You can select several types of representation: wireframe, ball-and-stick, and space-filling. The default view shown is the ball-and-stick view, in which atoms are represented by small spheres, and bonds represented by “sticks” of arbitrary width. This is the best view for most purposes. Under Surfaces , you can select Dot Surface to get an impression of the true size/shape of the molecule. Images are zoomable, either via mouse scroll wheel (or trackpad), or from the menu. You can measure molecular parameters such as bond lengths, bond angles, and dihedral (torsional, or twist) angles. A bond length is defined by two atoms, a bond angle by three atoms (the sequence ABC defines the angle between the AB and BC bonds, measured at B), and a dihedral angle by four atoms (the sequence ABCD defines the twist angle round the BC bond as the angle between the plane containing atoms ABC and the plane containing atoms BCD). Hold down the right mouse button to bring up the contextual menu, then choose Measurements followed by Click for X measurement . Distance, angle, and torsion are the three options. Then for example to measure a bond angle, click sequentially on the three atoms defining the bond (for example ABC to obtain the bond angle at B between bonds BA and BC). The default unit of bond length is nm, but you can select Å (Ångstrom) or pm. Remember that bond angles are typically greater than or equal to 90° - a smaller value usually means that you have selected atoms in the wrong order. If the image gets cluttered, you can choose Delete Measurements . The option Computation > Optimize structure allows some limited geometry optimization - we will have access to much better tools for this in Part B. Section I – VSEPR Sketch the molecules in each section, measure the bond angles, and compare them with the theoretical bond angles. a) Two regions of electron density
CHE151Lab9_ComputerModeling.doc Dr . Roderick M. Macrae CHE 151 b) Three regions of electron density (How do lone pair electrons explain the molecular geometry of SO 2 ? Note any differences between expected and measured bond angles.) c) Four regions of electron density (Compare the bond angles of CH 4 , NH 3 , and H 2 O. Do any of these molecules exhibit the ideal bond angles? Explain.) (This structure for H 2 O is actually quite poor. Try improving it with Optimize structure .) d) Five regions of electron density (How does lone pair repulsion explain the shapes of ClF 3 and SF 4 ?)
CHE151Lab9_ComputerModeling.doc Dr . Roderick M. Macrae CHE 151 e) Six regions of electron density (How does lone pair repulsion explain the shapes of XeF 4 and IF 5 ?) Section II – nitrosyl halides Sketch the four molecules shown and measure the nitrogen-halogen bond length in each. How do the results compare with the covalent radius/bond length data in your textbook?
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- Spring '14