Department of Chemistry The Intersection of Computational Chemistry and Experiment Structure, Vibrational and Electronic Spectra of Organic Molecules Angelo R. Rossi Department of Chemistry The University of Connecticut angelo.rossi@uconn.edu 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 on the molecule must first be performed. A typical Gaussian input file for optimizing the acrolein using coordinates is given below: %chk=acrolein-trans-opt-coord # HF/6-31g* opt gfinput gfprint pop=full Acrolein Ground state optimization 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 viewing 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 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 a vibrational 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 a graph of the two spectra and discussing similarities or differences. Explain which normal mode vibrations are allowed or forbidden, as well as whether they are only infrared active, only Raman active, or both active. Last Updated: February 4, 2017 at 6:51am 3
Wave Function Theory The experimental values for the first and second excited states are 3.73 ev and 6.41 ev, respectively Last Updated: February 4, 2017 at 6:51am 4
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 this is 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 are provided. Last Updated: February 4, 2017 at 6:51am 5
Excited-State Calculations Organic Molecules for Calculation of UV-Visible Spectra butadiene trans cis trans acrolein cis trans glyoxal cis Figure 1: trans- and cis-conformations of butadiene(top), acrolein(center), and glyoxal(bottom) Last Updated: February 4, 2017 at 6:51am 6
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 Density Functional Theory %oldchk=acrolein-trans-opt %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 Calculate the UV (vertical excitation) spectrum of acrolein using configuration interaction with single 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 a graph 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. Last Updated: February 4, 2017 at 6:51am 7
Excited-State Calculations (Continued) Analysis of Molecular Orbitals (MOs) Construct an MO excitation diagram for the appropriate highest occupied and lowest unoccupied MOs. Visualize the MOs with appropriate visualization software, and include them in the MO excitation diagram. Characterize the MOs by σ, σ, π, π, and n, i.e. bonding, antibonding, and non-bonding, and assign the 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 provides flexibility 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, and calculate the two lowest excited-states for a a rigid potential energy surface of rotation about the central C-C bond. Construct graphs comparing the ground-state rotational potential energy curves with the excitedstate results. Explain the trends observed in these graphs, and discuss whether or not excitations increase or decrease the rotational barriers. Last Updated: February 4, 2017 at 6:51am 8
Solvatochromism Examples of Gaussian input files for implicit polar and non-polar solvent calculations: Polar Solvent %oldchk=acrolein-trans-opt %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 Non-polar Solvent %oldchk=acrolein-trans-opt %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 Calculate the spectra of acrolein in polar and non-polar solvents using the continuum model of solvation, 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-polar solvents. Last Updated: February 4, 2017 at 6:51am 9