CHE 233 LAB

Percent yield

(Actual yield)/(theoretical yield) x100

In this (second) experiment, you will be recording IR spectra of 6,13-pentacenequinone and 6,13-dihexynylpentacene. Match the following functional groups with the approximate wavenumbers (cm-1) that you expect to see in the spectra. C = O ? C (triple bond) C ?

-- 1650-1780 -- 2100 - 2260

In the lactase encapsulation of macrocapsule part of the experiment, if the final maximum concentration of glucose was 0.00132 g/mL. Calculate the concentration of lactose in the volume of milk used in mg/dL. Show all calculation.

-1 glucose = 1 lactose - Convert to mg/dL -Divide by molar mass of glucose and multiply by molar mass of lactose

Chiral centers

-4 different groups attached to central C -not mirror superimposable -clockwise: R -counterclockwise: S

________ is used in experiment 3 as a coupling agent to bring about the formation of an amide (or peptide) bond that links two amino acids

Carbodiimide

At 4.33 ppm and 4.52 ppm on NMR it represents

Carbons adjacent to electronegative nitrogen (downfield) CH groups Multiplet for both Integration =1, makes sense bc only one H on the carbons in product

In the biodiesel experiment, the NaOCH3 serves as the ...

Catalyst

What is used as the solvent to develop the chromatographs in experiment 3?

Chloroform (CHCl3)

What are common impurities that you might see in your NMR spectrum? What are the chemical shifts for those impurities in your NMR spectrum?

Common impurities that I might see in my NMR spectrum include acetone, water, dichloromethane, methanol, and chloroform. I saw three impurities: methanol, chloroform, and the starting materials. Methanol has a chemical shift of 3.49 ppm. Chloroform has a chemical shift of 7.26ppm. Another common impurity was from the starting materials in triglyceride: the chemical shift is 4.15 and 4.3 ppm.

Amide bonds are formed by

Condensation of carboxylic acid and amine groups with elimination of water

What is the purpose of adding congo red?

Congo red is a pH indicator and helps visualize macrocapsules.

What is the limiting reagent?

Convert both reagents to moles of product. Pick smaller number (limiting)

Mixture of products are formed due to

Cross coupled condensation reactions

Alginate is particularly useful because it is easy to

Cross-link

In alginate, the more sodium atoms replaced by calcium, the more highly...

Cross-linked (dense, insoluble, strong) the polymer becomes

Assertion: Sodium alginate is insoluble in water Reason: Ionic salts are soluble in water A) Both the assertion and the reason are correct statements, and the reason is the correct explanation of the assertion B) Both the assertion and the reason are correct statements, but the reason is not the correct explanation of the assertion C) The assertion is correct, but the reason is an incorrect statement D) The assertion is wrong, but the reason is a correct statement E) Both the assertion and reason are incorrect statements

D

What is the difference between D-glyceraldehyde and L-glyceraldehyde

D — hydroxyl group at the stereogenic center is on the right L — hydroxyl group at the stereogenic center is on the left

Alginic acid is a block co-polymer of modified forms of the 2 carbohydrates:

D-Mannose and L-Gulose

Alginic acid is a block co-polymer of modified forms of two carbohydrates :

D-Mannose and L-Gulose

Hydrolysis of lactose yields

D-galactose and D-glucose

At 5.3 ppm on NMR it represents

DCM used to run reaction in (solvent)

Why use several solvents for workup? Experiment 3

HCl washing — remove unreacted amine (DMAP starting materials) NaHCO3 washing — remove unreacted acid (starting material) Water washing — to remove urea, any other salts (byproducts after the rxn) Brine washing — remove any water left in organic layer

HOMO vs LUMO

HOMO — highest occupied molecular orbital LUMO — lowest unoccupied molecular orbital

The elimination of water during the aldol condensation is named a(n) __________________ type elimination.

E1CB (elimination unimolar conjugate base)

The elimination step of the aldol condensation reaction is an example of:

E1cB

In the Aldol condensation reaction, the elimination that results in dehydration, proceeds via

E1cB mechanism

Since hydroxide is a poor leaving group in Aldol condensation, the elimination proceeds

E1cB mechanism

E1cB stands for

Elimination, unimolecular, conjugate base

Percent yield calculation

Experimental/theoretical x100

The top layer contains ______ with some ______ and the bottom layer (more viscous) contains _______

FAMEs; MeOH; glycerol

The triglycerides/ oils used in this experiment have variable solubility in methanol depending on the composition of oil. The products, ______ and _______, do not mix to a great extent, enabling phase separation. Since glycerol is much more soluble in _______ than the FAMEs, the top layer is rich in ______ and the bottom layer has the more dense _______.

FAMEs; glycerol; methanol FAMEs; glycerol

True or false: TLC was used in biodiesel experiment for monitoring progress of reaction because Boc-Phe is aromatic and UV active

False, it would be true if it said "dipeptide experiment"

True or false: the mobile phase used during the TLC analysis of dipeptide experiment was silica gel

False, stationary = silica gel and mobile = DCM solvent

Typical current carriers in organic semiconductors are ...

Holes (positively charge molecules) and electrons in pi-bonds

What type of reaction is the conversion of vegetable oils to FAMEs? Which base was used for this experiment?

Base-catalyzed transesterification with methanol is the reaction used to convert vegetable oils into FAMEs. Sodium methoxide was the base used for this experiment.

What happens when electrons absorb energy

Larger the energy jump, the lower the wavelength of light absorbed

What is the difference between saturated and unsaturated fatty acids?

