“WebMO is a simple, Web browser-based interface for using popular chemistry software packages, such as Mopac and Gaussian. You draw the molecule’s structure, and the output – including the molecule’s transition states and infrared and nuclear magnetic resonance spectra – appears in an easy-to-understand format.” Science, August 10, 2001 “WebMO is a Web-based interface to computational programs such as Gaussian, Gamess, and Mopac.
WebMO User’s Guide William F. Polik and Jordan R. Schmidt WebMO LLC 1281 Heather Drive Holland, MI 49423 USA www.webmo.
The information contained in this publication is believed to be accurate and reliable. However, no representation of warranty is made with respect to this document or the software described herein. No warranty of merchantability or fitness for any purpose is claimed by this document or software. Information described in this document is subject to change without notice and does not represent any future commitment.
Table of Contents 1. WebMO Introduction .......................................................................... 1 A. Overview......................................................................................... 1 B. Capabilities ..................................................................................... 1 C. Quickstart Tutorial...........................................................................
Table of Contents UV-Vis Spectrum Coordinate Scan (Pro) IRC Calculation Saddle Calculation Molecular Orbitals (Pro) NMR High Accuracy Methods Other C. D. E. F. Gamess ........................................................................................ 30 Gaussian....................................................................................... 32 Mopac ........................................................................................... 34 Failed Calculations................................
Table of Contents D. E. F. G. H. I. J. System Manager........................................................................... 62 Version Manager........................................................................... 63 Fragment Manager ....................................................................... 64 Remote Server Manager (Pro)...................................................... 64 Interface Manager.........................................................................
Table of Contents G. Partial Charge ............................................................................... 80 23. Partial Charge Analysis of Electrophilic Aromatic Substitution Reactions 24. Carbocation Intermediate Analysis of Electrophilic Aromatic Substitution Reactions H. Potential Energy Surface Scans ................................................... 82 25. Rigid Potential Energy Scan of CH Bond Dissociation (Pro) 26. Relaxed Potential Energy Scans of NH3 and H2O Inversion (Pro) I.
1. WebMO Introduction A. Overview WebMO is a web-based interface for computational chemistry programs. WebMO makes it possible to set up, run, and visualize state-of-the-art chemical calculations from any computer using only a web browser.
1. WebMO Introduction • • • • • • • • • • Saddle calculation Vibrational frequencies, spectra, and motions UV-VIS frequencies and spectra NMR frequencies and spectra Thermochemistry Molecular orbitals and electron density isosurfaces Electrostatic potentials Nucleophilic and electrophilic frontier orbital densities IRC calculation Coordinate scan C.
1. WebMO Introduction Job Manager After logging in, you will be on the WebMO Job Manager page. This page displays your account information (username and compute time limits), the number of currently queued jobs, and a list of jobs you have submitted and/or run. Click Create New Job near the bottom of the page to start a new job. WebMO Job Manager Page Build Molecule The Build Molecule page allows you to draw the 3-D chemical structure for which you wish to perform calculations.
1. WebMO Introduction WebMO Build Molecule Page Editor The WebMO Editor has 3 tools: • View: rotate, translate, or zoom molecule • Build: add new atoms, bonds, or fragments • Adjust: change bond lengths, bond angles, or dihedral angles IMPORTANT TIP: The status line at the bottom of the Editor indicates the current tool and the editing operations that are possible. on the toolbar) to start the build tool.
1. WebMO Introduction To further adjust the geometry (bond length, bond angle, or dihedral angle) of the molecule, choose Tools: Adjust ( ) to start the adjust tool. Select 2, 3, or 4 atoms by clicking the first atom and shift-clicking all subsequent atoms. Then choose Adjust: Bond Length ( ), Adjust: Bond Angle ( ), or Adjust: Dihedral Angle ( ), respectively. Enter the new desired value into the dialog box and click OK. Note that the first atom that was selected is the atom that is moved.
1. WebMO Introduction If more than one program is installed, choose which program to use. If the program is available on multiple computers, select the desired server. Click Job Options to continue. If only one computational chemistry program is installed then this page is skipped. WebMO Choose Computational Engine Page Configure Job Options The details of the Configure Job Options page depend on the specific computational engine chosen. In general, however, you will be able to: • Enter a Job Name, i.e.
1. WebMO Introduction WebMO Configure Job Options Page WebMO Advanced Options Page Job Manager Jobs submitted to WebMO are queued and then run at the first available opportunity. If no other jobs are currently queued or running, the submitted job will be run immediately. The Job Manager page will display the status of your submitted jobs as: Queued, Running, Completed, or Failed. Click the Refresh button on the bottom on the page to update the status of your jobs.
