WebMO – General Chemistry

These computational data are associated with the CHEM 103 – Molecular Geometry/WebMO Lab.  In the accordion panels below, you will find  clickable molecular images linked to WebMO pages that provide the designated computational output from Gaussian 09.  There are initial instructions for the Hydrogen (H2) and Water (H2O) molecules.  All subsequent molecules are associated with directions in your laboratory manual.

Index of Molecules

This is an accordion element with a series of buttons that open and close related content panels.

Hydrogen

Hydrogen (H2)

 

H2 H2_scan
hydrogen (H2) opt+vib hydrogen (H2) coordinate scan

Bond Length Measurement

  1. To measure the H-H bond distance, open the H2 opt+vib link.
  2. Click on the select tool () located on the left-hand side of Molecule Viewer.
  3. Click on each hydrogen atom and the measured distance will appear in bold/blue text in the bottom left of the Molecule Viewer window as shown below.

Coordinate Scan Viewinig

  1. To view the H-H bond distance scan, open the H2 coordinate scan link.
  2. Scroll down the window and locate the “Coordinate Scan” Table.
  3. To view an energy graph, click the graph tool icon ().  To view an animation of the scan showing the increasing H – H distance, click the movie icon ().

Water

Water (H2O)

 

h20 H2O scan
water (H2O) opt+vib

water (H2O) NBO

water (H2O) coordinate scan

Bond Angle Measurement

  1. To measure the H-O-H bond angle, open the water (H2O) opt+vib link.
  2. Click on the select tool(select_tool) located on the left-hand side of Molecule Viewer.
  3. Click on H, O, and H atoms in order and the measured angle will appear in bold/blue text in the bottom left of the Molecule Viewer.

Coordinate Scan Viewing

  1. To view the H-O-H bond angle scan, open the water (H2O) coordinate scan link.
  2. Scroll down the window and locate the “Coordinate Scan” Table.
  3. To view an energy graph, click the graph tool icon ().  To view an animation of the scan, click the movie icon ().

Lone Pair Viewing

  1. To view the O-atom lone pairs, open the water (H2O) NBO link.
  2. Scroll down to the final table, named “Natural Bond Orbitals”.
  3. To view each lone pair orbital, click the display tool icon () for orbitals 2 and 3, designated LP(1)O1 and LP(2)O1, respectively.
  4. Rotate them around to visualize their location relative to the atoms in the molecule.

H2O_NBO

Sulfur Oxides

Sulfur Oxyanions

Sulfur Oxyanions (SO32- & SO42-)

 

SO32- SO42-
sulfite (SO32-) opt+vib sulfate (SO42-) opt+vib

Methyl Anion, Methane, and Methyl Cation

Methyl Anion, Methane, and Methyl Cation (CH3, CH4, & CH3+)

 

CH3- CH4 CH3+
methyl anion (CH3) opt+vib methane (CH4) opt+vib methyl cation (CH3+) opt+vib

Amide Anion, Ammonia, and Ammonium Cation

Amide Anion, Ammonia, and Ammonium Cation (NH2, NH3, & NH4+)

 

NH2- NH3 NH4+
amide anion (NH2) opt+vib ammonia (NH3) opt+vib

ammonia (NH3) NBO

ammonium cation (NH4+) opt+vib

Hypervalent Compounds

Carbonate & Nitrate

Carbonate (CO32-) & Nitrate (NO3)

 

carbonate nitrate
carbonate (CO32-) opt+vib nitrate (NO3) opt+vib

Organic Molecules (Methanol, Methyl amine, Formamide)

Methanol (CH3OH), Methyl amine (CH3NH2), & Formamide (HCONH2)

 

methanol methylamine formamide
methanol (CH3OH) opt+vib methyl amine (CH3NH2) opt+vib formamide (HCONH2) opt+vib