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Chemistry LibreTexts

1: Intro Structure Determination

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Introduction to Structure Determination

The determination of the structure of a chemical is a critical laboratory skill for a chemist. This allows the chemist to know whether they have synthesized the molecule that they wanted or determine the structure of a molecule that has a specific biological activity.

Structure determination can be applied to a range of targets from very simple diatomic molecules to large complex biomolecules or polymers or even organometallic coordination complexes.

Due to the importance of these methods, chemists have developed several techniques to elucidate the structure of a molecule.

This course will introduce students to a wide range of methods including Infrared Spectroscopy, Ultraviolet Spectroscopy, Mass Spectrometry, and several Nuclear Magnetic Resonance Spectroscopic techniques.

Spectra are either from SDBS (Japan National Institute of Advanced Industrial Science and Technology) or simulated.

Introduction to Representing Molecules

Review Representations:

Before we begin to determine the structures of molecules, we will review methods for drawing potential structures and communicating them to others.

1. Lewis "Dot" Structures

Bond = an electron pair

Lewis structures can be cumbersome to draw, but they form the basis for devising all types of structures.

Methane (CH4) Formaldehyde (CH2O) Acetonitrile (CH3CN)

clipboard_efb848b21ebfe1301a7e1110ea0051bfc.png clipboard_e798d164fcb00caa92d53b38b0355234a.png clipboard_e46aaaae44ae2259aea1d130b340a3fd4.png

2. Bond-Line Structures

Bond = an electron pair = a line

This is just a slightly more convenient way of representing Lewis structures.

Methane (CH4) Formaldehyde (CH2O) Acetonitrile (CH3CN)

clipboard_e29a963d1561ba359ce848327e0802f37.png clipboard_ee5518bb3cf58a75f1965af5d786454b4.png clipboard_e8ed08a59ab64c79fa07d065a4a2e95e0.png

3. Condensed Formulas, Line-Bond, and Skeletal Representations

A shorthand method for drawing has developed.

a) All bonds are lines.

b) Every corner or end of a line is a carbon.

c) Every carbon is assumed to have four bonds. If there are not four bonds, the missing bonds must be to hydrogens.

d) All other atoms are shown.

  • Fill in the missing information in the table below:
Condensed Formula Line-Bond Skeletal

CH3CH3

clipboard_e65f2e9fa83dd848cd1c59ab54f6b0a1d.png

clipboard_ebb178bde3fb982c60c3ad19000b0b6af.png

CH3CH2OH

 

clipboard_e40f60a150e0cb02def71a8a575400b82.png

(CH3)2CHCH3 clipboard_e63292e70f6ae096dfe765a6c00b99e83.png  
CH3CH(NH2)CH3   clipboard_e7065762ebb4872d7533096ccf686db39.png
CH3(CO)CH3   clipboard_e5d8c7c21708e8dff8a73d7ce9fc41fe1.png
CH3CO2H clipboard_eeb4da99082c28f20c28834cbe1736be8.png  

4. Practice with Condensed Formulas

These structures are often used in textbooks because they fit nicely into lines of typed text.

a) The molecule is written in a single line of type that generally follows the longest continuous chain of atoms in the molecule.

b) Each chain atom is followed by all atoms attached to it and then by the next chain atom (no bonds are explicitly expressed).

c) When there is a branch in the primary chain, groups in the branch are enclosed in parentheses and follow the primary chain atom to which they are attached.

  • Draw a bond-line representation for each of the following:
CH3(CH2)3CH3 (CH3)2CHOCH2CH2CH2OH
 
CH3CH2CH2CH2CO2H Cl2CHCH(CH2SH)CH2CHO
 

5. Functional Groups

Functional Group Functional Group Name Example
C-C-H (only single C andHsingle bonds) alkane  
R-C=CH2 (R can be any carbon group) alkene  
R-C CH alkyne  
  aromatic ring  
  alcohol  
  ether  
  amine  
  phosphine  
  ketone (carbonyl refers to C=O)  
  aldehyde (carbonyl refers to C=O)  
  carboxylic acid (carbonyl refers to C=O)  
  ester (carbonyl refers to C=O)  
  amide (carbonyl refers to C=O)  
  sulfonate ester  
  phosphate ester  

This page titled 1: Intro Structure Determination is shared under a not declared license and was authored, remixed, and/or curated by Kate Graham.

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