PART I: Conformational analysis of polyhalogenated propanes I-A: Steric strain in the conformations of polyhalogenated propane derivatives Build your polyhalogenated propane with your assigned X/Y substituents for the propane derivative. Make sure that you do not interchange X and Y substituents, as this will reduce your lab report grade by 2 points. H3C H X where X will be assigned as one of F, Cl. Br, or I; and Y will be one of H, F, Cl, Br, or I. Building your assigned molecule: 1. Molecules are built by adding atoms to the workspace. Begin by clicking on the "Build" icon at the top of the screen. The atoms C, H, O and N are displayed. To add other atoms click on "other" display the periodic table and select your atom of interest. See to File G Edit Tools View Build Adjust Clean-Up Symmetry Huckel Help below sym 800 Periodic Table H Symbol: C He Build Adjust Li Be Atomic Number: 6 B C N o F Ne C Να Mg Al Si P S Cl Ar HON K Ca Sc Ti V Cr Mn Fe Co Ni Cu Zn Ga Ge As Se Br Kr Rb Sr Y Zr Nb Mo Tc Ru Rh Pd Ag Cd In Sn Sb Te I Xe N Other... Cs Ba La Hf Ta W Re Os Ir Pt Au Hg Tl Pb Bi Po At Rn Fr Ra Ac Fragment... Ce Pr Nd Pm Sm Eu Gd Tb Dy Ho Er Tm Yb Lu Th Pa U Np Pu Am Cm Bk Cf Es Fm Md No Lr Cancel Build Mode - C (click = add atom; drag = add bond; click & drag = add atom & bond; letter = change atom) Lookup Molecule Import Molecule Export Molecule -Select Database--- Open... 2. Select a carbon atom and you can now display the carbon on the screen by left clicking once in the workspace. On the screen you should now have a sphere representing a carbon atom. You can add another carbon atom by clicking in the workspace again. To generate a bond between atoms simply left click on one atom and drag to the second atom. You should see a line between the two atoms. 3. To add a halogen atom (F, Cl, Br, I) to the carbon atom select the appropriate halogen from the periodic table located under the Build option. To attach the halogen atom at a particular bond site of the carbon, left click once in a region on the screen near that atom and then generate a bond by clicking the atom and dragging towards the carbon. Do not add hydrogen atoms yet. 4. Continue to add the remainder of the atoms (except hydrogen atoms) of your molecule in a similar manner - use the periodic table to select each element and then 'bond' it to the other atoms. When all of the non-H atoms have been added, construction of the assigned structure is complete. The hydrogens will be added automatically in the next step. Before proceeding, make sure that the structure of your molecule is correct, and that each halogen atom has been bonded to the correct carbon centre. Pay particular attention to the position of each halogen: confirm that the assigned halogen X has been added to the same C which is bonded to the methyl group, and that the assigned halogen Y has been added to the C which is bonded to one hydrogen atom. 5. The icons and are called "comprehensive cleanup" and are responsible for the automatic hydrogen addition to your structure. Any empty valences on the carbon atoms of your molecule will be filled with hydrogen atoms by using this button. It is important to remember that once finished building a structure and before sending the job for a calculation to always select these icons interchengebly. 6. You can rotate the molecule by selecting the selecting the icon and you can magnify the molecule by icon: examine its three dimensional appearance. Make certain that you have correctly built your assigned molecule. If necessary you can use the undo icon t to correct your structure. If you need to start from the beginning select “File” and from the drop-down menu select "New." The Figure illustrates a sample below molecule. 7. To delete an atom when necessary, activate key on the keybord. icon, then select the atom and use the delete File Edit Tools View Build Adjust Clean-Up Symmetry Huckel Help View Mode Rotate (drag = rotate XY; alt-drag = rotate Z) Lookup Molecule Import Molecule ---Select Database--- Export Molecule Open... WebMO window showing the backbone of Br2HC - CC12CH3. I-B: Exploring the initial molecular structure Before optimizing your molecule's geometry, examine the structure while the carbon atoms still have their perfectly tetrahedral bonding. To measure bond lengths and angles in your molecule select the adjust icon from the toolbar, then select the first atom of interest, then hold the shift-key and then select the remaining atoms which define the bond or angle. The atoms you selected will appear colored while the non-selected atoms will be grey. The value of the chosen property is displayed at the bottom left corner of the screen: File Edit Tools View Build Adjust Clean-Up Symmetry Huckel Help 125 SX Adjust Mode - Bond Length: 1.816 Å Lookup Molecule Import Molecule Export Molecule ---Select Database--- Open... A H3C1 དཾ -''' H3C H Χ Χ The four atoms numbered above define the H3C-C-C-H dihedral (or torsion) angle of your molecule. View your molecule down the C²-C³ bond. To do this, rotate the molecule until your perspective corresponds to the Newman projection shown above right. Note the 'gauche' arrangement of the selected H-atom and the C-atom of the methyl group: the measured H3C-C- C-H dihedral (torsion) angle is exactly 60°, as expected for interconnected, perfectly tetrahedral carbon atoms. 1. To measure bond angles or dihedral angles, select the Adjust icon, then click on the terminal hydrogen (hydrogen on the carbon 3), and then hold the shift-key and select carbon 2 and then select carbon 1. This is the sequence that defines the dihedral angle of interest. Measure the dihedral angle for your constructed molecule. The measured value appears at the bottom left corner of the screen. 2. To measure a different molecular property simply click anywhere on the workspace. I-C: Optimizing the 'gauche' conformation geometry by geometry optimization You will now optimize the geometry of your molecule. Since the four substituents on carbons 2 and 3 are not all of the same size, Webmo will slightly move the substituents on each carbon atom away from a perfectly tetrahedral arrangement until the geometry of lowest energy is found. 1. To change the dihedral angle to 60° select the adjust icon from the toolbar, then select the hydrogen atom by first clicking on it and then hold the shift-key down and select C3, C2 and then C1. In total you have selected four atoms. At the bottom left of the screen you should see the words “Dihedral Angle” with a corresponding value. File Edit Tools View Build Adjust Clean-Up Symmetry Huckel N 18 52 CC !! Adjust Mode Dihedral Angle: 59.015* Help H Lookup Molecule Import Molecule --Select Database--- Export Molecule Open... ☑ 2. Then select the dihedral angle icon and you should see an applet appear as illustrated in Enter the value 60, select “Apply” and then select “Ok.” The applet should disappear once you have changed the angle. Adjust Dihedral Angle 60 OK Apply Cancel 3. Select the ; and click several times on it to clean up your structure. 4. To prepare your job for a geometry optimization calculation select the lower right of the screen. icon on the 5. On the next Job Options” window, for calculation select “Geometry Optimization.” For Theory select PM7. 6. You should be brought back to Job Manager and wait until your calculation changes status from "Queued" to "Complete." New Job▾ Show all Refresh Number Name 8669 C3H4C12Br2 Download ▾ Move To ▾ Delete <Utilities ▾ Logout Show all Show all Show all Description Date Status Time Actions Geometry Optimization - Mopac 2012 6/4/2014 13:49 Queued (1/1) 0.0 sec 7. Atoms were moved around by small amounts during geometry optimization in order to minimize steric interactions between them. Hence the H3C-C-C-H torsion angle of your 'gauche' conformation will no longer be exactly 60° the H atom and methyl group C atom will now be either closer together, or farther apart, than in the pre-optimization structure.