Bond user manual Podręcznik Użytkownika

“WebMO is a simple, Web browser-based interface for using popular chemistry software packages, such as Mopac and Gaussian. You draw the molecule’s st

1. WebMO Introduction • Saddle calculation • Vibrational frequencies, spectra, and motions • UV-VIS frequencies and spectra • NMR frequencies and

7. Exercises OH2CO Build ethyl enolate, by first building the corresponding alcohol and then deleting the alcohol H atom. Optimize the geometry with

7. Exercises C. Written report. Prepare a written report describing your project. The report should typically be 3-5 pages of written text, plus t

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 y

8. Appendices • Click 'Return to Admin' to return to the WebMO administration page. • Click 'interface_name Manager' to configu

8. Appendices $ cd WebMO.install $ perl upgrade.pl 7. Follow the directions that are given in the setup script and specify the absolute location

Notes 97

98 Notes

“WebMO is a simple, Web browser-based interface for using popular chemistry software packages, such as Mopac and Gaussian. You draw the molecule’s st

1. WebMO Introduction Job Manager After logging in, you will be on the WebMO Job Manager page. This page displays your account information (username

1. WebMO Introduction WebMO Build Molecule Page Editor The WebMO Editor has 3 tools: • View: rotate, translate, or zoom molecule • Build: add ne

1. WebMO Introduction To further adjust the geometry (bond length, bond angle, or dihedral angle) of the molecule, choose Tools: Adjust ( ) to start

1. WebMO Introduction If more than one program is installed, choose which program to use. If the program is available on multiple computers, select

1. WebMO Introduction WebMO Configure Job Options Page WebMO Advanced Options Page Job Manager Jobs submitted to WebMO are queued and then run at t

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 li

1. WebMO Introduction and other information. Clicking on a View button can graphically display: • Dipole Moment • Partial Charges • Normal Modes •

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 pac

2. Building Molecules A. Using Existing Structures Importing Structures The first step in running a computational chemistry job is to specify the mo

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 W

2. Building Molecules Some file formats lack bonding information or do not correctly indicate multiple bonds. In such cases, check the Generate Bond

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. T

2. Building Molecules Tool Action Description Click Add current atom (or fragment) Click on atom and drag Add bond and current atom Drag between a

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 b

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 w

2. Building Molecules • Zoom To activate a particular mode, choose View: Rotate (), View: Translate ( ), or View: Zoom (). The WebMO Editor status l

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,

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 co

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

WebMO User’s Guide William F. Polik and Jordan R. Schmidt WebMO LLC 1281 Heather Drive Holland, MI 49423 USA www.webmo.net

2. Building Molecules Fragment Library Dialog Box When adding a fragment to an existing molecule, it is often useful to move the fragment relative t

2. Building Molecules tool, selecting the fragment, and choosing Adjust: Rotate Selection or Adjust: Translate Selection. To find a selection, choose

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

2. Building Molecules J. Preferences Visual preferences of the editor can be set with the Preferences dialog box, which is called with File: Preferen

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

3. Running Jobs • Basis Set • Charge • Multiplicity There is also an Advanced Options page, on which less frequently used options can be specified. T

3. Running Jobs Geometry Optimization A Geometry Optimization calculation finds the nearest energy minimum by minimizing the energy. The resulting

3. Running Jobs Coordinate Scan (Pro) A Coordinate Scan calculation steps an internal coordinate (bond length, bond angle, or dihedral angle) and com

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 a

3. Running Jobs Entry Choices Job Name arbitrary name describing the calculation Molecular Energy Geometry Optimization Vibrational Frequencies Tran

The information contained in this publication is believed to be accurate and reliable. However, no representation of warranty is made with respect t

3. Running Jobs may be used instead. Note that Gamess carries out calculations in Cartesian coordinates by default, regardless of the coordinates us

3. Running Jobs Entry Choices Job Name arbitrary name describing the calculation Molecular Energy Geometry Optimization Vibrational Frequencies Opti

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, a

3. Running Jobs Configure Mopac Job Options Page Entry Choices Job Name arbitrary name describing the calculation Molecular Energy Geometry Optimiz

3. Running Jobs Advanced Mopac Options Page The Symmetry Number of the molecule may be specified for thermochemistry calculations. A Solvent may be

3. Running Jobs • Problem with geometry specification (choose Cartesian Coordinates from the Advanced Options, redefine the z-matrix, or specify GEO

4. Visualizing Results A. Molecular Geometry After the Job Manager indicates that a job has successfully completed, clicking the corresponding View

4. Visualizing Results • Reset Viewer: Return the molecule to its default viewpoint and configuration • Export Molecule: Export the displayed molec

4. Visualizing Results Calculated Quantities C. Dipole Moment and Partial Charges In addition to being listed as numerical values, some quantities

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.

Table of Contents 1. WebMO Introduction ... 1 A. Overview...

4. Visualizing Results C-H Stretching Normal Mode The entire infrared spectrum can be displayed by clicking the IR Spectrum View button. Computed p

4. Visualizing Results 13C and 1H NMR Spectra Infrared Spectrum 43

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 but

4. Visualizing Results Coordinate Scan Data View Coordinate Scan Download Coordinate Scan 45

4. Visualizing Results G. MOViewer (Pro) Molecular orbitals and their dependent functions may be viewed with the MOViewer helper application, which i

4. Visualizing Results When prompted to save the resulting .MO file, Internet Explorer users should choose to “Open this file from its current locati

4. Visualizing Results Electron Density and Electrostatic Potential Surfaces blue redblue Frontier density surfaces are computed from the magnitudes

4. Visualizing Results Electrophilic (HOMO) and Nucleophilic (LUMO) Frontier Density Surfaces blue blueSurface Color Interpretation Red/Blue occupie

4. Visualizing Results The appearance of the molecule can be controlled by varying the Atom Size. Checking Display Axes will display the cartesian a

4. Visualizing Results (http://www.mdlchime.com) or rasmol, to view .mol, .pdb, or .xyz files, checking Open in External Viewer will cause the molecu

Table of Contents UV-Vis Spectrum Coordinate Scan (Pro) IRC Calculation Saddle Calculation Molecular Orbitals (Pro) NMR High Accuracy Methods Other C.

