Mass spectrometry is a technique used to identify molecules based on their mass. It works by ionizing chemical compounds to generate molecular or fragment ions and measuring their mass-to-charge ratios. The document discusses the basic principles and components of a mass spectrometer, including ionization, separation of ions based on mass, and detection. It also covers common fragmentation patterns observed for different classes of compounds like hydrocarbons, alcohols, aromatics, and others. General rules for fragmentation are provided along with examples to illustrate how structural information can be determined.
Introduction
working principle
fragmentation process
general rules for fragmentation
general modes of fragmentation
metastable ions
isotopic peaks
applications
Introduction
working principle
fragmentation process
general rules for fragmentation
general modes of fragmentation
metastable ions
isotopic peaks
applications
MASS SPECTROSCOPY ( Molecular ion, Base peak, Isotopic abundance, Metastable ...Sachin Kale
CONTENT:
Molecular Ion Peak
Significance of Molecular ion & Graphically Method
Base Peak
Isotopic Abundance
Metastable Ion
Significance of Metastable ion
Nitrogen Rule & graphs
Formulation of Rule
Introduction & Definition, Theory, instrumentation, Continuous – wave (CW) instrument, The pulsed Fourier Transform [FT] instrument, Solvents, Chemical shift
i. Shielding and de-shielding
ii. Factors affecting chemical shift
PRINCIPLES of FT-NMR & 13C NMR
Fourier Transform
FOURIER TRANSFORM NMR SPECTROSCOPY
THEORY OF FT-NMR
13C NMR SPECTROSCOPY
Principle
Why C13-NMR is required though we have H1-NMR?
CHARACTERISTIC FEATURES OF 13 C NMR
Chemical Shifts
NUCLEAR OVERHAUSER ENHANCEMENT
Short-Comings of 13C-NMR Spectra
In mass spectrometry, fragmentation is the dissociation of energetically unstable molecular ions formed from passing the molecules in the ionization chamber of a mass spectrometer. The fragments of a molecule cause a unique pattern in the mass spectrum.
MASS SPECTROSCOPY ( Molecular ion, Base peak, Isotopic abundance, Metastable ...Sachin Kale
CONTENT:
Molecular Ion Peak
Significance of Molecular ion & Graphically Method
Base Peak
Isotopic Abundance
Metastable Ion
Significance of Metastable ion
Nitrogen Rule & graphs
Formulation of Rule
Introduction & Definition, Theory, instrumentation, Continuous – wave (CW) instrument, The pulsed Fourier Transform [FT] instrument, Solvents, Chemical shift
i. Shielding and de-shielding
ii. Factors affecting chemical shift
PRINCIPLES of FT-NMR & 13C NMR
Fourier Transform
FOURIER TRANSFORM NMR SPECTROSCOPY
THEORY OF FT-NMR
13C NMR SPECTROSCOPY
Principle
Why C13-NMR is required though we have H1-NMR?
CHARACTERISTIC FEATURES OF 13 C NMR
Chemical Shifts
NUCLEAR OVERHAUSER ENHANCEMENT
Short-Comings of 13C-NMR Spectra
In mass spectrometry, fragmentation is the dissociation of energetically unstable molecular ions formed from passing the molecules in the ionization chamber of a mass spectrometer. The fragments of a molecule cause a unique pattern in the mass spectrum.
Atomic absorption spectroscopy is a method of elemental analysis. It is particularly useful for determining trace metals in liquids and is most independent of molecular form of the metal in sample.
This power point was prepared based on Introduction to Spectroscopy by L. Pavia, Gary M. Lampman, and George S. Kriz. The language of this power point is Persian.
A mass spectrum (MS) is a graphical representation of the relative abundance of ions at different mass-to-charge ratios (m/z) in a sample. Mass spectrometry is a powerful analytical technique used to identify and characterize the chemical composition of a wide range of substances, including organic compounds, proteins, peptides, and even small molecules. Here's how a typical mass spectrum is generated and what it can tell you:
Ionization: In mass spectrometry, the sample is first ionized, meaning that the atoms or molecules are converted into ions (charged particles). Common ionization methods include electron impact, electrospray ionization, and matrix-assisted laser desorption/ionization (MALDI).
