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ADVANCED PHYSICAL
CHEMISTRY LABORATORY
LABORATORY MANUAL
These experiments are suites. Each suite consists of two or three experiments.
ID TOPIC EXPERIMENT
Activities of ions by electrochemistry (and some
A Activity coefficients
programming )*
Some of the material required for the experiments will not have been covered in any of your classes. Background research is
an essential part of the experiments.
GROUP #
Experiment Date/Time
Experiment/Group rotation.
Week →
1 2 3 4 5 6
Group No.Z
1
2
3
4
5
6
Introduction:2
CHEMISTRY LABORATORY SAFETY REGULATIONS
A chemical laboratory is a potentially dangerous environment; the most the sash! It defeats the whole point of the sash.
prevalent hazards are fire, chemical burns, cuts, and poisoning. • Do not wipe your face or eyes with gloves on!
NOTE: Safety rules only work if you obey them and encourage others to • Water play or squirting wash bottles will not be tolerated.
do so. Please familiarize yourself with the following regulations.
• Do not kneel or sit when preparing hazardous samples. If there’s a
NOTE: These regulations represent a minimum. A member of the lab
spill, you must be able to move fast and keep your face out of the way.
staff will inform you of variances and other regulations, or supply you
Use the center shelf of the lab bench to fill volumetric flasks to the line.
with appropriate references. If unsure about anything ask them.
NOTE: An eyewash station is available for the treatment of minor • Be sure you have received proper instruction in:
accidents. For first aid, phone local 78111 or 807-8111. In an emergency • Boiling of liquids (use boiling chips!)
(i.e. one requiring police, fire, ambulance or a hazmat team) phone 911 • Use of separatory funnels (don’t point them at anyone)
then phone local 78111 or 807-8111. A member of the lab staff will • Use of any unfamiliar equipment or chemicals
normally make such calls. • Insertion into or removal
1. Regulations of, glass tubing (rods,
• All accidents and incidents (near misses and spills) must be reported thermometers, pipettes
immediately to a member of the lab staff. etc.) rubber or plastic
items (tubing, pipette
• Students are not usually permitted to use the laboratory except during
bulbs, bungs etc.) e.g. see
their scheduled laboratory period.
figure for the correct way
• No student should attempt unauthorized experiments in the of inserting a pipette
laboratory, or modify any experimental apparatus. into a dispensing bulb.
• No student can work in a laboratory without a supervisor present • Do not wave
unless they have completed a WHMIS and the Chemistry Department pipettes around
Safety course, and then only with the supervisors consent. (especially Pasteur
• Any student deemed dangerously incompetent or intoxicated will be pipettes) around or you
required to leave the laboratory. An incident report will be filed. will spray residual any
• Keep walkways clear at all times. Do not leave cupboard doors open. material around.
2. Personal Safety. • Do not crush materials
• Many of the chemicals in the laboratory are poisonous, whether taken with stirring rods.
orally or absorbed through the skin. If any chemical is swallowed, the 2. Fire
supervisor should be summoned immediately. Immediately wash off • Students should be aware of the location and use of the fire
any chemical comes in contact with the skin with plenty of water. extinguishers in the laboratory.
Consult the MSDS data sheets for further information. Make sure you
• In case of fire, the flames should be extinguished with one of the
know the location of the eyewash station and emergency shower.
extinguishers and the supervisor notified immediately.
• As a minimum students MUST wear safety glasses at all times. You
• If a student's clothing or hair catch fire, use the emergency shower
must provide your own safety glasses. Contact lenses must not be worn.
(make sure you know its location). If this is not possible, smother the
Other protection such as side shields, goggles or face shields may be
flames immediately with a laboratory coat or a fire blanket (know the
required. Make sure your goggles are sealed against the face.
location of the latter)
• No food or drink may be bought into the laboratory. Do not chew gum
in the laboratory. 3. Breakages, spillages and fumes
• There must be no smoking in the laboratory. • Immediately report all breakages and minor spills of chemicals to the
• Students should keep their arms, legs and torso covered. Students supervisor or technician. A spill kit is available if needed. Know it’s
should keep their arms, legs and torso covered. Wearing 100% cotton lab location. Spills will normally be dealt with by the laboratory staff. Failure
coats is required. Most chemicals will stain or burn your clothing. to report mercury spills may result in a reprimand.
• You are not permitted to wear open toed shoes in the lab. • Remember that broken class is the sharpest material known.
• Long hair should be tied back at all times. • Any experiment involving the evolution of toxic materials, or pungent
or unpleasant odors or fumes, must be carried out in the fume hood.
• Unless otherwise informed assume all “unknown samples” are
dangerous, that is you must wear goggles, gloves and lab coat while • Don’t wear aftershave or cologne in the labs. It interferes with our
handling them. ability to detect fumes (they are fumes) and can mess up analyses.
• Assume all chemicals are corrosive or toxic by ingestion, and take 4. Disposal
appropriate precautions. • Make sure all broken glass or sharps are disposed of in the appropriate
• Never handle chemicals with your bare hands. container.
• While heating a substance in a vessel with a narrow mouth (e.g. a test • Make sure all materials are disposed of in the appropriate container
tube) ensure that the mouth of the vessel is not pointing at anyone, (solids, organics, halogenated solvents or inorganics)
including yourself. • Beware of materials that hydrolyze rapidly, e.g. SOCl2 and acid
• When using compressed gas, vacuum equipment, high temperature or anhydrides; they cannot be disposed of in containers containing
high voltage equipment be especially careful. Ask the laboratory alcohol or water.
instructor for help if you are uncertain of any procedure. Strongly • Never add hydrogen peroxide, nitric acid or any other oxidants to
corrosive or toxic materials should only be handled in the fume hood, organic materials (unless instructed) or into the organic disposal
with the sash down, and suitable gloves on. Do no kneel to look under container. Acetone and alcohol are a particular problem.
Introduction:3
MARKING POLICIES
Allocation of marks will be different from usual labs. and tabulate your original data points (that is working data
may vary with the experiment. As above, you start with one point; for instance there is no need to reproduce the data
or two marks less than the maximum otherwise an from time-runs, only the data points that arises form the
unrealistic spread of marks will occur. The follow ‘items’ time-runs) at the start of the report. Also, at the end,
will be considered when marking labs. tabulate your calculated results and the literature values.
TECHNIQUE. This mark will be assigned for things like Error discussion is required for each lab. Error analysis may
speed (finishing time), sloppiness, preparation (did you also be required. Make sure you indicate the algorithms
read the lab. before arrival?), contribution to the laboratory used for doing calculations, particularly if you used a
discussions, breakage’s, record of original data in your lab. computer. Marks are given for extra background research
notebook, attentiveness and attitude, as well as pipetting, and any insightful comments. (415 is a research based lab.
weighing, titrating and other standard lab. skills. These so these are part of your main mark, not an opportunity for
experiments are all straightforward and in many cases you brownie points as with most labs.) Marks are deducted for;
have done them before so odd factors like attitude will arithmetic errors, incorrect answers, failure to answer
weigh heavily – quietly sitting in a corner, noisily sitting in questions, failure to comment on results; incomplete error
a corner, or slipping out for a pint – will be viewed dimly. discussion, lack of literature values, bad organization and
Also, you will be marked on how you solved the problem extreme untidiness, excessive neatness, and of course
and the computer techniques used; e.g. proper choice of handing in the lab. report late. Be sure to answer all
data ranges, checking convergence criteria, use of special questions given. Not all reports are equally easy, marks
features rather than brute force (e.g. for Excel; in-cell allocated to a report may vary from 10 to 15 to 20,
iterations versus huge tables or use of named ranges). depending on the length and difficulty of the calculations
and questions.
