* Using Rule of 13:
* Molecular mass = 128
* 128/13 = 9 with remainder of 8
* So the hydrocarbon formula is C9H9+8 = C9H17
* It is given that there are 8 hydrogens
* So remove 8 hydrogens from C9H17 to get C9H9
Therefore, the molecular formula is C9H9
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
For UG students of All Engineering Branches (Mechanical Engg., Chemical Engg., Instrumentation Engg., Food Technology) and PG students of Chemistry, Physics, Biochemistry, Pharmacy
The link of the video lecture at YouTube is
https://www.youtube.com/watch?v=t3QDG8ZIX-8
Mass Spectrometry (MS) is an analytic technique used to determine the relative masses of molecular ions and fragments by calculating the degree of deflection of charged particles in a magnetic field.
It provides a great deal of information with very small amount of samples.
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
For UG students of All Engineering Branches (Mechanical Engg., Chemical Engg., Instrumentation Engg., Food Technology) and PG students of Chemistry, Physics, Biochemistry, Pharmacy
The link of the video lecture at YouTube is
https://www.youtube.com/watch?v=t3QDG8ZIX-8
Mass Spectrometry (MS) is an analytic technique used to determine the relative masses of molecular ions and fragments by calculating the degree of deflection of charged particles in a magnetic field.
It provides a great deal of information with very small amount of samples.
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
Mass Analyzers for example Magnetic Sector Mass Analyzer, Double Focusing Mass Analyzer, Quadroupole Mass Analyzer, Time of Flight Mass Analyzer and Applications of Mass Analyzer were explained
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
Mass Analyzers for example Magnetic Sector Mass Analyzer, Double Focusing Mass Analyzer, Quadroupole Mass Analyzer, Time of Flight Mass Analyzer and Applications of Mass Analyzer were explained
mass spectrometry, also called mass spectroscopy, analytic technique by which chemical substances are identified by the sorting of gaseous ions in electric and magnetic fields according to their mass-to-charge ratios.
Mass spectroscopy is an analytical technique used to measure the mass-to-charge ratio (m/z) of one or more molecules present in a sample. It can be used to identify unknown compounds via molecular weight determination, quantify known compounds, and determine the structure and chemical properties of molecules.2 Mass spectroscopy is also useful for studies on protein-protein interactions. The basic principle involves fragmentation of a compound or molecule into charged species, which are accelerated, deflected, and finally focused on a detector according to their mass and charge ratio.Mass spectroscopy is an instrumental method for identifying the chemical constitution of a substance by means of the separation of gaseous ions according to their differing mass and charge.
Richard's aventures in two entangled wonderlandsRichard Gill
Since the loophole-free Bell experiments of 2020 and the Nobel prizes in physics of 2022, critics of Bell's work have retreated to the fortress of super-determinism. Now, super-determinism is a derogatory word - it just means "determinism". Palmer, Hance and Hossenfelder argue that quantum mechanics and determinism are not incompatible, using a sophisticated mathematical construction based on a subtle thinning of allowed states and measurements in quantum mechanics, such that what is left appears to make Bell's argument fail, without altering the empirical predictions of quantum mechanics. I think however that it is a smoke screen, and the slogan "lost in math" comes to my mind. I will discuss some other recent disproofs of Bell's theorem using the language of causality based on causal graphs. Causal thinking is also central to law and justice. I will mention surprising connections to my work on serial killer nurse cases, in particular the Dutch case of Lucia de Berk and the current UK case of Lucy Letby.
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.
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.
Slide 1: Title Slide
Extrachromosomal Inheritance
Slide 2: Introduction to Extrachromosomal Inheritance
Definition: Extrachromosomal inheritance refers to the transmission of genetic material that is not found within the nucleus.
Key Components: Involves genes located in mitochondria, chloroplasts, and plasmids.
Slide 3: Mitochondrial Inheritance
Mitochondria: Organelles responsible for energy production.
Mitochondrial DNA (mtDNA): Circular DNA molecule found in mitochondria.