1. WebMO Introduction If necessary, you may terminate a queued or running job by clicking the Kill button. Jobs that exceed a user’s compute time limits are automatically terminated. When the job is finished, the status will either be Completed or Failed, depending on the whether the underlying program was able to complete the requested calculation. To view the results of a completed calculation, click the View button.
1. WebMO Introduction and other information. Clicking on a View button can graphically display: • Dipole Moment • Partial Charges • Normal Modes • Infrared Spectrum • UV-Vis spectrum • NMR Spectrum A new job may be started using the final geometry of the current calculation by clicking New Job Using This Geometry. The final geometry may be exported into a variety of formats using the Export Molecule button.
1. WebMO Introduction WebMO View Job Page (part 2/2) D. WebMO Pro WebMO Pro is a commercial add-on to the freeware WebMO computational chemistry package. It features a variety of powerful enhancements that are suitable for advanced education, research-level, or commercial users.
2. Building Molecules A. Using Existing Structures Importing Structures The first step in running a computational chemistry job is to specify the molecular structure for which the calculation should be performed. Sometimes a structure will already exist, e.g., on the web, in a database, or as a previous calculation. At other times, the user will have to create the structure (see next section). Many molecular structures are already available as files or web documents in a variety of formats.
2. Building Molecules Using Chime to Save a Molecule to Local Disk Once a molecule is saved to the local hard disk, it can be imported into WebMO. From the ) near the WebMO Job Manager page, click the Create New Job button ( bottom of the page to reach the Build Molecule page. Click the Import Molecule button ( ) to bring up the Import Molecule dialog box.
2. Building Molecules Some file formats lack bonding information or do not correctly indicate multiple bonds. In such cases, check the Generate Bonds box for WebMO to automatically generate bonds of the imported structure using simple distance relationships. It is wise to then check the structure and possibly open the editor to make any necessary changes. When importing a molecule, it is possible to skip the step of saving the structure to the local hard disk.
2. Building Molecules WebMO 3-D Molecular Editor All features of the WebMO Editor are available from the menu along the top of the editor window. The most common operations are also available on the toolbar along the left side of the window. The status line at the bottom of the window offers continuous help on currently permitted operations.
2. Building Molecules Tool Build Action Click Click on atom and drag Drag between atoms Multiple drag between atoms Build: Other... Click on atom Build: Fragment... View (Rotate) Drag Shift-drag View (Translate) Drag View (Zoom) Drag up Drag down Adjust Click on background Click on atom Shift-click on atom Select 2 atoms, Adjust: Bond Length... Select 3 atoms; Adjust: Bond Angle... Select 4 atoms; Adjust: Dihedral Angle...
2. Building Molecules C. Build Tool The build tool is used to add new atoms, bonds or fragments to a molecule. Once the WebMO Editor is opened, the build tool is invoked with Tools: Build, or by clicking on the toolbar. The WebMO Editor status line indicates the current atom, which is initially carbon. The status line also indicates what operations are permitted at the current time. To add an atom, simply click in the editor window.
2. Building Molecules Build Tool Periodic Table Dialog Box One does not need to add hydrogen atoms or worry about precise bond lengths and angles when building a molecule. The cleanup tool ( ) may be used at anytime to add hydrogen atoms and idealize all bond lengths and angles. It may be useful to the rotate ( ), translate ( ), or zoom ( ) the structure when building a molecule.
2. Building Molecules • Zoom To activate a particular mode, choose View: Rotate ( ( ). ), View: Translate ( ), or View: Zoom The WebMO Editor status line indicates which view mode is active, as well as how to manipulate the molecule in the current mode. In rotate mode, dragging the mouse rotates the molecule about the x and y axes (in the plane of the screen), and control-drag rotates the molecule about the z axis (perpendicular to the screen).
2. Building Molecules The WebMO Editor status line states that the adjust tool is active and indicates how to select atoms. Once atoms are selected, the status line displays the corresponding bond length, bond angle, or dihedral angle. A B A θ C A φ B Bond Length r Bond Angle θ C B r D Dihedral Angle φ Definitions of Bond Length, Bond Angle, and Dihedral Angle The adjust tool acts on selected atoms. To select multiple atoms, click the first atom and shiftclick all subsequent atoms.
2. Building Molecules Adjust Tool and Dihedral Angle Dialog Box To adjust the order of a bond, ctrl-click the bond to bring up a bond order context menu, from which the desired bond order (single, double, triple) may be chosen. To adjust the hybridization of an atom, ctrl-click the atom to bring up a hybridization context menu, from which the desired hybridization (sp, sp2, sp3, dsp3, d2sp3) may be chosen. Bond Order and Atom Hybridization Context Menus F.
