Analytical Chemistry Lesson of the Day – Accuracy in Method Validation

In pharmaceutical chemistry, one of the requirements for method validation is accuracy, the ability of an analytical method to obtain a value of a measurement that is close to the true value. There are several ways of assessing an analytical method for accuracy.

  1. Compare the value from your analytical method with an established or reference method.
  2. Use your analytical method to obtain a measurement from a sample with a known quantity (i.e. a reference material), and compare the measured value with the true value.
  3. If you don’t have a reference material for the second way, you can make your own by spiking a blank matrix with a measured quantity of the analyte.
  4. If your matrix may interfere with the analytical signal, then you cannot spike a blank matrix as described in the third way.  Instead, spike your sample with an known quantity of the standard.  I elaborate on this in a separate tutorial on standard addition, a common technique in analytical chemistry for determining the quantity of a substance when matrix interference exists.  Standard addition is an example of the second way of assessing accuracy as I mentioned above.  You can view the original post of this tutorial on the official JMP blog.

Potato Chips and ANOVA, Part 2: Using Analysis of Variance to Improve Sample Preparation in Analytical Chemistry

In this second article of a 2-part series on the official JMP blog, I use analysis of variance (ANOVA) to assess a sample-preparation scheme for quantifying sodium in potato chips.  I illustrate the use of the “Fit Y by X” platform in JMP to implement ANOVA, and I propose an alternative sample-preparation scheme to obtain a sample with a smaller variance.  This article is entitled “Potato Chips and ANOVA, Part 2: Using Analysis of Variance to Improve Sample Preparation in Analytical Chemistry“.

If you haven’t read my first blog post in this series on preparing the data in JMP and using the “Stack Columns” function to transpose data from wide format to long format, check it out!  I presented this topic at the last Vancouver SAS User Group (VanSUG) meeting on Wednesday, November 4, 2015.

My thanks to Arati Mejdal, Louis Valente, and Mark Bailey at JMP for their guidance in writing this 2-part series!  It is a pleasure to be a guest blogger for JMP!



Potato Chips and ANOVA in Analytical Chemistry – Part 1: Formatting Data in JMP

I am very excited to write again for the official JMP blog as a guest blogger!  Today, the first article of a 2-part series has been published, and it is called “Potato Chips and ANOVA in Analytical Chemistry – Part 1: Formatting Data in JMP“.  This series of blog posts will talk about analysis of variance (ANOVA), sampling, and analytical chemistry, and it uses the quantification of sodium in potato chips as an example to illustrate these concepts.

The first part of this series discusses how to import the data into the JMP and prepare them for ANOVA.  Specifically, it illustrates how the “Stack Columns” function is used to transpose the data from wide format to long format.

I will present this at the Vancouver SAS User Group (VanSUG) meeting later today.

Stay tuned for “Part 2: Using Analysis of Variance to Improve Sample Preparation in Analytical Chemistry“!



Analytical Chemistry Lesson of the Day – Linearity in Method Validation

In analytical chemistry, the quantity of interest is often estimated from a calibration line.  A technique or instrument generates the analytical response for the quantity of interest, so a calibration line is constructed from generating multiple responses from multiple standard samples of known quantities.  Linearity refers to how well a plot of the analytical response versus the quantity of interest follows a straight line.  If this relationship holds, then an analytical response can be generated from a sample containing an unknown quantity, and the calibration line can be used to estimate the unknown quantity with a confidence interval.

Note that this concept of “linear” is different from the “linear” in “linear regression” in statistics.

This is the the second blog post in a series of Chemistry Lessons of the Day on method validation in analytical chemistry.  Read the previous post on specificity, and stay tuned for future posts!

Analytical Chemistry Lesson of the Day – Specificity in Method Validation and Quality Assurance

In pharmaceutical chemistry, one of the requirements for method validation is specificity, the ability of an analytical method to distinguish the analyte from other chemicals in the sample.  The specificity of the method may be assessed by deliberately adding impurities into a sample containing the analyte and testing how well the method can identify the analyte.

