Comput. Chemistry Lab

Part B: Phosporous Trichloride

Introduction

Now you are going to calculate the inversion potential energy surface for PCl₃. PCl₃ is a toxic corrosive liquid that reacts violently with water. Phosphorus trichloride is a remarkably versatile reagent and is used to introduce chlorine or phosphorus into a wide range of inorganic and organic precursors. It is an important industrial chemical and produced in the millons of tons yearly, mostly for herbicides, insecticides, plasticisers, water processing chemcials and surfactants. Approximately 70% of the PCl₃ produced is used in the manufacture of organophosphorus pesticides including glyphosate, the active component of Roundup (chlorine is lost in the manufacturing process as HCl).

In this part of the lab you will gain experience in using non-standard basis sets and pseudo-potenitals, essential skills if you want to use computational chemistry to study inorganic systems, especially catalysis or main group metal containing compounds.

Diffuse functions allow the electron density to extend out a little from the molecule. Polarization functions allow the electron density to become polarized to one side of a molecule. Both types of function are important for an accurate description of transition states and structures that are not optimised ground state structures. In reactions the electron density is moving around and basis sets must be good to accommodate this ebb and flow.

Activities

(B1) Calculate the C_3v ground state and D_3h transition state of PCl₃, for the following basis sets and pseudo-potentials, in each calculation add the additional keyword "gfinput". Gfinput turns on the printing of the basis sets and pseudo-potentials in the output file.

• Start by carrying out a low level calculation to get a roughly correct structure using: B3LYP/6-31G
• now add polarization and diffuse functions: B3LYP/6-31+G(d,p)

What difference has adding polarisation and diffuse functions made to:

• the final geometry and barrier height?
• how many steps were there in the optimisations?
• how long did the optimisations take?
• is there any difference in the final structures?
• how many basis functions are there in each calculation?

  This information is found in the .log file, look for "Two-electron integral symmetry is turned on." for example:

  Two-electron integral symmetry is turned on. 36 basis functions, 56 primitive gaussians, 37 cartesian basis functions 5 alpha electrons 5 beta electrons nuclear repulsion energy 11.9101813716 Hartrees.

  this tells you how many "basis functions", "primitvie gaussians" and how many electrons are explicitly computed (ask the demonstator if you have problems.

(B2) Psuedo potantials replace the core electrons on an atom by a much simpler function. They are necessary for systems with a large number of electrons because the difficulty of a calculation scales with the number of electrons.

To use the basic pseudo-potential, just choose "LANL2DZ" out of the pull-down menu for basis sets.

To use the extra basis functions with a pseudo-potential requires that you edit the input file manually outside of gaussview. Pseudo-potentials always come with their own basis sets, you cannot use standard basis sets with pseudo-potentials, and thus they also come with special polarisation and diffuse functions.

• copy your previous run .com file to a new name ready for editing
• add to the command line (the line beginning with a hash) the key word "PSEUDO=READ
• replace the method/basis set specification with "B3LYP/GEN"
• leave the geometry keywords and gfinput keywords alone
• after the geometry section leave a blank line and add the following:

  P 0
  LANL2DZ
   P   1  1.00
        0.298000000E-01      1.00000000
   D   1  1.00
        0.364000000          1.00000000
   ****
  Cl 0
  LANL2DZ
   P   1  1.00
        0.467000000E-01      1.00000000
   D   1  1.00
        0.648000000          1.00000000
   ****
  
   P 0
   LANL2DZ
   Cl 0
   LANL2DZ
  						

  the first part adds the new basis functions, the second part adds the pseudo-potentials, make sure you add both!

• be sure to leave a blank line at the end of this section once you have added it to the input file.

There is an example file (pcl3_c3v_pp.txt) however you need to use the same starting geometry for all of these jobs so that they can be directly compared, so don't use my geometry!!

what difference has adding the pseudo-potential made to:

• the final geometry and barrier height?
• how many steps were there in the optimisations?
• how long did the optimisations take?
• is there any difference in the final structures?
• how many basis functions are there in each calculation?

you might want to make up a table comparing all this data.
Here are a few questions to answer.

• explain the basis set and pseudo-potential output seen in the .log file
• explain the functional form of polarization and diffuse functions
• explain using diagrams what polarization and diffuse functions do

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