reflection 1

Using robust details and ample evidence, create a reflection essay that describes 4 learning objectives you met while performing this experiment. View the learning objectives from the lab manual provided and select four to focus your writing on.

 
Virtual Lab Manual
Nucleophilic Substitution
Reaction: Alkyl halide Substrate
Synopsis
If reactions were flavors – substitution would be tutti-frutti! In this simulation, you will
explore the factors that affect substitution reactions and learn how to promote different
mechanisms of substitution. Put your substitution expertise to the test by using
retrosynthesis and reaction design principles to create an assortment of aroma molecules
in developing exciting new beverage flavors for a craft brewery!
Flavor chemistry saves the day
Help Corey the microbrewery barista attract more customers by designing flavor molecules
in the brew lab. Students will get hands-on in learning about substitution – getting
immersed in the mechanisms, exploring the factors that affect different types of
substitution and how it relates to changes in reaction energy profiles. In order to design
their own substitution reactions, students will first develop their theoretical and
mechanistic understanding and apply this to practical experimental design.
Exploring substitution mechanisms
Interact with both SN2 and SN1 reactions at a molecular level with our 3D reaction
visualizer. Identify the reactive components in substitution reactions, trigger the reaction
and replay or rewind at your leisure to spot the mechanistic differences. Be immersed in
the mechanistic principles to help lock in molecular-level reactivity concepts and
considerations.
Investigate substitution variable factors
Become acquainted with the factors that can affect substitution – and develop your SN2
versus SN1 prediction skills. Investigate why the selection of solvent, leaving groups and
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substrate size can either promote or prevent substitution. You’ll get to know superstar
substrates – the alkyl halides – and their reactivity preferences in substitution reactions.
Delving into reaction energy diagrams along the way, you’ll probe and predict the effect of
changing these factors to find the energetically most favorable reaction conditions.
Substitution: Synthesis design!
To successfully complete the mission, you’ll select the necessary chemical ingredients to
synthesize five flavor molecules using substitution. Can you mix and match alkyl halides,
nucleophiles and solvents to come up with the perfect recipe for each unique flavor?
Learning Objectives
At the end of this simulation, you will be able to…
● Demonstrate a detailed understanding of nucleophilic substitution reactions, both SN1
and SN2 and explain the difference between them
● Draw the mechanisms of both the SN1 and SN2 nucleophilic substitution reactions
● Describe the variables in substitution reactions and the effects of changing substrate
(steric effects), solvent, nucleophile, and leaving group
● Consider the stereochemistry of the product to determine the likely reaction
mechanism
● Describe the reactive properties of the alkyl halide group
Techniques in Lab
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Retrosynthesis
Reaction energy diagrams
Theory
Substitution Reactions
A substitution reaction is any reaction in which an atom, ion or functional group in a
molecule is substituted by another atom, ion or group. An example is the reaction in which
the bromine atom in a bromomethane molecule is displaced by a hydroxide ion, forming
methanol.
Figure 1: Example of a substitution reaction
Organic compounds with good leaving groups, such as alkyl halides, serve as excellent
starting materials for substitution reactions.
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Depending on the type of atom or group that acts as a substituent, substitution reactions
generally fall into three classes:
● Nucleophilic substitution where a nucleophile – or electron-pair donor – reacts with
an electron-deficient atom to eject a leaving group.
● Electrophilic substitution reactions see an electrophile displace a functional group.
Hydrogen atoms typically act as the electrophile – but not always.
● Radical substitution is a substitution reaction that involves free radicals as reactive
intermediates.
Reaction terminology
Here is a list of terms used in the description of chemical reactions, along with an
explanation of their correct uses.
● Catalyst
A catalyst is a component in a chemical reaction, which increases the reaction rate
by changing the reaction mechanism. A catalyst is not used in the reaction and thus
is often effective in sub-stoichiometric amounts.
● Curly arrow
A curly arrow is a special type of arrow used to denote the movements of the
electrons when describing the reaction mechanism of a chemical reaction.
● Electrophile
An electrophile is a species which will accept donation of electrons to create a new
bond.
● Intermediate
An intermediate, or more precisely a reaction intermediate, is a chemical species
which is formed from the reactants but continues to react to form the product(s) or
other intermediates. Reactions that contain more than one step will also have
reaction intermediates. A reaction intermediate represents a local minimum on a
reaction energy diagram.
● Leaving group
A leaving group is a part of a molecule which breaks away from the substrate during
the reaction, taking with it the electron pair that made up the bond which is being
broken.
