CHEM 542 10/12/01 INSTRUCTIONS FOR AB-INITIO CALCULATIONS Prepared by: Dr. Cynthia HARWOOD, Ahu AKIN, Prof. Tim KEIDERLING SETTLING IN: - Type your login name : Chem542 and press Enter - Type your password and press Enter - On the upper left corner of the screen you will see a vertical menu bar, Toolchest. With the left mouse button: Click on Desktop. Another menu will open. Click on Open Unix Shell (in this new menu) NOTE: The LogOut button under Open Unix Shell is used to log out of the system when you are finished. - A window will open on the screen. Type ls. This will list the directories and files in CHEM542 account. - Find the directory named after your lastname. At the prompt type cd followed by a space and then your lastname. You changed directory and are in your own directory now. - At the prompt, type cerius2 and press Enter. - Now, three windows will open: Cerius2 Models window: you will draw your structures on this window Cerius2 Visualizer Module, with a horizontal main menu bar (MMB) that lists File Edit Build, etc. Winterm, a terminal window that will update you on the progress of every process you invoke from Cerius 2. Important Note: In order to log out of Cerius 2 and the workstations please refer to the instructions on page 9. GETTING READY: - Examine the Visualizer module. The right half of the module contains names of utility menus decked vertically, with the heading printed on a yellow button at the very top. By default, Cerius2 opens BUILDERS1 deck with different options on different menus. - Click on BUILDERS1 (the yellow button) and drag the mouse down to Quantum1. This will open QUANTUM1 deck. - Select GAUSSIAN menu by clicking on it. 1
BUILDING MOLECULES: - On the Visualizer main menu, click on Build. - Select the 3D-Sketcher. - Right now your mouse cursor is in Select mode. To sketch your molecule, click on the green button to the left of Sketch with. The color of the button will turn blue and a scale in Angstroms will appear on your model window. - Examine the right side of the Sketch with statement: you will see a yellow button (with a bar) that is a pull down menu and a button with the periodic table symbol next to it. You will use this to pick the atom type. For H 2 : - Click on the yellow bar. Select H. You will see H in the blue box. - Move the mouse cursor into the model window. It will become /\. Click on the window. You have your first H which looks like a +! - Move cursor to the right, click once again. This is your second H bonded to the first. - Now move the cursor out of the model window. This will help you get rid of the green dashed line that keeps following your cursor! - At the very bottom of your Sketcher module observe a blue button with CLEAN written on it. Click and hold the mouse button until you don t see a movement in the model window. - To make your molecule look prettier you may want to change its display format. Close your Sketcher module by double clicking on the left topmost bar in brown. Click on the yellow button under and between File and Edit options on Visualizer MMB. It is in STICK mode by default. Change it to other modes and choose what you like best. - To translate, rotate and resize your molecule use the following mouse actions: Translate: click on the middle mouse button and drag the mouse in any direction you prefer Rotate: click on the right mouse button and drag left or right Resize: click on both the right and the middle mouse buttons and drag in any direction - To measure bond lengths and angles : Choose STICK format. Click on Geometry on the Visualizer menu bar. Click on Measurements. In the new window, click on the green button of interest (Distance, Angle, Torsion, etc.) 2
Use Guide? button to learn how to make the measurements you are interested in. Practice on the molecules you draw and that you optimize. Cerius 2 has on-line help available for all buttons/commands. To use this help just place the mouse over the button or option that you want to know more about and click with the right mouse button. SETTING UP AB-INITIO CALCULATIONS THROUGH CERIUS 2 : H 2 : Geometry optimization - Draw your H 2 molecule. - On GAUSSIAN menu click on Geometry and then on Z-Matrix. o Click on COMPLETE Z-Matrix lines. This will translate your input geometry (i.e. your drawing) into the format that Gaussian program can understand. o Close the Z-Matrix Editor window. - On GAUSSIAN menu click on Run. A module named Run Gaussian will open: Select the version of Gaussian program to run by clicking on the default GAUSSIAN92 and selecting GAUSSIAN94 from the pull down menu. Select your Task for H 2 : Click on the yellow button to the left of Task which highlights Single Point Energy by default. Drag the mouse to Geometry Opt. and release the mouse button. Select your Method as HF. Select your Basis Set to be 3-21G. Change your File Prefix (2 nd line) to a name you prefer. This will be the name of all files that are used or generated by the Gaussian program for this job (you may choose anything, I like to use initials and molecule identity and the trial # e.g. takh2_1). Click on the Output Options at the bottom left corner of the Run Gaussian module (which you are currently on). A window will open, giving you choices of what to output, mainly the information you would like to get out of your calculations apart from the default output. Click on Output Atomic Distance Matrix and Punch Molecular Orbitals buttons. Close Gaussian Output Options window. Go back to the GAUSSIAN menu. Select Job Control. You need to select a host workstation to run your job on. Click on the blue button to the left of Hosts. Select either Marvin or Zaphod. Close Job control window. 3
