Experiment 2 Pre Laboratory Assignment For Group

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Due Dates:

22 Feb / 23 FebA
15 Feb / 16 FebB

WebMO on Sunbird

All of the calculations for this experiment and future experiments will be completed using Gaussian09 using WebMO.  It can be accessed via the UW Chemistry Departmental Cluster.  You must know your username and password which you will recieve approximately 1 week prior to your scheduled lab date.  It is critical that your web browser and Java installations are up-to-date in order for your WebMO experience to be relatively smooth.

Day 1 Pre-Lab Requirements:

Before the first day you are schedule to work on Experiment 4,  you will need to have completed/confirmed the following:

  • Confirmed that you receieved your username and password via email.
  • Logged into WebMO on the departmental cluster successfully.
  • Viewed and taken notes on lectures 1 and 2 on molecular modeling.  You are encouraged to log into WebMO and build the molecules as shown in lecture 2.  These videos were recorded using an older version of WebMO, but the interface and images have changed only slightly.
  • Read Chapter 4 in the lab manual.

Lecture 1 - Molecular Modeling (56:20)

Lecture 2 - Molecular Modeling (1:10:39)

Lecture note-taking slides

Day 2 Pre-Lab Requirements:

Before the second day you are scheduled to work on Experiment 4, you need to watch lecture 3 on molecular modeling.

Lecture 3 - Molecular Modeling (37:48)

Required/Recommended Course Software:

Mozilla Firefox Latest Version

Google Chrome

ChemDraw Pro 15 Free Download

MestReNova

1H-NMR & 13C-NMR FID Data & Example MestreNova Workup Videos (no audio, old file structure)

Chem 344 MestReNova Guide

4'-hydroxyacetophenone 1H-NMR and 13C-NMR fid data

Folder 1 in the zip file is the 1H-NMR spectral data and folder 2 in the zip file is the 13C-NMR spectral data.

4'-hydroxyacetophenone 1H-NMR and 13C-NMR Sample Spectra (Not available for submission for credit)

Molecular Modeling Lecture Calculations:

All of the following calculations were completed using WebMO with Gaussian09 at a B3LYP/6-31G(d) level.

Frequently Asked Questions:

Q1) Why do I need to optimize a structure?  What does the program do when optimizing?

A1)  Put very simply, optimzing the structure allows Gaussian09 to calculate a good geometry for the molecule.  An optimized geometry should give reasonable energies, orbital occupancies, and other properties that you may wish to calculate.  In the process of optimizing, Gaussian will adjust the paramters of the molecule (distances, angles, and dihedral angles) until the energy of the structure settles into a local minimum on the potential energy surfcace.  If you are starting from a good guess of a starting structure, these changes will be relatively subtle and the calculation time will be small. 

Q2)How can I tell if my output is reasonable?

A2)  This is one of the hardest questions to answer and is a question that computational chemists ask every time they look at the output files of a calculation. 

  1. Make sure the calculation has finished properly.  WebMO will display a status of Complete for all successfully complete jobs.
  2. Confirm that the level of theory, basis set, and job type are the desired ones.
  3. Use your chemical intution and determine whether or not the structure looks reasonable.
  4. If you are looking for a reactant, product, or intermediate check to see that all of the molecules vibrational frequencies are positive values.  If you are looking for a transition state, check to see that exactly one vibrational frequency is negative or imaginary.

Q3) How can I predict whether or not VSEPR will adequately predict a molecular geometry?

A3) Valence-Shell Electron Pair Repulsion Theory (VSEPR) is a useful tool for predicting molecular geometries.  As we saw for water (see the LP orbitals in the NBO job above) it can often get the rightmolecular geometry (bent) even when it fails to predict the correct electron geometry.  Unlike the two equivalent lone pairs predicted by VSEPR, a quick molecular orbital calculation of water reveals two distinct lone pairs, one of which is in a p orbital.  Furthermore, as we saw with anisole, VSEPR fails to predict a reasonable bond angle for th Me-O-Ph angle which is far closer to 120 ° than 109.5 ° VSEPR alone would suggest.  This can make it confusing and difficult to know when VSEPR is likely to give the wrong electron geometry and when it is likely to give the wrong electron and molecular geometry.