● Lone-pair
A lone-pair is a pair of valence electrons which do not partake in bonding.
● Nucleophile
A nucleophile is a chemical species which will donate electrons to an electrophile to
form a new bond during a chemical reaction.
● Product
A product is the outcome of a chemical reaction.
● Reactant
A reactant is the species that is transformed into the product in a chemical reaction.
A reactant is also referred to as a substrate.
● Reaction conditions
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The reaction conditions of a reaction include factors like: The temperature at which
the reaction should occur; if any particular atmosphere should be used (for example
Argon or Nitrogen for air-free conditions); the pressure the reaction should run at (if
different from atmospheric pressure); the stirring speed (if important); the reaction
time.
Reagent
A reagent is a substance added to a reaction to cause the chemical transformation
of the reactant(s) to occur, or to test for the presence of a particular compound. A
reagent is consumed during the cause of the reaction, in opposition to a catalyst,
which is not consumed.
Solvent
A solvent is a chemical substance that dissolved a compound, which is then the
solute. A solvent is usually a liquid, but can also be a gas or a supercritical fluid.
Solvents usually do not partake in a chemical reaction.
Substrate
A substrate is a chemical species that is consumed during a chemical reaction to
give a product. A substrate can also be referred to as a reactant; however, in
catalytic reactions substrate is the correct term.
Transition state
The transition state of a chemical reaction represents the highest energy point on
the path from reactants to products. A transition state is not a stable species and
cannot be isolated. A transition state should not be confused with an intermediate!
Correct use of certain terms:
One or more reactants (also referred to as the substrate), dissolved in a solvent, are
transformed into products, either spontaneously or through the action of a reagent or
a catalyst. If the reaction has multiple steps, then intermediates will form after each
step, except for the last one which forms the final product. Every reaction step passes
through a transition state, which represents the highest energy point on the path from
reactants to products.
Overview of common functional groups
This image provides you with an overview of the most common functional groups in organic
chemistry. You can read more about each of the functional groups below the image.
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Alkane: A hydrocarbon that has no functional groups. Alkanes are named with the
suffix -ane, e.g. butane.
Alkene: A hydrocarbon that has at least one C-C double bond. The double bond is
nucleophilic, which makes the alkenes substrates in electrophilic addition reactions.
Alkenes are named with the suffix -ene, e.g. butene.
Alkyne: A hydrocarbon that has at least one C-C triple bond. The triple bond is
nucleophilic, which makes the alkynes substrates for electrophilic addition
reactions. If the alkyne is terminal, the proton is slightly acidic and acetylide anions
can be formed. Alkynes are named with the suffix -yne, e.g. butyne.
Arene: Also called aromatics, are hydrocarbons that contain at least one phenyl
group. Aromatic rings have a high electron density and are nucleophilic, which makes
them substrates for electrophilic aromatic substitution. Aromatics can contain other
functional groups and are named with the prefix phenyl- or with the suffix -benzene,
e.g. phenylamine and chlorobenzene.
Haloalkane: A compound that contains a halogen (main group VII in the periodic
table) substituent. The halogens are more electronegative than carbon, and are good
leaving groups, making haloalkanes good substrates for SN1/SN2 and E1/E2 reactions.
Haloalkanes are named with the prefix halo-, e.g. bromobutane.
Aldehyde: A compound that contains a C-O double bond, where one of the
substituents on the carbon atom is a hydrogen atom and the other is a carbon atom.
The C=O bond is polarized towards oxygen, making the carbon atom electrophilic
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and thus aldehydes are substrates for nucleophilic addition reactions. Aldehydes are
named with the suffix -al, e.g. butanal.
Ketone: A compound that contains a C-O double bond, where both of the
substituents on the carbon atom are carbon atoms. The C=O bond is polarized
towards oxygen, making the carbon atom electrophilic and thus ketones are
substrates for nucleophilic addition reactions. Ketones are named with the
suffix -one, e.g. butanone.
Alcohol: A compound with a hydroxy (-OH) substituent to saturated carbon. Alcohols
can be deprotonated to create a good nucleophile, or protonated to transform the
-OH into a good leaving group (OH2), thereby making the alcohols suitable substrates
for SN1/SN2 and E1/E2 reactions. Alcohols are named with the suffix -ol, e.g. butanol.
Note that a hydroxy (-OH) group on an aromatic ring yields the functional
group phenol, which has slightly different reaction properties.
Ether: A compound that contains a C-O-C bond. Ethers are generally not very
reactive and are often used as solvents. Ethers are named with the suffix ether,
e.g. diethyl ether.