Open or go to Run Gaussian window and click on Run button. o Your job will be running interactively. A small window will appear with blinking diamonds in it. This window is on when calculation is in progress and it disappears when the calculation is done. All you need to do is relax and wait at this point! You could read ahead or bring a book. o A window named filename.log will appear as soon as the calculation starts running. This is the file you need to extract geometries and MO information from. Later you will print this file. o When the job is finished the little diamond window will disappear and your molecule s geometry will be updated to the calculated and optimized geometry. It may now be interesting to measure the bond length between the two hydrogens and compare it with the initial and the experimental value you may look up in a reference. o Close the filename.log window. - It s orbital time! Close the Run Gaussian window and go to the GAUSSIAN menu. - Click on Analyze. Select Orbitals. A window named Gaussian Orbitals will pop up. By default HOMO is selected. Observe the orbital energy on the right (in Hartrees). Select HIGH Resolution. Click on the blue (dot in square) button next to Calculate. This will start your orbital calculation. Note: If you didn t choose Punch Molecular Orbitals in the Output Options of your job, this calculation will not work. In this case, you must run the H 2 Gaussian calculation again. When the job is done, you will see a blue egg on your model window. Believe it or not, this is your HOMO. - On GAUSSIAN menu, click on Analyze and select Surfaces. Change Transparency (%) to 50.0 from 0.0. Now you will be able to see your H 2 in the egg because your MO surface is 50% more transparent. Increase the isosurface value to 0.5. Click on Create New Surface blue dot button. Try other isosurface values to learn impact of this parameter. - Go to Analyze on GAUSSIAN menu and select Slices. Click on Create New Slice blue dot button. Observe your model window.your H 2 molecule will be sliced through the bond by a plane. 4
Click on Create Slice Plot in Graph Window blue dot button. A new window called the graph window will open which will show a contour plot of the wavefunction in real space. The wavefunction for HOMO will be most positive between two hydrogen nuclei and will become less positive as it extends further away from the nuclei in either direction on the slicing plane. Make sure you understand the contours and their color variation, especially where they change sign (important for higher orbitals). You can experiment with different isosurface values and the rest of the orbitals (LUMO, 3, and 4) from this point on. Be ready to describe them in terms of extent, sign pattern, symmetry, energy and component atomic orbitals. - To print out your orbitals and contour plots : On Visualizer MMB go to File then Print Click on Model Window button for orbitals and Graph Window button for contour plots. You may wish to change the background to grey and orbital colors to blue (-) and red (+). Go to Page Setup and make the following changes: Click on Include Cerius 2 logo thereby uncheck this option. Type your user name and a title text descriptive of what you are printing. Close this window. Click on Print. - To print out your log file:[warning this is quite long, editted version may be more useful] Open a new unix shell from Toolchest At the prompt, type ls to list all the files you created. Pay attention to the files with.log extension. Type: enscript 2jr filename.log For example, if you named your H 2 calculation files as H2 then type enscript 2jr H2.log To access your editted log file: (see instructor) H 2 bond length effect on MO s: - Go back to GAUSSIAN Geometry Z-Matrix. - Click on line #2 in the Z-Matrix Editor window. - Below the window, under Bond/X type the new stretched H 2 bond length, e.g. 2 Angstroms. - Close the window. 5
- Go to GAUSSIAN Run Task and choose Single Point Energy. - Change your file prefix to a new name! Otherwise the new calculation will overwrite the existing files and you will lose your optimization log file and orbitals that you still may want to print and compare to these results. - Run your job and analyze MO s energies, shapes and slice contours, contrast to optimized H 2. NOTE: The other parameters, output options, basis set, etc. are preserved from your first calculation. - To delete slices and surfaces in Cerius2 Models window open each under GAUSSIAN Analyze and click the blue dot button by Delete. CO: Geometry optimization, frequency, MO s, potential energy scan - Draw your CO molecule o Select the BALL & STICK format. o Draw a C-C and replace one of the carbons by an oxygen atom: Open a new model window by clicking on the + on the menu bar underneath the big Cerius 2 logo Open the 3D-Sketcher module Sketch a C-C. Go back to Select mode by clicking on the green button with an arrow on it, located at the top left corner of Sketcher module. Click on the green button to the left of Edit Element. Select O from the pull down menu on the right of this statement. On the model window, click on one of the carbon atoms. It will become smaller and turn red from gray. Click on the yellow button to the right of Edit Bond and select TRIPLE [To see that this happened you may need STICK format_ just select it, no need to restart]. Move your cursor into the model window. The cursor looks like an arrow. Click on the carbon then oxygen. Your single bond will turn into a triple bond. NOTE: It is not absolutely necessary for you to represent the bonds correctly for Gaussian to understand your molecule. It will however help the clean function give you a more realistic C-O bond length. Go back to Select mode. Clean your structure. - Flip back few pages, set up a similar calculation to the H 2 case but choose geometry optimization & freq. and run it. - Scroll through the log file to determine the vibrational frequency for CO. Determine how it will change for 13 C 16 O and 12 C 18 O. 6
