Newsletter #2 | August 2008
Responding to customer feedback there is a new documentation and free webinar center now available on the website replacing the former Learning Center which is no longer in use.
Detailed training manuals relating to the various CrossFire Commander versions (from 6.0 to 7.1) and to the CrossFire databases (CrossFire Beilstein, CrossFire Gmelin and Patent Chemistry Database) are available for download. Customers can also register for free web-based seminars. Each webinar, tailored specifically to a different aspect of the CrossFire databases, has been designed to ensure greater insight into the best possible usage of the databases. Access the training center where you will find useful 'How Do I...' guides giving clear instructions on the different steps required to acheive common tasks within the CrossFire databases.
Register for the free online CrossFire training webinars. Save valuable time and quickly learn how to get the most out of the CrossFire databases. Each webinar, tailored specifically to a different aspect of the CrossFire databases, has been designed to ensure greater insight into the best possible usage of the databases. Every webinar is run by an experienced customer care expert – direct contact which ensures total clarity on all topics.
The webinars, 'How Do I' guides and manuals are an effective and easy way to brush up on CrossFire knowledge, ensuring maximum results with minimum effort. Following the recent enhancements such as multi-step reactions and bi-directional linking with Scopus, the webinars ensure end users are always up-to-date. Don't hesitate to contact us with questions about the webinars or documentation.
Experimental texts in the Patent Chemistry Database
The detailed description of a synthetic method in any type of publication is one of the most meaningful items to check the feasibility of the method for yourself and thus the relevance of the original publication for your work. It puts the content - the reaction itself - into the context of the conditions used.
The Patent Chemistry Database makes these texts available for all indexed reactions from Patents from 1976 to today, allowing the selection of the most appropriate synthesis for a given task, saving end users from reading irrelevant patents.
The information supplied is detailed enough to allow researchers to conduct the reaction sometimes without even needing the original publication – saving both time and money. Analytical data such as NMR Peaks - are also indexed in this section - enable a quick check analysis of the end product.
Alongside the information about the method used, the location inside the patent and the Example Number are also listed, meaning that the information in the original document can be quickly located if needed.
Full Text Linking
What is Full Text Linking? As the name implies, full text linking gives access to the full text articles, i.e. the original journal articles or patent documents. CrossFire Commander 7.1 uses a free-of-charge CrossFire Linking Service which is available through the default web browser. As a result, once researchers have decided that the information presented in CrossFire is relevant they can then quickly and efficiently access the original article.
For users of versions of < 7.1 CrossFire Commander it is still possible to use the CrossFire Linking Service, despite the fact that the services of Litlink and Discovery Gate literature linking service are no longer available. We recommend that you contact us so that we can help you with a detailed and tailored description of the necessary procedure.
CWA - what you think
Customers have been reacting very positively about the new licensing model for the CrossFire Databases. Since the end of 2007 Corporate Wide Access (CWA) – access based on IP addresses instead of single usernames – has been available and has become the favoured model for CrossFire customers of all sizes.
Dr. Marc Thommen, Head of Small Molecules Business Unit at Polyphor Ltd., has praised the flexibility of the model, which allows occasional users to benefit from the CrossFire Databases in addition to the regular users. Polyphor has been using CWA since March 2008, recognizing that the CWA model provides an additional ROI by increasing the availability of CrossFire within the company, in turn giving faster access to results.
Polyphor Ltd is a privately held biotech company, headquartered in Allschwil (near Basle), Switzerland. The company provides innovative, high quality products and services to the pharmaceutical and biotech industry. In the area of small molecules, Polyphor offers scaffold-rich screening libraries, exclusive, custom made libraries and medicinal chemistry services. Furthermore Polyphor has developed clinically enabled Protein Epitope Mimetics (PEM) derived from its proprietary PEM Technology. Internal R&D efforts are focused on Protein Epitope Mimetics as novel clinical drug candidates. These efforts have led to a balanced portfolio of drug discovery projects.
If you have anything to add please share it with us.
