chemical buffers and their importance in biological systems ©2011 university of illinois board of...

Chemical buffers and their importance in biological systems

©2011 University of Illinois Board of Trustees • http://islcs.ncsa.illinois.edu/copyright

About this module Author : Nathan Kenyon, first-year medical

student at the College of Medicine at Urbana-Champaign

Institute for Chemistry Literacy through Computational Science

Intended Audience Grade Level: High school chemistry

teachers, beginning undergraduate students

Keywords Subject Areas: Buffer solution, Molecular Orbitals


What are acids and bases? The Arrhenius definition of acids/bases:

Acid: substance when dissolved in water produces hydrogen ions

Base: substance when dissolved in water produces hydroxide ions


Common Acids and Bases

AcidsHCl (hydrochloric)H2SO4 (sulfuric)

HNO3 (nitrous)

H2CO3 (carbonic)

HC2H3O2 (acetic)

H3C6H5O7 (citric)

BasesNaOH (sodium hydroxide) KOH (potassium hydroxide) NH4OH (ammonium hydroxide) Ca(OH)2 (calcium hydroxide) Mg(OH)2 (magnesium hydroxide)

-Remember that an acid will produce H+ ions while a base will produce OH- when placed in solution


Strong Acids and Bases Some acids and bases

are termed “strong” Dissociate completely in

solution HA(aq) → H+

(aq) + A−(aq)

Strong Acids Strong Bases

HClO4

Perchloric acid

LiOH

HClHydrochloric acid

KOH

H2SO4

Sulfuric acid

NaOH

HBrHydrobromic acid

RbOH

HNO3

Nitrous acid

CsOH


Definition of pH pH scale: determine how acidic or basic a

solution is

pH is a measure of the hydrogen ion concentration of a solution and defined by the below equation:

pH=-log (H+)

pH scale goes from 0 to 14 – Acids: 0 to 7 – Bases: 7 to 14– middle point of the pH scale is 7

-distilled water is exactly 7 (neutral)


Mixing an acid and base

If an acid and base are mixed:

H+ + OH- H2O (l)

-termed a neutralization reaction-water and salt produced-can determine concentration of acid or base in

solution using this equation


Indicator Indicator: chemical that changes color within

a certain pH range Methyl red, phenolphthalein, phenol red, etc.


Acid-Base Titration To titrate an unknown acid/base solution, take a

certain amount of the unknown solution and add a standard reagent of the known concentration until neutralization reaction is completed

equivalence point: number of hydrogen ions and hydroxide ions are equal

-use an indicator or a pH meter to determine

Using data of volume of standard reagent used, concentration of unknown solution can be calculated


Exercise on Acid-Base titration

Virtual Chemistry Lab experiment

http://lrs.ed.uiuc.edu/students/mihyewon/chemlab_experiment.html


Chemical Buffer Many chemical reactions are affected by the

acidity of the solution in which they occur In order for a particular reaction to occur at an

appropriate rate, the pH of the reaction medium must be controlled

Buffer solutions-tend to resist changes in pH -aqueous solution consisting of a mixture

of a weak acid and its conjugate base or a weak base and its conjugate acid

-pH of solution changes very little when a small amount of acid or base is added to it


Acid Base Titration using chemical buffer

http://michele.usc.edu/java/acidbase/acidbase.html

In this example, we will mix a weak acid with a strong base (NaOH)

Using the tabs on the right-side, select “NaOH” for add and select “acetate” as the buffer.

-NaOH is a strong base, meaning it nearly completely dissociates to Na+ and OH-


Change the amount of conjugate acid [HA] to 0.4 and amount of conjugate base [A-] to .05

Select “methyl red” as the indicator Indicator: substance that changes color upon

a certain pH-For example, methyl red is red under a pH of 4.4 but will turn yellow upon reaching a pH of 6.2-visible evidence of a change in pH


As you add the NaOH, note how the buffer pH gradually changes and turns to yellow at approximately 6.2

there is a sharp increase in pH at a value of 9

equivalence point: there is an equal concentration of acid and base

Equivalence point©2011 University of Illinois Board of Trustees • http://islcs.ncsa.illinois.edu/copyright

Questions

During the acid base titration, a strong base (NaOH) was added to a weak acid in the presence of a buffer, acetate. Roughly what was the value of the buffer pH after a large amount of base had been added?

What is molarity in terms of its standard units?

How many times more concentrated is a solution that is 10M versus one that is 1M?


Biological Buffer In multicellular organisms, fluid within cells

have a characteristic and nearly constant pH One important biological buffer system is

carbonic acid system In blood plasma, the carbonic acid and

hydrogen carbonate ion equilibrium buffers the pH

-Carbonic acid (H2CO3) is the hydrogen-ion producer (acid)

-Hydrogen carbonate ion (HCO3-) is the

hydroxide-ion producer (base)

H2CO3(aq) H+(aq) + HCO3

-(aq)

Carbonic acid

Hydrogen carbonate ion©2011 University of Illinois Board of Trustees • http://islcs.ncsa.illinois.edu/copyright

Carbonic Acid Buffer System

In blood plasma, concentration of hydrogen carbonate ion is about twenty times concentration of carbonic acid: HCO3

-(aq) >

H2CO3 (aq)

Hydrogen carbonate ion concentration controlled slowly by kidneys (excretion)

Carbonic acid concentration controlled quickly by respiration (breathing through lungs)