2. Building Molecules • Geometry: Bond lengths and angles are set to ideal values These steps should be carried out in order, since each step relies on the previous step having already been completed. To invoke all three clean-up steps with a single command, choose Clean-Up: Comprehensive ( ). Before and After Comprehensive Clean-Up The rules used for cleaning-up structures are based on stable organic molecules.
2. Building Molecules Fragment Library Dialog Box When adding a fragment to an existing molecule, it is often useful to move the fragment relative to the molecule. Choose the adjust tool, and select the fragment by dragging a box around it or by selecting an atom and choosing Adjust: Select Molecule. Then use the Adjust: Rotate Selection and Adjust: Translate Selection menu items. The fragment library can be extended by the WebMO system administrator using the Fragment Manager.
2. Building Molecules tool, selecting the fragment, and choosing Adjust: Rotate Selection or Adjust: Translate Selection. To find a selection, choose Adjust: Find Selection. The zoom factor is adjusted, and the selection is centered and oriented in the editor. In addition, the center of the selected atoms becomes the rotation origin when the Adjust: Rotate Selection or View: Rotate are used. To delete a selection, choose Adjust: Delete Selection which deletes the selected atoms and bonds from the molecule.
2. Building Molecules Z-Matrix Editor Dialog Box Two steps are required to change the z-matrix for the current molecule: first reorder the atoms as desired, and second adjust the connectivity definitions. These steps must be done in this order. To reorder the atoms, change the numbering in the Order column (negative and decimals are OK) and click the ReOrder button. The atoms will be resorted in numerical order. Note that the connectivity definition will likely change during this process.
2. Building Molecules J. Preferences Visual preferences of the editor can be set with the Preferences dialog box, which is called with File: Preferences... or by clicking the preferences button ( ) on the toolbar. The Atom Size and Bond Size with which atoms and bonds are drawn may customized. The Background Color of the editor may be specified. White is useful when copying the editor window to the Windows clipboard with Alt-Print Screen and pasting the bitmap image into other applications.
3. Running Jobs A. Overview After a molecule is built and appears on the Build Molecule page, the next step is to choose the computational engine to carry out the desired job. WebMO supports the following computational chemistry programs: • Gamess • Gaussian • MOPAC These programs are not part of WebMO and must be installed separately by the system administrator (see http://www.webmo.net/support for instructions).
3. Running Jobs • • • Basis Set Charge Multiplicity There is also an Advanced Options page, on which less frequently used options can be specified. The different Calculation types are described in the next section. The Job Options and Advanced Options pages for each computational engine are described in subsequent sections. The Configure Job Options page has a Preview Input File box that can be checked.
3. Running Jobs Geometry Optimization A Geometry Optimization calculation finds the nearest energy minimum by minimizing the energy. The resulting energy, electronic properties (dipole moment, partial charges, bond orders), and new geometry are reported. The optimized geometry is the nearest local minimum, which is not necessarily the global minimum. Transition State Optimization A Transition State Optimization calculation finds the nearest stationary point by minimizing the gradient.
3. Running Jobs Coordinate Scan (Pro) A Coordinate Scan calculation steps an internal coordinate (bond length, bond angle, or dihedral angle) and computes the energy at each point. The remaining coordinates can be all optimized (relaxed scan), all fixed (rigid scan), or a combination of both. The Z-Matrix Editor is used to define the coordinate to be scanned (S), and whether the remaining coordinates should be optimized (O) or fixed (F).
3. Running Jobs NMR A NMR calculation computes the absolute NMR shifts of each atom in the molecule. The NMR shifts of H and C relative to TMS are also provided for the default basis sets. Proton and carbon NMR spectra can be visualized from the job results page. High Accuracy Methods A High Accuracy Method is a compound method, such as G2, which results in energy calculations that are accurate to within several kcal/mol for most molecules. Other A user specified calculation type may be specified, e.g.
3. Running Jobs Entry Job Name Calculation Choices arbitrary name describing the calculation Molecular Energy Geometry Optimization Vibrational Frequencies Transition State Optimization IRC Calculation Molecular Orbitals Other Theory RHF UHF GVF Other Basis Set Minimal: STO-3G Basic: 3-21G Routine: 6-31G(d) Accurate: 6-311+G(d,p) MNDO AM1 PM3 Other Charge ..., -2, -1, 0, 1, 2, ... Multiplicity Singlet, ...