More on multi-step reactions
Seeing every step in a multi-step reaction has many benefits especially in several specific lab situations. For example, sometimes a single-step reaction with an extremely high yield uses a dangerous or hard-to-get catalyst or reagent, but a multi-step reaction with a commercially available reagent and an acceptable overall yield could prove more useful. Alternatively chemists working in natural product synthesis who need ten or more synthesis steps to produce a specific compound will appreciate seeing the whole n-step-process on a summary page and be able to compare different synthesis processes for one product.
The figure multi-step-reaction with 8 steps summarizing the reaction details:
To see the full reaction scheme with all steps (see image below) you need to click on the link “multi-step scheme” as shown above.
If the link “multi-step scheme” does not connect it could be that this is because you are using a CrossFire Commander version below 7.1. The link for multi-step reactions works only with CrossFire Commander 7.1, with all previous versions the corresponding link is inactive.
Reaction Dossiers: reactions which synthesize a specific product “Z” from the same reactant “A” (A -> Z) are merged into one reaction hit record independent from the number of steps. This means all potential synthesis methods which have been published are available in one single overview.
Apple Macintosh users cannot currently view multi-step reaction schemes, but this will change with Reaxys – the innovation from CrossFire Beilstein: a brand new workflow tool for chemists. Read about Reaxys below.
Tips and Tricks
See for yourself how easy it is to search using R-groups - taking the example of searching for mono-substituted aromatic rings, with the position of the attachment being undetermined.
In order to search for a monosubstituted aromatic rings, with undetermined position of the substitution you need to use R-Groups.
Using toluene as example and using the methyl group as reference for the substation position below are the required steps.
Add an R group in position ortho, meta and para to the methyl group, all the same R-group, and define R as your desired substituent, here bromene.
Note: In Commander the R-groups are converted to “G”-Groups.
In ISIS Draw now select the menu Chemistry/R-Query: R-Logic, and set R1 to the occurrence of “1”.
If you are using the CrossFire Structure Editor please create G-Groups instead of R-Groups in the similar way. Than select a G1-Group, and chose the menu “Query: Generic Frequency” from the Structure Editor Menus.
Set G1 to the frequency of 1.
More Tips and Tricks
The grouping and sorting feature of CrossFire Commander 7.1 comes with some valuable new features, for example the limit to and exclude capability as featured in the previous edition of this newsletter.
The groups can also be ranked by group size or population.
In order to decide how to group a larger hitset or limit to/exclude certain groups it is important to understand which groups are the most populated ones. For this the groups already in the grouping window can be sorted by size in order to determine which grouping items are prominent and which are not.
This option can be found at the bottom of the grouping options window:
This setting is then transferred to Commander, where the groups can be explored one by one.
This feature enables users to sort for example reaction hitsets by solvent, or compounds groups by logP, to see which groups are mostly populated. Also, if grouping a citation hitset by Journal or Author it is very useful to have the most populated group on top.
Where to find us
Following the successful Tetrahedron conference in Berkeley, California last month, members of the CrossFire team will be present at ACS Fall, Philadelphia, 17-21 August. Visit booth 717 to learn more about the products and to gain a personal insight into the next step beyond the CrossFire Databases. Register for the workshop 'From query to lab: using CrossFire to enhance synthesis planning' on either Monday 18th or Tuesday 19th August. The free workshop demonstrates how to reduce time spent on locating and reviewing synthesis data using CrossFire Commander 7.1.
Save the evening of Monday 18th August for a special Elsevier reception at the Philadelphia Marriott hotel where greater details on the next step beyond CrossFire will be revealed. Ask for more details at the booth.
The next European event with a CrossFire presence is the International Symposium on Medicinal Chemistry, Vienna 31 August – 4 September.
Reaxys - innovation from CrossFire Beilstein
Reaxys is a brand new workflow tool for chemists. It is designed to support the optimization of synthetic processes and offers a valuable resource for accurate and validated experimental reaction and substance data.
It is a web-based service with an interface that is easy to work with. Bi-directional linking with Scopus as well as convenient analysis and planning tools offer expedient functions which help scientists to make research and discovery of new compounds more efficient. Learn more about Reaxys and sign up for the Reaxys newsletter to stay up-to-date with future developments.
