Chemistry Cumulative Exam - April 22, 2017

General Instructions Department of Chemistry Cumulative Examinations April 22, 2017 You may choose to answer any exam from any area covered in the examination booklet. Each exam may contain multiple parts. You may answer more than one exam but each exam is scored separately and is treated as an individual examination result. Thus, answering parts of two exams with a score of 50% would not yield a 100% grade for this cumulative exam. Instead you would receive 50% on each examination attempted. This booklet contains five examinations. Analytical Cumulative Examination Biochemistry Cumulative Examination Inorganic Cumulative Examination Organic Cumulative Examination Physical Cumulative Examination On your examination booklet: Print your student ID number. Print the Exam Booklet number. Print the question number you are answering. Print the Exam Date. Do not write your name anywhere on the examination booklet. Each exam will be scored anonymously. If you attempt more than one exam, you must use a separate examination booklet for each examination. When you complete the examination, return the examination and your answer booklet to the proctor. Exam results will be posted on bulletin board #2B on the north side of the hall near BRWN 2124. Analytical Chemistry Cume Exam Topic: Analytical data evaluation; IR, Florescence, and Absorption spectroscopy A) (10 points) Define or give a mathematical equation for the following terms: Accuracy Precision Determinate error Absolute uncertainty Mode (of a distribution) Gaussian distribution Method of Least squares Degrees of Freedom Primary Standard Back titration B) (10 points) While doing a measurement you get the following 4 numbers for the concentration of iron in a sample: 0.1015, 0.0991, 0.1016, and 0.1017. What is the mean, the 95% confidence interval for normally distributed noise, and the relative standard deviation for this data set? (see equations and table at the end of the exam). C) (5 points) You calculate a relative standard deviation in the previous question. I usually regard the relative standard deviation as a measure of the relative error on your mean. You also calculated a confidence interval, which is also a measure of the uncertainty of the mean. Compare and contrast these numbers. Which is the better measure of experimental uncertainty? D) (15 points) Carbon has two common isotopes, ¹²C and ¹³C, with relative isotopic abundances of, respectively, 98.89% and 1.11%. (a) What are the mean and standard deviation for the number of ¹³C atoms in a molecule of cholesterol given binomial probability distribution? (b) What is the probability of finding a molecule of cholesterol (C₂₇H₄₆O) containing no atoms of ¹³C? (c) What is the probability of finding a molecule of cholesterol (C₂₇H₄₆O) containing one atom of ¹³C? (see equations at the end of the exam). E) (10 points) Describe three methods for performing an IR measurement on different sample types (e.g. liquids vs powders)? F) (10 points) The IR spectrum shown below belongs to a compound with formula C₄H₈O. Assign the peaks at ~2900 cm⁻¹ and ~1200 cm⁻¹, and determine the identity of the compound. [An IR spectrum is shown with Relative transmittance on the y-axis and Wave number (cm⁻¹) on the x-axis. There are strong, sharp peaks just below 3000 cm⁻¹, and a very strong, broad peak around 1200 cm⁻¹.] G) (10 points) Primary amino acids can be detected by fluorescence spectroscopy after derivatization with a molecular tag that is a strong fluorophore. Would the following derivative reaction produce a fluorophoric amino acid? Why or why not? [A reaction scheme shows a phthalaldehyde derivative reacting with R₁-NH₂ and a thiol (Fg-SH) to form a substituted isoindole derivative.] H) (10 points) Assuming the above derivative is fluorophoric, design a laser-induced fluorescence detection system for it that might be coupled to HPLC. Draw the schematic. I) (10 points) Write an equation for the laser-induced fluorescence intensity and indicate the variables. Indicate two ways the quantum efficiency (Φ) of a fluorophore be increased in an experiment? J) (10 points) The drug tolbutamide (MW = 270.0 g mol⁻¹), a treatment for type 2 diabetes, has a molar absorptivity of 703 M⁻¹cm⁻¹ at 262 nm. One tablet was dissolved in 250.00 mL of water. A 10.00 mL aliquot of this solution was diluted to 100.00 mL in a volumetric flask. This diluted solution exhibited an absorbance of 0.275 at 262 nm in a 1.00-cm cell. Calculate the mass (in mg) of tolbutamide in the tablet. Equations c = λν E = hν = hc/λ A=εbc Normal distribution: s² = [Σ(xᵢ - X̄)²] / (n-1) μ = X̄ ± (ts/√n) Binomial distribution: P(X,N) = [N! / (X!