Inheritance Pattern: Maternally inherited, meaning it is passed from mothers to all their offspring.
Diseases: Examples include Leber’s hereditary optic neuropathy (LHON) and mitochondrial myopathy.
Slide 4: Chloroplast Inheritance
Chloroplasts: Organelles responsible for photosynthesis in plants.
Chloroplast DNA (cpDNA): Circular DNA molecule found in chloroplasts.
Inheritance Pattern: Often maternally inherited in most plants, but can vary in some species.
Examples: Variegation in plants, where leaf color patterns are determined by chloroplast DNA.
Slide 5: Plasmid Inheritance
Plasmids: Small, circular DNA molecules found in bacteria and some eukaryotes.
Features: Can carry antibiotic resistance genes and can be transferred between cells through processes like conjugation.
Significance: Important in biotechnology for gene cloning and genetic engineering.
Slide 6: Mechanisms of Extrachromosomal Inheritance
Non-Mendelian Patterns: Do not follow Mendel’s laws of inheritance.
Cytoplasmic Segregation: During cell division, organelles like mitochondria and chloroplasts are randomly distributed to daughter cells.
Heteroplasmy: Presence of more than one type of organellar genome within a cell, leading to variation in expression.
Slide 7: Examples of Extrachromosomal Inheritance
Four O’clock Plant (Mirabilis jalapa): Shows variegated leaves due to different cpDNA in leaf cells.
Petite Mutants in Yeast: Result from mutations in mitochondrial DNA affecting respiration.
Slide 8: Importance of Extrachromosomal Inheritance
Evolution: Provides insight into the evolution of eukaryotic cells.
Medicine: Understanding mitochondrial inheritance helps in diagnosing and treating mitochondrial diseases.
Agriculture: Chloroplast inheritance can be used in plant breeding and genetic modification.
Slide 9: Recent Research and Advances
Gene Editing: Techniques like CRISPR-Cas9 are being used to edit mitochondrial and chloroplast DNA.
Therapies: Development of mitochondrial replacement therapy (MRT) for preventing mitochondrial diseases.
Slide 10: Conclusion
Summary: Extrachromosomal inheritance involves the transmission of genetic material outside the nucleus and plays a crucial role in genetics, medicine, and biotechnology.
Future Directions: Continued research and technological advancements hold promise for new treatments and applications.
Slide 11: Questions and Discussion
Invite Audience: Open the floor for any questions or further discussion on the topic.
This pdf is about the Schizophrenia.
For more details visit on YouTube; @SELF-EXPLANATORY;
https://www.youtube.com/channel/UCAiarMZDNhe1A3Rnpr_WkzA/videos
Thanks...!
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.
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 .
THE IMPORTANCE OF MARTIAN ATMOSPHERE SAMPLE RETURN.Sérgio Sacani
The return of a sample of near-surface atmosphere from Mars would facilitate answers to several first-order science questions surrounding the formation and evolution of the planet. One of the important aspects of terrestrial planet formation in general is the role that primary atmospheres played in influencing the chemistry and structure of the planets and their antecedents. Studies of the martian atmosphere can be used to investigate the role of a primary atmosphere in its history. Atmosphere samples would also inform our understanding of the near-surface chemistry of the planet, and ultimately the prospects for life. High-precision isotopic analyses of constituent gases are needed to address these questions, requiring that the analyses are made on returned samples rather than in situ.
2. Introduction
• Mass spectrometry is an analytical technique that measures the
mass-to-charge ratio of ions.
• Mass spectrometry is a powerful analytical technique used to
quantify known materials, to identify unknown compounds within a
sample, and to elucidate the structure and chemical properties of
different molecules.
• The complete process involves the conversion of the sample into
gaseous ions, with or without fragmentation, which are then
characterized by their mass to charge ratios (m/z) and relative
abundance.
• A mass spectrometer generates multiple ions from the sample
under investigation, it then separates them according to their
specific mass-to-charge ratio (m/z), and then records the relative
abundance of each ion type.