Saturated fatty acids do not have carbon-carbon double bonds. Unsaturated fatty acids have one or more carbon-carbon double bonds.

What is used to monitor reaction progress in experiment 3?

TLC — thin layer chromatography —under UV lamp, depending on eluent, TLC will show all the spots that are UV active

True or false? If unprotected amino acids are used for dipeptide formation, there is a possibility of formation of mixture of products instead of a single product due to cross coupled condensation reactions.

TRUE

What are fatty acids? What are FAMEs?

Fatty acids are carboxylic acids with long non polar hydrocarbon groups around 8-18 carbons long. FAMEs are long-chain fatty acid methyl esters produced through the transesterification of oils containing methanol.

Where is FAMEs, Glycerol, deuterated chloroform, methanol, and pipets disposed of in the first experiment?

First 4 — organic liquid hazardous chemical waste Piept — broken glass waste container

What is on the bottom of the rxn mixture?

Glycerol

Which amino acid does not have a chiral center

Glycine

Disaccaharides have _____ linkages. What do they do?

Glycosidic linkages; a covalent bond joining carbohydrate with another group

Coupling constant _____ = space between coupled peaks, depends on number of interfering bonds

H

N-protected amino acid used in this experiment

H

At 5.0 ppm and 6.40 ppm on NMR it represents

H connected to N NH Integration = 1, which makes sense bc NH Doublet

We will use ______ spectrum to analyze the FAMEs produced

H-NMR

How is the product characterized in experiment 3?

H-NMR spectroscopy

Determining color change in acid and base conditions for capsules

You will take 10 capsules and put them in 2 ml 0.1 M HCl and record your observations. Then you will filter and wash them with DI water and place them into 2ml 1M NaOH and record your observations.

Technical definition of biodiesel

a fuel comprising long-chain fatty acid methyl esters (FAMEs) derived from vegetable oils or animal fats, designated B100 and meeting standard requirements.

percent yield

actual yield/theoretical yield x 100

A more typical type of co-polymer comprised of different segment of random lengths of monomer "A" and monomer "B", alternating along the polymer chain is an [Blank 1] co-polymer.

alternating block

A more typical type of co-polymer is ...

alternating block, which is comprised of different segment of random lengths of monomer "A" and monomer "B", alternating along the polymer chain

where would HCl be disposed of?

aqueous liquid hazardous chemical waste container

where would brine solution be disposed of?

aqueous liquid hazardous chemical waste container

where would you dispose of the liquid waste after filtration of the macrocapsules?

aqueous liquid hazardous chemical waste container

Cross-linking significantly reduces the

the solubility of a polymer - highly cross-linked polymers are almost impossible to dissolve in any solvent

The properities of polymers are determined by...

the various functional groups present in the polymer chain, as well as the presence or absence of bonds between other polymers in the material

Products in H-NMR

— Prominent Peak due to -OCH3; singlet — Disappearance of peaks due to triglyceride -CH2- or -CH- (Ha, Hb, Hc protons).

Saturated fatty acids

do not have C=C bonds in the chain. These fatty acid chains follow the CnHn+2 rule for unsaturation.

In lab 4, because the spheres are porous, we will explore the formation of...

encapsulated enzymes. The guest molecule will be the enzyme Lactase.

Name the only achiral amino acid.

glycine

Unsaturated fatty acids

have one or more C=C bond (mono-unsaturated or poly-unsaturated, respectively) in the chain. These chains are called unsaturated because an equivalent of molecular hydrogen has been removed from the C-C bond. Naturally-occurring unsaturated fats usually contain Z (cis) C=C bonds, unlike artificial transfats which contain E (trans) C=C bonds.

Rf =

height of sample spot from origin/height of solvent front from origin

The simplest polymers consist of

individual repeat units of monomer covalently bonded to each other (as in Poly A). This is one of the most common types of polymer found in the world today

difference between intra-chain and inter-chain

intra -- within same polymer inter -- between 2 seperate polymers

At a basic level, a polymer is simply a

large (macro) molecule composed of repeating sub-units called monomers.

What is the full name of LiHMDS?

lithium hexamethyldisilazide

a polymer is a ______________ made of _____________, known as _________. polymers can be natural such as ___________ or synthetic such as __________

macromoleucle; many repeated subunits; monomers; glucose; plastics

what are the effects of cross-linking in polymers?

makes the polymer stronger and more dense

What is the mass of encapsulated CaCl2 solution in 10 macrocapsules (g)?

mass of encapsulated capsules - mass of crushed capsules

What is the volume of encapsulated CaCl2 solution in 10 macrocapsules (mL)?

mass/density = volume density of water

what is the unit of glucose concentration on the glucometer?

mg/dL

where would CHCl3 be disposed of?

organic liquid hazardous chemical waste container

Compounds such as functionalized pentacenes are useful as

organic semiconductors

sp2 C-H's ('vinylic' hydrogens) appear much farther downfield at ...

5-6 ppm

SiO2 column tips (second experiment: pentacene)

-before adding your sample, add 2mL of solvent to the column to pack down SiO2 -a clear fraction will come out first, the 2nd fraction is blue (Pentacene), the last fraction is green. -note the volume of solvents used to elute different fractions -after collecting the fractions, evaporate the blue colored solution by gently blowing air into the solution

Product from step 1 in the second experiment (pentacene)

-use Buchner filtration set up to filter the precipitate -after filtering, washing and drying -product = pentacene quinone

If in a reaction using 0.25mL of phenylacetylene and 0.7mL of 2.3 M solution of LDA in THF, 0.15 g of lithium phenylacetylide is obtained, what is the percent yield?