RESULTS. Clearly, the better your technique, the better
your results should be, but since some of these experiments PROBLEMS. Some labs. have lots of questions to answer.
are designed to produce bad results so you can use fancy In fact, some look like a lab. with a problem set attached to
techniques to fix them up a bit, this mark is a little odd. the end. The problems carry significant weight.
However, the experiments do often have built in checks, SAFETY. Normally, physical chemistry experiments are
there are certain errors that can only be achieved by designed to work with safe chemicals and equipment. For
incompetence – this mark will address these. advanced courses this is neither possible nor desirable.
PRESENTATION. This will be an opportunity to Place a small section in your lab. report giving toxicity
demonstrate your word-processing skills, HAND- information and precautions for each (and every one) of the
WRITTEN REPORTS WILL NOT BE ACCEPTED for any chemicals used (starting material, products and by-
lab. reports. You will be marked on presentation e.g. clear products). Look it up, don’t guess. If you don’t take this
format, data properly identified, clear use of labels, proper seriously I won’t let you in the lab. However, remember to
choice of axes on graphs, clear comments (in Maple). use credible sources as some sources tend to over exaggerate
Proper placement and sizing of titles, captions and graphs. the hazards for legal reasons (i.e. beware of the
You MUST record your original data and any in lab. notes in manufacturers literature). The WHIMIS CD-ROM is a
an approved lab. book. Do not submit this book with your good place to start.
reports, but I will wish to see it and assign marks according PLAGIARISM. See the separate section for details.
to it’s clarity and completeness. (The supplementary Basically, if you copy from somebody else or allow
questions may involve a lot of pictures or derivation in that somebody else to copy from you, you will get zero for that
case it may be acceptable to hand-write that section – lab. report. Repeated infractions may get you suspended.
check with the instructor). Discussion of ideas is permitted, but the write ups must be
REPORT. See the appropriate section for a description of independent.
the format of your report. Most importantly, do example
calculations for one sample and tabulate the final, and some
intermediate data, for the rest of the samples. Be sure to
Introduction:4
THE FORMAT OF A LABORATORY REPORT
IDENTIFICATION. All labs. reports should have a front systematic error, and estimate their limits (guesswork!). In
sheet that gives: Your name, the course number (Chem.309) general, don't make the discussion too detailed, unless you
and section no. Name of partner (if any). Full date of are told that an error analysis is required for that
experiment (e.g. Tue. May 10th 2018). Experiment number. experiment. If you are told to do a full error analysis you
Lab. Profs. name. need the formula in Table 3 of the Error Analysis section).
TITLE. This should give both the substance or system For most purposes an error analysis using Table 2 of that
studied and the method of physical measurement made, or section will suffice. Error analysis should be done along with
of property determined. your calculations. Discussion is done as a separate section.
OBJECT OR PURPOSE. One sentence; may not be CONCLUSIONS. Your major findings in a few lines. This
necessary if it just duplicates the title. section may not be necessary if you have them clearly set
out at the beginning or end of the "discussion" section. Be
PRINCIPLE OF METHOD. Briefly discuss the theory sure that you have answered all questions in the text. Also,
underlying the laboratory and briefly give the principle of make any comments about the findings and there
the method, and use this as opportunity to write down any implications for errors in this and related experiments
equations you will use in results and calculations.
QUESTIONS. The question may be in the body of the
PROCEDURE. You may refer to the lab. manual for this, main body or given in a separate section at the end of the
but you should any modifications to the procedure and experiment. Clearly identify, separate and answer the
indicate possible improvements and sources of errors or questions at the end of your report. Do not embed the
other general problems. Draw diagrams of apparatus setup questions in the discussion or conclusions or in a long
if required. rambling paragraph at the end. Text answers should be
RESULTS AND CALCULATIONS. Tabulating usually typed. Numeric or algebraic questions can be hand-
saves a lot of time and space and keeps the prof. happy. Draw written.
graphs using a computer, unless otherwise stated. Embed REFERENCES. Place any references, in the standard
both the graphs and tables in the text. Be sure to make the A.C.S. format, in this section. WEB references, with the
graphs readable, say 6x5 in minimum size For repeated exception of the CHEMBOOK site are NOT acceptable. See
calculations, give one example and one only, in full. The the section on the Internet elsewhere.
example calculation should be embedded in the text, but
may be hand written (try doing one by typing to see what a
pain it is). This should come more naturally than in the past Please feel free to discuss report format and other problems
as you should be using Excel for calculations and will need with the instructor, but do not expect detailed explanations
to explain them. Make sure you always compare your results or corrections written on your laboratory reports.
with the literature values when available. Make sure you
See the A.C.S. Authors Guide (in library) for further details
indicate the algorithms or programs used for doing on style and format of chemistry documents.
calculations.
DISCUSSION. This is a discussion of the results and their
errors in the context of the data processing methods used.
Benefits and shortcomings of the methods should be
discussed.
ERROR DISCUSSION/ANALYSIS. For any quant-ity
for which you have found a numerical value, give an
estimate of error limits. Do not propagate the errors in your
calculations unless an error analysis is required. Estimate
random errors from observed scatter of data either visually,
or by statistical computation. List possible sources of
Introduction:5
SOME NOTES ON TYPE SETTING REPORTS
All lab. reports are to be typed using a computer. I j) Watch for l’s (ells) they look like 1’s (ones). In sans serif
recommend Word (and Word on the Mac at a push). Make you get l’s (ells), 1’s (ones) and I’s (eyes).
sure the equation editor is installed (and you know how to k) Number the pages just in case the staple falls out.
use it). If you have last minute printing problems, see me, I
may accept a disk copy. For the purposes of proofing your If you need any help with word processing don’t hesitate to
reports I recommend printing them out. I will supply you come and see me – it’s part of the course. Office 2007 is
with a symbol font that contains nearly all the symbols
almost useless for lab. reports get a copy of Office 2003.
you’ll need for chemistry, and a Greek font with some
modifications suitable for scientific work (the standard
symbol font has Greek characters, but they have to be
italicized). I usually assign some keystrokes to a macro to
turn them on or off. I will also give you some macros you
might want to use. I want you to follow some basic
typographic conventions for your report (or you’ll loose
marks). They are as follows.
a) The main body of text should be in a proportionally-
spaced (e.g. not Courier) western (e.g. not Cyrillic) serif
font (e.g. Times New Roman, Garamond, School Book),
not a sans serif font (e.g Arial) or any decorative font (e.g.
