ccdc 操作方法

Searching the Cambridge Crystallographic Database
(CCDC ConQuest)
The Cambridge Crystallographic Database is continually growing database consisting of over 300,000 crystallographically characterized molecules. The database includes many pieces of important information about a published compound, including: •Journal Name (volume, page, year)
•Author’s Names
•Chemical Name and Formula
•Physical Properties (melting point, color)
•Crystal Information
o Space Group
o Unit Cell Parameters (a, b, c, α, β, γ)
o Reduced Cell Parameters
o Molecular Volume
•Known Polymorphs (same sample crystallized in a different way)
•Experimental Detail
o Collection Temperature
o Crystal Density
o R factor (indication of quality of structure)
o Average Sigma (C-C) for bond distances
o Whether or not the structure contains disorder
•Diagrams (ChemDraw and 3D view)
Unlike Scifinder and Beilstein, the CCDC only contains articles with structurally characterized compounds. The major advantage to this database is that you can find structural information (bond lengths, bond angles, molecular geometry, and hydrogen bonding interactions to name a few) quite quickly without having to search through every article published about a certain compound. One obvious disadvantage is that if the compound has not been structurally characterized, it will not be present in the database.
A second disadvantage is that the database in not a web-based database; rather periodic updates (every 3 months) are need to keep the database current.
Many groups on campus have a license for the database. If your group does not have a license, you can use the database in the X-ray Crystallography Lab (S146) during normal operational hours (8-5 daily); though, due to the cost of getting the database, there is a fee for non-licensed users ($57). See either: the director, Victor Young, or the TA, Ben Kucera if you have any questions.
To search the database, first click on the icon “ConQuest1.7” (or whatever version is present in your lab).
The first screen you come to will look like this:
This screen shows you all of the available search options. The following list is a brief description of each function.
•“Draw” is a drawing program
•“Peptide” allows you to specify amino acid linkages
•“Author/Journal” allows you to search for a particular author or in a particular journal
•“Compound Name” allows you to search based on the published name
•“Elements” allows you to specify certain elements to search for
•“Formula” allows you to search based on a specific formula
•“Space Group” allows you to search for a specific space group
•“Unit Cell” allows you to find samples based on the unit cell and reduced cell parameters
•“Z/Density” allows you to search for a particular crystal density or a particular number of molecules in the unit cell
•“Experimental” allows you to search for samples based on experimental data, such as data collection temperature, R factor, and average sigma (C-C) •“All Text” allows you to search based on keywords and phrases
•“Refcode (entry ID)” allows you to search based on the 6 letter CCDC code that each entry has
Each function will now be described in further detail.
DRAW
The first feature of the database is a Draw program. This Draw function is structured similar to ChemDraw.
Like ChemDraw, the Draw function contains a periodic table to select elements, as well as templates for various functional groups (C, H groups; C, H, O groups; N, H groups; and aromatic groups to name a few). The template feature of the Draw function is not as in depth as ChemDraw; however, what cannot be found in the templates can be drawn by hand.
The Draw function contains four ring structures already drawn for you (cyclopentane, cyclohexane, benzene and cyclopentadienyl). The program also contains a “RingMaker” feature that allows you to specify any size ring, along with selecting types of bonds (single, double, triple, aromatic) present in the ring.
Another feature of the Draw function is the option to choose a group of elements. For example, you can search for all cyclopentadienyl complexes of group 6 metals simply
by selecting group 6 (6B) from the “other elements” option under the “More…” tab and attaching a cyclopentadienyl ring. You can also specify “Any Metal”, “Any Non-metal”, or “Any Transition Metal” under the “More…” tab as desired.
Like any other database, the level of complexity of your drawing will affect the number of hits you receive. The more specific the drawing, the fewer hits you will receive and vice versa. To increase the number of hits for a specific molecule, highlight the molecule and select the “any” option under the “Bond” tab. This will allow the program to search for all combinations of those atoms, in the structure specified, regardless of whether the atoms are held together by single, double, triple or aromatic bonds.
Once you have drawn the molecule, hit the “Search” button. The following screen will come up.