3. Running Jobs may be used instead. Note that Gamess carries out calculations in Cartesian coordinates by default, regardless of the coordinates used to specify the molecular geometry. CPU% specifies what fraction of the CPU this job should consume. Specifying 100% claims exclusive use of the computational server, whereas specifying 50% would permit another 50% job to run simultaneously on the same server. Additional Keywords permits the specification of additional keywords on the control card.
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3. Running Jobs Advanced Gaussian Options Page The level of raw output may be specified as Terse, Normal, or Verbose. A Solvent may be specified, although this significantly increases the calculation time. The input geometry may be read from an existing Checkpoint File, and/or a checkpoint file for the calculation may be created. For a Saddle Calculation, the Second Geometry must be specified by supplying its job number.
3. Running Jobs Configure Mopac Job Options Page Entry Job Name Calculation Choices arbitrary name describing the calculation Molecular Energy Geometry Optimization Vibrational Frequencies Thermochemistry Transition State Optimization Saddle Calculation IRC Calculation (Forward) IRC Calculation (Reverse) Coordinate Scan Molecular Orbitals Other Theory PM3 AM1 MINDO/3 Other Charge ..., -2, -1, 0, 1, 2, ... Multiplicity Singlet, ...
3. Running Jobs Advanced Mopac Options Page The Symmetry Number of the molecule may be specified for thermochemistry calculations. A Solvent may be specified, although this significantly increases the calculation time. For a Saddle Calculation, the Second Geometry must be specified by supplying its job number. The default specification of molecular geometry is with a z-matrix; however, Cartesian Coordinates may be used instead.
3. Running Jobs • • Problem with geometry specification (choose Cartesian Coordinates from the Advanced Options, redefine the z-matrix, or specify GEO-OK in Mopac) Optimization failed to converge (Restart the job or start from a different initial geometry) If a job has failed, it is possible to restart the job from the last valid geometry, which could be either the initial geometry or the last step of a geometry optimization, by clicking Restart in the Job Manager.
4. Visualizing Results A. Molecular Geometry After the Job Manager indicates that a job has successfully completed, clicking the corresponding ) will display the job results in graphical and tabular form. View button ( At the top of the job results page is the job number, title, calculation type, and computational engine. The final molecular geometry is shown in a 3-D display.
4. Visualizing Results • • • Reset Viewer: Return the molecule to its default viewpoint and configuration Export Molecule: Export the displayed molecule in a variety of formats Output Files: View and download all input and output files (Pro) B. Calculated Quantities The quantities that are calculated are specific to the calculation type and computational engine. Information that can be displayed in tabular form includes: • Symmetry • Energy (HF, MP2, MP4, CCSD, CBS-4, G2, Heat of Formation, etc.
4. Visualizing Results Calculated Quantities C. Dipole Moment and Partial Charges In addition to being listed as numerical values, some quantities may be displayed visually. Clicking the View button corresponding to Dipole Moment or Partial Charges will display the quantity in the 3-D display.
4. Visualizing Results The dipole moment vector is centered at the center of mass and its length is set such that 1 Debye corresponds to 1 Angstrom. When viewing partial charge, the radius of each atom is proportional to its partial charge, and negative atoms are colored red while positive atoms are colored blue. This color code is consistent with the MOViewer convention of small↔large values being mapped onto red↔blue colors.
4. Visualizing Results C-H Stretching Normal Mode The entire infrared spectrum can be displayed by clicking the IR Spectrum View button. Computed peak positions and intensities are used, and the peak width is controlled by the Peak Width value. E. NMR, UV-Vis, and Infrared Spectra In addition to peak position listed in tabular form, computed spectra are available after performing their corresponding calculations.
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4. Visualizing Results UV-Vis Spectrum Spectra can be customized in the Spectrum Viewer window. To zoom into a defined region, click the Zoom in button and then define a zoom box by dragging. To zoom out, click the Zoom out button and then click on the spectrum. To return to the default zoom, click the Reset Zoom button. The Options button offers control over the line color, line type, range of the plot, and axis labels. To close the Spectrum Viewer window, click the Close button.
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4. Visualizing Results G. MOViewer (Pro) Molecular orbitals and their dependent functions may be viewed with the MOViewer helper application, which is compatible with Microsoft Windows (and Linux under WINE). Because of the intensive calculations required to compute and render 3-D surfaces are intensive, MOViewer is a client application that must be installed on each client computer. To install MOViewer on a computer, perform any Molecular Orbitals calculation, e.g.
4. Visualizing Results When prompted to save the resulting .MO file, Internet Explorer users should choose to “Open this file from its current location” to open the file in MOViewer and then click Open to open the file in MOViewer. To automatically open orbitals in MOViewer, unselect the “Always ask before opening this type of file” option at the bottom of the dialog. This will cause .MO files to be opened automatically without further prompts.