2AISC/SBS/MSc-I
3. The formed ions are separated by Deflection in magnetic
field according to their Mass to charge (m/z)
Ions formed Further break up into smaller ion
(Fragment ions or Daughter ions formed)
Mass Spectroscopy
Basic Principles
3
Molecules converted into highly energetic positively charged
ions (Molecular ions or Parent ions)
Organic Molecules are bombarded with electron
Mass Spectrum
m/z ratio Vs intensity (relative abundance of peak)
AISC/SBS/MSc-I
4. Basic Principle
• The first step in the mass spectrometric analysis of compounds is the production of
gas phase ions of the compound, basically by electron ionization with bombarded
of electron to form molecular ions or parent ion.
• This molecular ion undergoes fragmentation to from positively charged ions and
neutral ions or radicals.
• Each primary product ion derived from the molecular ion, in turn, undergoes
fragmentation, and so on.
• The ions are separated in the mass spectrometer according to their mass-to-
charge ratio, and are detected in proportion to their abundance.
• A mass spectrum of the molecule is thus produced.
• It displays the result in the form of a plot of ion abundance versus mass-to-charge
ratio.
• Ions provide information concerning the nature and the structure of their
precursor molecule.
• In the spectrum of a pure compound, the molecular ion, if present, appears at the
highest value of m/z (followed by ions containing heavier isotopes) and gives the
molecular mass of the compound.
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5. • In MS technique, molecules are bombarded with a beam of energetic
electrons.
• The molecules are ionized into ions and broken up into many fragments,
some of which are positive ions.
• Each kind of ion has a particular ratio of mass to charge, i.e. m/e
ratio(value).
• For most ions, the charge is one and thus, m/e ratio is simply the
molecular mass of the ion.
5AISC/SBS/MSc-I
7. Working of MS
• There are four key stages in the process for
Mass Spectrometry.
– Ionization
– Acceleration
– Deflection
– Detection
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8. Stage 1: Ionisation
8
• The initial sample may be a solid, liquid, or gas.
• The sample is vaporized into a gas and then ionized by the ion source, usually by
losing an electron to become a cation
• Electro Ionisation is the most common type of ionisation.
• The sample is bombarded by electrons which come from a heated filament.
• When the sample passes through the electron stream, the high energy electrons in
the stream knock electrons out of the sample to form ions.
• The ionization chamber is kept in a vacuum so the ions that are produced can
progress through the instrument without running into molecules from air.
Stage 2: Acceleration
• Acceleration is a simple step where the ions are placed between a set of charges
parallel plates.
• The ions will then be repelled by one plate and attracted to the other.
• There is a slit cut in the plate which the ions are attracted to. the force of
attraction and repulsion forces the ions through the slit at an accelerated rate.
• The speed of acceleration can be adjusted by changing the charge on the plates.
• The purpose of acceleration is to give all species the same kinetic energy, like
starting a race with all runners on the same line.
AISC/SBS/MSc-I
9. Stage 3: Deflection
• Ions are deflected by the magnetic field surrounding the instrument.
• The amount of deflection depends on the mass and charge of the ions.
• Lighter components or components with more ionic charge will deflect in the field
more than heavier or less charged components.
• The heavier ions, are deflected the least (Ion stream C)
• The lightest ions are deflected the most (Ion Stream A)
• The ions at the correct mass and charge travel to the detector. (Ion Stream B)
• The mass to charge ratio (m/z) is determined from the ion that hits the detector.
9
Step 4: Detection
• When the ion stream reached the detector the hit a wire. On hitting the
wire they become neutralised by an electron jumping from the metal wire
to the ion.
• The amplifier picks up on this current being created between the wire and
the ion and amplifies the signal being detected.
• The computer picks up on this and converts it to mass/charge ratio and a
spectrum is produced.
AISC/SBS/MSc-I
10. •Ionizing technique and their source in MS
There are many types of ionization methods are used in mass spectrometry
methods.
Gas Phase Sources. (Sources)
• Electron Impact Ionization (EI). (By Energetic electrons)
• Chemical Ionization (CI). (By reagent gaseous ions)
• Field Ionizations (FI). (By high potential electrodes)
Desorption Sources.