Statistics is an important tool in analytical chemistry, and, ideally, there is no overlap in the vocabulary that is used between the 2 fields.  Unfortunately, the above definition of specificity is different from that in statistics.  In a previous Machine Learning and Applied Statistics Lesson of the Day, I introduced the concepts of sensitivity and specificity in binary classification.  In the context of assessing the predictive accuracy of a binary classifier, its specificity is the proportion of truly negative cases among the classified negative cases.

Physical Chemistry Lesson of the Day – What is the Primary Determinant of the Effective Nuclear Charge for Outer Electrons?

Electrons in the inner shells of an atom shield the electrons in the outer shells pretty well from the nuclear charge.  However, electrons in the same shell don’t shield each other very well.  If an electron spends most of its time below another electron, then the first electron can shield the second electron.  However, this is not the case for electrons in the same shell – they repel each other because they are all negatively charged, and they are at roughly the same average distance from the nucleus.

Thus, the difference between

  1. the charge of the nucleus
  2. and the charge of the core electrons

is the primary contributor to the effective nuclear charge that the outer electrons experience.

Analytical Chemistry Lesson of the Day – Method Validation in Quality Assurance

When developing any method in analytical chemistry, it must meet several criteria to ensure that it accomplishes its intended objective at or above an acceptable standard.  This process is called method validation, and it has the following criteria* in the pharmaceutical industry:

  • specificity
  • linearity
  • accuracy
  • precision
  • range
  • limit of detection
  • limit of quantitation
  • robustness**

As I will note in future Chemistry Lessons of the Day, these words are used differently between statistics and chemistry.

*These criteria are taken from Page 723 of the 6th edition of “Quantitative Chemical Analysis” by Daniel C. Harris (2003).

**The Food and Drug Administration does not list robustness as a typical characteristic of method validation.  (See Section B on Page 7 of its “Guidance for Industry Analytical Procedures and Methods Validation for Drugs and Biologics“.)  However, it does mention robustness several times as an important characteristic that “should be evaluated” during the “early stages of method development”.  

Organic Chemistry Lesson of the Day – The 4 Conformational Isomers of Butane

In a previous Chemistry Lesson of the Day, I introduced the simplest case of conformational isomerism – the staggered and eclipsed conformations of ethane.  The next most complicated case of conformational isomerism belongs to butane.  Here are the Newman’s projections of the 4 possibilities.

butane conformers

Modified image courtesy of Avitek from Wikimedia.

The conformational isomers are named with respect to the proximity of the 2 methyl groups.  The dihedral angle between the 2 methyl groups, θ, is below each Newman projection.  From left to right, the conformational isomers are:

  • fully eclipsed (θ = 0 degrees)
  • gauche (θ = 60 degrees)
  • eclipsed (θ = 120 degrees)
  • anti (θ = 180 degrees)

Clearly, the fully eclipsed conformation has the most steric strain* between the 2 methyl groups, so its internal energy is highest.

Clearly, the anti conformation has the lowest steric strain between the 2 methyl groups, so its internal energy is lowest.

The gauche conformation has less steric strain than the eclipsed conformation, so its internal energy is the lower of the two conformations.

From lowest to highest internal energy, here is the ranking of the conformation isomers:

  1. anti
  2. gauche
  3. eclipsed
  4. fully eclipsed

This can be visualized by the following energy diagram.

butane energy diagram

Image courtesy of Mr.Holmium from Wikimedia.

*As mentioned in my previous Chemistry Lesson of the Day on the 2 conformational isomers of ethane, there is some controversy about what really causes the internal energy to increase in eclipsed conformations.  Some chemists suggest that hyperconjugation is responsible.

Eric’s Enlightenment for Thursday, May 21, 2015 – A Special Edition on the Mental Health of Chemistry Graduate Students

Today, combining

  • my passion for chemistry,
  • my experienced knowledge of university culture in North America,
  • and my deep concern for mental health issues,

The Chemical Statistician will feature a collection of writing about the struggles that graduate students in chemistry face during their studies, and how those struggles affect their mental health.  This is a special edition of Eric’s Enlightenment.