A reasonable guidline is to assume that VSEPR will often give a good prediction for the molecular geometry when steric repulsion of lone and bond pairs of electrons is the major or only factor involved.  If conjugation of orbitals, orbital mixing, hyrogen bonding, or any other factor impacts the geometry, VSEPR may not do very well.

Importantly, VSEPR will fail to predict the proper electron geometry for all atoms that possess two or more lone pairs.

Shown above is the molecule oseltamivir optimized at B3LYP/6-31G(d) with no imaginary vibrational frequencies.  This molecule is interesting in that it showcases the successes and limitations of VSEPR geometry prediction within the same molecule.  If you click on the optimized structure, WebMO will allow you to measure the bond angles and dihedral angles throughout the molecule. 

VSEPR works well to predict the molecular geometries of the carbon atoms.  The amine nitrogen atom appears to be well predicted by VSEPR and displays a trigonal pyramidal shape.  The amide nitrogen atom has a lone pair in conjugation with the neighboring carbonyl group π bond.  The C-N-C bond angle that results is 121.5 ° and the nitrogen-atom is nearly trigonal planar.  Likewise the geometry of both oxygen atoms which have bonds to two different atoms are poorly described by VSEPR.  The ether oxygen atom has a C-O-C angle of about 114.0 ° and the ester oxygen atom attached to the ethyl group has a C-O-C angle of about 115.8 °.

Q4) What are symmetry point groups and what do I need to know about them for Chem 344?

A4)  Symmetry point groups are geometric designations that identify all of the symmetry elements within a structure of that group.  It is not critical for Chem 344 that you understand the point group symmetry elements or are able to assign point groups.  A lengthy description can be found on wikipedia, but shown below are point groups that you'll encouter a lot in this course.

Point GroupExample(s)Key Characteristics
C1

(R)-2-butanol

Molecules in this point group lack internal mirror planes or symmetric points.  It is the most common point group.
Cs

anisole

toluene

Molecules in this point group contain an internal mirror plane.  This occurs when the molecules is planar and any atoms out of plane are matched by atoms out of plane on the other face of the molecule.
C2v

water

nitrobenzene

These molecules contain an internal mirror plane like the CS point group, but also contain a second mirror plane perpendicular to the first cutting the molecule in equal halves.
C∞v

HCN

Linear molecules with different atoms in each half of the molecule fit into this point group
D6h

benzene

The image displaying the symmetry elements for benzene appears really complicated.  Essentially this it is a D6h structure which means that it is planar with a six mirror planes that are perpendicular to the molecular plane.  Each atom has a counterpart opposite it from the center of the molecule.