• Field Desorption (FD). (By high potential electrodes)
• Electrospray Ionization (ESI). ( by high electric field)
• Matrix assisted desorption/Ionisation (MALDI). (By laser beam)
• Plasma desorption (PD). (by fragments from 253Cf)
• Fast Atom Bombardment (FAB). (by energetic atomic beam)
• Thermospray Ionization (TS). (By high temperature)
• Secondary Ion Mass Spectrometry (SIMS). (energetic atomic beam)
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12. Types of Peaks in MS
• Molecular ion Peak
• Base Peak
• Metastable peak
• Fragment ion peak
• Rearrangement ion peak
• Multicharged ion
• Negative ion peak
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13. Molecular ion Peak
• When a any sample is bombarded with electrons of 9
to 15 eV energy, the molecular ion is produced by loss
of single electron. It is denoted by M (or M)
• When the vaporized organic sample passes into the
ionization chamber of a mass spectrometer, it is
bombarded by a stream of electrons. These electrons
have a high enough energy to knock an electron off an
organic molecule to form a positive ion. This ion is
called the molecular ion. (sometimes the parent ion.)
• Molecular ion peak gives molecular weight of
compounds
M M 2e+
e
molecular ion
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15. Mass spectrum of Pentane
(Molecular weight = 72)
15AISC/SBS/MSc-I
16. High Resolution Molecular ion peak
• A unique molecular formula can often be derived accurate
mass measurement alone in High Resolution Mass
spectrometry (HRMS). So molecular ion in HRMS are called
high resolution molecular ion peak. In HRMS masses
obtained up to four or five decimal places.
• The unique molecular formula possible because the nuclide
masses are not integer.
• Exact masses of some nuclides
H 1.00783
C 12.0000
N 14.0031
O 15.9949
•
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17. Precise mass determination
• if we have molecular formula C6H12O then its HRMS molecular ion
mass is unique at 100.0888
• Mass = (number of Carbon X Mass of Carbon) + (number of hydrogen X
Mass of Hydrogen )+ (number of Oxygen X mass of Oxygen)
• Mass = 6 X Mass of Carbon + 12 X Mass of Hydrogen + 1 X mass of Oxygen
= 6 x 12.0000 + 12 x 1.00783 + 1 x 15. 9949
= 72.0000 + 12.09396 + 15.9949
=100.08886
• For molecular formula C5H8O2
• Mass = 5 x Mass of Carbon + 8 x Mass of Hydrogen + 2 x mass of Oxygen
= 5 x 12.0000 + 8 x 1.00783 + 2 x 15. 9949
= 60.0000 + 8.06264 + 31.9898
= 100.05244
AISC/SBS/MSc-I 17
18. Significance / Use of the Molecular Ion (M)
• By using rule thirteen for molecular ion peak, one can determine the
molecular formula.
• From Molecular ion peak, it gives idea of isotopic element if present.
• It gives idea of odd nitrogen present in compound (nitrogen rule).
• The molecular ion along with other information from IR and NMR spectra
can allow the identity of an unknown to be determined.
• Now a days, Once the identity of the molecular ion has been determined
much can be learned about the compound. One extremely valuable piece
of information that can be determined from a high resolution mass
spectrometer is the molecular formula of an unknown analyte.
• If a molecular ion was identified to be at m/z 80 on an instrument with
unit resolution little could be determined about the molecular formula.
For example, some of the many possible molecular formulas include
C4H4N2 (80.0375), C5H4O(80.0262), and C6H8 (80.0626).
• A high resolution instrument measurement of this peak at 80.0372 ±
0.0005 would indicate that the empirical formula is C4H4N2.
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19. Base peak
• The most intense ion peak or tallest peak in mass
spectrum is assigned an abundance of 100, and it is
referred to as the base peak.
• The relative abundance of the tallest peak or
base peak ion is assigned a value of 100, and the
abundances of all other ions plotted in that mass spectr
um are normalised to that value.
• The base peak is not necessarily the same as the parent
molecular ion peak.
