1. Alkyl halides can undergo nucleophilic substitution or elimination reactions. Nucleophilic substitution reactions include SN2 and SN1 mechanisms, while elimination reactions include E1 and E2 mechanisms.
2. The type of reaction depends on factors like the structure of the alkyl halide, the nucleophile, the base, and the solvent. Primary alkyl halides favor SN2, while tertiary alkyl halides favor SN1 or E1/E2 in protic solvents.
3. The chapter examines these reaction mechanisms in detail to understand how they occur and how their characteristics can be used to predict and control reaction outcomes.
Pinacol pinacolone rearrangement involves conversion of 1,2 - diols to carbonyl compounds in presence of acid catalyst with change in carbon skeleton. It is an example of whitmore shift.
Pinacol pinacolone rearrangement involves conversion of 1,2 - diols to carbonyl compounds in presence of acid catalyst with change in carbon skeleton. It is an example of whitmore shift.
B.Pharm I Year II Sem. SN1 and SN2 reactions, kinetics, order of reactivity of alkyl halides, stereochemistry and rearrangement of carbocations.
SN1 versus SN2 reactions, Factors affecting SN1 and SN2 reactions.
Structure and uses of ethylchloride, Chloroform, trichloroethylene, tetrachloroethylene,
dichloromethane, tetrachloromethane and iodoform.
Alcohols, Qualitative tests for Alcohol, Structure and uses of Ethyl alcohol, chlorobutanol, Cetosterylalcohol, Benzyl alcohol, Glycerol, Propylene glycol
This is the contents of this presentation-
• The arenium ion mechanism,
• Orientation and reactivity,
• Energy profile diagrams.
• o/p ratio,
• Orientation in benzene ring with more than one substituent, orientation in other ring systems.
• ipso attack
• Diazonium coupling,
• Gatterman-Koch reaction,
• Reimer-Tiemann reaction,
• Pechman reaction,
• Houben –Hoesch reaction,
• Kolbe Schmitt reaction,
• Recapitulation of halogenation, nitration, sulphonation, and F.C. reaction.
(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.
Professional air quality monitoring systems provide immediate, on-site data for analysis, compliance, and decision-making.
Monitor common gases, weather parameters, particulates.
The increased availability of biomedical data, particularly in the public domain, offers the opportunity to better understand human health and to develop effective therapeutics for a wide range of unmet medical needs. However, data scientists remain stymied by the fact that data remain hard to find and to productively reuse because data and their metadata i) are wholly inaccessible, ii) are in non-standard or incompatible representations, iii) do not conform to community standards, and iv) have unclear or highly restricted terms and conditions that preclude legitimate reuse. These limitations require a rethink on data can be made machine and AI-ready - the key motivation behind the FAIR Guiding Principles. Concurrently, while recent efforts have explored the use of deep learning to fuse disparate data into predictive models for a wide range of biomedical applications, these models often fail even when the correct answer is already known, and fail to explain individual predictions in terms that data scientists can appreciate. These limitations suggest that new methods to produce practical artificial intelligence are still needed.
In this talk, I will discuss our work in (1) building an integrative knowledge infrastructure to prepare FAIR and "AI-ready" data and services along with (2) neurosymbolic AI methods to improve the quality of predictions and to generate plausible explanations. Attention is given to standards, platforms, and methods to wrangle knowledge into simple, but effective semantic and latent representations, and to make these available into standards-compliant and discoverable interfaces that can be used in model building, validation, and explanation. Our work, and those of others in the field, creates a baseline for building trustworthy and easy to deploy AI models in biomedicine.
Bio
Dr. Michel Dumontier is the Distinguished Professor of Data Science at Maastricht University, founder and executive director of the Institute of Data Science, and co-founder of the FAIR (Findable, Accessible, Interoperable and Reusable) data principles. His research explores socio-technological approaches for responsible discovery science, which includes collaborative multi-modal knowledge graphs, privacy-preserving distributed data mining, and AI methods for drug discovery and personalized medicine. His work is supported through the Dutch National Research Agenda, the Netherlands Organisation for Scientific Research, Horizon Europe, the European Open Science Cloud, the US National Institutes of Health, and a Marie-Curie Innovative Training Network. He is the editor-in-chief for the journal Data Science and is internationally recognized for his contributions in bioinformatics, biomedical informatics, and semantic technologies including ontologies and linked data.
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 .
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.
A brief information about the SCOP protein database used in bioinformatics.
The Structural Classification of Proteins (SCOP) database is a comprehensive and authoritative resource for the structural and evolutionary relationships of proteins. It provides a detailed and curated classification of protein structures, grouping them into families, superfamilies, and folds based on their structural and sequence similarities.
