Periodic trends

20 Apr 2012

The Periodic Table of Life

Submitted by Kathy Franz, Duke University, Department of Chemistry
Description: 

A little more than 5 slides, this is a video I made for a colleague to use in General Chemistry as an intro, or hook, into exciting topics in chemistry (in this case, bioinorganic).  I use these slides as an intro to my junior/senior Inorganic course on the first day of class, to ask the question "What is Inorganic Chemistry?" and get them to think about the "living" parts of "inorganic".  Topics include an overview of essential, toxic, and medicinally active elements of the periodic table, key examples of metalloprotein active sites, and an overview of the functional roles of biological inorganic elements.

Corequisites: 
Prerequisites: 
Learning Goals: 

Learning goals from this lecture include:

1.  Students will think about what the term "inorganic chemistry" means.

2. Students will have an appreciation for the breadth of bioinorganic chemistry

3. Students will see how core principles of inorganic chemistry can be applied in a biological setting.  The list of Functional Roles of Biological Inorganic Elements can be tied to many principles professors typically cover in an inorganic (or even general chemistry) course (acid/base, redox, catalysis, energy storage, structure/function). 

Implementation Notes: 

The video can be downloaded for free from iTunes U.  Follow the link below, which will take you to the Duke University "Core Concepts in Chemistry" course (another great resource, by the way!).  "The Periodic Table and Life" video is listed as lecture #4.  Click on "view in iTunes" to get to the content.  You should be able to access the site on any device with iTunes (computer, iPad, iPhone, iPod touch).

http://itunes.apple.com/us/course/the-periodic-table-and-life/id495047302?i=109398734

Time Required: 
10 min
Evaluation
Evaluation Methods: 

Students could be asked to provide some of the information presented in the "learning goals" section above as part of an exam or in-class activity.

25 Jun 2011
Evaluation Methods: 

Upon completion of the assignment, each group of students gives a short PowerPoint presentation (10-15 minutes) describing their assigned computational project. Their results are described, reporting computed energetic and spectroscopic differences, and using calculated molecular orbital diagrams to explain key intrinsic differences between their computed compounds.

Description: 

Groups of 2-4 students (depending on class size) are each assigned a different collaborative project that involves using DFT calculations to evaluate some of the principles of inorganic structure and bonding developed in lectures throughout the semester.  Each “project” involves comparing the computed properties (spectroscopic (IR), geometric,or relative energies) of a series of molecules and drawing conclusions about the observed differences using concepts developed in class. For each project, a handout is provided, describing the assigned task and providing insightful questions to guide their group discussions. Examples of assignments and the corresponding handouts are attached below.

Molecules are constructed and Gaussian 09 calculations are set up using the user-friendly Gaussview interface.  Each group project involves 4-8 calculations,enough that each student gets practice setting up a calculation.  Upon completion of their DFT calculations,each group of students collects their data and together they explain the IR results using concepts they learned in class.  

Learning Goals: 

Upon completion of this assignment, students will be familiar with:

  •  the computational methods typically utilized in inorganic chemistry
  • the types of information that can (and cannot) be extracted from computational outputs.

Students will also be:

  • able to understand and interpret the computational results presented in papers in the current literature
  • familiar with procedures for setting up, running, and interpreting computational results using density functional theory (DFT) implemented by Gaussian 09.
Prerequisites: 
Corequisites: 
Course Level: 
Equipment needs: 

Assignment is written with Gaussian 09 in mind, but it is certainly adaptable to Spartan or WebMO.

25 Jun 2011
Evaluation Methods: 

Students turned in the lab reports for grading.  Nearly all students completed the lab report - a few needed extra time after the lab period to finish up calculations. 

We also asked students their opinion of the usefulness of the MO exercise on the lab evaluation form.  I comment on these more in the next section.

Evaluation Results: 

Of the five lab exercises done during the semester (some were multi-week) the MO exercise received the lowest marks from students on the lab evaluation form.  A significant fraction of students in the class (15 out of 45) included comments about this lab that indicated that many of the students did not understand the point of the calculations or how it related to what we were discussing in the course.  As a result of these comments I will be implementing this exercise in the Fall 2011 offering of Chem 111 as part of the regular course meetings rather than the lab so it can be closely integrated with the class sessions on molecular orbitals.