Brush Script) or anything weird (e.g. Tekton). Use a normal
face, not italicized, hollow or bold. Type size should be 12,
13 or 14pt.
b) Titles should be bold, serif or sans serif, and larger than
the main text; don’t bother with anything fancy.
c) There should be a maximum of three fonts in a report
(the main text, titles, symbols). If you want some variation
on the title page you can use bold and italic (sparingly).
d) Keep it simple, no curly borders or color (except maybe
in graphs). Use bold or italic for emphasis, do not
underline.
e) Use tables for your data, don’t rely on tabs etc. Do not
box the table, a couple of lines here and there usually does
the job.
f) Note that stuff like 13 CO 2+3 can only be typed in using
the equation editor – learn to use it.
g) The main body should be double or triple spaced (with
a 1” margin all round) so I can insert comments. However, I
will tolerate single spaced reports.
h) Diagrams can be drawn by hand, but keep them neat.
They should be captioned by a line of type. Equations must
be typed in, I suggest you reference the manual (e.g. Exp. G
eq.3) to reduce this burden. All graphs must be done by
computer, but you can manually cut and paste them into
your report if you wish (OLE works nicely, but only on fast
machines with lots of memory).
i) Do not cut and paste lumps of text from your partner’s
reports. I want to see some originality; in both the content
and the formatting (Also see the section on plagiarism).
Introduction:6
TYPOGRAPHIC CONVENTIONS FOR PAPERS
All journals have conventions that you must adhere to in for comments.
order to get a paper published in them. These conventions • Use a fly page.
vary from journal to journal, although there are some • Insert diagrams, graphs and tables into the text rather
common conventions to all journals. Below is a set of than on separate pages. (Use cut and paste).
conventions that you must adhere to for your lab. report to
• Number the pages.
be accepted. (These are over and above the format
conventions laid out elsewhere in this manual). The • Do not start sentences with numerals (use the word).
conventions are based on those for A.C.S. journal and are • Breaks and indenting for paragraphs are your choice.
detailed in the A.C.S. style guide (along with a grammatical • Number graphs, figures and tables clearly.
guide and conventions for hyphenation, abbreviations, • You should use the equation editor for equations.
capitalization etc., well worth a peek at). Conventions for Calculations can be inserted into the text in hand writing
other journals are usually laid out in the front of the journal. though (they are a real pain to type).
Fonts and case. Equations, Tables & Figures.
• Use 12 pt Roman (or similar). • Equation numbers should be at the left margin. The
• Do not used bold or italic except as indicated below. equation should be centered. Refer to the equation as eq.n.
• Do not underline – ever. • Label figures and tables underneath. The caption should
• Lower case Greek letters are always italicized. Upper not exceed the with of the figure or table and should be
Greek letters case are not. centered. Refer to them as Figure.n or Table.n.
• Mathematical variables and constants are italicized. References. Any consistent referencing scheme will do,
• Numbers and operators are not italicized. but the following is recommended. References should
• Vectors and tensors are bold. preferably be numbers and grouped at the end of the report.
• Math variables are never case sensitive (like in the Do not use MS Word’s Endnote facility. Placing references in
moronic C). d and D are the same. footnotes is ok though. References should be referred to by
• Element symbols are not italicized. just a number in parenthesis or an author and a number.
• Use italics for emphasis. Use bold for titles. Increasing Journals.
font size is also useful for emphasis. 1) For sequentially numbered volumes : Name, M. Y.; Other,
• When defining a new word it is common to italicize it. A.N. , Journal Abbrv. Year, volume, pages. .
• Italicize latinates (actually optional, but I tend to do it). 2) For individually number volumes: Same, M. Y. , Journal
• Try to make superscripts and subscripts 10pt (there’s a Abbrv. Year, volume(issue), pages.
macro on the disk for this). Books.
• Symbols and axis labels in graphs should be 12pt. 3) No editors: Name, M. Y.; Other, A.N. Title of the Book;
Publisher: City, Year, Chap. or page refs.
Abbreviations and units. 4) Editor only: Title of the Book; Ed. Name; Publisher; City,
• Units are never capitalized when spelt out. Year, Chap. or page refs.
• Abbreviations for units should be spaced, e.g. 10 km hr-1 5) Author and editor: Author. A. N. In Title of the Book;
not 10km.hr-1. I tend to ignore this rule as it leads Editor Name, Ed.; Publisher; City, Year, Chap. or page refs.
orphaned or widowed units. Web pages.
• A list of approved abbreviations are in the A.C.S. Guide.
You should not take reference material from the web as it is
• All abbreviations, except as listed below, must be defined not peer reviewed and not a permanent medium. Do look
at their point of first use. around the page to see if it has a formal reference (most
a) The symbols for the elements. government pages will) or has a reference from which the
b) the latinates (i.e., e.g., etc.). material is taken. If not, note down the URL of the page and
c) at. wt., w/w, w/v, v/v, vol. the date you obtained the information.
Layout. Consult the Format section for other details. For reference to other types of materials see the A.C.S. style
• If the report is double-spaced I can insert comments guide. (For which you have no reference, notice how
easily, but single space is OK. I use 14pt exactly. irritating that is) – it’s in the library). Abbreviations for
• Use one inch margins all round. That leaves some space journal are also in the A.C.S. guide.
Introduction:7
TYPE SETTING TECHNICAL DOCUMENTS
Introduction. Font Size.
For hints on typesetting in general, see Robin Williams book As can be seen in the section above that different fonts have
The Non-Designers Design Book. She also has a number of different widths, heights, weights and spread, even though
useful tips at www.eyewire.com/magazine/columns/robin. they have the same point size. Times is large and open
Some more information can also be found under and Caslon small and cramped so Times works well at
www.microsoft.com/typography/ . The hints below refer
10pt, Caslon does not. On the other hand Caslon works
specifically to type setting lab. reports. or lab. manuals. I’ve fine at 14pt, and so does Times. I use 12pt for lab.
attempted to set up this page according to these hints, even manuals since they are usually read standing up (and I’m a
if the rest of the manual is not setup that way (do as I say
little short sighted). For reports 10pt is ok if you have a laser
not as I do). printer, for inkjets 12pt is better.
Emphasis and Titling. Spacing.
Do not use underline or ALL CAPS for emphasis or titling, Spacing between lines is usually set to single (which is
they are a hangover from the typewriter days. However, I actually variable). For plain text this is ok, but is poor when
still find it useful to use a liberal sprinkling of DO NOT’s in
you’re using super/subscripts or symbols. I find spacing at
lab. manuals.
exactly 14pt (for 12pt text) works well if the “don’t center
For emphasis in text use italic, bold italic or bold. exact height lines” option in Word is off. If you’re writing a
Occasionally, using a small font surrounded by white space draft, double or triple spacing can be useful to allow for
works well as does using a larger font. annotations.
For titling use a larger font, normal, bold or italic. If your
Spacing between words is set by using left justification (no
main text is serif (as it should be) then a larger Sans
extra spacing) or by using full justification (spacing filled so
Serif font is good. Placing a line across the page (as above) line exactly fits the line). Full justification is fine as long as
also works well in moderation. The lines may be various
you don’t use narrow columns (a fine example of what can
weights or doubled.
go wrong is in the opening paragraph).
Typeface. Misc.