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.
THE IMPORTANCE OF MARTIAN ATMOSPHERE SAMPLE RETURN.
Chapter11
1. 11. Reactions of Alkyl Halides:
Nucleophilic Substitutions and
Eliminations
Based on McMurry’s Organic Chemistry, 7th
edition
2. Alkyl Halides React with
Nucleophiles and Bases
Alkyl halides are polarized at the carbon-halide bond,
making the carbon electrophilic
Nucleophiles will replace the halide in C-X bonds of
many alkyl halides(reaction as Lewis base)
Nucleophiles that are Brønsted bases produce
elimination
3. Why this Chapter?
Nucleophilic substitution, base induced
elimination are among most widely occurring
and versatile reaction types in organic
chemistry
Reactions will be examined closely to see:
- How they occur
- What their characteristics are
- How they can be used
4. 11.1 The Discovery of Nucleophilic Substitution
Reactions—Walden
The reactions alter the array
at the chirality center
The reactions involve
substitution at that center
Therefore, nucleophilic
substitution can invert the
configuration at a chirality
center
The presence of carboxyl
groups in malic acid led to
some dispute as to the
nature of the reactions in
Walden’s cycle
5. 11.2 The SN2 Reaction
Reaction is with inversion at reacting center (substrate)
Follows second order reaction kinetics
Ingold nomenclature to describe characteristic step:
S=substitution
N (subscript) = nucleophilic
2 = both nucleophile and substrate in characteristic
step (bimolecular)
Nucleophile Electrophile
Leaving Group
6. Reaction Kinetics
The study of rates of reactions is called kinetics
Rates decrease as concentrations decrease but the
rate constant does not
Rate units: [concentration]/time such as L/(mol x s)
The rate law is a result of the mechanism
The order of a reaction is sum of the exponents of the
concentrations in the rate law
A + B -----> C + D
Experimentally determine the effect of increasing A/B
First Order: rate = k[A] (only depends on [A], not [B])
Second Order: rate = k[A][B] (depends on both [A],[B])
Third order: rate = k[A]2
[B]
7. SN2 Process
The reaction involves a transition state in which both
reactants are together
Rate = k[ROTs][OAc]
NucleophileElectrophile
Leaving Group
8. SN2 Transition State
The transition state of an SN2 reaction has a planar arrangement of the
carbon atom and the remaining three groups
9. 11.3 Characteristics of the SN2
Reaction
Occurs with inversion of chiral
center
Sensitive to steric effects
Methyl halides are most
reactive
Primary are next most reactive
Secondary might react
Tertiary are unreactive by this
path
No reaction at C=C (vinyl
halides)
10. Steric Effects on SN2 Reactions
The carbon atom in (a) bromomethane is readily accessible
resulting in a fast SN2 reaction. The carbon atoms in (b) bromoethane
(primary), (c) 2-bromopropane (secondary), and (d) 2-bromo-2-
methylpropane (tertiary) are successively more hindered, resulting in
successively slower SN2 reactions.
11. Order of Reactivity in SN2
The more alkyl groups connected to the reacting
carbon, the slower the reaction
12. The Nucleophile
Neutral or negatively charged Lewis base
Reaction increases coordination at nucleophile
Neutral nucleophile acquires positive charge
Anionic nucleophile becomes neutral
13. Relative Reactivity of Nucleophiles
Depends on reaction and conditions
More basic nucleophiles react faster
Better nucleophiles are lower in a column of the periodic table
Anions are usually more reactive than neutrals
14. The Leaving Group
A good leaving group reduces the barrier to a reaction
Stable anions that are weak bases are usually excellent
leaving groups and can delocalize charge
15. Poor Leaving Groups
If a group is very basic or very small, it prevents reaction
Alkyl fluorides, alcohols, ethers, and amines do not typically
undergo SN2 reactions.