0.0016 mol x 108.07 g = 0.17g 0.15g/0.17g x100 = 88.23%

Pentacene derivatives: organic semiconductors (2)

1) Acenes: linear polycyclic aromatic hydrocarbons with fused benzene rings 2) Pentacene: is a polycyclic aromatic hydrocarbon of 5 linearly fused benzene rings (penta = 5)

Aldol condensation key features (3)

1) Base catalyzed reaction 2) basic sodium hydroxide reacts with acidic α-hydrogen of 1,4-cyclohexadione to produce a nucleophilic enolate anion 3) the nucleophillic enolate attacks the electrophilic carbonyl carbon of phthalaldehyde

Name the solutions that were used to wash the reaction mixture during the work up and explain their roles. (dipeptide lab experiment 4)

1) HCl was used in washing to remove unreacted amino (DMAP starting materials). 2) NaHCO3 was used in washing to remove unreacted acid (starting material). 3) Water was used in washing to remove urea, any other salts (byproducts after the reaction). 4) Brine was used in washing to remove any water left in the organic layer.

Basic idea of lab 1 (transesterification)

1) Two layers = MeOH top and glycerol bottom 2) H NMR spectrum to determine identity of unknown oil

Lab 4 beginning

1) dissolve sodium alginate in water, then add indicator. This is solution A 2) by syringe, slowly drop solution into beaker of CaCl2/H2O. This is solution B 3) gently swirl solution 4) filter capsules 5) weigh

Waste disposal for experiment 3

1) excess methylene chloride — liquid organic hazardous chemical waste 2) excess solid chemicals — solid hazardous chemical waste 3) all aqueous waste generated during extraction (HCl, NaHCO3, brine, water) — hazardous aqueous liquid acidic and basic chemical waste 4) used Pipettes — broken glass waste

Waste disposal in second lab

1) filtrate into organic liquid hazardous chemical waste container 2) disposal of Sn salts — the aqueous filtrate will go into aqueous liquid hazardous chemical waste container

Basic idea of lab 2 (Pentacene)

1) prepare pentacenequinone 2) prepare 6,13-dihexnylpentacene 3) recording IR products of 1&2

Reactants for pentacenequinone (2)

1,4-cyclohexanedione Phthalaldehyde

Observations to note in step 1 of the second experiment (pentacene)

1. Adding starting materials to isopropanol 2. Starting materials dissolved in isopropanol 3. Quinone precipitates upon addition of aq NaOH

Name three common types of co-polymers that are discussed in this experiment.

1. Alternating co-polymers 2. Block co-polymers 3. Alternating block co-polymers

Coupling reagents and their roles for experiment 3 (4)

1. Carbodiimide (EDCl) is used for the activation of carboxylic acid group 2. EDCl used in this reaction is water soluble (as it is a HCl salt) 3. EDCl gives water soluble urea byproduct that can be easily superheated from product 4. DMAP acts as a base/activator

Avoiding racemization in experiment 3

1. HOBt reacts with O-acylurea to form an active ester which is less reactive and so less prone to racemization 2. Sometimes DMAP also acts as a racemization suppressor

Name two other techniques other than TLC used in this experiment. (experiment 4 dipeptide)

1. Purification -- liquid liquid solvent extraction 2. H-NMR analysis

General dipeptide synthesis

1. Two amino acids condense with elimination of water 2. A dipeptide formed; but mixture of products are possible

sp3 C-H's that are not near any functional group are ...

1.0 ppm

Fatty acids are carboxylic acids (R-CO2H) whose unbranched nonpolar hydrocarbon R-group is

8-18 carbon atoms long

C=O IR spectrum

1650-1780

How many amide bonds are there in a tripeptide?

2

Dipeptides are shortest peptides consisting of

2 amino acids joined by a single peptide bond

Like E1 elimination, E1cB requires _____ _____. Unlike E1 though, the intermediate in E1cB is a ______, not a carbocation

2 steps; carbanion

sp3 C-H's that are adjacent to the C=C bonds (called the allylic positions) appear downfield at ...

2.0 ppm

methylene protons immediately adjacent to the carboxylate group appear at ...

2.3 ppm

Polyunsaturated fats like linoleic acid have a unique pair of hydrogens that are allylic to two different C=C bonds, and these 'doubly (or bis) allylic' resonances are even farther downfield., appearing around ...

2.7 ppm

sp (C≡C) IR spectrum

2100-2250

sp3 C-H IR spectrum

2850-3000

A molecule with n chiral centers will have...

2^n possible stereoisomers. Depending on the overall symmetry of the molecule, some of these structures may be identical

Congo red is a ph indicator and helps visualize macrocapsules. Approximate pH range for color change for Congo-red is ...

3.0-5.0 Low pH color = blue-purple High pH color = red

sp2 C-H IR spectrum

3000-3100

Calculate molecular weight for 6,13-pentacenequinone in appropriate units.

308 g/mol

C-protected amino acid using in experiment 3

A

alginic acid is a block co-polymer of modified forms of the 2 carbohydrates (A and B). identify A and B

A -- D-Mannose B -- L-Gluose

TLC for experiment 3

A = origin B = DMAP C = Boc phenylalanine D = dipeptide E = solvent front

How will the concentration of lactose be measured and what assumptions must be made?

