High-Throughput Experimentation: Palladium-Catalyzed Suzuki-Miyaura Cross-Coupling

By: Jingyuan Ma


This lab introduced techniques used in the Penn/Merck High-Throughput Experimentation Center. The Suzuki-Miyaura reaction was implemented using 4 reagents, an assigned inorganic base, an assigned solvent, and pre-dosed phosphine ligands. TLC and HPLC were used to qualitatively analyze the reactivity trends of 24 reaction screens, which were all conducted under room temperature and controlled settings. The following overall reaction was conducted to catalyze sp2-sp2 carbon-carbon bonding through the use of a palladium catalyst:


The following is a more detailed introduction to the Suzuki-Miyaura reaction, beginning with the very initial reaction conducted by Suzuki and Miyaura:


The following is an example of a reaction that could be conducted using the Suzuki-Miyaura reaction, including a more specific mechanism:

specific mechanism

After the rate determining step of oxidative addition, where the palladium catalyst oxidizes from 0 to II and couples with the alkyl halide to produce an organopalladium complex that isomerizes from the cis to trans complex (for allylic and benzylic halides as shown previously in the two reactions), while vinyl halides retain their stereochemistry during oxidative addition. The main focus of this lab report introduction will, however, be the transmetallation step after oxidative addition.


In this step of the reaction mechanism, the ligands are transferred from one location to another, from the organoboron species to the PdII complex. The exact mechanism is not completely resolved, although the base is expected to activate the organoboron compound, because organoboron compounds are very covalent and unless there is a base, the transmetalation does not occur. Boronate complexes form with a negatively charged base via quaternization of the boron as shown in Fig 3.[i]

The transmetalation mechanism is still under research, as seen in the 2011 JACS publication regarding the possible pathways for the transmetalation to occur. The two ways that could be possible is that the organoboron compound is converted to a nucleophili boronate by base and attacked by a palladium halide complex or the palladium halide is converted to a nucleophilic palladium hydroxo complex that then reacts with the neutral organoboron complex.[ii] Carrow and Hartwig show that the transmetalation is between the palladium hydroxo complex and a boronic acid, not the palladium halide complex and a trihydroxyborate. This was determined by comparing stoichiometric reaction rates between isolated species. The pathway that is correct for the transmetalation within the Suzuki Miyaura cross-coupling is the one producing the largest product of the rate constant and the largest concentration of palladium complex and boron reagent.

Other recent research aims to provide the same reaction for the desired product and basis of further research of pharmaceuticals such as anticancer gossypol and antibiotic vancomycin, without the ligands. In that case, the phosphine side reactions would not exist and the reaction could be under aerobic conditions. Kumbhar, et al discovered a way for the Suzuki-Miyaura coupling reaction to occur ligand-free with the use of zeolite immobilized palladium.[iii]



Day one was used to assemble 24 well blocks and lid with Teflon liner, clearly labeled with initials. Obtained five 4 mL vials with caps. The reagents provided and used were Pd(OAc)2, 4-chloroanisole, 4-bromoanisole, 4-fluorophenylboronic acid; inorganic bases: potassium phosphate and sodium carbonate, phosphine ligands in 1000uL vials. 7.2mg (ended up being 9.09mg) Pd(OAc)2, a rusty orange powder, was measured carefully into 4 mL vials, carefully labeled. 60.2mg and 60.3mg respectively of the white powder 4-fluorophenylboronic acid was weighted into each of 2 vials, carefully labeled one “4-chloroanisole” and the other “4-bromoanisole”. 2.4mmoles of the selected base was weighed into the fourth vial, however, in this case the base was pre-prepared as well as the 24 reaction vials of predosed ligands and thus the reaction setup and vials were moved to the “wet box” to prepare stock solutions. To the vial with palladium acetate, 4mL of THF was added. The vial was sealed and shaken to dissolve the palladium acetate, which dissolved completely. Using 20-100 uL pipette, 25 uL of the Pd(OAc)2 solution was dosed to each 24 predosed reaction vials. The box was then transferred back to the dry box and the blowdown tool used to remove THF solvent to leave behind palladium and ligand. While the solvent was being removed, the reaction solutions were prepared. However, in this case, the solvent and base solutions were already premade (0.890 mL of selected solvent: THF, 1.8 mL of water was added to the assigned base K2CO3 for a 1.2M base solution (premade) and for the individual step, 0.890mL of THF was added to both the 4 mL vials A and B containing the 4-fluoroboronic acid. 4.90 uL of 4-Chloroanisole was added to the 4mL vial. 50 uL of 4-bromoanisole was added to the 4mL vial B. After blowdown, transferred reaction blocks back to wet box. 50uL of the 4-chloroanisole reagent solution Vial A was dosed to each of the 12 vials A1-A6 and B1-B6. 50 uL of the 4-bromoanisole reagent solution in vial B was dosed to each of the 12 vials C1-C6 and D1D6. 50 uL of the aqueous base was dosed to each of the 24 vials A1-D6. Reaction block was caped and the lid tightened with a power screwdriver, starting from the screw in the center and working in a crisscross pattern. The box was removed from the glovebox and placed on a tumble stirrer overnight until moved into the fridge in the morning to halt the reaction.


Second day was used for TLC analysis. Plate 1 consisted of (in order): A1-6, product standard, 4-chloroanisole standard, B1-6. Plate 2 consisted of (in order) C1-C6, product standard, 4-bromoanisole standard, D1-6. In 95:5 hexanes:ethylacetate mobile phase, the TLC plates were ran and the solvent line was marked. The plate results were marked and compared. The HPLC calibration curve was prepared by Dr. Rarig (tared 10 mL vial, added 8-15mg of 4,4dimethylbiphenyl, added 8-15mg of product standard, 4-fluoro-4’methoxybiphenyl, added 8mL acetonitrile to vial, capped vial and shook for dissolution, transfered 1.5-2mL of this solution to HPLC vial, injected 5uL of this sample onto HPLC, recorded area under peak for the product standard (Rf=4.78 min) and the internal standard (Rf=5.64 min)).

Samples were prepared for HPLC. Using 100-1000uL multi-channel pipette, 500 uL of prepared 0.02M solution of 4,4-dimethylbiphenyl in acetonitritle was dosed into your reaction mixture. The cap was replaced on reaction block, tightened and placed on the stirplate in order to ensure all dissolved into acetonitrile. Using the 100-1000uL multichannel, 700 uL of acetonitrile was dosed into each of 24 wells on a 96 well HPLC block. The reaction block was shared between all members of the experiment, so each quadrant was well marked. After 12-13 hours, the data took about 10min per person to extract.



Each solvent and base applied during the experiment is extremely important as a combination for analyzing the Suzuki coupling reactions. For this experiment, the assigned solvent was THF and the assigned base was K2CO3. It was observed in literature, Wolfe and Singer, that KF was ineffective in toluene, but most efficient promoter of coupling in THF. [iv] It was hypothesized that while biphasic solvent systems generally give poor results compared to those without water and while a combination may be a poor choice, for example, K3PO4 was less compatible with THF, reaction catalyst loads can be ran at higher (boiling point of water) temperatures in toluene for better results.

After the reaction processed, the qualitative analysis consisted of two parts: TLC and HPLC. TLC plates were visualized and produced Rf values presented in the Product Characterization section. For the quantization of which lanes consumed the aryl halide starting material and which had not. Some lanes contained multiple spots (for A6, B2, C6, D1, D5), which indicated a messy reaction. In comparison between 4-chloroanisole and 4-bromoanisole, it was concluded that reactions with 4-bromoanisole reagent (C and D vials) produced far more visible reactions via TLC as well as results within HPLC, quantized by the highest P/IS value, which correleated with the basic TLC runs (C1-5 and D1-3, 5), which did not include any of the 4-chloroanisole reagent reactions. This can be used to determine that the 4-bromoanisol reagent with THF solvent and K2CO3 base produced better results.