If you are preparing a long document readability is very Lines of text should not be more than (on average) eight-
important. In print readability is best achieved by using a nine words long. For large format pages that means two or
classic serif font such as Times Roman, Caslon, more columns. Large margins can also help. Setting up
Garamond, Baskerville or similar (This manuals text is double columns can be a little awkward and slows down the
set in a slightly narrow Roman font – Adobe Minion). Don’t computer. Some of the lab. manual is not set that way so I
use anything fancy. If you are type setting a Web page or don’t expect it in lab. reports.
have a lousy printer then a san-serif font such as Arial may
work better. I avoid Arial because of the confusion between I
(eye) l (el) and 1 (one). Check for appearance on screen vs.
the printer, the fonts named above (except Minion) look
quite different on screen than they do in this text. Also,
check the numbers for a given font in Times you get
1234567890 with Bulmer you get 1234567890, which
is a little ugly (especially on screen).
In general, one should not use more than two or three
typefaces per page, typically one for body text, one for titles,
one for symbols. One may add one more font to represent
computer or instrument input, Courier is usually used
for that purpose.
Introduction:8
PLOTTING GRAPHS.
Example Graph Most graphics packages give half decent graphs, however Excels
defaults settings are setup for Business slides (i.e. for appearance
Specific Heat
40.00 not content.) However, the plots can be readily customized. Below
20.00
Series1 are a set of refinements which can also be used to as general
Series2 guidelines for plotting.
0.00
-4.00 1.00 6.00 The top graph is Excels default scatter plot. The scales are wrong,
Time(s) the annotation too large and the plot cluttered. It is almost useless.
You should setup a custom graph in a proper format and use that as
the default..
Example Graph
For the first step we get rid of the grid lines (only leave grid lines if
Specific Heat
40.00 you need to read data of the graph) and the gray background which
reduces contrast. The legend is also deleted. Again, legends are
20.00
useful when working off the graphs, but for reports the legend
0.00 should be below the graph along with other information. Note how
0.00 2.00 4.00 6.00 the graph rescales when the legend is removed.
Time(s)
30.00 normal typeface. If you intend to reduce the figure you should scale
the annotation accordingly. For reports annotation should match
20.00
your text size (10-12pt). If you are making slides, overheads or
10.00 reducing graphs, it will need to be bigger (18-24 pt often works).
The title has been moved to the bottom and numbered.
0.00
0.00 1.00 2.00 3.00 4.00 Most of these changes are accessible by left clicking on the graph,
Time(s)
then right clicking to access the various properties.
Figure 1. Example Graph
The final step is to remove both figure and axis boxes, they serve no
35 purpose. The title has been removed and replaced by text from
Word because you can’t do anything fancy in Excel - in this case
Specific Heat
simply to put the legend in. Note that it is centered below the graph.
30
The axes have been tidied up, the span has been corrected, decimal
places reduced and tick marks added. The least square fit lines have
25 been added. The data points have been changed to black and made
easily distinguishable.
20 These graphs have been cut and paste in. If you do that, make sure
0 1 2 3 4 they are a decent size, including the annotation. (see exp.P for some
Time(s) bad examples. Graphs can be presented on a separate
page if necessary.
Figure 1. A plot of Cv vs. Vent time for the Clement –
Desormes’. Dots at 20C, squares at 30C
Introduction:9
PRESENTING TABLES.
Time(s) P1 (cmHg) Cv Excel’s default tables are nearly as poor as the graphs. Here
4.03 76.49 28.04099 we will illustrate how to tidy them up.
3.25 76.67 26.34766
Generally you should cut and paste in from Excel in-line to
3.32 76.57 26.65888
the text, but if the table is very large it should be presented on
3.06 76.73 26.85892 a separate page, in landscape mode if neccessary. Either way
2.6 76.63 26 the default cut & paste table is poorly laid out with lots of
2.28 76.52 25.06601 clutter and white space.
1.75 76.6 25.01056
1.31 76.58 24.84336
0.96 76.6 24.65
0.66 76.51 24.25748
P1 Center the text and the table. The number of decimals are
Time(s) (cmHg) Cv made uniform to clean up the appearance and allow a more
4.03 76.49 28.04 meaningful column alignment and spacing. The heavy grid
3.25 76.67 26.35 has also been removed. The grids can serve a purpose in
3.32 76.57 26.66 large multicolumn data look-up table, but generally they just
3.06 76.73 26.86 clutter the table.
2.60 76.63 26.00
2.28 76.52 25.07
1.75 76.60 25.01
1.31 76.58 24.84
0.96 76.60 24.65
0.66 76.51 24.26
Vent Pressure, P1 Cv
The final step is to tidy up the table headings (centered
Time(s) (cmHg) J/mol-1 vertically and horizontally) and add subscripts. Use the
equation editor if necessary. A caption has also been added
4.03 76.49 28.0
along with a light grid.
3.25 76.67 26.4
3.32 76.57 26.7 Number formatting has been changed to reflect the correct
3.06 76.73 26.9 number of significant figure. You may want to change the
2.60 76.63 26.0 font type and size to match your text as well.
2.28 76.52 25.1
1.75 76.60 25.0
1.31 76.58 24.8
0.96 76.60 24.7
0.66 76.51 24.3 A final note: Try to avoid E or exponential notation if
necessary rescale your data to µM or whatever. e.g. use 0.234
Table 2. Vent times, initial pressure, P1, and not 2.34E-01 or 2.34x10-1 (the latter is the lesser of two
calculated specific heat, Cv , for the Clement- evils). Use 0.345µM, not 3.45x10-7M and certainly not
Desormes experiment. 0.000000345M. Also remember to limit the number of
decimal places, Excel defaults to something too large.
Introduction:10
USING FIGURES
Figures are rarely prepared in situ they are usually prepared Scanning is great – when it works. You use somebody else’s
separately then cut and paste (manually or electronically) pictures and just cut and paste them electronically into you
into the document. The only real exceptions are sketches in report. There are three problems though, one is copyright,
your lab. notebook. Regardless of the type of figure they all they are, after all, somebody else’s pictures. Resolution is
need a figure number and caption placed beneath it. The another, and color is the last. Copyright is usually not a
caption should be no wider than the figure. problem for one-off lab. reports, but for anything you sell
(such as lab. manuals) you have to get copyright permission,
There are a number of ways of preparing figures for formal which may of may not be free. Resolution is a serious
reports, each with advantages and disadvantages. problem. Grayscale pictures may give acceptable results at
a) Hand drawn 300dpi (check by printing a rough copy out), but even then
b) Drafted they will be huge (on disk). Line drawings need at least
c) Computer drafted. 600dpi or you get jaggies. Scaling down often exacerbates
d) Scanning. the problem. Color also creates a problem. Most reports are
Hand-drawn figures are not usually used in formal reports, in black and white with perhaps grayscale pictures. Color
but they are fast and convenient. does not always converts to grayscale well, and almost never
convert to good line drawings (black and white). Basically
Drafting involves special pens, templates, drawing boards any picture with a colored background will be unusable.
etc. The usual approach is to draw an oversize figure and
Xerox reduce it (that cleans it up a lot). You then manually As an exercise go through this manual and see if you can
cut and paste it into a prepared gap in the report and Xerox determine which figures are hand drafted and scanned,
that page. This process is very labor intensive (the chem. computer drafted, scanned from other sources, bitmaps
dept at UBC has two graphic artists for this purpose), but it from other programs or OLE links.
is the only way to do some types of pictures.
