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Website Help System

Reaction Database

 Using the Search Applet

The Search Applet is comprised of two main search areas that can be used separately or in conjunction with one another. Structure based searching is available on the left and text and numeric based searching is available on the right.

Customizing Hitlist Reporting

Two dropdown fields are available above the text and numeric searching area that allow the user to specify the number of hits per page and the number of total hits. Hits per Page can be set to 5 (default), 10, 25, and 50. Total Hits can be set to 100 (default), 250, and 500. Depending upon machine and network specifications, the values set in these fields may influence observed performance.

 Structure Based Searching

The structure based search system utilizes an integrated JME Molecular Editor© window for straightforward structure and reaction composition.

Reactant Search

Substructure

To search for reactions with a major reactant having a structure containing a given substructure:

  1. Examine the "Search reactions by:" field located above the JME Molecular Editor© to ensure that "Substructure match" (default) is selected
  2. Draw the desired substructure to the left of the arrow in the JME Molecular Editor©
  3. Click the Search Button

Exact structure

To search for reactions with a major reactant having the exact structure drawn:

  1. Select "Exact structure match" from the "Search reactions by:" field located above the JME Molecular Editor©
  2. Draw the desired structure to the left of the arrow in the JME Molecular Editor©
  3. Click the Search Button

Product Search

Substructure

To search for reactions with a product having a structure containing a given substructure:

  1. Examine the "Search reactions by:" field located above the JME Molecular Editor© to ensure that "Substructure match" (default) is selected
  2. Draw the desired substructure to the right of the arrow in the JME Molecular Editor©
  3. Click the Search Button

Exact structure

To search for reactions with a product having the exact structure drawn:

  1. Select "Exact structure match" from the "Search reactions by:" field located above the JME Molecular Editor©
  2. Draw the desired structure to the right of the arrow in the JME Molecular Editor©
  3. Click the Search Button

Reaction Search

Substructure

To search for reactions specifying a substructure that must exist in a major reactant and a substructure that must exist in the product:

  1. Examine the "Search reactions by:" field located above the JME Molecular Editor© to ensure that "Substructure match" (default) is selected
  2. Draw the desired reactant substructure to the left of the arrow in the JME Molecular Editor©
  3. Click the à button on the JME Molecular Editor© (structure is copied to product side)
  4. Alter the copied product substructure as desired on the right side of the arrow in the JME Molecular Editor©
  5. Click the Search Button

Exact structure

To search for reactions specifying exact structures for a major reactant and product:

  1. Select "Exact structure match" from the "Search reactions by:" field located above the JME Molecular Editor©
  2. Draw the desired reactant structure to the left of the arrow in the JME Molecular Editor©
  3. Click the à button on the JME Molecular Editor© (structure is copied to product side)
  4. Alter the copied product structure as desired on the right side of the arrow in the JME Molecular Editor©
  5. Click the Search Button

 Text and Numeric Based Searching

The text and numeric based searching area is comprised of a series of labeled fields that can be used separately or in conjunction with one another to create powerful search queries.

Text Searches

The general text searches available are journal author, journal name, journal volume, keywords, product name, and reactant name. All of these fields perform a "like" search on the string of text that is input. This means that a search for "product name: benzene" would return reactions where the product name or synonym contains the word benzene (e.g. benzene and 1,2-dimethylbenzene and 1,2-benzenediamine).

Numeric Searches

The numeric searches search fields in the database that contain numeric data. The numeric search fields are journal year, product weight, reactant weight, product yield, and product purity. For journal year, values should be entered in YYYY format, and for the weight, purity, and yield fields, only numeric data should be entered, no units or percent signs. Numeric fields have an operator associated with them that allows ranges of values to be searched. Operator values of between, = (equals), < (less than), and > (greater than) can be chosen. The default operator value of "between" results in two fields separated by an ampersand. This allows the entry of the minimum and maximum value for the range being searched. When another operator is selected, the second field and ampersand are removed automatically.

CAS Number and Formula Searches

The product and reactant CAS and product and reactant formula fields are also available in this area. CAS numbers must be entered in standard CAS format (i.e. #####-##-#) with the hyphens. For instance the CAS number for benzene must be entered 71-43-2, and not 71432.

Data input into formula fields must adhere to the proper case restrictions for elemental symbols. Two letter symbols must have a capital first letter and lowercase second letter (e.g. Ni3 means three Nickel atoms, but NI3 means one nitrogen and 3 iodine atoms). The numeric atom quantity must be entered after the element symbol. Thus the correct formula entry for 1,2-dichlorobenzene would be C6H4Cl2.

There are three operators available for formula searches "contains at least" (default), "has exactly", and "no more than". The "contains at least" operator searches for any formula that has the respective elements in the specified quantity or greater. The "no more than" operator searches for any formula that has the respective elements in the specified quantity or less. The "has exactly" operator searches for any formula that contains the specified elements in their specified quantities.

Formula searches are performed with an understood "any other element" principle. This means that elements other than those specified may appear in the formulae of search hits as long as the specified formula is present.

 Combining Searches

The search applet has been designed in such a way that any of the aforementioned search methods can be combined with one another. The search page can be considered a search composition form. Any field that is filled out on the form (including structure/reaction drawings) constitutes a separate search. All searches that exist on the form are combined (using the Boolean AND operator) when the search button is clicked, and the resulting hitlist provides only hits that satisfy all the search terms. The combination possibilities are endless, but beware that excess constraint may exclude all hits.

At any point, the entire search form may be cleared by clicking the Clear button.

 Reaction Hitlists

Layout

The reaction hitlists are designed in a two column format with link bars at the top and bottom of the list. The number of hits per page, and the number of total hits returned are configurable on the search page. The left column contains compound properties for the products of the reactions returned. The right column contains the reaction scheme image. Results are sorted by product molecular weight by default.

