A web page containing Jmol applets

Once the molecule file is fully loaded, the image at right will become live. At that time the "activate 3-D" icon will disappear.

Phenol (C6H5OH)

The geometry optimizations for the three highest levels of theory are shown below for phenol. The levels of theory used were 621G, 631G, and DZV. The buttons below display the bond lengths and the bond angles for each level of theory respectively.

Table 1: This table displays the bond lengths for phenol taken from the literature⁴.

Bond Type	Bond Length in Angstroms
C-C	1.398
C-H othro	1.084
C-H meta	1.076
C-H para	1.082
C-O	1.364
O-H	0.956

The two buttons above display the bond lengths and angles for the 621G optimization.

The two buttons above display the bond lengths and angles for the 631G optimization.

The two buttons above displays the bonds lengths and angles for the DZV optimization. The values calculated from the DZV theory was determined to be the best optimization for the bond lengths and angles.
The overall percent error in the total bond lengths was 5.74%.

This displays the Highest Occupied Molecular Orbital found at orbital 25. The orbitals were calculated by adding all of electrons in the molecule and dividing it by two.

This displays the Lowest Unoccupied Molecular Orbital found at orbital 26. The electrons will transition to this orbital when excited with enough energy.

This button displays the electrostatic potential. The electron cloud ranges in color from red to blue. Red being areas of high electrostatic potential and blue being areas of low electrostatic potential. Since the oxygen atom (hydroxyl group) is more electronegative, thus pulling the electrons closer to it (Red area).

The partial atomic charge on each atom is shown in this diagram. They are created by the asymmetric distribution of electrons in a chemical bond. The sum of these charges equal to zero.

The vibrational frequencies were calculated using the highest level of theory, DZV. The IR-spectrum for Phenol is displayed below retrieved from the NIST website⁴.

IR Spectrum for Phenol taken from the NIST website

Figure 1:
This is an IR-Spectrum of phenol displaying the vibrational frequencies of the bonds⁴.

Table 2: This tables displays the vibrational frequencies for the bonds in phenol taken from the literature¹.

Type of Vibration	Wavelength in cm^-1
C-H bend	680-900
C=C stretch	1440-1620
C-H stretch	3000-3100
O-H stretch	3350-3650

C-H bend

C=C stretch

C-H stretch

O-H stretch

The buttons above display the vibrations calculated from the highest level of theory. All values calculated using DZV were overestimates giving large percent errors of 6.53%, 0.087% (this was a very good estimate), 9.68%, and 11.96% respectively.

UV-Vis spectra values were calculated with the highest level of geometry optimization theory.

Table 3: This table contains values of constants taken from NIST used for UV-Vis calculations below⁶.

Constant	Value of Constant
Planck's Constant (h)	6.62606957x10^-34 Js
Speed of Light (C)	2.99792x10^8 m/s

Energy = Planck's constant x speed of light / wavelength
Wavelength = Planck's constant x speed of light / Energy

Table 4: This table displays the oscillator strength and wavelengths for phenol.

Oscillator Strength (unitless)	Wavelength in nanometers (nm)
ground to 1st = 0.046723	1979
ground to 3rd = 1.311125	1465
ground to 4th = 1.106149	1445
1st to 15th = 0.000002	2569

The dipole moments of phenol were calculated with all levels of theory and compared to the literature values.

Table 5: This table displays the dipole moment of phenol taken from the literature⁵.

Molecule	Dipole moment value from literature
Phenol	1.40 +/- 0.03

Table 6: This table displays the dipole moments of all levels of theory for phenol.

Level of Geometry Optimization Theory	Dipole moment value
621G	1.645541
631G	1.767432
DZV	1.814355

The best optimization for the dipole moment of phenol was calculated from 621G giving a percent error of 17.5%.

Based on template by A. Herráez as modified by J. Gutow

Page skeleton and JavaScript generated by export to web function using Jmol 14.2.12_2015.01.22 2015-01-22 21:48 on Mar 7, 2015.

