A structure or substructure query can be taken from Structure Editor, Database Manager or a fragment copied in Fragments & Mechanism window.

Structure and substructure searches are very important features for retrieving library entries. The structure search is the most straightforward method for finding compounds in a library. Since the rules of systematic nomenclature need not necessarily lead to a unique name for each compound, name search can be, in many cases, very ineffective. It is much easier to draw or import a structure query than to type a complicated name. It is also more natural for a chemist to deal with structures rather than names or CAS numbers.

While a structure search (Identity search) provides an exact match of query and library structure, Substructure search retrieves compounds that contain a common structural subset, called substructure. The exact substructure must be embedded in each molecule retrieved. The exact match, in structure and substructure searches, has a notable exception - that stereo bonds are ignored, since optical activity does not play a significant role in mass spectrometry. All other structural features such as bond multiplicity, atom state and skeletal arrangement must match exactly. Charge, radical and unspecified charge site can be optionally ignored. Also isotopes can be optionally disregarded.

Substructure search offers two additional search options: Substructure Best Match and Substructure Match Ring Bonds. A substructure can sometimes fit at several locations of a larger structure. The Substructure Best Match option that represents the closest match will be found and displayed in red in the Structure tab. Please note that this option will lengthen calculation times. Since fragmentation mechanisms on rings significantly differ from acyclic moieties, it is useful to search substructures that exactly match the ring membership for each bond. This option can be set in the Search Type group box. This option will also lengthen calculation times.

Substructure search can be used for a variety of purposes. It allows you to study mass spectra of structurally related molecules. If you want to positively identify an unknown, or you need help in interpreting a mass spectrum, compounds retrieved by substructure search can provide analogies to the fragmentation processes in the spectrum under consideration.

When searching structures with an unspecified charge site or substituents, please note the search rules that apply