Introduction to stereochemistry, Representation of 3D molecules, R/S nomenclature, D-L and M-P convention, Topicity, Prochirality, Allenes, Biphenyls, Spiranes, Hemispirane.
more chemistry contents are available
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2. YouTube: https://www.youtube.com/channel/UCKxWnNdskGHnZFS0h1QRTEA
3. Facebook: https://web.facebook.com/Chemist.Rabia.Aziz/
4. Blogger: https://chemistry-academy.blogspot.com/
ORGANIC CHEMISTRY
Geometric isomerism of alkenes, cyclic compounds: cis-trans and (E)-(Z) system of
nomenclature
b) Conformational isomers: Open chain and cyclic system
c) Chirality of molecules: Enantiomers, diastereomers, racemic modification, Meso
compound, R & S configuration, sequence rule, Optical rotation
d) Asymmetric synthesis: Preparation of enantiomers by asymmetric synthesis & optical
resolution method
e) Stereo selective and stereo specific reaction
f) Pharmaceutical importance of studding stereochemistry
Introduction to stereochemistry, Representation of 3D molecules, R/S nomenclature, D-L and M-P convention, Topicity, Prochirality, Allenes, Biphenyls, Spiranes, Hemispirane.
more chemistry contents are available
1. pdf file on Termmate: https://www.termmate.com/rabia.aziz
2. YouTube: https://www.youtube.com/channel/UCKxWnNdskGHnZFS0h1QRTEA
3. Facebook: https://web.facebook.com/Chemist.Rabia.Aziz/
4. Blogger: https://chemistry-academy.blogspot.com/
ORGANIC CHEMISTRY
Geometric isomerism of alkenes, cyclic compounds: cis-trans and (E)-(Z) system of
nomenclature
b) Conformational isomers: Open chain and cyclic system
c) Chirality of molecules: Enantiomers, diastereomers, racemic modification, Meso
compound, R & S configuration, sequence rule, Optical rotation
d) Asymmetric synthesis: Preparation of enantiomers by asymmetric synthesis & optical
resolution method
e) Stereo selective and stereo specific reaction
f) Pharmaceutical importance of studding stereochemistry
This is for UG students. In this unit concept of stereochemistry is explain in easy way. The content are shown below:
-Stereochemistry
-Isomerism and their classification
-stereochemistry and their classification
-Geometrical Isomerism
-Optical isomerism
-Confirmational Isomerism
Geometric isomerism of alkenes, cyclic compounds: cis-trans and (E)-(Z) system of
nomenclature
b) Conformational isomers: Open chain and cyclic system
c) Chirality of molecules: Enantiomers, diastereomers, racemic modification, Meso
compound, R & S configuration, sequence rule, Optical rotation
d) Asymmetric synthesis: Preparation of enantiomers by asymmetric synthesis & optical
resolution method
e) Stereo selective and stereo specific reaction
f) Pharmaceutical importance of studding stereochemistry
Nutraceutical market, scope and growth: Herbal drug technologyLokesh Patil
As consumer awareness of health and wellness rises, the nutraceutical market—which includes goods like functional meals, drinks, and dietary supplements that provide health advantages beyond basic nutrition—is growing significantly. As healthcare expenses rise, the population ages, and people want natural and preventative health solutions more and more, this industry is increasing quickly. Further driving market expansion are product formulation innovations and the use of cutting-edge technology for customized nutrition. With its worldwide reach, the nutraceutical industry is expected to keep growing and provide significant chances for research and investment in a number of categories, including vitamins, minerals, probiotics, and herbal supplements.
Richard's entangled aventures in wonderlandRichard 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.
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.
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 .
What is greenhouse gasses and how many gasses are there to affect the Earth.moosaasad1975
What are greenhouse gasses how they affect the earth and its environment what is the future of the environment and earth how the weather and the climate effects.
Professional air quality monitoring systems provide immediate, on-site data for analysis, compliance, and decision-making.
Monitor common gases, weather parameters, particulates.
(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.
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.
3. Why we need
stereochemistry?