4. Visualizing Results blue red blue Electron Density and Electrostatic Potential Surfaces Frontier density surfaces are computed from the magnitudes of molecular orbitals available for attack by an electrophile, nucleophile, or radical. The result is a “bull’s eye” pattern with blue representing the largest probability of attack. For example, the electrophilic (HOMO) frontier density surface of formaldyhde, H2CO, is blue (maximum value) around the oxygen.
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4. Visualizing Results The appearance of the molecule can be controlled by varying the Atom Size. Checking Display Axes will display the cartesian axes, so that orbitals can be more easily identified. The Colors of the Background, Occupied Orbital, and Unoccupied Orbital can be customized. Continuous varying quantities, e.g., electrostatic potentials and frontier densities, are painted on the specified electron density isosurface so that color represents the value of the quantity.
4. Visualizing Results (http://www.mdlchime.com) or rasmol, to view .mol, .pdb, or .xyz files, checking Open in External Viewer will cause the molecule to be automatically opened in the chosen program. Export Molecule Dialog Box Exported Molecule as Text and into External Viewer I. Spreadsheet Summary (Pro) Job results can be exported into a spreadsheet by selecting the jobs and clicking the Spreadsheet button on the Job Manager page.
4. Visualizing Results Spreadsheet Display of WebMO Jobs J. Output Files (Pro) Every file related to a job can be individually viewed or downloaded using the Output Files button on the job results page. Click the Output Files button on the job results page to display a directory listing of all input and output files for the job. Choose whether you wish to view the file as text or download the file as binary, and then click the filename.
5. Job and Profile Management A. Job Manager The central tool for managing submitted and completed computational chemistry jobs is the Job Manager. The top of the Job Manager displays account information (username, total time limit , job time limit) and the current number of queued jobs. The main portion of the Job Manager is a list of completed and submitted jobs, which can be managed with various actions.
5. Job and Profile Management • • Import Job: Transfer jobs from your local computer to WebMO Edit Profile: Change your user preferences Other buttons on the Job Manager are: • Refresh: Update the list of jobs • About WebMO: Display version information • Help: Display online help • Logout: Logout of WebMO WebMO Job Manager B. Folders (Pro) WebMO Pro allows users to organize their jobs by creating folders for storing completed jobs. WebMO users have only Inbox and Trash folders.
5. Job and Profile Management To create a new folder, click the Folders button at the bottom of the Job Manager job listing. Enter a Folder name and click the Create button. A green “Folder successfully created” message is displayed confirming that the new folder has been created. Either create additional folders or click the Return to Job Manager button. To rename a folder, select an existing folder as the Target folder, specify a new name as the New Folder, and click the Rename button.
5. Job and Profile Management Deleted jobs are moved from the current folder to the Trash folder, but not actually deleted from the file system. To permanently delete a job from the file system, display the Trash folder and delete the jobs again. C. Download Completed jobs may be downloaded from the WebMO server to the user’s local machine.
5. Job and Profile Management Importing an Output File or WebMO Archive E. Rename To rename a job, check the corresponding checkbox and click the Rename button. The new name can be entered into the pop-up dialog box. Renamed jobs appear with their new names in the WebMO environment. However, the raw output file, which contains the original job name as a job title, remains unchanged. Renaming a Job F.
5. Job and Profile Management To permanently delete jobs from the server file system, display the Trash folder by selecting the Trash folder and clicking the Move To button. Check the checkboxes corresponding to the jobs to be permanently deleted, and click the Delete button. Confirm that the selected jobs will be permanently deleted by clicking the OK button. Jobs that are permanently deleted cannot be restored.
6. WebMO Administration A. Overview After the initial installation, all WebMO configuration and administration is done through a web browser interface. To access the WebMO administration webpages, login as the user “admin” with the admin password.
6. WebMO Administration B. User Manager To add, edit, disable, or delete users, click the User Manager link on the WebMO Administration page. An alphabetized list of WebMO users is displayed. To add a new user, click the New User button. On the New User page, specify a username and password, and confirm the password. Optionally provide an email address. If appropriate, specify total and job time limits. Click the Submit button. A confirmation message is displayed.
6. WebMO Administration C. Job Manager The Job Manager allows the administrator to monitor all queued and running jobs and to view, download, and delete any completed job. The administrator Job Manager is very similar to a user’s Job Manager.
6. WebMO Administration Administrator Job Manager D. System Manager The WebMO daemon and WebMO preferences are controlled by the System Manager. The status of the WebMO daemon is displayed as either “Not running” or “Running”. Note that the WebMO daemon only runs when jobs are queued and/or running. When there are no queued or running jobs, the WebMO daemon does not run. Under normal conditions, the daemon status should not be changed.
