:
    1. Click the Range toggle to turn on the range option.
    2. Enter the minimum number of elements in your substance in the Min number of elements field.
    3. Enter the maximum number of elements in your substance in the Max number of elements field. If the maximum number of elements is lower than the minimum number of elements an error will be displayed.

Elements and ratios​

The elements and ratios section of the Elemental Composition tab allows you to select and configure the elements that your material contains using selections from a periodic table. You can specify which elements must be included, can be included or elements which must be excluded from results. For each element you can also specify a ratio, using a value between 0 and 1 which indicates the relative proportion of the element in the substance.

When you select elements in the periodic table, they are added to the chosen dropdown where they can be further configured. You can manually expand the dropdowns to view the selected elements, or you can choose to have these automatically expand as new elements are added by selecting or deselecting the Auto expand dropdowns when selecting check box beneath the Must include elements dropdown.

You can increase and decrease the size of the periodic table to help make your selections easier by selecting small, large, and largest from the Table size section beneath the Exclude elements dropdown.

To select elements to include or exclude from your substance search:

  • To select elements that must be included in your search:

    1. Click on the Must include elements dropdown. A border is displayed around the dropdown to indicate it is selected.
    2. Click on the element in the periodic table. The element is added to the dropdown list.
    3. Optional: To set the relative proportion of the element in the substance:
      1. Click the Set ratio button beneath the element name.
      2. Enter a value between 0 and 1 in the min field in the Enter ratio limits: section. For example, use a value of 0.1 if the minimum amount of the element in the substance must be 10%.
      3. Enter a value between 0 and 1 in the max field in the Enter ratio limits: section.
      4. Click OK to set the ratio.
    4. Repeat step i and ii to add new elements to the Must include elements list and set their ratios.

  • To select elements that may be included in your search, but are not required:

    1. Click on the Can include elements dropdown. A border is displayed around the dropdown to indicate it is selected.
    2. Click on the element in the periodic table. The element is added to the dropdown list.
    3. Optional: To set the relative proportion of the element in the substance:
      1. Click the Set ratio button beneath the element name.
      2. Enter a value between 0 and 1 in the min field in the Enter ratio limits: section.
      3. Enter a value between 0 and 1 in the max field in the Enter ratio limits: section.
      4. Click OK to set the ratio.
    4. Repeat step i and ii to add new elements to the Can include elements list and set their ratios.

  • To select elements that must not be included in your search:

    1. Click on the Exclude elements dropdown.
    2. Click on the element in the periodic table. The element is added to the dropdown list.

The ratios of individual elements can be changed by selecting the element in the appropriate dropdown and clicking the Set ratio button. To remove an element from one of the categories, click on the X next to the element in the dropdown list. To remove all elements from a particular category, select the appropriate dropdown and click the Clear all button.

If you are ready to search, go to Selecting data sources to search for instructions on how to select the data sources before you perform this search. If you would like to add more constraints to your query, use the information in the following sections to help.

Periodicity and Symmetry​

Crystals exhibit periodicity, meaning their atomic or molecular structures repeat in space. This repeating nature arises from the symmetry present in the crystal, such as translational symmetry (repetition along specific directions), rotational symmetry (rotations that leave the crystal unchanged), and reflection symmetry (mirror planes within the structure). These symmetries define the pattern and geometry of the crystal. The Periodicity and Symmetry tab enable your search query to be constrained by these properties of crystals.

Periodicity​

You can select periodicity constraints of your query by clicking on one or more of the following options:

  • 0, e.g. a single molecule
  • 1, e.g. a carbon nanotube
  • 2, e.g. a 2D slab or surface
  • 3, e.g. a bulk crystal structure

Selected periodicity options are displayed as white text on a dark blue background. Click on a selected option to deselect it.

tip

If you want to configure properties for symmetry as part of your search, you must select the 3 value for periodicity.