Description: 

In Haverford College's course Chem 111:Structure and Bonding, we have included a workshop exercise that guides students through their first experience using electronic structure calculations.  We use the WebMO interface along with Gaussian03, but the exercise could be adapted for other electronic structure programs. The general structure of the exercise is as follows:

  • Each student in the class performs an MO energy calculation on an H2 molecule with a different H-H distance in the range of 0.5 to 2.0 Å.  The class data is used to construct an E vs. r graph for the H-H bond.  The students then verify that the "optimize geometry" calculation will find the minimum energy configuration of the H2 molecule.
  • The students perform similar calculations for O2 and discover that the triplet state is lower than the singlet state (in addition to learning what "singlet" and "triplet" mean).  Then using the O2 molecule they learn to visuallize the molecular orbitals and learn how the "isovalue" affects the appearance of the MOs.
  • The students each take a different HX molecule with X from 2nd or 3rd row and calculate dipole moments, atomic (Mulliken) charges, and bond distances.  Then as a class the students use their data to construct an electronegativity scale and see how their scale compares with the Pauling scale.  They also use the bond lengths to construct a table of atomic covalent radii, and discuss the periodic trends.
  • The students are given some suggestions for further topics to explore using electronic structure calculations.  Suggestions include (1) Calculating the shapes and bond angles in various XYn molecules and comparing them to VSEPR predictions.  (2) Discovering inductive effects on the partial charge on atoms depending on electronegativity of atoms several bonds away.  (3) Shapes of MOs in CO (vs. those in O2).  (4) Shapes and energies of MOs in benzene.

In the Fall of 2010 these activities all were part of a 3 hour laboratory period devoted to computational chemistry.  The report form for this activity is included as an attachment.  I've also attached a slightly modified version of the description of the exercise from the Fall 2010 lab manual for the course.  My plan for next semester is to implement this as a 1 hour recitation exercise followed by a series of homework activities.  Stay tuned.

Learning Goals: 
  • Students will learn how to carry out and interpret electronic structure calculations for real and hypothetical small molecules
  • Students will learn how to visualize molecular orbitals and electronic potential surfaces derived from electronic structure calculations
  • Students will relate results from electronic structure calculations to properties such as atomic radius and electronegativity
  • Student's prior learning about periodic trends in atomic radius and electronegativity will be reinforced
Prerequisites: 
Corequisites: 
Course Level: 
Equipment needs: 

Students can use their own laptops or institution-owned computers.  Institution supplies computer cluster operating WebMO and Gaussian software.

Time Required: 
3 hours (or 3-4 1 hour sessions)
19 Mar 2011
Evaluation Methods: 

This was done as an in-class activity during my conference section, so I did not collect or formally evaluate student work.  I made the solutions available after class for students to check on their own time.  During the conference, I circulated among the groups, answering questions and gently guiding them towards the right answer if necessary.  The solutions to this activity are posted as a Problem Set learning object type (see Related Activities above) and can be downloaded by VIPEr Faculty Users that are logged in.

To assess the learning goal of whether this activity helped students learn the names of the pnicogen elements, I asked a Clicker Question in lecture the day after this conference activity on which group of elements belonged to the pnicogens.  The choices were (A) As, Bi, P; (B) Bi, Sb, Te; (C) As, Bi, Pb; or (D) S, Se, Po.  Out of 19 students, 11 (58%) chose the correct answer.

 

Evaluation Results: 

The students had a more difficult time with these problems than I had anticipated, in particular coming up with a Lewis structure for the [XeF]+[BiF6] ion-pair.  A useful hint that I would provide was to consider that there is a new “covalent” bond that forms between the ions, or at least covalent in the sense of a shared pair of electrons in the Lewis structure.  Some groups would draw Lewis structures without the correct number of electrons, caught most easily by summing the formal charges or they would propose Lewis structures with “less favorable” distributions of formal charges.  This led to quite interesting discussions about whether or not formal charges were “real” and if not, then why did we bother with them.