(N-X)!)] * pˣ * (1-p)ᴺ⁻ˣ where P(X,N) is the probability that a given outcome will occur X times during N trials, and p is the probability that the outcome will occur in a single trial. Mean: μ = Np Variance: σ² = Np(1-p) Values of t for the 95% Confidence Interval | Degrees of Freedom | t | | :----------------- | :----- | | 1 | 12.71 | | 2 | 4.30 | | 3 | 3.18 | | 4 | 2.78 | | 5 | 2.57 | | 6 | 2.45 | | 7 | 2.36 | | 10 | 2.23 | | 12 | 2.18 | | 14 | 2.14 | | 16 | 2.12 | | 18 | 2.10 | | 20 | 2.09 | | 30 | 2.04 | | 50 | 2.01 | | ∞ | 1.96 | Biochemistry Cumulative Exam Title: Nucleic Acids April 22, 2017 (10 points) Why using bromo-deoxyUTP instead of TTP can lead to mutations in DNA? (10 points) Provide all the steps of rRNA processing in prokaryotes. (20 points) Provide any four differences between a miRNA and a siRNA. (10 points) Define the following terms in 2-3 sentences: (a) Riboregulators (b) Riboswitches. (10 points) Provide any one mechanism by which a double stranded DNA break is repaired in cells. (20 points) (a) How fast does template DNA spin (expressed in revolutions per second) at an E. coli replication fork? (b) What is the velocity of movement (in micrometers per second) of DNA polymerase III holoenzyme relative to the template? (10 points) Telomerase is not active in most human cells. Some cancer biologists have suggested that activation of the telomerase gene would be a requirement for the cells to become cancerous. Explain why this might be the case? (10 points) Provide all the steps for generating a cDNA library from human liver cells. Inorganic Cume Organometallic Chemistry April 22, 2017 Please answer the following questions as completely as possible. Partial credit will be given in instances where work and thought process is shown. 1. (15 points-5 points each) The dimeric compound [(η⁵-C₅Me₅)Cr(CO)₂]₂ (A) obeys the 18 electron rule and shows IR absorptions around 1870 cm⁻¹. A on treatment with excess CO at 1200-1450 psi and 175 °C for 10 hrs gave another dimeric chromium compound B which also obeys the 18 electron rule and also showed absorptions around 1876 cm⁻¹. Photolysis of A with UV radiation was found to result in a 17 electron dimeric compound C along with the release of CO gas. IR spectrum of C showed a single band at 1788 cm⁻¹ and analysis showed it to have the same bond order as compound A between the chromium atoms. Draw the structures of A, B and C clearly indicating Cr-Cr bond order and nature of CO bonding. 2. (40 points-8 points each) Reaction of OsO₄ with CO at 125 °C and 75 atm was found to result in a stable compound A with the empirical formula OsC₄O₄. Compound A was found to contain 3 metal-metal bonds. Reaction of A with excess of sodium metal followed by treatment with H₃PO₄ was found to result in compound B with the molecular formula OsH₂C₄O₄. Heating of B was found to result in the release of a colourless gas and formation of a compound C with empirical formula OsH₂C₄O₄. C on treatment with MeI was found to get converted to D with release of a hydrocarbon gas. D on further treatment with Na/Hg followed by MeI gave E with the empirical formula Os₂C₁₀H₆O₈. Compounds A-E obey 18 electron rule and all of them show infrared absorptions in the vicinity of 2000 cm⁻¹. No bridging ligands were also observed. Suggest structures for compounds A-E. 3. (15 points-5 points each) The reaction of Pt(PEt₃)₃ with 1 mole of biphenylene over a period of 10 days at 80 °C was found to result in a 16 electron compound A along with the release of PEt₃. Compound A on further reaction at 80 °C with one more mole of biphenylene was found to give a 16 electron compound C through an 18 electron intermediate B. Reaction of C with PEt₃ at 113 °C was found to give tetraphenylene along with Pt(PEt₃)₃. Write the structures of A, B and C. Indicate type of reactions happening at all stages. [A reaction scheme is shown depicting the sequential reaction of biphenylene with a platinum complex.] 4. (30 points-5 points each) Provide the oxidation state, d electron count, and valence electron count for the following molecules: [Six complex organometallic structures are shown for analysis.] Organic Division Exam April 2017 (Note: Questions in this section refer to an attached journal article: Shenvi and Reiher, J. Am. Chem. Soc. 2017, 139, 3647-3650) 1. Shenvi and Reiher have carried out the following reactions as shown in the attached article. [Reaction scheme shows compound 7 reacting with DMF-DMA to form compound 8, which then reacts with TBSOTf to form compound 5.] a. Write down the full name and chemical structures of DMF•DMA. b. Show the stepwise mechanism of formation of compound 8. c. Write the stepwise mechanism for the formation of TBS ester 5. 