BOND LENGTH WITH HYPERCHEM LITE
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1 BOND LENGTH WITH HYPERCHEM LITE LAB MOD2.COMP From Gannon University SIM INTRODUCTION The electron cloud surrounding the nucleus of the atom determines the size of the atom. Since this distance is somewhat fuzzy, the atomic radius of an atom is used to measure the size of the atom. Bond length is the distance between two bonded atoms or the sum of the radii of the two bonded atoms. Bond lengths are usually measured in angstroms, Å (1 Å = m). or picometers, pm (1pm = m). HyperChem Lite is a molecular modeling and simulation program that uses a computer and CD-ROM based software to predict physical and chemical properties of molecules. This software allows covalent bonds to be considered as if they were springs connecting atoms. PURPOSE The purpose of this experiment is to learn to measure bond length and to examine the impact of multiple bonds on bond length. EQUIPMENT/MATERIALS Laptop computer with HyperChem Lite installed Wireless Printer and Paper HyperChem Lite CD SAFETY Keep goggles on hand for use when dealing with glass, chemicals and/or fire. MOD2.COMP-1
2 PROCEDURE The HyperChem Lite Window 1. To start HyperChem Lite, put cursor in the HyperChem Lite Icon, then double click on left mouse. The HyperChem Lite window will open the following list of features: a. Menu Bar: contains the different HyperChem Lite menus which include: File, Edit, Build, Display, Set-up, Compute, Cancel and Help. b. Tool Bar: the left side of the screen contains the tools to draw, select, display and move atoms and molecules. c. Workspace: displays current atoms or molecules. d. Status Line: show a brief description of menu item selected and information about drawing. e. Title Bar: shows name of file working on. f. Control Menu Button: contains commands to move, resize, maximize, and close HyperChem Lite windows. It also contains the switch command, which lets you activate other windows. Measuring Bond Length Carbon-Nitrogen Bonds Target molecules: HCN, CH 2 NH and CH 3 NH 2 To build HCN, CH 2 NH and CH 3 NH 2, follow these steps: 1. Left-double click on the draw icon ( ). The element table dialog box will appear. Left-double click on carbon (C) in the periodic table. 2. Left click in the workspace. A carbon atom will appear in the workspace. 3. Left-double click on the draw icon. The element table dialog box will appear. Left-double click on nitrogen (N) in the periodic table. 4. Left click in the workspace. A nitrogen atom will appear in the workspace. 5. Left click on carbon and drag cursor to N once to draw a single bond, twice for a double bond and three times for a triple bond, depending on structure being built. 6. Left click on Build. Left click on Add Hydrogens. A complete molecule will appear. Left click on Display. Left click on Renderings. Select balls and cylinders, shaded and highlighted. Left click OK. 7. Under Setup, Left click on molecular mechanics 8. Select Compute. Left click on Geometry Optimization. Select Polak-Ribiere. Left click OK. The molecule model is now complete and geometrically correct. MOD2.COMP-2
3 9. To measure the bond length. Left click on Selection Tool. Left click on carbon and drag cursor to nitrogen. The bond length will appear on the lower left below the workspace. 10. Record bond length for the C-N bond, in Angstroms, on the Data Sheet. 11. Clear the molecule by left clicking in an open area of the workspace. All the atoms will turn green. Select Edit and left click on clear. Select yes to remove the previous molecule. 12. Repeat steps 1-9 to build other C-N molecules. Record bond length. Clear molecule. Oxygen-Oxygen Bonds Target molecules: H 2 O 2, O 2 and O 3 To build H 2 O 2, O 2 and O 3, follow these steps: 1. Left-double click on the draw icon ( ). The element table dialog box will appear. Left-double click on oxygen (O) in the periodic table. 2. Left click two times in the workspace. Two oxygen atoms will appear in the workspace. 3. Click and drag to form a single bond between the two oxygen atoms. 4. Left click Build. Left click on Add Hydrogens. A complete molecule will appear. 5. Left click on Display. Left click on Renderings. Select balls and cylinders, shaded and highlighted. Left click OK. 6. Under Setup, left click on molecular mechanics. 7. Select Compute, left click on Geometry Optimization. Select Polak-Ribiere. Left click OK. H 2 O 2 molecule model is now complete and geometrically correct. 8. To measure the bond length. Left click on Selection Tool. Left click on one oxygen and drag cursor to the other oxygen. The bond length will appear on the lower left below the workspace. 9. Record bond length for the O-O bond, in Angstroms, on the Data Sheet. 10. Clear the molecule by left clicking in an open area of the workspace. All the atoms will turn green. Select Edit and left click on clear. Select yes to remove the previous molecule. MOD2.COMP-3