Unformatted text preview: CHEMISTRY 112 – Experiment 2 Chemistry of Smell Pre-Lab Assignment (16 pts) - must be submitted on Canvas by the beginning of lab Our chemical system of interest in lab this week will be the sense of smell. Consider your own understanding of what happens when you smell something. Do not look up any information to write this initial explanation. The ideas that you provide will not be judged on their scientific correctness (unless specified in the question). Your score will be based on completeness and how well you follow the directions for what to include in the assignment as outlined below. In your assignment: 1. (4 pts) Describe what you think happens at the molecular‐level when your nose detects a smell. 2. (2 pts) As an extension of your explanation above, explain why two chemical substances might smell different from, or similar to, each other. 3. (2 pts) Based on your own prior experiences, what are some examples of specific evidence that helps support your molecular‐level ideas about odors and the sense of smell? If you do not think you have any evidence, explain why you think a lifetime of smelling odors does not count as specific evidence. 4. Watch the video of the April Fools’ Day prank which introduced Google Nose (https://www.youtube.com/watch?v=VFbYadm_mrw). Based on this video, answer these questions: a. (2 pts) On a scale of 1 to 10, with 1 = “pure science fiction” and 10 = “technology already exists”, how close do you think we are from realistic development of this type of technology? Briefly explain your choice. {Note: The accuracy of your responses on questions (b) and (c) will be graded – so watch the video and answer carefully.} b. (4 pts) According to the video, how large is the database of smells that has been created by the fictional Google “mobile aroma indexing program”? Convert this number into megabytes of data (show your work). c. (2 pts) The video describes temporarily aligning molecules to create a particular scent. What two things does it claim are combined to make alignment of molecules possible? Page | 16 Chem 112 Laboratory Manual © 2017 Colorado State University Department of Chemistry In-Class Activities (24 pts) Activity I – EXPERIMENT 1. Start this activity by sketching out a very large table in your lab notebook with the following headings: Vial Chemical Name Smell Classification 2. 3. 4. 5. Molecular Formula Structural Formula Leave enough space below the headings so that you can fill in rows of data for at least 16 different samples. Depending on your handwriting style, you will probably want to have this table cover two pages in your lab notebook with 8 rows on each page. As you perform activities throughout this experiment, this large master table will help you look at all of the information more comprehensively rather than having small parts of similar data spread throughout different pages of your lab notebook. It is advisable to have a large column width for Structural Formula as you will draw molecules in this column. Now that you have your master data table ready, your group will be given a set of vials labeled A‐ E. Your TA will also demonstrate the proper method for observing smells (“wafting”). Each group member should: a. Smell each vial and record observations about the associated smell. b. Classify the smell for each vial into one of five possible categories: MINTY, FISHY, SWEET, PUTRID, CAMPHOR Note: Categories can be used for more than one vial, and some categories may not be used at all. For instance, you might say all five vials smelled minty. Also, the “camphor” category may be one that is less familiar to you. To help identify the “camphor” smell, vials of pure camphor have been provided for reference. Discuss the smell observation and classification identified by each member of your group. Reconcile any differences in classification, and reach a group consensus on the classification of the smell. Place this group classification into your master data table. Also, record any issues/reasons why the group had difficulty identifying the odor or agreeing on the classification. Be prepared to share your group smell classifications with the rest of the class. Activity II – ANALYZE AND DISCUSS 1. Your TA will provide you with the chemical names and formulas of the substances in vials A‐E. Record these names and formulas in your lab notebook. 2. In your group, compare the chemical name and formula information to the smell classification that you agreed upon, and try to come up with at least 5‐7 patterns in the data. Which noticeable patterns could help you predict the smells of other substances? 3. Participate in a class discussion about these initial patterns. Chemistry of Smell © Colorado State University Department of Chemistry Page | 17 Activity III – PREDICT AND TEST 1. Your TA will provide you with the chemical names and formulas of the substances in vials F‐J. Record these names and formulas in your lab notebook. 2. Using your patterns and current molecular‐level understanding of smell, predict what these substances will smell like. Write these predictions down in your lab notebook with an appropriate heading for your TA. You can also add your predictions into your master data table under “smell classification.” Be sure to label which smell is your prediction and which smell is your actual classification (once you have smelled the vials). Be prepared to share your predictions with the class if asked to do so by your TA. For your predictions: Classify each substance using one of the five smell categories. Identify whether your confidence level in each prediction is low, medium, or high. State a clear reason for each prediction’s confidence level being low, medium, or high. Suggest any other experimental or chemical information you might want available to help strengthen your predictions. 