Product Characterization

Vial Ligand used: Observation: P Value P/IS Value
A1 1: Ataphos Yellow



A2 2: Butyldi-1-adamantylphosphine Milky white



A3 DPPF Yellow/orange- cloudy



A4 DTBPF Orange with percipitate



A5 P(o-toluyl)3 Peach with side precipitate



A6 P(PPh3)3 Brown-orange clear



B1 P(tBu)3 HBF4 Clear with white precipitate



B2 RuPhos Yellow with yellow precipitate



B3 S-Phos Brown



B4 Xantphos Yellow



B5 X-Phos Clear with white precipitate



B6 None Black precipitate



C1 Ataphos Orange precipitate



C2 Butyldi-1-adamantylphosphine Brown-grey precipitate



C3 DPPF Brown-red



C4 DTBPF Orange clear



C5 P(o-toluyl)3 Grey-yellow



C6 P(PPh3)3 Brown murky



D1 P(tBu)3 HBF4 Grey



D2 RuPhos Yellow-green



D3 S-Phos Yellow clear



D4 Xantphos Yellow murky



D5 X-Phos Yellow



D6 None Grey-black



Calibration - -



            0.01165 g of recrystallized product was combined with 0.01229 g of pure 4,4′-dimethylbiphenyl (internal standard) and the mixture was dissolved in 8 mL of acetonitrile.  This solution was then shot on the HPLC for analysis. These values were used for the calculation of the above P/IS values (calculation show in Question and Answer section).

Rf values from TLC- Chlorine: (solvent front: 3.15cm)

Spotting Rf Value
A1 0
A2 0
A3 0
A4 0
A5 0
A6 0.79, 0.86
Product 0.60
4-Chloroanisole reagent 0
B1 0
B2 0.57, 0.83
B3 0.57
B4 0.57
B5 0.54
B6 0

Rf values from TLC- Bromine: (solvent front: 3.10cm)

Spotting Rf Value
C1 0
C2 0.48
C3 0.45
C4 0
C5 0
C6 0.48, 0.94
Product 0.45
4-Bromoanisole reagent 0
D1 0.13, 0.29, 0.48
D2 0.58
D3 0.81
D4 0.81
D5 0.55, 0.84
D6 0.52


Upon comparison of the Rf values and HPLC data obtained for each reaction vial, the spotting values/characteristics did not match that of the HPLC integration values. Therefore, there must be cases of sources of error, especially in the TLC method. The TLC data most likely did not reflect the HPLC due to over-spotting, which occurred some of the trials. This resulted in blobs of spots in between lanes, which made the deciphering of the Rf values difficult. According to the HPLC, the first 6 runs of “A” or 4-chloroanisole reagent with THF solvent, K2CO3 base, and 1-6 ligand, had zero integration peaks or a no reaction, which was also reflected in the TLC in comparison to both the starting material and the product spot, except for A6. This A6 inconsistency may be due to a source of error, perhaps a poor cleaning of the thin TLC pipette, a over running of a side spot, or contamination of the plate. Visual observation of the product formation showed that although the HPLC confirmed zero integration peak, there was still visibly a precipitate, indicating that a visualization of the process is not enough for complete analysis of the 24 reactions. Ligand, solvent, and reagent combinations that produced high P/IS values were C1-5 and D1-3, 5.



According to research the use of certain types of ligands led to enhanced rate of oxidative addition while the catalytic cycle was also sped up unlike the common result of one step speeding and another slowing down. The ligands are therefore successful in their purpose of applying their electron-richness to the palladium and their bulkiness to increase the rate of reductive elimination and increase the amount of L1Pd complexes to increase the rate of transmetalation. The following experiment using the High-Throughput Experimentation Center allowed for the further understanding of screening multiple reactions within a limited amount of time, analyzing the results, and comparing the effectiveness of different solvents, ligands, and bases. Understanding each factor that contributes to the reaction process helps develop future experiment protocols and develop ideal conditions for desired reactions.

Assigned Questions

  1. See introduction
  2. Values from your calibration solution (reaction product and internal standard), calculate P/IS value that corresponds to complete conversion. Molar ratio of product to internal standard in your calibration solution? What was the relative area ratio for that sample? What is the molar ratio of theoretical product formation to our internal standard that we dosed into each reaction vial?

Molar ratio: theoretical product formation: 0.01165g/[202.228 g/mol]= molar quantity of product theoretical=5.8e-5mol. Internal standard (pure 4,4′-dimethylbiphenyl) of 0.01229g/[182.26g/mol]=6.74e-5mol internal standard.

Relative area ratio: product peak integration: internal standard peak integration approximate to product: internal standard molar ratio.

 internal standard molar ratio.

areaAny observed reactivity trends. Compare qualitative TLC assessment with quantitative HPLC data. What are the shortcomings of the TLC? Benefits? Short comings and benefits of HPLC?

TLC assessments are a way to observe reactivity trends. They were used to quickly assess each of the 24 reactions, which allowed the assessment to be a fast and easy way to visually compare the reactivities. However, TLC plates are also not completely reliable because the plates don’t have long stationary phases and the detection limit is high. The data obtained would just be a rough estimate and other chromatographic techniques may be used. Also, the plates were crudely placed in a beaker with solvent and the system was somewhat open, only slightly covered by aluminum foil. The many environmental factors and high likelihood of dots being overspotted, running into each other, streaking, and uneven solvent front all contribute to the shortcomings of the TLC technique.

HPLC can be run for many reactions at a fast rate and with far more accuracy. The results are easily reproducible and easy to operate. It can also be used for more complex molecules and However, these are very expensive to obtain, use, and maintain in a laboratory.

Any problems? What would you change to improve the experience?

The experience was great in the laboratory. The groups were split up well so that everyone got a section of the glovebox and took turns in a timely fashion. The calendar was poorly organized in that there were due dates that were different between the groups and I felt that I had to turn in 3 labs without getting feedback on them, which lost me a few points on technical issues.

[1] N. Miyaura and A. Suzuki, “Palladium-Catalyzed Cross- Coupling Reactions of Organoboron Compounds,” Che- mical Reviews, 1995, 95, 7, 2457-2483.

[1] Coletta, Chris, and Andrew Haidle. “The Suzuki Reaction.” Havard Chemistry 215. N.p., n.d. Web. 22 Nov. 2013. <http://www.chem.harvard.edu/groups/myers/handouts/12_Suzuki.pdf>.

[1] Carrow, Brad P., and John F. Hartwig. “Distinguishing Between Pathways for Transmetalation in Suzuki-Miyaura Reactions.” Journal of the American Chemical Society 2011, 133, 2116-119.

[1] Kumbhar, Arjun, Santosh Kamble, Anand Mane, Ratnesh Jha, and Rajashri Salunkhe. “Modified Zeolite Immobilized Palladium for Ligand-free Suzuki–Miyaura Cross-coupling Reaction.” Journal of Organometallic Chemistry 2013, 738, 29-34.Science Direct. Web. 20 Nov. 2013. <http://www.sciencedirect.com/science/article/pii/S0022328X13002325>.

[1] Wolfe, J.P.; Singer, R.A.; Yang, B.H.; Buchwald, S.L. Journal of American Chemistry Society 1999, 121, 9550-9561.



I. Purpose

To study how stress affects a system’s equilibrium and to determine the concentration of the complex ion in solutions of unknown concentration as well as the equilibrium constant.

  1. Procedure

LeChatelier’s Principle

Part 1

Solid sodium chloride was poured into a test tube and the test tube was then filled ¾ full of distilled water.  The solution was then decanted into a second test tube and Cl- ions in the form of concentrated HCl were added.

Part 2

A small test tube was filled about half full of distilled water.  Several drops of bromthymol blue indicator solution and 5 drops of 0.1 molar hydrochloric acid were added, and the resulting color was noted.  0.1 molar sodium hydroxide was then added drop by drop with stirring until no further color changed occurred. The color was then noted.  The attempt was then made to add the right about of acid to the test tube to cause the solution to be green in color after stirring.

Part 3

About 25 mL of 0.0020 molar KSCN solution was poured into a beaker.  25 mL of distilled water and 5 drops of 0.20 molar Fe(NO3)3 solution were then added and swirled.  The color of the KSCN and Fe(NO3)3 solutions were noted, as well as the color of the resulting complex ion. Equal amounts of the solution were poured from the beaker into four test tubes.  The solution in the first test tube was the reference solution.  To the second test tube 2-3 crystals of KSCN were added and the results were described.  To the third test tube 6 drops of Fe(NO3)3 solution were added, and the solution was stirred and the results noted.  To the fourth test tube small crystals of Na2HPO4 were added a few at a time and stirred into the solution; the results were noted.