Poor Leaving groups can be made into good leaving groups
“Tosyl chloride”
16. The Solvent
Solvents that can donate hydrogen bonds (-OH or –NH) slow SN2
reactions by associating with reactants
Energy is required to break interactions between reactant and solvent
Polar aprotic solvents (no NH, OH, SH) form weaker interactions with
substrate and permit faster reaction
S
O
CH3H3C
DMSO
Dimethyl Sulfoxide
P
O
(H3C)2N
N(CH3)2
N(CH3)2
HMPA
Hexamethylphosphoramide
C
O
CH3H3C
Acetone
C
O
HN
H3C
CH3
DMF
Dimethylformamide
17. 11.4 The SN1 Reaction
Tertiary alkyl halides react rapidly in protic solvents by a
mechanism that involves departure of the leaving group
prior to addition of the nucleophile
Called an SN1 reaction – occurs in two distinct steps while
SN2 occurs with both events in same step
If nucleophile is present in reasonable concentration (or it
is the solvent), then ionization is the slowest step
18. SN1 Energy Diagram and Mechanism
Rate-determining step is
formation of carbocation
rate = k[RX]
19. Stereochemistry of SN1
Reaction
The planar
intermediate
leads to loss of
chirality
A free
carbocation is
achiral
Product is
racemic or has
some inversion
20. SN1 in Reality
Carbocation is biased to react on side opposite leaving group
Suggests reaction occurs with carbocation loosely associated
with leaving group during nucleophilic addition (Ion Pair)
Alternative that SN2 is also occurring is unlikely
21. 11.5 Characteristics of the SN1 Reaction
Substrate
Tertiary alkyl halide is most reactive by this mechanism
Controlled by stability of carbocation
Remember Hammond postulate,”Any factor that stabilizes a high-
energy intermediate stabilizes transition state leading to that
intermediate”
Allylic and benzylic intermediates stabilized by delocalization of charge
Primary allylic and benzylic are also more reactive in the SN2
mechanism
22. Effect of Leaving Group on SN1
Critically dependent on leaving
group
Reactivity: the larger
halides ions are better
leaving groups
In acid, OH of an alcohol is
protonated and leaving group
is H2O, which is still less
reactive than halide
p-Toluensulfonate (TosO-
) is
excellent leaving group
23. Nucleophiles in SN1
Since nucleophilic addition occurs after
formation of carbocation, reaction rate is not
normally affected by nature or concentration
of nucleophile
24. Solvent in SN1
Stabilizing carbocation also stabilizes associated transition
state and controls rate
Protic solvents favoring the SN1 reaction are due largely to
stabilization of the transition state
Protic solvents disfavor the SN2 reaction by stabilizing the
ground state
Polar, protic and unreactive Lewis base solvents facilitate
formation of R+
25. 11.7 Elimination Reactions of
Alkyl Halides: Zaitsev’s Rule
Elimination is an alternative pathway to substitution
Opposite of addition
Generates an alkene
Can compete with substitution and decrease yield,
especially for SN1 processes
26. Zaitsev’s Rule for Elimination Reactions
In the elimination of HX from an alkyl halide, the more
highly substituted alkene product predominates
Mechanisms of Elimination Reactions
E1: X-
leaves first to generate a carbocation
a base abstracts a proton from the carbocation
E2: Concerted transfer of a proton to a base and
departure of leaving group
27. 11.8 The E2 Reaction
A proton is
transferred to base
as leaving group
begins to depart
Transition state
combines leaving of
X and transfer of H
Product alkene forms
stereospecifically
Rate = k[RX][B]
28. Geometry of Elimination – E2
Syn arrangement requires eclipsed conformation = disfavored
Anti arrangement allows orbital overlap and minimizes steric interactions
Overlap of the developing π orbital in the transition state requires
periplanar geometry, anti arrangement
29. Predicting Product
E2 is stereospecific
Meso-1,2-dibromo-1,2-diphenylethane with base gives cis-1,2-diphenyl
RR or SS 1,2-dibromo-1,2-diphenylethane gives trans 1,2-diphenyl
30. E2 Reactions and Cyclohexene Formation
Abstracted proton and leaving group should align trans-diaxial
to be anti periplanar (app) in approaching transition state
Equatorial groups are not in proper alignment
31.
32. 11.10 The E1 Reaction
Competes with SN1 and E2 at 3° centers
Rarely have “clean” SN2 or E1 single products
Rate = k [RX], same as SN1
33. Comparing E1 and E2
Strong base is needed for E2 but not for E1
E2 is stereospecifc, E1 is not
E1 gives Zaitsev orientation
34. E1cB Reaction
Takes place through a carbanion intermediate
Common with very poor leaving group (OH-)
HO-C-C=O fragment often involved
35. Summary of Reactivity: SN2, SN1, E1, E2
Alkyl halides undergo different reactions in competition, depending on
the reacting molecule and the conditions
Based on patterns, we can predict likely outcomes
Primary Haloalkanes
SN2 with any fairly good nucleophile
E2 only if Bulky, strong base
Secondary Haloalkanes
SN2 with good nucleophiles, weak base, Polar Aprotic Solvent
SN1/E1 with good LG, weak Nu, Polar Protic Solvent
E2 with strong base
Tertiary Haloalkane
SN1/E1 with good LG, no base (solvolysis)
E2 with strong base
Good L.G.
2o
alkyl halide
Poor Nucleophile
Polar Protic Solvent
SN1 and E1 products