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.
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.
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.
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.
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
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
Depending on sample preparation, adduct ions can be present on a mass spectrum. The goal of the elucidator is to identify whether an adduct ion(s) is present and its contribution to the mass (or elemental composition) of the unknown compound.
The example ESI+ mass spectrum below exhibits 2 ion clusters at m/z 951.305 and 973.287, corresponding to ions [M+H]+ and [M+Na]+ respectively. For this spectrum, sodiation is identified by taking the difference between the two masses at 21.982 g/mol and comparing it to the mass of a sodium ion at 22.989 g/mol minus the mass of a proton at 1.007 g/mol. The mass of the unknown at 950.298 g/mol is calculated by subtracting the contribution of the sodium adduct or the mass of a proton at 1.007 g/mol from the respective peak.