Part 4

About 10 mL of ethanol was measured in to a beaker.  Solid cobalt (II) chloride was examined, with its color and formula noted, then a small amount was dissolved in the beaker of ethanol.  About 2 mL of the alcoholic cobalt solution was added into each of 3 small test tubes.  To the first test tube, 3 drops of distilled water were added, one drop at a time with stirring.  3 drops of distilled water were added to the other 2 test tubes and the effect was noted.  Using the first test tube as a control, 5 drops of 12 molar HCl was added one drop at a time with stirring and the result was noted.  To the third test tube a few crystals of sodium chloride were added and stirred.  The remainder of alcoholic cobalt solution from the beaker was put into a fourth test tube.  10 drops of 0.1 molar silver nitrate solution were added one drop at a time, and the color of the solution was noted.  A sealed Beral pipet containing some of the alcoholic cobalt chloride-water system was obtained and the large end of the pipet was immersed in some hot water and the color change was noted.  The Beral pipet was then chilled in an ice bath to see if the color change in the previous step was reversible.

Equilibrium Constant of FeSCN

Part 1                                                           

Using burets or pipets, 2.0, 3.0, 4.0, 5.0, and 6.0 mL of 2.0 X 10-3 M KSCN  in 0.50 M  HNO3 was measured into 100 mL volumetric flasks and diluted to 100 mL with 0.20 M Fe(NO3)3 in 0.50 M HNO3 and mixed well.  The concentration of FeSCN in each flask was then calculated, assuming the all of the SCN had reacted.  The absorbance of each of the standard solutions were measured at 445 nm, using distilled water as the reference in the spectrophotometer.  The molar concentration of FeSCN was then plotted against absorbance and the best fitting line was drawn through the data points.

Part 2

Using a buret or pipet, the following quantities were measured into 5 test tubes.  The solutions were mixed well with a glass rod and the absorbance of each was measured at 445 nm using distilled water as a reference.


2.0 X 10-3 M Fe(NO3)3 in 0.50 M HNO3

2.0X10-3 M KSCN in 0.50 M HNO3

0.50 M HNO3


5.0 mL

1.0 mL

4.0 mL


5.0 mL

2.0 mL

3.0 mL


5.0 mL

3.0 mL

2.0 mL


5.0 mL

4.0 mL

1.0 mL


5.0 mL

5.0 mL

0.0 mL

 II. Data

LeChatelier’s Principle

Part 1

A white solid precipitated at the top of the test tube.

Part 2

The result of step 1 is a yellow solution.  The number of drops of acid needed to create a lime green color is 40 drops.

Part 3

KSCN is a colorless solution.  Fe(NO3)3 is a purple solid.  The second test tube was blood red, the third test rube was a burnt orange color, the fourth test tube was clear, and the resulting complex ion was an orange color.

 Part 4

Step 8 caused the solutions to become more purple.  Step 9 caused the solution to become bright blue.  When placed in an ice bath, the solution turned pink.  When placed in a hot water bath, the solution reversed back to blue.

Equilibrium Constant of FeSCN
Part 1


mL 2.0*10-3 M KSCN in 0.50 M HNO3

% Transmittance


Concentration FeSCN, M





4.0 X 10-5





6.0 X 10-5





8.0 X 10-5





1.0 X 10-4





1.2 X 10-4

                                                Part 2


mL 2*10-3 Fe3+ in 0.50 M HNO3

ML 2*10-3 SCN- in 0.50 M HNO3

% Transmittance


Initial moles Fe3+
































Initial moles SCN-

Concentration FeSCN2+, M

Moles FeSCN2+ at Equilibrium

Moles Fe3+ at Equilibrium

Moles HSCN at Equilibrium


































Concentration HSCN at Equilibrium, M

Concentration Fe3+ at Equilibrium, M

Concentration H+ at Equilibrium, M

Equilibrium Constant Kc



























 Average Kc = 98

Calibration Curve for Absorbance

 IV. Calculations


Equilibrium Constant of FeSCN

(See Data section for complete list of final calculation answers)

Part 1

Concentration of FeSCN

Equilibrium Constant

Concentration Fe at Equilibrium

9.7*10-6 / 0.1 L = 9.7*10-5 M Fe

Equilibrium Constant

Equilibrium Constant

V. Conclusions and Error Analysis

LeChatelier’s Principle


In this experiment the effect of stress on a system’s equilibrium was observed.  As more HCl was added in the second part, the equilibrium shifted to move the reaction in the reverse direction. In the third part, the color of the solution shifted as more of either KSCN or Fe(NO3)3 were added, shifting the equilibrium.  In the fourth part, the effect of temperature on equilibrium was observed.  As the solution sat in the ice bath, it turned pink because equilibrium shifted in the reverse direction because it had a ΔH of 50 kJ/mol.  As the solution warmed back up in the hot water bath, the reaction shifted again to favor the products.  In the first part of the experiment, the effect of a change in concentration was observed.  The HCl that was added reacted with the sodium chloride to form more solid sodium chloride on the top of the solution do to over-saturation.


Equilibrium Constant of FeSCN
The average Kc obtained was     . From the data it can be concluded that the concentration of FeSCN is inversely proportional to the absorbance and directly proportional to the amount of SCn used as a reactant.


Based on the obtained R2 value of     it can be inferred that only a small amount of error was obtained up to this point.  However, some explanations for the small amount of error that did occur are not setting the features of the Spec 20 correctly, contamination of the chemicals, and aging of the chemicals.  If the chemical were aged or contaminated, this would affect the molarity and therefore the absorption.  If the settings on the Spec 20 were incorrectly adjusted, this would affect the absorption number obtained.  If an error was made in the calculation for the concentration of FeSCN using the data from the graph, this would affect the calculated number of moles of FeSCN, and therefore affect the calculations of the number of moles and concentrations of the Fe and SCN, as well as the Kc value.


Ways to prevent these types of error are to double check the Spec 20 settings before use and to use only fresh chemicals to avoid aging and impurities.


Because 100. mL of solution was mixed in a volumetric flask after being measured in a graduated cylinder, some of the solution may have been retained in the cylinder and was therefore unable to react with the other chemicals in the solution, which would affect the absorbency.  Because such small quantities of solution were used in part 2, any error in measurement would greatly affect the absorption.


Some ways to avoid this type of error are to be as accurate as possible when measuring and making allowances in calculations for lost or spilled solutions.

VI. Discussion of Theory  


Equilibrium occurs when the forward reaction and the reverse reaction are acting at the same rate.  In the first experiment, the effects of temperature, saturated solutions, and the addition of more of either reactants or products were observed.  As stress is applied to a system, the system responds accordingly in order to maintain a state of equilibrium.  For example, if an endothermic reaction were cooled, the reaction would shift in favor of the reactants in order to relieve the stress, as demonstrated in the following equation:

form 1


In the second experiment, the equilibrium constant was determined for a reaction taking place in solutions of unknown concentration.  The average calculated value of the equilibrium constant (98) is relatively high, which indicates that the reaction’s equilibrium favors the products side of the reaction as shown in the following equation:

form 2

A spectrophotometer is an electronic device that measures the absorbance and percent transmittance of a solution by comparing the light waves accepted by the standard solution to the control solution (in this case distilled water).  The standard solutions were obtained by diluting particular amounts of a solution of known molarity in order to obtain a percent transmittance.  The molarity of the diluted solution is then obtained by using the formula M1V1 = M2V2, which is

then plotted against the absorbance to produce a calibration curve graph.  This graph is then used to calculate the number of moles and concentrations of the FeSCN, Fe, and SCN solutions, as well as the Kc values. Three significant figures including one estimated digit can be obtained using the spectrophotometer.  The major source of error that stems from using the apparatus is that it can be unreliable if the absorption is measured using the device rather than calculating it from the percent transmittance.  Other experiments in which a spectrophotometer would be useful are those which are designed to determine a chemical substance’s identity by using the color transmitted by its electrons.



Throughout the experiment, 0.5 molar nitric acid was used in all solutions in order to maintain a constant molarity of H+.  If a higher concentration of nitric acid had been used, this would have caused the Kc value to increase due to the fact that the hydrogen was a product, and therefore a numerator in the Kc calculation.

The Diels-Alder Reaction

By: Kayla Powers and Jakkrit Suriboot


Introduction Diels-Alder reactions are used for synthesizing new carbon-carbon bonds and more specifically, six-membered cyclic compounds. In addition, this reaction synthesizes compounds that are otherwise difficult to obtain, such as bridged bicyclic compounds.  A key characteristic of these reactions is their stereospecificity.  Based on the interaction between a conjugated diene and a dienophile, different stereoisomeric compounds are formed.   The Diels-Alder reaction is categorized as a pericyclic reaction, which involves the overlap of spatial orbitals as well as the hybridization and delocalization of the molecules.1  As a unique characteristic, this reaction is characterized as a concerted cycloaddition reaction indicating a lack of intermediate in the mechanism.