 

Description: 

This Lewis structure and VSEPR problem is based on a paper from Inorganic Chemistry in 2010 reporting the crystal structures of a series of salts of the [XeF]+ cation.  The [MF6] and [M2F11] anions (M = As, Sb, Bi) were used as counterions, and in all cases, the [XeF]+ cation interacts with the anion via a weak bond between the Xe and a fluoride of the anion to form an ion-pair in the crystalline solid.  These somewhat unusual ions provide an interesting application of the predictive powers of Lewis structures and VSEPR theory to molecular structure, backed up by experimental data on bond distances and bond angles and can provide an opening to the descriptive chemistry of the heavier pnicogens.  These ions also provide interesting examples to discuss the model and utility of assigning formal charge in Lewis structures and how to describe the bonding in molecules with expanded octets. Although not specifically addressed in the attached problem, which focuses on the bismuth salts, one could extend the discussion to periodic trends in these salts with different counter ions from the pnicogen group.  The reference to the original paper is Inorg. Chem. 2010, 49, 8504-8523.

 

Learning Goals: 
In answering these questions, a student will:
  • Practice drawing Lewis structures for molecules with expanded octets and assigning (sometimes unusual) formal charges
  • Gain experience applying VSEPR to predict the molecular structure and approximate bond angles in different molecules
  • Relate the predictions of relatively simple theories to actual experimental results obtained from X-ray crystallography
  • Learn the names of the heavier pnicogen elements
Prerequisites: 
Course Level: 
Subdiscipline: 
Implementation Notes: 

This was assigned as a problem to be worked at the board by small groups during a conference session for a second-year inorganic chemistry course. 

 

Time Required: 
~30 minutes
3 Sep 2010

First Isolation of the AsP3 Molecule

Submitted by Anne Bentley, Lewis & Clark College
Evaluation Methods: 

The students’ written answers to the questions and presentations of the questions were graded.

Evaluation Results: 

Because we discussed this article at the end of the semester, the stretching mode analysis was not fresh in the students’ minds.  They appreciated the chance to review earlier portions of the course. 

Description: 

Early in 2009, Christopher Cummins’ group at MIT reported (in Science) the synthesis of AsP3, a compound that had never been isolated at room temperature.  Later that year, a full article was published in JACS comparing the properties and reactivity of AsP3 to those of its molecular cousins, P4 and As4.  The longer article is full of possibilities for discussion in inorganic chemistry courses, with topics including periodic trends, NMR, vibrational spectroscopy, electrochemistry, molecular orbital theory, and coordination chemistry.

Corequisites: 
Prerequisites: 
Learning Goals: 

After reading and discussing this paper, a student should be able to:

•    recognize the general names used for groups 15, 16, and 17
•    derive the expected number of Raman resonances for the AsP3 and P4 molecules
•    outline the trend observed in P–P vs As–P bond strength
•    compare the reactivity of P4 and AsP3 in at least one example and make predictions regarding As2P2 and As3P reactivity

Subdiscipline: 
Implementation Notes: 

This learning object was developed as one of five journal article discussions included in a small (5 student) senior-level inorganic course in the spring of 2010.  This course is the only inorganic course (aside from a separate inorganic laboratory) offered in our curriculum.

The literature discussions were interspersed throughout the semester.  This journal discussion was the final one in the semester, and we discussed questions 1-4 as a group before each individual presented the results of the reactivity studies they had chosen (question 5).  Student presentations were informal; it was a good opportunity for them to learn how to condense information.   

Time Required: 
30 minutes as implemented. A larger class might take more time.
17 Jul 2010
Evaluation Methods: 

Upon completion of the experiment the student pairs submit a brief summary of their results and plans to developing a formal report. A draft report is then written in the style and format of an American Chemical Society journal article; the draft must be thoroughly referenced. The instructor reads the draft and returns it to the students with suggestions for revisions. The final version of the report is evaluated in accord with criteria presented in the policy section of the laboratory manual.

 

Evaluation Results: 

Given the integrated nature of this exercise, the laboratory reports indicate whether or not the students have mastered the essential ideas of coordination chemistry. The reports reveal skill in laboratory technique through the percent yield and quality of the products and recording infrared and electronic absorption spectra and in interpretation of the spectra. Although reports are often of high quality and reflect considerable insight, some students seem not to grasp the distinction between molecular and electronic structure. A somewhat larger number have difficulty synthesizing the reaction observations and the measurements, computation, and database results into a comprehensive narrative. That requires further discussion with the instructor. Many students need to learn when to reference statements appropriately.

