KATHMANDU UNIVERSITY

Dhulikhel, Kavre

Course: Genomics & Proteomics (BIOT 414)

Assignment: 02

Submitted to:
Mr. Simon Kumar Shrestha
Department of Biotechnology
Kathmandu University
Dhulikhel, Kavre

Submitted by:
Reeha Neupane (20)
B. tech in Biotechnology
4th year, 2nd semester
Kathmandu University

Date of Submission: November 11, 2020

Questions:

1. A gas was known to contain only elements from the following list:

1H 1.0078

12C 12.0000

14N 14.0031

16O 15.9949

The gas had a molecular ion peak at m/z = 28.0312 in a high-resolution mass spectrometer.
What was the gas?

ANSWER: Three gases have relative formula mass of 28 which include N2, C0 and C2H4 which
contain the above mentioned elements. So, for obtaining the accurate relative mass of 28.0312
we can proceed as follows:
For C0 = 12+15.9949 =27.9949 =28
For N2 = 14.0031 *2 = 28.0062
For C2H4 = (12*2 + 1.0078*4) = 28.0312
So, we can conclude from the above calculation that the gas is ethylene (C2H4).

2. The mass spectra below are for pentan-2-one and pentan-3-one, but not necessarily in
that order Pentan-2-one is CH3COCH2CH2CH3. Pentan-3-one is CH3CH2COCH2CH3.
Decide which is which, explaining your thinking as fully as possible. (Fragmentation)
ANSWER: The figure a represents mass spectrum of pentane-2-one and figure b represents that
of Pentane-3-one.
In my opinion, pentane-2-one with molecular formula (CH3COCH2CH2CH3) is likely to fragment
giving positive ions on the CO group by giving two different ions as follows:
1. [CH3CO]+
2. [COCH2CH2CH3]+
The peak in figure a would give us strong lines at m/z = 43 and 71 which is due to the above two
ions that have been formed after fragmentation, which can therefore be concluded to be
pentane-2-one.

Similarly, molecular formula of Pentan-3-one is CH3CH2COCH2CH3 and the fragmentation of

pentane3-one gives one ion [CH3CH2CO] as such:

The base peak, at m/z=57, in figure b is due to the [CH3CH2CO]+ ion. Similarly, the m/z = 29 peak is
produced by the ethyl ion - which once again could be formed by splitting the molecular ion either
side of the CO group as follows.

Since different molecules have different mass spectrum because of the different fragmentation
patterns that can occur, we can differentiate the mass spectrum of pentane-2-one and pentane-
3-one.

3. The mass spectrum of a mystery compound is shown below. The figures in red show the m/z
values for a few of the lines.

a. What is the m/z value for the molecular ion?

- The m/z for molecular ion is 46.
b. There are several organic compounds which have a molecular ion with that value. Use
the approximate values for the relative isotopic masses in the table below to find as
many of these compounds as you can.
You should draw the full structural formulae of each compound so that you are sure
that such a compound can exist. For example, you might think that C3H10 would be a
possible compound, but any attempt to draw a structure would show that to be
impossible.

ANSWER: Using the relative isotopic masses of the elements we can get C2H6O=
(12*2+6*1.0078+15.9949) = 24+6.0468+15.9949 = 46.0417.
Similarly calculating for CO2H2 we get 46.0054, C2H3F we get 46.021 and for CH6N2 we
get 46.059.
Drawing the structures for the compounds we get

For C2H6O,

For CO2H2,

For C2H3F,

For CH6N2,

c. A high resolution mass spectrum for this compound has an M+ line at m/z = 46.0054.
Which of the structures that you have drawn in part (b) corresponds to this compound?
(Note: If you don't have a compound which gives this value, then you have missed at
least one! Think again.)
 ANSWER: As, calculated above in question b the only compound that corresponds to the m/z
value of 46.0054 is HCOOH, formic acid, so we can conclude this acid to be the compound that
has M+ line at m/z= 46.0054.

d. Write an equation to show the formation of the molecular ion from this compound.
The molecular ion formed fom formic acid is as follow:
ANSWER: HCOOH [HCOOH]+ + e-

e. What fragments are represented by the lines at 17, 28, 29 and 45?

In short chain acids, peaks due to the loss of OH (molecular ion less 17) and COOH
(molecular ion less 45) are prominent due to cleavage of bonds next to C=O.
Therefore the fragmentation represented by the lines are
- 17: [OH]+
- 28: [CO]+
- 29: [HCO]+
- 45: [HCOO]+ / [COOH]+

4. The following mass spectra are taken from the SDBS (SDBSWeb : http://sdbs.db.aist.go.jp
(National Institute of Advanced Industrial Science and Technology, 8/8/2014).
For each spectrum, work out as far as you can which substance produced it, giving as much
supporting evidence as you can.
Remember the relative isotopic masses of the various atoms you might be interested in

The two small lines at m/z 79 and 81 could possibly be bromine atom with 2 of its isotopes. Similarly, we
can see other two pairs of similar lines at (107 and 109) and at (136 and 138).
So, if we remove bromine, 79 from 136 or 81 from 138 we are left with a value of 57 which ends up with
a compound with 4 carbon atoms and 9 hydrogen atom with molecular formula C4H9. Likewise
removing bromine from the 107/109 fragments leaves a mass of 28, ending up with compound with 2
carbon atom and 4 hydrogen atom C2H4. So after removing bromine we can assume the compound
with molecular mass of 28 to be either [CH2CH2Br]+ or [CH3CHBr]+ . The two conformations are
possible depending on where the bromine atom is located either at the end or at the middle of the
chain. Similarly, the strong line at 41 would correspond to a [C3H5] + fragment, which ends up nowhere.
But the line at 29 is useful, because it corresponds to a [C2H5] + fragment. So, the molecule probably
contains a CH3CH2 group.

Keeping all the fragments together the molecule could be CH3CH2 CH2CH2Br or CH3CHBrCH2CH3.

In the m/z = 39 and 41 region there are two lines with their lengths in the ratio that looks like 3:1. There
are also two similar lines at m/z = 63 and 65. This may indicate the presence of a single chlorine atom in
the molecule, with its two isotopes with masses 35 and 37 in a 3:1 ratio. If we remove 37 from 80 (or 35
from 78), we have a molecular mass of 43. That could be, a C3H7 group. Also, a strong line at 43
suggests a C3H7 + fragment giving [CH3CH2CH2] + or [CH3CHCH3] +. If we remove 35 and 37 the
chlorine isotopes from 63 and 65 we are left with a mass of 28, suggesting the fragment being either
[CH3CHCl]+ or [CH2CH2Cl]+. Since there is no line at 29, CH3CH2 group cannot be there as it would be
seen if the chlorine was attached at the end of the chain in the compound, so ending up with
CH3CHClCH3 as our compound which is 2-chloropropane.
The pattern of three lines in the molecular ion region at m/z = 84, 86 and 88 and with peak heights in
the ratio of 9:6:1 suggests a typical molecule with 2 chlorine atoms. So, taking 2 x 35 from we are left
with 14 - a CH2 group. So the compound must be Chloromethyl (CH2Cl2).