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
this ppt contain all basic information related to the mass spectrometry like introduction, principle of MS, type of ions, fragmentation processes eg. mcLafferty rearrangement, alpha clevage, sigma bond clevage, retro-diels-alder reaction
THE MASS SPECTROSCOPY IS AN ANALYTICAL TECHNIQUE USED IN INDUSTRIES FOR ANALYSING THE THE MOLECULAR WEIGHT OF COMPOUND ALSO TO ODENTIFY THE STRUCTURE OF UNKNOWN COMPOUND.
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
this ppt contain all basic information related to the mass spectrometry like introduction, principle of MS, type of ions, fragmentation processes eg. mcLafferty rearrangement, alpha clevage, sigma bond clevage, retro-diels-alder reaction
THE MASS SPECTROSCOPY IS AN ANALYTICAL TECHNIQUE USED IN INDUSTRIES FOR ANALYSING THE THE MOLECULAR WEIGHT OF COMPOUND ALSO TO ODENTIFY THE STRUCTURE OF UNKNOWN COMPOUND.
TYPES OF PEAKS IN MASS SPECTROSCOPY.pptxAnupamaCp2
Types of peaks in mass spectroscopy.
Molecular ion or parent peak.
base peak.
fragment ions.
rearrangement ion.
multiple charged ion.
negative ion.
metastable ion.
isotopes ion.
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.
This slide discusses the principle, instrumentation, process, detectors, sample ,solvents used in mass spectroscopy and also its applications and limitations.
TYPES OF PEAKS IN MASS SPECTROSCOPY.pptxAnupamaCp2
Types of peaks in mass spectroscopy.
Molecular ion or parent peak.
base peak.
fragment ions.
rearrangement ion.
multiple charged ion.
negative ion.
metastable ion.
isotopes ion.
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.
This slide discusses the principle, instrumentation, process, detectors, sample ,solvents used in mass spectroscopy and also its applications and limitations.
It is an analytical technique useful for the determination of molecular mass, molecular formula and fragmentation pattern of particular molecule and compounds. It has greater application in pharmaceutical and medicinal fields.
Introduction, Basic Principles, Terminology, Instrumentation, Ionization techniques (EI, CI, FAB, MALDI, and ESI), Mass Analyzer (Magnetic sector instruments, Quadrupole, TOF, and ICR ), and Applications of Mass Spectrometry.
it is an analytical technique that measures the mass-to-charge ratio of ions. The results are typically presented as a mass spectrum, a plot of intensity as a function of the mass-to-charge ratio.
Theories of coordination compounds, CFSE, Bonding in octahedral and tetrahedral complex, color of transition metal complex, magnetic properties, selection rules, Nephelxeuatic effect, angular overlap model
Cancer cell metabolism: special Reference to Lactate PathwayAADYARAJPANDEY1
Normal Cell Metabolism:
Cellular respiration describes the series of steps that cells use to break down sugar and other chemicals to get the energy we need to function.
Energy is stored in the bonds of glucose and when glucose is broken down, much of that energy is released.
Cell utilize energy in the form of ATP.
The first step of respiration is called glycolysis. In a series of steps, glycolysis breaks glucose into two smaller molecules - a chemical called pyruvate. A small amount of ATP is formed during this process.
Most healthy cells continue the breakdown in a second process, called the Kreb's cycle. The Kreb's cycle allows cells to “burn” the pyruvates made in glycolysis to get more ATP.
The last step in the breakdown of glucose is called oxidative phosphorylation (Ox-Phos).
It takes place in specialized cell structures called mitochondria. This process produces a large amount of ATP. Importantly, cells need oxygen to complete oxidative phosphorylation.
If a cell completes only glycolysis, only 2 molecules of ATP are made per glucose. However, if the cell completes the entire respiration process (glycolysis - Kreb's - oxidative phosphorylation), about 36 molecules of ATP are created, giving it much more energy to use.
IN CANCER CELL:
Unlike healthy cells that "burn" the entire molecule of sugar to capture a large amount of energy as ATP, cancer cells are wasteful.
Cancer cells only partially break down sugar molecules. They overuse the first step of respiration, glycolysis. They frequently do not complete the second step, oxidative phosphorylation.
This results in only 2 molecules of ATP per each glucose molecule instead of the 36 or so ATPs healthy cells gain. As a result, cancer cells need to use a lot more sugar molecules to get enough energy to survive.
