Thermodynamics and Kinetics

Independent Investigation

 

Investigations will span the last several weeks of laboratory and will result in a detailed report, a Web based summary of key findings, and a formal presentation to the class during the final days of class.  The first week of the investigation will be spent preparing a two page proposal which will include rational for the investigation with references (3-5) to the literature and a detailed plan including a timeline and a list of materials and equipment.   Use RefWorks to format your citations in the ACS Jouranl of the American Chemical Society format (see http://gustavus.edu/academics/library/search/refworksguide.html ). Provide catalog numbers, quantity, and pricing for necessary materials after making sure that they are not available in the stockroom (see http://gustavus.edu/academics/chem/Chemistry%20Stockroom.htm and download Excel spreadsheet) and checking with the instructor.

 

Resources

ACS Electronic Journals: Searching and Web Editions
Journal of Chemical Education Online
Gustavus Library Resources Databases
SIGMA-Aldrich Online Catalog

http://bert.chem.gac.edu/  Gustavus Computational Cluster

 

Outlines of Other Investigations

Kinetics of Isomerization Through NMR Lineshape
Kinetics of Fluorescence Quenching Laser based Investigation

Computational investigation on SN2 reaction from solution kinetics investigation

 

Project Topics

Kinetics of Methylene Blue Reduction by Ascorbic Acid

Mowry, Sarah; Ogren, Paul J. Kinetics of Methylene Blue Reduction by Ascorbic Acid J. Chem. Educ. 1999 76 970. (carried out by: Kelly Devine and Justin Mattson previously)

Supramolecular chemistry: Host-Guest interactions

Hernández-Benito, Jesús; González-Mancebo, Samuel; Calle, Emilio; García-Santos, M. Pilar; Casado, Julio. A Practical Integrated Approach to Supramolecular Chemistry. I. Equilibria in Inclusion Phenomena. J. Chem. Educ. 1999 76 419.

Jesus Hernandez-Benito, Samuel Gonzalez-Mancebo, Emilio Calle, M. Pilar Garcia-Santos, and Julio Casado*. A Practical Integrated Approach to Supramolecular Chemistry. II. Kinetics of Inclusion Phenomena J. Chem. Educ. 1999 76 422.

A Practical Integrated Approach to Supramolecular Chemistry III. Thermodynamics of Inclusion Phenomena

Jesús Hernández-Benito, M. Pilar García-Santos, Emma O'Brien, Emilio Calle, and Julio Casado
Departamento de Química Física, Universidad de Salamanca, Facultad de Química, E-37008 Salamanca, Spain

Computational study of the pKa of biological systems

http://bert.chem.gac.edu/pkapage.html

Computational molecular dynamics study of Prion proteins: Pr^C (normal) vs. Pr^SC (refolded).

Viles, Cohen, Prusiner, Goodin, Wright, and Dyson, Copper binding to the prion protein: Structural implications of four identical cooperative binding sites, Proc. Natl. Acad. Sci. USA, 96, 2042-2047, March 1999.

Scientific American: Detecting Mad Cow Disease [ BIOTECHNOLOGY ]

New tests can rapidly identify the presence of dangerous prions--the agents responsible for the malady--and several compounds offer hope for treatment

http://www.bscbioinformatics.com/Stu/Pro/Prions.htm

http://www.rcsb.org/pdb/cgi/explore.cgi?pid=169611100367377&page=0&pdbId=1E1G

Some relevant structures include: 1E1G, 1E1J, 1B10, and 1HQQ

Use Gustavus Amber calculator (http://bert.chem.gac.edu/comptools.html) coupled to VMD.

Rotational Barriers in Push–Pull Ethylenes:

An Advanced Physical-Organic Project Including

2D EXSY and Computational Chemistry

Dwyer, Tammy J.; Norman, Julia E.; Jasien, Paul G. Rotational Barriers in Push-Pull Ethylenes: An Advanced Physical-Organic Project Including 2D EXSY and Computational Chemistry J. Chem. Educ. 1998 75 1635.

An integrated upper-division physical-organic experiment for chemistry majors has been developed. It involves the determination and mechanistic interpretation of the C=C and CN rotational barriers in a push-pull ethylene. In the course of the experiment students will synthesize an organic compound, acquire variable temperature 1D and 2D NMR spectra, and use computational quantum chemistry to gain a deeper understanding of the unique electronic features of the molecule. Low temperature 2D EXchange SpectroscopY (EXSY) is used to quantitate the rotational barriers in a series of solvents. The quantum mechanical calculations provide a means to compare the properties of the push-pull ethylene with a similar non-push-pull system. Analysis of the experimental and theoretical results leads to a nearly complete picture of how substituent effects can influence bond lengths, rotational barriers, and the electronic distribution in these ethylenes.