Amine: A compound that contains an amino substituent. The amine can be primary
(R-NH2), secondary (R-NHR’) or tertiary (R-NR’R”). Amines are alkaline and often used
as bases or nucleophiles. Amines are named with the suffix amine, e.g. triethyl
amine.
Carboxylic acid: A compound with a -COOH substituent. Carboxylic acids and their
derivatives (below) can be transformed into each other through nucleophilic
substitution reactions. Carboxylic acids are named with the suffix -oic acid,
e.g. butanoic acid.
Acid anhydride: A compound with a -COOCO- component. Acid anhydrides are
derivatives of carboxylic acids, structurally resembling two carboxylic acids that have
been merged with the elimination of a water molecule. Acid anhydrides are named
with the suffix -oic anhydride, e.g. butanoic anhydride.
Ester: A compound with a -COOR substituent. Esters are derivatives of carboxylic
acids, structurally resembling a carboxylic acid that has been merged with an
alcohol by the elimination of a water molecule. Esters are named with -yl -oate,
e.g. butyl butanoate.
Amide: A compound with a -CONHR substituent. Amides are derivatives of carboxylic
acids, structurally resembling a carboxylic acid that has been merged with an amine
by the elimination of a water molecule. Amides are named with the suffix amide,
e.g. butanamide.
Acyl halide: A compound with a -COX substituent, where the X is a halogen. Acid
halides are derivatives of carboxylic acids, where the hydroxy substituent has been
replaced with a halogen atom. Acyl halides are named with the suffix -oyl halide,
e.g. butanoyl chloride.
Stereochemistry
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Stereochemistry relates to the three-dimensional arrangement of atoms and molecules and
the effect of this spatial arrangement on chemical reactions. Stereoselectivity is the
preference for a reaction to occur on one molecular face over another, resulting in the
preferential formation of one stereoisomer. If there’s more than one stereoisomer possible
from a reaction, and the configuration of at least one chemical bond is not known, that
bond can be represented with a wavy bond.
Figure 2: Stereoselectivity in bromide ion addition to a carbocation. Note the solid and
hashed wedged bonds.
A reaction is said to be stereoselective if the reaction mechanism selects the formation of
one stereoisomer over the other. In contrast, a stereospecific reaction is a reaction which
only allows the formation of one stereoisomer (e.g. the stereochemistry is already set by
the starting material).
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Virtual Lab Manual
Electrophilic Addition: Explore
Reactions of Hydrocarbons
Synopsis
Buckle up for a chemistry journey a billion kilometers away! In the Electrophilic Addition
simulation, you will identify some natural hydrocarbon resources on Saturn’s moon, Titan,
and explore their most significant reactions. Hydrocarbons may be the simplest organic
molecules – but they provide great building blocks for chemical synthesis!
Investigate hydrocarbons on Titan
Join Dr. Smith in the Titan lab to begin identifying hydrocarbons that could be used to
synthesize more complex substances and materials. Discover which hydrocarbons and
reactions are the most synthetically useful for our colonization mission. We’ll delve deeper
into understanding the electrophilic addition reaction and its wide-ranging applications.
Perform and visualize addition reactions
Be immersed at a molecular level in our 3D reaction visualizer. There you’ll engage
interactively with the reaction components and carry out the electrophilic addition reaction
mechanism in 3D. Get better acquainted with reaction principles and selectivity and see the
reaction happen before your very eyes!
In our lab, you’ll perform the bromine test for hydrocarbon unsaturation on Titan samples
before carrying out investigative electrophilic addition reactions in the fume hood. Find the
equipment you need to perform electrophilic addition reactions on two alkene isomers
simultaneously and use your knowledge to predict the products. With replenishing pipettes
and the option to reset – there are opportunities to repeat experimental steps quickly in
our virtual lab!
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Explore selectivity – and the colony
At the end, you will analyze the results of your electrophilic addition experiments and
investigate possible products in our 3D molecular visualizer. Will you be able to identify and
synthesize hydrocarbon materials that we can use to build a colony?
Learning Objectives
At the end of this simulation, you will be able to…
● Describe the reactions of simple alkanes, alkenes and alkynes
● Describe the reaction of simple alkenes with electrophiles
● Demonstrate a detailed mechanistic understanding of addition reactions
● Predict which way an electrophile will add to an alkene using Markovnikov’s Rule and
an understanding of carbocation stability
● Predict the major product of the main different types of addition reactions
Techniques in Lab
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Bromine Test
GC data analysis
Gas-liquid reaction
Theory
Hydrocarbons
Hydrocarbons are a subgroup of organic compounds, which contain only carbon and
hydrogen. Examples of hydrocarbons can be seen in Figure 1. Salicylic acid, shown in Figure 2,
is an organic compound, but it’s not a hydrocarbon as it contains oxygen groups.