Unlike healthy cells that "burn" the entire molecule of sugar to capture a large amount of energy as ATP, cancer cells are wasteful.
Cancer cells only partially break down sugar molecules. They overuse the first step of respiration, glycolysis. They frequently do not complete the second step, oxidative phosphorylation.
This results in only 2 molecules of ATP per each glucose molecule instead of the 36 or so ATPs healthy cells gain. As a result, cancer cells need to use a lot more sugar molecules to get enough energy to survive.
introduction to WARBERG PHENOMENA:
WARBURG EFFECT Usually, cancer cells are highly glycolytic (glucose addiction) and take up more glucose than do normal cells from outside.
Otto Heinrich Warburg (; 8 October 1883 – 1 August 1970) In 1931 was awarded the Nobel Prize in Physiology for his "discovery of the nature and mode of action of the respiratory enzyme.
WARNBURG EFFECT : cancer cells under aerobic (well-oxygenated) conditions to metabolize glucose to lactate (aerobic glycolysis) is known as the Warburg effect. Warburg made the observation that tumor slices consume glucose and secrete lactate at a higher rate than normal tissues.
Seminar of U.V. Spectroscopy by SAMIR PANDASAMIR PANDA
Spectroscopy is a branch of science dealing the study of interaction of electromagnetic radiation with matter.
Ultraviolet-visible spectroscopy refers to absorption spectroscopy or reflect spectroscopy in the UV-VIS spectral region.
Ultraviolet-visible spectroscopy is an analytical method that can measure the amount of light received by the analyte.
This presentation explores a brief idea about the structural and functional attributes of nucleotides, the structure and function of genetic materials along with the impact of UV rays and pH upon them.
(May 29th, 2024) Advancements in Intravital Microscopy- Insights for Preclini...Scintica Instrumentation
Intravital microscopy (IVM) is a powerful tool utilized to study cellular behavior over time and space in vivo. Much of our understanding of cell biology has been accomplished using various in vitro and ex vivo methods; however, these studies do not necessarily reflect the natural dynamics of biological processes. Unlike traditional cell culture or fixed tissue imaging, IVM allows for the ultra-fast high-resolution imaging of cellular processes over time and space and were studied in its natural environment. Real-time visualization of biological processes in the context of an intact organism helps maintain physiological relevance and provide insights into the progression of disease, response to treatments or developmental processes.
In this webinar we give an overview of advanced applications of the IVM system in preclinical research. IVIM technology is a provider of all-in-one intravital microscopy systems and solutions optimized for in vivo imaging of live animal models at sub-micron resolution. The system’s unique features and user-friendly software enables researchers to probe fast dynamic biological processes such as immune cell tracking, cell-cell interaction as well as vascularization and tumor metastasis with exceptional detail. This webinar will also give an overview of IVM being utilized in drug development, offering a view into the intricate interaction between drugs/nanoparticles and tissues in vivo and allows for the evaluation of therapeutic intervention in a variety of tissues and organs. This interdisciplinary collaboration continues to drive the advancements of novel therapeutic strategies.
Introduction:
RNA interference (RNAi) or Post-Transcriptional Gene Silencing (PTGS) is an important biological process for modulating eukaryotic gene expression.
It is highly conserved process of posttranscriptional gene silencing by which double stranded RNA (dsRNA) causes sequence-specific degradation of mRNA sequences.
dsRNA-induced gene silencing (RNAi) is reported in a wide range of eukaryotes ranging from worms, insects, mammals and plants.
This process mediates resistance to both endogenous parasitic and exogenous pathogenic nucleic acids, and regulates the expression of protein-coding genes.
What are small ncRNAs?
micro RNA (miRNA)
short interfering RNA (siRNA)
Properties of small non-coding RNA:
Involved in silencing mRNA transcripts.
Called “small” because they are usually only about 21-24 nucleotides long.
Synthesized by first cutting up longer precursor sequences (like the 61nt one that Lee discovered).
Silence an mRNA by base pairing with some sequence on the mRNA.
Discovery of siRNA?
The first small RNA:
In 1993 Rosalind Lee (Victor Ambros lab) was studying a non- coding gene in C. elegans, lin-4, that was involved in silencing of another gene, lin-14, at the appropriate time in the
development of the worm C. elegans.
Two small transcripts of lin-4 (22nt and 61nt) were found to be complementary to a sequence in the 3' UTR of lin-14.
