Computer modeling

17 Jul 2010

Synthesis and Molecular Modeling of Sodium Tetrathionate

Submitted by Kim Lance, Ohio Wesleyan University
Evaluation Methods: 
Our inorganic laboratory program involves a rotation through a series of four experiments – and this is one of those experiments. Each student’s laboratory notebook is collected every four weeks and graded on a grading rubric which will be added later. I have the students rotate through the experiments and rotate through the final report – either written or oral. The written report is in the format of the American Chemical Society Style Book Guidelines for submitting a paper to JACS. The oral report is in the format of an ACS national meeting where each student is introduced, given 15 minutes to talk and five minutes for questions and answers.
Description: 
This experiment is a computational supplement to synthesis of sodium tetrathionate described in "Macroscale Inorganic Chemistry:  A Comprehensive Laboratory Experience".*  Students will synthesize one sulfur oxyanion (tetrathionate), optimize and compute IR spectra for their synthesized product.   In addition, students will predict (using symmetry arguments) and then compute the IR vibrational modes for six additional sulfur oxyanions.  A comparison of theoretical (IR spectra), experimental (IR spectra) and computational data ( IR spectra) will aid them in determining the most in identifying the S-O vibrations in their experimental spectrum. * Szafran, Z.; Pike, R.; Singh, M. Microscale Inorganic Chemistry:  A Comprehensive Laboratory Experience; Wiley:  New York, 1991. 
Course Level: 
Prerequisites: 
Learning Goals: 
A student will be able to successfully perform a titration;

A student will be able to quantitatively synthesize a sulfur oxyanion;

A student will be able to draw the Lewis structures of a series of sulfur oxyanions;

A student will be able to determine the point groups and number of vibrational modes in a series of sulfur oxyanions;

A student will be able to use computational methods to determine the number of vibrational modes in a series of sulfur oxyanions;

A student will successfully obtain an infrared spectrum for each in a series of sulfur oxyanions;

A student will be able to interpret the infrared spectra of the sulfur oxyanions including the labeling of the vibration responsible for the frequency;

A student will be able to explain the change in the frequency with respect to the oxidation number in a series of sulfur oxyanions;

Subdiscipline: 
Equipment needs: 
100 mg iodine/student
1.5 g potassium iodide/student
300 mg sodium thiosulfate pentahydrate/student
1% starch solution/1 mL per student
10 mL beaker/student
25 mL beaker/student
2 mL ethanol/student
0.500 mL diethyl ether/student
Hirsch funnel/student
10 mL filter flask/student
sodium sulfate (1 mg/student for IR)
sodium sulfite(1 mg/student for IR)
sodium thiosulfate(1 mg/student for IR)
sodium bisulfite(1 mg/student for IR)
potassium peroxodisulfate(1 mg/student for IR)
sodium dithionite(1 mg/student for IR)
infrared spectrophotometer
dry potassium bromide
molecular modeling software
Time Required: 
Two or Three three-hour laboratory periods
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
21 Jan 2010

Exploring Molecular Orbitals With Spartan

Submitted by Maggie Geselbracht, Reed College
Evaluation Methods: 

This activity was “spot-graded” meaning that I looked carefully at all of the answers for several questions but skipped over others.  This is my new solution to too much grading.  On this assignment, I “spot-graded” the LiH/HF question and the CO2 part of question 2

Evaluation Results: 

The following results are out of 24 students that completed the assignment.  On the LiH/HF question: 6 out of 24 students scored 85% or above, 11 out of 24 students scored 67–84%, and 7 students scored below 66%.  The most common problem was misunderstanding the composition of the LiH molecular orbitals, particularly the role of sp mixing on Li.  

On the CO2 part of question 2, 16 of 24 students scored above 90%, 4 students scored 67–85%, and 4 student scored below 66%.  The main problems were identifying the labels and types of molecular orbitals (bonding, nonbonding, antibonding, gerade, ungerade, etc.).
 