Description: 

This experiment, intended for an upper-level inorganic chemistry course, involves classical transition-metal coordination compounds. The purpose of the exercise is to compare the physical and chemical properties of coordination complexes containing copper(II) and silver(II) ions bound to the anion of pyridine–2–carboxylic acid, also known as picolinic acid, picH. The metallic elements copper and silver are in the same family in the periodic table, but their chemical properties are quite different. Although Cu(II) is the stable oxidation state in aqueous solution, Ag(II) is powerfully oxidizing in water. The conjugate base of picH, pyridine–2–carboxylate or picolinate ion, acts as a ligand toward these metal ions, binding to them in chelating mode through the pyridine ring nitrogen atom and one of the carboxylate oxygen atoms. The compounds are synthesized in water at room temperature. In both cases picolinic acid is deprotonated to give picolinate ion, which then binds to Cu2+ and Ag2+, yielding products formulated as M(pic)2. For silver, Ag+ must be oxidized to Ag2+. Molecular and electronic structural characterization is accomplished through infrared, electronic absorption, and electron spin resonance spectroscopy and density functional calculation. Available crystal and molecular structure information is surveyed using the Cambridge Structure Database. 

Prerequisites: 
Course Level: 
Subdiscipline: 
Learning Goals: 

• Students will discover that two structurally similar transition metal compounds can be synthesized cleanly from water solutions.

• Students will engage in the molecular and electronic structural characterization of both compounds. They should appreciate the need to employ a variety of physical measurements to develop a comprehensive structural understanding of a molecule.

• Students will develop an appreciation of differences arising from position in the first vs. second vs. third transition series (the gold(II) compound does not exist).

• Students will learn to do an electronic structure calculation on a transition metal compound and to explore a crystallographic database.

Equipment needs: 

• Pyridine-2-carboxylic acid (picolinic acid), copper(II) acetate hydrate, silver(I) nitrate, ammonium peroxodisulfate, sodium carbonate, deionized water

• Beakers, magnetic stirrers, magnetic stirring bars, filtering funnels, filtering, vacuum drying capability, vials

• FTIR spectrometer (mineral-oil/NaCl or KBr disks or KBr and press for pellet making), UV/Visible spectrometer (quartz cell, water), ESR spectrometer (quartz tubes)

• Access to density functional theory computation software (Spartan, for example) and to Cambridge Structure Database

Implementation Notes: 

Students do this experiment in pairs. The synthetic reactions are easily accomplished. The copper reaction gives either the anhydrous material or the monohydrate. The reaction filtrate will yield large crystals, but this requires several weeks at room temperature. The silver compound that does not precipitate from the initial reaction will decompose in solution within a few days at ambient temperature. We store the silver compound in a refrigerator and allow the storage vial to warm to room temperature before removing a sample for physical measurements. The IR measurements are straightforward. We record both solid-state and solution electronic absorption spectra for comparison with the IR spectra (solid state) and to obtain molar absorptivity values. Both compounds give strong ESR spectra for solid-state samples, and a procedure for data analysis is provided. The density functional calculation for the copper compound works well using low-level Spartan software; for silver the number of electrons is too large for successful calculation. Students should understand that generally the simple Spartan DF computation applies to the molecules in the gas phase.

Time Required: 
• One and a half hours for syntheses by a pair of students. • Two-three hours for spectroscopy.
15 Jul 2010

Element Jeopardy!

Submitted by Keith Walters, Northern Kentucky University
Evaluation Methods: 

I typically include a quick question or two on each test that covers some of the content that's been presented in recent games.

Evaluation Results: 

Students typically do well on these questions. In addition, many have tried to fold content learned in the game into other answers on homework assignments and exams. The integration of this material into the core content of the course shows that they are seeing the connection of the science and the story. Of course, there are some students that don't "get it" and merely treat the exercise as an extra credit opportunity that they don't need. However, the majority of the students do enjoy the activity.