Figure 1: Structure of the hydrocarbons methane, propane, and 1-butene.
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Figure 2: Structure of salicylic acid.
Bromine test
The bromine test is used to test for an unsaturated carbon carbon bond, such as an alkene
or alkyne. The test uses a type of chemical reaction called addition, where a reactant, here
bromine, is added to an organic compound to break a double or triple bond.
For example the addition of bromine to but-2-ene:
Bromine has an orange-brownish color when in solution, so the color of the solution is lost
when an alkene or alkyne is present for bromine to react with. Bromine will also react with
aromatic compounds, such as phenol, but it can’t react with alkanes as they contain only
single bonds, and therefore there is no color change when these are mixed. Benzene can
react with bromine in the presence of a catalyst, but not without a catalyst since it is not
reactive enough. Phenol is more reactive than benzene so can react with bromine without a
catalyst. This is because the alcohol group donates electron density into the delocalized
benzene ring.
Materials
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Test tubes
Test tube rack
Carbon tetrachloride
Chloroform
Bromine water
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Compound to be tested
Safety information
Bromine is corrosive, toxic, and an environmental hazard. Bromine causes eye and skin burns,
as well as digestive and respiratory tract burns. It may be fatal if inhaled and is a strong
oxidizer. Contact with other material may cause a fire. Corrosive to metal. Carbon
tetrachloride is toxic. Chloroform is harmful. This test should be performed at room
temperature.
Procedure
1.
Dissolve 0.1 g or 5 drops of organic compound in 2 mL of carbon tetrachloride. If you
do not have carbon tetrachloride, a solvent such as chloroform or water can be used
to dissolve the organic compound.
2. Add 2% solution of bromine water drop by drop with continuous shaking.
3. If the bromine solution becomes colorless then there is an unsaturated carbon carbon
bond in the organic compound. This test should be confirmed with the baeyers test.
Electrophilic Addition Reaction
An addition reaction is an organic reaction where two or more molecules combine to form
a larger molecule as the only product. The electrophilic addition reaction is the most
common reaction of C-C multiple bonds. The C-C double bond is a region of high electron
density making it nucleophilic in nature which can make it susceptible to attack
from electrophiles. Electrophilic addition reactions are typical of unsaturated organic
compounds e.g. alkenes (which contain a C-C double bond) or alkynes (which contain a C-C
triple bond).
Figure 4: General addition reaction scheme
The reaction is driven by the conversion of the weaker pi bond (C=C) into two new stronger
sigma bonds. Conceptually, addition is the reverse of elimination which can be used to
prepare alkenes.
A wide variety of reagents can undergo addition reactions to provide a diversity of chemical
products. There are 3 factors that could potentially influence the outcome of an addition
reaction:
1. Overall functional group conversion (e.g. C=C to new functional group)
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2. Regioselectivity – if the two atoms that add to C=C are different
3. Stereochemistry – if the two atoms that add to C=C are different
Chromatography
Chromatography is a technique used for the separation of a mixture by passing it through a
medium in which the mixture components move at different rates.
The word chromatography comes from the Greek words chroma, which means color,
and graphos, which means to draw. This name was chosen by the Russian botanist, Tswett.
He separated different pigments from a plant extract by loading a sample mixture onto a
calcium carbonate column.
Figure 5: Tswett’s method of separating a mixture of pigments from a plant extract.
By passing solvent (a mobile phase) through the column (stationary phase) the different
components of the sample moved at different rates down the column due to their
chemical and physical properties. As a result, Tswett separated and collected each of the
three dye molecules that make up chlorophyll and developed a now widely used and
versatile technique. It’s now widely used as a purification or analytical technique in
chemistry.
How to draw reaction mechanisms
Reaction mechanisms are drawn using curly arrows to denote the movement of the
electrons in each step of the reaction. It is very important that the arrow starts where the
electrons are and points towards where the electrons go. A curly arrow with
a whole arrowhead represents the movement of an electron pair, whereas a curly arrow
with a half arrowhead represents the movement of a single electron, typically in a radical
reaction. The two types of curly arrows are shown in figure 6.
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Figure 6: The curly arrow with a whole arrowhead (left) represents the movement of an
electron pair.
The curly arrow with half an arrowhead (right) represents the movement of a single
electron.