- Calculate MO s and prepare the contour plots. - Note that in H 2 the first two orbitals, lowest two energies, were the HOMO and LUMO. In CO there are several orbitals lower than the HOMO. Analyze the variation in energy, orbital makeup, symmetry and size to answer the Lab homework questions. - Analyze vibrations: Analyze vib animate CO Potential Energy Surface: - Go to GAUSSIAN Geometry Constraints. Examine this z-matrix and compare it with the Z-Matrix Editor s version. You will see one symbol: r2. r stands for internuclear distances. This is the Name for the bond distance Variable for CO. - Go back to GAUSSIAN Run Task and select Scan Potential Surface. - Click on More button to the right of the Task statement: Type the variable name of your bond length into Variable Name box Type 0.5 into the Start box Type 1.0 into the Stop box Type 10 into the Steps box Now you can exit this window. You have setup a one-dimensional scan, for larger molecules you can setup two-dimensional scans by varying a second variable in your z-matrix. - Go to GAUSSIAN Run. - Run! - Print out and examine your log file. The bond length vs. potential energy data may be found at the very end. - After this job has completed, go to GAUSSIAN Run and click on More button next to Task which is Scan Potential Energy. - Implement the following changes : Type 1.0 into the Start box Type 3.0 into the Stop box Type 10 into the Steps box Change the file prefix. - Run this job and examine the output. - Take all bond distance vs. HF Energy values and plot them. C 2 H 4 : torsion angle analysis STEP A: Geometry optimization, frequencies, orbitals, energies - Build your C 2 H 4 o Open a new model window. o Select the STICK format. o Draw a C-C. 7
o Change the single bond to a double bond. On the Sketcher Module: Click on the green button to the left of Edit Bond statement o Click on the yellow button to the right of Edit Bond and select DOUBLE. o Move your cursor into the model window. The cursor looks like an arrow. o Click on one carbon then the next. Your single bond will turn into a double bond. o Go back to Select mode (button at top of Sketcher with diagonal arrow). o To add the 4 H atoms, click on the blue H ADJUST button on the Sketcher Module. o CLEAN your structure. - Run a geometry optimization & freq. Job with options (Punch MO s,output atomic distances, etc) set equivalent to the previous jobs. - Carry out routine geometry, frequency, and MO analysis, prepare contour plots, have fun! STEP B: Torsion angle vs. potential energy plot - You will use the optimized C 2 H 4 geometry for this second job step, which is on your current model window. - Choose STICK format and label your atoms. - Go to GAUSSIAN Geometry Z-Matrix. Examine the Z-Matrix Editor. A typical Z-Matrix line for C 2 H 4 looks like this: H4 1.074 121.90 180.0 C1 C2 H3 H4: the atom we consider as reference 1.074: bond distance between H4 and C1 in Angstroms_ H4 is directly bonded to C1 121.90: angle between H4-C1-C2 _ H4 is directly bonded to C1 which is directly bonded to C2. 180.0: torsion angle between H4-C1-C2-H3_ H3 may or may not be directly bonded to C2. - Go to GAUSSIAN Geometry Constraints. Examine this z-matrix and compare it with the Z-Matrix Editor s version. You will see symbols like r1, a4, t6, etc. r stands for internuclear distances, a stands for angles, and t stands for torsion angles. These are the Name s for each Variable. - Examine the connectivities and match each torsion angle with its variable name. - Select a H-C-C-H torsion angle and it variable name. You will vary this angle in steps of 20 degrees for a total of 180 degrees (9 steps) and examine the potential energy surface. - Go back to GAUSSIAN Run Task and select Scan Potential Surface. - Click on More button to the right of the Task statement: Type the variable name of your torsion angle into Variable Name box Type 0.00 into the Start box Type 180.00 into the Stop box Type 9 into the Steps box 8
- Click on Ignore Symmetry Changes box. - Go to your Output Options menu in Run Gaussian window. Deselect Punch Molecular Orbitals. - Change the file prefix for this job. - Run! - Print out and examine your log file. The torsion variable vs. potential energy data may be found at the very end. ENDING YOUR SESSION YOU MUST DO THESE EACH TIME BEFORE LOGGING OUT! - CLEANUP your window so that you end up with the three windows you started with. - Go to File on Visualizer MMB and click on Exit. This should be the first and only way you exit Cerius 2 interface. - Click on Exit once again on the pop-up blue window that confirms the exit process. Your model and Visualizer windows will disappear and you will have a unix shell left. You may close it as well. - Go to Toolchest_LogOut and click. Wait. - A small confirmation window will pop up. Say YES and wait until you are really logged out of the system. 9