Fragmentation and mass spectra of Esters

• Molecular ion peak is weak but noticeable.
• The most characteristic peak results from McLafferty rearrangement. 
  
• Other important Peaks results from bond cleavage next to C=O.
  
• gives an easily recognizable peak for esters.
• Easters, in which the acid portion is the predominant portion of molecule, the fragmentation pattern is same as described for the fragmentation pattern of free acid.
  
• Easters, in which the alcohol portion is the predominant portion of molecule, eliminate a molecule of acid on fragmentation.
• lets check spectrum of methyl octanoate
  

Fragmentation and mass spectra of Aliphatic Acids

• Molecular ion peak is weak but noticeable.
• In short chain acids, cleavage of bonds next to C=O results prominent peaks at M-OH and M-CO₂H.
• In long chain acids, the spectrum consists of two series of peaks resulting from cleavage at each C-C bond with retention of charge either on the Oxygen containing fragment or the alkyl containing fragment.
• The most characteristic peak is m/z 60 resulting from the McLafferty rearrangement. Branching at α carbon enhance this cleavage.
  

lets examine spectrum of decanoic acid 

Fragmentation and mass spectra of Aldehydes

• Molecular ion peak is very weak.
• M-1 peak is good diagnostic peak, even for long chain Aldehyde.
• In lower aldehydes, α-cleavage is prominent with retention of charge on oxygen.
• In straight chain Aldehydes, the other diagnostic peaks are at 

1. M-18 because loss of water
2. M-28 because loss of ethylene
3. M-43 because loss of CH2=CH-O
4. M-44 because loss of CH2=CH-OH

Fragmentation and mass spectra of Ketone

• The mass spectrum of a ketone generally has an intense molecular ion peak.
• Ketones fragment homolytically at the C-C bond adjacent to the C=O bond, which results in the formation of a cation with a positive charge shared by two atoms. The alkyl group leading to the more stable radical is the one that is more easily cleaved.

• If one of the alkyl groups attached to the carbonyl carbon has γ hydrogen, a cleavage known as a McLafferty rearrangement may occur.
  

lets interpret this spectrum

Fragmentation and mass spectra of Ethers

• Molecular ion peak is small.
• The presence of oxygen atom can be deduced from strong peaks at m/z31,45,59,73 ect. These peaks represents the RO⁺ and ROCH₂⁺fragments.
• Fragmentation of the resulting molecular ion occurs in two principal ways:

1. A C-O bond is cleaved heterolytically, with the electrons going to the more electronegative oxygen atom. 
   
2. A C-C bond is cleaved homolytically at the position because it leads to a relatively stable cation in which the positive charge is shared by two atoms (carbon and oxygen).
   

Now try to this interpret spectrum

Fragmentation pattern and mass spectra of Alcohols

·        Molecular ion peak of primary and secondary alcohol is quite small and for tertiary alcohol is undetectable.

·        Molecular ion peak is formed by the removal of one electron from the lone pairs on the oxygen atom of primary and secondary alcohol.

·        Cleavage of C-C bond next to the oxygen (α cleavage) is of general occurrence.

o   Thus primary alcohol  show a prominent peak resulting from oxoniumion (m/z 31)

o   secondary alcohol show a prominent peak resulting from (m/z 45,59,73 etc)

o   tertiary alcohol show a prominent peak resulting from(m/z 59, 73, 87 etc)

·     A distinct and sometimes prominent peak can usually be found at M-18 from loss of H₂O.

·     In primary alcohol elimination of water, together with elimination of alkene, accounts for the presence of a peak at M-(alkene+ H₂O) ie (m/z 46, 74, 102 etc)

lets examine spectrum of 1-pentanol

examine spectrum of  secondary alc. 2-pentanol

now examine spectrum of  tertiary alc. 2-methyl-2-butanol

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Fragmentation pattern of Aromatic hydrocarbon in mass spectra

·        Molecular ion peak is fairly noticeable because an aromatic ring better stabilizes the molecular ion.

·        If the aromatic ring is substituted by an alkyl group, a prominent peak is formed at m/z 91. This highly stabilized fragment is result from rearrangements.

·        Next frequently observed peak at m/z 65 results from elimination of neutral acetylene molecule from tropylium ion.

·        When alkyl group is longer than two carbon peak at m/z 92 is observed, accounts for hydrogen migration with elimination of neutral alkene molecule.

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How to Interpret Mass Spectra?

Here we learn how to interpret mass spectra?
As you know mass spectrum is a presentation of the masses of the positively charged fragments versus their relative concentrations. The most intense peak in the spectrum, called the ‘Base peak’ is assigned value of 100%, and the intensity of other peaks, are reported as percentage of the base peak.
The commonly used technique in mass spectrometry is ‘Electron Impact’. On electron impact, the molecules are energized sufficiently to eject an electron, thus produces molecular ion "M+"; which further fragments to more daughter ions.
Fragmentation fallow general principles of stability of organic molecule.
Interpretation of mass spectrum is just like to solve puzzle. You have to think all possible ways in which molecular ion can fragment, and form more stable daughter cation. More stable daughter cation gives more abundant peak.
Lets work out this spectrum of alkane.

1. Identify molecular ion peak. Here it is 72. 
2. find out carbon skeleton corresponds to molecular ion. Here it may be C5H(12-1)ion
3. Find out all possible carbon frames. Here we find 3 possibilities..
4. Identify base peak in given spectra. Here it is 43 and corresponds to the major fragment ion. 
5. Now its puzzle time:) you have to work with every possible skeleton. 