Because lin-4 encoded no protein, she deduced that it must be these transcripts that are causing the silencing by RNA-RNA interactions.
Types of RNAi ( non coding RNA)
MiRNA
Length (23-25 nt)
Trans acting
Binds with target MRNA in mismatch
Translation inhibition
Si RNA
Length 21 nt.
Cis acting
Bind with target Mrna in perfect complementary sequence
Piwi-RNA
Length ; 25 to 36 nt.
Expressed in Germ Cells
Regulates trnasposomes activity
MECHANISM OF RNAI:
First the double-stranded RNA teams up with a protein complex named Dicer, which cuts the long RNA into short pieces.
Then another protein complex called RISC (RNA-induced silencing complex) discards one of the two RNA strands.
The RISC-docked, single-stranded RNA then pairs with the homologous mRNA and destroys it.
THE RISC COMPLEX:
RISC is large(>500kD) RNA multi- protein Binding complex which triggers MRNA degradation in response to MRNA
Unwinding of double stranded Si RNA by ATP independent Helicase
Active component of RISC is Ago proteins( ENDONUCLEASE) which cleave target MRNA.
DICER: endonuclease (RNase Family III)
Argonaute: Central Component of the RNA-Induced Silencing Complex (RISC)
One strand of the dsRNA produced by Dicer is retained in the RISC complex in association with Argonaute
ARGONAUTE PROTEIN :
1.PAZ(PIWI/Argonaute/ Zwille)- Recognition of target MRNA
2.PIWI (p-element induced wimpy Testis)- breaks Phosphodiester bond of mRNA.)RNAse H activity.
MiRNA:
The Double-stranded RNAs are naturally produced in eukaryotic cells during development, and they have a key role in regulating gene expression .
Earliest Galaxies in the JADES Origins Field: Luminosity Function and Cosmic ...Sérgio Sacani
We characterize the earliest galaxy population in the JADES Origins Field (JOF), the deepest
imaging field observed with JWST. We make use of the ancillary Hubble optical images (5 filters
spanning 0.4−0.9µm) and novel JWST images with 14 filters spanning 0.8−5µm, including 7 mediumband filters, and reaching total exposure times of up to 46 hours per filter. We combine all our data
at > 2.3µm to construct an ultradeep image, reaching as deep as ≈ 31.4 AB mag in the stack and
30.3-31.0 AB mag (5σ, r = 0.1” circular aperture) in individual filters. We measure photometric
redshifts and use robust selection criteria to identify a sample of eight galaxy candidates at redshifts
z = 11.5 − 15. These objects show compact half-light radii of R1/2 ∼ 50 − 200pc, stellar masses of
M⋆ ∼ 107−108M⊙, and star-formation rates of SFR ∼ 0.1−1 M⊙ yr−1
. Our search finds no candidates
at 15 < z < 20, placing upper limits at these redshifts. We develop a forward modeling approach to
infer the properties of the evolving luminosity function without binning in redshift or luminosity that
marginalizes over the photometric redshift uncertainty of our candidate galaxies and incorporates the
impact of non-detections. We find a z = 12 luminosity function in good agreement with prior results,
and that the luminosity function normalization and UV luminosity density decline by a factor of ∼ 2.5
from z = 12 to z = 14. We discuss the possible implications of our results in the context of theoretical
models for evolution of the dark matter halo mass function.
Multi-source connectivity as the driver of solar wind variability in the heli...Sérgio Sacani
The ambient solar wind that flls the heliosphere originates from multiple
sources in the solar corona and is highly structured. It is often described
as high-speed, relatively homogeneous, plasma streams from coronal
holes and slow-speed, highly variable, streams whose source regions are
under debate. A key goal of ESA/NASA’s Solar Orbiter mission is to identify
solar wind sources and understand what drives the complexity seen in the
heliosphere. By combining magnetic feld modelling and spectroscopic
techniques with high-resolution observations and measurements, we show
that the solar wind variability detected in situ by Solar Orbiter in March
2022 is driven by spatio-temporal changes in the magnetic connectivity to
multiple sources in the solar atmosphere. The magnetic feld footpoints
connected to the spacecraft moved from the boundaries of a coronal hole
to one active region (12961) and then across to another region (12957). This
is refected in the in situ measurements, which show the transition from fast
to highly Alfvénic then to slow solar wind that is disrupted by the arrival of
a coronal mass ejection. Our results describe solar wind variability at 0.5 au
but are applicable to near-Earth observatories.
