Introduction to ADF

ADF (Amsterdam Density Functional) is a Fortran program for calculations of atoms and
molecules (in gas phase or solution). The underlying theory is the Kohn-Sham approach to
Density-Functional Theory (DFT). This implies a one-electron picture of the many-electron
systems but yields in principle the exact electron density (and related properties) and the total
energy. ADF can be used for the study of such diverse fields as molecular spec troscopy, organic
and inorganic chemistry, crystallography and pharmacochemistry. In this exercise, you will use it
to study the thermodynamic properties of simple reactions.
As a powerful DFT calculation package, ADF has diverse functionalities, of which the following
will be used in your assignments:
Geometry optimization: find the optimized geometry for the desired molecule
Transition state calculation: find the transition state or activation barrier between
reactants and products and observe the corresponding structure transition
Frequency and thermodynamic properties: verify that the global optimized structure has
zero imaginary frequency and transition structure has exact one imaginary frequency;
provide thermal properties, entropy, internal energy and constant volume heat capacity,
of the molecule

Input File Structure

In order to run ADF, an input file structured by keywords is a must. A keyword is a string of
characters that does not contain a delimiter (blank, comma or equal sign). Keywords are not case
sensitive. Input is read until either the end-of-file condition (eof) becomes true, or until a record
END INPUT is encountered, whichever comes first. In the sample input files for all three types of
calculations, geometry optimization, transition state search and frequency calculations, the
structured blocks begin with the keyword followed by its the arguments. Blocks are closed by a
record containing (only) the wordEND.Please use the space instead of tab for delimiter. Tab will
cause errors.
The input file starts with a TITLE keyword, which is followed by the specification of the
calculation that user can define for his convenience, like the name of the molecule and the
corresponding type of calculation. Remember to keep all the TITLE information in one line.
The following block begins with UNIT keyword, which specifies the units used for the molecule
geometry, saying angstrom for bond length and degrees for bond angle.
The usage of keyword RESTRICTED or UNRESTRICTED depends on the molecule to be
calculated. If the molecule is in singlet state, closed shell molecule (no unpaired electron for the

molecule), RESTRICTED keyword is used. Otherwise, for all the open shell molecules (systems
with unpaired electrons), the UNRESTICTED keyword is used. For your assignments, please be
cautious with the unpaired electrons for your systems and then select the correct keyword.
The block beginning with ATOMS Z-MATRIX/CARTESIAN contains the internal or Cartesian
coordinates of the atoms in the system. In the assignment, you are more concerned with this part
since it changes with different systems to be calculated. In this block, one atom is specified in a
line with geometric specification regarding to the previous atoms. For example, the ATOMS ZMATRIX BLOCK for ammonia (NH3) is:
Atoms Z-matrix
1 N 0 0 0 0.0 0.0 0.0 f=N/1
2 H 1 0 0 r2 0.0 0.0 f=H/1
3 H 1 2 0 r3 a3 0.0 f=H/2
4 H 1 2 3 r4 a4 t4 f=H/3
End
here the columns in italic denote atoms positions with respect to the origin atom, the first atom (1
N). The columns in bold specify the geometry parameters, bond length, bond angle and dihedral
angle, according to the position parameters in the italic columns. For example, the second line 2
H 1 0 0 r2 0.0 0.0 f=H/1 specifies the first H atom (2 H) is bonded with the first atom (1
N), denoted by 1 0 0 in the italic column, with bond length of r2. Since so far there are just two
atoms, there are no bond angle and dihedral angle denotations in the bold columns. In the third
line of Z-matrix, 3 H 1 2 0 r3 a3 0.0 f=H/2, the second H atom (3H) is bonded with the first
N atom (1 N) and has a bond angle with the first N and H atoms, denoted by 1 2 0 in the italic
columns, with bond length and bond angle of r3 and a3 in the bold columns respectively. In order
to determine the geometric position of the third H atom, the dihedral angle, t4, is introduced for
the third H atom in the fourth line of Z-matrix in addition to the bond length and angle parameters.
It is the dihedral angle between plane of 4(H) 1(N) 2(H) and plane of 1(N) 2(H) 3(H).
The next block is the GEOVAR block. It contains the geometry parameters of the atoms specified
in the ATOMS Z-MATRIX block.
The BASIS block specifies the fragments used in the calculations, in which different basis sets are
specified. In your assignments, the double-zeta basis sets with polarization functions will be used.
The GEOMETRY block determines the types of calculation and sets up their corresponding
environment variables. For geometry optimization calculation, use:
Geometry
Optim Internal All
End
For transition state search calculations, use:
Geometry
Optim Internal All
Transitionstate
End