Stereochemistry represents a major component of the Diels-Alder reaction.  Due to the interaction and arrangement of a cyclic diene and a dienophile, an endo and exo product can be formed characterizing the reaction as stereo- and regioselective. By analysis of NMR spectroscopy and physical properties of the specific isomers, the difference between the possible products can be identified.

Interesting products of the Diels-Alder reaction are cyclic compounds with chlorine-containing substituents that act as powerful insecticides.  Insecticides have been commonly used to treat pests in various types of fruits, vegetables, and crops.  Because of the negative affect on the environment, certain pesticides have remained unused and alternative methods involving the elimination of pests have been investigated.  Strategies, such as using hormones have been explored with haste because of the potential damage many pests have on agricultural produce.2  These compounds have been researched and related back to their concerted cycloaddition mechanism.

Reaction Mechanism The scheme below depicts the concerted mechanism of the Diels-Alder reaction of cyclopentadiene and maleic anhydride to form cis-Norbornene-5,6-endo-dicarboxylic anhydride.

diels-alder reaction

Results and Discussion When combining the reagents, a cloudy mixture was produced and problems arose in the attempt to completely dissolve the mixture.  After heating for about 10 minutes and magnetically stirring, tiny solids still remained. The undissolved solids were removed form the hot solution by filtration and once they cooled, white crystals began to form. Regarding the specific reaction between cyclopentadiene and maleic anhydride, the endo isomer, the kinetic product, was formed because the experiment was directed under mild conditions.   The exo isomer is the thermodynamic product because it is more stable.3

A total of 0.47 g of the product was collected; a yield of 27.6%. The melting point was in the range of 163-164 °C which indicates the absence of impurities because the known melting point of the product is 164 °C.

Cis-Norbornene-5-6-endo-dicarboxylic anhydride

The 1H NMR spectrum of the product revealed a peak in the alkene range at 6.30 ppm, H-2 and H-3 (Figure 1).  In addition, it exhibited two peaks at 3.57 and 3.45 ppm because of the proximity of H-1, H-4, H-5, and H-6 to an electronegative atom, oxygen.  Finally, two peaks at 1.78 and 1.59 ppm corresponded to the sp3 hydrogens, Hb and Ha, respectively.  Impurities that appeared included ethyl acetate at 4.03, 2.03, and 1.31 ppm as well as acetone at 2.16 ppm.

Regarding the 13C NMR, a peak appeared at 171.3 ppm, accounting for the presence of two carbonyl functional groups, represented by C-7 and C-8 in Figure 1.  The alkene carbons, C-2 and C-3, exhibited a peak at 135.5 ppm, while the sp3 carbons close to oxygen, C-5 and C-6, displayed a peak at 52.7 ppm.  Finally, peaks at 46.1 and 47.1 ppm accounted for the sp3 carbons, C-1 and C-4, and C-9.  Impurities of ethyl acetate appeared at 46.6, 25.8, and 21.0 ppm accompanied with acetone at 30.9 ppm.

The IR spectrum revealed a peak at 2982 cm-1 representing the C-H stretches.  A peak at 1840 cm-1 accounted for the carbonyl functional group, while a peak at 1767 cm-1 accounted for the alkene bond.  A peak at 1089 cm-1 represented the carbon-oxygen functional group.

In order to distinguish between the two possible isomers, properties such as melting point and spectroscopy data were analyzed.  The exo product possessed a melting point in the range of 140-145 °C which is significantly lower than the endo product.  The observed melting point in this experiment supported the production of the endo isomer. The 1H NMR spectum exhibited a doublet of doublets at 3.57 ppm for the endo isomer.  The exo isomer would possess a triplet around 3.50 ppm due to the difference in dihedral angle between the hydrogen molecules of H-1 and H-4, and H-5 and H-6 (Figure 1).  A peak at 3.00 ppm would appear in the exo isomer spectra as opposed to a peak at 3.60 ppm as shown in the observed endo product.3 This is because of the interaction and coupling with the H-5 and H-6, as displayed in Figure 1.


Conclusion Through the Diels-Alder reaction, 27.6% yield of cis-Norbornene-5,6-endo-dicarboxylic anhydride was produced. The distinction of the presence of the endo isomer was proven by analyzing physical properties of both possible isomers.



General: All reagents were provided by Sigma-Aldrich from Texas A&M University Chemistry Department. 1H and 13C spectra were taken on a Mercury 300 MHz NMR spectrometer.  An IR spectrum was recorded on PerkinElmer UATR Two Spectrophotometer.


Cis-Norbornene-5,6-endo-dicarboxylic anhydride Cyclopentadiene was previously prepared through the cracking of dicyclopentadiene and kept under cold conditions.  In a 25 mL Erlenmeyer flask, maleic anhydride (1.02 g, 10.4 mmol) and ethyl acetate (4.0 mL) were combined, swirled, and slightly heated until completely dissolved.  To the mixture, ligroin (4 mL) was added and mixed thoroughly until dissolved.  Finally, cyclopentadiene (1 mL, 11.9 mmol) was added to the mixture and mixed extensively.  The reaction was cooled to room temperature and placed into an ice bath until crystallized.  The crystals were isolated through filtration in a Hirsch funnel.  The product had the following properties: 0.47 g (27.6% yield) mp: 163-164 °C (lit: 164 °C).  1H NMR (CDCl3, 300 MHz) δ: 6.30 (dd, J=1.8 Hz, 2H), 3.57 (dd, J=7.0 Hz, 2H), 3.45 (m, 2H), 1.78 (dt, J=9.0,1.8 Hz, 1H), 1.59 (m, 1H) ppm.  13C NMR (CDCl3, 75Hz) δ: 171.3, 135.5, 52.7, 47.1, 46.1 ppm.  IR 2982 (m), 1840 (s), 1767 (s), 1089 (m) cm-1.

Supporting information IR, 1H NMR and 13C NMR spectra of cis-norborene-5,6-endo-dicarboxylic anhydride are attached.

1 Martin, J.; Hill, R.; Chem Rev, 1961, 61, 537-562.

2 Pavia, L; Lampman, G; Kriz, G; Engel, R. A Small Scale Approach to Organic Laboratory   Techniques, 2011, 400-409.

3 Myers, K.; Rosark, J. Diels-Alder Synthesis, 2004, 259-265.


Determining a Reaction Intermediate

By: Jaime Rodriguez


In this experiment, the concentrations of KMnO4 in each test tube were considered similar if their respective colors were similar. This step is what made it possible to calculate the amount of hydrogen peroxide in the original solution of melted ice. Unfortunately, the human eye is not keen to accurately detect the change in color intensity; therefore the colors in both test tubes may not have been very similar at all. Besides this method, there is another, more accurate, method that could determine when all of the hydrogen peroxide was consumed in the reaction. With the use of a ph monitor, the total consumption of the hydrogen peroxide could be determined. ( ph of H2O2 Solutions). In the reaction, the addition of the hydrogen peroxide turns the solution from basic to acidic. After all of the hydrogen has been consumed, the solution will return to a base. If the shifts in ph are monitored, it can accurately be determines when all of the hydrogen peroxide has been consumed.


No changes were made to the procedure. It was followed as it was written.

Data and Results:

detecting a reaction intermediateDetecting a reaction intermediate 2

Table of results:

Table of results

The number of moles of excess MnO4- present was calculated by taking the concentration of KMnO4 from the test tube with deionized water, and multiplying it by the total volume of solution in the test tube with melted ice.

6.87*10^-7M * .00552L

=3.8*10^-8 moles

The number of moles of MnO4- which reacted was found simply by subtracting the number of moles in excess by the number of moles added.

1.008*10^-7 moles  – 3.8*10^-8 moles

=6.28*10^-8 moles

The moles of H2O2 which reacted was found by using the stoichiometric ratio of number of moles of H2O2  to number of moles of MnO4- .

6.28*10^-8 moles of MnO4- * (5 moles of H2O2/2 moles of MnO4- )

=1.57*10^-7 moles

Finally, the concentration of H2O2  in the original melted ice solution was calculated by dividing the number of moles of H2O2  which reacted by the volume of melted ice.

1.57*10^-7 moles/.00472L

=3.33*10^-5 M

The reaction between H2O2  and MnO4- might proceed more slowly at the end because by this time, almost all of the H2O2  is being consumed in the reaction. The concentration of hydrogen peroxide that was measured was 3.33*10^-5 M

To calculate the free energy of the reactions for hydrogen gas reacting with gaseous water to form gaseous hydrogen peroxide, and gaseous hydrogen peroxide reacting with hydrogen gas to form water, were found by using the Gibbs free energy equation.

