Mass spectrometry...an introduction

Mass spectrometry is based on slightly different principles to the other spectroscopic methods.The physics behind mass spectrometry is that a charged particle passing through a magnetic field is deflected along a circular path on a radius that is proportional to the mass to charge ratio, m/e. In an electron impact mass spectrometer, a high energy beam of electrons is used to displace an electron from the organic molecule to form a radical cation known as the molecular ion. If the molecular ion is too unstable then it can fragment to give other smaller ions. The collection of ions is then focused into a beam and accelerated into the magnetic field and deflected along circular paths according to the masses of the ions. By adjusting the magnetic field, the ions can be focused on the detector and recorded.

• Probably the most useful information you should be able to obtain from a MS spectrum is the molecular weight of the sample.
• This will often be the heaviest ion observed from the sample provided this ion is stable enough to be observed.

Terminology 
 

Molecular ion	The ion obtained by the loss of an electron from the molecule
Base peak	The most intense peak in the MS, assigned 100% intensity
M+	Symbol often given to the molecular ion
Radical cation	+ve charged species with an odd number of electrons
Fragment ions	Lighter cations formed by the decomposition of the molecular ion. These often correspond to stable carbcations.

Spectra

The MS of a typical hydrocarbon, n-decane is shown below. The molecular ion is seen as a small peak at m/z = 142.  Notice the series ions detected that correspond to fragments that differ by 14 mass units, formed by the cleaving of bonds at successive -CH₂- units

The MS of benzyl alcohol is shown below. The molecular ion is seen at m/z = 108.  Fragmentation via loss of 17 (-OH) gives a common fragment seen for alkyl benzenes at m/z = 91.  Loss of 31 (-CH₂OH) from the molecular ion gives 77 corresponding to the phenyl cation. Note the small peaks at 109 and 110 which correspond to the presence of small amounts of 13C in the sample (which has about 1% natural abundance).

Isotope patterns

• Mass spectrometers are capable of separating and detecting individual ions even those that only differ by a single atomic mass unit.
• As a  result molecules containing different isotopes can be distinguished.
• This is most apparent when atoms such as bromine or chlorine are present (⁷⁹Br : ⁸¹Br, intensity 1:1 and ³⁵Cl : ³⁷Cl, intensity 3:1) where peaks at "M" and "M+2" are obtained.
• The intensity ratios in the isotope patterns are due to the natural abundance of the isotopes.
• "M+1" peaks are seen due the the presence of ¹³C in the sample.

The following two mass spectra show examples of haloalkanes with characteristic isotope patterns.

The first MS is of 2-chloropropane. Note the isotope pattern at 78 and 80 that represent the M amd M+2 in a 3:1 ratio.
Loss of ³⁵Cl from 78 or ³⁷Cl from 80 gives the base peak a m/z = 43, corresponding to the secondary propyl cation. Note that the peaks at m/z = 63 and 65 still contain Cl and therefore also show the 3:1 isotope pattern.
 

 

The second MS is of 1-bromopropane. Note the isotope pattern at 122 and 124 that represent the M amd M+2 in a 1:1 ratio. Loss of ⁷⁹Br from 122 or ⁸¹Br from 124 gives the base peak a m/z = 43, corresponding to the propyl cation. Note that other peaks, such as those at m/z = 107 and 109 still contain Br and therefore also show the 1:1 isotope pattern.
 

N-Benzoylbenzoxazepine

The ¹H NMR spectrum showed extreme line broadening for almost all signals in the aliphatic and aromatic regions. Raising the temperature to 375K in D₆-DMSO resulted in sharpening of all resonances and the aromatic region was readily assigned as shown. Line broadening at room temperature was therefore particularly evident in the o-protons of the benzoyl ring as well as H8 and H9 on the benzoxazepine skeleton. Full ¹H and ¹³C NMR assignments in D₆-DMSO are shown below.

Conformational isomerism in the oxazepine ring

When ¹H NMR spectra of benzoyl derivatives, (1)-(3) were run at lower temperatures (220-230K), all three exhibited clearly defined axial and equatorial protons for the benzylic protons and the methylene adjacent to oxygen in the benzoxazepine ring. Below room temperature these molecules undergo a slowing down of a different form of isomerism resulting in separate chemical environments for all six aliphatic ring protons. The spectrum of (1) at 219K as illustrated below shows the axial protons at positions C3 and C5 resonating as triplets at d4.42 and d3.4 respectively while the associated equatorial protons are doublets at d4.6 and d3.0. The methylene protons at position 4 resonate at very similar chemical shifts and are not resolved at 300MHz.

It is clear that the slow isomerism at these temperatures involves flipping between energetically identical chair conformations similar to that observed in the solid state or predicted by AM1 calculations.

The anisotropic shielding of aromatic protons at C8 and C9 adjacent to nitrogen in the benzoxazepine ring confirm that the oxygens arecis.

The pivaloyl substrate (5), in which only one isomer was prevalent at room temperature, also froze to a chair conformation below 250K as did the benzenesufonyl derivative (7) and in the latter case there was no evidence for slowing of isomerisation about theN�Sbond although chemically distinct methylene protons were broader than in the case of the benzoyl substrates.