Compound Properties

This column lists properties for the product such as name, molecular formula (MF), molecular weight (MW), CAS number, MDL number, yield, and catalog information. There are also several reaction properties listed including reaction scale, year, citation, and keywords. A button is available by the product name that launches reaction relay for that product.

Reaction Scheme

The reaction scheme for each result is shown in the right column. The scheme is limited to a default size, but if that size is exceeded, scrollbars are available to view any obscured portions. There is also a Zoom In link that opens a larger version of the reaction scheme in a separate window. The yield and product role are shown under the product image, and the arrow is stamped with either ‘Detailed Reaction’ in blue (for a Synthematix reaction) or ‘Summary Reaction’ in purple (for an InfoChem reaction). Click the reaction arrow to open the scalable reaction run sheet in a separate window.

Other Links and Functionality

The link bars at the top and the bottom contain navigational links and information. This area displays the set of reactions being viewed (e.g. Reaction 1-5 of 100) and contains previous and next links for navigation between pages of results when applicable. The New Search link opens a new, blank search page in the same window, and the Return link functions like the Back button on the browser, returning to the search page with the search data still intact.

 Reaction Run Sheet

The reaction run sheet is the detailed view of the reaction that shows the reagent quantities, procedural steps, equipment used, and other information as it was entered into the database. The calculator section is scalable, allowing reaction amounts to be quickly adjusted based upon user-defined mol scales. Reactions may also be exported as PDF worksheets or as SRZIP files for import into Arthur™ systems.

Layout

The reaction run sheet is comprised of eight sections. These are arranged from top to bottom as listed below:

  • Product Information: At the top is the product information section. The product names, formulae, molecular weights, CAS numbers, and catalog information (if available) are printed in a grey bar above the reaction scheme. There are also buttons that display substance properties, search the product structure as a reactant, and launch reaction relay for the product.
  • Reaction Scheme: Below the product information bar is the reaction scheme. Here the major reactants and products are depicted in A + B à C format, with the yield and product role information displayed below the product image.
  • Useful Information/Keywords: Any keywords associated with the reaction appear in this section.
  • Mol Scale Entry/Yield Display: This section allows the mol scale value that controls the scalable calculator to be input. This is also the section in which the product yield and purity are displayed.
  • Chemicals Needed: This section provides reagent information as well as amounts and ratios used in the reaction. The text boxes update with appropriate values according to the mol scale entered in the previous section. Buttons exist for each reactant that link to substance properties, searching the reactant structure as a reactant, searching the reactant structure as a product, and launching reaction relay for the reactant. Reactant names may also be linked to reactions that produce them.
  • Equipment Needed: This section displays the list of equipment saved when the reaction was created.
  • Procedure: This section displays the procedural steps recorded for the reaction. Any text boxes that appear in this section also get updated with appropriate values when a mol scale is added above.
  • References: This section lists both bibliographic and laboratory notebook reference information for the reaction.

Scaling Reactions

To scale a reaction, enter the desired mol scale into the ‘Enter Mol Scale:’ field, and click the Calculate button. Upon doing so, the blank text boxes in the reactant calculator, procedure steps, and yield will all update with the appropriate values based upon the mol scale entered.

Info Buttons

Info buttons appear in the button bar underneath substance names. The buttons are either blue (Synthematix substance) or purple (InfoChem substance) circles with a white "i" in the center. When these buttons are hovered, the substance image appears. When these buttons are clicked, the reactant details window, providing substance property information, appears.

Structure Search Buttons

Structure search buttons are also located in the button bar underneath substance names. Products have only a ‘search as reactant’ button, while reactants have both ‘search as reactant’ and ‘search as product’ buttons. When these buttons are clicked, an exact structure search is launched for the structure of the chosen substance. Depending on which button is clicked, the search will examine products or reactants and display the conforming reactions in a hitlist within a separate window.

Reaction Relay

The final button in the button bar underneath the substance name is the reaction relay button. Clicking this button launches the reaction relay applet in a separate window. The properties for the chosen substance are displayed in the upper right frame, and a diagram of the substance and its nearest neighbors in transform space appears in the upper left frame. The substances shown are all either major reactants or products, and the directions of the arrows indicate the direction of the reaction. The numbers that appear within the arrowheads indicate the number of reactions that exist with that particular starting material and product. Navigation within reaction relay is simple:

  • To view the properties of another substance, click any substance in the relay diagram
  • To expand the diagram around a substance, double-click the substance
  • To collapse the diagram around an expanded substance, double-click the substance
  • To view reaction details in the lower frame, click any arrowhead

Within the lower frame, previous and next links will appear when there is more than one reaction for a given set of substances. These links can be used to move among the reactions. The summary information includes the reaction scheme, a list of any other reagents used, and the reference information. To open a reaction run sheet for the current reaction, simply click the View Details link or click the reaction arrow in the reaction scheme.

PDF Worksheet

A PDF worksheet of a reaction can be created by clicking the View as PDF button at the top of the run sheet. If the button is clicked prior to scaling the reaction, the original amounts appear in the PDF. If the reaction has been scaled prior to clicking the button, the scaled values appear in the PDF. This file can then be saved or printed as the user sees fit.

Reaction Export

A reaction can also be exported in SRZIP format. The SRZIP file format is a proprietary means of transferring committed reactions between Arthur™ databases. When the Get Reaction button is clicked, a file save dialog appears allowing the user to pick the location in which to save the file. This file can then be imported into an Arthur™ database using either Reaction Planner, or the web interface. Upon import, the file is committed immediately to the database in the same state as it was committed originally. This means that the original database values remain in the calculator, regardless of whether or not the reaction was scaled prior to clicking the Get Reaction button.