1: Intro Structure Determination
- Page ID
- 309304
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\(\newcommand{\avec}{\mathbf a}\) \(\newcommand{\bvec}{\mathbf b}\) \(\newcommand{\cvec}{\mathbf c}\) \(\newcommand{\dvec}{\mathbf d}\) \(\newcommand{\dtil}{\widetilde{\mathbf d}}\) \(\newcommand{\evec}{\mathbf e}\) \(\newcommand{\fvec}{\mathbf f}\) \(\newcommand{\nvec}{\mathbf n}\) \(\newcommand{\pvec}{\mathbf p}\) \(\newcommand{\qvec}{\mathbf q}\) \(\newcommand{\svec}{\mathbf s}\) \(\newcommand{\tvec}{\mathbf t}\) \(\newcommand{\uvec}{\mathbf u}\) \(\newcommand{\vvec}{\mathbf v}\) \(\newcommand{\wvec}{\mathbf w}\) \(\newcommand{\xvec}{\mathbf x}\) \(\newcommand{\yvec}{\mathbf y}\) \(\newcommand{\zvec}{\mathbf z}\) \(\newcommand{\rvec}{\mathbf r}\) \(\newcommand{\mvec}{\mathbf m}\) \(\newcommand{\zerovec}{\mathbf 0}\) \(\newcommand{\onevec}{\mathbf 1}\) \(\newcommand{\real}{\mathbb R}\) \(\newcommand{\twovec}[2]{\left[\begin{array}{r}#1 \\ #2 \end{array}\right]}\) \(\newcommand{\ctwovec}[2]{\left[\begin{array}{c}#1 \\ #2 \end{array}\right]}\) \(\newcommand{\threevec}[3]{\left[\begin{array}{r}#1 \\ #2 \\ #3 \end{array}\right]}\) \(\newcommand{\cthreevec}[3]{\left[\begin{array}{c}#1 \\ #2 \\ #3 \end{array}\right]}\) \(\newcommand{\fourvec}[4]{\left[\begin{array}{r}#1 \\ #2 \\ #3 \\ #4 \end{array}\right]}\) \(\newcommand{\cfourvec}[4]{\left[\begin{array}{c}#1 \\ #2 \\ #3 \\ #4 \end{array}\right]}\) \(\newcommand{\fivevec}[5]{\left[\begin{array}{r}#1 \\ #2 \\ #3 \\ #4 \\ #5 \\ \end{array}\right]}\) \(\newcommand{\cfivevec}[5]{\left[\begin{array}{c}#1 \\ #2 \\ #3 \\ #4 \\ #5 \\ \end{array}\right]}\) \(\newcommand{\mattwo}[4]{\left[\begin{array}{rr}#1 \amp #2 \\ #3 \amp #4 \\ \end{array}\right]}\) \(\newcommand{\laspan}[1]{\text{Span}\{#1\}}\) \(\newcommand{\bcal}{\cal B}\) \(\newcommand{\ccal}{\cal C}\) \(\newcommand{\scal}{\cal S}\) \(\newcommand{\wcal}{\cal W}\) \(\newcommand{\ecal}{\cal E}\) \(\newcommand{\coords}[2]{\left\{#1\right\}_{#2}}\) \(\newcommand{\gray}[1]{\color{gray}{#1}}\) \(\newcommand{\lgray}[1]{\color{lightgray}{#1}}\) \(\newcommand{\rank}{\operatorname{rank}}\) \(\newcommand{\row}{\text{Row}}\) \(\newcommand{\col}{\text{Col}}\) \(\renewcommand{\row}{\text{Row}}\) \(\newcommand{\nul}{\text{Nul}}\) \(\newcommand{\var}{\text{Var}}\) \(\newcommand{\corr}{\text{corr}}\) \(\newcommand{\len}[1]{\left|#1\right|}\) \(\newcommand{\bbar}{\overline{\bvec}}\) \(\newcommand{\bhat}{\widehat{\bvec}}\) \(\newcommand{\bperp}{\bvec^\perp}\) \(\newcommand{\xhat}{\widehat{\xvec}}\) \(\newcommand{\vhat}{\widehat{\vvec}}\) \(\newcommand{\uhat}{\widehat{\uvec}}\) \(\newcommand{\what}{\widehat{\wvec}}\) \(\newcommand{\Sighat}{\widehat{\Sigma}}\) \(\newcommand{\lt}{<}\) \(\newcommand{\gt}{>}\) \(\newcommand{\amp}{&}\) \(\definecolor{fillinmathshade}{gray}{0.9}\)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 (\(CH_4\)) Formaldehyde (\(CH_2O\)) Acetonitrile (\(CH_3CN\))
2. Bond-Line Structures
Bond = an electron pair = a line
This is just a slightly more convenient way of representing Lewis structures.
Methane (\(CH_4\)) Formaldehyde (\(CH_2O\)) Acetonitrile (\(CH_3CN\))
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 |
|
\(CH_3CH_3\) |
 |
|
|
\(CH_3CH_2OH\) |
|
|
| \((CH_3)_2CHCH_3\) |  |
|
| \(CH_3CH(NH_2)CH_3\) |  |
|
| \(CH_3(CO)CH_3\) |  |
|
| \(CH_3CO_2H\) |  |
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:
| \(CH_3(CH_2)_3CH_3\) | \((CH_3)_2CHOCH_2CH_2CH_2OH\) |
| \(CH_3CH_2CH_2CH_2CO_2H\) | \(Cl_2CHCH(CH_2SH)CH_2CHO\) |
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 |