A lactose column is used to cycle milk through a syringe. At the end of each cycle, the concentration of the glucose converted by the encapsulated lactase is calculated through a glucometer. Assuming that one molecule of lactose produces one molecule of glucose, lactose concentration in the original milk can be calculated.

What type of polymer is alginic acid? Which two modified carbohydrate units make up the basic building block of this polymer

Alginic acid carbohydrate-based polymer, an anionic polysaccharide, and a block co-polymer. Two modified carbohydrate units that make up the basic building block of this polymer are D-Mannose and L-Gulose

What is an amino acid? Explain zwitter ions.

Amino acids are building blocks of proteins. Amino acids consist of a central carbon bonded to R group, an amino group, a carboxyl group, and a hydrogen. At near neutral pH, amino acids exist as zwitterion as they are both acidic and basic functional group. Zwitterion is a neutral molecule with formal +ve and -ve charges on different atoms of the same molecule.

Anhydride in experiment 3?

Another potent acylating agent

At the end of second day of the experiment (synthesis of 6,13-dihexynylpentacene ), where would you dispose the waste containing tin salts?

Aqueous liquid hazardous chemical waste container

From the above derived equation, as the absorption maximum (λmax) for a molecule increases to a longer wavelength (for example from 300 to 700 nm), how does this affect the energy for the electronic transition?

As the absorption maximum for a molecule increases to a longer wavelength, the energy for the electronic transition decreases. Longer wavelengths are lower in energy.

Calculating average total volume and actual volume of macrocapsules

Average = 4/3(pi)r^3 Actual =You can then determine the volume of the encapsulated solution based on the mass difference and the density of water

Congo red was used in polymer macrocapsule experiment: A) as a cross-linking agent B) as a pH indicator C) as an enzyme to convert lactose to glucose D) for membrane capsule test E) to measure concentration of glucose

B

Organic electronics: possible future

Bendable microprocessor composed of plastic substrate, gold circuits, organic dielectric and a pentacene organic semiconductor

At 3.08 ppm on NMR it represents

Benzylic hydrogens (CH2Ph) Integration = 2 and that makes sense bc of CH2 Multiplet

A type of fuel synthesized by breaking down lipids from natural sources

Biodiesel

General definition of biodiesel

Biodiesel is a domestic, renewable fuel for diesel engines derived from natural oils like soybean oil, and which meets certain requirements specified by international standards

Why is BocPhe used for comparison in TLC?

BocPhe is used for comparison in TLC because it is aromatic and shows UV-visible absorption. It is also the limiting reagent.

Urea is the ______ in both pathways for experiment 3

Byproduct

DCM was used in peptide synthesis as: A) dehydrating agent B) protecting group C) solvent D) electrophile E) base

C

Which of the following methods CAN be used to prepare fatty acid methyl esters (FAMEs): A. Aldol Condensation B. E1cB mechanism C. Base-catalyzed transesterification D. Acid-amine coupling E. Condensation reaction

C

TLC observed after 0, 10, and 20 minutes in experiment 3

C, F, A

Peak at 1673 cm-1 in IR is most likely due to ...

C=C or C=O

Why was CaCl2 used and not NaCl in the preparation of macrocapsule?

Ca2+ ion is divalent ion which can effectively form the cross linked polymer

What is the role of Ca+2 ion during macrocapsule formation? How are the properties changed after addition of Ca+2?

Ca2+ ions form the macrocapsule core by cross linking with sodium alginate. By replacing the Na+ ion with Ca2+, bridging ionic bonds are formed between polymer strands that serve as strong cross-links. This allows the negative charge to be stabalized by the Ca2+ cation. The more sodium atoms replaced by calcium, the more highly cross-linked (structurally rigid, insoluble, and dense) the polymer becomes. The properties of the macrocapsule after the addition effects the stability and pore size of the beads, making it more dense and less soluble.

The more cross-links present in a polymer, the more

Dense and structurally rigid the material will be

What is the purpose of adding base in the aldol condensation reaction?

Deprotonate α-carbon to generate nucleophile

Which organic solvent is used to extract the product during the work up of the reaction in experiment 3

Dichloromethane

How are dipeptides formed?

Dipeptides are the shortest peptides consisting of 2 amino acids joined by a single peptide bond. This happens via a condensation reaction. General dipeptide synthesis consists of 1) two amino acids condensing with elimination of water and 2) a dipeptide is formed, but a mixture of products are possible.

How will you characterize your product in this experiment? What specific differences will you be looking for compared to the starting material?

Disappearance of -CH2 peak due to triglyceride and appearance of peak due to -OCH3

What major differences would you be looking for in the IR spectra of 6,13-pentacenequinone and 6,13-dihexynylpentacene?

Disappearance of peak due to C=O in 6,13-pentacenequinone and appearance of peak due to C≡C from 6,13-dihexynylpentacene.

In alginate, by replacing the monovalent sodium counter ion with ______ _______, what is formed?

Divalent calcium. Bridging ionic bonds are formed between polymer strands that serve as strong cross-links

In lab 4, mixtures of sodium alginate and a molecule of interest (guest) will be dropped into solutions of CaCl2. In our experiment the guest molecules will be ...

Dropped into solutions of CaCl2. In our experiment the guest molecules will be congo red dye or the enzyme lactase.

UV-Vis trends of acenes

In general, the greater the length of a conjugated system in molecule, the nearer the λmax comes to the visible region

Driving force for E1cB elimination is the

Increased conjugation

Briefly explain why is LiHMDS such a strong base relative to hydroxide ion.