The equation states that,  delta G=delta H-delta S(T). To find delta S and H, the values of H and S for each of the reactants and products were found. Then, the sum of the products was subtracted by the sum of the reactants. Once this was done, the values were put in to the Gibbs free energy equation, and the temperature used was 198.15 K, room temperature. The free energy values were -105.5kJ, and -351.5kJ, respectively. The free energy values for these two equations should be equivalent to the free energy associated with the combustion of hydrogen, since both are intermediate reactions, with hydrogen peroxide being the reaction intermediate. Below is the corresponding potential energy diagram.

reaction coordinate


The experiment was easy, relatively quick, and yielded good quality data. Some of the calculations got confusing, but they were eventually figured out. There were really no issues with the experiment, and it was overall relatively enjoyable.


pH of H2O2 solutions? | H2O2.com – US Peroxide – Technologies for Clean Environment.” US Peroxide – Technologies for a Clean Environment. N.p., n.d. Web. 22 Apr. 2013. <http://www.h2o2.com/faqs/FaqDetail.aspx?fId=26>.


Determination of Mn in Steel

By: Juno Kim and Nicole


            The goal of this experiment was to determine the mass percent of manganese in an unknown steel sample using methods of visible spectroscopy and volumetric analysis. The two methods were then analyzed and compared to decide the better method for determining the composition of Mn in the unknown steel. In both methods, the unknown steel was digested in hot concentrated Nitric acid, HNO3, and analyzed for transition metals. An accurate analysis of steel composition is important because the mass percent of carbon and transition metals in the steel determine its properties such as strength, conductivity, ability to be altered by heat, and corrosiveness that ultimately decide the steel’s usage. An alloy is a mixture of two or more elements, one of them being a metal, and steel is an alloy of iron containing small amounts of transition metals. Adding carbon to iron creates steel which has versatile uses for its general properties.

Pertaining to this lab, knowing the composition of steel reveals the best form of usage. For example structural steels contain alloying elements like Mn that can be used to produce complex structures and machine parts while tool steels have higher carbon mass percentage and contain alloying elements such as chromium. Compared to iron, steel is tougher with high strength and has the ability to greatly alter form through heat treatment. Adding Chromium to steel produces stainless steel that resists corrosion and adding silicon to steel creates silicon steel used for electronic purposes. The composition of steel must be determined and double checked prior to its intended use to avoid consequences as large as a bridge collapsing due to the use of inadequate steel. The methods of determining the composition of steel can also be used to analyze the strength and durability of already standing structures that have been subject to corrosion and weathering as well. The main objective of the experiment was to determine the manganese composition of the steel unknown by the methods of standard additions, involving visible spectroscopy, and volumetric analysis, involving back titration.

Experimental Methods

I. Standard Addition

The standard addition method used visible spectroscopy to determine the concentration of

manganese in the unknown steel sample. Standard addition is used to account for the potentially interfering ions from other transition metals.2 To start with, the sample of unknown steel was digested in hot nitric acid. Precisely 1.0437g of steel unknown and 50 mL of 4M nitric acid, HNO3, were added to a 250mL beaker and brought to a gentle boil. The beaker was covered with the watch glass to avoid losing its contents through splattering. It took close to an hour for all of the unknown steel to dissolve so excess 4M HNO­3 was added during the digestion to displace the evaporated liquid and keep the volume close to 50 mL. After digestion, 1.0 g of ammonium peroxydisulfate, [(NH4)2S2O­8], was slowly added to the beaker and put to boil for 15 minutes. During the boil, peroxydisulfate oxidizes any carbon in the sample in the reaction shown below:

2S2O82- + C + 2H2O -> CO2 + 4SO42- + 4H+

Following the procedure, 0.1 g of sodium bisulfate (NaHSO3) was added while heating and the resulting solution was left to cool to room temperature and transferred to a 250 mL volumetric flask where it was diluted with distilled water to the mark. Note that NaHSO3 solution was added to reduce any permanganate that may have formed through this reaction:

5HSO3- + 2MnO4- + H+ -> 2Mn2+ + 5SO42- + 3H2O

            Following the steel digestion, the standard Mn solution was prepared. For that 100 mg of Mn was dissolved in 10 mL of 4M HNO3 and put to boil to remove nitrogen oxides. The resulting solution was diluted to the mark with DI water in a 1 L volumetric flask.

After the necessary solutions were prepared, standard additions took place. Total of seven samples were prepared for the spectroscopy and in each sample 20 mL aliquot of the digested steel was put into a 250 mL beaker. Then 5 mL of 85% phosphoric acid was added to eliminate iron(III) as a source of interference when taking the spectroscopy. Samples of standard Mn2+ and solid potassium periodate were added to the beaker according the table I provided below:

Table I: Calibration Standard Sample Volumes




Standard Mn



20 mL

5 mL

0 mL



20 mL

5 mL

0 mL



20 mL

5 mL

1 mL



20 mL

5 mL

2 mL



20 mL

5 mL

3 mL



20 mL

5 mL

4 mL



20 mL

5 mL

5 mL


Upon heating, KIO4 oxidizes Mn2+ to a permanganate ion in the reaction given below:

2Mn2+ + 5IO4- + 3H2O -> 2MnO4- + 5IO3- + 6H+

Each of the samples were boiled for 5 minutes and cooled before being diluted in a 50 mL volumetric flask. Then, using the UV-Visible spectrometer, absorbance at the max wavelength for permanganate ion was measured. The max wavelength for the permanganate ion is 525 nm and the analyzers are designed to measure the absorbance in a particular wavelength band1. Small aliquots of each sample were added to a cuvette to measure the absorbance and a linear graph was expected with no absorbance value greater than 1.0 for any of the samples. At the end, the absorbance of the blank solution, containing no Mn or KIO4, was deducted from the other samples’ absorbance values. The line of best fit for the plot of concentration of added Mn2+ vs. the absorbance was drawn to find the x-intercept which represented the concentration of Mn in the unknown steel sample. The concentration of added Mn2+ was calculated by using the concentration of the standard Mn solution as shown below:

100.0 ppm * (mL of Mn added/50 mL) = concentration of Mn in ppm

II. Volumetric Analysis

            Determination of Mn in the unknown steel through volumetric analysis involved titrations. A standard potassium permanganate (KMnO4), standard Ferrous Ammonium Sulfate (Fe(NH4)2(SO4)2), and an unknown steel sample were prepared in lab for the titration of the unknown steel sample.

The KMnO4 solution was prepared by glass filtering 100 mL of 0.1 M KMnO4 solution through a sintered glass filter. The resulting solution was then transferred to a 1 L volumetric flask and diluted to the mark with DI water. To standardize this solution, solid sodium oxalate was put to dry in an oven for an hour. Then three 100 mg samples of dried sodium oxalate were transferred to 250 mL beakers along with 100 mL of 0.9 M sulfuric acid (H2SO4) and heated. While heating, a burette was filled with the permanganate solution and its initial volume was recorded. A single drop of the permanganate solution was added to each of the beakers while heating and the titrations commenced once the pink color from the permanganate disappeared. The reappearance of the pink color marked the end of titrations. The reaction of permanganate with oxalate is as follows:

2MnO4- + 5C2O42- + 16H+ -> 2Mn2+ + 10CO2 + 8H2O

Using stoichiometry, the concentration of MnO4- in the solution was calculated using the formula:

0.100g C2O4- * (1 mol/88.01928g C2O4-) * (2mol MnO4-/5 mol C2O4-) *(1/L of MnO4- used)

Taking the average of the three trials yielded a MnO4- concentration of 0.0148 M in the standard solution.

For the preparation of standard Fe(NH4)2(SO4)2 solution, about 12 grams of ferrous ammonium sulfate hexahydrate were added to a 1L volumetric flask and dissolved in 1:20 sulfuric acid (H2SO4). The solution was diluted to the mark with 1:20 H2SO4. For the standardization process, 25 mL of 1:30 nitric acid (HNO3) was added to a 250 mL Erlenmeyer flask using a volumetric pipette. Then 25 mL of Fe(NH4)2(SO4)2 was added and the resulting solution was titrated with KMnO4 until the pale pink endpoint. The ferrous ions react with MnO4- in the redox reaction given below:

MnO4- + 5Fe2+ + 8H+ -> Mn2+ + 5Fe3+ + 4H2O

Using stoichiometry, the concentration of the ferrous ion, Fe2+, was calculated using the formula:

(Volume of KMnO4 used) * 0.0148M KMnO4 * (5 M Fe2+/1 M MnO4) * (1/volume of sample)

Taking the average concentrations of four trials yielded a Fe2+ concentration of 0.0466 M in the standard solution.