4. Visualizing Results Spreadsheet Display of WebMO Jobs J. Output Files (Pro) Every file related to a job can be individually viewed or downloaded

5. Job and Profile Management A. Job Manager The central tool for managing submitted and completed computational chemistry jobs is the Job Manager.

5. Job and Profile Management • Import Job: Transfer jobs from your local computer to WebMO • Edit Profile: Change your user preferences Other butt

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

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

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 Re

5. Job and Profile Management To permanently delete jobs from the server file system, display the Trash folder by selecting the Trash folder and clic

6. WebMO Administration A. Overview After the initial installation, all WebMO configuration and administration is done through a web browser interfa

6. WebMO Administration B. User Manager To add, edit, disable, or delete users, click the User Manager link on the WebMO Administration page. An alp

6. WebMO Administration C. Job Manager The Job Manager allows the administrator to monitor all queued and running jobs and to view, download, and del

Table of Contents D. System Manager... 62 E. Version Manager...

6. WebMO Administration Administrator Job Manager D. System Manager The WebMO daemon and WebMO preferences are controlled by the System Manager. The

6. WebMO Administration Click the Submit button to implement preference changes. System Manager E. Version Manager The version, license number, and

6. WebMO Administration F. Fragment Manager The Fragment Library permits users to insert fragments when building molecules with the WebMO Editor. The

6. WebMO Administration $ rsh -l webmo compserver.domain.edu ls should list the files on the remote computational server, where webmo is the acco

6. WebMO Administration Remote Server Manager H. Interface Manager The Interface Manager enables and disables the computational engines supported by

6. WebMO Administration Interface Manager I. Computational Engine Managers Computational Engines are configured with the corresponding {Computation

6. WebMO Administration Gamess, Gaussian, and Mopac Managers J. Customization Look and Feel Aspects of WebMO’s look and feel may be customize

6. WebMO Administration The name of the WebMO computational server displayed on the Choose Computational Engine page is specified as the Server name

7. Exercises A. WebMO Editor 1. Creating Structures Using WebMO Use the WebMO Editor to build the following molecules. A. Propene, CH3CH=CH2 B. A

7. Exercises Import Molecule button. On the Import Molecule page, choose the proper format, browse to the saved file, and click the Import Molecule

Table of Contents G. Partial Charge... 80 23. Partial Charge Analysis of

7. Exercises 5. Molecular Orbitals of Formaldehyde (Pro) Build formaldehyde, H2CO, using WebMO. Perform a Molecular Orbital Hartree-Fock STO-3G cal

7. Exercises compound Couter Cinner butane 13.4 25.2 trans-2-butene 17.6 126.0 2-butyne — 73.6 Silverstein, Bassler, and Morril, Spectroscopic Identi

7. Exercises Cl FFFClFFFCl FFFplanarteepyramidal To build a particular geometry, construct ClF5, set the hybridization of the central Cl atom to dsp3

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

7. Exercises despite the short distance between the H atoms.] Close the Advanced Job Options window. Check Preview Input File and submit the job. D

7. Exercises CC H HHNHHCCHHHNHHplanarpyramidal For planar vinyl amine, adjust the hybridization of N to sp2 and then clean up the geometry. Be sure

7. Exercises CCCHHFHHHCCCFHHHHHCCCHHHHFH Do not do a comprehensive cleanup, as the Add Hydrogens function uses rules that are applicable to stable mo

7. Exercises Compute ∆rxnH from your calculations by appropriately combining H298 values and converting to kcal/mol. 1 Hartree = 627.5095 kcal/mol.

7. Exercises 21. Compound Method Calculation of Ozone Destruction by Atomic Chlorine Use Gaussian to perform CBS-4M calculations on atomic Cl (doubl

7. Exercises NO2+NO2NO2NO2Cl+NO2ClNO2 Product ortho meta para C6H4N2O4 6% 93% 1% C6H4NO2Cl 30% 1% 69% Build nitrobenzene such that the nitro group

1. WebMO Introduction A. Overview WebMO is a web-based interface for computational chemistry programs. WebMO makes it possible to set up, run, and

7. Exercises 24. Carbocation Intermediate Analysis of Electrophilic Aromatic Substitution Reactions Aromatic substitution reactions proceed via a car

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 s

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 perform

7. Exercises COHH49.4°112.5°1.583Å1.102Å1.151Å Double check your geometry before proceeding. Perform a Transition State Optimization Hartree-Fock 3-2

7. Exercises Locate the transition state for this reaction by first building the norbornene product. Perform a PM3 geometry optimization of the prod

7. Exercises Start with the norbornene transition state in the previous exercise. Open the molecule in the WebMO Editor, and make appropriate substi

7. Exercises View the results of the saddle calculation, choose New Job Using This Geometry. Perform a PM3 Transition State Optimization calculation

7. Exercises perform a Vibrational Frequencies calculation at the same level of theory and with Excited State option checked. Complete the following

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 proto

7. Exercises MOViewer application. The electrostatic potential is painted onto an electron density isosurface, with red being negative and blue bein