Introductory WebMO Exercises

Transcription

1 Introductory WebMO Exercises These directions assume no prior knowledge of e WebMO interface and provide detailed, click by click instructions on building molecules and setting up calculations. Use your provided login credentials to login to WebMO Exercise 1 - Study of H-X-H Bond Angles Structure of CH 4 Click New Job, en Open Editor. A small window opens where you build molecules. Click on e Periodic Table icon (5 down e left side). Choose C by clicking on it. Click once in e center of e workspace. A gray carbon atom appears. Choose Clean-Up > Comprehensive Mechanics. You should now have meane. Experiment wi e Rotate, Translate, and Zoom tools (Top 3 icons on left side). Click Close Editor in e main WebMO window. Meane now appears in e Build Molecule window. This structure contains idealized bond lengs and angles. A more accurate structure can be found by carrying out an energy minimization using molecular mechanics, semiempirical meods, or ab initio calculations. To reduce e time required for e calculations and to obtain reasonable results, e semi-empirical meod PM3 will be used. This meod is available in most molecular modeling programs. Click e blue continue arrow in e lower right side of e Build Molecule window. Choose Mopac as e computational engine. Choose first available in e select server pull-down menu. Click e blue continue arrow. Type in/choose e following: Job Name: CH4PM3 Calculation: Geometry Optimization Theory: PM3 Charge: 0 Multiplicity: Singlet Click on e blue continue arrow. You should now see your job listed. To kill or stop a job, you would click on e red X under Actions on e right side. Click Refresh (every ~10 seconds) until you see at your job is Complete (under Status). Click on e hyperlinked name (CH4PM3) to open e View Job window. Choose e Select arrow (4 icon down on left). Click on one of e H atoms in e structure (e oer atoms and bonds will fade ). Shift and Click e C atom (bo atoms are now highlighted). The bond leng is displayed just below e molecule. Record e value of e C-H bond leng Å (1.091 Å literature). Check e oer C-H bond lengs. Click on one of e H atoms, en Shift and click e C atom, followed by anoer H atom. The bond angle is displayed just below e molecule. Record e value of e H-C-H bond angle ( literature). Check e oer H-C-H bond angles. Scroll down and review e information under Calculated Quantities. When finished, click e Job Manager link under Actions (to e left of e molecule display). To delete files, click e box to e left of e desired file and choose Delete on e menu. To continue on to e next exercise, choose New Job > Create New Job.

2 Structure of NH 3 Build NH 3 using e above procedure. Use Job Name H3NPM3, and perform e geometry optimization as before (PM3). Record e value of e N-H bond leng Å (~0.999 Å, Å literature). Record e value of e H-N-H bond angle (~107.8, literature). Scroll down and review e information under Calculated Quantities. Return to Job manager, and choose New Job > Create New Job. Structure of H2O Build H2O using e above procedure. Use Job Name H2OPM3, and perform e geometry optimization as before (PM3). Perform e PM3 geometry optimization as above. Record e value of e O-H bond leng Å (~0.951 Å, Å literature). Record e value of e H-O-H bond angle (~107.7, literature). Return to Job Manager. What conclusion(s) can you make concerning e H-X-H bond angle and e number of unshared (lone) pairs of electrons around e central atom X? What conclusions can you make concerning e size of e central atom X and e X-H bond leng? Exercise 2 - Study of e Molecular Orbitals in Eene, CH2CH2 Click New Job, en Open Editor. Click on e Periodic Table icon (5 down e left side). Choose C by clicking on it. Click once in e workspace. A gray carbon atom appears. Click on is atom and drag to one side and release. You should now have C-C. Click and Drag from e center of one C atom to e center of e oer C atom to form e double bond. Choose Clean-Up > Comprehensive Mechanics. You should now have eene. Click Close Editor in e main WebMO window. Click e blue continue arrow in e lower right side of e Build Molecule window. Choose Mopac as e computational engine. Choose First available in e select server pull-down menu. Click on e blue continue arrow. Use Job Name C2H4PM3, and perform e geometry optimization as before (PM3). Once e job is complete, click on e hyperlinked name (C2H4PM3) to open e View Job window. Click e New Job Using This Geometry button, click e blue continue arrow, choose Mopac. and First available, and type in/choose e following: Job Name: C2H4PM3Orb Calculation: Molecular orbitals Theory: PM3 Charge: 0 Multiplicity: Singlet Click on e blue continue arrow. You should now see your job listed. Once e job is complete, click on e hyperlinked name (CH4PM3Orb) to open e View Job window. Scroll down to e Molecular Orbitals table. Using e energy values as your judge, identify

3 e HOMO and LUMO. View ese orbitals by click on e magnifying glass icon. The orbitals can be rotated by clicking and dragging in e viewer window. Were your choices correct? View some of e oer orbitals. Note at all orbitals viewed appear as a tab in e MOViewer. Clicking on e tab brings at orbital back into e window. Close e viewer window and return to Job Manager. Exercise 3 - Study of Rotation Barrier Energy about Carbon-Carbon Bonds Build C2H 6 using e above procedure. Be sure to do e Clean-Up as before. Choose Tools > Z-matrix to open e Z-matrix Editor window. In is window, each atom is numbered. The corresponding number appears on e molecule sketch in e WebMO Editor window. Identify e two H atoms at form a dihedral angle (H-C-C-H) of ~180 (or -180 ). It may help to rotate e molecule. In e pull-down menu to e right of is listed dihedral angle, choose S (See below for H7 and H3): As shown above, enter e Start (-180) and Stop (180) scan values, along wi 72 steps, en click OK to close e Z-Matrix Editor window. Click Close Editor, en click e blue continue arrow. Choose Mopac. Use e following Job Options: Job Name: C2H6PM3Angle Calculation: Coordinate Scan Theory: PM3 Charge: 0 Multiplicity: Singlet Click e blue continue arrow. You should see e job in e queue. When e job is complete, click on e linked name. Scroll down to e Coordinate Scan table and click on e magnifying glass on e table title bar. A Coordinate Scan window opens showing e plot of Energy vs. dihedral angle. Choose Options > Axes and in e Options window change e x-axis settings to Start (-180), Stop (180), and Interval (60). Click OK. Does e graph make sense? Describe e relationship between e dihedral angle and energy you observe. View a movie of e dihedral angle rotation by scrolling to e Geometry Sequence box. Choose Loop in e pull down menu, en click e film in e upper right corner of e box. You can use e controls to e left of e molecule to control ings.