For the preparation of steel unknown sample, 0.2351 g of the unknown steel sample was added to a 250 mL beaker. The manual states a whole gram of the unknown steel should be used, but after a few failed trials with the first method, only 0.2351 g of the unknown steel was left for analysis. Then 50 mL of nitrous acid free 1:3 HNO3 was added to the beaker and the contents were put to a gentle boil under a watch glass cover. Once all the steel dissolved, the beaker was removed from heat and 0.5 g of sodium bismuthate (NaBiO3) was added. After the addition of NaBiO3, the contents were boiled for another five minutes which after, the solution turned purple so there was no need to add additional grams of NaBiO3. The resulting purple solution was removed from heat and drops of sodium sulfite (NaSO3) were added until the purple color disappeared (3 drops used). Then the solution was put to boil and became rust orange in color after 5 minutes. The beaker was cooled in an ice bath and allowed to chill and after, 0.7 g of NaBiO3 was added to form a solid NaBiO3 inside a purple solution. The reaction of bismuthate with manganese ion is shown below:

2Mn2+ + 5BiO3- + 14H+ -> 2MnO4- + 5Bi3+ + 7H2O

To transfer the solution, a sintered glass filter was used instead of filter paper which the Mn could react with. The filter was washed with 1:30 HNO3 and the solution inside the beaker was filtered into a flask. After filtration 4 mL of 85% phosphoric acid (H­3PO4) was added to the filtrate and mixed. The resulting solution was then transferred to a 100 mL volumetric flask and diluted to the mark with 1:30 HNO3.

After the necessary solutions were prepared, the titration of the unknown steel 64 commenced. 25 mL of the (Fe(NH4)2(SO4)2) solution as well as 25 mL of the steel unknown solution were added to an Erlenmeyer flask using a volumetric pipette. The purple color disappeared as the steel unknown reacted with the ferrous ions. Then the solution was back titrated to the pink endpoint with the standard KMnO4 solution. In this back titration, an excess of standard (Fe(NH4)2(SO4)2) was added to the steel unknown, turning the color clear as the ferrous ions reacted. Then the excess (Fe(NH4)2(SO4)2) was titrated with the standard KMnO4 until the endpoint which was signaled by the reemergence of the pale pink color. Once all the Fe2+ ions have reacted, MnO4- remained in the solution to signal the end of the back titration with the pale pink endpoint. The net ionic equation is:

MnO4- + 5Fe2+ + 8H+ -> Mn2+ + 5Fe3+ + 4H2O

The percentage Mnin the steel unknown was calculated by the formula below:

the formula


The results from the two different methods were synchronized. The Mn contents of all the unknowns vary from 0.10% to 1.00% so both methods gave an acceptable result.

The Beer’s law states that absorbance is proportional to concentration. The calibration plot of UV-Vis supports the law. Beer’s law:

A = εlc

‘A’ represents absorbance with no units. ε is the molar absorption coefficient with units Lmol-1cm-1. ‘l’ represents the path length of the cuvette and ‘c’ is the concentration of the compound in solution expressed in molL-1. Another form of Beer-Lambert’s law is:

I = I010^-εcL 3

‘I’ is the transmitted intensity, varying with the length L and I0the incident intensity.2 UV and visible spectra are plots of absorbance against the wavelength in nanometers. Its absorbance is related to concentration by the Beer-Lambert’s law.4

A = log(I0/I) = εlc 4


            The weight percentage of Mn in the unknown steel sample was calculated as .51% with 95% confidence interval of 0.71 from the visual spectroscopy method. The absorption of the blank sample containing no standard Mn or KIO4 was measured to be 0.0395. The measurement of the second sample yielded absorption value of 0.4020. After subtracting the blank absorption value the first sample’s absorption was 0.3625. This was a lot higher than 0.1 absorption value the second sample should be at so the absorption values along with the steel sample volume were adjusted through division by 4. The 95% confidence interval value of 0.71 is very high. The cause of error in this method most likely resulted from the fact that the steel unknown solution had small precipitates that would not dissolve. Such error may be alleviated by letting the solution sit for a period of time until the precipitates fall to the bottom of the flask. Then samples could be taken from the top of the solution without any precipitate using a pipette. The steel unknown sample took 45 minutes longer than anticipated to digest during the lab and even after the digestion there were some particles left in the solution. This could be from impurities of the unknown steel sample. The digestion process could be sped up next time by preparing a hot HNO3 to digest the steel unknown.

The volumetric analysis also gave a Mn concentration of 0.51% in the unknown steel with the 95% confidence interval of 0.16. For this experiment, judging from the lower value for the confidence interval, this method of back titration gave more reliable concentration of Mn in the steel #64. Note that instead of using 1 g of the unknown steel sample, only 0.2351 g was used because that is what was left available. The volumes of KMnO4 used to back titrate the mixture of 25 mL unknown steel solution and 25 mL (Fe(NH4)2(SO4)2) were very consistent and consequently, they yielded consistent Mn weight percentage values in the three trials. The weight percentages of Mn for the three trials were found to be 0.52%, 0.51%, and 0.50% with the low variance of 0.02. The standard deviation, 0.1414, was calculated by square rooting the variance. The standard error, which was multiplied by 1.96 to give 95% confidence margin of error, was calculated by dividing the standard deviation by the square root of the number of trials. The confidence interval, calculated as 0.16, is still high considering the precise Mn percentage values. This could be amended by increasing the number of trials which would bring down the values (assuming the same, precise Mn percentages are calculated).

Comparing the two, both methods gave a very precise concentration of Mn in the unknown steel. The volumetric analysis had a much lower value for its confidence interval so for this experiment the back titration proved to be the better method. The visual spectroscopy method was easier in a sense that the UV-Visible spectrometer measured the absorbance for each of the prepared cuvette samples left to be graphed and analyzed. However the slight problem with this method is the fact that it relies on the line of best fit to find the concentration of Mn in the sample, making it more prone to errors by inaccurate measurements.

The volumetric analysis involved preparing two standard solutions and an unknown steel solution before the titration of the steel unknown. This method gave the experiment more control because the standard solutions were made in lab and their concentrations were calculated using stoichiometry from the redox equations. It was also easy to tell if a certain titration has gone wrong by looking at the volumetric data and noticing an outlier among the volumes used for the same titration. In this method it was critical to keep the prepared solutions from being affected by impurities. That was achieved by transferring small amounts of the standard solutions into beakers and drawing samples from the beakers. That prevented the standard solutions from being contaminated through multiple aliquots drawn by a pipette.


The purpose of the experiment was to find the concentration of Mn in an unknown steel sample through the method of standard additions, involving visible spectroscopy, and volumetric analysis, where the concentration was calculated through back titration. The volumetric analysis proved to be a better method since the standard addition method’s calibration plot of the UV-Visible spectrometer yielded a faulty 0.71 margin of error under a 95% confidence level. Such margin of error is unacceptable considering the Mn concentration falls outside probable range between 0.1% and 1% after just one standard deviation away from the mean. After back titrations, the Mn concentration in the unknown steel was found to be 0.51% with 0.16 margin of error under a 95% confidence. Adding Mn to steel increases the steel’s toughness and strength and analysis of the concentration of Mn or other transition metals in steel as well as carbon can reveal the properties of the steel and its practical usage.



1 Laverman, L.E. Experiments in Analytical, Physical and Inorganic Chemistry, 3rd Edition; p.


2 Green, Don W., Perry, Robert H. Perry’s Chemical Engineer’s Handbook, 8th Edition;

McGraw-Hill: New York, 2008, p. 8-62.

3 Atkins, Peter., Paula, Julio de. Physical Chemistry, 9th Edition; W.H. Freeman and Company:

New York, 2010, p. 490.