Mass-to-Charge Ratio (m/z): After ionization, the ions are separated based on their mass-to-charge ratio (m/z). This ratio is a dimensionless quantity, and it represents the mass of the ion (in atomic mass units, amu) divided by its charge (in elementary charge units, e).
Ion Separation: The ions are separated by a mass analyzer, such as a magnetic sector, time-of-flight (TOF), quadrupole, or ion trap, depending on the specific instrument used. The mass analyzer sorts ions according to their m/z values.
Detector: As the ions exit the mass analyzer, they are detected, and their abundance is recorded. The detector measures the number of ions at each m/z value.
Data Output: The data from the detector is then used to create a mass spectrum. The x-axis of the mass spectrum represents m/z values, while the y-axis represents the relative abundance or intensity of ions at each m/z value.
A typical mass spectrum might have peaks at specific m/z values, and these peaks can provide valuable information about the sample:
Base Peak: The peak with the highest intensity in the spectrum is called the base peak. It represents the most abundant ion.
Molecular Ion Peak: The peak at the highest m/z value (farthest to the right) often represents the molecular ion, which can provide insight into the molecular weight of the compound.
Fragment Peaks: Peaks at lower m/z values are often fragment ions resulting from the breaking of chemical bonds within the original ions. These fragment ions can provide information about the structure of the compound.
Isotopic Peaks: Some elements have natural isotopes, and their presence can result in multiple peaks with slightly different m/z values. These isotopic peaks can also provide information about the composition of the sample.
Interpreting a mass spectrum involves analyzing the positions and intensities of these peaks to identify the compound and its structure. Mass spectrometry is widely used in various fields, including chemistry, biochemistry, environmental science, and forensic analysis, for tasks such as identifying unknown substances, quantifying the amounts of specific compounds, and studying chemical reactions.
Finding Transition States Algorithmically for Automatic Reaction Mechanism Ge...Richard West
A presentation given by Prof. Richard West at the 8th International Conference on Chemical Kinetics in Seville, Spain, on 12th of July 2013.
The slides were designed to accompany the oral presentation and do not quite stand alone, so please email if you have any questions.
3. Introduction to Mass Spectrometry
Sample
introduction
Ionization
Minimize
collisions,
interferences
Separate
masses
Count ions
Collect results
3
4. Principle
It is also called as positive ion spectra or line spectra Sample is
bombarded with the high electron beam produce the positive
ions.
They travel in straight path
When a magnetic field or electric field is applied then travels
in curved path
The fragments of different masses are separated based on the
radius of curvature.
m/e α r2
4
5. How does a mass spectrometer work?
Sample Plate
Target
HPLC
GC
Solids probe
MALDI
ESI
IonSpray
FAB
EI/CI
SFA
DFA
Quadrupole
FTMS
Faraday cup .
Electron Mult.
Photomultiplier
5
7. Mass Spectrometry Needs
Ionization-How the protein is injected in to the MS
machine
Separation-Mass and Charge ?
is determined
Activation-Protein are broken into smaller fragments
(peptides/AAs)
Mass Determination- m/z ratios are determined for the
ionized protein fragments/peptides 7
8. FRAGMENTATION
The process of Breaking Molecules /ions into
fragments is known as fragmentation.
This can be seen in the form of peaks in mass spectra
Methanol can be divided in to 4fragments
e.g.
CH3OH CH3OH⁺ +e¯
CH3OH CH3⁺ + OH¯
CH3OH CH2OH⁺+ H¯
CH3OH CHO⁺ + H2¯
.