It is a strong base because nitrogen is less electronegative than oxygen, so the negative charge is less stable on NH2 than OH. The methyl groups also donate electron density which increases basicity.

Discuss what alginic acid is why we are using it in experiment 4

It is commonly found in the cell walls of algae, and is also a major structural component of seaweed. It is produced by nature in such large amounts that it is currently farmed for use as a food additive and in many over-the-counter pharmaceuticals. Alginic acid is an anionic polysaccharide. It is incorporated into many products. For example, it can function as a dehydrating agent for paper manufacturing or as a thickening agent in ice creams.

Why is it important to keep macrocapsules uniform in size and shape?

It is important to keep macrocapsules uniform in size and shape because it ensures reproducibility of valid and reliable results.

Determine the limiting reagent and excess reagent in the reaction you will preform in this biodiesel experiment

LR = triglyceride ER = methanol

What is LeChatelier's Principle? How it is applicable in this experiment (1) ?

LeChatelier's Principle states that when a system is in equilibrium and a stress is added to the system, the system will shift in order to alleviate itself of the stress in order to return to equilibrium. Stresses could include concentration changes, temperature changes, or pressure changes. In this experiment, the sample of oil is heated on the hotplate. When this happens, equilibrium is disturbed. The reaction will shift in order to re-establish equilibrium. In addition, the concentration changes when adding excess methanol which shifts the equilibrium to the right.

Pentacene is not very stable, has poor solubility, ...

Limiting its applications

Liquid waste in lab 4

Liquid aqueous hazardous chemical waste container. Macrocapsules in the trash

What is a ogliosaccharide

Made of few monosaccharide units(2-10) e.g. disaccharides, trisaccharides, etc. For example, Lactose is a disaccharide made of glucose and galactose

Evaporate excess _______ at 60*C

Methanol

At 1.35 ppm on NMR it represents

Methyl (CH3) Doublet because there is only 1 different hydrogen neighboring it (n+1) Integration is about 3 — so 3 equal neighboring hydrogens (CH3 makes sense)

Protecting groups in experiment 3

Methyl ester as a way to block reactivity of one carboxylic acid group, and we will use a "Boc" protecting group to block the amino group on the other amino acid

How would you prepare 10 mL of the required solvent system to run TLC for this experiment (experiment 3)

Mixing 1 mL of methanol with 9 mL of chloroform

Block co-polymers

Monomer "A" polymerizes first, then a chain of polymer "B" grows off of this initial chain, leading to a polymer comprised of two large "blocks" of different composition

Many of the most common biopolymers are derived from carbohydrates —

Monomers with the basic formula C6H12O6

3 classifications of carbohydrates

Monosaccharides, ogliosaccahride, polysaccharide

Number of peaks =

N+1, where n=number of equivalent neighbor H's

Difference between H-NMR and IR

NMR — molecules chemical structure IR — functional groups

Zwitterion

Neutral molecule with formal +ve and -ve charges on different atoms of the SAME molecule. At iOS electric point (pl), the net charge is zero.

Saturated fatty acids have

No C=C bond

NMR =

Nuclear magnetic resonance

Hexynide lithium reacts with 6,13-pentacenequinone via:

Nucleophilic addition to carbonyl

Size of each integral for each signal corresponds to the

Number of hydrogens in each chemical environment

At 1.42 ppm on NMR it represents

OC(CH3)3 Singlet Integration = 9 because there are 3 CH3 groups neighboring it

At 3.71 ppm on NMR it represents

OMe Singlet integration = 3, makes sense bc of CH3

Unsaturated fatty acids have

One (or more) C=C bonds

After completion of the experiment, where do you dispose of FAMES?

Organic liquid hazardous chemical waste container

Organic vs inorganic electronics

Organic: —semi-conductive materials which are carbon based —polymers are lighter, more flexible, less expensive Inorganic: —inorganic semiconductors = silicon —brittle, inflexible, expensive to produce

In alginic acid, the primary alcohol functional group has been...

Oxidized to the carboxylic acid

Generally a molecule with 50 amino acid units or less is considered a _______, and one with more is a ________

Peptide; polypeptide

At 7.2-7.3 ppm on NMR it represents

Ph Multiplet Integration = 6, higher than usual because of residual chloroform at 7.24 ppm

The energy of the HOMO-LUMO gap corresponds to the

Photons of wavelength absorbed

Carbohydrates are ________ _________ or ________

Polyhydroxy aldehydes or ketones

Proteins are

Polypeptides made up of one, or sometimes more than one polypeptides linked together and have a peptide backbone

Spectrum reported as chemical shifts in units of ______, referenced against TMS=0

Ppm

2 steps in the second experiment of pentacene

Prepare pentacenequinone Prepare 6,13-dihexynylpentacne

SiO2 column for _____ of crude _______

Purification; pentacene Collect blue colored fraction in Erlenmeyer flask

4-way Aldol produces

Quinone

Reactants, reagents, and solvent of the 3rd experiment (dipeptide)

Reactants — Alanine methyl ester and Boc phenylalanine Reagents — 1-ethyl-3-(3 dimethylaminopropyl)carbodiimide and N,N-Dimethyl 4-aminopyride Solvent — dichloromethane methylene chloride (DCM)

Fatty acid molecules with single bonds between all carbons

Saturated fatty acid

Chromatography is a method for the

Separation and identification of substances (solutes) based upon their differential mobility on a supporting medium (stationary phase) under the influence of a flowing medium (mobile phase), which may be a gas or liquid

Peptides are

Short polymers of amino acids linked by peptide/amide bonds

The more conjugated the scene, the

Smaller the HOMO-LUMO gap

Addition of _____ immediately gives a ____ color

SnCl2; blue Product formation

The addition of water to sodium methoxide produces...