Symmetry​

Three properties can be configured to constrain your search query for crystal substances:

Hall space group symbols​

Hall symbols are a concise notation used to describe the symmetry of space groups in crystallography. They provide detailed information about the symmetry operations and the lattice type of a crystal. The symbols are separated by spaces to clearly distinguish different components, such as the lattice type and symmetry elements. The format is useful in computational crystallography for unambiguously defining space groups.

For example, the Hall symbol: P 2yb -1 would translate to:

  • P indicates the lattice type (primitive)
  • 2yb specifies a twofold rotation along the y-axis with a b-glide
  • -1 represents an inversion center Other examples include:
  • P 2c -2ac
  • -I 4bd 2ab 3
  • P 2yb (-1/2*x+z,1/2*x,y)
  • -I 4 2 (1/2*x+1/2*y,-1/2*x+1/2*y,z)

For more information about Halls symbols, see Space-group notation with an explicit origin, Concise Space-Group Symbols, and Extension of Hall symbols of crystallographic space groups to magnetic space groups.

To enter a symmetry properties using a Hall space group symbol, enter the appropriate symbol in the Hall symbols separated by space field.

Space group number​

A space group number is a unique identifier assigned to each of the 230 distinct space groups in crystallography. These space groups describe the symmetry of crystalline structures in three-dimensional space, including their rotational, translational, and reflectional symmetry operations. The numbering system is standardized in the International Tables for Crystallography, where space groups are numbered from 1 to 230. For example:

  • Space group 1 corresponds to P1, the simplest space group with no symmetry except a translational lattice.
  • Space group 230 corresponds to Ia-3d, a highly symmetric cubic space group.

To enter a space group number, enter an integer between 1 and 230 in the Space group number field.

Number of sites​

In crystallography, the number of sites refers to the distinct atomic or molecular positions within a unit cell that are defined by symmetry operations of the crystal's space group. These sites represent the unique positions occupied by atoms or ions in the crystal structure. For example, in a primitive lattice (like in a simple cubic structure), there is typically one site per unit cell because the lattice points are at equivalent positions. In more complex crystal structures there may be multiple unique sites representing atoms at different positions or symmetrically equivalent arrangements.

You can choose to enter a specific number of sites, a minimum number of sites, or a range for the number of sites that you would like to use in your search.

  • To select a specific number of sites: Enter the number of sites for your substance in the Number of sites field. This value must be an integer number.
  • To select a minimum number of sites:
    1. Click the Range toggle to turn on the range option.
    2. Enter the minimum number of sites for your substance in the Min number of sites field. This value must be an integer number.
  • To select a range for the minimum number of sites:
    1. Click the Range toggle to turn on the range option.
    2. Enter the minimum number of sites for your substance in the Min number of sites field. This value must be an integer number.
    3. Enter the maximum number of sites for your substance in the Max number of sites field. This value must be an integer number. If the maximum number of sites is lower than the minimum number of sites an error will be displayed.

If you are ready to search, go to Selecting data sources to search for instructions on how to select the data sources before you perform this search. If you would like to add more constraints to your query, use the information in the following sections to help.

Crystal Cell Parameter​

Crystal cell parameters are the essential dimensions and angles that define the geometry of a unit cell, which is the smallest repeating unit of a crystal lattice. These parameters determine the symmetry, packing, and atomic arrangement in the crystal, influencing its physical and chemical properties:

  • Unit cell lengths (a, b, c): The lengths of the three edges of the unit cell, typically measured in angstroms (Å).
  • Unit cell angles (α, β, γ): These are the angles (measured in degrees) between the edges of the unit cell. α: Angle between the b and c axes. β: Angle between the a and c axes. γ: Angle between the a and b axes.

