Organic Molecular Modeling Lab coat and goggle are not necessary - PowerPoint PPT Presentation

Organic Molecular Modeling  Lab coat and goggle are not necessary 2016/03/20 revised  Self-prepare digital camera  Download Avogadro and Chemsketch free software (reference expt.) Collect and check contents: MOLYMOLD Organic Set White ball: 20 Green ball: 4 Black ball: 12 Yellow ball: 2 Red ball: 6 Grey ball: 1 Blue ball: 4 Purple ball: 1 Short white link: 26 Medium grey link: 26 Long grey link: 12 Link remover: 1 1

Purpose  Construct and learn spatial arrangement of organic molecules  Use MOLYMOLD  organic set to build  Ball-and-stick model  Observe the conformers and isomers  Use free software to sketch the chemical structures (reference expt.)  Chemsketch  Avogadro 2

Chemical Structure of Organic Compound H H  Lewis structure Wedge- H C H and-dash C H H H H  Ball-and-stick  Space-filling 3

MOLYMOLD  Organic Set Specific color for element Ball-and-stick C H O N Single Multiple bond bond Cl Space-filling Link remover 4

Flow Chart I. Organic Molecular Modeling MOLYMOD ball-and-stick model Check the contents in the set Draw chemical structures MOLYMOD organic set Construct ball-and-stick model Compare and take picture After lab, recheck the set Ball-and-stick model 5

I. Newman Projection  For ethane, C 2 H 6 Newman Projection 1. Staggered 1 2 1 1 2 2 1 2. Eclipsed 2 1 1 2 1 2 1 6

II. Conformation  Conformation  Rotate single bond to change the spatial arrangement Eclipsed, higher energy Staggered, lower energy 2 2 More stable 1 1 7

II. Chair and Boat Form of Cyclohexane  Cyclohexane, C 6 H 12 : chair and boat form Chair form Boat form 4 1 4 3 2 2 3 6 5 6 5 1 More stable H H H H H H H H H H H H H 8

III. Isomers Same formula, but Isomers different structures Same skeleton, Different Structural Stereoisomers but different spatial skeleton isomers arrangement Skeletal Functional Positional Geometric group isomers isomers Enantiomers isomers isomers CH 3 O CH Cl Cl Cl Cl CH 3 CH 2 OH Cl Cl 9

Geometric Isomers Geometric isomers ( cis , trans -isomers)  Molecule with C=C double bond or ring structure  cis : on the same side  trans : on the other side H Cl H H C C C C Cl Cl Cl H Cis -form Trans -form Cis -form Trans -form 1,2-Dichloroethene 1,4-dimethylcyclohexane 10

Enantiomers  Chiral carbon Chiral carbon *  Carbon with four different substituents *  Labeled as C *  Enantiomers (optical isomers)  Molecule with chiral carbon is non-superimposable with its mirror image, named enantiomers  Enantiomers could rotate plane-polarized light with same angle but different direction, and named optical isomers • Rotate clockwise, i.e. dextrorotatory, represent as (+) or d - • Rotate counterclockwise, i.e. levorotatory, represent as (-) or l - 11

Naming Stereocenters- The R , S System Priority rules:  Higher atomic number with higher priority (assign 1) 2 2 4 4 1 3 1 3 Counter- Clockwise clockwise Enantiomers of 2-butanol  S-  R- OH OH  * * C C  H H H 3 C   CH 3  CH 3 CH 2  CH 2 CH 3   25 25 [ ] +13.52 [ ] -13.52 D D 12 ( S )-( ＋ )-2-Butanol ( R )-( － )-2-Butanol IUPAC

Compare the Enantiomers 1. Assemble the molecules 2. Compare and take picture 3. Determine the R - or S - configurations 13

Notice  Construct the molecules and take pictures in the lab  Use link remover to take the constructed model apart to avoid breaking the links  After lab, check the contents of MOLYMOD set, hand-in and rechecked by GTA  Hand-in lab report with IUPAC systematic names, the chemical structures and pictures of modeling next week Hand-writing or draw by software 14

Flaw Chart II: Free Software for Chemical Structures (Reference)  Chemsketch http://www.youtube.com/watch?v=5kaU5iEqifQ  Draw chemical structure CH 2 H 3 C  Avogadro http://www.youtube.com/watch?v=ohdMhGaaP68  Show three-dimensional structure  Calculate bond-angle, bond-length, and bond energy 15