intensity 5 10 15 20 25 30 35
m/e 8
120
100
80
60
40
20
0
CHO⁺
CH3OH⁺
CH3⁺
CH2OH⁺
9. Fragmentation rules in MS
1. Intensity of MM..++ is LLaarrggeerr ffoorr lliinneeaarr cchhaaiinn than for branched
9
compound
2. Intensity of MM..++ ddeeccrreeaassee with IInnccrreeaassiinngg MM..WW.. (fatty acid is an
exception)
3. Cleavage is ffaavvoorreedd aatt bbrraanncchhiinngg
44.. AArroommaattiicc RRiinnggss,, DDoouubbllee bboonndd,, CCyycclliicc ssttrruuccttuurreess ssttaabbiilliizzee MM..++
55.. DDoouubbllee bboonndd ffaavvoorr AAllllyylliicc CClleeaavvaaggee
6. Saturated Rings lose a Alkyl Chain (case of branching)
7.. AArroommaattiicc CCoommppoouunnddss CClleeaavvee iinn bb
Resonance Stabilized TTrrooppyylliiuumm
8.. CC--CC NNeexxtt ttoo HHeetteerrooaattoomm cleave leaving the cchhaarrggee oonn tthhee
HHeetteerrooaattoomm
99.. CClleeaavvaaggee ooff ssmmaallll nneeuuttrraall mmoolleeccuulleess ((CCOO22,, CCOO,, oolleeffiinnss,, HH22OO ……..))..
RReessuulltt oofftteenn ffrroomm rreeaarrrraannggeemmeenntt -- MMccLLaaffffeerrttyy rreeaarrrraannggeemmeenntt 9
10. General rules of Fragmentation
1.Hydrocarbons
•Hydrocarbons give clusters of peaks.
•Molecular ion peaks of very low abundance are observed for linear hydrocarbons.
•For branched hydrocarbons give a low intensity at M+.
•Intensity of (CnH2n+1) peaks decreases with increasing mass.
10
11. General rules of Fragmentation
2.Cleavage at Branched carbon
Cleavage at branched carbon is favored due to higher stability
at tertiary carbocation.
H
C > C
> C
H
H
>
H
C
H
H
tert. sec. primary methyl
11
12. CH3
1 2 3 4 5 6 7 8
+
cleavage at 6-1
cleavage at 6-2
cleavage at 6-3
C4H9
C H
C3H7
+
CH3
C H
C4H9
+
CH3
C H
C3H7
+
(F1)
(F2)
(F3)
H3C CH2 CH2 C
H
CH2 CH2 CH2 CH3
Eg.
Produces thre secondary cations, the most favored fragments
at C-4 of
4- methyl octane.
Note that C4 is common for fragments (F1)(F2) And (F3). 12
13. General rules of Fragmentation
3.Rule of b cleavage
Most important rule covers 70% of mass fragmentation.
X C1 C2 R X CH
a b
Cleavage favored at b bond leaving positive charge on C1.
13
14. H3C CH2 O CH2 CH3
H3C CH2 O CH2 CH3
CH2 O CH2
m/e = M-15
1.
H3C
2.
CH2 CH2 CH3
H3C CH2 N CH2
N
C2H5
C3H7
H2C
N
C2H5
H2C
H2C
m-57 m-29
N
CH2
C3H7
m-15
CH2
tert.amine
B1
B3 B2
e.g.: A) (x) = O, N, S.
14
15. 3.
CH2 S CH2 CH2 CH3
H2C S
CH2
H2C S
M-71 C3H7
M-29
B2 B1
B1
B2
17. O
+
O C CH + 3
m/e = M-R m/e = M-15
Simarly for x= N & S
+
Very common fragment for ester
C. Allylic Cleavage
H2C
M-31 = methyl ester
M-45 = ethyl ester
R
m/e = M-R stable allyliz cation
O
H3C CH3
R CH3
R C O
i)
ii)
O
R C OCH3
R C O
m/e = M-31
+
17
18. General rules of Fragmentation
4 Rule of elimination of small neutral molecule
A) b - Elimination
The high temperature and high vacuum are quite favourable for elimination reaction
H
C
C
OH
C C
+
+ H2O
m/e M - 18
and hence
i)Loss of water (H2O) for alcohols (M-18) is a prominent fragment.
Tertiary alcohols lose the water so fast that in many cases M.I. Peak is absent.
18
19. ii)Loss of Ammonia (NH3)(M-17) for primary amines and primary
and secondary alkyl ammonia derivatives
For
C C
NH
C C + NH2
M - 46
C2H5
C2H5
H
C
C
NH2
C C +
M - 17
NH3
19
20. iii)Elimination at Hydrogen sulphide (H2S)[M-34] confirms thiols
(mercaptons)
H
C
C
SH
C C + H2S
M - 34
iv)Elimination of Hydrogen cyanide (HCN)[M-27] confirms nitriles.