Description: 

Molecular models and selected molecular orbital surfaces and slices were calculated with Spartan for HF, LiH, CO2, XeF2, and BF3, and the results were used by students in an in-class activity (covering several class sessions) to answer a series of questions.

Learning Goals: 

By examining the calculated molecular orbitals on Spartan and comparing these with MO energy diagrams, a student will:

  • Gain experience predicting the atomic orbital contributions to a given molecular orbital.
  • Discover, in some cases, the unanticipated role of sp mixing.
  • Interpret the implications of molecular orbital occupation on bond polarity and bond order.
  • Consider the meaning of 3 center, 2 electron bonds in hypervalent molecules such as XeF2.
  • Explain the bonding and Lewis acidity of BF3 from the perspective of molecular orbitals.

Corequisites: 
Course Level: 
Equipment needs: 

Computers with Spartan molecular modeling software

Prerequisites: 
Implementation Notes: 

Spartan models, selected molecular orbital surfaces and slices were calculated in advance for the students using an appropriate level of theory.  Students were already familiar with the use of Spartan to visualize molecular orbitals from a previous conference activity (a one hour session) examining the MOs of N2 and CO.  The detailed “help sheet” and handout for this conference activity is attached below.  Although many of the details in these handouts are particular to our computer lab, I left them in to show the level of detail that I provide for students in the instructions.  

I have assigned these same questions as problem set questions in previous years (usually no more than one per year), but in this iteration, I assigned all three as an extensive in-class activity for students to complete while I was away at the ACS meeting.  I anticipated a minimum of 3 hours for this activity to compensate for 3 missed class sessions.  In my understanding, this was mostly accurate for time required, although some students spent longer.  

The textbook that I was using in this particular year was Housecroft & Sharpe, 3rd edition.  I usually point them to the appropriate MO diagrams in their text to compare to the Spartan results.  Obviously, the MO diagrams vary from text to text, and it is helpful to look at these in advance in case you need to change the hints at all on various questions.

A solutions key is posted for this learning object under “Problem Sets.”  You must have approved “Faculty” status on VIPEr to access these.
 

Time Required: 
3 hours
31 Aug 2009

Computational Organometallic Chemistry

Submitted by Thomas R. Cundari, University of North Texas, Chemistry, CASCaM
Evaluation Methods: 
A student should be able to better evaluate computational inorganic/organometallic papers in the literature after this lecture. Also, a student should be able to identify potential issues in their own calculations, and those who are primarily experiments should be able to better interface with their computational chemist colleagues.
Evaluation Results: 
N/A
Description: 
Lecture given at NSF-CENTC 2008 workshop on modeling in organometallic chemistry.
Learning Goals: 

A student should be able to better evaluate computational inorganic/organometallic papers in the literature after this lecture. Also, a student should be able to identify potential issues in their own calculations, and those who are primarily experiments should be able to better interface with their computational chemist colleagues.

http://depts.washington.edu/centcweb/flashvideos/

Subdiscipline: 
Course Level: 
Equipment needs: 
None.
Topics Covered: 
Prerequisites: 
Implementation Notes: 
Flash video is needed.
13 Mar 2009

d-orbitals in a variety of ligand geometries

Submitted by William F Coleman, Wellesley College
Description: 

I developed this Jmol page to help my students see the relationship(s) between the ligands and metal d-orbitals in a number of different geometries.  Since the images are all rotatable, students who have difficulty looking at flat images and drawing appropriate conclusions have that barrier reduced or eliminated.  I have now used the application twice - this past fall in the second semester of introductory chemistry and a few weeks ago when I began ligand field theory in my inorganic course.  In both classes I received favorable comments.  A number of students in the inorganic course, who had not had me in previous courses, remarked that they wish that they had seen this in their introductory course.

http://www.flicksstuff.com/Jmol/jsmol/ligandfield.html

Cheers,

Flick

(Note that the link above has been updated to the current correct link by Anthony Fernandez on 12 December 2018.)