Observation of Io’s Resurfacing via Plume Deposition Using Ground-based Adapt...Sérgio Sacani
Since volcanic activity was first discovered on Io from Voyager images in 1979, changes
on Io’s surface have been monitored from both spacecraft and ground-based telescopes.
Here, we present the highest spatial resolution images of Io ever obtained from a groundbased telescope. These images, acquired by the SHARK-VIS instrument on the Large
Binocular Telescope, show evidence of a major resurfacing event on Io’s trailing hemisphere. When compared to the most recent spacecraft images, the SHARK-VIS images
show that a plume deposit from a powerful eruption at Pillan Patera has covered part
of the long-lived Pele plume deposit. Although this type of resurfacing event may be common on Io, few have been detected due to the rarity of spacecraft visits and the previously low spatial resolution available from Earth-based telescopes. The SHARK-VIS instrument ushers in a new era of high resolution imaging of Io’s surface using adaptive
optics at visible wavelengths.
Observation of Io’s Resurfacing via Plume Deposition Using Ground-based Adapt...
Mass spectrometry
1. Mass Spectrometry
Dr. Krishnaswamy. G Page 1
MASS
SPECTROMETRY
Prepared By
Dr. G. Krishnaswamy
Faculty
DOS & R in Organic Chemistry
Tumkur University
Tumakuru
2. Mass Spectrometry
Dr. Krishnaswamy. G Page 2
Mass Spectrometry is an analytic technique that utilizes the degree of deflection of charged
particles by a magnetic field to find the relative masses of molecular ions and fragments. It is a
powerful method because it provides a great deal of information and can be conducted on tiny
samples. Mass spectrometry has a number of applications in organic chemistry, including:
- Determining molecular mass
- Finding out the structure of an unknown substance
- “Verifying the identity and purity of a known substance”
- Providing data on isotopic abundance.
The mass spectrometer performs three essential functions. First, it subjects molecules to
bombardment by a stream of high energy electrons, converting some of the molecules to ions
which are accelerated in an electric field. Second, the accelerated ions are separated according to
their mass to charge ratios in a magnetic or electric field. Finally the ions that have a particular
mass to charge are detected by a device which can count the number of ions striking it.
A graph of the number of particles detected or relative abundance as a function of mass to charge
ratio is-Mass spectrum.
A sample studied by mass spectrometry may be gas, a liquid or a solid can be introduced into the
ionization chamber through sample inlet system which converts sample to vapor state to obtain
stream of molecules that must flow into the ionization chamber. Once the stream of molecules
has entered the ionization chamber, a beam of high energy electron bombards it emitted from a
filament heated to several thousand degrees Celsius. The emitted electrons have energy of about
70 eV which is routinely used method called electron ionization (EI).These high energy
electrons strike the stream of molecules and ionize the molecules in the stream by removing the
electrons from them; the molecules are thus converted to radical cation (M+.).
3. Mass Spectrometry
Dr. Krishnaswamy. G Page 3
The energy requiredtoremove an electron from an atom or molecule depends on its ionization
potential. Most of the organic molecules have ionization potentials ranging from 8 and 15 eV.
However, a beam of electrons does not create ions with high efficiency until it strikes the stream
with a potential of 50 to 70 eV.
A repellar plate which carries a positive electrical potential directs the newly created ions
towards a series of accelerating plates. A large potential difference ranging from 1 to 10 kV
applied across these accelerating plates produces a beam of rapidly traveling ions. One or more
focusing slits direct the ions into a uniform beam.
From the ionization chamber the beam of ions passes through a short field free region. From
there it enters the mass analyser, the region where the ions are separated according to their mass
to charge ratios.
The kinetic energy of an accelerated ion is equal to
Where m = mass of the ion, v = velocity of the ion, e = charge on the ion and V = potential
difference of the ion accelerating plates.
In the presence of a magnetic field, a charged particle describes a curves flight path. The
equation which yields the radius of curvature of this path is
Where r = radius of curvature of the path and H = strength of the magnetic field. If these two
equations are combined to eliminate the velocity term, the result is
4. Mass Spectrometry
Dr. Krishnaswamy. G Page 4
This is the important equation that governs the behavior of an ion in the mass analyzer portion of
the mass spectrometer.