Overall there are three different types of curly arrows:
● Arrows that break bonds. The arrow root is drawn to begin in the bond which is
broken. The arrowhead points to the atom or part of the molecule which will accept
the electron pair from the bond. In the example below, a bromine atom breaks away
from tert-butyl bromide. The electrons that made up that bond leaves with the
bromine atom, creating a negatively charged bromine ion and a carbocation.
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Arrows that make bonds. The arrow root is drawn to begin in the lone-pair or the
negative charge of the nucleophile which will attack. The arrowhead is drawn to
point at the electrophile where the nucleophile will attack or the new bond which
will be formed as a result of the reaction. In the example below, a lone-pair on the
oxygen atom of a water molecule attacks the electrophilic carbon atom of the
carbocation. The result is a protonated tertiary alcohol.
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Arrows that make and break bonds at the same time. The arrows root is drawn to
begin in the bond which is being broken and the arrowhead is drawn to point at the
electrophile where the nucleophile will attack or the new bond which will be formed.
In the example below, the bond between the carbon and hydrogen is being broken,
and the electrons from that bond are used to create a new bond between that same
carbon atom and the positively charged carbon atom. The result is an alkene and a
proton.
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Notice that for all the reaction mechanisms drawn, charge is conserved, just as when
writing reaction schemes. Drawing reaction mechanisms is an accounting system, so no
electrons or charges can suddenly appear or disappear.
Regioselectivity
The term regioselective can be used to describe any process that favors bond formation at
a particular atom over other possible atoms. The ‘Regio-’ prefix comes from the Latin for
‘Region’ or an area of something.
A reaction can be said to have high regioselectivity when one major product dominates due
to the reaction being highly favored at one atomic position over another.
In the addition reaction example below the preferential formation of a stable tertiary
carbocation at the 2-position results in the reaction proceeding to give 2-Chlorobutane as
the major product.
Figure 7: Regioselectivity in the hydrochlorination of but-1-ene.
Stereochemistry
Stereochemistry relates to the three-dimensional arrangement of atoms and molecules and
the effect of this spatial arrangement on chemical reactions. Stereoselectivity is the
preference for a reaction to occur on one molecular face over another, resulting in the
preferential formation of one stereoisomer. If there’s more than one stereoisomer possible
from a reaction, and the configuration of at least one chemical bond is not known, that
bond can be represented with a wavy bond.
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Figure 8: Stereoselectivity in bromide ion addition to a carbocation. Note the solid and
hashed wedged bonds.
A reaction is said to be stereoselective if the reaction mechanism selects the formation of
one stereoisomer over the other. In contrast, a stereospecific reaction is a reaction which
only allows the formation of one stereoisomer (e.g. the stereochemistry is already set by
the starting material).
Titan – a hydrocarbon world
Titan is Saturn’s largest moon and is the only moon in our Solar System known to have a
dense atmosphere. It’s also the only other place in the Universe where clear evidence of
stable bodies of surface liquid has been found. This makes it one of the most interesting
locations to explore chemistry in space.
Figure 9: Titan appears orange due to its thick organonitrogen atmosphere. Image Courtesy
of NASA JPL-Caltech
Titan has an Earth-like methane cycle where methane clouds form rain and even produce
storms on the surface of the moon. The Cassini-Huygens mission gave us a closer look at
Titan and its chemistry – detecting the presence of an organonitrogen surface haze and
liquid hydrocarbon seas. Data also suggested the possible presence of cryovolcanoes that
erupt cold liquid methane or ammonia!
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Titan’s upper atmosphere is rich with methane and nitrogen. When exposed to sunlight or
highly energetic particles these small molecules are broken into ions and electrons. These
charged species trigger a cascade of chemical reactions that produce a diverse range of
hydrocarbons and other organic molecules. Data from the Cassini-Huygens mission
detected not only alkanes, alkenes and alkynes in Titan’s atmosphere but complex
polycyclic aromatic hydrocarbons. This demonstrates an evolution of chemical processes as
the compounds generated in upper atmospheric levels fall closer to Titan’s surface.
Scientists believe that the heaviest of these molecules fall to Titan’s surface. These organic
compounds eventually end up in the sea whether they fall there directly from the air, via
hydrocarbon rain or transportation by rivers. A recent study adds evidence that Titan’s large
seas consist of pure methane and is likely to have a seabed of organic compounds.
Compounds that are insoluble in the methane sea, such as benzene or nitrile compounds,
sink to the seafloor to create a thick hydrocarbon sludge.
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