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20. Base peak in pentane
20
In the mass spectrum for pentane, the positive ion with m/z = 43 produces
the tallest spectrum. It is base of given spectrum.
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21. Mass Spectrum of ethyl Benzene
(Base peak = 91)
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22. Metastable peaks
22
• Metastable Ions: Fragment of a parent ion will give rise to a new ion (daughter)
plus either a neutral molecule or a radical.
• Fragment ion produced in the analyzer follows abnormal flight path on its way to
detector. This ions appear at an m/e ratio depend on its masses as well as the
masses of original ions from which it formed. Such ions are called Metastable ions.
• For example
• M1
+ M2
+ + non charged fragment
• An intermediate situation is possible; M1
+ may decompose to M2
+ while being
accelerated.
• The resultant daughter ion M2
+ will not be recorded at either M1 or M2, but at a
position M* as a rather broad, poorly focused peak. Such an ion is called a
metastable ion.
AISC/SBS/MSc-I
23. • Metastable ions have lower kinetic energy than normal ions and
metastable peaks are smaller than the M1 and M2 peaks and also broader.
These metastable ions arise from fragmentation that takes place during
the flight down through ion rather than in the ionization chamber.
Molecular ions formed in the ionization
• Significance of Metastable ions:
• Metastable ions are useful in helping to establish fragments routes.
• Metastable ion peak can also be used to distinguish between
fragmentation Processes, which occur in few microseconds.
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24. Fragment ion peak
• Molecular ion peak in MS further undergo
fragmentation gives new daughter ion peaks
such peak produced in MS called as fragment
ion peaks.
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25. Negative ion peak
25
• Negative ions are formed from electron bombardment of
sample. These results due to the capture of electron by a
molecule during collision of molecules .
• Molecular ions observed in negative ion chemical ionization
mass spectra are usually M or [M-H]-.
• In the negative ion mode operation peaks corresponding to
deprotonated analyte molecules are observed.
• The formation of negative ions is very rare .
AISC/SBS/MSc-I
26. *Nitrogen rule in Mass spectroscopy*
• When m/z for M has an odd mass (odd number
of amu), the corresponding molecular formula
has an odd number of nitrogen atoms (1, 3, 5,
etc.).
• When m/z for M has an even mass (even
number of amu), the corresponding molecular
formula has no / zero nitrogen or an even
number of nitrogen atoms (0, 2, 4, etc.).
• This is called nitrogen rule.
• Nitrogen rule is very useful for determining the
nitrogen content of an unknown compound.
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28. Calculate Mass and tally with Nitrogen rule
28
NH2 NO2 NH2
mass
nitrogen
odd / even
odd / even odd / even odd / even
odd / even odd / even
H3C H3C
H2N
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29. Calculate Mass and nitrogen
29
NH2 NO2 NH2
NO2
mass
nitrogen
odd / even
odd / even odd / even odd / even
odd / even odd / even
AISC/SBS/MSc-I
30. *Rule of 13*
• The Rule of 13 is a simple procedure for tabulating possible
chemical formula for a given molecular mass.
• The first step in applying the rule is to assume that only carbon and
hydrogen are present in the molecule and that the molecule
comprises some number of CH "units" each of which has a nominal
mass of 13.
• If the molecular weight of the molecule in question is M, the
number of possible CH units is n and
• where r is the remainder.
• The base formula for the molecule is CnHn+r
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31. 31AISC/SBS/MSc-I
Q2 ) for a m+ = 106,
n=8 (106/13) with r of 2.
A possible molecular formula for this ion C8H8+2 = C8H10
33. The nominal mass of a substance is 140.
What is its molecular formula?
• By using The rule of 13:
• Divide the nominal mass by 13:
• A hydrocarbon with this molecular weight
would have 10 C atoms
• Multiply the remainder by 13: 0.769*13 = 9.997 or 10;
• A hydrocarbon with this molecular weight
would have (n+r) (10+10) or 20 hydrogens
• ‘CH’Molecular formula will be C10H20
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34. By using rule of 13, molecular formula
determination with other element.
