Required Reading & Assignments:

"Molecular Modeling & Molecular Mechanics" in Pavia, 6th Ed. p. 158-162
"Computational Chemistry--an Initio and Semiempirical Methods" in Pavia, 6th Ed. p. 168-175
0B THEORY: Introduction to Molecular Modeling

Introduction to WebMO:

WebMO is a free web-based interface for operating computational chemistry packages. A three dimensional model of a molecule can be created using an editor. The molecular model can then be refined using a geometry optimization (see animation below for process behind geometry optimization); this can be accomplished with a variety of methods from molecular mechanics calculations (WebMO uses MM2) to semi-empirical methods (PM3, AM1, MNDO/3); read the sections in the lab manual above to learn more about molecular mechanics and semi-empirical methods. Once optimized, the resulting molecular model can be used calculate bond angles, bond lengths, thermodynamic parameters and other useful quantities describing the electronic structure of the molecule (molecular orbital energies, electrostatic potential energy maps, etc).

Geometry Optimizatin with WebMO.gif

The goal of this activity is to introduce you to the fundamentals of WebMO. You will learn how to use the interface to build models of molecules, perform geometry optimizations, and analyze the results. Later in the course, we will expand on these molecular modeling techniques to make predictions on the rates and outcomes of chemical reactions.

WebMO Tutorial:

To get practice using WebMO, the tutorial below walks you through how to build, geometry optimize, and analyze 4 molecular models: methane, ethanol, trans-1,2-dichloroethene and cis-1,2-dichloroethene.

WebMO Basics
Methane
Ethanol
Trans-1,2-dichloroethene
Cis-1,2-dichloroethene

Log in to WebMO by navigating to http://butane.cabrillo.edu/~webmo/cgi-bin/cabrillo/login.cgi. Your username is the first two letters of your first name followed by your last name with lowercase letters; include the hyphen if your name is hyphenated. For example, if your name was Jane Doe-Smith, your username would be jadoe-smith. Your password is "chem12". If you have any difficulties with WebMO, don't hesitate to ask a question in Piazza or stop by office hours via Zoom.

To build a new molecular model: At the top of the WebMO Job Manager Page, click on the "New Job" button. This will bring up the Molecule Builder page:

The list below summarizes each tool on the Molecule Builder page and how to use them properly. Once a tool is selected by clicking once on the icon, the information bar at the bottom of the window provides instructions on the use of each tool.

BUILD: When this icon is selected, atoms will be added with a left click in window. Left click, hold down on an atom, drag and release and another atom will be added; repeat this process between two existing atoms to form double or triple bonds.
PERIODIC TABLE: Click this icon and a periodic table will pop up; click the element that you would like to add with the BUILD icon.PRO TIP: you can also use the keyboard to switch from one element to another: just type the element symbol and the program will automatically switch to adding that element.
ROTATE: Use this icon to rotate the model; hold down the left click anywhere in the window and drag to rotate the model in 3 dimensions.
TRANSLATE: Use this icon to move the model left, right, up or down. Hold down left click and drag.
ZOOM: Use this icon to zoom in or zoom out; either use the scroll wheel or hold down left click and drag up to zoom in, drag down to zoom out.
SELECT: This icon allows specific atoms to be highlighted when left click is used. Left click and drag to select multiple atoms simultaneously; left click on white space to de-select atoms:
- With two atoms selected, the corresponding bond length will be displayed in the white bar below the model (see below for example).
- With three atoms selected, the corresponding bond angle will be displayed in the white bar below the model (see below for example).
  - The order in which you select the atoms defining the bond angle matters. See the animated gif below for more information:
Once atoms are selected, the ADJUST icons below can be used to adjust charges, bond lengths, bond angles and dihedral angles:
- ADJUST CHARGE: With one atom selected, this icon will allow you to manually adjust the charge on the selected atom.
- ADJUST BOND LENGTH: With two atoms selected, this icon will allow you to manually adjust the bond length between the selected atoms.
- ADJUST BOND ANGLE: With three atoms selected, this icon will allow you to manually adjust the bond angle between the selected atoms.
- ADJUST DIHEDRAL ANGLE: With four atoms selected, this icon will allow you to manually adjust the dihedral angle between the selected atoms (we will use this later in the course when we study conformations of molecules).
CLEANUP: COMPREHENSIVE: IDEALIZED: Clicking this icon will add any implied hydrogen atoms to build a neutral molecule with complete octets. The system will fix molecular geometries based on VSEPR theory and set bond lengths/angles to pre-defined values based on tables of experimental values.
CLEANUP: COMPREHENSIVE: MECHANICS: This icon is similar to the COMPREHENSIVE IDEALIZED clean-up except the system will use molecular mechanics calculations (MM2) to minimize the energy of the molecule. The resulting model will be more accurate, but will still benefit from a geometry optimization using semi-empirical methods.
SYMMETRIZE: Clicking on this icon, WebMO will identity the closest point group (a term used to describe the symmetry of the molecule) and then adjust the model to have this exact symmetry. This is helpful to perform prior to semi-empirical calculations since quantum chemistry programs can take advantage of molecular symmetry to speed up calculations and reduce memory requirements. Thus, it is usually desirable to symmetrize nearly symmetric molecules prior to a calculation. WebMO will warn the user if one exits the Build Molecule page with a nearly symmetric molecule.
SHOW SYMMETRY: Clicking on this icon will show the symmetry elements associated with the model; we will rarely use this feature.
ORBITALS: Clicking on this icon will display the molecular orbitals and their associated energies.
UNDO: Click this icon to undo the last change to the model. Alternative, press "Control + Z" on the keyboard.
REDO: Click this icon to return to the last version prior to clicking UNDO.
PREFERENCES: Click this icon to adjust preferences. This is rarely necessary as the default settings are fine for most situations.