Introduction:11
KEEPING A LABORATORY NOTEBOOK
Basically, you need to record what, with what, when, where, Pre-Laboratory Preparation.
how and how long, all in relation to your laboratory a) Write in any directions, calculations, diagrams, flow
activities. An outline of the information you should record charts, molecular weights, cautions, weights and
(by category) is given below (you don’t need to put such volumes.
titles in the book). The laboratory book should have
numbered duplicate pages. The duplicates should be Instruments
removed and stored in a separate place from the laboratory a) Record instrument settings (scan time, resolution, scan
book. If you have a laboratory, the laboratory book should width, temp. etc. etc. – anything that can be varied).
be locked up in the laboratory. Keep the duplicates at home Anything that doesn’t have a value, indicate any
or in your office. Increasing amounts of data are kept on changes. E.g. lamp height was optimized for the
computers, be sure to backup the disks and record file standard sample.
names in your laboratory book. The lab. Manual contains b) State sample cells used (try and get your own). If they
some ‘NOTES’ sheets, they are an artifact of production. break record that (different cells give different results).
They are useful as scratch sheets, but anything of c) If there are any power glitches or the signal seems very
significance should be written in the lab. notebook, only. noisy, indicate those along with the time. E.g. at UBC it
Incidentally, the examples given are real, not made up for used to be impossible to work at 4.30, when everybody
your entertainment. was turning their instruments off. There was also
trouble with big lasers firing; recording times will help
General you track these things down.
a) Each page should be dated and titled. Start each new d) Record the computer file names that any data is held in.
date on a new page, unless the entries are less than ¼ of Make them useful, have a convention. If the OS
a page. The title should be short, but descriptive and supports long file names use them. I find it useful to
placed in an index at the front of the book. use a convention like XXYYnnnn.mmm – where XX is a
b) Entries should be neat and in water insoluble pen. two letter month code, YY is the day (number), nnnn is
c) Entries should be organized – start new topics on a new a code for the experiment/sample type, mmm is the
line. extension, usually you won’t have a choice about that.
d) Mistakes should be deleted with one line (leaving the E.g. JL09dx12.spc might mean a spectrum (spc) taken
mistake clear – it might not be a mistake). Do not July 09, of a doxyl-12 spin probe. Most computers are
delete or change entries after the fact. pretty good about keeping the file date correct so you
e) Place any literature references against appropriate may want to just use an 8-letter code instead. However,
entries. it’s often easier to search for a file name than for a file
f) Note any modifications to any standard procedures. date. I like to use an extension nnn where nnn was 000,
g) Keep your notes legible. Dalton may have been a great 001, 002 etc. for a sequence of files. It can be very
chemist, but his lab. notes weren’t that great as seen difficult to locate three month old data, especially if you
below. generate 100 files a day.
Preparation
a) Record the chemicals, grades, weights and volumes
used.
b) Record the order in which the chemicals were added. I
once did a preparation with three chemicals, which
gives three possible orders (assuming the order of a
given pair is irrelevant). Not only did two of the
combinations give the wrong product, the reactions
were explosive. The order was not given in the original
instructions.
c) Draw, or otherwise indicate the equipment used.
(Some reactions depend on the size and shape of the
flasks). Something a little more auspicious that the
efforts of the Greek alchemist shown below, but drafting
is not required.
Introduction:12
(almost a flash) then went pale yellow, the color before
freezing. (In this case the pale yellow turned out to be iron
contamination from the cheap stainless steel syringe
needles used to deliver into reactants to the sample). 2) Fine
white needles formed in the acetone wash bath after two
days of use. (They turned out to be acetone peroxide, a
contact explosive, even when wet).
Computers.
REMEMBER TO BACK UP ALL YOUR COMPUTER
DATA IMMEDIATELY. Computers generate huge amounts
of information and it’s silly to reproduce it in a notebook.
There are some exceptions, X-ray data and spectra typically
find their way into special libraries. For your work, you can
restrict yourself to the following items.
a) Record filenames used in a given experiment. Record
d) If any of the bottles have old labels, broken caps, or any data that the instrument doesn’t put into it’s files.
discolored contents, record that. Some chemicals just b) If doing simulations setup a table of filenames, input
don’t work when old. Hydrogen peroxide is really bad parameters and comments on success or whatever.
for that, check the bottle date. c) Computers are finicky, record any difficult to remember
e) Record any changes to the preparation procedures. E.g. procedures (say for importing data) into your book.
200mL flask used instead of recommended 50mL flask. d) Paste in things like ASCII tables or program procedures
f) Note the course of reaction and other details. E.g. 1) into the lab. book.
reaction proceeded smoothly and was complete in e) Record the computer type and program version nos.
10mins. 2) Reaction proceed rapidly and blew a bung Bugs are often undetected for a long time, this data will
out (replaced rapidly). 3) Some silicone grease dripped help you decide their relevance.
into the reaction vessel. 4) Reaction turned green after f) Make sure you indicate the algorithms used for doing
30 min (instead of yellow at 45min.). Mixture
calculations, particularly if you used a computer.
detonated after 32min. (The student who noted the
latter dropped chemistry and became a lawyer). 5)
Initial preparation showed traces of NO2. Reaction
vessel was flushed with nitrogen again to remove
oxygen. 6) Foul smell, sample stored in fume hood.
Times
Time is more important than you think. One preparation in
my laboratory, at UBC, didn’t work on sunny winter days,
but worked fine on sunny summer days. This was because
the sun would shine into the laboratory at 4pm, in winter,
just when the silver salts were added to the reaction (it was
an 8hr prep.). In the summer, the sun was to high to shine
in. Record reaction times, flushing times, reflux times, start
times, end times, just about any time you can think of.
Results
a) Record basic physical data; total mass, state, % yield,
m.p.t. etc.
b) Record any other data including program and version
number, if the result is produced by a computer. Be sure
to record any file names.
Miscellany
Record anything else you notice. e.g. 1) samples were yellow
when removed from freezer, but turned a transient red
Introduction:13
PLAGIARISM
You cheat,
You’re dead meat.
For a detailed discussion of plagiarism see the OUC Guide to Plagiarism available from the bookstore. The policy is
basically one of zero tolerance. The penalty for plagiarism is usually a zero for the work involved and a letter of
reprimand. Penalties for theft of papers or repeated plagiarism may be expulsion.
Avoiding plagiarism in chemistry labs. is quite simple; don’t copy other peoples work ! That is, do not copy
or read the whole or sections of another person laboratory report, draft or final.