For frequency calculations, use:

Geometry
Optim Internal All
Frequency
End
The first line of this block, Optim Internal All, means the optimization is performed on all atoms
of the Z-matrix. The transition state search calculation is performed with keyword of
transitionstate in this block. For frequency calculations, keyword of Frequency is specified in this
block.
The block of XC (exchange-and-correlation functional) specifies the Functional used in the
calculations. It consists of an LDA and a GGA part. LDA stands for the Local Density
Approximation, which implies that the XC functional in each point in space depends only on the
(spin) density at the same point. GGA stands for Generalized Gradient Approximation and is an
addition to the LDA part, by including terms that depend on derivatives of the density. Below is
the list of options for XC:
Fortheexchangeparttheoptionsare:
Becke
:thegradientcorrectionproposedin1988byBecke[3].
PW86x
:thecorrectionadvocatedin1986byPerdewWang[4].
PW91x
:theexchangecorrectionproposedin1991byPerdewWang[5].
Forthecorrelationparttheoptionsare:
Perdew

:thecorrelationtermpresentedin1986byPerdew[6].

PW91c

:thecorrelationcorrectionofPerdewWang(1991),see[5].

LYP

:theLeeYangParr1988correlationcorrection,[79]

SomeGGAoptionsdefinetheexchangeandcorrelationpartsinonestroke.Theseare:
PW91

:thisisequivalenttopw91x+pw91ctogether.

Blyp

:thisisequivalenttoBecke(exchange)+LYP(correlation).

LB94

:thisreferstotheXCfunctionalofVanLeeuwenandBaerends[10].Thereareno

separateentriesfortheExchangeandCorrelationpartsrespectivelyofLB94.

In your assignment, you will try two functionals from the list above, Becke and Perdew for LDA
and PW91 for GGA, and discuss how they affect the energy and geometry calculations of the
system.
The next block begins with CHARGE and just has one line. The first part of CHARGE is related
to the charges of the system and the second part is concerned with the multiplicities of the system:
i.e. the number of unpaired electrons. For example, the multiplicity for H atom is 1 but 0 for H 2
since electrons in H2 are paired. In your assignment, please be cautious with the multiplicity of
your systems since every molecule can have several states, singlet or doublet or triplet or , and
only one of them is the ground state.

Reference:
1. ADF examples: http://www.scm.com/Doc/Doc2002/Examples.pdf
2. ADF User Manual: http://www.scm.com/Doc/Doc2002/ADFUsersGuide.pdf
3. Becke, A.D., Physical Review A, 1988. 38: p. 3098.
4. Perdew, J.P. and Y. Wang, Accurate and simple density functional for the electronic exchange
energy: generalized gradient approximation. Physical Review B, 1986. 33(12): p. 8800.
5. Perdew, J.P., et al., Physical Review B, 1992. 46: p. 6671.
6. Perdew, J.P., Density-functional approximation for the correlation energy of the
inhomogeneous elctron gas. Physical Review B, 1986. 33(12): p. 8822.
7. Lee, C., W. Yang, and R.G. Parr, Development of the Colle-Salvetti correlation-energy
formula into a funcitonal of the electron density. Physical Review B, 1988. 37(2): p. 785.
8. Johnson, B.G., P.M.W. Gill, and J.A. Pople, The performance of a family of density funcional
mehtods. Journal of Chemical Physics, 1993. 98(7): p. 5612.
9. Russo, T.V., R.L. Martin, and P.J. Hay, Density Functional calculations on first-row transition
metals. Journal of Chemical Physics, 1994. 101(9): p. 7729.
10. van Leeuwen, R. and E.J. Baerends, Exchange-correlation potential with correct asymptotic
behaviour. Physical Review A, 1994. 49(4): p. 2421-2431.