4 Exercise 4 - Study of C-C Bond Lengs at e Semi-empirical Level of Theory In is experiment we will investigate e trend of e C-C bond leng in simple organic compounds containing single, double, and triple bonds at e PM3 Semi-empirical Level of Theory. Literature values: Compound Name r e/(å) H3C - CH3 Eane H2C = CH2 Eene (Eylene) HC CH Eyne (Acetylene) C6H6 Benzene Better results can be obtained by using higher levels of eory wi larger basis. Eane H3C-CH3 Construction of H3C-CH3 Click New Job. After e tool bar appears at e left of e Build Molecule window, click Open Editor. The WEBMO Editor window opens. Click e Build icon (4 down). Click in e workspace to place a C atom. Click and drag from e C to form C-C wi a single bond. st Click e Rotate icon (1 down) to be sure at e staggered structure is formed. If necessary, click Clean-Up / Comprehensive-Mechanics again. Click e Close Editor button in e Build Molecule window. Optimize H3C-CH3 Click e right blue arrow (Continue). Choose Mopac as e desired Computational Engine and default Server Name. Click e right blue arrow (Continue). Click Job Options and choose: C2H6xxx where x = your initials (for identification) for Job Name. Geometry Optimization for Calculation. PM3 for Theory. Basic: 3-21G or default if asked for a Basis Set. Leave Charge as 0 and Multiplicity as Singlet. You may click e oer tabs for advanced properties and to preview e input file. Click e right blue arrow (Continue). Your file will appear on e WEBMO Job Manager screen as eier qued, running, or finished. After a short period of time, click Refresh until e job is complete. Measure Properties of H3C-CH3 Click e View Job icon for your job (magnifying glass). The View Job output screen will list various Calculate Quantities and e optimized model. Click e Select icon (4 down).

5 Click on one of e C atoms and Shift/Click on e oer C atom. Record e C-C bond leng Å and compare to e literature value. Click Job Manager. Eene H2C=CH2 Construction of H2C=CH2 Click New Job and Open Editor. Click e Build icon (4 down). Click in e workspace to place a C atom. Click and drag from e C to form C-C wi a single bond. Repeat e click/drag operation to form C=C wi a double bond. Click e Close Editor button in e Build Molecule window. Optimize H2C=CH2 Optimize by clicking e right blue arrow (Continue), choosing Mopac as e desired Computational Engine, clicking e right blue arrow (Continue) and choosing C2H4xxx where x = your initials (for identification) for Job Name, Geometry Optimization for Calculation, PM3 for Theory, Basic: 3-21G or default if asked for a Basis Set, and leaving Charge as 0 and Multiplicity as Singlet. Click e right blue arrow (Continue). Measure Properties of H2C=CH2 Click e View Job icon for your job. Click e Select icon (4 down) and measure and record e C=C bond leng Å and compare to e literature value. Click Job Manager. Eyne HC CH Construction of HC CH Click New Job and Open Editor. Click e Build icon (4 down). Click in e workspace to place a C atom. Click and drag from e C to form C-C wi a single bond. Repeat e click/drag operation two more times to form C C wi a triple bond. Click e Close Editor button in e Build Molecule window. Optimize HC CH Optimize by clicking e right blue arrow (Continue), choosing Mopac as e desired Computational Engine, clicking e right blue arrow (Continue) and choosing C2H2xxx where x = your initials (for identification) for Job Name, Geometry

6 Optimization for Calculation, PM3 for Theory, Basic: 3-21G or default if asked for a Basis Set, and leaving Charge as 0 and Multiplicity as Singlet. Click e right blue arrow (Continue). Note at linear molecules are difficult for some lower level eories to handle and is calculation may fail. Measure Properties of HC CH Click e View Job icon for your job. Click e Select icon (4 down) and measure and record e C C bond leng Å and compare to e literature value. Click Job Manager. Benzene C6H6 Construction of C6H6 Click New Job and Open Editor. Click e Build icon (4 down). Click in e workspace to place a C atom. Click and drag from e C to form C-C wi a single bond. Repeat e click/drag operation until you have generated a hexagon of singlebonded C atoms. The last operation is made by dragging onto e first C atom. Construct ree double bonds by click/drag between alternate sets of C atoms. Click e Close Editor button in e Build Molecule window. Optimize C6H6 Optimize by clicking e right blue arrow (Continue), choosing Mopac as e desired Computational Engine, clicking e right blue arrow (Continue) and choosing C6H6xxx where x = your initials (for identification) for Job Name, Geometry Optimization for Calculation, PM3 for Theory, Basic: 3-21G or default if asked for a Basis Set, and leaving Charge as 0 and Multiplicity as Singlet. Click e right blue arrow (Continue). Measure Properties of C6H6 Click e View Job icon for your job. Click e Select icon (4 down) and measure and record e C-C and C=C bond lengs and Å and compare to e literature value. Why does is representation for benzene better represent e bonding between e C atoms an e representation at uses alternating single and double bonds?