L2_gaussian_gaussview

2. Z-matrix coordinates:
• also called internal coordinates • specify positions of atoms relative to one another using bond lengths, angles and dihedral angles (3N-6 variables) • one section specifies connectivity, second section specifies values of variables corresponding to bond lengths, etc. • Gaussian expects values in Angstroms and degrees • convenient for PES scans because bonds and angles are defined explicitly
8. Blank Line: -tells program the input file is done
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Gaussian Input File
example input for water
link 0 commands route line
charge and multiplicity
geometry in cartesian coordinates
• • • • specifies type of calculation that is to be performed line starts with „#‟, can only be 80 characters in length can have multiple lines line contains method, basis set and keywords with options in parentheses:
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Gaussian Input File
the Gaussian input file has the following form (/g_ur/m_input.htm): 1. Link 0 Commands: -set up memory limits, etc. Line starts with %. Optional. 2. Route Section: -specifies the details of the calculation
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Z-matrix Input
connectivity specification:
C C H H H H 1 1 1 2 2 B1 B2 B3 B4 B5
H3
H5
2 2 1 1
A1 A2 3 D1 A3 3 D2 A4 5 D3
H4
C1
C2
H6
• 1st column specifies atom type • 2nd column defines a bond, e.g. the „1‟ in line 2 indicates that atom 2 is bonded to atom 1 • 3rd column gives the label of a variable corresponding to the bond length
-can be multiple lines with max. 80 characters -each line in Route Section must start with #
3. Blank Line: -tells program Route Section is done
4. Title
• 4th column defines an angle, e.g. the „2‟ in line 3 indicates that the 3rd atom forms a 3-1-2 (H3-C1-C2) angle
• 5th line gives the label of a variable containing the value of the dihedral angle • 6th line defines a dihedral angle, e.g. the „3‟ in line 4 indicates that the 4th atom forms a dihedral 4-1-2-3 (H4-C1-C2-H3) dihedral angle • 7th line gives the label of a variable containing the value of the dihedral angle 7
CHEM 834: Computational Chemistry
Exploring the Potential Energy Surface with Gaussian/Gaussview
March 9, 2008
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Topics
Last time: • overview of computational chemistry • exploring potential energy surfaces Today: • gaussian/gaussview overview and tutorial Reminders: • projects should be selected and approved by March 13 • assignment 1 is optional, but you can hand it in to me if you want comments
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How to Explore the PES with Gaussian/Gaussview
Gaussian (): • computational chemistry software package • performs molecular mechanics, ab initio, density functional theory, and semi-empirical molecular orbital calculations • calculates a wide range of properties • performs geometry optimizations and frequency calculations Gaussview (): • graphical user interface for Gaussian • can build molecules, set-up input files, submit Gaussian calculations, and visualize results Gaussian03 and Gaussview are available on department computer cluster (Rm. 100) Gaussian03 and Gaussview can be installed on other department owned computers (ask me)
5. Blank Line: -tells program Title is done 6. Charge and Multiplicity 7. Molecular Geometry: -provide the atomic coordinates
-Cartesian or Z-matrix format
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Z-matrix Input
connectivity specification:
C C H H H H 1 1 1 2 2 B1 B2 B2 B2 B2
H3
H5
A3 C1 D2 C2 B4
2 2 1 1
A1 A1 3 D1 A1 3 D2 A1 5 D3
H4
variables:
B1=1.5 B2=1.1 A1=120.0 D1=0.0 D2=0.0 D3=180.0
• careful, though
• assigning the same label to two or more geometric variables means they have to remain equal throughout entire calculation
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Route Line
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Z-matrix Input
connectivity specification:
C C H H H H 1 1 1 2 2 B1 B2 B3 B4 B5
H3
H5
A3 C1 D2 C2 B4
2 2 1 1
A1 A2 3 D1 A3 3 D2 A4 5 D3
H4
variables:
B1=1.5 B2=1.1 B3=1.1 B4=1.1 B5=1.1 A1=120.0 A2=120.0 A3=120.0 A4=120.0 D1=0.0 D2=0.0 D3=180.0
/g_ur/keywords.htm
• relevant keywords for exploring the PES: • scan perform a scan along predefined coordinates • opt perform a geometry optimization to a minimum or transition state • freq perform a frequency/normal mode calculation
Z-matrix Input
connectivity specification:
C C H H H H 1 1 1 2 2 B1 B2 B3 B4 B5
H3
H5
A3 C1 D2 C2 B4
2 2 1 1
A1 A2 3 D1 A3 3 D2 A4 5 D3