Using directory /Volumes/ZAC'S DRIVE/Spring 2015/Pchem Website Ryan and Larry/Phenol page
  adding JmolPopIn.js
  ...jmolApplet0
      ...adding Bond_Length_621G_Phenol.png
copying and unzipping jsmol.zip directory into /Volumes/ZAC'S DRIVE/Spring 2015/Pchem Website Ryan and Larry/Phenol page
      ...copying
file:/Volumes/ZAC'S DRIVE/Lab 2 QM Calculations /Phenol_621G_opt.log
         to
      ...compressing large data file to
/Volumes/ZAC'S DRIVE/Spring 2015/Pchem Website Ryan and Larry/Phenol page/Phenol_621G_opt.log.gz
/Volumes/ZAC'S DRIVE/Spring 2015/Pchem Website Ryan and Larry/Phenol page/Phenol_621G_opt.log.gz
      ...adding Bond_Length_621G_Phenol.spt
  ...jmolApplet1
      ...adding Bond_Length_631G_Phenol.png
copying and unzipping jsmol.zip directory into /Volumes/ZAC'S DRIVE/Spring 2015/Pchem Website Ryan and Larry/Phenol page
      ...copying
file:/Volumes/ZAC'S DRIVE/Lab 2 QM Calculations /Phenol_631G_opt.log
         to
      ...compressing large data file to
/Volumes/ZAC'S DRIVE/Spring 2015/Pchem Website Ryan and Larry/Phenol page/Phenol_631G_opt.log.gz
/Volumes/ZAC'S DRIVE/Spring 2015/Pchem Website Ryan and Larry/Phenol page/Phenol_631G_opt.log.gz
      ...adding Bond_Length_631G_Phenol.spt
  ...jmolApplet2
      ...adding Bond_Length_DZV_Phenol.png
copying and unzipping jsmol.zip directory into /Volumes/ZAC'S DRIVE/Spring 2015/Pchem Website Ryan and Larry/Phenol page
      ...copying
file:/Volumes/ZAC'S DRIVE/Lab 2 QM Calculations /Phenol_DZV_opt.log
         to
      ...compressing large data file to
/Volumes/ZAC'S DRIVE/Spring 2015/Pchem Website Ryan and Larry/Phenol page/Phenol_DZV_opt.log.gz
/Volumes/ZAC'S DRIVE/Spring 2015/Pchem Website Ryan and Larry/Phenol page/Phenol_DZV_opt.log.gz
      ...adding Bond_Length_DZV_Phenol.spt
  ...jmolApplet3
      ...adding Bond_Angles_621G_Phenol.png
copying and unzipping jsmol.zip directory into /Volumes/ZAC'S DRIVE/Spring 2015/Pchem Website Ryan and Larry/Phenol page
      ...adding Bond_Angles_621G_Phenol.spt
  ...jmolApplet4
      ...adding Bond_Angles_631G_Phenol.png
copying and unzipping jsmol.zip directory into /Volumes/ZAC'S DRIVE/Spring 2015/Pchem Website Ryan and Larry/Phenol page
      ...adding Bond_Angles_631G_Phenol.spt
  ...jmolApplet5
      ...adding Bond_Angles_DZV_Phenol.png
copying and unzipping jsmol.zip directory into /Volumes/ZAC'S DRIVE/Spring 2015/Pchem Website Ryan and Larry/Phenol page
      ...adding Bond_Angles_DZV_Phenol.spt
  ...jmolApplet6
      ...adding HOMO_Phenol.png
copying and unzipping jsmol.zip directory into /Volumes/ZAC'S DRIVE/Spring 2015/Pchem Website Ryan and Larry/Phenol page
      ...adding HOMO_Phenol.spt
  ...jmolApplet7
      ...adding LUMO_Phenol.png
copying and unzipping jsmol.zip directory into /Volumes/ZAC'S DRIVE/Spring 2015/Pchem Website Ryan and Larry/Phenol page
      ...adding LUMO_Phenol.spt
  ...jmolApplet8
      ...adding Electrostatic_Potential.png
copying and unzipping jsmol.zip directory into /Volumes/ZAC'S DRIVE/Spring 2015/Pchem Website Ryan and Larry/Phenol page
      ...adding Electrostatic_Potential.spt
  ...jmolApplet9
      ...adding Partial_Atomic_Charge_Phenol.png
copying and unzipping jsmol.zip directory into /Volumes/ZAC'S DRIVE/Spring 2015/Pchem Website Ryan and Larry/Phenol page
      ...adding Partial_Atomic_Charge_Phenol.spt
  ...jmolApplet10
      ...adding 958_79_cm_-1_C-H_bend.png
copying and unzipping jsmol.zip directory into /Volumes/ZAC'S DRIVE/Spring 2015/Pchem Website Ryan and Larry/Phenol page
      ...copying
file:/Volumes/ZAC'S DRIVE/Lab 2 QM Calculations /Phenol_Vib_DZV.log
         to
      ...compressing large data file to
/Volumes/ZAC'S DRIVE/Spring 2015/Pchem Website Ryan and Larry/Phenol page/Phenol_Vib_DZV.log.gz
/Volumes/ZAC'S DRIVE/Spring 2015/Pchem Website Ryan and Larry/Phenol page/Phenol_Vib_DZV.log.gz
      ...adding 958_79_cm_-1_C-H_bend.spt
  ...jmolApplet11
      ...adding 1621_42_cm_-1_C_C_aromatic_stretch.png
copying and unzipping jsmol.zip directory into /Volumes/ZAC'S DRIVE/Spring 2015/Pchem Website Ryan and Larry/Phenol page
      ...adding 1621_42_cm_-1_C_C_aromatic_stretch.spt
  ...jmolApplet12
      ...adding 3400_cm_-1_C-H_aromatic_stretch.png
copying and unzipping jsmol.zip directory into /Volumes/ZAC'S DRIVE/Spring 2015/Pchem Website Ryan and Larry/Phenol page
      ...adding 3400_cm_-1_C-H_aromatic_stretch.spt
  ...jmolApplet13
      ...adding 4086_64_cm_-1_O-H_stetch.png
copying and unzipping jsmol.zip directory into /Volumes/ZAC'S DRIVE/Spring 2015/Pchem Website Ryan and Larry/Phenol page
      ...adding 4086_64_cm_-1_O-H_stetch.spt

This will be the viewer still of jmol image

If your browser/OS combination is Java capable, you will get snappier performance if you use Java