Determine molar extinction coefficient for an analyte ... Materials & Reagents ... Prepare a plot (Figure 1) of absorbance (y-axis) vs. wavelength for the pH 9.0 sample using ... figure has a legend, axes are labeled and units are indicated where ...
Photometry CHEM4401 Biochemistry I Laboratory (Please see Photometry laboratory in your manual for additional background material) Purpose -Principles of spectrophotometry - Determine optimal absorption wavelength for an analyte - Determine molar extinction coefficient for an analyte - Determine pKa for analyte from data and Henderson-Hasselbach equation Spectrophotometry Versatile method: - usually nondestructive (unless photochemical rxn occurs) - can be very specific for compound or functional group of interest - fast - sensitive to low concentrations Large number of biomolecules absorb light in UV or visible spectrum - compounds with conjugated double bonds (-C=C-C=C-) -nucleotides (purines and pyrimidines) -aromatic compounds (amino acids, metabolites, pigments, etc.) - etc. Absorption of light of a particular wavelength is related to concentration via the Lambert-Beer Law Io = εbc I Abs = absorbance Abs = log
I = incident light (light falling on absorbing medium) € I = transmitted light e = molar extinction coefficient b = path length of cell containing absorbing compound c = concentration of absorbing compound o
Caution! - various factors can affect accuracy of measurement” - light must be monochromatic (specific wavelength) - side reactions in cell can change concentration of absorbing species - pH stability of compound - temperature stability of compound Today - Using a spectrophotometer to follow dissociation of p-nitrophenol
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OH
O-
+ H+
NO2
HA
(p-nitrophenol)
NO2
A
+
H+
(phenolate ion, absorbing species)
Q: If [p-nitrophenol] = [phenolate ion] when pH = pKa, what will happen to the [p-nitrophenol] when pH increases? Blanks: blanks are used to obtain baseline readings for your instrument. Usually NOT H O. Blanks contain all components except the compound of interest (analyte). 2
Laboratory goals: 1. Determine optimal wavelength for measurement of phenolate ion (λmax) 2. Determine molar extinction coefficient (ε) for phenolate ion 3. Estimate pKa for p-nitrophenol dissociation reaction (graphically)
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CHEM4401 Biochemistry I Laboratory Photometry Materials & Reagents p-nitrophenol (0.2 mM) Tris buffer (0.5 M, pH 9.0) NaH2PO4 (0.05 M) Na2HPO4 (0.05 M Tris HCl (0.05M) Tris Base (0.05M) 13 x 100 mm glass test tubes Spectrophotometer
(per student group) 6 ml (fresh daily, pH 9.0 Tris buffer (0.05M) (Make a 2mM soln, then dilute 1:10 to 0.2 mM) 500 ml (for 0.05M solutions of p-nitrophenol) 50 ml 50 ml 20 ml 20 ml 12/group (6 blanks, 6 w/ p-nitrophenol) 1/group
Experimental Procedure 1. Student groups (6) will prepare 100 ml of each buffer listed in the table below. 2. Set up six test tubes as follows:
3. Determine the optimal wavelength (λmax) for measurement of the phenolate ion (see attached instructions for proper operation and blanking of spectrophotometer) a. Set the spectrophotometer wavelength to 360 nm. b. Blank the machine using pH 9.0 buffer solution (5 ml, no p-nitrophenol) c. Replace the blank with tube # 6 (pH 9.0 buffer plus p-nitrophenol). Record the absorbance d. Set the spectrophotometer wavelength to 365 nm. e. Repeat step b. f. Repeat step c. g. Increase the spectrophotometer wavelength by another 5 nm and repeate steps b and c. Continue on at 4 nm intervals until you reach a wavelength of 430 nm. h. Determine the wavelength at which maximum absorbance of tube # 6 occurs. Be sure you obtain an absorbance value > 0.6 for your λmax reading. Otherwise your extinction coefficient (ε) value will be too low and you will get a negative value of [HA] for some pH values. If it is too low, repeat your absorbance readings using more p-nitrophenol (2 vs 1 ml, etc.).