  1. Chemjobber began a dialogue with Vinylogous about mental health and graduate studies in chemistry in 2013.  It started with this blog post as Part 1, containing reflections of Chemjobber’s own experience and thoughts on general issues on this subject.
  2. In Part 2 of their dialogue, Vinylogous responds to Chemjobber with a very detailed post on his conjectures of why graduate studies in chemistry is so hard on a student’s mental health.
  3. In Part 3 of their dialogue, Chemjobber responds to some of Vinylogous’ main points and addresses possible solutions to mental health challenges for chemistry graduate students.  He/She also begins to answer the question “Is a graduate degree in chemistry worth the sacrifice?”.
  4. In Part 4 of their dialogue, Vinylogous examines some alternative issues in this subject, including possible benefits of chemistry graduate studies for mental health, how some research supervisors aggravate mental health problems, and differences between sub-fields of chemistry.
  5. Finally, in Part 5, Chemjobber concludes this discussion by trying to answer some of the key questions that this dialogue generated and summarizes some of the key points that they learned.
  6. I am surprised that I never learned about this sad story during my studies as a chemistry student: Jason Altom was an accomplished and well-liked doctoral student in chemistry at Harvard University, yet he committed suicide at age 26, citing excessive pressure from abusive research advisers, including his supervisor, Nobel Laureate Elias Corey.  Notably, his suicide notes contained policy recommendations on how academic departments can better protect their students.

The dialogue between Chemjobber and Vinylogous was very productive, with many other chemistry bloggers adding valuable perspectives in their own blog posts.  I highly encourage you to read those articles, too.

I also highly recommend you to read the comments in all 5 blog posts – they add great diversity to the perspectives and experiences about this complicated topic.

Here are some key quotations that I gathered from these articles:

Chemjobber – in Part 1 of the dialogue with Vinylogous.

After weeks and weeks of long hours and frustration in the lab in either my 2nd or 3rd year of graduate school, I remember walking into my apartment bathroom, smashing the mirror with my fist and sitting on the edge of the bathtub. I seem to recall yelling at the top of my lungs “What am I going to do!?!?” about whatever reaction sequence of my total synthesis that simply was not going anywhere.

I can easily say that was one of the darkest periods of my time in graduate school. I am not sure if I was depressed — I’m a synthetic chemist, not a clinical psychologist. Close to ten years later, it’s mostly an unpleasant memory, with little recall of the details that set me off. But I can remember sitting on that bathtub edge, the deep despair of a project that wasn’t going well and the feeling that my entire life was an utter failure. Now, of course, I don’t feel that way at all. I can leave my work at work (mostly, anyway), and my self-worth is not entirely reliant on the yield of my last reaction. But there was a lot of pain in between then and now.

Vinylogous – in Part 2 of the dialogue with Chemjobber.

At one point during my previous degree, when I was doing research, taking classes, and teaching, my advisor told me frankly that my productivity needed to increase. It needed to double. At that point I already felt that I was at my absolutely limit in what I could accomplish in a week. At that point, I had nowhere near enough data for a paper and barely enough for a mediocre conference poster. Weekends had been given up, as had hobbies. When I mentioned to my advisor the many demands on my time, his response was short: “Sometimes you need to prioritize what’s important to you.” (The subtext: stop caring about class and teaching and hobbies). It was an existential moment. I managed somehow to increase my productivity and my efficiency, and within a year or so I had three first-author manuscripts. I defended my M.S. and graduated, moving to another (higher tier) school for a Ph.D. But I left with a pre-conditioned bitterness towards graduate work.

Organic Chemistry Lesson of the Day – The 2 Conformational Isomers of Ethane

The simplest case of conformational isomerism belongs to ethane, C2H6.

ethane conformers

Newman projections of the 2 conformational isomers of ethane.

Image courtesy of Mr.Holmium via Wikimedia.

In the Newman projections above, you can see that the dihedral angle between any 2 vicinal hydrogens plays a key role in the stability of ethane.  In particular, there are 2 extrema in that plot of the change in Gibbs free energy vs. the dihedral angle:

  • The minimum is attained when the dihedral angle is 180 \times (2n + 1) \div 3 degrees, where n is any integer (n = 0, \pm 1, \pm 2, \pm 3, ...).  In other words, the vicinal hydrogens are as far apart from each other as possible.  This conformation is called the staggered conformation.
  • The maximum is attained when the dihedral angle is 180 \times (2n) \div 3 degrees, where n is any integer (n = 0, \pm 1, \pm 2, \pm 3, ...).  In other words, the vicinal hydrogens are as close to each other as possible.  This conformation is called the eclipsed conformation.