2. Ester 9 was converted to diethylphosphonate derivative 6 in a two-step sequence. [Reaction scheme shows compound 9 reacting with LDA and PhSeCl to form intermediate A, which then reacts with H₂O₂ to form compound 6.] a. Draw the product intermediate A for the first step reaction with LDA and (EtO)₂P(O)-CH₂CH₃ followed by the addition of PhSeCl. b. Show the mechanism for the second step reaction with H₂O₂. 3. Write the full name and draw the chemical structures for DMDO, TFAA, TMSCN, TBSOTf, and HFIP. 4. Treatment of 2a (protokalihinol) with V(O)(OEt)₃, TBHP followed by a reaction with Zn, EtCO₂H and NaI, EtCO₂Na provided tetrahydrofuran derivative 15 and its diastereomer in 48% yield and diastereomeric ratio (dr) of 93:7. [Reaction scheme shows compound 2a reacting to form compound 15.] a. Show stepwise formation of the tetrahydrofuran intermediate formed with V(O)(OEt)₃, TBHP (before deoxygenation with Zn, EtCO₂H and NaI, EtCO₂Na). b. Draw the structure of the minor (7%) diastereomer formed after these reactions. 5. Tetrahydrofuran derivative 15 was converted to nitrile derivative 25 in three-step sequence through the intermediates B and C. [Reaction scheme shows compound 15 converted via intermediates B and C to compound 25.] a. Draw the product structures for B and C with proper stereochemistry. b. Propose a mechanism for the reaction of C with TMSCN and Sc(OTf)₃ leading to the formation of nitrile 25. 6. Tetrahydrofuran derivative 25 was converted to Kalihinol (1) in a three-step sequence through intermediates D and E. [Reaction scheme shows compound 25 converted via intermediates D and E to compound 1.] a. Identify intermediates D and E with appropriate stereochemistry. b. Rationalize why products D and E are formed stereoselectively. Physical-Chemistry Cume Notation: C: Acid concentration pC = -log(C) ; for example, pC = 1.0 for a 0.10M solution. pKₐ = -log(Kₐ), where Kₐ is the equilibrium constant for acid dissociation in water. pKw = 14, for water dissociation. Before starting: Please use a full page to draw a square plot of pH vs. pC, like the one below. The Y-axis should be labeled pH and run from 0 to 10. The X-axis should be labeled pC and also run from 0 to 10. Draw a grid line at every unit of pH and pC. [An empty 10x10 grid is shown with pH on the y-axis (0-10) and pC on the x-axis (0-10).] 1. Diluting a strong monoprotic acid (Use filled circles, ⚫, to indicate your answers on the pH vs. pC plot). (a) What is the pH of a 0.10M solution of HCl in water? Add your answer on the plot. [5 points] (b) Now dilute the solution of part (a) by a factor of a thousand, so that pC = 4.0. Calculate the pH of the resulting solution and indicate it on your plot. [10 points] (c) Now dilute the solution of part (b) by another factor of a thousand. Calculate the pH of the resulting solution and indicate it on your plot. [10 points] (d) Draw a continuous solid line for the entire range of pC from 0 to 10. If you trust your previous three answers, the line should pass through those points. [5 points] 2. Diluting a weak monoprotic acid of pKₐ = 4.76 (This is the value for acetic acid). (Use open circles, ⚪, to indicate your answers on the pH vs. pC plot). (a) What is the pH of a 0.10M solution of acetic acid in water? Add your answer on the plot. [10 points] (b) Now dilute the solution of part (2a) by a factor of a thousand, so that pC = 4.0. Calculate the pH of the resulting solution and indicate it on your plot. [10 points] (c) Now dilute the solution of part (2b) by another factor of a thousand. Estimate the pH of the resulting solution, and indicate it on your plot. [10 points] (d) Draw a dashed line for the entire range of pC from 0 to 10. If you trust your previous three answers, the line should pass through those points. [5 points] (e) To calculate the answer to part (2c) correctly to two significant figures, you would need to find the real solutions of a cubic equation of the type: x³ + ax² + bx + d = 0 If x represents the concentration of hydronium ions, please provide expressions for the coefficients a, b, and d in terms of Kₐ, Kw, and C. [30 points] (f) Sketch your best guess for the percent dissociation of the acid vs. pC. The X-axis should be pC from 0 to 10. The Y-axis should be %dissociation of the acid from 0 to 100. Why is acetic acid referred to as a "weak acid" ? [5 points]