There are cases where it is acceptable to copy other peoples work, in which case you should note the following:
a) If you wish to copy blocks of text from some source, put it in quotes and reference the source. You should not do this a
lot or you will be penalized for poor style. The source of material must not be another students lab. report or from a
‘tutoring service’.
b) If you use any source to assist in writing your labs. make sure you reference those sources in your write up. If you
paraphrase the text from these sources, try to do it as loosely as possible (i.e. keep it close to your personal style). If the
paraphrasing is too similar to the original you may be open yourself to a plagiarism charge. I find it best to read two or
more sources, close those sources and then write out what I understand of what I’ve just read. Again, the sources must
not be other students lab. reports, profs. notes etc.
c) You may discuss labs. with other students and you may compare original data and graphs. At a pinch, you can
compare calculations to track down errors. Under no circumstances should you read or copy other students lab. reports
(final or draft), that is considered plagiarism. If you read another students report (but not necessarily copy) it will taint
the style of your write up. It is quite shocking how easy that is to detect, particularly is small classes – so don’t do it!
d) Do not copy other students graphs or tables either electronically or by Xeroxing. Producing your own graphs and
tables is an important part of this course. (This may be acceptable in other courses, but not this one).
HOUSE KEEPING
Before starting an experiment, wash, and if necessary dry, any glassware, before use. Remember, the last person to use
the glassware was a student.
At the end of the experiment be sure to clean and wash any glassware. If you found it on the bench, in the cupboard, the
draws, the outside and return it there. If it came from a stock cupboard , put it on the drying rack. Make sure you leave
the balances clean. If any equipment was disassembled when you got it, disassemble it again and return to where you
found it. Leave any equipment or chemicals that the instructor/technician gave you on the bench. Clean up any spills,
paper towels, or any other mess you make. Report any breakages or depleted reagents so we can make replacements.
Failure to do this housekeeping may result in marks being deducted.
QUESTIONS.
1) The mechanism is more complex than the simple
Michaelis-Menten one so we cannot determine if the
Malathion is competitive or non-competitive using a
© P.S.Phillips 31/10/2011 Exp. E. Enzyme Kinetics:9
NOTES
where Vao is the initial volume of the analyte, cbo is the initial CALCULATIONS.
concentration of analyte, Vb is the volume of titrant added, Do the following calculations for both the titrations.
cbo is the concentration of titrant and 1) Determine the end-point and hence the pKa‘s of both
the acids directly from a plot of pH vs. VNaOH.
co f c o K (1- f )
a = a ) Ka b= a a ) Kw 2) Determine the pKa of both the acids from a plot of
1) rf 1) rf
dpH/dV vs. VNaOH. That is, setup Excel to do a simple
where r = cao / cbo , and the fraction of analyte titrated, f, is derivative using dy / dx » ( yi)1 - yi )/(xi)1 - xi ) . You may
f = Vb cbo / Vaocao . These equations enable us to extract Ka have to drop the first few points of the amino acid titration.
using the whole titration curve rather than just the one ill- Typical results are shown in figure 1.1 below.
defined end-point.
3) Repeat the two plots of the titration curve using
PROCEDURE. This is a simple pH titration. First, you CurveFit (if provided by the instructor) with the cubic spline
need to calibrate the pH meter, using the provided standard (with and without tension) and Akima spline. One method
buffers (pH 4.00, pH 7.00 and pH 9.00 or 10.00). You will be works better than the other.
shown how to do this. Make sure you don’t get cross
© P.S.Phillips October 31, 2011 EXPERIMENT G:1
4) Fit the titration curve to a cubic (in the vicinity of each glycine. This lab. illustrates the complexity of such
pKa and get α and β in (1.1) and hence the pKa’s. apparently simple experiments. In fact, we will have to take
some short cuts and make use of literature values or we
5) If you were asked to do a titration using conductivity,
wouldn’t have time to do it all.
repeat the process with the conductivity data using the
method of broken lines and the derivative method. THEORY. Here, we are interested in the enthalpy of
protonation ( DH proton of glycine, HGly) in aqueous
solution, that is
H+(aq) + HGly (aq) ] H2Gly+(aq) (2.1)
This is characterized by pK a2 for glycine. Note that this
reaction is not the dissociation of glycine (or the reverse),
that is given by
HGly (aq) ] H+(aq) + Gly-(aq) (2.2)
and characterized by the pK a1 for glycine.
Figure 1.1 Typical titration curve and the I have dropped the superscript “o” from the enthalpies for
differential. The weaker the acid (or base) the less convenience, they do, however, refer to standard conditions.
well defined the inflection point becomes.
We can obtain DH proton from the temperature dependence
5) Get the pKa using a Gran plot. That is, plot [H+]VNaOH of the pKa . Here we will obtain it from calorimetric reaction
vs. VNaOH. The slope of the line is –Ka and the x-axis cycles:
intercept is the equivalence point. Compare those values
with those obtained by the other methods. You may want to Reaction 1.
use the robust LSF to fit the data (CurveFit again). At the DH (Gly)
HGly(s) ) H+ (aq) ¾¾ dissoln
¾¾¾¾ ® HGly(aq) ) H+ (aq)
very least, you may have to eliminate points from the plot
ends before fitting. Note you cannot use this plot over the DH rx1 DH proton (HGly(aq))
whole range: select data from around the end-points H2Gly + (aq)
QUESTIONS. This is the dissolution of glycine in hydrochloric acid and it’s
1) Compare your data to the literature values. Does the pKa subsequent protonation. The protonation is not complete
in the 0.3M NaCl differ from water or its literature value? and has to be accounted for. In the presence of excess acid,
there is no significant dissociation of glycine so this is
2) We often talk about sharp and fuzzy to describe slope ignored.
changes or breaks. The formal terms to describe lines are
smoothness, monotonicity and continuity. Briefly, describe Reaction 2.
DH (Gly)
the correct descriptions for the terms and support with HGly(s) ¾¾ dissoln
¾¾¾¾ ® HGly(aq)
DHdissoc (HGly(aq))
some math. Be sure to distinguish between the informal and
formal definitions of smooth. DH soln
3) The conductivity data will go through a minimum. Gly-(aq) ) H+
Explain this and the general structure of the titration curve. This is simply the dissolution of glycine and it’s subsequent
dissociation, normally referred to as the heat of solution. The
Part 2. SOLUTION THERMODYNAMICS dissociation is not complete and has to be accounted for; see
INTRODUCTION. As elegant as thermodynamics is later. The protonation of glycine is not significant under
(everything follows from the first two laws) there is no way these circumstances and can be ignored. Note the
of predicting enthalpies or entropies; they must be distinction between enthalpy of solution (just adding
measured. Some simplification occurs because we measure glycine to water) and enthalpy of dissolution.
state functions so data that are not directly measurable are
accessible via what I call the cycle method (just a variation Reaction 3.
of Hess’s Law). In this experiment, we will measure the heat NH2CH2COOH + NH3CH2COO-
of protonation of an amino acid (glycine) in aqueous
That is, dissociation to the zwitterion. It turns out that
solution via its heat of solution and heat of reaction for solid
EXPERIMENT G:2 © P.S.Phillips October 31, 2011
glycine only exists as the zwitterion in solution. This is made while a sample of glycine is dissolved in the acid. The
discussed below. temperature is recorded continuously throughout the course
By examining these schemes above you can see that to get of the experiment. The heat change is determined by
the enthalpy of protonation ( DH proton ) one needs the comparison with a standard run (of adding TRIS to 0.1M
enthalpy of dissolution ( DH dissoln ) and the enthalpy of HCl). Since we will be using solid glycine, we have to do a
dissociation ( DH dissoc , see the appendix). The enthalpy of third run to establish the heat of solution of the glycine.