Sodium hydroxide and methanol

In the first reaction, we will be using _____ ______ as our base catalyst

Sodium methoxide (NaOCH3)

In commercial form, the alginic acid polymer is sold as ...

Sodium salt of the carboxylic acid referred to as sodium alginate. In this form, the ionic material is reasonably soluble in water

What is the aim of experiment 1 (biodiesel)? Which three oils were used in the experiment?

The aim of the experiment is to create biodiesel through transesterification. In this experiment, a mixture of glycerol esters (triglycerides) and methanols are converted into a mixture of methyl esters and glycerol. This process converts cooking oils into FAMEs (fatty acid methyl esters). FAMEs can be used as biodiesel. H-NMR was used to analyze the product. The three oils that were used in this experiment were canola, olive, or vegetable oils.

What was the approximate shape of the macrocapsules?

The approximate shape of the macrocapsule is circular spheres.

What is the driving force for elimination of water during the reaction to form pentacenequinone?

The driving force for elimination of water during the reaction to form pentacenequinone is from the stabalization of increased conjugation. The increased conjugation makes elimination increase.

Was the experiment successful/unsuccessful? Why? BIODIESEL

The experiment was successful because, there was transesterification of vegetable oil to produce vegetable oil FAMEs (bio diesel). This experiment created a substitute for petroleum-based diesel fuel. The H' NMR spectrum shows no glycerol present; the FAMEs were successfully seperated. Even despite the starting materials still present, the H-NMR spectrums between the product and vegetable oil are extremely similar.

HOMO-LUMO

The hoppping of the charge carriers between molecules depends on the overlap of the frontier orbitals of adjacent molecules

What might happen if the pentacenequinone was not dried completely of methanol and/or any residual water it might have absorbed, before reacting it with hexynyl lithium? What would the result be?

The methanol or water would react with the strong base (hexynyl lithium) forming a byproduct that could affect the production of the pentacene derivative. This could result in low yield of the product. The synthesis in step 2 would be affected and the desired reaction would not occur.

The following data were obtained for different concentrations of sodium alginate and CaCl2. What could you infer from these data? Provide an explanation for these results.

The more sodium alginate and CaCl2 used takes longer time for the macrocapsule to change color. This makes sense because thicker capsules should result from more concentrated solutions, thus resulting in increased time necessary for the color change to occur. Batch 3 took the most time to change color, followed by batch 2, then batch 1. Batch 3 had the thickest membrane capsules, which had higher sodium alginate and CaCl2 concentrations. The diffusion of OH- and H+ will occur a different rates based on the thickness of the macrocapsule shell. The time change for NaOH took longer for 5 minutes in HCl soak, than regular NaOH, because the pH changed more drastically after a long soak.

What is the importance of using protected amino acids during dipeptide formation? Name two protected amino acids that were used in this lab. Draw and upload the images of their structures.

The names of the 2 protected amino acids are alanine methyl ester and boc phenylanine. It is important to use protected amino acids during dipeptide formation because they avoid cross coupling reactions. Protected amino acids is a chemical modification of a functional group in order to get chemo selectivity in a particular chemical reaction. NH2 of phenylalanine is protected as t-butoxycarbonyl (Boc) and COOH of alanine is protected as methyl ester. If unprotected amino acids are used for dipeptide formation, there is a possibility of formation of mixture of products instead of a single product due to cross coupled condensation reactions.

Is your plot of the number of cycles vs glucose concentration linear? Explain how it relates to this experiment.

The plot of the number of cycles vs glucose concentration is approximately linear. The graph levels off at the 10th cycle because there is less lactose available to be converted into glucose. Originally, the graph is linear (as expected) because about the same amount of lactose is converted into glucose in each cycle through the column.

Major advantage of using EDC over other carbodiimide is

The urea byproduct is water-soluble and can be easily removed from the product mixture after the reaction

Based on the limiting reagent,

Theoretical yield is calculated

When large structured acenes are used,

They absorb light in the visible region and generate charges.

Capsule membrane test

Thicker capsules should result from more concentrated solutions, thus resulting in increased time necessary for the color change to occur. You will be testing three different concentrations. The diffusion of OH- & H+ will occur at different rates based on the thickness of the macrocapsules shell

What was the purpose of using thin-layer chromatography in this experiment (dipeptide experiment 4)

Thin-layer chromatography is used to monitor the reaction progress. TLC allows us to determine if the reaction has been run to completion or if there is still remains from the starting material. TLC allows us to observe the progress of the reaction without actually stopping the reaction. All components of the reaction are present in the TLC, but only aromatic compounds are visible under the UV light.

What would be the effect of placing the macrocapsule in 4 mL of 1 M NaOH instead of 2 mL of 1 M NaOH as described in the procedure?

Time for color change will not change

Role of aqueous sodium bicarbonate during the work up of the reaction in experiment 3

To remove unreacted acid

Role of acqueous hydrochloride acid during the workup of the reaction in experiment 3

To remove unreacted amine, DMAP

Role of water during the workup in the reaction of experiment 3

To remove urea, any other salts (byproducts after the reaction)

Role of sodium sulfate during the workup of the reaction in experiment 3

To remove water from the organic layer

During the FAMEs synthesis, a mixture will be assed to a vial and 2 layers will form. Identify the components of each layer

Top = FAMEs and methanol Bottom = glycerol

A chemical reaction in which an ester is converted into a new type of ester is...

