Searching for Unknowns via the Internet

Searching for unknowns across an internal library or database can serve as a major time saver. A more accessible database is the Internet. Many chemists and elucidators search the World Wide Web using a mass, a molecular formula or a fragment.

Be aware that proprietary data sent over the Internet runs the risk of being intercepted.

Searching the Internet via Google™ for the molecular formula C17H11N5 produced 787 hits with Letrozole appearing in the first dozen hits or so. Using a variation of the molecular formula C17 H11 N5 with the elements spaced out produced over 34,000 hits without any clear reference to Letrozole.

Searching for Unknowns via the Internet

Searching for unknowns across an internal library or database can serve as a major time saver. A more accessible database is the Internet. Many chemists and elucidators search the World Wide Web using a mass, a molecular formula or a fragment.

Be aware that proprietary data sent over the Internet runs the risk of being intercepted.

Searching the Internet via Google™ for the molecular formula C17H11N5 produced 787 hits with Letrozole appearing in the first dozen hits or so. Using a variation of the molecular formula C17 H11 N5 with the elements spaced out produced over 34,000 hits without any clear reference to Letrozole.

Milestone for P2C2E

February 1, 2009 marked the 1 year anniversary of the weblog with the first post on ‘The Intricacies of solving for an unknown structure using solution NMR data’. The blog went live on February 15, 2008 with the second blog ‘Dealing with Mixture in a 13C NMR spectrum’.

 

I would like to thank all the blog readers; I truly appreciate the support and dedication.

  

As of January 17, 2009, the web counter marked 14,968 hits with an average of ~46 hits per day. January 18, 2009 had the most hits at 218.

Milestone for P2C2E

February 1, 2009 marked the 1 year anniversary of the weblog with the first post on ‘The Intricacies of solving for an unknown structure using solution NMR data’. The blog went live on February 15, 2008 with the second blog ‘Dealing with Mixture in a 13C NMR spectrum’.

 

I would like to thank all the blog readers; I truly appreciate the support and dedication.

  

As of January 17, 2009, the web counter marked 14,968 hits with an average of ~46 hits per day. January 18, 2009 had the most hits at 218.

Limiting the Atom Ranges

In a previous blog, the atoms C, H, O, and N were limited to a specific range, 0-50, 0-100, 0-10 and 0-10, respectively. Starting from a wide atom count range ensures molecular formulae are not overlooked. The ranges for the atom count can be restricted further using additional information such as NMR, IR, etc.

A common tactic for elucidating compounds containing nitrogen is to acquire a 15N NMR experiment to assist in setting a narrower range for nitrogen count. The 1H-15N HMBC experiment below indicates the presence of at least 2 nitrogen atoms. Therefore, the nitrogen range can be set to 2-10 atoms and thus reduce the number of candidate molecular formulae.

    

Limiting the Atom Ranges

In a previous blog, the atoms C, H, O, and N were limited to a specific range, 0-50, 0-100, 0-10 and 0-10, respectively. Starting from a wide atom count range ensures molecular formulae are not overlooked. The ranges for the atom count can be restricted further using additional information such as NMR, IR, etc.

A common tactic for elucidating compounds containing nitrogen is to acquire a 15N NMR experiment to assist in setting a narrower range for nitrogen count. The 1H-15N HMBC experiment below indicates the presence of at least 2 nitrogen atoms. Therefore, the nitrogen range can be set to 2-10 atoms and thus reduce the number of candidate molecular formulae.

    

Fitting a Molecular Formula to a Mass

With a monoisotopic mass identified from a mass spectrum, the next step is to fit a molecular formula (or elemental composition) to the unknown. For organic compounds, the starting elements of choice are Carbon, Hydrogen, Oxygen, Nitrogen and sometimes Sulfur. Information from starting material and known derivatives can also help when deciding what elements and valences to work with.

The mass of an unknown organic compound is 950.298 g/mol accurate to 0.002 Da. If the elements C(0-50), H(0-100), O(0-10) and N(0-10)—atoms ranges are listed within the brackets—are used, then no molecular formula fits this mass. For this case, expanding the elemental list to include sulfur will produce a list of 54 candidate MFs. The top 9 MFs, based on lowest error, are displayed below.

No.     Formula         Monoisotopic Mass     Error

1     C42H78OS11         950.2980             0.0000

2     C27H82N8OS13     950.2981             -0.0001

3     C28H88NO6S13     950.2981             -0.0001

4     C20H84N7O9S12     950.2979             0.0001

5     C41H58N8O8S5     950.2981             -0.0001

6     C34H74N6O4S10     950.2979             0.0001

7     C21H96N3O3S16     950.2983             -0.0003

8     C49H62N2O5S6     950.2983             -0.0003

9     C35H72N3O10S8     950.2983             -0.0003

Fitting a Molecular Formula to a Mass

With a monoisotopic mass identified from a mass spectrum, the next step is to fit a molecular formula (or elemental composition) to the unknown. For organic compounds, the starting elements of choice are Carbon, Hydrogen, Oxygen, Nitrogen and sometimes Sulfur. Information from starting material and known derivatives can also help when deciding what elements and valences to work with.

The mass of an unknown organic compound is 950.298 g/mol accurate to 0.002 Da. If the elements C(0-50), H(0-100), O(0-10) and N(0-10)—atoms ranges are listed within the brackets—are used, then no molecular formula fits this mass. For this case, expanding the elemental list to include sulfur will produce a list of 54 candidate MFs. The top 9 MFs, based on lowest error, are displayed below.

No.     Formula         Monoisotopic Mass     Error

1     C42H78OS11         950.2980             0.0000

2     C27H82N8OS13     950.2981             -0.0001

3     C28H88NO6S13     950.2981             -0.0001

4     C20H84N7O9S12     950.2979             0.0001

5     C41H58N8O8S5     950.2981             -0.0001

6     C34H74N6O4S10     950.2979             0.0001

7     C21H96N3O3S16     950.2983             -0.0003

8     C49H62N2O5S6     950.2983             -0.0003

9     C35H72N3O10S8     950.2983             -0.0003