H
C
C
CN
C C + HCN
M - 27
20
21. v)Elimination of Hydrogen halide(HX),
Common for tertiary halides.
H
C
C
X
C C
m/e = M - HX
X = F, Cl, Br, I
21
22. General rules of Fragmentation
5.Rule – retro Diel’s Alder reaction
High temperature high vacuum highly favorable for(DA) common for all
these six membered cyclic mono olefins.
+
O
O
O
O + O
O
diene dienophile
22
23. MCLAFFERTY REARRANGEMENT:-
Rearrangement ions are fragments, they are formed
due to the result of intermolecular atomic
MMccLLaaffffeerrttyy
rearrangement H
during fragmentation
x
To undergo this CH2
rearrangement the molecule must
posses heteroatom, CH2
one double bond and hydrogen atom
CH2
O
C
Y
+
YY HH,, RR,, OOHH,, NNRR22
IIoonn SSttaabbiilliizzeedd
bbyy rreessoonnaannccee
x
CH2
CH2
H
CH2
O
C
Y
-- CCHH22==CCHH22
x
CH2
O
C
Y
H
x
+
CH2
O+
C
Y
H
x
CH2
O
C+
Y
H
23
24. NITROGEN RULE:-
It is used for determination of molecular mass of
compounds and its elemental composition
Molecules having odd mass number contain odd
number of nitrogen atoms.
H3C
Molecules having even mass number contain even no
H3C of nitrogen CH3
atoms.
H
MMWW == 5599
((oodddd))
MMWW == 5588
((eevveenn))
IIoonniissaattiioonn
[[MM++HH]]
[[MM++HH]]
MMWW == 6600
MMWW == 5599
CH3
N
H3C CH3
24
25. Nitrogen:
Odd number of N = odd MW
CH3CN
M+ = 41
SDBSWeb : http://riodb01.ibase.aist.go.jp/sdbs/ (National Institute of
Advanced Industrial Science and Technology, 11/2/09)
25
27. Fragmentation Patterns
Alkanes:
Fragmentation often splits off simple alkyl groups:
Loss of methyl M+ - 15
Loss of ethyl M+ - 29
Loss of propyl M+ - 43
Loss of butyl M+ - 57
Branched alkanes tend to fragment forming the
most stable carbocations.
27
34. Fragmentation Patterns
Alcohols
Fragment easily resulting in very small or missing
parent ion peak
May lose hydroxyl radical or water
M+ - 17 or M+ - 18
Commonly lose an alkyl group attached to the
carbinol carbon forming an oxonium ion.
1o alcohol usually has prominent peak at m/z =
31 corresponding to H2C=OH+
35. Fragmentation Patterns
MS for 1-propanol
M+-18 M+
CH3CH2CH2OH
H2C OH
SDBSWeb : http://riodb01.ibase.aist.go.jp/sdbs/ (National Institute of
Advanced Industrial Science and Technology, 11/28/09)
36. Fragmentation Patterns
Ethers
a-cleavage forming oxonium ion
Loss of alkyl group forming oxonium ion
Loss of alkyl group forming a
carbocation
37.
38. Fragmentation Patterns
Aldehydes (RCHO)
Fragmentation may form acylium ion
RC O
Common fragments:
M+ - 1 for
M+ - 29 for
RC O
R (i.e. RCHO - CHO)
39. Fragmentation Patterns
Ketones
O
Fragmentation leads to formation of
acylium ion:
Loss of R forming
Loss of R’ forming
R'C O
RC O
RCR'
40. Fragmentation Patterns
MS for 2-pentanone
O
CH3CCH2CH2CH3
CH3CH2CH2C O
M+
CH3C O
SDBSWeb : http://riodb01.ibase.aist.go.jp/sdbs/ (National Institute of
Advanced Industrial Science and Technology, 11/28/09)
41. Fragmentation Patterns
Esters (RCO2R’)
Common fragmentation patterns
include:
Loss of OR’
peak at M+ - OR’
Loss of R’
peak at M+ - R’
42. Fragmentation Patterns
M+ = 136
77 105
O
C
O CH3
105
77
SDBSWeb : http://riodb01.ibase.aist.go.jp/sdbs/ (National Institute of
Advanced Industrial Science and Technology, 11/28/09)