6. WebMO Administration Click the Submit button to implement preference changes. System Manager E. Version Manager The version, license number, and total jobs run are displayed by the Version Manager. The Version Manager also checks whether the most recent version of WebMO is running and informs you if an update is available. A link is provided to the WebMO download area for obtaining updates. When updating WebMO, the location of the globals.int configuration file must be specified.
6. WebMO Administration F. Fragment Manager The Fragment Library permits users to insert fragments when building molecules with the WebMO Editor. The WebMO administrator can add fragments to the Fragment Library with the Fragment Manager. The source of the fragment must be an existing WebMO job. To add a fragment, specify the Job number from which to import the fragment geometry, specify a Category for the fragment, e.g., rings, and specify a Fragment name, e.g., benzene.
6. WebMO Administration $ rsh -l webmo compserver.domain.edu ls should list the files on the remote computational server, where webmo is the account under which the webserver cgi scripts run. Detailed instructions for configuring a remote computational server may be found by clicking the Help button on the Remote Server Manager. Briefly, insure that the above pre-requisites are met, and test that the webserver can execute remote commands on the compserver.
6. WebMO Administration Remote Server Manager H. Interface Manager The Interface Manager enables and disables the computational engines supported by WebMO. Since WebMO Pro supports multiple computational servers, if the desired server is not displayed at the top of the page, it must first be selected selecting the remote server and clicking the Change button. The current status of each interface is displayed as either Disabled or Enabled.
6. WebMO Administration Interface Manager I. Computational Engine Managers Computational Engines are configured with the corresponding {Computational Engine} Manger. Since WebMO Pro supports multiple computational servers, if the desired server is not displayed at the top of the page, it must first be selected selecting the remote server and clicking the Change button. The {Computational Engine} Manger varies with each computational chemistry program.
6. WebMO Administration Gamess, Gaussian, and Mopac Managers J. Customization Look and Feel Aspects of WebMO’s look and feel may be customized with the System Manager, which is accessible from the admin account. The Registered user is an arbitrary string displayed on the WebMO Login page. The Background graphic is the filename for the background image on all WebMO pages. The Table background is the color for all tables displayed by WebMO.
6. WebMO Administration The name of the WebMO computational server displayed on the Choose Computational Engine page is specified as the Server name in the System Manager. The name of each remote computational servers is specified as the Server name in the Remote Server Manager. It is possible to edit the *.html files in the {htmlBase} directory of a WebMO installation, so long as only the displayed text is changed, i.e., form and javascript variables may not be changed..
7. Exercises A. WebMO Editor 1. Creating Structures Using WebMO Use the WebMO Editor to build the following molecules. A. Propene, CH3CH=CH2 O OH O B. Aspirin, C9H8O4 O Use the Fragment Library (Build: Fragment...) in the WebMO Editor to create the following molecules. When working with two fragments, it is often useful to select one fragment, and then rotate or translate just the selected fragment with Adjust: Rotate Selection or Adjust: Translate Selection.
7. Exercises Import Molecule button. On the Import Molecule page, choose the proper format, browse to the saved file, and click the Import Molecule button E. Taxol, C47H51NO14 F. Buckminsterfullerene, C60 USEFUL TIP: In Windows, Alt-Print Scrn copies the active window to the clipboard as a bitmap graphic image. This is very useful for inserting WebMO images into other applications, such as Microsoft Word or PowerPoint.
7. Exercises 5. Molecular Orbitals of Formaldehyde (Pro) Build formaldehyde, H2CO, using WebMO. Perform a Molecular Orbital Hartree-Fock STO-3G calculation on it. From the energies, shapes, and composition of the molecular orbitals, classify each molecular orbital as bonding, anti-bonding, non-bonding or core. Provide images of the HOMO−1, HOMO and LUMO. Describe each of these orbital as sigma or pi and as bonding, anti-bonding, or nonbonding.
7. Exercises Cinner compound Couter butane 13.4 25.2 trans-2-butene 17.6 126.0 2-butyne — 73.6 Silverstein, Bassler, and Morril, Spectroscopic Identification of Organic Compounds, 5th ed. (Wiley, New York, 1991), Tables 5.2, 5.6, 5.8 D. Geometry Optimizations 7. Conformers of n-Butane Use the WebMO Editor to build n-butane, C4H10. Set the initial C1-C2-C3-C4 dihedral angle to 30°. Perform a Geometry Optimization calculation on the molecule, and record the optimized dihedral angle and energy.
