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Department of Chemistry

The Intersectionof

Computational Chemistryand

Experiment

Structure, Vibrational and Electronic Spectraof

Organic Molecules

Angelo R. RossiDepartment of Chemistry

The University of [email protected]

Spring 2017

Last Updated: February 4, 2017 at 6:51am

Exercises

Frequency Calculations and Vibrational Analysis

Geometry Optimization

Before a frequency calculation or vibrational analysis can be performed, a geometry optimization onthe molecule must first be performed. A typical Gaussian input file for optimizing the acrolein usingcoordinates is given below:

%chk=acrolein-trans-opt-coord

# HF/6-31g* opt gfinput gfprint pop=full

Acrolein Ground state optimization

0 1

O -1.242755 -1.344192 0.000000

C 0.000000 0.741186 0.000000

C 1.219202 1.332734 0.000000

C -0.110617 -0.794819 0.000000

H -0.885875 1.341286 0.000000

H 0.775207 -1.395005 0.000000

H 1.296116 2.400016 0.000000

H 2.105077 0.732634 0.000000

• Optimize the molecular structure with the Gaussian program using Wave Function Theory: HF/6-31g∗ and Density Functional Theory: B3LYP/6-31g∗.

• Check the optimization convergence with appropriate visualization software, as well as directly view-ing the output of the Gaussian log file.

Last Updated: February 4, 2017 at 6:51am 2

Frequency Calculation

A typical Gaussian input file for performing a frequency calculation by using the data from a restart file:

%oldchk=acrolein-trans-opt-coord

%chk=acrolein-trans-vib

# HF/6-31g* opt gfinput gfprint freq=raman pop=full guess=read geom=allcheck

Acrolein Vibrational Analysis at the Optimized Geometry

0 1

• Perform a frequency analysis with the Gaussian program using Wave Function Theory: HF/6-31g∗

and Density Functional Theory: B3LYP/6-31g∗.

• Verify that the optimization reached a minimum on the potential energy surface by performing avibrational analysis at the optimized geometry.

All calculated frequencies must be positive at the optimized geometry.

Analysis of a Calculated IR Spectrum

• Visualize the vibrational normal modes with appropriate visualization software applications.

• Assign the character of the normal modes (e.g. stretching, in-plane bending, out-of-plane bending,other deformations), and assign the symmetry of corresponding vibration.

Also, look for IR intensity and Raman activity in the Gaussian log file.

• Compare the calulated vibrational spectrum with the one experimentally obtained by providing agraph of the two spectra and discussing similarities or differences.

• Explain which normal mode vibrations are allowed or forbidden, as well as whether they are onlyinfrared active, only Raman active, or both active.


Wave Function Theory

The experimental values for the first and second excited states are 3.73 eV and 6.41 eV, respectively


Density Functional Theory

The experimental values for the first and second excited states are 3.73 eV and 6.41 eV, respectively

• Time Dependent Density Functional Theory (TDDFT) tends to be more accurate than CIS, but thisis sensitive to choice of functional and certain special situations.

• Charge-transfer transitions are particularly problematic,

• For TDDFT, no wave function is created, but eigenvectors analogous to those predicted by CIS areprovided.


Excited-State Calculations

Organic Molecules for Calculation of UV-Visible Spectra

butadienetrans cis

acroleintrans cis

glyoxaltrans cis

Figure 1: trans- and cis-Conformations of butadiene(top), acrolein(center), and glyoxal(bottom)


Gaussian input files for performing a vertical excitation using the data from a restart file:

Wave Function Theory (WFT) - Configuration Interation with Singles (CIS)

%oldchk=acrolein-trans-opt

%chk=acrolein-trans-ex-gas.chk

# CIS(nstates=6)/6-31g(d) 5d gfinput gfprint pop=full guess=read geom=allcheck

Acrolein: UV spectrum calculated with CIS at the optimized trans conformation

0 1

Density Functional Theory


%chk=acrolein-trans-ex-gas.chk

# b3lyp/6-31G(d) td(nstates=6) 5d gfinput gfprint pop=full guess=read geom=allcheck

Acrolein: UV spectrum calculated with time TDDFT at the optimized trans conformation

0 1

• Calculate the UV (vertical excitation) spectrum of acrolein using configuration interaction withsingle excitations using both Wave Function Theory: HF/6-31g∗ and Density Functional Theory:B3LYP/6-31g∗.

• Characterize the type of excitations (π → π∗, ...) for the first few excited states.

• Compare the calulated excitation spectrum with the one experimentally obtained by providing agraph of the two spectra and discussing similarities or differences.

• Which excitations are allowed or forbidden? Why? Use symmetry arguments.

Why can excitations which are forbidden appear in the experimental spectrum?

• Compare the results of the CIS (wave function theory) and TDDHF (Density Functional Theory)calculations by providing a graph of the two spectra and discussing similarities or differences.


Excited-State Calculations (Continued)

Analysis of Molecular Orbitals (MOs)

• Construct an MO excitation diagram for the appropriate highest occupied and lowest unoccupiedMOs.

Visualize the MOs with appropriate visualization software, and include them in the MO excitationdiagram.

Characterize the MOs by σ, σ∗, π, π∗, and n, i.e. bonding, antibonding, and non-bonding, and assignthe symmetry representation for each orbital.

Both visualized MOs and energy levels should be included.

Rotational Potential Energy Curves for Excited States of Organic Molecules

Another way to input the coordinates of a molecule is through the use of a Z-matrix which providesflexibility in the ability to change structural parameters and easily calculate potential energy surfaces.

• Perform excited-state calculations on butadiene, glyoxal, and acrolein, as shown in Figure 1, andcalculate the two lowest excited-states for a a rigid potential energy surface of rotation aboutthe central C-C bond.

• Construct graphs comparing the ground-state rotational potential energy curves with the excited-state results.

• Explain the trends observed in these graphs, and discuss whether or not excitations increase ordecrease the rotational barriers.


Solvatochromism

Examples of Gaussian input files for implicit polar and non-polar solvent calculations:

Polar Solvent


%chk=acrolein-trans-ex-water

# B3LYP/6-31G(d) guess=read geom=allcheck 5D td(nstates=6) SCRF=(SMD, Solvent=Water)

gfinput gfprint pop=full

Acrolein: UV spectrum at the optimized geometry in water

0 1

Non-polar Solvent


%chk=acrolein-trans-ex-heptane

# B3LYP/6-31G(d) guess=read geom=allcheck 5D td(nstates=6) SCRF=(SMD, Solvent=Heptane)

gfinput gfprint pop=full

Acrolein: UV spectrum at the optimized geometry in heptane

0 1

• Calculate the spectra of acrolein in polar and non-polar solvents using the continuum model ofsolvation, and compare these results with experimental data.

Look for solvent shifts, and rationalize the results.

• Which of the molecules in Figure 1 will be significantly impacted from solvation in the excited state?

Explain. Justify any discussion by performing calculations on these molecules in polar and non-polarsolvents.


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