The steps below describe how to build a model of methane (CH₄), perform a geometry optimization, then display and analyze the results. Record the partial charges on the carbon and hydrogen atoms; this information will be needed for the THEORY assignment.

Login to WebMO and create a new job.
Click once in the Editor window. This will draw a single carbon atom.
Click once on CLEANUP: COMPREHENSIVE: MECHANICS. This will add four hydrogen atoms to your carbon atom, with sp³geometry, and you will have a complete methane molecule.
To perform a geometry optimization using semi-empirical calculations, click on the "Job Options" link to the left of the model window or the arrow to the right on the bottom of the screen (see RED highlights below).
On the "Configure Mopac Job Options" page, adjust the fields below:
- JOB NAME: give your molecule its standard IUPAC name, followed by an underscore and an identifier of your choice, such as methane_practice. Use any identifier you like, as long as the molecule name begins with the IUPAC name and an underscore.
- CALCULATION: Select Geometry Optimization from the Calculation drop-down menu. This will calculate the minimum energy conformation for your molecule.
- THEORY: Select AM1 from the Theory drop-down menu.
- CHARGE: Leave the charge at 0.
- MULTIPLICITY: Leave the multiplicity at Singlet.
Click on the Submit Job link to the left of the window or click the right arrow at the bottom of the screen (see RED highlights below)
This will return you to the Job Manager Page, where you will see your job listed. In the status column you will see "Running" in orange.
Click on the Refresh button at the top-left corner of the screen. Your job's status should now say "Complete" in green.
Click on the Magnifying Glass icon to the right of the job's status to see the results of the calculation.
SCROLL DOWN to view the various results available from the completed job page (example shown below):
- Job Number & Name: The Job number and name are at the top of the page. Job numbers are in order of all of the jobs run on the server, each job has a unique
  number.
- Molecule Viewer: The molecule is displayed with the optimized geometry.
- Route (Keywords): The keywords the computational engine used to optimize the molecule are displayed.
- Symmetry: The symmetry point group to which the molecule belongs is displayed
- Heat of Formation: The calculated Heat of Formation for the molecule is displayed in kcal/mol.
- Dipole Moment: The calculated Dipole Moment of the molecule is displayed in Debye and can be visualized by clicking the adjacent magnifying glass icon.
- Partial Charges: The calculated partial charge on each atom of the molecule is given in table format. The partial charges can be visualized by clicking the adjacent magnifying glass button. Record the partial charges on the carbon and hydrogen atoms; this information will be needed for the THEORY assignment.
- Bond Orders: The calculated bond orders (strength of bonding interaction) are displayed. Values less than one indicate no existing bond. Values approximately one indicate a single bond interaction between the two
  atoms. Values approximately two and three indicate a double or triple bond interaction, respectively.

The steps below describe how to build a model of ethanol (CH₃CH₂OH), perform a geometry optimization, then display and analyze the results. Record the partial charges on oxygen and the attached hydrogen atom; this information will be needed for the THEORY assignment.