4 Mohrig, J.M., Hammond, C.N., Schatz, P.F. Techniques in Organic Chemistry, 3rd Edition; W.

H. Freeman and Company: New York, 2010, p. 429.

Diffraction Patterns from Polystyrene Beads and from Breath Figures

By: Ludmila Novikova


Before X-ray diffraction of crystals was applied to determine the arrangement of atoms in 1913, little was known about the geometric and stereochemical shape of molecules and about the science of crystallography in general. In fact, the atomic theory of matter was not completely accepted because there was no theory available to explain the existence of compounds of the same composition (Flack, 372). X-ray crystallography presented us with methods that would allow us to strike a chosen crystal with a beam of X-rays so that we could measure and interpret the diffraction patterns that would be produced from the crystal. The calculations of the angle of diffraction, wavelength paths and distances between the atoms in the crystal are useful in determining the positions of atoms in a crystal, their chemical bonds, electron density, and much more.  The resulting information is then used to analyze the structure and function of bio molecules. We can already get a sense of how important and advantageous the study of crystallography is, and one of the primary objectives in this chemistry project was to study diffraction patterns of crystals to better understand diffraction phenomena.  Throughout the semester, I worked with small sizes of polystyrene beads to analyze, compare, and interpret the outcomes of the scattering and diffraction patterns given out by the crystallites. The size of the beads had to small because they would create diffraction patterns that could have defined and distant spacing lengths between “points” of the crystal. These polystyrene beads ranged from .5mm to 3 mm in diameter and they were diluted in different mixtures of water, ethanol, glycerol, cationic surfactant, and even with a small amount of potassium chloride solids. They were then delivered onto glass slides, covered with glass cover slips so that then they could be placed into an apparatus that held the slide in place. A helium-neon laser was then used to shoot a beam of emitted photons of the same wavelength (632.8nm) so that diffraction patterns could be produced. It should be noted that the monochromatic light had to pass through a magnifying lens that focused in on one sample of the microscope slide. The goal in this crystallography project was to create a monolayer of polystyrene beads on the glass slides to see hexagonal packing. Measurements of the angle of diffraction and distances between a set of “points” could then be carried out and the calculations could then be applied to make an analogous method for finding protein structures. Towards the end of this project, it was also found that diffraction patterns could also be given out by breath figures. The condensed tiny droplets of water formed an epitaxial film on the glass slides and this observation turned out to be useful because breath figures are smaller than .1mm.  Overall, much was learned about the study of crystals, spectroscopy, diffraction gratings, and breath figures to come to the conclusion of how X-ray crystallography can help us study internal structure of crystalline materials.

That we find a crystal or a poppy beautiful means that we are less alone, that we are more deeply inserted into existence than the course of a single life would lead us to believe.”    ~John Berger


Let us start off with the definition of a crystal. A crystal is a crystalline solid whose atoms are arranged in a repeating pattern. At a nano scale, the crystals’ complex arrays of atoms rarely have a perfect internal structure, and most often the crystals have misalignment of the arrangement of these atoms.

In theory, if we take a crystal (using high tech equipment) and we want to determine its crystal structure, we have to apply mathematical equations to the diffraction patterns it gives off when X-rays are shot at it. In X-ray crystallography, the X-rays are waves of electromagnetic radiation that are scattered by atoms. The X-rays essentially produce a diffraction pattern because their wavelength is typically the same order of magnitude as the spacing between the diffracting planes and the spacing between the points of the atoms. These patterns can be seen on some type of slide that shows the image of the diffraction pattern.

The diffraction pattern is produced because the electromagnetic waves from the X-rays interfere with each other constructively and destructively which results in the image we see when the X-ray light interacts with the crystallites.

When we finally determine the crystal structure of the crystal we’re studying, we can correlate its structure to the structure of bio molecules such as proteins. The applications of X-ray crystallography can help us better understand the structure of the proteins, and since “structure” of proteins is related to their “function”, we may also learn more about the function of the various proteins we might be studying.

Background Chemistry:

Crystal Structure Determination: A crystal’s structure may be determined if we take a sample of a small crystallite and measure the variations of the intensity of radiation passing through a portion of the crystal. We must then find the angle of diffraction between the diffracting planes and we must measure the path lengths of the rays.

There are many definitions for different terms when we’re discussing various locations on a crystal. Below is a list of the basic definitions applied to all crystals.

  1. Lattice: An infinite array of points in space. The points have identical surroundings to all other points.
  2. Crystal Structure: The periodic arrangement of atoms in the crystal.
  3. Unit Cell: The smallest component of the crystal. Many unit cells compromise the crystal.
  4. Asymmetric Unit: Fraction of a unit cell

As for the mathematical equations that are applied to the diffraction patterns, most of them branch off from Bragg’s Law of diffraction. The Bragg’s Law of diffraction gives the angles for coherent and incoherent scattering from a crystal lattice.

Bragg’s Law of Diffraction: nλ=2dsinθ

It is for this law that we can confirm the existence of real particles at the atomic scale. Why? Because the tiny particles we’re observing scatter light. And although white light (400-700nm) consists of waves that have different intensities, the objects that scatter this light have different scattering patters. This is important to note because tiny objects usually do not give significant scattering of the light, but if we use a beam of X-rays, which have a wavelength of 10-35nm, we’ll then be able to see the scattering pattern from those tiny molecules. This is true because the size of the tiny objects correlate to the wavelength of the X-rays. Low wavelength (like X-ray wavelength) correlates to high energy. We can conclude that a lot of energy is proportional to high frequency.

Diffraction is the interaction of radiation with matter. In this project, the “matter” refers to polystyrene crystallites and the “radiation” refers to monochromatic light from a laser.

Polystyrene Beads: Beads of aromatic polymers. Polystyrene is commonly used in the industry of plastics. It is also solid at room temperature and the chemical formula is C8H8.


In this project, we are using monochromatic light because its wavelength is 632.8nm, it has a narrow frequency, and the energy levels are not strong enough to melt the polystyrene beads. Basically, if the wavelength is increased into the range of white light, we will not see any diffraction points. We must keep the wavelength 1.33 X 10-6  or lower to be able to see diffraction points. When the laser light is shot out at a crystal, the crystallites emit and absorb energy as they jump from an excited energy state to a ground state. The emitted and absorbed radiation occurs because of the interaction between the beads and the monochromatic light.

When many polystyrene beads are atop of one another, and monochromatic light is shot at the beads, the scattering pattern presents us with circular diffraction, called powder patters. These powder patterns are circular because the polystyrene beads are the same size and they’re giving out diffraction patterns in all directions. When there is a monolayer of polystyrene beads, you get a diffraction pattern. If you take a picture of this diffraction pattern, you can find the angle of diffraction using your knowledge of the wavelength of the laser, and your knowledge of the size of the polystyrene beads, and your measurements of the spacing between the “points” on the diffraction pattern.

One of the problems in X-ray crystallography, when determining crystal structure, is the issue of observing a crystal that is too small. It takes time to grow the perfect crystal and once you’ve finally chosen the crystal you’d like to study, you must keep in mind that when the crystal is placed on the goniometer head (X-ray crystallographic device), the crystal is rotated in the X-ray beam, so that it gives off diffraction patterns that reflect the radiation at different levels of absorption. This absorption depends on the path lengths of the X-rays through the crystal and it changes as the crystal is oriented. The mathematics is done through a computer programed system, but factors such as these are crucial in order to understand how the crystal structure correlated to the structure of various bimolecular chemicals.

To avoid crystallography problems in our experimentation, you must make sure to keep the different sizes of the polystyrene beads away from each other because they might mix in with each other and you will never know because the beads are tiny.





Pre-Laboratory Quiz:

1)      What is a crystal?

A crystal is a crystalline solid whose atoms are arranged in a repeating pattern.

2)      What is diffraction?

Diffraction is the interaction of radiation with matter

3)      Why do we need to use monochromatic light when observing 1mm polystyrene beads?

We are using monochromatic light because its wavelength is 632.8nm, it has a narrow frequency, and the energy levels are not strong enough to melt the polystyrene beads

4)      What would happen if we used white light to observe the diffraction patters from the polystyrene beads?

We would not see any diffraction patterns because the wavelength of the white light would be too long and it would not correlate to the size of the beads.

5)      What is the name of the X-ray crystallographic device that is used to determine the crystals’ structure?


6)      Name one problem that scientist might encounter when working with crystals?

The crystal might be too small to have its structure determined. It takes time to grow enough of the crystal for it to be observed and analyzed.

7)      What is the Bragg’s law of diffraction?


8)      What are powder patters?

Powder patterns are circular diffraction patterns because the polystyrene beads (for example) are the same size and they’re giving out diffraction patterns in all directions.

9)      What is the chemical formula for polystyrene?


10)    What is one benefit from determining the crystal structure of the crystal being studied?

We can use the crystal structure to understand the structure of proteins.