dissolution can then be obtained from reaction cycle 2: You will be dealing with changes in temperature of less than
DH proton = DH rx1-DH soln+ DH dissoc a degree so you should be definitely trying to get better than
There are three problems, however: The first is that the 1% accuracy for the various individual measurements. A
reaction (1) is done in a 0.3M HCl solution. This is strong temperature measurement to 0.01C may look impressive to
enough to influence the activities, and thus the reaction you, but it is not much good for this experiment. The
enthalpy. This is overcome by doing the enthalpy of solution thermocouple is precise to 0.001C, if correctly used. You
(reaction (2.2)) in a solvent of the same ionic strength, in will have to be very careful to get decent results.
this case, 0.3M KCl. CALORIMETER DISASSEMBLY/ASSEMBLY. The
The second problem is quite insidious. Neutral glycine does apparatus contains some very fragile glass bits. Be careful
not exist in solution (at least only 1 in ¼ million) it exists as when handling them, you'll need a bank balance with five
the zwitterion. However, since it’s always in this form no significant figures to repair them. If the calorimeter is
parameter relating to neutral glycine appears in the assembled (see Figure 2.1), disassemble as follows: If the
equations, so it actually doesn’t matter. However, this is not glass push rod is raised, push it down gently to eject the
true of other amino acids where the zwitterion may not sample dish. Disengage the drive belt if on. Then gently lift
dominate. the whole assembly out of the calorimeter and place it in the
The third problem is that glycine is not a very acidic so it retort ring provided. NOTE: that the thermocouple is
plugged into the back of the calorimeter so don't expect to
does not completely dissociate in solution. We thus have to
be able to move the assembly very far without unplugging it
adjust for the degree of dissociation. We can get K1 for
dissociation from the appendix. For n moles of glycine we first. Hold the glass plunger rod and pull off the Teflon
have the ‘ICE’ calculation sample cup while twisting it and then slide out the glass rod.
Inspect the sample cell and sample dish for dirt and water.
HGly(aq)]H+(aq) + Gly- (aq) Carefully clean and dry if necessary. Now, carefully lift out
n 0 0 the Dewar flask and clean and dry if necessary. Reverse the
n-α –α -α process (including cleaning and drying) to assemble the
and apparatus. If the calorimeter is already disassembled,
familiarize yourself with each of the components and the
[H+ ][Gly-]
K1 = order in which they fit.
[HGly]
from which we get
α2
K1 =
(n − α )0.1
Equilibrium constants are for concentrations, not moles, so
the factor of 0.1 is to correct for the 100mL solution. Hence
we get the factor, 1/α, to multiply the enthalpy of
dissociation by to correct for incomplete dissociation (1/α
should be about 500).
BASIC PROCEDURE. The calorimeter is a Dewar flask
containing a rotating sample cell and a thermocouple (see
fig.1) attached to a data processing unit. A known amount of
acid (about 100g) will be measured into it, the stirrer will be
run continuously, and calorimetric measurements will be Figure 2.1. Schematic of solution calorimeter.
23.8
ERROR ANALYSIS. A full error analysis will drive you
squirrelly so proceed as follows:
23.7 a) Identify the errors an all quantitative measures and
23.6 estimate their size and whether they are systematic or
random.
23.5
-2 0 2 4 6 8 10 12 14 16 18
b) Errors in ∆T can be estimated as indicated earlier. All
Time (s) others can be made using the tables in the error analysis
time at which the temperature was at 60% of the net change. section. Identify all other error sources and estimate their
(the vertical line in figure 3.5). Do an Excel fit to the pre- rough size (in this case they will be small or negligible) and
and post run temperatures. Only use the linear part of the whether they are systematic or random.
post-run (about 11sec onward in figure 3.5 – the fit shown c) Identify the largest error and propagate that. Be sure to
is not quite correct). Make sure you do a full Excel fit to get pay attention to subtractions.
QUESTIONS. Suppose each sodium ion has a solvation THEORY. The partition coefficient for a solute X, is
shell of six waters – we will call this “bound “water. How defined as
much “free” water is there in a 5M NaCl solution (ignore the [X]octanol
K ow =
chloride ion)? Now consider a 1mM solution of a model [X]water
protein of molar mass 100kDa (say poly glycine). Would
there be enough water to hydrogen bond this molecule So Kow tends to be large for non-polar species. Kow is, of
completely (assume 2 H-bonding sites per base). Is it course, an equilibrium constant, albeit for a physical process,
possible that we the effect is not due to hydrophobicity rather than a reaction. The corresponding free energy
changes, but a loss of H-bonding? DG o =-RT ln K ow
Part 3. PARTITIONING is just the free energy change when one mole of X is
INTRODUCTION. In the last two sections we looked at transferred from water to octanol.
the mutual solubility of two liquids. Here we will look at how One widely overlooked fact is that, for acids and bases
a solute distributes between two immiscible solvents, and (and amphiphiles), Kow depends on pH. For instance, acetic
the effect of pH. acid (CH3COOH) is quite soluble in non polar solvents. It’s
You’ve all heard the expression “oil and water” don’t mix. also soluble in water because of H-bonding and also
To be more specific, oil and water are immiscible and form a because the conjugate base (CH3COO-) is very polar. The
two phase system. The reason for this is the hydrophobic degree of dissociation depends on the pH. For a sufficiently
effect, discussed above. high pH, acetic acid will cease to partition into the non-
You’ve also heard the phrase “like dissolves like”. Again, polar phase because it’s completely dissociated. This means
to be more specific, polar materials dissolve in polar solvents that partition coefficients for organic acids and bases vary
and non-polar materials dissolve in non-polar solvents. with pH. The tabulated values (which are for arbitrary
There are of course many exceptions, acetone dissolves concentrations of the acid or base) are completely useless for
freely in hexane and water, although these two solvents are environmental or biochemical work where the aqueous
immiscible. This then begs the question, what happens if phase is nearly always buffered to near neutral.
you mix acetone, water and hexane? The answer is that the The system is a parallel (as opposed to sequential)
acetone will dissolve in both; it will partition itself between equilibrium:
the two solvents. The degree of partitioning will relate to the
polarity of the solute and the relative polarity of the two Ka
HA(aq) ←→ H + (aq) + A − (aq)
solvents. This apparently mundane observation is rather
important: we exploit it in the chemistry laboratory (and ↑ K ow
industrially) to extract the non-polar species from aqueous ↓
solution (by shaking with a non-polar solvent and HA(oct )
decanting the non-polar solvent off). Similarly, we can which is described by two equations
extract polar species using water. In environmental science
it’s important to know how various chemicals (a.k.a. [H + ][A + ]
Ka =
pollutants) distribute themselves between water (highly [HA]
polar), mud (polar) and fish (partly non-polar). In and
¶G ö÷ ¶G ö÷ m
¶G ö÷÷
G º H -TS dG = ÷÷dT )) ÷÷ dP ...... å ÷÷ dni (4)
¶T ø P ,n1 ,n2 ,... ¶P ø T ,n1 ,n2 ,... i=1
¶ ni ÷ø T ,P ,all n
\ dG = dH -TdS - SdT k¹i
We define the last term as the chemical potential, µ, the
H º U + PV variation of G with composition i.e.
but
\ dH = dU + PdV + VdP ¶G ö÷
ki º ÷
¶ni ÷÷øT ,P ,all n
k¹i
so dG = dU + PdV + Vdp -TdS - SdT so (4) becomes
m
¶G ö÷ ¶G ö÷
but U º q +w dG = ÷ dT + ÷ dP
¶T ÷ø P ,n1 ,n2 ,... ¶P ÷ø T ,n1 ,n2 ,...