4 11. Repeat steps 1-3 for the next target molecule, drawing in double or triple bonds. Omit step 4 since the molecule does not contain hydrogen. 12. Continue with steps 5-10 above. Carbon-Oxygen Bonds Target molecules: HCOOH, CO, and CO 2 To build HCOOH, CO, and CO 2, follow these steps: 1. Left-double click on the drawing icon ( ). The element table dialog box will appear. Left-double click on oxygen (O) in the periodic table. Left click twice in the workspace. Two oxygen atoms will appear in the workspace. 2. Left-double click on the draw icon ( ). The element table dialog box will appear. Left-double click on carbon (C) in the periodic table. 3. Left click in the workspace. A carbon atom will appear in the workspace. 4. Left click on carbon and drag cursor to one oxygen to draw a single bond, Left click and drag cursor to other oxygen twice for a double bond. 5. Left click Build. Left click on Add Hydrogens. A complete molecule will appear. 6. Left click on Display. Left click on Renderings. Select balls and cylinders, shaded and highlighted. Left click OK. 7. Under Setup, left click on molecular mechanics. 8. Select Compute, left click on Geometry Optimization. Select Polak-Ribiere. Left click OK. HCOOH molecule model is now complete and geometrically correct. 9. Measure the bond length. Left click on Selection Tool. Left click on carbon and drag cursor to oxygen. The bond length will appear on the lower left below the workspace. 10. Record bond length and clear molecule. 11. Repeat steps 1-10 to build CO and CO 2, omitting step 5 and adjusting the number of oxygen atoms as needed. MOD2.COMP-4
5 Carbon-Carbon Bonds Target molecules: C 2 H 6, C 2,H 4, and C 2 H 2 To build C 2 H 6, C 2 H 4, and C 2 H 2, follow these steps: 1. Left-double click on the draw icon ( ). The element table dialog box will appear. Left-double click on Carbon (C) in the periodic table. L-click in the workspace twice. Two carbon atoms will appear. 2. Left click on one carbon and drag to next once to build a single bond, twice for a double bond and three times for a triple bond. 3. Left click Build. Left click on Add Hydrogens. A complete molecule will appear. 4. Select Compute, Left click on Geometry Optimization. Select Polak-Ribiere. Left click OK. C 2 H 6 molecule model is now complete and geometrically correct. 5. Left click on Display. Left click on Renderings. Select Balls and cylinders, Option, shade and highlighted. Left click OK. 6. To measure the bond length. Left click on Selection Tool. Left click on one carbon and drag cursor to the other carbon. The bond length will appear on the lower left below the workspace. 7. Record bond length for the C-C bond, in Angstroms, on the Data Sheet. 8. Clear the molecule by left clicking in an open area of the workspace. All the atoms will turn green. Select Edit and left click on clear. Select yes to remove the previous molecule. MOD2.COMP-5
6 DATA SHEET Name Name Period Class Date BOND LENGTH WITH HYPERCHEM LITE DATA A. Bond distance for Carbon-Nitrogen bonds: HCN CH 2 NH CH 3 NH 2 B. Bond distance for group Oxygen-Oxygen bonds: H 2 O 2 O 2 O 3 C. Bond distance for Carbon-Oxygen bonds: CO CO 2 HCOOH D. Bond distance for Carbon-Carbon bonds: C 2 H 6 C 2 H 4 C 2 H 2 MOD2.COMP-6
7 EXTENSION: POLARITY AND MOLECULAR SHAPE Underlined molecules can be found already built in the HyperChem Lite sample file. To access file left click on File, left click Open, left-double click Samples, left-double click Vsepr. Structure is already built and geometrically optimized. To Measure bond Angle: 1. Left click on Selection Tool. 2. Left click on one atom and drag cursor to other atom. The bond angle will appear on the lower left below the workspace. FORMULA BOND ANGLE SHAPE POLAR (YES/NO) BeCl 2 BF 3 SO 2 CH 4 NH 3 SCl 2 PF 5 Second angle for PF 5 SF 4 ICl 3 I 3 SF 6 IF 5 XeF 4 MOD2.COMP-7
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