Molecular Graphics. Molecular Graphics Expt. 1 1

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1 Molecular Graphics Expt. 1 1 Molecular Graphics The study of organic chemistry has for more than a century and a half focussed on the relationship between the structure of an organic molecule (its three-dimensional shape, bonding and electron distribution) and the properties of that molecule. Structure-activity relationships form the basis for new drug discoveries (AIDS therapies, anti-cancer agents, and pain-relievers that don't cause ulcers are but a few examples of structure-driven drug discoveries). The structure of molecules helps chemists design new polymers for unusual applications. Generally, we will look at three important facets of organic structure: shape (for each atom in the molecule and for the molecule itself), flexibility, and charge distribution. I suspect that only one of these issues is obvious: the overall shape. However, you will learn that the other two issues are often extremely important. Sometimes they are far more important than the overall shape. There are two activities that you will be doing frequently while learning about organic chemistry. The first is called "visualization." This involves some formalized kinds of drawing that have been developed for the convenience of practicing chemists. The second activity, which is often used in the pursuit of the first, is structural prediction. We use some simple but powerful rules to predict structural features in small areas of molecules. From these predictions, we can predict the structures of entire molecules. Molecular graphics can help to relieve some of the tedium of building models of molecules. With the ease of switching between model styles, 1 molecular graphics can highlight the relationship between different aspects of a molecule (for example, the relationship between the skeleton and the overall volume). One cautionary note: most structures that one sees using molecular graphics are wrong in one important aspect. The natural flexibility of most molecules cannot be easily displayed. Remember that single bonds allow free rotation. In addition, the structures posted may or may not be in the "best" conformation (whatever that is). We will still have to use some judgement in evaluating the structures. 1 For examples and explanation, see

2 2 Molecular Graphics Websites that take advantage of free molecular graphics software can also provide value other than 3D structures. Several of the sites also provide other properties, such as physical data, biological activity, industrial use, etc. Most sites can be searched by standard name or synonym, and some can look by empirical formula or other properties. General Purpose of This Lab One important goal of this lab is to empirically examine structural issues that we talk about in class. We will explore hybridization and bonding types, and their relationship to things which can be measured on molecules, such as bond lengths and bond angles. In doing so, you should learn the basics of using molecular graphics software and the utilities associated with it. You should also become familiar with a few of the many helpful websites available for your aid in learning organic chemistry. As you explore these molecules, you should be alert to the strengths and weaknesses of the tools you are using. These tools include both the software and website combinations and the model styles that you use. Perhaps the most important skill to be improved is the ability to convert structures from a 2-dimensional representation to a 3- dimensional one, or from 3-D to 2D. The ability to visualize molecules is crucial to understanding many of the fundamental concepts in organic chemistry. We will also begin to investigate the difference between theoretical values and real-world values for such things as bond angles and bond lengths. Angles and lengths in a complex molecule are a compromise between the desired, or "ideal" value and the need to fit more awkward structures together. For example, small rings cause bond angle strain, while larger rings might have "torsional" strain, or non-standard dihedral angles. Unusual bond lengths are a bit more difficult to find [you might consider why this is], but can occur. Software and websites used We will use both the free Chime plugin and the SpartanView and SpartanBuild packages that you got with your textbook. Websites used for 3D molecular models include

3 Molecular Graphics Expt. 1 3 [This is a terrific database for exploring visualization, but some measurements can not be made.] Links to an overview of Chime and structure description can be found at Procedure 1. Write a generic form of the functional group along with the name of the functional group in the left column of a table in your notebook. The table should be big enough to receive a decent sized molecular structure and notes about that structure. Groups studied during this lab will be: Group 1 Group 2 Group 3 Alkane Alkane Alkane Alkene Alkyne Aromatic Ketone Ether Alcohol Acid Ester Amide Amine with saturated carbon attached to N Nitrile Amine with unsaturated carbon attached to N 2. Using one of the structure databases listed above, find examples of molecules which contain at least one of each functional group from the list in part 1. There should be one example per item in the list (a total of 5 examples). One example should have a molecular weight of greater than 150 amu, one should have a weight smaller than 60 amu, one should be a compound found on a label from a product you use. 3. Write a 2-dimensional representation of the molecule. 4. For each example, measure bond lengths for the atoms involved in the functional group. Compare them to the standard values found in your text For each example, measure bond angles that will help tell you what the hybridization or shape is for each atom in the functional group. Note that you do not have to measure all the angles in the molecule. 2 Or at

4 4 Molecular Graphics 6. For each of the examples that occur in your functional groups, measure dihedral angles around: R-C-C-R in an alkane R-C=C-R in an alkene C-C=O in ketone or aldehyde C-O in alcohol, ether, carboxylic acid and ester C-N in amine and amide H-C-C-H in aromatic ring. 7. Using molecular models provided in lab, your group should make a physical model of one of the molecules you are looking at using molecular graphics. You should be prepared to discuss your models with the instructor. 8. Using the Learning through Modeling CD provided with your text, examine the three allyl cations (SpartanView). Measure the charges on each atom. Where is the bulk of the positive charge? 9. Using the SpartanBuild function, build one of your examples from part 2 above. How does the minimized structure compare with the structure posted? Note: When you write 2-dimensional structures, use the following format for bond lengths and angles: Bond Length 151 pm OH 109 Bond Angle

5 Molecular Graphics Expt. 1 5 Notebook instructions The laboratory write-up should include the following: A. A table of data for each functional group, including: 1. Name of group and a generic structure for the group. 2. Name of substance 3. Two dimensional structure of the substance, marked up with bond lengths and angles. 4. Comments on the structure B. The answers to the following questions should be completed prior to the laboratory. 1. Describe your web access away from the Science building. Do you own your own computer? Do you access the web/ daily, or less frequently? 2. Predict the answers to questions C1 and C2 (in the postlab questions). C. The answers to the following questions should be completed after finishing the experiment. 1. For each functional groups which you studied, identify the hybridization of each carbon (sp 3, sp 2, sp). You should base this identification on the data you found, and back it up with the measurement that allowed you to make your conclusion. Were there any differences between this answer and your predictions made in part B? 2. For one of your compounds (ideally one that has noticeably odd bonding), explain differences between values that you measured and what is predicted for "standard" hybridization. 3. What is your best guess for the hybridization of the following atoms? Justify your answer with a relevant measurement or two Ṫhe oxygens in alcohols and in ethers. Both oxygens in a carboxylic acid. The nitrogens in amines (there may be more than one type, depending on the kind of carbon to which it is attached). The nitrogen in amides. 4. Summarize the benefits and drawbacks of the major types of molecular display (wireframe, stick, ball and stick, and spacefill). Base this summary on your experience.