GAUSSIAN 09W TUTORIAL - McGill University

1 GAUSSIAN09W TUTORIALAN INTRODUCTION TOCOMPUTATIONALCHEMISTRY USINGG09 WANDAVOGADRO SOFTWAREAnna is a quick TUTORIAL that will help you to make your way through thefirst steps of computational chemistry using GAUSSIAN 09W software (G09).The TUTORIAL is oriented to beginners and describes in detail the most usedcalculations done using G09. However, the theoretical basis of these cal-culations will not be covered here. If you are interested in understadingthe details, please refer to textbooks targeting this subject. I found [1] and[2] very helpful, and strongly recommend to take a look at these TUTORIAL - ATpage 1 of 34 CONTENTS1 Program Input .. Output .. Visualization .. Computation model ..52 First look at a EXAMPLE 1: Single Point Energy of Water ..53 GAUSSIAN Input Link 0.

2 Route Section .. Molecular Structure ..84 Theoretical What is a theoretical model? .. initiomethods .. Examples ofAb initiomethods .. Semiempirical methods .. Examples of semiempirical methods .. Density Functional Theory .. Examples of DFT methods .. Molecular Mechanics .. Examples of MM methods .. 105 Basis What is a basis set and why is its selection important? .. A bit of theory: Slater VS GAUSSIAN .. Types of Basis Sets and Notation .. Minimal .. Split Valence .. Correlation-consistent .. Useful Tips from David Sherrill[5].. Comparison between Pople and CC basis sets .. 136 Types of Geometry Optimization .. What is it? .. For your Job .. What information do you get out of this calculation?

3 Single point energy .. What is it? .. For your Job .. What information do you get out of this calculation? .. Frequencies and Thermochemistry .. What is it? .. For your Job .. What information do you get out of this calculation? .. 17G09 TUTORIAL - ATpage 2 of Stability check .. What is it? .. In G09 .. For your Job .. Molecular Orbitals and Population Analysis .. What is it? .. For your Job .. What information do you get out of this calculation? .. UV-Vis and Electronic transitions .. What is it? .. For your Job .. What information do you get out of this calculation? .. Potential Energy Surface .. What is it? .. For your Job .. Solvation effect.

4 What is it? .. For your Job .. Other Molecular Properties .. Polarizability .. Forces on Nuclei .. Molecular Volume .. NMR analysis .. Electrostatic potential and Electron density .. 227 For a successfull Main steps of a successfull computational study .. Step 1: Define the boundries .. Step 2: Set up you computer .. Step 3: Define a good way to name the jobs .. Step 4: Define a parent molecule.. Step 5: Succesfull sequence of calculations .. Step 6: Read the output .. 248 Batch files: avoid waiting What are Batch Files? .. How to create a .bcf file? .. Batch File Generator .. 259 EXAMPLE 1: SP of H2O .. EXAMPLE 2: Opt of Ethanol .. EXAMPLE 3: Molecular Orbitals Calculation and Visualization of EXAMPLE 4: The Energy of Stereisomers and Scaling Factors (butene) 2910 Convergence cannot be achieved?

5 My job froze, what can I do to avoid restarting from scratch? .. A double bond disappeared from the structure after computation? .. My batch file does not run properly, why? .. 30G09 TUTORIAL - ATpage 3 of 3411 Appendix3112 References33G09 TUTORIAL - ATpage 4 of 341 PROGRAM SPECIFICATIONSG aussian 09W (G09) is a computational chemistry program that runs on any mod-ern Windows 32-bit PC. If you want to install G09 on a 64bit PC, there is a specialprocedure you must follow:1. Insert the CD with G09 and copy its content onto you computer. Any folderwill do; I copied directly into the :C\ Open directory containing G093. Find the file4. Right click on exe file, select Properties, a new window should appear5. Go into the Compatibility menu6. Put a checkmark next to : Run as administrator (this should enable othercheckboxes)7.

6 Put a checkmark next to : Run this program in compatibility with (selectWindows version that you are using)The installation requires the GAUSSIAN CD and a registration (ChemBio 3D Ultra) and Avogadro ( )softwares can be used for you prefer watching video tutorials for a better understand-ing, please see below: Part 1: Part 2: Part 3: Part 4: Part 5: search for "Avogadro with GAUSSIAN TUTORIAL " in INPUTThe input for G09 can have the following extensions: GAUSSIAN Input File: .gjf Batch Control File: .bcf Avogadro Input File: .com Text File: .txtG09 TUTORIAL - ATpage 5 of 34 The input can be done manually or come from another software, such as Chem-Draw (3D) or Avogadro. G09 s input consists of the following parts, shown onFigure 1:Figure 1: G09 input windowThis window appears when you click on File Open.

7 In the main G09window. The first line : specifies the path to the file you just loaded. Section: specifies the name of the checkpoint file (.Chk) Route Section: specifies the basis set, the theoretical model and the type ofjob you want to perform Title Section: specifies the name of the job (for the user s ease only) Charge, Multipl.: specifies the charge and spin multiplicity of the currentmolecule separated by a space. Molecule Specification: specifies the atoms and their coordinates this iswhat we want from the ChemDraw and Avogadro input, otherwise, we wouldneed to calculate the coordinates by details on each section of the input is available in section ( )G09 TUTORIAL - ATpage 6 of OUTPUTTo run the G09 job, click on the RUN button, on the right panel of the Job Entrywindow (Figure 1).

8 The output has only one extension: .out. You will be promptto save the output file before closing G09 VISUALIZATIONThis TUTORIAL will use Avogadro software for visualization of the G09 output. Openthe .out file in Avogadro, your input molecule should appear on the view detailed demostration of Avogadro is available in the first two parts of the you try to visualize things you have not calculated using G09, the programwill freeze! COMPUTATION MODELThe mathematical models used to do the computations are called FEM (FinalElement Method) and Symplex method. Using matrices, this method cuts the N-dimensional space into small sub-systems that can be described by N linear equa-tions. These equations can be solved as soon as one of them is solved. Therefore,one must take a guess of the solution and then, recursively solve all the other all solutions are obtained, the initial guess can be modified and the calcula-tions repeated.

9 This process is run until the new solution outputs the same resultas in the previous iteration. This is called the initial guess can be very far off the real value, many thousands ofiterations are often needed. The basis set selected influences, among other, thequality of the guesses, while the theoretical model influences the type of calcula-tions that the matrices will be subjected calculation stops as soon as the result converges, however convergence doesnot mean that the system reached its minimum. It is very likely that the minimumoutputted is actually only a saddle point on the potential surface, but the programwill not be aware of this. The user must be careful with this, and always performa check of stability of the system. This is done by perturbing the "stable" systemand re-calculating the minimum.

10 If the output is the same, one can assume thatthe energy obtained is the total MORE DETAILS ON THE MATH:[3]2 FIRST LOOK AT A COMPUTATIONThis section will describe how to do a simple calculation in G09 using the parts of this procedure (and more) are explained more in details in corre-sponding sections. Let s take a EXAMPLE 1: SINGLEPOINTENERGY OFWATERLet s calculate the Single point energy of water. For this, we will first open Avo-gadro and draw the molecule (Figure 2).If you think you will reuse this molecule in Avogadro, you can save it with is good practice to save all parts of your job along the way!G09 TUTORIAL - ATpage 7 of 34 Figure 2: water molecule in AvogadroNow, find the Extensions button on the top task bar, and select " "under this tab. A new window should appear (Figure 3).