H2CO3(aq) H+(aq) + HCO3-(aq)


Carbonic Acid Buffer System Carbonic acid-hydrogen carbonate ion buffer works throughout body to maintain pH of blood plasma at 7.4

Body maintains buffer by eliminating either acid (carbonic acid) or base (hydrogen carbonate ions)

Changes in carbonic acid concentration occur within seconds through increased or decreased respiration

region of greatest buffering capacity outside normal blood pH


Carbonic Acid (H2CO3) Important biological buffer in blood plasma Used in making soda, champagne, bubbly

drinks In equillibrium with carbon dioxide dissolved

in water H2CO3 ⇌ CO2 + H2O

Carbonic Acid Carbonic Acid 3D structure (WebMO)


Investigating structure of Carbonic Acid (H2CO3)

1. Use the guest account (username: guest, password: guest) to log in the WebMO demo site.

2. Click New Job -> Open Editor. A small window opens where you build molecules.

3. Add C atom in the workspace. Click on the Periodic Table icon (5th down the left side). Choose "C" by clicking on it and click once in the center of the workspace. A gray carbon atom appears. Click on the Periodic Table icon and choose “O”. Click to add three total O atoms around the carbon as shown below:


3. Now, click and hold to draw bonds between the carbon and oxygen. There should be one carbon-oxygen double bond as shown below:

4. Choose Clean-Up -> Comprehensive Mechanics. You should now have carbonic acid. Experiment with the Rotate, Translate, and Zoom tools (Top 3 icons on left side)


5. Click Close Editor in the main WebMO window. Carbonic acid now appears in the Build Molecule window. This structure contains idealized bond lengths and angles. To reduce the time required for the calculations and to obtain reasonable results, the semiempirical method PM3 will be used.

6. Click the blue "continue" arrow in the lower right side of the Build

Molecule window.

7. Choose Mopac as the computational engine.

Choose the following settings:

Job Name: CH2O3 PM3Geom Opt. Calculation: Geometry OptimizationTheory: PM3Charge: 0Multiplicity: Singlet.

8. Click on the blue continue arrow. You should now see your job listed. To kill or stop a job, you would click on the red "X" under Actions on the right side. Click Refresh (every ~5 seconds) until you see that your job is Complete (under Status).


9. Click on the hyperlinked name (CH2O3 PM3 Geom Opt) to open the "View Job" window. Choose the Select arrow (4th icon down on left). Click on one of the O atoms in the structure (the other atoms and bonds will "fade"). Shift and Click the C atom (both atoms are now

highlighted). The bond length is displayed just below the molecule.

Record the value of the C-O bond length: ___________A Record the value of the C=O bond length: ___________A

Click on the C atom, then Shift and click an O atom, followed by another O atom. The bond angle is displayed just below the molecule. Record the value of the O=C=O bond angle ___________degrees.

What accounts for the difference between the C-O and C=O bond

lengths?


1. When finished, click the Job Manager link under Actions (to the left of the molecule display). To continue on to the next exercise, choose New Job -> Create New Job.

2. Click the blue continue arrow in the lower right side of the Build Molecule window. Choose Mopac as the computational engine and click the blue continue arrow.

3. Use Job Name H2CO3PM3, and perform the geometry optimization as before (PM3). Once the job is complete, click the hyperlinked name (C2H4PM3) to open the View Job window.

4. Click the New Job Using This Geometry button, click the blue continue arrow, choose Mopac, and choose the following:

Job Name: H2CO3 PM3 MOCalculation: Molecular orbitalsTheory: PM3Charge: 0Multiplicity: Singlet

5. Click on the blue continue arrow. You should now see your job listed. Once the job is complete, click on the hyperlinked name (H2CO3 PM3 MO) to open the View Job window.


6. Scroll down to the Molecular Orbitals table. Using the occupancy values as your judge, identify both the Highest Occupied Molecular Orbital (HOMO) and Lowest Unoccupied Molecular Orbital (LUMO). View these orbitals by clicking on the magnifying glass icons.


Electronegativity

Electronegativity (the ability of an atom to pull electrons near itself) increases while going upwards and right along the periodic table.

Note that oxygen is more electronegative than carbon and carbon more than hydrogen

Electronegativity: O>C>H


7. The orbitals can be rotated by clicking and dragging in the viewer window. If you hold down the Shift key while clicking and dragging, you can zoom in and out. The HOMO is the pi orbital between the carbon atoms. The LUMO is the anitbonding pi* orbital. View some of the other orbitals. Note that all orbitals viewed appear as a tab in the MOViewer. Clicking on the tab brings that orbital back into the window. Close the viewer window and return to Job Manager.

Region of greatest electrostatic potential(=O)


Questions

Oxygen is a very electronegative element. How does this explain the distribution of the electrostatic potential around the oxygen in carbonic acid (H2CO3)? Refer to the WebMO image.

Additionally, why are the bond lengths different in this molecule?

Discuss the equation involving carbonic acid and how it functions as a buffer in blood plasma.


References

http://www.chemistry.wustl.edu/~edudev/LabTutorials/Buffer/Buffer.html

http://lrs.ed.uiuc.edu/students/mihyewon/chemlab_experiment.html

http://michele.usc.edu/java/acidbase/acidbase.html


chemical buffers and their importance in biological systems ©2011 university of illinois board of...

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