This screen gives you the option of shrinking down your search by specifying which crystallographic features (disorder, errors, ions, powder structures) to remove. You can
search based on the R factor, as well as specifying only organic or only organometallic structures.
Once the search is completed, a screen like the following will appear. This search was the result of drawing a cyclopentadienyl ring bonded to a 6B metal using “any” bonds, as well as single bonds to three 7B elements (any halogen atom).
The hit list on the right contains all matches in the database for the molecule specified. The six letter code is the Refcode given to each molecule upon addition to the database. On the left are the tabs containing the information specific to the molecule shown in the center picture (journal, authors, data collection information, crystal system, etc.). Each search option described after this will come up to the same type of screen, with the same information and options.
Peptide
The Peptide feature allows you to specify a certain amino acid sequence to search for.
This feature also allows you to search for chemically modified sequences; peptide and non-peptide bonding; and cyclic or acyclic sequences.
Author/Journal
The Author/Journal feature allows you to search for the database entries for a specific author in a specific journal.
Compound Name
This option allows you to specify a compound name to search for.
Elements
This feature allows you to search for compounds containing a list of specified elements. The hits for this feature will include all compounds containing, at minimum, the atoms selected.
The elements can be in either the same molecule, or in the same crystalline lattice. You can also specify the heaviest atom present in order to limit the search results.
This feature allows you to specify a certain formula to search for.
The formula can pertain to either a single molecule or all parts of the structure (cation and anion, solvent, etc.).
Space Group
This feature allows you to specify a specific space group to search for. This feature is generally not useful for looking for a particular molecule unless you are looking for an enantiomerically pure sample (which could crystallize in a chiral space group).
The Unit Cell feature allows you to search the database for specific unit cell dimensions. This feature is not useful for finding specific molecules in a general search.
This feature is of great importance to those who are actively collecting data in the X-ray Crystallography Lab. After collecting your unit cell matrix frames, you can determine if the crystalline sample you have has already been structurally characterized. The unit cell of a compound is generally very specific (unless polymorphs are present), so a match of the structure and unit cell dimensions in the database indicates that you have the same material.
A reduced cell search is strongly recommended because this will allow you to find the alternate settings of a crystalline sample. This is important because the database contains entries from the early beginnings of X-ray crystallography, before generally accepted unit cell conventions were established.
Along with entering a, b, c, α, β, and γ, you can specify the lattice type (primitive (P), A-centered, B-centered, C-centered, Face-centered (F), body-centered (I), and a rhombohedral setting (R)) of the unit cell (if known).
This feature allows you to specify the number of molecules per asymmetric unit and per unit cell.
Not all entries in the database have 3D coordinates, so if you are interested in bond lengths, bond angles, or other 3D related information, specifying atoms with 3D coordinates is important.
You can also search based on a calculated density and the number of chemical units in the cell.
Experimental
This feature allows you to search for molecules containing a specific set of experimental conditions.
You can search for molecules based on R-factor, data collection temperature and radiation source (X-rays, neutrons, or any).
You can also search based on disorder, errors in the solution, powder structures, and average e.s.d.’s of C-C bonds.
All Text
This option allows you to search every part of the database for a particular word or phrase. This word or phrase can be found in any part of the results list from
“Author/Journal” to “CSD internals.”
Refcode (entry ID)
This option allows you to search the database for a specific Refcode entry.
As stated earlier, each entry in the database has a unique Refcode. There is no set system for assigning Refcodes, so using this option for a search is only useful if you already know the Refcode (acquired from an earlier search or from a journal).
Once you have completed your searches, you can combine queries, as well as manage the searches that you have already done.
Combine Queries
This feature allows you to find similarities or differences between different searches, as a way to trim down the number of hits to a more manageable level.
Manage Hitlist
This feature is similar to the “Combine Queries,” however, it allows you to combine searches to form a third search that can be renamed and saved for future use.
Additional information can be obtained by clicking on the “Help” tab in the toolbar and selecting either the “Help Index” option or the “Tutorials” option. Also feel free to ask either Victor Young or Ben Kucera for help.。