Description: 

Like many inorganic faculty (especially those faced with trying to teach "all" of inorganic chemistry in a one-term junior/senior course), I have found it increasingly difficult over the years to include any significant descriptive chemistry content in my course. Moreover, I have a constant interest in trying to convey some of the "story behind the story" in chemistry, which in this area centers on the discovery of the elements. I was mulling this over at an ACS meeting one time and happened to be in an inorganic teaching session where Josh van Houten (St. Michael's College) gave a great presentation on using a Jeopardy activity to spend time every week in lecture on descriptive chemistry. The light bulb turned on, and I figured that I could combine both of the above concerns into a single activity (thanks, Josh!).

I've been using "Element Jeopardy!" in my lecture for the past three years, and every time it's a little different. Students seem to be very interested in participating (probably because the points they score turn into extra credit at the end of the term), and I regularly would see them looking for information on the elements online prior to lecture. I would typically devote 10-15 minutes in the last lecture period of every week to a new game. I rotate between students for each question (there's no buzzing in, because I want everyone to have a chance).

The games were broken down by group for the s and p block elements, plus one game just for hydrogen and one game for each of the three transition metal periods. This combination gave me one game every week for an academic term if we didn't play during test weeks. For the periodic group games, each element got its own category (with the more obscure elements grouped together, like Cs/Fr). For the other games, categories were created based on history, usage, properties, common ores (for the transition metal games), and "fun facts." I initially used different Powerpoint presentations to run the games, but I was never happy with the way things looked. Last year I stumbled across the BYOJeopardy freeware program, and it does a great job in writing and running game boards (including daily double questions!). I have included my games and a link to the software below (PC only, see below for Mac options).

The sources of information for the games have varied as I've created the games, and they change a little bit every year. Initially I used our current lecture textbook, which was fine for the physical properties and reactivity of the elements but left much to be desired in the other categories. I dug into some of my history of chemistry materials (particularly The Periodic Table by Eric Scerri, Oxford Press) to find some of the historical details. I have also resorted (horrors...) to using Wikipedia as a starting point for other material on the different elements, as well as some judicious web searching. The absolute best place for "I didn't know that" information, however, is the excellent Chemistry In Its Element podcast (http://www.rsc.org/chemistryworld/podcast/element.asp), which is an excellent listen (and one that every chemistry educator should utilize). Many of the daily double questions come from these podcasts.

 You will notice as you look at the games that I ask some very easy questions (that hopefully students with a basic understanding of the periodic table can get) as well as some questions that I probably couldn't answer. The hard questions are there more to inform than to be a source of extra credit points, and I've picked them to surprise the students (and I'll provide additional information on the question slide where appropriate). Many times students will say "Is that really true?" or "I never imagined it could do that!" during the course of the game. This stimulation of curiosity and an increase in the appreciation of the diversity of the periodic table (and how we discovered the elements that fill its boxes) is the true heart of the exercise.

Learning Goals: 

A student should be able to understand basic properties of the groups of the periodic table as well as the history behind the discovery of the elements. Students should also gain an appreciation of the uniqueness of the elements that constitute the periodic table.

Corequisites: 
Equipment needs: 
Prerequisites: 
Related activities: 
Implementation Notes: 

To use the software after installation: 1. Open the BYOJeopardy program, then open one of the unzipped game boards using File>Open 2. Select "Player must answer in the form of a question" in the Game Format popup, then click OK 3. The game board should be on the screen. Click the category/point value to see the answer, then the button at the bottom of the answer to see the question 4. If you want to change the gameboard, use File>Edit to open the editor The software listed is for PCs only, unfortunately. BYOJeopardy does have an online version that should work with any browser, but since games are accessible by anyone on the site with an account I'm a little hesitant to post the games there (my students can be very resourceful!). In the zip file I've provided .html files of all the games so that you can use the questions in whatever delivery system you choose.

Time Required: 
10-15 minutes weekly
20 Mar 2010
Evaluation Methods: 

The "post-lab" analysis for this experiment was collected the following week and consisted of answers to the questions included in the attached "MO Lab Instructions" sheet.  

79 students completed the lab activity, and they were split into lab sections of approximately 20 students per section.    The post-lab was worth 50 points, with points split between the Pre-Lab Assignment, and their answers to the procedural directions while they were working on the computers. 

Evaluation Results: 

The majority of the students were able to answer each question well based on the outputs from GaussView.  Many of their paper sketches of the Lewis Dot structures for molecules such as C2 varied from double bonded atoms (with a lone pair of electrons on each C) to triple bonded atoms (with a single electron on each C).  Students had to be reminded while they were working on the computers to sketch into their notebooks the outputs from the screen, and, specifically, to differentiate between the positive and negative portions of the wavefunctions. 

