{"id":2251,"date":"2018-06-19T20:23:28","date_gmt":"2018-06-19T20:23:28","guid":{"rendered":"https:\/\/courses.lumenlearning.com\/suny-potsdam-organicchemistry\/chapter\/structure-of-organic-molecules\/"},"modified":"2019-09-13T13:42:27","modified_gmt":"2019-09-13T13:42:27","slug":"1-3-representing-structures","status":"publish","type":"chapter","link":"https:\/\/courses.lumenlearning.com\/suny-potsdam-organicchemistry\/chapter\/1-3-representing-structures\/","title":{"raw":"1.4. Representing structures","rendered":"1.4. Representing structures"},"content":{"raw":"

Representing a chemical structure<\/strong><\/h2>\r\n
Chemical structures are the essential building blocks in organic chemistry. They make up the \u201cwords\u201d of every organic chemistry sentence, so it is vital to understand how to read and write structures.\u00a0 Chemical structures are usually represented by the skeletal formula, which provides a graphical representation of the molecule with most hydrogens omitted for clarity.\u00a0 Full Lewis structures are used only rarely, when a more complete drawing is needed, because they are often harder to read than skeletal structures.\u00a0 Sometimes structures need to be represented in other ways, such as a name or other identifier.\u00a0 Fig. 1 illustrates some of the most common representations for the compound with the name 1-bromobutane.\"\"<\/section>
Fig. 1: Representations of 1\u2013bromobutane: Skeletal structure, Lewis\u2013type structure, InChI string, InChIKey, SMILES[1]<\/strong><\/a> and CAS Registry Number.[2]<\/strong><\/a><\/em><\/section>
Here you will learn how to understand, write and draw organic molecules. Why were different drawing techniques developed? Organic molecules can get complicated and large. It is tedious to constantly draw out every detail, especially when not necessary, so organic chemists developed ways to make it more convenient and easy. In addition, some of these shorthand ways of drawing molecules give us insight into the bond angles, relative positions of atoms in the molecule, and some eliminate the numerous hydrogens that can get in the way of looking at the backbone of the structure.\r\n
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Introduction to structure drawing<\/h3>\r\nObserve the following drawings of the structure of retinol<\/span><\/a>, the most common form of vitamin A. The first drawing follows a Lewis-based structure which is helpful when you want to look at every single atom; however, showing all of the hydrogen atoms makes it difficult to compare the overall structure with other similar molecules and makes it difficult to focus in on the double bonds and OH group.\r\n\r\n[caption id=\"\" align=\"aligncenter\" width=\"454\"]\"vitamin Retinol: Lewis-type straight-line drawing[\/caption]\r\n\r\nThe following is a skeletal (a.k.a. line-angle) formula for retinol. With this simplified representation, one can easily see the carbon-carbon bonds, double bonds, OH group, and CH3<\/sub> groups sticking off of the the main ring and chain. Also, it is much quicker to draw this than the one above.\r\n\r\n[caption id=\"\" align=\"aligncenter\" width=\"314\"]\"vitamin Retinol: Skeletal formula[\/caption]\r\n\r\n<\/div>\r\n
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Importance of structure<\/h3>\r\nLearning and practicing the basics of organic chemistry will help you immensely in the long run as you learn new concepts and reactions. Some people say that organic chemistry is like another language, and in some aspects, it is. At first it may seem difficult or overwhelming, but the more you practice looking at and drawing organic molecules, the more familiar you will become with the structures and formulae. Another good idea is to get a model kit and physically make the molecules that you have trouble picturing in your head.\r\n\r\nThrough general chemistry, you may have already experienced looking at molecular structure. The different ways to draw organic molecules include Lewis-type<\/strong>, condensed formulae<\/strong>, and skeletal formulae<\/strong>. It will be more helpful if you become comfortable going from one style of drawing to another, and look at drawings and understanding what they mean, than knowing which kind of drawing is named what.\r\n\r\nAn example of a drawing that incorporates all three ways to draw organic molecules would be the following additional drawing of retinol. The majority of the drawing uses the skeletal formula, but the -CH3\u00a0<\/sub>are written as condensed formulae, and the -OH group is written in Lewis-type form.\r\n\r\n\"retinol.jpg\"\r\n

Drawing the structure of organic molecules<\/h3>\r\n<\/div>\r\n
\r\n\r\nAlthough larger molecules may look complicated, they can be easily understood by breaking them down and looking at their smaller components.\r\n\r\nAll atoms want to have their valence shell full, a \"closed shell.\" Hydrogen has a full shell with only 2 e-<\/sup> whereas carbon, oxygen, and nitrogen want to have 8 e-<\/sup>(an \"octet\"). When looking at the different representations of molecules, keep in mind the Octet Rule<\/a>. Also remember that hydrogen can bond one time, oxygen can bond up to two times, nitrogen can bond up to three times, and carbon can bond up to four times.\r\n