Laboratory Experiments: Flowchart of the Experiments


Section A: Powder Patterns

Section B: Diffraction Grating

Section C: .5mm Polystyrene Diffraction Pattern

Section D: 3mm Polystyrene Diffraction Pattern

Section E: Breath Figures

Section A: Powder Patterns

Goal: To recognize powder patterns and understand how and why they form.

Powder patterns are patterns of circular diffraction given out by many crystallites that are superimposed on each other, clumped together, and atop of one another.


1)      Set up a helium-neon laser

2)      Tape a magnifying lens to the opening of the laser

3)      Stack 3 1X96 well-trays atop of one another 10 cm in from of the laser opening.

4)      Place 4 straws into the top tray so that they can hold the glass slide. (Look at picture below)

5)      Set up a white slide 3 feet away from the apparatus to look at the diffraction patterns.

6)      Deliver one drop of .5mm polystyrene beads onto the glass slide and spread the beads with a brush.

7)      Let the mixture dry.

8)      Take the slide and place it between the 2 straws on each side.

9)      Look at the slide to observe the scattering pattern.

Apparatus Diagram:

Apparatus Diagram

The apparatus in the middle holds the slides.

The pattern should appear to have circular concentric rings around the undiffracted beam (the most intense beam) This pattern is called a powder pattern, and you should be able to see it because the drop of the polystyrene beads from the hydrophobic solvent were not diluted in water. If the polystyrene beads were highly diluted, you would see hexagonal packing in the diffraction pattern.



Section B: Diffraction Grating

Goal: To apply Bragg’s law of diffraction to find the angle of diffraction from a diffraction grating that has 75000 grooves per cm.

A diffraction grating is a piece of a plastic slide with many tiny spaced slits in it that diffract laser beam light into an order of points that have different intensities.  (Refer to picture below)

diffraction grating

When we use diffraction gratings with a laser, we know that the points displayed are 2-dimentional. Because the points are 2-dimentional, we use the Bragg’s law of diffraction that is not 3-dimentional. This equation comes out to be nλ=dsinθ. The wavelength of the laser was 632.8nm, the distance between the grooves was 75000 grooves per cm, and the integer number was 1. If we plug this information into the equation, we can find the angle of diffraction.


1)      Place a piece of diffraction grating 10cm away from the laser.

2)      Mark the points of interaction between the laser light with the diffraction grating.

3)      The mathematical procedure of finding the angle of diffraction is written out below.

The calculations should show that there was constructive interference between the grooves. The grooves allowed the light to pass through and as the light passed through, it separated between the slits. The angle of diffraction also depends on the wavelength of light. From previous experimentation, we can also conclude that the relationship between the angle of diffraction and wavelength determines the color we see.


Question to consider: If there was destructive interference between the rays, would the equation of nλ=dsinθ be true? No, the nλ would not equal dsinθ because the rays would cancel each other out.

Section C: .5mm Polystyrene Diffraction Pattern

Goal: To create a monolayer of .5mm polystyrene beads on a glass slide and prove that the wavelength of the laser correlates to the size of the polystyrene beads.


.5mm is a very small size. From the introduction and background chemistry, we may recall that is preferable to work with small crystallites because they give out a more precise image of the diffraction patterns. The beads give out “points” onto the slide whose spacing can be measured easily because it is not clumped together. The smaller the beads are, the more distant the spacing is between the points is. This is what we would like to prove in this experiment and in the next one where we will be using 3mm polystyrene beads.



1)      Get out a clean microscope slide with a clean cover slip and set them aside.

2)      .55mm polystyrene beads need to diluted in lots of water and ethanol. To prepare the mixture, you must deliver 1 drop of the beads from a pulled micropipette into a well in the 1X24 well tray.

3)      You must then add 20 drops of water and 10 drops of ethanol into this tray and mix them all together.

4)      Suck up the solution using a clean micropipette and deliver 1-2 drops of this solution onto the microscope slide.

5)      Make a wet mount by placing the cover slip over the solution. Try to avoid any air bubbles.

6)      Place the slide into the apparatus that holds microscope slides.

7)      Find a monolayer on the slide

8)      Observe the diffraction patterns.

9)      What do you see? (If you see scattering patterns, this means that the beads are not diluted enough)

10)   Mark the spots on the slide. Keep the recorded markings on the slide for further comparison with the 3mm polystyrene bead diffraction patters.

To get a defined image from the polystyrene beads, it is also useful to cut out a hole in the slide (paper) for the undiffracted beam to go through. This will allow you to see the different intensities of the various points on the image.  Also, make sure to record your data immediately after you have found a clear diffraction pattern because from experimentation, it was noticed that the polystyrene beads were moved by the laser light and the beads were also melted. It is hard to avoid these problems because the magnifying glass directs a lot of energy onto a sample on the microscope slide.  High energy is what is responsible for moving and melting the beads.




Section D: 3mm Polystyrene Diffraction Pattern

Goal: To compare the diffraction patterns from the 3mm polystyrene beads to the diffraction patterns from .5mm polystyrene beads.

The diffraction patterns from 3mm polystyrene beads should come out to be smaller, more clumped (packed) together and the spacing between the points should be small as well. In the following experiment, we want to prove that the spacing between the crystallites can be interpreted knowing the size of the polystyrene beads. The primary objective here is to show that the bigger the polystyrene beads are, the harder it is to detect a diffraction pattern. If the beads are bigger than the wavelength of the monochromatic light, we will not be able to see the diffraction patterns at all.


1)      Repeat everything from Section C using 3mm polystyrene beads.

2)      What diffraction pattern do you see?

Compare the diffraction patterns from both experiments and explain what you would expect to see if we used .01mm polystyrene beads.

schematic representation of what the

Section E: Breath Figures

Breath figures are condensed tiny droplets of water formed that form an epitaxial film on the glass slides. They are useful in our research because breath figures range from .1mm to .01mm. In theory, we may obtain diffraction patterns that have distant spacing between the water molecules. In the following experiment, we will observe breath figures.


1)      Take a styrofoam cup and fill it with hot water of 65°C

2)      Place the top lid of a petri dish onto the opening of the cup and let it sit there until a cloud forms underneath the lid

3)      Place the lid back onto the bottom half of the petri dish

4)      Allow laser light to pass through a sample of the cloud

5)      Observe and record diffraction patterns.

The diffraction patterns should come out to be well defined because the size of the water droplets ranges from .1mm to .01mm.

To continue on with these experiments, we can observe diffraction patterns from various chemicals like the interaction between HCl and NH3. As a chemical front is formed off the surface of the NH3 drop, smoke will fill the petri dish and the NH4Cl particles will form small solid crystallites that will too give off diffraction patterns.

6)      Take a clean petri dish and place one drop of NH3 on the top and one drop of the HCl onto the bottom half of the petri dish

7)      Close petri dish

8)      Allow the smoke to fill the petri dish

9)      Shoot laser light through the petri dish

10)   Compare the diffraction patterns given off by HCl and NH3 and water molecules from water vapour.

An advantage of studying diffraction patterns from breath figures rather than from polystyrene beads is that it is cheaper. The price to gather the apparatus materials for polystyrene beads came out to be over a $100. Thanks to Dr. Thompson, I was able to study diffraction patterns through the use of these micron sized polystyrene beads.







Works Cited

“Bragg’s Law.” Wikipedia, the Free Encyclopedia. Web. Feb. 2011. <http://en.wikipedia.org/wiki/Bragg’s_law>.

Clegg, William. Crystal Structure Determination. Oxford: Oxford UP, 1998. Print.

“Crystallography.” Wikipedia, the Free Encyclopedia. Web. 28 Jan. 2011. <http://en.wikipedia.org/wiki/Crystallography>.

“Epitaxy.” Wikipedia, the Free Encyclopedia. Web. 18 Apr. 2011. <http://en.wikipedia.org/wiki/Epitaxy>.

Feynman, Richard P. QED: the Strange Theory of Light and Matter. Princeton, NJ: Princeton UP, 1985. Print.

Flack, H. D. “Louis Pasteur’s Discovery of Molecular Chirality and Spontaneous Resolution in 1848, Together with a Complete Review of His Crystallographic and Chemical Work.” Web. Jan. 2011. <http://library.epfl.ch/en/periodicals/?recId=12869839>.

Taylor, Charles Alfred. Images: a Unified View of Diffraction and Image Formation with All Kinds of Radiation. London: Wykeham Publications, 1978. Print.

Thompson, Stephen. Chemtrek: Small-scale Experiments for General Chemistry. Englewood Cliffs, NJ.: Prentice Hall, 1989. Print.