Transesterification

Base-catalyzed biodiesel production utilizes...

Transesterification

A molecule made up of glycerol connected to 3 fatty acid chains

Triglyceride

What is the origin of the fatty acids in plant oils?

Triglycerides are biosynthesized by phosphorylated glycerol and enzyme functionalized fatty acid esters. Triglycerides are produced by enzymatic transesterification

True or false? The excess reagent in this reaction is required to shift the equilibrium to the right

True

What are allylic and vinylic hydrogens? Explain briefly using examples.

Unsaturated acids have sp2 C-H's (vinylic hydrogens) that appear much farther downfield on the NMR spectrum (5-6 ppm). Vinylic hydrogens are directly related to the carbon-carbon double bond unit. Also, unsaturated acids have sp3 C-H's that are adjacent to the carbon-carbon double bond (allylic hydrogens) that appear near 2.0 ppm.

Fatty acid molecules with single bonds between some carbons and double bonds between some carbons

Unsaturated fatty acid

Using your NMR spectrum that you obtained, identify the oil given to you for the experiment. Also, compare the observations with the standard NMR spectrum for the oil.

Using the NMR spectrum I obtained, I decided that vegetable oil was used in this experiment. In order to determine which oil was used, a ratio of integrals (methoxy protons/bis-allylic protons) was conducted. My experiment: -OCH3 integral = 0.22 bis-allylic protons = 0.11 0.22/0.11 = 2 Olive oil ratio = 8.0 - 8.5 Canola oil ratio = 2.5 - 3.0 Vegetable oil ratio = 1.5- 2.0, so the oil used in this experiment was most likely vegetable oil. Also, comparing the observations with the standard NMR spectrum for vegetable oil are very similar. Both spectrums show the bis-allylic proton as a triplet. This peak pattern matches vegetable oil bis-allylic proton.

Using the information provided below, derive an expression to show that the energy of an electronic transition measured from UV-VIS spectroscopy is a function of the wavelength of the light absorbed using the equations below. ν λ = cΔE = hν where E is the energy for the transition, ν is the frequency of light, λ is the wavelength, c and h are the speed of light and Plank's constant respectively (both constants).

V = c/λ

What was the purpose of varying the concentrations of sodium alginate and CaCl2?

Varying concentrations of sodium alginate and CaCl2 were used to determine the relationship between changing concentrations and its affects on the thickness of the capsules. Different concentrations of each may produce different macrocapsule shell thickness.

List all possible fatty acid methyl esters in your unknown oil.

Vegetable oil FAMEs include methyl oleate, methyl linoleate, and methyl stearate.

Inter chain cross link

between 2 seperate polymers

What was the color of the macrocapsule after the addition of 0.1 M HCl?

blue

where would capillary tubes be disposed of?

broken glass waste container

in lab 4, what will be used to achieve crosslinking

calcium chloride

General structure of an amino acid

central carbon bonded to R group, amino group, carboxyl group and hydrogen

If two different monomers are used in polymers, the resulting material is called a

co-polymer and a variety of different arrangements can arise

what are the 2 guest molecules used in polymer encapsulation

congo red dye and enzyme lactase

What is a polysaccharide

contain more than 10, or even thousands of monosaccharide units. e. g. Starch, cellulose, cotton. These are biopolymers

In lab 4, the surface of the droplet will immediately begin to ...

cross-link, forming a stable macrocapsule that traps the guest inside. The formation of the capsule is accompanied by replacement of the Na+ ion with Ca2+.

Goal for lab 4 is to determine the relationship between ...

cross-linking time and concentration with regards to the properties of the capsules including capsule thickness and volume.

Another structural parameter that has significant impacts on polymer properties is

cross-linking. Cross-linking has bonds between adjacent polymer chains, or between "loops" within a single polymer chain

true or false? The tin(II)chloride in the synthesis of pentacene derivative works as an oxidizing agent.

false

true or false? in this (2nd) experiment, LiHMDS acts as an acid

false

What type of electrons are responsible for the photophysical properties of pentacene?

pi

What was the color of the macrocapsule after the addition of 1 M NaOH?

red

In lab 4, lactase will be used to hydrolyze the lactose found in milk, producing glucose that can be easily detected and measured. You will determine the concentration of glucose through a ...

series of runs on a column containing the lactase encapsulated macrocapsules

Column chromatography uses a stationary and a mobile phase to separate compounds. What is the stationary phase in the column chromatographic purification of crude pentacene derivative?

silica gel

What is a monosaccharide

simplest unit. e. g. glucose, fructose, etc. They cannot be hydrolyzed to smaller molecules by water.

where would TLC plates be disposed of?

solid hazardous chemical waste

true or false? In a block co-polymer, all of monomer "A" polymerizes first, then a chain of polymer "B" grows off this initial chain, leading to a polymer comprised of two large "blocks" of different composition

true

true or false? Increasing the conjugation will decrease the energy of absorption.

true

true or false? macrocapsules can be disposed in the regular trash

true

true or false? solubility of the polymer decreases as cross-linking increases

true

Alternating co-polymers simply consist of

uniformly alternating "A" and "B" monomers, and are among the most common type of co-polymers

Alternating co-polymers consist of [Blank 1] alternating monomers and are among the most [Blank 2] of co-polymers.

uniformly; uniform

Intra chain cross link

within same polymer

In lactose, D-galactose and D-glucose are joined by ...

