Calculating

Molecular
Properties
from molecular orbital calculations

Geometric Properties
Bond length
Bond angle
Dihedral angle

A single lowest energy

equilibrium structure is
generally the result of a
geometry optimization;
actual molecules exist as
an ensemble (mixture) of
conformations which is
temperature dependent.

Experimental measurements of geometry (X-ray, ED,

NMR, ND) measure different aspects of structure.

Molecular Properties
Many are first, second or third derivatives of

the Hartree-Fock energy with respect one or

more of the following:
external electric field (F)
nuclear magnetic moment (nuclear spin, I)
external magnetic field (B)
change in geometry (R)

Examples
external electric field (F):
Raman intensity
E/RF2
nuclear magnetic moment (nuclear spin, I)
ESR hyperfine splitting (g)
E/I
NMR coupling constant (Jab)
E/IaIb

Examples...
external magnetic field (B) and (nuclear spin, I)
NMR shielding (

E/BI
Change in geometry (R)
Energy Gradient
E/R
Hessian (force constant; IR vibrational
frequencies)
E/R

Other Properties
Ionization energy (IP)
Neg. of HOMO energy (Koopmans theorem)
Electron affinity (EA)
LUMO energy
UV-Vis spectra
Est. (poorly) by HOMO-LUMO energy difference

UV-Vis Spectra
Can be estimated as the HOMO-LUMO energy

difference
Generally not very accurate, but useful for
relative wavelengths, and to predict trends
Difficult to model effects of solvent, especially
on excited states, about which little is known.
Density functional theory (to be discussed
later) generally does a better job at predicting
UV-Vis spectra.

Problems with UV-Vis

spectra
The energy required to promote an

electron from MO i to MO j is not simply

equal to the energy difference e(j) - e(i).
The promotion energy E(i-->j) can be
expressed as:
E(i-->j) = e(j) - e(i) - v(i,j)
The wavefunction |i-->j> of an excited
electronic configuration is not a good
approximation to an eigenfunction of the
many-electronic Hamilton operator H.
Excited configurations tend to interact,
and a proper description must include

Other Properties...
IR spectra (bond vibrational frequencies)
frequencies are over-estimated by H-F theory; a
scaling factor of 0.89-0.91 must be applied to
reproduce observed values
Proton affinity (related to basicity, but is

calculated in the gas phase rather than in

aqueous solution)

RNH2

+ H

RNH3

Other Properties...
Acidity

RCO 2H

RCO 2

Gibbs Free energy (G)

Includes Enthalpy (H) and Entropy (S)
A frequency calculation must be performed
on an energy minimized structure to
obtain thermal corrections, which allow
calculation of entropy and other values. (later)

Other Properties...
(topic of a
Charges on Atoms in Molecules
later lecture)
meaning of charge is ill-defined
value depends on definition
several commonly used charge estimations
Mulliken
Natural population analysis
Charges fit to electrostatic potential
Atoms in molecules (AIM)
ChelpG

NMR chemical shift

calculations
(in ppm)
calc.
CH3CH2CH2CH3
C2 23.7
CH3CH=CHCH3
C2
benzene (C6H6)

expt.*
C1
15.9

13.4

25.2
C1

18.4

124.7

17.6

126.0
128.9

130.9
* in CDCl3 solution

NMR: Effect of Basis Set

Calculated chemical shifts (ppm) and
difference from gas phase experimental
values as a function of basis set
Shift
Diff.
HF/6-31G(d)
127.3
-3.6
HF/6-31G(d,p)
128.4
-2.5
HF/6-31++G(d,p)
128.9
-2.0
(observed)
130.9
--

IR Frequency Calculations
O
Formaldehyde
C
H
H
C-H bend C=O stretch
Computed Frequency 1336 cm-1
2028
cm-1
Reduced mass
1.37
7.25
Relative intensity
0.4
150.2
Freq. scaled by 0.89 1189 cm-1
1805
cm-1

IR Frequencies (cm-1, gas phase)

Scaled Frequency

O
H

O
CH3

1799 1737
CH3

1850 1822

O
CH3

Cl

O
CH3

1805 1746

OCH3

1797 1761

Expt.