Low temperature ¹H NMR spectra of acetylbenzoxazepine (4) and 2-methylpropanoylbenzoxazepine (6) indicated the presence of chair conformers for both theEandZ-isomers. A spectrum of the acetyl compound (4) at 220K diplayed overlapping equatorial and axial benzylic resonances at d2.85 and d3.15 and in one isomer the methylene hydrogens adjacent to oxygen resonate normally at d4.2 (axial) andd4.4 (equatorial). The same protons in the other amide isomer also overlap at ~ d4.4.

The 2-methylpropanoyl compound (6) displayed a similar spectrum at 230K but, in addition, separate methine and methyl resonances were evident. Two sets of diasteriotopic isopropyl methyls were evident. The upfield pair correlating with the methine at d2.5 and the downfield pair correlating with a methine overlapping the axial benzylic proton at d3.3. A NOESY spectrum at 230K indicated that the upfield methine correlated with aromatic protons and therefore corresponded to the isomer in which the isopropyl group was over the aromatic ring (oxygenscis)

The unsubstituted benzoxazepine (8) exhibited a chair conformation at lower temperatures than the other benzoxazepines and at 220K, only the benzyl protons were clearly resolved into distinctly different environments. Isomerisation in this substratewould be expected to be a faster process when compared toN-acylated derivatives.

Each of theEandZ-isomers ofN-acetylnaphthoxazepine (9) was conformationally stable at room temperature. Axial and equatorial benzylic and oxymethylenic hydrogens are clearly discernable for each isomer. Resonances for the major isomer (red) and minor isomer (blue) are depicted in the accompanying COSY spectrum of the aliphatic region.

It is clear that relative to the benzoxazepines (1) to (8), the bay orientation of the acetyl substituent results in a strong steric barrier to ring inversion due to interference with the peri hydrogen. Though not measured, this barrier must be high as even at 398K in D₆-DMSO the ring methylenes and acetyl methyls are still extremely broad .

In the low temperature NMR spectra of benzoyl derivatives (1)-(3), and particularly in the 8-methylderivative (3), a second low temperature conformer is evident. A low temperature COSY spectrum at 220K is shown below and satellite resonances for axial and equatorial hydrogens of the oxymethylene ( d3.75 and d4.05) as well as the benzylic methylenes ( d3.05 and d2.80) are evident and correlated through the methylene at C4. 

Variable temperature studies indicated that the the C3 hydrogens coalesced at very low temperature and that the resultant signals ultimately coalesced with the respective coalesced methylenes from the chair conformation. Thus this minor conformation can clearly convert into the chair conformation but itself isomerises with a lower barrier. (Table 2, Tw-bt DG ^ý= 11.2 kcal mol ^-1). Careful analysis of models and AM1- optimised geometries indicates that this must be an intermediate twist-boat conformation. The twist-boat structure results in distinctly axial and equatorial proton environments at both the benzylic and 3-positions. In the boat structure, the benzylic protons and the 4-methylene protons are however largely eclipsed (Table 3). Axial and equatorial environments are interchanged through interconversion between equivalent forms.

Pseudo-rotation

Models indicate that a twist-boat to twist-boat interconversion can proceed through a pseudo-rotation via one boat conformation.

In seven-membered rings, this is normally extremely facile but fusion with the benzene ring slows this process and the high E_Apseudorotation also involves an energetically unstable transition geometry in which the nitrogen substituent is coplanar with the aromatic ring.

Chair-to-chair interconversion involves a comparatively strained flipping to the nearest boat conformer (but with minimal change at nitrogen), a high E_Apseudo-rotation via one twist-boat form to the alternative boat followed by flipping once again.

METHYL ACETOACETATE

H-1 NMR spectrum of methyl acetoacetate

C-13 NMR spectrum of methyl acetoacetate

STYRENE

A more complex splitting than we saw before can happen in alkene (e.g. styrene) or in a saturated cyclic compound. For example in styrene, signals may be split by adjacent protons, different from each other, with different coupling constant. H_B of styrene which is split by an adjacent H trans to it (J = 17 Hz) and an adjacent H cis to it (J = 11 Hz).

p-Ethoxytoluene

 

Fig.2

¹ H-NMR spectrum of Ethoxytoluen with numbering of the signals (rollover: with integrals)

For the evaluation of spectra are best places to a table where all interesting information can be entered.

Table 1

Information for spectra analysis

///////////pics do the talking

signal1 delta 1.38, triplet

signal2 delta 2.27, singlet

signal3 delta 3.98, quadrplet

signal4 delta 6.79, multiplet

signal5 delta 7.05, multilet

................

 





 





signal 2

signal 1,3






signal 4,5

Structural determination using isotopes is often performed using nuclear magnetic resonance spectroscopy and mass spectrometry

Source: Boundless. “Structural Determination.” Boundless Chemistry. Boundless, 25 Nov. 2014. Retrieved 07 Dec. 2014 from https://www.boundless.com/chemistry/textbooks/boundless-chemistry-textbook/nuclear-chemistry-19/use-of-isotopes-139/structural-determination-549-10548/

https://www.boundless.com/chemistry/textbooks/boundless-chemistry-textbook/nuclear-chemistry-19/use-of-isotopes-139/structural-determination-549-10548

13C NMR spectrum of DMEA plus CO2 at 300 psig

http://pubs.rsc.org/en/content/articlelanding/2011/ee/c0ee00506a#!divAbstract



13C NMR spectrum of DMEA plus CO2 at 300 psig (referenced to dissolved CO2