• From parent hydrocarbon which is derived
from rule of 13, other elements (like O, N) can
be added to that hydrocarbon.
• For addition of oxygen / nitrogen we have to
remove same mass of oxygen or nitrogen from
hydrocarbon formula.
• For addition of ‘O’ remove CH4
• For addition of ‘N’ remove CH2
• For addition of ‘C’ remove 12 H
34AISC/SBS/MSc-I
35. Q) A carboxylic acid of molecular ion peak (m/z) at 122. find its
molecular formula with the help of rule of 13.
• M = 122
• Therefore become
:. CH Molecular formula CnHn+r = C9H14
Carboxylic acid contain at least 2oxygen to form –COOH group
C9H14
+O -CH4
C8H10O
+O -CH4
C7H6O2
35
:. Molecular formula for give mass 122 is C7H6O2
AISC/SBS/MSc-I
36. Q) A hydrocarbon compound with mass 128 and 8 hydrogen.
find its molecular formula with the help of rule of 13
36
• M = 128
• Therefore become
:. CH Molecular formula CnHn+r = C9H20
C9H20
remove12H add C
C10H8
AISC/SBS/MSc-I
37. Q) A hydrocarbon compound with mass 109 and PMR shows
7 hydrogen. find its molecular formula with the help of rule
of 13
37
• M = 109
• Therefore become
:. CH Molecular formula CnHn+r = C8H13
mass is odd there it contain odd no. of Nitrogen (Nitrogen Rule)
C8H13
+N -CH2
C8H11N
+O -CH4
C7H7ON
:. Molecular formula for give mass 109 is C7H7ON
AISC/SBS/MSc-I
38. Genesis of m/z fragments:
Alkanes (cyclic and acyclic), alcohols, amines
38AISC/SBS/MSc-I
• Genesis means mode of formation of something.
Here in MS, it is used for formation of fragments
from molecular ions. Fragments which having
positive charge (cations) which detected in MS
and shows peak in mass spectrum.
• In this we have to show how fragment for a given
value of m/z is formed from parent ion or by
daughter ions.
• Some compounds follows fragmentation rule for
particular function groups to gives new
fragments.
39. Formation of molecular ion M+
and
Fragmentation of the molecular ion
AISC/SBS/MSc-I 39
• When a any molecule / sample is bombarded with electrons, the
molecular ion is produced by loss of single electron with same mass of its
molecular weight. Molecular ion is also denoted by a radical cation as
below
A B
e
A B
M o le c u la r io n
M
2 e
• These Molecular ion or a radical cation undergo fragmentation to break a
bond between A&B to form a radical and a cation as given below.
• Only cations or fragment with positive charge is detected in MS.
Molecular ion
a radical cation
A B
A + B
A + B
radical
radical cation
cation
40. Fragmentation of Alkanes
40AISC/SBS/MSc-I
• Fragmentation of straight chain alkane is observed by
breaking of any C-C bond from molecular ion.
• Alkane gives following m/z fragments due loose of
group
M-15 (due to loose of -CH3 methyl group)
M-29 (due to loose of –CH2CH3 ethyl group)
M-43 (due to loose of -CH2CH2CH3 propyl group)
• Lose of largest substituent is more fevered due to
stability .
• Stability of cation :
• methyl < primary < secondary < tertiary
42. Q.2) Give the genesis for pentane
Mass (m/z): 15, 29, 43(100%), 57, 72
42AISC/SBS/MSc-I
Molecular ion
m/z = 72
CH3CH2CH2CH2CH3
e
CH3CH2CH2CH2CH3
MW =72
Answer
43. Another way it is also written like this
AISC/SBS/MSc-I 43
45. Fragmentation of Branched alkane
• Genesis of 2-methyl pentane:
• m/z = 15, 29, 43 (100%),71, 86
AISC/SBS/MSc-I 45
46. Q) Show the genesis for following branched alkanes.
AISC/SBS/MSc-I 46
47. Fragmentation of Cycloalkanes
• Loss of side chains if present, by cleavage
• Loss of ethylene or double bond fragment
from ring
• Cleavage takes place by homolytic fasion
(show single headed arrow mechanism)
AISC/SBS/MSc-I 47
52. Fragmentation of Alcohols
52AISC/SBS/MSc-I
• The molecular ion of alcohols is usually small and
sometimes undetectable especially in tertiary alcohols.