The stability of ethane is dependent on this dihedral angle.

  • If the vicinal hydrogens are far part from each other (in a staggered conformation, for example), then there is less torsional strain* between the 2 carbon-hydrogen bonds, resulting in more stability.
  • If the vicinal hydrogens are close to each other (in an eclipsed conformation, for example), then there is greater torsional strain* between the 2 carbon-hydrogen bonds resulting in less stability.

*In my undergraduate education, I learned that the greater stability in the staggered conformation is due to less torsional (steric) strain.  However, Vojislava Pophristic & Lionel Goodman (2001) argued that the effect is actually due to the stabilizing effect of hyperconjugation.  Song et al. (2005) and Mo and Yao (2007) rebutted this argument in separate publications.  Read these articles as searched under “ethane hyperconjugation steric strain” on Google Scholar for more information.


  • Pophristic, V., & Goodman, L. (2001). Hyperconjugation not steric repulsion leads to the staggered structure of ethane. Nature, 411(6837), 565-568.
  • Song, L., Lin, Y., Wu, W., Zhang, Q., & Mo, Y. (2005). Steric strain versus hyperconjugative stabilization in ethane congeners. The Journal of Physical Chemistry A, 109(10), 2310-2316.
  • Mo, Y., & Gao, J. (2007). Theoretical analysis of the rotational barrier of ethane. Accounts of chemical research, 40(2), 113-119.

Organic and Inorganic Chemistry Lesson of the Day – Conformational Isomers (or Conformers)

Conformational isomerism is a special type of stereoisomerism that arises from the rotation of a single bond.  Specifically, 2 molecules are conformational isomers (or conformers) if they can be interconverted exclusively by the rotation of a single bond.  This type of isomerism differs from configurational stereoisomerism, whose isomers can only be interconverted by breaking certain bonds and reattaching* them to produce different 3-dimensional orientations.  Examples of configurational isomers include enantiomers, diastereomers, cis/trans isomers and meso isomers.

Different conformers are notable for having different stabilities, depending on the electrostatic interactions between the substituents along the single bond of interest.  I will talk about these differences in greater depth in future Chemistry Lessons of the Day.

*Such reattachment of the bonds must not result in different connectivities (or sequence of bonds); otherwise, that would result in structural isomers.

Café Scientifique – Materials Science Seminar by Neil Branda on Wednesday, November 19, 2014

If you will attend the following seminar, please do come and say “Hello”!  The event is free, but registration is required!  For more information, visit the SFU Café Scientifique’s web site!

SFU Café Scientifique

Time: 7:00 -8:30 pm

Date: Wednesday, November 19, 2014

Place: Boston Pizza, 1045 Columbia Street, New Westminster, BC

Title: It’s a Materials World – From Sticks and Stones to Nanotechnology, how materials have changed our world

Speaker: Neil Branda – Professor of Chemistry at Simon Fraser University, Executive Director of 4D LABS, and Chief Technology Officer of SWITCH Materials


Since the beginning, understanding how materials can be used for specific tasks has resulted in some of the biggest changes to civilizations. Modern society is becoming more and more dependent on the development and use of advanced materials. From the basics to the controversial, how materials have affected they way we live and play will be discussed.

Biography of Speaker:

Dr. Neil Branda is a professor of Chemistry and a Canada Research Chair at Simon Fraser University, the Executive Director of 4D LABS, a research centre for advanced materials and nano-scale devices, CTO of SWITCH Materials Inc., a company he founded to commercialize his molecular switching technology and Founder and Director of the NanoCommunity Canada Research Network, a community of nanotechnology researchers committed to sharing knowledge and working collaboratively to advance applications in medical diagnostics, therapeutics, renewable energy and advanced materials.


Organic and Inorganic Chemistry Lesson of the Day – Stereoisomers

Two molecules are stereoisomers if they

  • have the same molecular formula
  • have the same sequence of bonds between each molecule’s constituent atoms
  • have different 3-dimensional (spatial or geometric) orientations of the constituent atoms

Examples of stereoisomers include

It is important to emphasize that stereoisomers are defined for 2 or more molecules.  Consider 3 isomers, A, B and C.