Prerequisites: 
Corequisites: 
8 Mar 2009

Interactive Spreadsheets for Inorganic Chemistry

Submitted by Lori Watson, Earlham College
Description: 

This web site contains a number of interactive spreadsheets, most of which are applicable to inorganic chemistry (or a physical chemistry class that uses inorganic examples).  Here's the list of the most relevant for most inorganic classes:

 

ABC kinetics - interactively plot concentration versus reaction extent for A, B and C in A -> B -> C by varying k values

angular overlap model - explore the angular overlap model for d-orbital splitting in complexes by designing various geometries of complexes and varying the parameters es and ep

complexation of silver ion - explore the concentration of various silver species in ammonia as a function of ammonia concentration - can be generalized by varying the Ksp and formation constants interactively

general complexation - explore the distribution of complex species as a function of the concentration of ligand X for MXn with n = 1 - 6 by varying the formation constants

reducing irreducible representations - interactive spreadsheet for reducing reducible representations of 12 common point groups

reversible kinetics - explore concentrations of A and B for A <=> B as a function of time by varying k values - also shows the reaction quotient, Q, and the ratio of Q/K


Prerequisites: 
Corequisites: 
Learning Goals: 

Depends on which spreadsheet you're using!  

Implementation Notes: 

Some of these spreadsheets require Visual Basic which is apparently not supported on Excel 2008 for Mac.  You can use all PC versions of Microsoft Office, however, and may be able to use other products to convert to a Mac-readable format.

8 Mar 2009
Evaluation Methods: 
Answers to the discussion questions are collected and graded as part of a problem set.  Students are allowed to go back and edit their answers after the small/large group discussion.
Evaluation Results: 
Generally they do well on the direct questions, but need prompting to think about extensions of the research or why the authors might be interested in this topic.
Description: 
This is a guided set of questions for the paper: Group 10 and 11 Metal Boratranes (Ni, Pd, Pt, CuCl, AgCl,
AuCl, and Au+) Derived from a Triphosphine-Borane.  It was used to help students integrate the study of a variety of techniques (for example NMR, X-ray, computational studies) and basic organometallic chemistry into reading a "real" paper.
Prerequisites: 
Corequisites: 
Subdiscipline: 
Learning Goals: 
A student should be able to use the experimental techniques he or she is familiar with, combined with basic information concerning d-block complex reactivity, and basic MO theory to understand the synthesis and reactivity of the complexes discussed in the paper.  Additionally, the student will gain confidence in reading the primary literature.
Course Level: 
Implementation Notes: 
The paper and the accompanying questions are assigned as part of a problem set.  We then spend about 20 minutes in class discussing the paper in small groups, and answer one or two of the questions as a whole class based on small group responses.
Time Required: 
20 minutes in class plus about 1-2 hr out of class for the student
8 Mar 2009

Using Computational Chemistry to discuss backbonding to CO

Submitted by Lori Watson, Earlham College
Evaluation Methods: 

Student learning is primarily assessed by means of a written report describing their calculations and results. Related concepts of pi-backbonding, pi donor/acceptor, trans effect, etc. are the subject of problem set and exam questions.

Evaluation Results: 

Typically they do well with this, and enjoy calculating "real" molecules--once they get the hang of the software. Some students do not enjoy learning new software programs and find drawing the molecules and editing the z-matrices tedious and difficult. Students universally like to see the vibrational animations! I am careful to discuss "error bars" of computational calculations--especially the qualitative vs. exact quantitative CO frequencies--as students will otherwise assume the computational results are more accurate than the experimental ones.

Description: 

This activity uses Gaussian with the WebMO interface to investigate the role of the metal in backbonding to CO as well as effects of the trans ligands. It can also be used as a way of introducing computational chemistry in an inorganic course.