• The identification of the molecular ion is complicated
by the prevalence of a M-1 peak caused by the loss of a
single hydrogen from the α carbon in primary and
secondary alcohols.
• Fragmentation pattern in alcohol
– -Bond Cleavage to oxygen
– loss of water molecule Dehydration
– Rearrangement and loss of water molecule
– -Bond Cleavage to oxygen giving m/z= 31
53. -cleavage in alcohol
• The most important fragmentation reaction in
alcohols is the loss of an alkyl group which are
.
• Example
or
AISC/SBS/MSc-I 53
e-
molecular ion
i)
ii)
OH
+
+
OH
+
OH OHa-cleavage
54. • In tertiary alcohol, there are chances of
braking each all three -bond to alcohol
• Alcohols also undergo dehydration to loss
water molecule either 1,2 elimination oe 1,4
elimination resulting (M-18) peak.
AISC/SBS/MSc-I 54
1,2 elimination
1,4 elimination
55. • Alcohols also frequently undergo the rearrangement resulting in a
M-18 peak from the loss of water. This peak is most easily visible in
primary alcohols but can be found in secondary and tertiary
alcohols as well. Primary alcohols also can lose both water and an
alkene.
• Alcohol containing four or more carbon may undergo such
rearrangement simultaneous loss water and ethylene as
AISC/SBS/MSc-I 55
Or
56. • Alcohols also frequently cleave to give resonance
stabilized cations due to the breaking of the β
bond. As a result of this cleavage, alcohols show a
prominent peak at m/z 31
AISC/SBS/MSc-I 56
62. • Primary amine that are not branched at the
carbon next to nitrogen, the most intense
peak occurs at m/e = 30. it arises from
cleavage.
AISC/SBS/MSc-I 62
64. Questions to solve
64AISC/SBS/MSc-I
• Q1. Give Genesis for Ethyl amine
mass (m/z) = 30 (100%) , 44, 45.
• Q2. Give Genesis for diethyl amine
mass (m/z) = 30, 58 (100%) , 72, 73.
• Q1. Give Genesis for triethyl amine
mass (m/z) = 30, 58, 86 (100%) , 100, 101.
65. Applications of Mass Spectrometry
• Mass Spectrometry as a technique can be coupled with
other techniques such as HPLC and GC.
• As it is used in the identification of compounds it is
used in all areas of science.
• Some of its uses are:
• Trace Gas Analysis
• Pharmaceutical Industry
• Space Exploration
• Forensic Toxicology
• Archaeological Dating.
65AISC/SBS/MSc-I
69. Calculation of intensity of isotopic (M+1) peak
• M+1 peak possible due to isotopes of C, H, and N.
M+1 peak intensity can be calculated by number of
atoms present with their isotopic abundance
• The formula for calculating the intensity of the
M+1 peak is as follows
• % (M+1) = 1.1 X number of C atoms +
0.016 X number of H atoms +
0.38 X number of N atoms +…
AISC/SBS/MSc-I 69
70. What will be the M+1 intensity for
propene C3H6
• Propene C3H6
• % (M+1) = 1.1 X number of C atoms + 0.016 X number of H atoms +
0.38 X number of N atoms +…
% (M+1) = 1.1 x 3 + 0.016 x 6
= 3.3 + 0.096
= 3.396 %
Calculate intensity of M+1 peak for Aniline
Aniline C6H7N
% (M+1) = 1.1 X number of C atoms + 0.016 X number of H atoms +
0.38 X number of N atoms +…
% (M+1) = 1.1 x 6 + 0.016 x 7 + 0.38 x 1
= 6.6 + 0.112 + 0.38
= 7.1 %
AISC/SBS/MSc-I 70