  • A and B may be stereoisomers.
  • A and C may not be stereoisomers.  They may be structural isomers, which have the same atoms but different sequences of bonds.

Organic and Inorganic Chemistry Lesson of the Day – Optical Rotation is a Bulk Property

It is important to note that optical rotation is usually discussed as a bulk property, because it’s usually measured as a bulk property by a polarimeter.  Any individual enantiomeric molecule can almost certainly rotate linearly polarized light.  However, in a bulk sample of a chiral substance, there is usually another molecule that can rotate light in the opposite direction.  This is due to the uniform distribution of the stereochemistry of a random sample of the molecules of one compound.  (In other words, the substance consists of different stereoisomers of one compound, and the proportions of the different stereoisomers are roughly equal.)  Because one molecule’s rotation of the light can be cancelled by another molecule’s optical rotation in the opposite direction, such a random sample of the compound would have no net optical rotation.  This type of cancellation will definitely occur in a racemic mixture.  However, if a substance is enantiomerically pure, then all of the molecules in that substance will rotate linearly polarized light in the same direction – this substance is optically active.

Organic and Inorganic Chemistry Lesson of the Day – The Difference Between (+)/(-) and (R)/(S) in Stereochemical Notation

In a previous Chemistry Lesson of the Day, I introduced the concept of optical rotation (a.k.a. optical activity).  You may also be familiar with the Cahn-Ingold-Prelog priority rules for designating stereogenic centres as either (R) or (S).   There is no direct association between the (+)/(-) designation and the (R)/(S) designation.  In other words, an (R)-enantiomer can be dextrorotary or levorotary – it must be determined on a case-by-case basis.  The same holds true for an (S)-enantiomer.

(R)/(S) can be used to distinguish between enantiomers in one exception: If the stereoisomer has only 1 stereogenic centre, then this designation can also serve as a way to distinguish between 2 enantiomers.

Furthermore, note that the designation of optical rotation applies to a molecule, whereas the R/S designation applies to a particular stereogenic centre within a molecule.  Thus, a molecule with 2 stereogenic centres may have one (R) stereogenic centre and one (S) stereogenic centre.  However, a chiral compound consisting purely of one enantiomer can rotate linearly polarized light in only one direction, and that direction must be determined on a case-by-case basis by a polarimeter.

Organic and Inorganic Chemistry Lesson of the Day – DO NOT USE THE PREFIXES (d-) and (l-) TO CLASSIFY ENANTIOMERS

In a recent Chemistry Lesson of the Day, I introduced the concept of optical rotation, and I mentioned the use of (+) and (-) to denote dextrorotary and levorotary compounds, respectively.

Some people use d- and l- instead of (+) and (-), respectively.  I strongly discourage this, because there is an old system of classifying stereogenic centres that uses the prefixes D- and L-, and the obvious similarity between the prefixes of the 2 systems causes much confusion.

This old system classifies stereogenic centres based on the similarities of their configurations to the 2 enantiomers of glyceraldehyde.  It is confusing, non-intuitive, and outdated, so I will not discuss its rationale or details on my blog.  (If you are interested, here is a good explanation from the University of Maine’s chemistry department.)

Also, note that D- and L- classify stereogenic centres, whereas d- and l- classify enantiomers – this just adds more confusion.

In short,

  • DO NOT use d- and l- to classify enantiomers; use (+) and (-) instead.
  • DO NOT use D- and L- to classify stereogenic centres; use the Cahn-Ingold-Prelog priority rules (R/S) instead.

Organic and Inorganic Chemistry Lesson of the Day – Optical Rotation (a.k.a. Optical Activity)

A substance consisting of a chiral compound can rotate linearly polarized light – this property is known as optical rotation (more commonly called optical activity).  The direction in which the light is rotated is one way to distinguish between a pair of enantiomers, as they rotate linearly polarized light in opposite directions.

Imagine if you are an enantiomer, and linearly polarized light approaches you.