3. Once you have completed your predictions, use the same procedure that you used for vials A‐E to smell vials F‐J. Record your smell observations in your master data table. Activity IV – ANALYZE AND DISCUSS 1. In your groups, discuss your smell observations for vials F‐J. While discussing, record responses to the following bullets in your lab notebook: Examine the smell data. Note which smell classifications for F‐J are consistent with your predictions and which are not consistent. Closely compare the following pairs of smells: D/F, G/H, and I/J. What do you think can account for the smells you identified for each of these pairs? What changes should you make to the patterns that you used to make your F‐J predictions? How do the smell observations support those changes in your patterns? 2. Your TA will provide you with cards containing structural formulas of the substances in vials A‐J. Record these structural formulas in your master data table. 3. In your group, sort the cards in a way that makes sense to you. Look for, and write down, any new patterns that you see in the data. Which noticeable patterns could help you predict the smells of other substances? Activity V – PREDICT AND TEST 1. Your TA will provide you with the chemical names, formulas, and structural formulas of the substances in vials K‐O. Record all of this information in your master data table. 2. Using your patterns and current molecular‐level understanding of smell, predict what these substances will smell like. Write these predictions down in your lab notebook with an appropriate heading for your TA. Again, you can combine predictions and actual smells within the master data table. Be prepared to share your predictions with the class if asked to do so by your TA. For your predictions: Classify each substance using one of the five smell categories. Identify whether your confidence level in each prediction is low, medium, or high. State a clear reason for each prediction’s confidence level being low, medium, or high. Page | 18 Chem 112 Laboratory Manual © 2017 Colorado State University Department of Chemistry Suggest any other experimental or chemical information you might want available to help strengthen your predictions. 3. Once you have completed your predictions, use the same procedure that you used for vials A‐J to smell vials K‐O. Record your smell observations in the master data table. Activity VI – ANALYZE AND DISCUSS 1. In your groups, discuss your smell observations of vials K‐O. While discussing, record responses to the following bullets in your lab notebook: Examine the smell data. Note which smell classifications for F‐J are consistent with your predictions and which are not consistent. What changes should you make to the patterns that you used to make your smell predictions? How do the smell observations support those changes in your patterns? Activity VII – EXPLORE 1. In this part of the experiment, you will examine molecular models of the substances in vials A‐O. Physical models of the eight molecules listed in the table below are provided in the room. A l‐carvone C amyl propionate D isoamyl acetate I isopentanoic acid K citronellol L fenchol N menthol O borneol Additionally, using the laptop at your lab station, virtual 3D models of all of the substances can be viewed and explored at http://sites.chem.colostate.edu/genchemlabs/chem112/chem112.htm. Use these models to explore the 3D shape of these substances. 2. As a group, look for patterns in the molecular models that can be used to predict the smells of molecules. Record any patterns or observations in your lab notebook. 3. In your group, identify at least three (3) aspects of chemical structure that you think impacts the smell of a substance. Record these aspects in your lab notebook. Chemistry of Smell © Colorado State University Department of Chemistry Page | 19 Activity VIII – PREDICT AND TEST 1. Your TA will provide you with a notecard containing the chemical name, formula, and structural formula of the last sample, vial P. Record thisinformation in your master data table. 2. Using your patterns and current molecular‐level understanding of smell, predict what the substance in vial P will smell like. Like previous predictions, record this information in your lab notebook. Be prepared to share your prediction with the class. For your prediction: Classify the substance using one of the five smell categories. Identify whether your confidence level in the prediction is low, medium, or high. State a clear reason for confidence level being low, medium, or high. Suggest any other experimental or chemical information you might want available to help strengthen your prediction. 3. Once you have completed your prediction, use the same procedure that you used for vials A‐O to smell vial P. Record your smell observations. 4. Smell vials A and P side‐by‐side. Record a description of the similarities and differences you notice between these two vials. 5. Observe the 3D models of substances A and P, and note the similarities and differences in your lab notebook. Activity IX – ANALYZE AND DISCUSS 1. In your groups, discuss the structures and your smell observations of vial P in comparison to vial A. While discussing, record responses to the following bullets in your lab notebook: What do you think might account for the different smells of the two molecules with the same formula and basic connectivity of atoms? How can you explain this outcome? What changes should you make to the patterns you used to make your smell predictions? How do the smell observations support those changes in your patterns? Are there any revisions you can make to the three (3) aspects of chemical structure that you think impact the smells of different substances? What questions about smells remain, or what new questions have developed? What experiment(s) could you propose to help answer some of the remaining questions? 