The range for crystal cell lattice constants can vary widely depending on the material and its atomic structure, for example:

  • Small molecules: Lattice constants are often in the range of 2–10 Å (angstroms). For example, simple salts like NaCl or molecular crystals fall within this range.
  • Macromolecules or Complex Systems: For larger biological or polymeric structures, lattice constants can extend up to 100 Å or more.
  • Minerals and metal alloys: These tend to have lattice constants in the range of 3–15 Å, influenced by their atomic packing and chemical composition.
  • Materials with open frameworks: Some materials, like zeolites or metal-organic frameworks, can have much larger lattice constants, sometimes exceeding 20–30 Å.
warning

If you configure any of the parameters on the Crystal Cell Parameter tab, the data sources that you can search will be restricted because these fields are only applicable to data sources that include crystallographic data. Currently this will restrict your search to the following data sources: Crystallography Open Database (COD), Theoretical Crystallography Open Database (TCOD), and the Cambridge Structural Database (CSD).

To configure the crystal cell parameters for your substance:

  1. Enter values for the unit cell lengths in the a, b, and c fields in the Unit cell lengths section.
  2. Optional: Configure a tolerance for the unit cell lengths, by entering a value in the Tolerance field. This will retrieve results for all substances that fall the range of minimum and maximum bounds generated by this value.
  3. Enter values for the unit cell angles in the α, β, and γ fields in the Unit cell angles section.
  4. Optional: Configure a tolerance for the unit cell angles, by entering a value in the Tolerance field. This will retrieve results for all substances that fall the range of minimum and maximum bounds generated by this value.

If you are ready to search, go to Selecting data sources to search for instructions on how to select the data sources before you perform this search. If you would like to add more constraints to your query, use the information in the following sections to help.

Molecule​

The Molecule tab enables you to search for a molecule using InChI or SMILES chemical identifiers. You can either enter or paste chemical identifiers directly into the Identifier field, or you can draw a molecule using the ChemDoodle application. Within ChemDoodle you can import and transform an existing molecule from an alternative format:

  • Canonical SMILES
  • InChI
  • MDL MOL
  • SMILES
  • ChemDoodle JSON
warning

If you add a chemical identifier on the Molecule tab, the data sources that you can search will be restricted because these fields are only applicable to data sources that include molecule data. Currently this will restrict your search to the to the following data sources: ChASe, Propersea, Chemotion, Crystallography Open Database (COD), Theoretical Crystallography Open Database (TCOD), and the Cambridge Structural Database (CSD).

To create a chemical identifier using ChemDoodle:

  1. Click Draw a Molecule. The 2D ChemDoodle interface will be displayed within the Molecule tab.
  2. Choose whether to represent your molecule as a SMILES or InChI by selecting the appropriate radio button at the bottom of the page. The molecule you draw or import will be displayed in SMILES or InChI format at the bottom of the page.
  3. Optional: Draw a molecule in the 2D ChemDoodle tab. For guidance on how to use the 2D Sketcher functionality in ChemDoodle, see the Sketcher Canvas Tutorial.
  4. Optional: If you do not want to draw a molecule from scratch you can import an existing molecule using :
    1. Click on the Import tab to display the import options
    2. Choose your input format from the Select input format list
    3. Choose 2D or 3D coordinates from the Select coordinates list
    4. Enter or paste the molecule in the selected input format in the Data to import field.
    5. Click the Import button to import the molecule. The molecule is displayed in the 2D ChemDoodle tab.
  5. Make any required changes to the molecule in the 2D ChemDoodle tab.
  6. Optional: You can use the 3D ChemDoodle tab to inspect your molecule.
  7. When you have finished drawing your molecule, click on the Done button in the 2D ChemDoodle tab. The Chemical identifier from ChemDoodle is automatically entered into the Identifier field.

If you are ready to search, go to Selecting data sources to search for instructions on how to select the data sources before you perform this search. If you would like to add more constraints to your query, use the information in the following sections to help.