β-glycosidic bond between C1 of galactose and C4 of glucose

Enzyme encapsulation in lab 4

—In this experiment, you will encapsulate the lactase enzyme within your alginate macrocapsules. —You will then use this encapsulated, solid-supported enzyme to convert lactose from milk to glucose. —While there is no simple test for checking the presence of lactose, the decomposition of lactose by the lactase enzyme produces glucose, which is easily monitored with glucose test strips. —You will determine the concentration of glucose converted by lactase over several cycles. There should be a linear relationship between the number of cycles and glucose concentration. A linear relationship results due to lactase activity from the macrocapsules. The conversion to glucose should be directly proportional.

Reaction of interest in experiment 3 (2 protections)

—NH2 of phenylalanine is protected as t-butoxycarbonyl (Boc) —COOH of alanine is protected as methyl ester

Absolute configurations

—R and S —priorities are based on atomic number —keep the lowest priority group away from the viewer — if the first 3 groups appear in clockwise order, then it is a R chiral center — if the first 3 groups appear in anti clockwise order, then it is a S chiral center

How is the DMAP spot assigned in the TLC for experiment 3?

—TLC plates are coated with SiO2 (Lewis acid) that has a fluorescent indicator added —compounds that enhance or diminish the fluorescence of the indicator will be visible under UV light —only aromatic compounds are visible (EDCl is not visible) —DMAP is aromatic so it is visible under UV light —DMAP is a base it has a strong interaction wit the Lewis acidic TLC plate. So it will have a lower Rf than all other reaction components

To avoid cross coupling reactions (mixture of products)...

—Use protecting groups —chemical modification of functional group in order to get chemo selectivity in a particular chemical reaction —most widely used in multi-step organic synthesis —the amino or carboxylic acid groups become inactive to facilitate desired reaction and products —single desired product is formed without other significant products

Lactase column in lab 4

—You will be taking a standard amount of the microcapsules (25) and inserting them inside an empty syringe (10 mL). —You will be running milk through the syringe and collecting and recycling the milk. After each cycle of running milk through syringe, you will be measuring the concentration of glucose converted by the encapsulated lactase using a glucometer. —Assuming that one molecule of lactose produces one molecule of glucose, calculate the lactose concentration in the original milk.

What are amino acids?

—amino acids are molecules containing an amine group, a carboxylic acid group and a side-chain that varies with different amino acids —building blocks of proteins —20 naturally occurring amino acids encoded by universal genetic code —all natural amino acids, except glycine, are chiral —all natural amino acids, except proline, are 1* amines

A number of analytical techniques can be used to characterize the product of a reaction (experiment 3)

—comparison of physical properties such as melting point, boiling point, optical rotation etc to a known compound —more widely used methods for identification and characterization are spectroscopic methods such as NMR, IR, mass spectroscopy, etc that measure the interactions of the compound with the electromagnetic radiation of various wavelengths We are using H-NMR of the protected dipeptide produced

Relative configurations

—d and l relate to optical rotation —clockwise = dextrorotatory or d or (+) —counterclockwise = levorotatory or l or (-) —DO NOT MIX UP WITH D AND L

LiHMDS is a strong base sooooo

—in THF —strong nucleophillic base that is extremely flammable —reacts vigoursly with water and acids (any protic solvent) —severly corrosive to skin, eyes, and respiratory system

Organic electronics

—involves development of carbon-based materials in microelectronics —aces are used as organic semiconductors — such devices include transistors, solar cells, and diodes

Essential amino acids

—of 20 natural, 9 are essential amino acids —essential amino acids cannot be synthesized by human body; need to be supplemented by food —at near neutral pH, they exist as zwitterion as they both have acidic and basic functional group. This pH is also called pl(is o electric point)

Workup and purification in experiment 3

—product is a mixture containing other undesired components —need to purify the product; easily done by liquid liquid solvent extraction —bottom layer will be organic (DCM is denser than water) —top layer is aqueous

TLC observations of experiment 3

—ran every 20 minutes —starting material BocPhe in DCM —reaction mixture in DCM

Fischer projection

—relates to 3D spatial arrangement of groups at chiral center —designated as D or L; possible extension of Fischer notation of carbohydrates —L has NH2 on the left —D has NH2 on the right

Electronic materials in experiment 2

—various metals and solid crystalline substances that have electrical conductivity —used as base material for computer chips and electronic devices —traditional electronics are silicon-based

Commercial methods for making fatty acid methyl esters (FAMEs)

• Base-catalyzed transesterification of the oil with methanol (approach we will use) • Acid-catalyzed esterification of the oil with methanol • Saponification of the oil to yield free fatty acids, followed by acid catalyzed esterification

Remember the 4 things for H-NMR

• Number of SIGNALS : how many different kinds of protons are present • The POSITION of peak (chemical shift): how shielded or deshielded is the proton • The INTENSITY : number of protons of a particular type • Peak SPLITTING: number of neighboring proton(s)

Starting materials of ex1

• ONE of three oils (canola, olive or vegetable oil) • Methanol • Sodium Methoxide

Majority of FAME production utilizes base-catalyzed method because it is the most economic (in lab and in industry) for several reasons:

• Relatively low reaction temperature (1500F; 65.50C) and pressure (20 psi). • Rapid and efficient conversion (98%) with minimal side reactions. • One-step reaction—no inconvenient intermediate reactions. • No need for exotic starting materials, equipment or esoteric procedures. • Faster than acid-catalyzed. • Bases typically used are less corrosive than the acids required for acid- catalyzed production.