Cis, butanoic acid “maleic acid” essential for plants and ani
trans, butanoic acid “fumaric acid” toxic to tissue
4. contents
1- isomers types
2- stereoisomers
3- chirality center
4- Cahn-Ingold-Prelog R/S system
5- optical activity
6- Fischer projections
5. isomers
Compounds that have the same molecular
formula but different chemical structures .
isomers contain the same number of atoms
of each element, but have different
arrangements of their atoms
Isomers are classified to different types
depending on what differences there are
between the structures
7. Isomers types
1. Constitutional : isomers differ in the order
in which the atoms are connected so they
can contain different functional groups and
/ or bonding patterns (e.g. branching)
example: 1-propanol, 2-propanol and ethyl
methyl ether (C3H8O)
8. 2. Stereoisomers: have the same functional
groups and the same atoms order, they
differ only in the arrangement of atoms
and bonds in space.
14. Geometric isomers
(also named cis-trans isomers) :
These isomers occur where you have
restricted rotation somewhere in a
molecule ( ex double bond) or across
a ring system
16. If you don't know :
mirror images are the reflections of an
object.
If two objects are superimposable, it means
you can not tell them apart, they are identical.
If two objects are non-superimposable, then
you can always distinguish them.
Bring these together, and it means we are
comparing an object with it's mirror image to
see if the object can be distinguished from it's
mirror image or not.
17. Enantiomers
any pair of stereoisomers that are
non-superimposable mirror images of
each other.
A molecule that can exist as a pair of
enantiomers has the
property of chirality
(described as chiral)
18. Left hand and right hand
enantiomers can not be
superimposed, you can always tell a
left from a right (I hope !).
Therefore, since your left
and right hands are
non-superimposable
mirror images,
then they are a pair of enantiomers
19. Diastereomers
can be superposed ( no difference
between original object and it’s mirror
image) (not an enantiomers).
They have quite different physical and
chemical properties from one another.
This is important as it allows them to
be separated
21. The Chirality Centre
for an atom
Also named asymmetric, stereogenic
or chiral center .
chiral center is defined as a carbon
atom bearing 4 different atoms or group
of atoms
23. The Cahn-Ingold-Prelog
system
it is a system that is used for the
naming of enantiomers and
diastereomers .
It is also known as
R & S naming system.
24. How R & S naming system
works?
Step 1: find your stereocenter
the carbon with four different substituents
F
25. Step 2 : assign a priority to the four groups
bonded to the chiral center
a- look at the first atom of the group
higher atomic number = higher priority
F 1
2
3
4
26. b- if there is a tie , you keep going out
one bond at a time until you break the
tie.
27. c- isotopes atoms have the same
atomic number, if you have isotopes
higher atomic weight = higher priority
D
1 2
3
4
28. Step 3 : Position the lowest priority group away
from you,
as if you were looking along the C-(4) s bond.
Step4 : For the other 3 groups, determine the
direction of high to low priority (1 to 3)
If this is clockwise,
then the center is R (Latin= right)
If this is counter clockwise,
then it is S (Latin = left)
30. The Chirality Centre
For Molecules With More Than One Chiral
Center
If there are two chiral centers in a single
molecule, there are four possible
stereoisomers. This is because each carbon
atom can be in one of two possible forms (R
or S).
If a molecule is symmetric (have the same
substituents on both chiral atoms ) so that
two of the four possible stereoisomers are
identical (the S,R is identical to the R,S) this
form of the molecule is called the meso form
31. How to determine Whether
Molecules Are Enantiomers,
Diastereomers or Meso
Compounds ?
1- determine whether the chiral center
is R or S ( using the previous
explained method )
32. 2- Use the following table to determine
relationship.
33. 3- If the molecule have symmetry (same
substituents on both chiral centers ) ,
check for meso compound
only the R,S or S,R molecules can be
meso (the S,S and R,R forms of even
symmetric molecules are not meso
compounds, they are enantiomers).
35. Optical Activity
it is the ability of a chiral molecule to
rotate the plane of plane-polairsed
light, measured using a polarimeter.
A simple polarimeter consists of :
1- a light source
2- polarizing lens
3- sample tube
4- analyzing lens.
37. Polarimeter principle
light passes through a sample that can
rotate plane polarized light
the light appears to dim because it no
longer passes straight through the
polarizing filters.