The molecular ion or parent ion:
The simple removal of an electron from a molecule like highest occupied orbital of aromatic
system and non bonding electron oxygen and nitrogen atoms yields an ion whose mass is the
actual molecular weight of the original molecule. This ion is the molecular ion and symbolized
as M+. The intensity of the molecular ion peak depends on the stability of the molecular ion. The
most stable the molecular ions are those of purely aromatic systems. If the substituents that have
favorable modes of cleavage are present, then the molecular ion peak will be less intense and
fragment peaks relatively more intense.
In general the following group of compounds will in order of decreasing ability give
prominent peaks:
Aromatic compounds >conjugated alkenes >cyclic compounds >organic sulfides >short, normal
alkanes > mercaptans.
The molecular ion is frequently not detectable in aliphatic alcohols, nitriles, nitrites, nitrates and
in highly branched compounds.
The most abundant ion formed in the ionization chamber gives rise to tallest peak in the
mass spectrum called the base peak.
Metastable ion peak:
The ions appear at an m/z ratio that depends on its mass as well as the mass of the original ion
from which it formed. Such an ion is called Metastable ion peak. It is formed due to abnormal
flight path on its way to the detector.
m* = apparent mass of the Metastable ion, m1 = mass of the original ion and m2 = mass of the
new fragment ion.
Characteristics of Metastable ion:
They do not necessarily occur at the integral m/z values
5. Mass Spectrometry
Dr. Krishnaswamy. G Page 5
These are much broader than the normal peaks and
These are relatively less abundance.
Example:Consider the formation of Metastable peak in the mass spectrum of toluene. Two
strong peaks at m/z 91 and at m/z 65 are formed. The peak at m/z 91 is due to formation of
tropylium ion which loses a molecule of acetylene to give C5H5
+ of m/z 65.
-H+ Rearrangement
-C2H2
m/z = 91 m/z = 65
(m1) (m2)
Suppose the transition C7H7+ to C5H5+ occurs, then a Metastable peak is formed. The position of
the broad Metastable peak is determined as
= 65 x 65/ 91 = 46.4
A Metastable peak appears at 46.4 in case of toluene mass spectrum.
Ionization techniques
1. Electron Ionization (EI)
2. Chemical ionization (CI)
3. Field Desorption (FD)
4. Fast Atom Bombardment (FAB)
5. Electron sprayIonization (ESI)
6. Matrix Assisted Laser Desorption/ Ionization (MALDI)
Electron Ionization (EI): Mass spectra are routinely obtained at an electron beam energy of
70 eV. The simplest event that occurs is the removal of single electron from the molecule in the
gas phase by the electron of the electron beam to form the molecular ion, which is a radical
cation.
Chemical Ionization (CI): The vaporized sample is introduced into the mass spectrometer
with anlarge excess of reagent gas (1000 – 10000 times) is introduced (Methane, ammonia,
isobutane) at a pressure of about 1 torr. The excess carrier gas is ionized by electron impact to
the primary ions CH4+.and.CH3. These react with the excess methane to give secondary ions like
CH5+, C2H5+ and C3H5+. The secondary ions react with the sample.Chemical ionization mass
spectra show peaks one mass unit higher than those expected in electron impact spectra [M+H]+.
The stability of M+ 1 peak is usually greater than that of the molecular ion.
electronswithninteractiouponformedareCHandCH 34
6. Mass Spectrometry
Dr. Krishnaswamy. G Page 6
Field Desorption (FD): Stable molecular ions are obtained from a sample of low volatility
which is placed on the anode of a pair of electrode between which there is an intense electric
field. Desorption occurs and molecular and quasimolecular ions are produced with insufficient
internal energy for extensive fragmentation. Usually the major peak represents the [M+ H]+
ion.Synthetic polymers with molecular weights on the order of 10, 000 Da have been analyzed.
Fast Atom Bombardment (FAB): Polar molecules such as peptides with molecular weight
upto 10, 000 Da can be analyzed by a soft ionization technique called Fast atom bombardment.
The bombarding beam consists of xenon (or Argon) atoms of high translational energy.This
beam is produced by first ionizing xenon atoms with electrons to give xenon radical cation.The
compound of interest is dissolved in a high boiling solvent such as glycerol, a drop is placed on a
thin metal sheet and the compound is ionized by the high energy beam of xenon atoms.
Ionization by translational energy minimizes the amount of vibration excitation and this results
in less destruction of the ionization molecule.