7. Exercises F F Cl F F F Cl F F Cl F F tee planar pyramidal To build a particular geometry, construct ClF5, set the hybridization of the central Cl atom to dsp3 with the Adjust tool by control-clicking on Cl, choose Clean-Up: Geometry (not Comprehensive!), and finally delete the undesired F atoms. If a particular geometry optimization calculation fails to converge, click the Restart button in Job Manager, and view the last computed geometry.
7. Exercises For one of these jobs, report the keywords that control the type of calculation being run. Also report the text from the corresponding output file indicating that the optimization has converged. Discuss the physical meaning of the convergence criteria. 11. Transition State of Vinyl Alcohol Build an approximate transition state for the isomerization of vinyl alcohol-0° and vinyl alcohol180° as follows.
7. Exercises despite the short distance between the H atoms.] Close the Advanced Job Options window. Check Preview Input File and submit the job. Describe the general appearance of the input file. Specifically, how does it differ from other input files? Submit the job. Provide a picture of the transition state for this reaction.
7. Exercises H H H N H H H C C H H pyramidal C C H planar N H For planar vinyl amine, adjust the hybridization of N to sp2 and then clean up the geometry. Be sure to adjust the dihedral of the amine group appropriately for each molecule. For each conformation, optimize the geometry and calculate vibrational frequencies with a PM3 (or Hartree-Fock 6-31G(d) or better) calculation. Make a table with columns for conformation, energy, and type of stationary point.
7. Exercises H H H H H H C C C F H H H C C H C H F H C C C H H H F Do not do a comprehensive cleanup, as the Add Hydrogens function uses rules that are applicable to stable molecules, not transition states. Instead, manually add the hydrogens, including a hydrogen that is bonded to both C1 and C3. Adjust the hybridization of C2 to sp2, and clean up the geometry only. Adjust the H-C2 bond angle appropriately so it is symmetric with respect to the ring.
7. Exercises Compute ∆rxnH from your calculations by appropriately combining H298 values and converting to kcal/mol. 1 Hartree = 627.5095 kcal/mol. Compute ∆rxnH from the experimental data by appropriately combining ∆fH. Comment on the agreement between calculation and experiment by comparing Cp, S, and ∆rxnH values in a table. F. Model Chemistry 19.
7. Exercises 21. Compound Method Calculation of Ozone Destruction by Atomic Chlorine Use Gaussian to perform CBS-4M calculations on atomic Cl (doublet), O3 (bent geometry, singlet), OCl (doublet), and O2 (triplet). [It has been observed that OCl must be built with oxygen as the first atom; otherwise, the CBS-4M portion of the calculation fails.] When configuring Gaussian job options, set Calculation = “Other(CBS-4M)”, Theory = “Other()”, and Basis Set = “Other()”.
7. Exercises NO2 + Cl + Product C6H4N2O4 C6H4NO2Cl NO2 NO2 NO2 Cl NO2 NO2 ortho 6% 30% meta 93% 1% para 1% 69% Build nitrobenzene such that the nitro group lies in the molecular plane and has equal NO bond lengths. Pre-optimize this structure with a PM3 calculation. [If using Gaussian, disable symmetry using the Advanced Job Options. The NoSymmetry keyword prevents the job from terminating if the molecular symmetry changes during calculation.
7. Exercises 24. Carbocation Intermediate Analysis of Electrophilic Aromatic Substitution Reactions Aromatic substitution reactions proceed via a carbocation intermediate. The product distribution of an aromatic substitution reaction may be predicted from the relative stabilities of the carbocation intermediates. The aldehyde group is meta-directing for aromatic substitution reactions.
7. Exercises Repeat the coordinate scan with various levels of theory and basis sets, up to a MP2 6-311+G(p,d) calculation. Download the coordinate scans and use Excel to plot these potential functions in the same figure. Comment on the relative energies of these plots. Calculate the CH bond dissociation energy in kcal/mol by taking the difference between the minimum and separated energies. Compare your results to an experimental value from a general or organic chemistry textbook.
7. Exercises View the output and click New Job Using This Geometry. Run a Gaussian Bond Order calculation at the same level of theory, which performs a NBO (Natural Bonding Orbital) analysis of the Bond Order. Starting with the same same geometry, run a Gamess Molecular Energy UHF (Unrestricted Hartree-Fock) 3-21G calculation of this doublet molecule. Finally, starting with the same geometry, run a Mopac Geometry Optimization job at the PM3 level of theory.
7. Exercises H 1.583Å H 49.4° 1.102Å 112.5° C 1.151Å O Double check your geometry before proceeding. Perform a Transition State Optimization Hartree-Fock 3-21G calculation. View the Results, click New Job Using This Geometry, and perform a Vibrational Frequencies job with the same geometry and theory. Report the value of any negative (imaginary) frequencies. Note the energy and H-H bond length. Using the transition state geometry, perform a Forward IRC calculation with the same theory.