Interpretation of the Output File

Once your geometry optimization and transition structure search jobs are done, output files with
the name you specified are generated. The output files contain much more information than what
you need in your assignments. Below is the part of the information on the convergence of the
calculation and the optimized geometry parameters calculated. In addition to the optimized
geometry, the total bonding energy is also very important and listed in several units, such as
hartree, ev, kcal/mol and kj/mol. In your assignments, please use kcal/mol for convenience. In
order to get the desired information quickly, please use the search function in editors like pico, vi
or emacs and search for the keyword like Final Geometry and Total Bonding Energy to locate
the optimized geometry and energy for ground state structure and transition state structure.

As for the output file from the frequency calculation, it has the same name with the input file but
with the file extension of out. The part of information that includes the calculated frequencies is
shown below:
List of All Frequencies:

Intensities
===========

Frequency
cm-1
----------

Dipole Strength
1e-40 esu2 cm2
----------

Absorption Intensity (degeneracy not counted)

km/mole

----------

-1165.478453

764.071305

-223.211317

298.194636

1213.123186

90.674005

459.284720

1414.641735

162.857039

589.037030

505.329568

74.609715

705.055800

676.149880

119.493570

1210.179005

46.629461

14.144516

1801.529386

570.845596

257.773386

3421.622715

13.308611

11.414133

3740.869138

560.651872

525.707124

Assignment 1: Thermo-chemistry Study of Simple Reaction

Calculate the enthalpy for the following reaction:
2H2 + O2 2H2O
1. Calculate the reaction enthalpy for the reactants and products using the LDA by Becke and
Perdew functional and the GGA by PW91 functional. Calculate the enthalpy for the whole
reaction. The sample input file of Geometry Optimization calculation is provided in your
account under directory of ADFAssignment and contains the minimum. Compare your results
with the experimental data and assess the accuracy of your calculations and effects of
different functionals.
2.

Compare the optimized structures of reactants and products from your calculation with those
from the experimental data.

3.

Play around the molecular visualization tool, ViewerLite, and draw the optimized structures
for reactants and products from your preferred tool.

Hints:

The functional specification for LDA by Becke and Perdew in the input file is:
XC
LDAVWN
GradientsPostSCFBECKEPERDEW
End

The functional specification for GGA by PW91 in the input file is:
XC
GGAPW91
End

The experimental data for molecule structures and formation enthalpy can be obtained
from NIST database: http://srdata.nist.gov/cccbdb/

Be careful with the multiplicity of O2 molecule when calculating its ground state. The
different states and find the ground one.

Assignment 2: Transition Structure Calculation of the

Hydrogen Shift Reaction
1.

Calculate the reaction enthalpy for Formaldehyde transforming into trans form of
Hydroxycarbene with LDA by Becke and Perdew. Verify the optimized geometries of
reactant and product with frequency calculations and tabulate their corresponding
frequencies: use the optimized geometry from your geometry optimization result as the input
geometry parameters for frequency calculation. The optimized geometry is verified by
showing zero imaginary (negative) frequency in your frequency calculation result:
H2CO HCOH

2.

Calculate the transition structure of the Hydrogen shift from the Carbon terminal of
Formaldehyde (H2CO) to the Oxygen terminal of hydroxycarbene (HCOH). Verify that your
transition structure with frequency calculation by showing there is exact one imaginary
frequency in your frequency calculation result. The guessed geometry of transition structure
looks like:

Formaldehyde

3.

C
H

H-Shift TS

C
H

Hydroxycarbene

Plot the potential energy surface (PES) of this reaction by three points you calculated, the
enthalpies of reactants, transition state and products. The PES shows activation barrier
(saddle point) for the reaction from reactant to product. Explain the height of the PES.