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Experimental Results (17 pts) 1. Prepare a plot (Figure 1) of absorbance (y-axis) vs. wavelength for the pH 9.0 sample using the Microsoft Excel “Graph Wizard” (or similar program). Note the λmax on your plot. Be sure figure has a legend, axes are labeled and units are indicated where appropriate (4 pt). 2. Plot (by hand is OK) the absorbance values for the pH 6.0, 6.5, 7.0, 7.5, and 8.0 samples on figure 1 (1 pt). 3. Calculate the Molar Extinction Coefficient (ε) for your sample (2 pt). According to Beer’s Law, A = ε.b.c may be rearranged as:
ε= where:
A bc
ε = the molar extinction coefficient A = the absorbance of the pH 9.0 sample at λmax € b = the path length of the spectrophotometer chamber (1 cm) c = concentration of the phenolate ion
The concentration of the phenolate ion is directly dependent upon the concentration of pnitrophenol. Recall that 1 ml of 0.2mM p-nitrophenol was added to 4 ml of buffer, for a total volume of 5 ml. It’s concentration in the pH 9.0 solution can be determined using the dilution equation C1V1 = C2V2 (0.2mM)(1 ml) = C2.(5 ml) C2 = 0.04 mM = 0.00004M Let’s assume that the p-nitrophenol (HA) is completely ionized (100% in the phenolate ion (A) form) when the pH = 9.0. The extinction coefficient for phenolate ion may then be calculated as:
ε=
Absorbance of pH 9.0 sample (1 cm)(0.00004 M)
Final units should be in cm-1.M-1 (2 pt). 4. Prepare a tabe (No.1) as follows: €
(phenolate ion [A]) can be calculated for each sample using Beer’s law. Since the total concentration of p-nitrophenol and the phenolate ion remains constant, [HA] can be calculated as:
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[HA] = total conc. (0.00004M) – [A] Show one set of example calculations for the determination of [A], [HA] and log [HA]/[A]. Note: It’s OK to get negative values for some log [A]/[HA] values, especially at lower pH. This means that [HA] > [A], which we expect at lower pH. Table should be titled. (3 pt) 5. The pKa for any weak acid can be determined from the Henderson Hasselbach Equation [A] pH = pKa + log [HA] Notice that this equation is similar to that for a straight line: y = mx + b We can take advantage of this fact to find an estimate for the pKa of p-nitrophenol using data € if we make the following substitutions: from our table. For example, y = pH m = slope of the line = 1.0 ( each increase in pH represents a directly proportional increase in log [A]/[HA] x = log [A]/[HA] b = pKa then we can estimate the pKa for p-nitrophenol from a graph of pH vs. log [A]/[HA] Prepare a second graph (Figure 2) of pH (y-axis) vs. log [A]/[HA] (x-axis) using the values from Table 1. Use the “scatter” plot option in Microsoft Excel or similar and produce a line of best fit (regression) through the data points. Be sure to include a figure legend, label axes and indicate units where appropriate. (5 pt) 6. Lab performance (2 pt)
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Spectrophotometer Instructions (Spectronic 20+ spectrophotometer) 1) Turn the spectrophotometer on by turning the “Power Switch/Zero Control” knob (front left side of instrument) clockwise. Allow the spectrophotometer to warm up for 15 minutes. 2) Set the filter level to the position appropriate for your desired wavelength (340-599 nm or 600-950 nm). 3) Switch ‘mode’ to “Transmittance”. Adjust the spectrophotometer to 0% T (Transmittance) with the Power Switch/Zero Control knob. Make sure the sample compartment is empty and the cover is closed. • The purpose of this step is to zero the detector with the shutter closed and no light hitting the detector. 4) Fill a clean cuvette (test tube) with appropriate volume (about 2/3 of the cuvette) of your blank solution. Wipe the cuvette with a Kimwipe to remove liquid droplets, dusts, and fingerprints. 5) Place the cuvette in the sample compartment. Close the lid. 6) Adjust the spectrophotometer to 100 % T with the Transmittance/Absorbance Control knob (front, right side of instrument). 7) Remove the blank cuvette from the sample compartment. 8) Fill a new cuvette (test tube) with appropriate volume (about 2/3 of the cuvette) of test sample. Wipe with a Kimwipe. 9) Insert sample cuvette into the sample compartment and close the lid. Change mode to absorbance. 10) Read the appropriate value (% Absorbance). 11) When all measurement are completed, turn off the spectrophotometer by turning the Power Switch/Zero Control knob counterclockwise until it clicks. Place plastic cover on instrument.
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