7. Exercises Locate the transition state for this reaction by first building the norbornene product. Perform a PM3 geometry optimization of the product, and verify that the resulting geometry is reasonable. View the result, choose New Job Using This Geometry, and open the molecule in the WebMO Editor. Adjust the two carbon-carbon bond lengths that are formed in the reaction to 2.2 Angstroms, recalling that the first selected atom is the one that is moved. Open the Z-Matrix Editor with Tools:Z-Matrix....
7. Exercises Start with the norbornene transition state in the previous exercise. Open the molecule in the WebMO Editor, and make appropriate substitutions for the transition state to a particular product. Select only the changed atoms, choose Clean-Up: Selection Only, and then choose Clean-Up: Comprehensive. Perform a PM3 Transition State Optimization calculation, followed by a Vibrational Frequencies calculation if desired. Repeat for the other stereoproducts.
7. Exercises View the results of the saddle calculation, choose New Job Using This Geometry. Perform a PM3 Transition State Optimization calculation. View the results of the transition state optimization job, and choose New Job Using This Geometry. For cosmetic purposes, open the molecule in the WebMO Editor and adjust the bonds in the HOCC 4-membered rings to single bonds. Perform a PM3 Vibrational Frequencies calculation.
7. Exercises perform a Vibrational Frequencies calculation at the same level of theory and with Excited State option checked. Complete the following table, using the scaling factor of 0.8929 for Hartree-Fock 6-31G(d) frequency calculations.
7. Exercises 36. Solvation Energy of Glycine and its Zwitter Ion The amino acid glycine has a zwitter ion isomer, in which the carboxylic acid proton is transferred to the amino group. O HO C O CH2 NH2 O C CH2 NH3 Build glycine and perform a Geometry Optimization calculation. Using the resulting geometry, perform a Molecular Energy calculation at the same level of theory but using the Advanced Options to select water as the solvent.
7. Exercises MOViewer application. The electrostatic potential is painted onto an electron density isosurface, with red being negative and blue being positive. In Edit: Preferences..., adjust the Opacity of the surface to about 70%. Use the electrostatic potential image to determine which nitrogen is more basic, i.e., would more likely attract a proton.
7. Exercises O O H 2C Build ethyl enolate, by first building the corresponding alcohol and then deleting the alcohol H atom. Optimize the geometry with a Hartree-Fock STO-3G calculation. View the result, choose New Job Using This Geometry, and perform a Molecular Orbitals calculation at the same level of theory. On the job results page, view the HOMO (Highest Occupied Molecular Orbital), which opens the MOViewer application. Note that the electron density is delocalized across oxygen-carbon π system.
7. Exercises C. Written report. Prepare a written report describing your project. The report should typically be 3-5 pages of written text, plus tables and figures. The report will consist of a title, introduction, outline of calculations, results, discussion, conclusion and references. The calculations will be evaluated for appropriateness and correctness.
8. Appendices A. Installing WebMO 1. Obtain a WebMO license from http://www.webmo.net. A license number and download password will be emailed to you. 2. Download WebMO to your PC. 3. Upload the WebMO archive from your PC to your unix (Linux, IRIX, AIX, Solaris, etc.) web server. Do not uncompress the archive on your PC before uploading! 4. Login to your web server account, uncompress, and untar the WebMO archive. $ gunzip WebMO.3.3.00x.tar.gz $ tar xvf WebMO.3.3.00x.tar 5. Run the setup script. $ cd WebMO.
8. Appendices • • • • • • • Click 'Return to Admin' to return to the WebMO administration page. Click 'interface_name Manager' to configure any interfaces that were enabled in the Interface Manager. Make any necessary changes in the interface configuration and then click submit to commit the changes. Click 'Return to Admin' to return to the WebMO administration page. Click on the 'User Manager' and then the 'New User' button to create WebMO users. Create at least one user.
8. Appendices $ cd WebMO.install $ perl upgrade.pl 7. Follow the directions that are given in the setup script and specify the absolute location of your globals.int file. After the distribution files are copied, the command line portion of WebMO upgrade is complete. 8.
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Notes 98
“WebMO is a simple, Web browser-based interface for using popular chemistry software packages, such as Mopac and Gaussian. You draw the molecule’s structure, and the output – including the molecule’s transition states and infrared and nuclear magnetic resonance spectra – appears in an easy-to-understand format.” Science, August 10, 2001 “WebMO is a Web-based interface to computational programs such as Gaussian, Gamess, and Mopac.