1. n-pentane -The C2-C3 bond is more likely to break than the C1-C2 bond because C2-C3 fragmentation leads to a primary carbocation and a primary radical which is more stable than primary carbocation and methyl radical. Means major fragment will be (m/z=43) and other fragments may be (m/z=29, 15, 57). 
2. 2-methylbutane- The C2-C3 bond is more likely to break and forms secondary carbocation (m/z =43). And next probable fragment will form due to loss of methyl radical which leads to formation of secondary carbocation (m/z= 57). 
3. 2,2-dimethylpropane- major fragment will form by loss of methyl radical which leads to tertiary carbocation(m/z =57). 
6. Assess all possibilities.
1. n-pentane- base peak will be 43, and other major peaks will be 57, 29 and 15.
2. 2-methylbutane- base peak will be 43 and peak 57 should also have high abundance.
3. 2,2-dimethylpropane-base peak will be 57.
7. Correct answer will be n-pentane.

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Mass Spectra of Alkene

Molecular ion peak is intense in unsaturated compounds. Molecular ion represents the most stable cation formed by the removal of an electron from the parent molecule. In conjugated alkene, molecular ion is formed by the removal of one of the π electrons. The molecular ion, thus formed, is stabilized by the resonance. It means the burden of positive charge is shared between all atoms. Here we will study normal alkene. Let's try to solve the spectra of 3-heptne.

The other intense peak corresponds to the ion formed by McLafferty rearrangement. Let’s see what McLafferty rearrangement is. Molecules those have gama γ Hydrogen can undergo this rearrangement.

What does it mean by γ Hydrogen? Carbon atoms are labeled on the basis of their position in molecule with respect to the functional group. Carbon atom which bears functional group is called α carbon and Carbon atom placed next to the α carbon is called β carbon and the second next carbon is called the γ Carbon. The Hydrogen atoms attached to these carbon atoms are respectively called as α, β and γ Hydrogen. In McLafferty rearrangement, molecular ion splits from β Carbon and functional group gains the γ Hydrogen. Thus formed cation is stabilized by resonance and is represented by an intense peak in mass spectra.

The next stable cation is allylic carbocation. Allyl group is three carbon molecule with one double bond. It is formed when alkene undergoes allylic cleavage that means a cleavage which results in formation of allyl carbocation. This allyl cation is stabilized by resonance and appears as next highest peak to the molecular ion peak.

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Fragmentation and Mass Spectra of Alkane

• Molecular ion peak is always present although height of peak decreases as the molecular mass increases in the homologous series.
• C-C bond is weaker than C-H hence cleavage is favored at C-C bond.
• Fragmentation pattern is characterized by clusters of peak, and the corresponding peaks of each cluster are 14 mass units (CH₂) apart.
• Largest peak in each cluster represents a C_nH_2n+1 fragment and occurs at m/z= 14n+1
• Most abundant fragments are C₃ and C₄
• Fragment abundance decrease for [M- C₂H₅]⁺ and [M- CH₃]⁺is very weak or missing.
• Compounds containing more than 8 carbons show similar spectra; identify them by M⁺peak.

Branched Alkane:

• Molecular ion peak is mostly not observed.
• Bond cleavage takes place preferably at the site of branching.
• The way a molecular ion fragments depends on the strength of its bonds and the stability of the fragments.
• Generally, largest substituent is eliminated readily as a radical. The radical achieves stability by the delocalization of lone electron. 

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What is Mass Spectrometry?

Mass spectrometry is not a true spectroscopic technique because absorption of electromagnetic energy is not involved in any way.

Mass spectrometry is use to characterized organic molecule in two principal ways:

        I.            To measure exact molecular weight, and by this, exact molecular formula can be determined.

      II.            To indicate the point at which molecule prefers to fragment; from this, the presence of certain structural units in the compound can be recognized.

A Mass spectrum is a presentation of the masses of the positively charged fragments versus their relative concentrations. The most intense peak in the spectrum, called the ‘Base peak’ is assigned value of 100%, and the intensity of other peaks, are reported as percentage of the base peak.

The commonly used technique in mass spectrometry is ‘Electron Impact’. In this mode spectrometer bombards molecules in the vapor phase with a high energy electron beam and record the result of electron impact as a spectrum of positive ions separated on the bases of mass/charge (m/z).  On electron impact, the molecules are energized sufficiently to eject an electron, thus produces molecular ion M^+.which further fragments to more daughter ions.

The molecular ion though it may be of low abundance gives highly useful information about the identity of an organic compound. Fragmentation pattern that is the break-up process of the molecular ion into smaller ions gives further information about the structure of compound.

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Electromagnetic Spectrum

Electromagnetic radiation is radiant energy having the properties of both particles and

waves. A continuum of different types of electromagnetic radiation—each type associated

with a particular energy range which constitutes the electromagnetic spectrum.

Visible light is the type of electromagnetic radiation with which we are most familiar, but

it represents only a fraction of the range of the entire electromagnetic spectrum.

X-rays and radio waves are other types of familiar electromagnetic radiation.

The electromagnetic spectrum is made up of the following components:

• Cosmic rays, which consist of radiation discharged by the sun, have the highest energy, the highest frequencies, and the shortest wavelengths.

• (gamma rays) are emitted from the nuclei of certain radioactive elements and, because of their high energy, can severely damage biological organisms.

• X-rays, somewhat lower in energy than are less harmful, except in high doses. Low-dose X-rays are used to examine the internal structure of organisms.

• Ultraviolet (UV) light is responsible for sunburns, and repeated exposure can cause skin cancer by damaging DNA molecules in skin cells.

• Visible light is the electromagnetic radiation we see.

• We feel infrared radiation as heat.

• We cook with microwaves and use them in radar.

• Radio waves have the lowest energy (lowest frequency). We use them for radio and television communication, digital imaging, remote controls, and wireless linkages for laptop computers. Radio waves are also used in NMR spectroscopy and in magnetic resonance imaging (MRI).

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