Electron spray Ionization (ESI): Electron sprayinvolves placing an ionizing voltage several
kilovolts across the nebulizer needle attached to the outlet. This technique is widely used on
water soluble biomolecules proteins, peptide and carbohydrates. Electron spray ionization is one
of several variations of atmospheric pressure ionization (API).
Matrix Assisted Laser Desorption/Ionization (MALDI): In the MALDI procedure is
mainly used for large biomolecules the sample in a matrix is dispersed on a surface and is
desorbed and ionized by the energy of a laser beam. The MALDI procedure is has been used in
several variations to determine the molecular weight of large protein molecule upto several
hundred kDa.
Determination of Molecular weight
The Nitrogen Rule states that if m/z for M is odd, then the molecular formula must have an
oddnumber of nitrogens. If m/z for M is even, then the molecular formula must have an even
number
of nitrogens (this includes 0).
EX: For 1-bromopropane, m/z for M=122. The even number is in accordance with theeven
number of nitrogens in the formula (zero).
The Hydrogen Rule states that the maximum number of hydrogens in the molecular formula is
2C+N+2
3544 CHCHCHCH
25243 HHCCHCH
45 CHMHCHM
4252 HCMHHCM
7. Mass Spectrometry
Dr. Krishnaswamy. G Page 7
C: No.of carbons, N: No of nitrogens
EX: For CH3CH2CH2Br, there are three carbons, so the max # of hydrogens is 2(3)+2=8
Index of hydrogen deficiency or Double Bond Equivalent
One Double Bond Equivalent (DBE) (also known as a degree of unsaturation) is one pi bondor
one ring. A triple bond counts as 2 DBE. Having 4 DBE indicates the possibility of a
benzenering, since benzene has three pi bonds plus one ring. The formula for DBE is the
following:
Index of hydrogen deficiency
or
DBE = C – (H/2) _ (X/2) + (N/2) + 1
C = No. of carbons, H = No. of Hydrogen, X = No. of Halogens & N = No. Nitrogen
Determination of Molecular Formulas
A. Precise Mass determination:
Most important application of high Resolution mass spectrometer is the Determinationof
very precise molecular weight of substances. We are accustomed to thinking of atoms as
having integral atomic massed for example H = 1, C = 12 and O = 16. However if we
determine the atomicmasses with sufficient precision we find thatthis not true.Depending
upon the atoms in a molecule it is possible for particle of the same nominal mass to have
slightly different measured masses when precise determinations are possible. Consider a
molecule with a molecular weight of 60 could be C3H8O, C2H8N2, C2H4O2 or CH4N2O.
These species have the following precise masses
8. Mass Spectrometry
Dr. Krishnaswamy. G Page 8
B. Isotope Ratio Data:
In this method of determining molecular formulas is to examine the relative intensities of
the peaks due to the molecular ion and related ion that bear one or more heavy isotopes.If
only C, H, N, O, F, p and I are present, the approximate expected percentage (M+1) and
(M+2) intensities can be calculated by use of the following formula.
Fragmentation:
General rules for predicting prominent peaks in EI spectra:
1. The relative height of the molecular ion peak is greatest for the straight chain compound
and decreases as the degree of branching increases.
2. The relative height of the molecular ion peak usually decreases with increasing molecular
weight in a homologous series.
3. Cleavage is favored at alkyl-substituted carbon the more substituted the more likely is
cleavage. This is consequence of the increased stability of a tertiary carbocation over a
secondary carbocation which in turn is more stable than a primary.
9. Mass Spectrometry
Dr. Krishnaswamy. G Page 9
R
C CR +
4. Double bonds, cyclic structures and especially aromatics rings (or heteroatoms) stabilize
the molecular ion and thus increase the probability of its appearance.
5. Double bonds favors allylic cleavage and give resonance stabilized allylic carbocation.
This rule does not hold good for simple alkenes because of ready migration of double
bond but it does hold for cycloalkenes.
6. Saturated rings tend to lose alkyl side chains at α bond.The positive charge tends stay
with ring fragment.
R
-R
Unsaturated rings can undergo a retro-Diels-Alder reaction.
-R
7. In alkyl substituted aromatic compounds cleavage is very probable at the β bond to the
ring, giving the resonance stabilized benzyl cation or the tropylium ion.
R
H
H
1,2-H shift
-R.
8. The C-C bonds next to a hetero atom are frequently cleaved, leaving the charge on the
fragment containing the heteroatom whose nonbonding electrons provide resonance
stabilization.
