How to apply the Nitrogen rule to organic compounds … Part 2

For MS data, the ionization method will dictate how the nitrogen rule is applied.

For example, if the ionizer is Electron Impact (EI) ionization, then the nitrogen rule is to be applied to the molecular ion [M]+* as follows:

-an odd nominal mass indicates an odd number of nitrogen atoms, e.g. 1,3,5

-an even nominal mass indicates an even number of nitrogen atoms, e.g. 0,2,4.

If the particles are charged using ElectroSpray Ionization (ESI), for example, then the nitrogen rule is to be applied to the molecular ion [M+H]+ or [M-H]- as follows:

-an odd nominal mass indicates an even number of nitrogen atoms

-an even nominal mass indicates an odd number of nitrogen atoms.

The chemical structure for Etifenin is shown below; the differences between the structures are displayed in red. The nominal mass for the [M+H]+ structure, shown on the left side, is odd and therefore the nitrogen rule dictates an even number of nitrogen atoms. For the M+* structure shown on the right side, the even nominal mass dictates an even number of nitrogen atoms.

How to apply the Nitrogen rule to organic compounds … Part 2

For MS data, the ionization method will dictate how the nitrogen rule is applied.

For example, if the ionizer is Electron Impact (EI) ionization, then the nitrogen rule is to be applied to the molecular ion [M]+* as follows:

-an odd nominal mass indicates an odd number of nitrogen atoms, e.g. 1,3,5

-an even nominal mass indicates an even number of nitrogen atoms, e.g. 0,2,4.

If the particles are charged using ElectroSpray Ionization (ESI), for example, then the nitrogen rule is to be applied to the molecular ion [M+H]+ or [M-H]- as follows:

-an odd nominal mass indicates an even number of nitrogen atoms

-an even nominal mass indicates an odd number of nitrogen atoms.

The chemical structure for Etifenin is shown below; the differences between the structures are displayed in red. The nominal mass for the [M+H]+ structure, shown on the left side, is odd and therefore the nitrogen rule dictates an even number of nitrogen atoms. For the M+* structure shown on the right side, the even nominal mass dictates an even number of nitrogen atoms.

How to apply the Nitrogen rule to organic compounds

The purpose of the nitrogen rule is to assist with deciphering how many nitrogen atoms are present without any prior information on the molecular formula. Depending on the ionization mode, an odd nominal mass indicates an odd number of nitrogen atoms, e.g. 1,3,5, whereas an even nominal mass indicates an even number of nitrogen atoms, e.g. 0,2,4.

The nitrogen rule can only be applied under the following conditions:

1. the m/z value is the molecular ion,

2. the unknown is an organic compound with any combination of hydrogen, carbon, oxygen, nitrogen, phosphorous, silicon, sulfur, fluorine, chlorine, bromine, iodine, and

3. the MS data is nominal data.

For a better way to tell if nitrogen is present, please visit this link to Fiehn’s Lab.

How to apply the Nitrogen rule to organic compounds

The purpose of the nitrogen rule is to assist with deciphering how many nitrogen atoms are present without any prior information on the molecular formula. Depending on the ionization mode, an odd nominal mass indicates an odd number of nitrogen atoms, e.g. 1,3,5, whereas an even nominal mass indicates an even number of nitrogen atoms, e.g. 0,2,4.

The nitrogen rule can only be applied under the following conditions:

1. the m/z value is the molecular ion,

2. the unknown is an organic compound with any combination of hydrogen, carbon, oxygen, nitrogen, phosphorous, silicon, sulfur, fluorine, chlorine, bromine, iodine, and

3. the MS data is nominal data.

For a better way to tell if nitrogen is present, please visit this link to Fiehn’s Lab.

Does my unknown structure contain Bromine?

MS and NMR are complementary elucidation tools. Knowing when to apply the correct tool can facilitate the elucidation process.

Compounds with bromine atoms exhibit a distinct ion pattern on a mass spectrum. The A+2 peak for a monobrominated compound appears at almost identical intensity to the 79Br peak due to the presence of 81Br (~49.3% natural isotope abundance). A compound with two bromines shows a distinct A+4 peak with an approximate ratio of 1:2:1.

The following EI mass spectra are for 3-bromopropanenitrile and (1Z)-1,2-dibromobut-1-ene with nominal masses at 133 and 212 Da, respectively. The top MS shows 3 identified fragments containing bromine (m/z 79/81, 93/95 and 133/135) as noted by the ~1:1 intensity of the ion clusters. The ion peak at m/z 54 does not show a 1:1 ratio since the fragment does not contain a bromine atom.

The MS for (1Z)-1,2-dibromobut-1-ene shows 4 identifiable fragments containing bromine (m/z 117/119, 133/135, 197/199/201 and 212/214/216). In particular, ion clusters at m/z 197/199/201 and 212/214/216 show the distinct ~1:2:1 intensity. This is a result of the varying amounts of the isotopes 79Br and 81Br, that is, the 3 peaks represent 79Br/79Br : 79Br/81Br : 81Br/81Br.

TIP: Check the fragment ion peaks too for the distinct pattern especially when the molecular ion peak is not visible.

Does my unknown structure contain Bromine?

MS and NMR are complementary elucidation tools. Knowing when to apply the correct tool can facilitate the elucidation process.

Compounds with bromine atoms exhibit a distinct ion pattern on a mass spectrum. The A+2 peak for a monobrominated compound appears at almost identical intensity to the 79Br peak due to the presence of 81Br (~49.3% natural isotope abundance). A compound with two bromines shows a distinct A+4 peak with an approximate ratio of 1:2:1.

The following EI mass spectra are for 3-bromopropanenitrile and (1Z)-1,2-dibromobut-1-ene with nominal masses at 133 and 212 Da, respectively. The top MS shows 3 identified fragments containing bromine (m/z 79/81, 93/95 and 133/135) as noted by the ~1:1 intensity of the ion clusters. The ion peak at m/z 54 does not show a 1:1 ratio since the fragment does not contain a bromine atom.

The MS for (1Z)-1,2-dibromobut-1-ene shows 4 identifiable fragments containing bromine (m/z 117/119, 133/135, 197/199/201 and 212/214/216). In particular, ion clusters at m/z 197/199/201 and 212/214/216 show the distinct ~1:2:1 intensity. This is a result of the varying amounts of the isotopes 79Br and 81Br, that is, the 3 peaks represent 79Br/79Br : 79Br/81Br : 81Br/81Br.

TIP: Check the fragment ion peaks too for the distinct pattern especially when the molecular ion peak is not visible.

Identifying a monosubstituted benzene fragment in a 1H NMR spectrum

Although peak crowding can be a nuisance, a monosubstituted benzene fragment can be identified by a 1H NMR. A good marker for a monosubstituted benzene ring, and thus how an elucidator can clue in to its presence for an unknown, is whether the sum of the relative integrals for the aromatic resonances add up to 5.

Below are 6 1H NMR spectra illustrating the various patterns for a monosubstituted benzene fragment. Although other possibilities can exist, these are the typical patterns to be on the lookout for in the aromatic region.