Introduction to GAUSSIAN 98W and GENNBOW 5'0

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Introduction to GAUSSIAN 98W and GENNBOW 5.0

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Outline 1. Basis sets of orbitals 2. Using
PCModel for molecular modeling and as an
interface with GAUSSIAN 98W 3. The forms of
GAUSSIAN 98W input and output files. 4.
Introduction to the theory of NBO 5. Introduction
to the NBO 3.0 program, implemented to GAUSSIAN
98W and its use for evaluation of stabilizing
orbital interactions 6. Introduction to the
standalone GENNBOW 5.0 program and its use for
the NRT theory
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1. Basis sets of orbitals
Molecular orbitals of a chemical system
(molecule, radical, ion, excited state etc.) are
build from a Basis Set of orbitals by the LCAO
method. A larger number of basis orbitals gives
more flexibility to the process of LCAO
optimization and provides a better set of
molecular orbitals. In Minimum Basis Sets each
Basis Orbital is Built from one atomic orbital,
in Split Basis Sets one or more basis orbitals
are built from one atomic orbital. Atomic
orbitals are well represented by Slater type
orbitals (STO), which are not convenient for
computations. Because of this, atomic orbitals
are constructed as a sum of one or more Gaussian
type orbitals (GTO).
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(For the right branch)
Minimum basis set STO-3G Each atomic orbital
represents a basis orbital and is
constructed from three GTO. total for carbon 5
basic functions, 15 GTOs
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Split Basis sets
Two basis functions are built from valence atomic
orbitals. One basis function is built from core
orbitals.
Example 3-21G basis set both core and valence
atomic orbitals are represented by three GTOs.
Total for carbon 9 basic functions, 15
GTOs. Split basis sets are superior vs. the
Minimum basis set, because they give more
flexibility to the optimization.
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Another example of split basis set 6-31G basis
set Core atomic orbitals are represented by six
GTOs, and valence atomic orbitals are represented
by four GTOs.
Total for carbon 9 basic functions, 22 GTOs.
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An example of a double split basis set 6-311G
basis set Core atomic orbitals are represented
by six GTOs, and valence atomic orbitals are
represented by five GTOs.
Total for carbon 13 basic functions, 26 GTOs.
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Polarized basis sets have additional basis
functions with L x 1, where x is the largest
quantum number L in the basis set. For instance,
to all elements of the 2nd period, 6 d-orbitals
are added, to all elements of the 1st period, 3
p-orbitals are added (each represented by one
GTO). For instance, the 6-31G basis set for
carbon (d-orbitals are added to all atoms, except
hydrogens) has (15 9 6) basis functions and
(28 22 6) GTOs. The basis set 6-31G basis
set is same as 6-31G basis set, but additional
functions are added to all atoms, including
hydrogens. Examples for hydrogen 6-31G basis
set 2 basis functions, 4 GTOs. 6-31G basis
set 5 basis functions, 7 GTOs.
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2. Using PCModel for molecular modeling and as an
interface with
GAUSSIAN 98W
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3. The forms of GAUSSIAN 98W input and output
files
HF/3-21G GAUSSIAN input file for the
molecule of water in Cartesian coordinates for a
single-point calculation 0 1 O
-0.226958 0.284685 -0.261528 H -0.232987
-0.718496 0.189196 H -1.104056
0.849609 0.087152
HF/3-21G OptZ-matrix GAUSSIAN input file
for the molecule of water in internal
coordinates for the optimization with the frozen
angle A3 0 1 O H,1,R2 H,2,R3,1,A3
Variables R21.099811 R31.796717
A335.242874
HF/3-21G OptZ-matrix GAUSSIAN input file
for the molecule of water in internal
coordinates for the full optimization 0 1
O H,1,R2 H,2,R3,1,A3 Variables
R21.099811 R31.796717 A335.242874
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4. Introduction to the theory of NBO
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5. Introduction to the NBO 3.0 program,
implemented to GAUSSIAN 98W and its use for
evaluation of stabilizing orbital interactions
Let us quantitatively compare the conjugation
with the carbonyl group in acetylchloride and
methyl acetate.
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Step 1. Build GAUSSIAN input files for both
molecules and run full optimizations for
them. Step 2. Read the output files using
PCModel, build new input files and include there
a command to call the implemented NBO 3.0 program.
HF/3-21G PopNBORead NBO input file for
methyl acetate 0 1 C -1.929142
-0.788266 -0.006665 C -0.501571 0.071299
0.031806 O 0.673270 -0.851462
-0.138486 O -0.358059 1.390747 0.188375
C 2.150399 -0.203161 -0.128225 H
-2.854980 -0.040890 0.129011 H -1.922437
-1.609506 0.871729 H -2.013291
-1.372720 -1.054194 H 2.899356 -1.122671
-0.279094 H 2.357685 0.348594
0.916046 H 2.264914 0.590656 -1.019625
NBO END
HF/3-21G PopNBORead NBO input file for
acetyl chloride 0 1 C 0.792521
-0.913172 0.048911 C 0.025056 0.366855
0.106067 Cl -1.735643 0.054661
-0.621798 O 0.298831 1.439743 0.490197
H 1.781962 -0.753227 0.453540 H
0.854823 -1.246274 -0.978191 H 0.269651
-1.668697 0.619460 NBO END
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Step 3. Find in the NBO section of the output
files the interactions of interest 17.45
kcal/mol for acetyl chloride and
49.19 kcal/mol for methyl acetate. The results
are consistent with intuitive considerations
(the lone pair on chlorine is less active, that
the lone pair on oxygen because of lesser 3n-2p
overlap).
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6. Introduction to the standalone GENNBOW 5.0
program and its use for the NRT theory
Now we will compare relative contributions of two
resonance Structures for the same pair of
molecules
Unfortunately the NBO 3.0 program, implemented to
GAUSSIAN, can not do the NRT analysis. We need to
use the GENNBOW 5.0 to run this type of
computations. We need to tell the NBO 3.0
program to create an input file for the GENNBOW
5.0 program by placing the following line to the
GAUSSIAN input file and run GAUSSIAN again NBO
ARCHIVE FILEfilename END
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How to specify connectivities for the resonance
structures of interest and tell it to the GENNBOW
5.0 program
Molecule 1 Acetyl chloride
NBO NRT END NRTSTR STR1 LONE 3 3 4 2 END
BOND S 1 5 S 1 7 S 1 6 S 1 2 S 2 3 D 2 4 END
END STR2 LONE 3 2 4 3 END BOND S 1 5 S 1 7 S
1 6 S 1 2 S 2 4 D 2 3 END END END
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Molecule 2 Methyl acetate
NBO NRT END NRTSTR STR1 LONE 3 2 4 2
END BOND S 1 6 S 1 7 S 1 8 S 1 2 S 2 3 S 3 5 S 5
10 S 5 11 S 5 9 D 2 4 END END STR2 LONE 3 1 4
3 END BOND S 1 6 S 1 7 S 1 8 S 1 2 D 2 3 S 3 5 S
5 10 S 5 11 S 5 9 S 2 4 END END END
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Finally, find in the scratch directory, which
belongs to GAUSSIAN, The archive files with the
extension .47. Open them and replace the NBO
END line with the specifications you have just
prepared. Save the files, run the GENNBOW 5.0
program and get the following results,
consisting with the intuitive considerations