Learning Goals: 

Learning Goals: After this exercise you will be able to…
•    Explain the effect of changing the metal on the CO stretching frequencies of a metal carbonyl complex
•    Understand the role of σ and π donors/acceptors in modifying the amount of π backdonation into a trans CO ligand
•    Predict the degree of backdonation into a trans carbonyl that will be observed with an unfamiliar ligand
•    Perform DFT calculations to find the minima and vibrational frequencies of a molecule using WebMO/Gaussian.

Corequisites: 
Subdiscipline: 
Course Level: 
Equipment needs: 

You will need some kind of computational program, preferably one that does DFT calculations. Gaussian with the WebMO interface is suggested.

Prerequisites: 
Implementation Notes: 

I have attached some of the Gaussian output files of the complexes. They can be imported into WebMO and used as starting geometries. If you do not have your own computational program, they can also be imported into the WebMO Demo site (http://www.webmo.net/demo/index.html) and students can look at the outputs and animate the vibrations, etc.

Time Required: 
If the students have never used WebMO/Gaussian before, 1-2 hours. If they have, it can be assigned as homework. The calculations (depending on how good their guesses are) take betwen 15minutes and 3 hours to complete.
8 Mar 2009

Basics of Computational Chemistry

Submitted by Lori Watson, Earlham College
Description: 

I would use this VERY brief introduction to computational chemistry in my inorganic course to preface a computational based assignment.  While one learning goal for such an assignment might be familiarity with WebMO/Gaussian, understanding the background and theory of computational chemistry would generally be beyond the scope of the inorganic course.  However, I certainly want students to have some idea of what they are doing when they perform a calculation (optimization and frequency analysis of metal carbonyls, for example).  I've also included here handouts I use to explain how to use WebMO and the "about computational chemistry" I include in the student's lab handouts

Topics Covered: 
Course Level: 
Learning Goals: 

A student should be able to explain what computational chemistry is and have a basic understanding of what choosing a method and a basis set means.  He or she should also gain a basic understanding of how Gaussian (or another computational chemistry program) "finds" the best geometry for a minimum or transition state.

Implementation Notes: 

Please see the instructors notes attached below.

Evaluation
Evaluation Methods: 

These resources are used to introduce computational chemistry and have students begin their own calculations in a lab or problem set setting (activities elsewhere on this site).  Student learning is assessed by how much understanding of what computational chemistry is as demonstrated by laboratory write-ups.

Evaluation Results: 

In our curriculum, this is generally the first introduction students have to computational chemistry.  Those students less comfortable with "jumping right in" with new computer programs can get stuck in the mechanics of submitting jobs.  The WebMO interface to Gaussian greatly reduces the need to  teach command line interface skills.  Students typically need to do several calculations (in Inorganic and P-Chem classes) to really gain an understanding of what all the method and basis set choices mean.

12 Jan 2009

House: Inorganic Chemistry

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

House (Inorganic chemistry):  The book is divided into 5 parts:  first, an introductory section on atomic structure, symmetry, and bonding; second, ionic bonding and solids; third, acids, bases and nonaqueous solvents; fourth, descriptive chemistry; and fifth, coordination chemistry.  The first three sections are short, 2-4 chapters each, while the descriptive section (five chapters) and coordination chemistry section (seven chapters covering ligand field theory, spectroscopy, synthesis and reaction chemistry, organometallics, and bioinorganic chemistry.) are longer.  Each chapter includes references (both texts and primary literature) for further reading, and a few problems (answers not available in the back of the book). 

I thought the text was generally good.  This text felt aimed at the introductory one-semester inorganic course offered at most schools rather than an advanced (senior/grad) course.  Although MO theory is developed in the text, most of the coordination chemistry is described using crystal field theory, though a short section on MO theory for complexes is included.  The sections on descriptive chemistry of the elements are very good and not overloaded with too much information, and the writing style (throughout the text) is easy to read and conversational.

My main complaint about the book, and this may seem petty, is that the molecular orbitals (throughout) do not accurately depict the way actual orbitals look;  they are too "pointy." 

The list price for the student text is $99.95 for a paperback, 864p version.

Prerequisites: 
Corequisites: 
Course Level: 

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