Login to WebMO (if you aren't already) and create a new job.
Click once near the center of the Editor window, this will set a single carbon atom. Click on the Carbon atom and hold the mouse button down. Now drag the mouse horizontally away from the first carbon in the direction where you would like to place the second carbon, all the while holding down the mouse button. Release the mouse button when the cursor resides where you would like to place the second carbon atom. Do not put the atoms too close together, or too far apart (about two to three atom diameters is about right) as this can cause problems during the calculations. Also do not rotate the molecule while building unless absolutely necessary, this often makes building more difficult.
Click on the PERIODIC TABLE icon on the left-hand menu and select oxygen from the table; alternative, press the "O" button on your keyboard.
Click once, and hold the mouse button down, on the carbon atom to which you would like to attach the oxygen atom. Now drag the cursor away from the carbon atom, approximating a good bond angle of 109.5o. Release the mouse button to place the oxygen atom, placing it two to three atom diameters away from the carbon.
Click once on the wrench icon, CLEANUP: COMPREHENSIVE: MECHANICS. This will add hydrogen atoms, and perform a molecular mechanics calculation to minimize the energy of the resulting ethanol molecule.
If you want to see the molecule from another angle, click on the ROTATE icon , and you will be able to click and drag to rotate the molecule. It is best not to do this until you are finished building the molecule.
To perform a geometry optimization using semi-empirical calculations, click on the "Job Options" link to the left of the model window or the arrow to the right on the bottom of the screen.
On the "Configure Mopac Job Options" page, adjust the fields below:
- JOB NAME: give your molecule its standard IUPAC name, followed by an underscore and an identifier of your choice, such as ethanol_practice. Use any identifier you like, as long as the molecule name begins with the IUPAC name and an underscore.
- CALCULATION: Select Geometry Optimization from the Calculation drop-down menu. This will calculate the minimum energy conformation for your molecule.
- THEORY: Select AM1 from the Theory drop-down menu.
- CHARGE: Leave the charge at 0.
- MULTIPLICITY: Leave the multiplicity at Singlet.
Click on the "Submit Job" link to the left of the window or click the right arrow at the bottom of the screen. This will return you to the Job Manager Page, where you will see your job listed. In the status column you will see "Running" in orange.
Click on the Refresh button at the bottom-left corner of the screen. Your job's status should now say "Complete" in green.
Click on the Magnifying Glass icon to the right of the job's status to see the results of the calculation.
SCROLL DOWN to view the various results available from the completed job page. Record the partial charges on oxygen and the attached hydrogen atom; this information will be needed for the THEORY assignment.

The steps below describe how to build a model of trans-1,2-dichloroethene (structure shown below), perform a geometry optimization, then display and analyze the results. Record the calculated dipole moment for this molecule; this information will be needed for the THEORY assignment.

Login to WebMO (if you aren't already) and create a new job.
Watch this short video to see a demonstration of how to build trans-1,2-dichloroethene in WebMO, or follow these steps: Start by drawing the two center carbons of the carbon=carbon double bond. Click once near the center of the Editor window, this will set a single carbon atom. Click on the Carbon atom and hold the mouse button down. Now drag the mouse horizontally away from the first carbon in the direction where you would like to place the second carbon, all the while holding down the mouse button. Release the mouse button when the cursor resides where you would like to place the second carbon atom. Do not put the atoms too close together, or too far apart (about two to three atom diameters is about right) as this can cause problems during the calculations. Also do not rotate the molecule while building unless absolutely necessary, this often makes building more difficult. To make the double bond, click once on the first carbon atom and hold the mouse button down while dragging to the second carbon atom. Release the mouse button while the cursor is over the second carbon atom. The two atoms should now be connected by a double bond.
Click on the PERIODIC TABLE icon on the left-hand menu and select chlorine (Cl) from the table.
Add one chlorine atom to each carbon atom at the approximate distances and angles; please one chlorine above the plane of the double bond and the other chlorine below--this will make the trans-alkene as needed (see structure above).
Click once on the wrench icon, CLEANUP: COMPREHENSIVE: MECHANICS. This will add hydrogen atoms, and perform a molecular mechanics calculation to minimize the energy of the resulting trans-1,2-dichloroethene molecule.
To perform a geometry optimization using semi-empirical calculations, click on the "Job Options" link to the left of the model window or the arrow to the right on the bottom of the screen.
On the "Configure Mopac Job Options" page, adjust the fields below:
- JOB NAME: give your molecule its standard IUPAC name, followed by an underscore and an identifier of your choice, such as trans-1,2-dichloroethene_practice. Use any identifier you like, as long as the molecule name begins with the IUPAC name and an underscore.
- CALCULATION: Select Geometry Optimization from the Calculation drop-down menu. This will calculate the minimum energy conformation for your molecule.
- THEORY: Select AM1 from the Theory drop-down menu.
- CHARGE: Leave the charge at 0.
- MULTIPLICITY: Leave the multiplicity at Singlet.
Click on the "Submit Job" link to the left of the window or click the right arrow at the bottom of the screen. This will return you to the Job Manager Page, where you will see your job listed. In the status column you will see "Running" in orange.
Click on the Refresh button at the bottom-left corner of the screen. Your job's status should now say "Complete" in green.
Click on the Magnifying Glass icon to the right of the job's status to see the results of the calculation.
SCROLL DOWN to view the various results available from the completed job page. Record the calculated dipole moment for this molecule; this information will be needed for the THEORY assignment
1. Dipole Moment: The calculated Dipole Moment of the molecule is displayed in Debye and can be visualized by clicking the adjacent magnifying glass icon.

Following the same steps as the previous models, build a model of cis-1,2-dichloroethene (structure shown below).

To create the desired cis- arrangement of chlorine atoms, be sure to position the chlorines so they both point in the same direction (see demonstration below). Perform a geometry optimization (again using the AM1 level of theory). View the results of the calculation and record the calculated dipole moment for this molecule; this information will be needed for the THEORY assignment.