....... + å mi dni
i=1
For a reversible change in a closed system of constant
composition (no reactions), with no non-expansion work, Also, for 1 mol, µ is just G so (2) can be written
this becomes
æPö
U = qrev - PdV m(P) = mo ) RT lnçç o ÷÷÷ (5)
çè P ø
but since qrev = TdS , substituting back into the expression
for dG we get It’s a little difficult to see why we would introduce chemical
potential; after all, we can only measure changes in it, which,
dG = TdS - PdV + PdV + VdP -Tds - SdT at constant T and P, is ∆G. There are a couple of reasons, but
the simplest is that it easier to talk about. Saying ∆Gvap is
hence we get dG = VdP - SdT (1) +ve is the same as saying the chemical potential of a liquid
is lower than the vapor. The latter is somehow clearer and
¶G ö÷ more intuitive (things roll downhill). Another example is,
so at constant T ÷ =V that at equilibrium the chemical potential of multiple phases
¶T ÷øT
have the same chemical potential. That statement captures
Integrating between P1 and P2 assuming P scales inversely the situation more easily than some description using free
with V (e.g. PV=nRT) energy. It also allows us to introduce non-ideality more
easily (chemical potential is also known as the partial molar
æP ö
G(P2 ) = G(P1) ) RT lnçç 2 ÷÷÷ (2) free energy). Lastly, (4) is the not whole equation, there are
çè P1 ø÷ other terms we won’t discuss here.
Solids and liquids are incompressible so the volume change Solutions.
with pressure is tiny, so the change is negligible (1-2 J), but The chemical potential of a substance is the same
for gases it’s quite large. throughout a sample at equilibrium, regardless of how many
If we measure changes in G with respect to some phases are present. This is very important because it allows
reference state, they become ∆G’s. To simplify things further, us to say something about complicated systems. In
we usually make P1 the reference state, so P1 become Po and particular, for a liquid/vapor system, if we know the
∆G(P1) becomes ∆Go , so we get for some pressure P chemical potential of the vapor, we know the chemical
æPö potential of the liquid. This is important because we can
DG(P) = DG o ) RT lnçç o ÷÷÷ (3)
çè P ø calculate (or measure) a lot about gases, even non-ideal
Chemical Potential. ones, but we know very little about liquids and, currently,
Gibbs Free Energy is a function of composition can calculate diddly-squat about them, but if we have the
(n1, n2 ,...nm ) , temperature, T and pressure, P, i.e. chemical potential of the vapor, we know everything we
need to know (thermodynamically) about the liquid.
G = f (T , P , n1, n2 ,...nm )
© P.S.Phillips October 31, 2011 EXPERIMENT H:7
Let’s consider a pure (denoted by a superscript *) we change X to activity.
solvent, A, in equilibrium with its vapor in a closed system
We can now rearrange this equation to give us the
(no air present), then chemical potential change for converting one mole of
mA* (vapor ) = mA* (liquid) o
solvent to a solution of concentration XA i.e. DGtransfer
Since the liquid is pure, and if we have one mole, it’s in its
standard state (the pressure is not one bar, it’s whatever its Raoult’s Law.
vapor pressure is, but we have shown elsewhere that this Raoult’s Law is empirical and only applies to cases where the
solution is dilute or the solute and solvent are very similar.
effect is negligible for liquids and solids so we can use the
standard state), so This problem can be side-stepped, in the usual way, by
stating “for dilute solutions.....”, however, that defeats the
mAo (liquid) = mA* (vapor ) purpose of studying non-ideal cases. The more useful way
is to define the activity aA(“apparent “ or thermodynamic
However, the chemical potential of the vapor is pressure concentration) as follows
dependent, (5). so if P* is the vapor pressure of the pure
liquid we get mA (solution) = mAo (liquid) ) RT ln aA
æ P * ö÷ The activity, aA, is purely empirical, but the equation is
mA (vapor , P ) = mA (vapor , P ) ) RT lnççç o ÷÷
* * o o
(6) exact. For dilute solutions of non-polar solutes aA → X A .
÷
çè P ÷ø
For dilute solutions of ionic compounds, the activity can be
The standard state for the vapor being the vapor at one bar calculated by Debye-Huckel theory or one of its extensions.
pressure. Some Nomenclature.
Now let’s consider a solution of solvent A and a single non- There are some evil forces at work that refer to the
volatile solute B (i.e. it has no vapor pressure). hydrophobic effect as hydrophobic forces, or worse bonds.
However, there are some sources of confusion. The first
mA* (vapor ) = mA (solution) being intermolecular vs. intramolecular. Intermolecular
refers to “between molecules” and intramolecular “within a
since the chemical potential of A must be the same in both
phases. Therefore from (5) molecule” (and is mainly responsible for protein folding).
The next is the distinction between forces, bonds and
æPö effects. A bond involves sharing of electrons and is
mA (solution) = mAo (vapor , P o ) ) RT lnçç o ÷÷÷ (7)
èç P ø directional. Forces are usually electrostatic in nature (ionic
bonds aren’t really bonds, they are an electrostatic force).
where P is now the vapor pressure over the solution. They may or may not be directional. Hydrogen bonds, π-
From (6) stacking etc. are electrostatic forces, which we collectively
call intermolecular forces (although they can be
æ P * ö÷ æ P ö÷ intramolecular forces. π-stacking is almost exclusively
mA (solution) = mA* (vapor , P o ) - RT lnççç o ÷÷ ) RT lnççç o ÷÷
èç P ø÷÷ èç P ø÷÷ intramolecular.) On the other hand the hydrophobic effect is
just that an effect (on entropy). It is caused by H-bonding,
æ P ÷ö but is not bonding, or even a force. To avoid confusion were
so mA (solution) = mAo (liquid) ) RT lnççç * ÷÷ call all the conditions that organize the structure of
çè P ÷÷ø molecules, covalent and ionic bond’s excepted,
intermolecular interactions.
but Raoult's Law for an ideal solution is
PA = X A PA*
That is, the solute lowers the vapor pressure of the solvent
(since XA is <1). Note that the identity of B is irrelevant;
vapor pressure is a colligative property. For a real solution,
This is what you get lots and lots of stuff (336 structures). You need to narrow it down.
Anyway lets click on 2HHb, or more specifically the the title next to it.
There are other viewing options so let’s scroll back up to see them.
http://en.bio-soft.net/3d.html
http://www.pdb.org/pdb/static.do?p=software/software_links/molecular_graphics.html