Zero-point energy
Energy due to
the fact that v0,
the lowest
vibrational state,
is above the
electronic energy
level of the
equilibrium
structure.

r0, r1, r2...

v3
v2

Energy

Usual calcc energy

v1
v0

zero point
energy

eq. bond length

Distance between atoms

Thermal Energy
Corrections
The following may be derived from the

results

of a frequency calculation:

Zero Point Energy (z.p.e.)

Free Energy at STP (G)
Free Energy at another Temperature, Pressure
Entropy (S)
Enthalpy (H) corrected for thermal

contributions
Constant-volume heat capacity (Cv)

Frequency calculation
Formaldehyde was optimized and a

frequency calculation performed in

Gaussian 98 at NCSC.
Zero-point correction=
0.028987 (Hartree/Particle)
Thermal correction to Energy=
0.031841
Thermal correction to Enthalpy=
0.032785
Thermal correction to Gibbs Free Energy=
0.007373
Sum of electronic and zero-point Energies=
-113.840756
Sum of electronic and thermal Energies=
-113.837902
Sum of electronic and thermal Enthalpies=
-113.836958
Sum of electronic and thermal Free Energies=
-113.862370

Frequency calculation...
Heat capacity Entropy
E (Thermal)

CV
Kcal/mol

cal/mol-Kelvin
TOTAL
53.483
ELECTRONIC
TRANSLATIONAL
36.130
ROTATIONAL
17.303
G = H
VIBRATIONAL

19.980

S
cal/mol-Kelvin
6.260

0.000
0.889

0.000
2.981

0.889

2.981

0.000

- TS 18.203

0.298
0.050
-113.862370 = -1 H 3.- 298.15 * 53.483 / 627.5095 * 1000
(in Hartrees)

(kcal/mol per Hartree)

Dipole Moment
(in Debyes)
Expt.

HF /
HF /
MP2 /
MMFF
AM1
PM3
3-21G*

6-311+G**

NH3

2.04 1.85 1.55 1.75 1.68 1.65 1.47

H2O

2.46 1.86 1.74 2.39 2.12 2.08 1.85

P(CH3)3

2.06 1.52 1.08 1.28 1.44 1.31 1.19

thiophene 1.32 0.34 0.67 0.76 0.80 0.47

(note that none are very accurate; this reflects two factors:
0.55
equilibrium geometry is only one of several, even many, in
an ensemble of conformations, and charges are ill-defined.

Conformational Energy Difference

(in kcal/mol)

Good:

Generally poor:

Expt.

Sybyl

HF /
HF /
MMFF AM1

acetone
(trans/gauche) 0.6 0.8
0.8

0.7

N-Me formamide
(trans/cis)
-1.8 2.6
2.5

0.4

1,2-diF ethane
(gauche/anti)
0.0
0.8 0.8

-0.6

MP2 /
PM3 3-21G*

0.5

6-311+G**

0.8

1.0

0.6

-0.5 3.9

2.7

2.7

-0.9

0.3

-0.5

1.4

Equilibrium(in )
Bond Length

Expt.

propane
(C-C single)
1.526

Sybyl

HF /
HF /
MMFF AM1

MP2 /
PM3
3-21G*

6-311+G**

1.551 1.520 1.501 1.512 1.541 1.525 1.526

propene
(C=C double) 1.334 1.334 1.331 1.328 1.316 1.316 1.336
1.318
1,3-butadiene
(C=C double)
1.338 1.338 1.335 1.331 1.320 1.320 1.342
1.345
propyne

Log P
Log of the octanol/water partition coefficient;
considered a measure of the bioavailability
of a substance
Log P = Log K

(o/w)

= Log [X]octanol/[X]water

most programs a use group additivity approach

some use more complicated algorithms,

including the dipole moment, molecular size and

shape
subject to same limitations as dipole moment

Conclusions
Many useful molecular properties can be

calculated with reasonably good accuracy.

Some properties (charges on atoms, dipole
moments, UV-Vis spectra) are not well
modeled, even by high level calculations.