Description: 

This laboratory exercise was developed to compliment several weeks of freshmen or sophomore level quantum chemistry lecture material at our institution. The students meet in a computer lab on campus and use the software package known as GaussView. We focus on molecular orbital calculations for a series of homonuclear diatomic molecules of the second row in the periodic table (Li2, B2, C2, N2, and F2).  The students view and compare pictures of the sigma and pi molecular orbitals so that they can readily observe the overall shapes of the atomic orbital lobes that result in bonding and antibonding interactions between atoms.  The students also look at electrostatic maps of their simple molecules to observe any trends in electron density across the series.

Prior to the computer portion of the lab, the students are also asked to determine electron configuration for the elements Li, B, C, N, and F.  They draw Lewis dot structures for the diatomic molecules Li2, B2, C2, N2, and F2.  Finally, they sketch molecular orbital shapes and diagrams on paper for the simple molecules included in the periodic series.

Corequisites: 
Prerequisites: 
Course Level: 
Learning Goals: 
  • Reinforce some simple molecular orbital theory for freshmen or sophomore undergraduate students
  • Students determine the MOs on paper for simple homonuclear diatomic molecules of the second row in the periodic table
    • Review of electron configuration and Lewis dot structures
  • Students use the software program GaussView to view the outputs of calculated molecular orbital energies and shapes
    • Compare the computational results to their paper sketches
    • Visualize the shapes of the MOs to compare sigma and pi bonds, and bonding and antibonding MOs
  • Students use the software program GaussView to view potentiostatic maps of the homonuclear diatomic molecules in Period 2
    • Detect trends in electronegativities of atoms across a period

 

Equipment needs: 
  • Computers with GaussView 4.1 molecular modeling software
Implementation Notes: 

Students had no prior experience with using molecular orbital computational software in preparation for this lab exercise.  Selected molecular orbitals were calculated in advance for the students using an appropriate level of theory.  The detailed "MO Lab Instructions" and "GaussView Instructions" sheets are attached.     

The first time for trying this lab exercise was during the fall 2009 semester.  The instructors for each section spent approximately 30 minutes doing a "pre-lab" lecture review of some simple molecular orbital theory.  Prior to viewing the computational outputs from GaussView, students were asked to form small groups and sketch on paper the molecular orbital energy level diagrams and the general shapes of the MOs that should result for the homonuclear diatomic molecules explored in this lab.  They then could compare the calculated surfaces to their paper sketches. 

At Washington & Jefferson College, students take a one semester Introduction to Inorganic Chemistry course in their sophomore year that serves as a General Chemistry course as well.  The text that we used for this past year was University Chemistry by Brian B. Laird.  The students brought their textbook to lab this day so that they could refer to the MO diagrams printed in the book.


Note to Instructors 

 While the visualization of molecular orbitals is instructionally a valuable tool in chemical education, the aim of computation chemistry is to produce accurate results efficiently.  The price of this accuracy is the loss of an intuitive understanding.  In order to maintain the conceptual value of molecular orbital theory, we only use the STO-3G minimal basis set, which limits both the core and valence atomic orbitals to a single basis function. We employed the restricted open-shell Hartree-Fock (ROHF) method. ROHF creates a single molecular orbital for each orbital that is doubly occupied, but it has the freedom to create separate orbitals for unpaired electrons.  The use of doubly occupied molecular orbitals limits the number of orbitals to the familiar set associated with MO theory discussed at the undergraduate level. At the same time, ROHF has the complexity necessary to describe the triplet states of diatomic boron and oxygen.

Time Required: 
3 hours
18 Mar 2010

Periodic Table of Haiku

Submitted by Adam R. Johnson, Harvey Mudd College
Description: 

This is a great website that was forwarded to me by a friend.  Broaden students' scientific communication skills by condensing the descriptive chemistry of an element down to a haiku.

Prerequisites: 
Corequisites: 
Learning Goals: 

As stated on the website, the goal of the activity was to integrate chemistry and creative writing.  Students will also learn some aspects of the descriptive chemistry of the element.

Course Level: 

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