10. Mass Spectrometry
Dr. Krishnaswamy. G Page 10
9. Cleavage is often associated with elimination of small stable neutral molecule such as
CO, Olefins, water, ammonia, hydrogen sulfide, hydrogen cyanide, mercaptans, ketenes
or alcohols with rearrangement.
McLafferty Rearrangements:
McLafferty rearrangement involves the migration of γ-hydrogen atom followed by the cleavage
of a β-bond. To undergo McLafferty rearrangement a molecule must possess an appropriately
located heteroatom, a π-system (usually double bond) and an abstractable hydrogen atom γ to the
C=O system.
The rearrangement leads to the elimination of neutral molecules and proceeds through sterically
hindered six membered transition state.
Y
O
H
Y
O
H
Y
O
H
+
Y
O
H
Transition State
Y = H, R, OH, OR, NR2
Example: 1-pentene contains γ-hydrogen atom undergoes McLafferty rearrangement
H
+
m/z= 42
Mass Spectra of some chemical classes:
1. (a) Alkanes:
The relative height of the parent peak decreases as the molecular mass increases
in the homologous series.
Groups of peaks in the mass spectrum are observed 14 mass units apart. The most
abundant peaks correspond to CnH+
2n+1 ion.
11. Mass Spectrometry
Dr. Krishnaswamy. G Page 11
The most intense peaks are due to C3 and C4 ions at m/z 43 and 57 respectively.
We also notice small peaks for CnH+
2n-1 and CnH+
2n
Example mass spectrum of octane.
(b) Branched chain alkanes:
Bond cleavage takes place preferably at the site of branching. Due to such
cleavage, a more stable secondary or tertiary carbocation ion results.
Generally largest substituent at a branch is eliminated readily as a radical.
With 2,2,4-trimethylpentane, the cleavage shown leads to formation of tert-butyl
carbocation. Since tertiary carbocations are the most stable of the saturated alkyl
carbocations, this cleavage is particularly favorable and accounts for the intense
fragment peak at m/z = 57.
2. Alkenes:
The molecular io peak in the unsaturated compounds is more intense than the
corresponding saturated analogues. The reason is the better resonance
12. Mass Spectrometry
Dr. Krishnaswamy. G Page 12
stabilization of the charge on the cation formed by the removal of one of the π
electrons.
The relative abundance of the molecular ion peak decrease with increasing
molecular mass.
The general mode of fragmentation induced by a double bond is the allylic
cleavage.
The CnH2n ions formed by McLafferty rearrangement are more intense.
H
+
m/z= 42
3. Alkynes:
Themass spectra of alkynes are very similar to those of alkenes. The molecular
ion peaks tend to be rather intense and fragmentation patterns parallel those of the
alkenes.
4. Cycloalkanes:
The relative abundance of the molecular ion of Cycloalkanes is more as compared
to the corresponding alkanes.
13. Mass Spectrometry
Dr. Krishnaswamy. G Page 13
It favors cleavage at the bond connecting the ring to the rest of the molecule.
The stability of the fragment ion depends upon the size of the ring.
+
+
M+
= 126 m/z = 83
m/z = 55
5. Cycloalkenes:
Cyclic alkenesusually show a distinct molecular ion peak involving retro Diels-
Alder reaction.
-R
6. Aromatic compounds:
The mass spectra of most aromatic hydrocarbons show very intense molecular ion
peaks.
If the aromatic ring is substituted by an alkyl group, a prominent peak is formed at
m/z 91, here benzyl cation formed spontaneously rearranges to tropylium cation.
14. Mass Spectrometry
Dr. Krishnaswamy. G Page 14
R
H
H
1,2-H shift
-R.
When the side chain attached to benzene ring contains three or more carbons ions
formed by a McLafferty rearrangement can be observed.
Example: Fragmentation pattern of n-propyl benzene
15. Mass Spectrometry
Dr. Krishnaswamy. G Page 15
CH2
-(CH3CH2)
M+
m/z = 120
m/z = 91
m/z = 65
HC CH-
7. Alcohols and Phenols:
The molecular ion peak of primary and secondary alcohol is usually low abundance. It is
not detected in tertiary alcohols.
The fragmentation of carbon-carbon bond adjacent to oxygen atom (α-bond) is the
preferred.
Fragmentation involves the loss of an alkyl group or the loss of a molecule of water
(M-18).
Alcohols containingfour or more carbons may undergo the simultaneous loss of both
water ad ethylene.
