Unformatted text preview: Molecular Modeling: Computer Aided Conformational Analysis The study of molecular conformations is used to better understand reactivity, interactions and properties of
molecules. Without modern computational power, conformational analysis of complex molecules would be too
time consuming to be useful. With current computational methods and a quality personal computer (though
having a supercomputer can’t hurt) large molecules including pharmaceuticals, proteins and polymers can be
analyzed. In order to perform computations on complex molecules, simple molecules are studied in great detail allowing
inferences to be made for larger molecules. READ THE ENTIRE HANDOUT. RECORD DATA IN YOUR LAB NOTEBOOK. Underlined words should be selected with mouse. “Words in quotes” should be typed. (Words in parentheses)
may or may not be needed. The mouse has THREE buttons: Left = select Holding Middle = rotate Holding Right = move
3) Draw methane.
Elle New (C|ick on Builder Window) ﬂ Return to Main &
“methanespa” Save As ( Oveiwrite ) b) Perform a geometry optimization. gem Calculations Task: Equilibrium Geometry Model: Molecular Mechanics M
gm M Job has been Submitted: Qﬂ Job has Completed: Q_i_< c) View different representations of methane.
me] Wig Mgd_e_l Ball and Wire Mel M
M Sgace Filling m Ball and Spoke You may view one or more representation for the other molecules in this exercise, also. Molecules can be rotated in three dimensions by holding the middle mouse button and moving the mouse, or in one dimension
by holding shift and the middle mouse button and moving the mouse. d) Record the C-H bond length. may W Select C and one H Record in Lab Notebook
e) Record the value of the H-C-H bond angle.
g Geometry Measure Angle Select H-C—H in order Record in Lab Notebook
An ideal tetrahedral bond angle is 109.5 °. However, bond angles vary with atom type and substitution.
3) Draw water.
Elle: Mg E112 Nﬂv (Click on Builder Window) file
Return to Main ﬂ “watenspa” Save As ( Oven/vrite)
b) Perform a geometry optimization.
Mg Calculations Task: E uilibrium Geomet Model: Molecular Mechanics §a_v_e
Mg M Job has been Submitted: gig Job has Completed: 95'
c) Record the 0-H bond length.
Geometgr Measure Distance Select 0 and one H Record in Lab Notebook Oxygen is more electronegative than carbon resulting in shorter bonds to hydrogen ...
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- Summer '08