  • If the light is rotated clockwise from your perspective, then you are a dextrorotary enantiomer.
  • Otherwise, if the light is rotated counterclockwise from your perspective, then you are a levorotary enantiomer.

In a previous Chemistry Lesson of the Day, I introduced the concept of diastereomers, and I used threose as an example.  Let’s use threose to illustrate some notation about optical activity.

D-threose.svg 2


  • Levorotary compounds are denoted by the prefix (-), followed by a hyphen, then followed by the name of the compound.  The above molecule is (-)-threose.
  • Dextrorotary compounds are denoted by the prefix (+), followed by a hyphen, then followed by the name of the compound.  The enantiomer of (-)-threose is (+)-threose.

A compound’s optical rotation is determined by a polarimeter.

I strongly discourage the use of the prefixes (d)- and (l-) to distinguish between enantiomers.  Use (+) and (-) instead.

Beware of the difference between designating enantiomers as (+) or (-) and designating stereogenic centres as either (R) or (S).

It is important to note that optical rotation is usually referred to as a bulk property.

Organic and Inorganic Chemistry Lesson of the Day – Cis/Trans Isomers Are Diastereomers

Recall that the definition of diastereomers is simply 2 molecules that are NOT enantiomers.  Diastereomers often have at least 2 stereogenic centres, and my previous lesson showed an example of how such diastereomers can arise.

However, while an enantiomer must have at least 1 stereogenic centre, there is nothing in the definition of a diastereomer that requires it to have any stereogenic centres.  In fact, a diastereomer does not have to be chiral.  A pair of cis/trans isomers are also diastereomers.  Recall the example of trans-1,2-dibromoethylene and cis-1,2-dibromoethylene:



Image courtesy of Roland1952 on Wikimedia.

These 2 molecules are stereoisomers – they have the same atoms and sequence/connectivity of bonds, but they differ in their spatial orientations.  They are NOT mirror images of each other, let alone non-superimposable mirror images.  Thus, by definition, they are diastereomers, even though they are not chiral.

Organic and Inorganic Chemistry Lesson of the Day – Meso Isomers

A molecule is a meso isomer if it

Meso isomers have an internal plane of symmetry, which arises from 2 identically substituted but oppositely oriented stereogenic centres.  (By “oppositely oriented”, I mean the stereochemical orientation as defined by the Cahn-Ingold-Prelog priority system.  For example, in a meso isomer with 2 tetrahedral stereogenic centres, one stereogenic centre needs to be “R”, and the other stereogenic centre needs to be “S”. )  This symmetry results in the superimposability of a meso isomer’s mirror image.

By definition, a meso isomer and an enantiomer from the same stereoisomer are a pair of diastereomers.

Having at least 2 stereogenic centres is a necessary but not sufficient condition for a molecule to have meso isomers.  Recall that a molecule with n tetrahedral stereogenic centres has at most 2^n stereoisomers; such a molecule would have less than 2^n stereoisomers if it has meso isomers.

Meso isomers are also called meso compounds.

Here is an example of a meso isomer; notice the internal plane of symmetry – the horizontal line that divides the 2 stereogenic carbons:

(2R,3S)-tartaric acid

(2R,3S)-tartaric acid

Image courtesy of Project Osprey from Wikimedia (with a slight modification).

Organic and Inorganic Chemistry Lesson of the Day – Racemic Mixtures

A racemic mixture is a mixture that contains equal amounts of both enantiomers of a chiral molecule.  (By amount, I mean the usual unit of quantity in chemistry – the mole.  Of course, since enantiomers are isomers, their molar masses are equal, so a racemic mixture would contain equal masses of both enantiomers, too.)

In synthesizing enantiomers, if a set of reactants combine to form a racemic mixture, then the reactants are called non-stereoselective or non-stereospecific.

in 1895, Otto Wallach proposed that a racemic crystal is more dense than a crystal with purely one of the enantiomers; this is known as Wallach’s rule.  Brock et al. (1991) substantiated this with crystallograhpic data.



Brock, C. P., Schweizer, W. B., & Dunitz, J. D. (1991). On the validity of Wallach’s rule: on the density and stability of racemic crystals compared with their chiral counterparts. Journal of the American Chemical Society, 113(26), 9811-9820.