\"possible<\/a>Lewis-type<\/h3>\r\n<\/div>\r\n
\r\n\r\nLewis-type structures are similar to traditional Lewis structures<\/a>, but instead of covalent bonds being represented by electron dots, the two shared electrons are shown by a line.\r\n\r\n(A) \"A\r\n\r\n(B)\"B\r\n\r\n(C)\"C\r\n\r\nLone pairs remain as two electron dots, but they are usually left out even though they are still there<\/em>. Notice how the three lone pairs of electrons were not draw in around chlorine in example B.\r\n\r\n<\/div>\r\n
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Condensed formulae<\/h3>\r\nA condensed formula is made up of the elemental symbols.\u00a0The order of the atoms suggests the connectivity. Condensed formulas can be read from either direction and H3<\/sub>C is the same as CH3<\/sub>, although the latter is more common because Look at the examples below and match them with their identical molecule under Kekul\u00e9 structures and bond-line formulas.\r\n\r\n(A)\u00a0 CH3<\/sub>CH2<\/sub>OH\u00a0\u00a0\u00a0\u00a0 (B)\u00a0 ClCH2<\/sub>CH2<\/sub>CH(OCH3<\/sub>)CH3\u00a0\u00a0\u00a0\u00a0\u00a0\u00a0 <\/sub>(C)\u00a0H3<\/sub>CNHCH2<\/sub>COOH\r\n\r\nLet's look closely at example B. As you go through a condensed formula, you want to focus on the carbons and other elements that aren't hydrogen.\u00a0The hydrogens are important, but are usually there to complete octets. Also, notice the -OCH3<\/sub> is in written in parentheses which tell you that it not part of the main chain of carbons. As you read through a a condensed formula, if you reach an atom that doesn't have a complete octet by the time you reach the next hydrogen, then it's possible that there are double or triple bonds. In example C, the carbon is double bonded to oxygen and single bonded to another oxygen. Notice how COOH means C(=O)-O-H instead of CH3<\/sub>-C-O-O-H because in the latter structure carbon does not have a complete octet and oxygens.\r\n\r\n<\/div>\r\n
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Skeletal formulae<\/h3>\r\nBecause of the typical (more stable) bonds that atoms tend to make in molecules, skeletal chains often end up looking like zig-zag lines. If you work with a molecular model kit you will find it difficult to make stick straight molecules (unless they contain sp<\/a> triple bonds), whereas zig-zag molecules and bonds are much more feasible.\r\n\r\n(A) \"A\r\n\r\n(B)\"B\r\n\r\n(C)\"C\r\n\r\nThese molecules correspond to the exact same molecules depicted for Lewis-type structures and condensed formulae. Notice how the carbons are no longer drawn in and are replaced by the ends and bends of a lines. In addition, the hydrogens have been omitted, but could be easily drawn in (see practice problems). Although we do not usually draw in the H's that are bonded to carbon, we do draw them in if they are connected to other atoms besides carbon (example is the OH group above in example A) . This is done because it is not always clear if the non-carbon atom is surrounded by lone pairs or hydrogens. Also in example A, notice how the OH is drawn with a bond to the second carbon, but it does not mean that there is a third carbon at the end of that bond\/ line.\r\n\r\n<\/div>\r\n
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Problems<\/h3>\r\n
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  1. \u00a0How many carbons are in the following drawing? How many hydrogens?\r\n\"prob<\/li>\r\n \t
  2. \u00a0How many carbons are in the following drawing? How many hydrogens?\r\n\"prob<\/li>\r\n \t
  3. \u00a0How many carbons are in the following drawing? How many hydrogens?\r\n\"prob<\/li>\r\n \t
  4. Look at the following molecule of vitamin A and draw in the hidden hydrogens and electron pairs.\r\n\"vitamin (Hint: Do all of the carbons have 4 bonds? Do all the oxygens have a full octet?)<\/li>\r\n \t
  5. How many bonds can hydrogen make?<\/li>\r\n \t
  6. How many bonds can chlorine make?<\/li>\r\n \t
  7. Dashed lines means the atomic bond goes ___________(away\/toward) you.<\/li>\r\n \t
  8. Draw ClCH2<\/sub>CH2<\/sub>CH(OCH3<\/sub>)CH3<\/sub> in Lewis and skeletal form.<\/li>\r\n<\/ol>\r\n[reveal-answer q=\"797621\"]Show Answer[\/reveal-answer]\r\n[hidden-answer a=\"797621\"]\r\n
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    1. \u00a0Remember the octet rule and how many times carbons and hydrogens are able to bond to other atoms.\r\n\"prob<\/li>\r\n \t
    2. \"prob<\/li>\r\n \t
    3. \"prob<\/li>\r\n \t
    4. Electron pairs drawn in blue and hydrogens drawn in red.\r\n\"vitamine<\/li>\r\n \t
    5. Hygrogen can make one bond.<\/li>\r\n \t
    6. Chlorine can make one bond.<\/li>\r\n \t
    7. Away<\/li>\r\n \t
    8. See (B) under Kekul\u00e9 and Bond-line (zig-zag) formulas.<\/li>\r\n<\/ol>\r\n<\/div>\r\n<\/div>\r\n[\/hidden-answer]\r\n\r\n<\/div>\r\n<\/div>\r\n
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      Further Reading<\/h3>\r\nCommunicating chemical structure with formulas and names<\/a>\r\n\r\n<\/div>\r\n

      References<\/h3>\r\n
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      \r\n\r\n[1]<\/a> http:\/\/www.chemspider.com\/Chemical-Structure.7711.html?rid=b8719dd4-7de2-4140-aebf-afb809c26dab<\/a>\r\n\r\n<\/div>\r\n
      \r\n\r\n[2]<\/a> http:\/\/www.commonchemistry.org\/ChemicalDetail.aspx?ref=109-65-9<\/a>\r\n\r\n<\/div>\r\n<\/div>\r\n3. Vollhardt, K. Peter C., and Neil E. Schore. Organic Chemistry: Structure and Function<\/u>. 5th ed. New York: W. H. Freeman Company, 2007. 38-40.\r\n\r\n4. Klein, David R. Organic Chemistry I As a Second Language<\/u>. 2nd ed. Hoboken, NJ: John Wiley & Sons, Inc, 2007. 1-14.\r\n\r\n<\/div>\r\n
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      Outside Links<\/h3>\r\n