Enzyme Kinetics of Yeast Invertase

Christine Torborg and Gina Kime

Iodine Clock Reaction

Creary, Xavier; Morris, Karen M. A New Twist on the Iodine Clock Reaction: Determining the Order of a Reaction J. Chem. Educ. 1999 76 530

A Thermodynamic Study of Azide Binding to Myoglobin

Marcoline, Anne T.; Elgren, Timothy E. A Thermodynamic Study of Azide Binding to Myoglobin J. Chem. Educ. 1998 75 1622.

The visible absorption spectrum associated with the heme protein myoglobin changes as a result of azide binding to the iron center. Therefore, a titration with azide can be monitored and concentrations of the myoglobin-azide adduct quantified. From these ligand binding data, the dissociation constant and number of binding sites can be determined using the Scatchard method for analysis. This laboratory project can be completed in two 3-hour lab periods. Evaluation of other thermodynamic properties is possible by exploring the temperature dependence of these binding data. A third lab period is required for students to probe the temperature dependence.

Synthesis and Kinetics of Hydrolysis of 3,5-Dimethyl-N-acetyl-p-benzoquinone Imine

Buccigross, Jeanne M.; Metz, Christa; Elliot, Lori; Becker, Pamela; Earley, Angela S.; Hayes, Jerry W.; Novak, Michael; Underwood, Gayl A. Synthesis and Kinetics of Hydrolysis of 3,5-Dimethyl-N-acetyl-p-benzoquinone Imine: An Undergraduate Laboratory J. Chem. Educ. 1996 73 364.

The synthesis of the title compound by a three-step procedure is described. The hydrolysis kinetics, which involve two consecutive psuedo-first-order processes, are also described. The synthesis and kinetics experiments described here are proposed for incorporation into undergraduate laboratory courses under a variety of formats. The compound described here is related to a toxic metabolite of the common analgesics acetaminophen and phenacetin.

Determination of Rates of Proton Exchange of Thiamine Hydrochloride by ¹HNMR Spectroscopy

T.E. Grys and A DeGreeff

Thiamine hydrochloride, a cofactor of vitamin B1, an essential nutrient that functions as a cofactor for several metabolic reactions. In this experiment, the rates of exchange of 2-carbon and 6-carbon protons of thiamine hydrochloride were measured by 1H NMR at 20C. Different rates were found by varying concentrations of acetate ion/acetic acid buffer in a total ionic strength of 2 M. A sample using DCl in place of the buffer was used as a control. The rates of exchange were found to be 7.93e-13 to 2.27e-15 in the 0.05 M to 1 M acetate buffers, respectively. First and second order rate constants, as well as equilibrium constants were also determined for reactions in each acetate buffer concentration

The Study of Historical Gunpowder Recipes by Bomb Calorimetry to Examine Their Thermodynamic Efficiency

Dave Savage and Eric Godfrey

Few chemical processes have had as much influence on the lives of mankind as the creation and usage of gunpowder. For over a thousand years, gunpowder has been writing the history of the world. Over the centuries, several mixtures have been proposed that would yield the "optimum" mixture. In this experiment we test three of these mixtures, two ancient recipes and a optimal mixture, for their heat of combustion using the bomb calorimetry. Our results are somewhat puzzling but seem to point towards the fact that the most optimal mixture of gunpowder will have a lower heat of combustion.

Synthesis and Analysis of a Thermochromic Compound: Spiropyra

Chris Krug and Sarah Spessard

In this investigation we first synthesize and then analyze the thermochromic properties of the compound 1,3,3-Trimethylindoline-2-spiro-6'-(2',3'-b-napthpyran), a spiropyran. Using a spectrophotometer, we measured the temperature dependence of the thermochromic equilibrium and calculated values for the Keq, DG0, DS0 and DH0. We also tested the dependence of the polarity of the solvent on the thermochromic equilibrium. Our data shows that more polar solvents tend to shift the equilibrium toward the quinonemethide and less polar solvents shift it toward the spiropyran. We also found a direct correlation between the Keq and the temperature of the system.

Flash Photolysis of Benzophenone: Triplet Decay

Churo, M. S.; Grela, M. A. Photochemistry of Benzophenone in 2-Propanol: An Easy Experiment for Undergraduate Physical Chemistry Courses J. Chem. Educ. 1997 74 436.

J. Chem. Educ. 1997 74 436.

(previously performed by Vanja Duric and Brent Olson)

 Enzyme catalyzed hydrolysis of an ester with alpha-chymotrypsin

See Experiment 24 Halpern

The Enthalpy and Entropy of Excimer Formation

See Experiment 36 Halpern

The thermochromism of Mercury (II) Dithizonate

See Experiment 28 Halpern