Cyclic alcohols may undergo fragmentation by at least three different pathways.
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Phenols typically loss the element of carbon monoxide to give strong peaks at m/z
values that are 28 mass units below the value for the molecular ion (M-28).
Phenols also lose the elements of the formyl radical (HCO.) to give strong M-29
peaks.M-29 is less intense than M-28
OH
H H
-H.
m/z = 108 m/z = 79
HO
-CO
Tropylium hydroxide
Benzyl alcohols exhibit intense molecular ion peaks. A favored mode of
fragmentation involves loss of a hydrogen atom, loss of a molecular carbon
monoxide and loss of a formyl radical.
8. Ethers:
The molecular ion peals of ether are rather weak. Principal modes of
fragmentation include α-cleavage, formation of carbocation fragment and loss of
an alkoxy group.
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Consider the mass spectrum of diisopropyl ether, loss of alkyl group gives rise a
peak at m/z = 87.
O O
-CH3
.
m/z = 87m/z = 102
A second mode of fragmentation involves cleavage of the carbon-oxygen bond of
ether to yield carbocation. Cleavage of this type in diisopropyl ether is responsible
for the C3H7+ fragment at m/z = 43.
O OH
+
m/z = 43
A third type of fragmentation occurs as a rearrangement reaction taking place on
one of the fragmentation ions rather than on the molecular ion itself.This type of
rearrangement is particularly favored when the carbon of the ether is branched. In
the case of diisopropyl ether this rearrangement gives rise to a C2H5O+ fragment
(m/z = 45)
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9. Aldehydes:
The molecular ion peak of an aliphatic aldehydes is usually observable may be
fairly weak.
The major fragmentation processes are α- and β- cleavages.
α- cleavages
β- cleavages
If the carbon attached to the carbonyl group contains at least three carbons,
McLafferty rearrangement is also observed.
Aromatic aldehydes exhibit intense molecular peaks. Consider the mass spectrum
of Benzaldehyde, the M-1 peak appears at m/z = 105. A peak at m/z = 77 which is
due to loss of the –CHO group to give C6H5+.
H O O+
-H. -CO
(M-1) m/z = 77 m/z = 51
+
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10. Ketones:
The mass spectra of ketones show intense molecular ion peak.
Loss of the alkyl groups attached to the carbonyl group is one of the most
important fragmentation processes. The pattern of fragmentation is similar to that
of aldehydes.
The larger of the two alkyl groups attached to the carbonyl group appears more
likely to be lost. Consider the mass spectrum of 2-butanone.
The peak at m/z = 43 is due to loss of the ethyl group is more intense than the peak
at m/z = 57 due to loss of methyl group.
When the carbonyl of a ketones attached to alkyl group that is three or more
carbon atom length, McLafferty rearrangement id possible.
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R O O+
-R. -CO
+
Cyclic ketones may undergo a variety of fragmentation and rearrangement processes.
Aromatic ketones undergo cleavage to lose alkyl group and form the C6H5CO+ ion
(m/z = 105). This ion loses the carbon monoxide to form the C6H5+ ion (m/z = 77).
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When larger alkyl group attached to the carbonyl group, McLafferty rearrangement
is possible.
11. Esters:
The most important of the cleavage reaction involves the loss of the alkoxy group
from an ester to form the corresponding acylium ion RCO+.
Benzyl esters undergo rearrangement to eliminate the neutral ketene molecule.
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12. Carboxylic acids:
Aliphatic acids generally show weak but observable molecular ion peaks.
Aromatic acids on the other hand show strong molecular ion peaks.
The principal mode of fragmentation resembles those of the methyl esters.
With short chain acids the loss of OH and COOH through α-cleavages on either
side of the C=O group may be observed.
13. Amines:
Aliphatic amines, the molecular ion peak may be very weak or even absent.
The most intense peak in the mass spectrum of a aliphatic amine arises from α
cleavage.
When there is a choice of R group to be lost through this process, the largest
group is lost preferentially.
Aromatic amines show intense molecular ion peaks. A moderately intense peak
appears at m/z value one mass unit less than that of the molecular ion, due to loss
of a hydrogen atom.
14. Amides:
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The mass spectra of amides usually show observable molecular ion peaks. The
fragmentation pattern of amides is quite to those of corresponding esters and acids.
The presence of the strong fragment ion at m/z = 44 is usually indicative of a primary
amide. The peak arises from α-cleavage.