2. Participate in a final class discussion (or smaller group discussion with your TA) about vials A and P as well as your final thoughts on the relationship between chemical structures and smells. Page | 20 Chem 112 Laboratory Manual © 2017 Colorado State University Department of Chemistry Post-Lab Assignment (70 pts) – maximum 4-page limit Note: The ideas you express in your explanations throughout the semester should be your own, not someone else’s ideas. Explain your ideas and your own understanding – you should NOT be trying to report the “right answer” or the thoughts of another person that you are getting from a friend, web, or textbook. You may use such outside resources to help supplement your own ideas, but you must properly cite and reference those information sources. 1. (8 pts) Based on the evidence you collected and the discussions you had during lab, re‐work your initial pre‐lab explanation about what happens when you smell something, incorporating your new information from your lab activities. Provide a clear molecular‐level explanation for what allows us to distinguish between different types of smells and why two substances might smell different from or similar to each other. Throughout your response, you must cite detailed and specific evidence/observations from the lab that support(s) your explanation. 2. (8 pts) Identify and describe how your explanations of what happens when you smell something have changed from the pre‐lab to the post‐lab. For your response, you must clearly explain what aspects of your explanation were revised based on the lab experiments performed, and you must cite detailed and specific evidence/observations from the lab that caused you to rethink your ideas. If you think none of your ideas have changed since your pre‐lab assignment, then cite detailed and specific evidence/observations from the lab that demonstrate(s) your original ideas can explain every observation made in the lab. 3. (12 pts total; 4 pts each molecule) Using the patterns from lab and your current molecular‐level understanding of smell, predict the smells of the following substances (X, Y, and Z). Classify the prediction using one of the five smell categories from lab, and include a complete, detailed molecular‐level explanation supporting your prediction. The most important part of this question is your explanation, not the accuracy of the prediction itself. Do not waste your time looking for answers online. In answering this question, you may find it helpful to refer to the 3D molecular models available at http://sites.chem.colostate.edu/genchemlabs/chem112/chem112.htm. Note: The device you use may not properly run the 3D modeling script. This might occur due to a number of different issues including your choice of web browser, installed plugins, and security settings. Unfortunately, we cannot troubleshoot your individual devices. If you try several browsers or devices and continue to have difficulty seeing the molecular models, you may need to use the computers in the CLeRC – Yates 412. Vial Chemical Name Molecular Formula X pulegone C10H16O Chemistry of Smell © Colorado State University Department of Chemistry Structural Formula Page | 21 Y citral C10H16O CH3 Z bornyl acetate C12H20O2 H2C H3C H3C H2C C H C CH3 O C C CH2 O C H 4. (10 pts) Generate a list of five (5) HIGH‐QUALITY unanswered scientific questions you (still) have about smells. All of your questions should be new or revised from previous questions. You should use the questions that you and your group generated during lab as starting points for your new questions. Be sure that you are considering scientific questions, not random, unfocused questions. 5. (32 pts total) Another student in the class decides to try to answer one of their own scientific questions that they have proposed: “What are differences in people’s ability to distinguish smells?” The student walks around the hallways of the Yates and A/Z buildings with a vial of l‐ carvone (vial A), asking people, “What does this smell like?” The student records the responses of different people on a piece of scrap paper with a pencil. Based only on this description of the student’s experimental design, answer the following questions. Consider the scientific question being asked: “What are differences in people’s ability to distinguish smells?” a. (2 pts) Identify whether the question asked is open‐ended or close‐ended. b. (2 pts) Rewrite the question to be in the opposite form (open‐ended changed to close‐ ended or vice versa). c. (4 pts) Consider the scientific value of the original question. Identify one specific strength and one specific weakness in how the question was structured. Be sure your response has sufficient detail. Consider the experimental method and procedure used: d. (4 pts) Identify two specific strengths of the method and procedure used. Be sure your response has sufficient detail. e. (4 pts) Identify two specific weaknesses of the method and procedure used. Be sure your response has sufficient detail. Page | 22 Chem 112 Laboratory Manual © 2017 Colorado State University Department of Chemistry Consider the data being collected: f. (4 pts) Identify what type of data will result from this experiment by providing some detailed examples of what the expected responses from participants might be. g. (4 pts) Explain whether or not the expected data is likely to provide any useful information to help answer the leading question. Be sure your explanation is thorough, and use the expected data you wrote above to support your explanation. Create an improved overall design for this experiment. Your new and improved experiment should include the following: h. (4 pts) Provide a revised scientific question for the experiment that corrects the weaknesses you identified in part (c) above. i. (4 pts) Provide a revised experimental procedure that corrects the weaknesses you identified in part (e) above. Chemistry of Smell © Colorado State University Department of Chemistry Page | 23 ...
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