The amount of rotation is quantified as the
number of degrees that the analyzing lens
must be rotated by so that it appears as if
no dimming of the light has occurred.
38. The rotation is affected by two factors :
1- path length (l, the time the light travels
through a sample)
2- concentration (c, how much of the
sample is present that will rotate the
light)
When these effects are eliminated a
standard for comparison of all molecules
is obtained, the specific rotation [ ]
39. the quantified rotation determined using
polarimeter is known as observed rotation
[ ] = 100 / c*l
concentration is expressed as: g sample /100ml solution
Enantiomers will rotate the plane of
polarisation in exactly equal amounts (same
magnitude) but in opposite directions.
Dextrorotary : d or (+), clockwise rotation
(to the right)
Levorotary : l or (-), anti-clockwise rotation
(to the left)
41. enantiomeric excess (ee%)
The optical purity or the enantiomeric excess (ee%) of a
sample can be determined as follows:
% enantiomeric excess = % enantiomer1 - % enantiomer2
= 100 [ ]mixture / [ ]pure sample
ee% = 100 ([major enantiomer] - [minor enantiomer]) /
([major enantiomer] + [minor enantiomer])
where
[major enantiomer] = concentration of the major
enantiomer
[minor enantiomer] = concentration of the minor
42. Example of optical activity
Consider that (S)-bromobutane has a specific
rotation of +23.1o and (R)-bromobutane has a
specific rotation of -23.1o
1- Determine the optical purity of a racemic
mixture.
Answer: The specific rotation, [ ], of the
racemate is expected to be 0, since the effect
of one enantiomer cancel the other .
Optical purity, % = 100 [ ]mixture / [ ]pure sample
= 100 (0) / +23.1o
= 0%
43. 2- Which isomer is dominant and what is the
optical purity of a mixture, of (R)- and (S)-
bromobutane, whose specific rotation was found
to be -9.2o?
Answer: The negative sign tells indicates that
the R enantiomer is the dominant one.
Optical purity, % = 100 [ ]mixture / [ ]pure sample
= 100 (-9.2) / -23.1o
= 40%
this indicates a 40% excess of R over S!
44. 3- What is the percent composition of
the mixture?
Answer:
The 60% leftover, which is optically
inactive, must be equal amounts of
both (R)- and (S)-bromobutane. The
excess 40% is all R so there is a total
of 70% (R) and 30% (S).
45. Newman projection
A representation of a molecule in which the
atoms and bonds are viewed along the axis
about which rotation occurs.
the molecule is viewed along an axis
containing two atoms bonded to each other
and the bond between them, about which the
molecule can rotate. Carbon-carbon bond
the "substituents" of each atom , can then be
viewed both in front of and behind the
carbon-carbon bond
46. Fischer Projection
representation of a 3D molecule as a
flat structure where a tetrahedral
carbon is represented as two crossed
lines.
the atoms that are pointed toward the
viewer would be specified with a
wedged
and the ones pointed away from the
viewer are specified with dashed
(4)
47. The Fischer Projection consists of :
1- horizontal lines represent the
wedged
2- vertical line represents the dashed .
The point of intersection between the
horizontal and vertical lines represents
the central carbon.
48. Fischer projection for structures
with more than one chiral center
In this case the tetrahedral carbons are
"stacked" on top of one another
The carbons are numbered from top
to bottom (starting with highly oxidized
carbon on he top )
49. Rotation of Fischer projection
Fischer Projection can be rotated by 180ᵒ
only!
(Rotation by 90 ° or -90 ° (270 °) invert
the stereochemistry) = change it from S
to R or from R to S
50. references
1- L. G. Wade Jr, Organic chemistry , 169-210
2- Ann Van Eeckhaut, Yvette Michotte,Chiral Separations by Capillary
Electrophoresis, pp 11
3- John Wiley & Sons, Organic Chemistry I For Dummies, pp 89
4- Shore, N. (2007). Study Guide and Solutions Manual for Organic
Chemistry (5th Ed.). New York: W.H. Freeman. (182-186)
5- INDAH PURNAMA SARYa,*, SISWANDONOb, TUTUK BUDIATIb
,International Journal of Pharmacy and Pharmaceutical Sciences ISSN-
0975-1491 ,Vol 7, Issue 3, 2015