Linked Publication Reference​

Some data sources include publication reference information associated with the substance data, and the Linked Publication Reference tab enables you to search for a substance using bibliographic information. The results that are returned using this search may be different to the results that are returned using the main Find a Publication Reference search.

warning

If you add a chemical identifier on the Linked Publication Reference tab, the data sources that you can search will be restricted because these fields are only applicable to data sources that include publication reference data associated with substance information. Currently this will restrict your search to the to the following data sources: Chemotion, Crystallography Open Database (COD), and the Theoretical Crystallography Open Database (TCOD).

You can constrain your search using as many or as few of the following fields in the Linked Publication Reference as necessary:

  • Author name: Add a full or partial name for the author, for example you can search using the surname only.
  • Title: Add a full or partial title for the publication, for example you can search using a keyword you expect to find in the title.
  • DOI: This must be the exact DOI of the publication.
  • Journal: Add a full or partial name for the Journal.
  • From year: Add a minimum value for year, this should be in the format of YYYY, for example 1979 or 2021.
  • Until year: Add a maximum value for year to create a range of time in which a reference was published. This should be a higher number than the value specified in the From year.
  • Volume: Add a value for the volume number of the publication, this must be the exact volume of the journals specified in the search.

If you are ready to search, go to Selecting data sources to search for instructions on how to select the data sources before you perform this search. If you would like to add more constraints to your query, use the information in the above sections to help.

tip

A tick icon is displayed next to each tab name at the top of the page for any section where you have configured any constraints. If you decide that you do not want to search using a set of constraints, go to the tab with the tick icon and remove the settings from the appropriate field. Once you have removed the settings, the tick icon is no longer displayed.

Once you have configured the constraints for your search query, you can choose the data sources that you want to search. The data sources available depend on the search parameters that you have configured. By default all of the relevant data sources are selected.

To change, add or remove data sources from the search:

  1. Click on the Select data sources to search button. A list of the available data sources to search is displayed with descriptions. All the available data sources are selected by default. Selected data sources are indicated with a tick icon to the left of the data source name.
  2. Optional: If you want to know more about a particular data source, you can click on the View resource catalogue link to read more about it.
  3. Optional: You can select or deselect all of the available data sources by clicking on the All or None buttons near the top of the list.
  4. Select the data sources that you want to search. You can search for specific data sources by scrolling through the list or by entering the name of the data source in the Filter data sources text field at the top of the list.
  5. When you have finished selecting the data sources for your search, click the cross (X) symbol at the top left of the list.

Once you have configured the constraints for your search query and selected the data sources you can click on the Search button to perform the search.

Search and Search Results​

When you click on the Search button to perform your search, the list of data sources you selected to search is displayed with the progress in retrieving the results for each one. A tick symbol next to the data source name indicates results were retrieved successfully. You can cancel the search if you want to stop and view the retrieved results by clicking the Cancel button. If all the data sources returned results successfully, the list of data sources is replaced by the list of results.

If a cross appears next to a data source, this indicates an error was returned from that data source. The list of data sources will remain on screen so that you can see which data sources returned an error. To view more details about the cause of the errors and to view successful results, click the Results button.

For each result returned by the search query, a 'result card' is displayed. The content of the result cards is determined by the fields that are returned by each data source, so not all information is available for every record. At the top right of each result card you can see from which data source the result originates.

You can configure the number of results that are displayed per page using the per page dropdown at the top left of the page. You can also configure how many results for each database are displayed using the per database dropdown at the top left of the page.

Some data sources enable you to view more information about the data or to download the data. For example, the Crystallographic Open Database (COD) allows you to view a visualisation of the molecule and to download the data. The controls for these additional functions can be found at the top right of the result card.

The Source tab in the result card provides the contents of the result record in JSON format.

What to do next​

There are multiple ways to search the data sources accessible through PSDI, find out how to use our other search methods:

Related links:

PSDI offers other ways to search for data that are not included in our Cross Data Search service. Explore these links to access additional data sources offered by PSDI:

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