C7800 Introduction to molecular modelling - seminar -1-
Projects
Project A - Water Dimer
Petr Kulhanek
kulhanek@chemi.muni.cz
National Center for Biomolecular Research, Faculty of Science
Masaryk University, Kotlářská 2, CZ-61137 Brno
C7800 Introduction to molecular
modelling - seminar
TSM Modeling of molecular structures
C7800 Introduction to molecular modelling - seminar -2Water
molecule
Water molecule dimer
Water molecule
➢ structure and energy
➢ basis set effect
➢ properties
Quantum-chemical calculations
Water molecule dimer
➢ structure and energy
➢ interaction energy
➢ basis set effect
➢ properties
C7800 Introduction to molecular modelling - seminar -3To
think about
➢ What effect does the basis set size have on the value of the absolute energy of a water
molecule?
➢ What effect does the basis set size have on the value of the absolute energy of the
water molecule dimer?
➢ What effect does the basis set size have on the value of the interaction energy of the
water molecule dimer?
C7800 Introduction to molecular modelling - seminar -4How
to process results
I recommend to summarize the results in the form of a brief protocol, which should have the
following requirements:
• Name and surname, name of the project and date
• For each thematic area:
• Brief summary of the topic, including a reaction scheme, if appropriate
• Software used, including versions
• Results (tables)
• Tables
• numbers aligned to the right
• energies with 6 decimal points (au) or 2 decimal points (kcal/mol)
• lengths with 4 decimal points (A)
• angles with 1 decimal points (deg)
• charges with 3 decimal points (au)
• Discussion of results in context of the course
• References (e.g., for experimental values)
C7800 Introduction to molecular modelling - seminar -5Water
molecule
(Almost) individual project
➢ Reference manuals
➢ Gaussian (QM calculations)
➢ Nemesis (preparation, visualization)
➢ CBS - Extrapolation to a complete basis set
➢ VMD (volumetric data visualization)
➢ Infinity (submitting jobs)
C7800 Introduction to molecular modelling - seminar -6-
Tasks
1) Create a model of water molecule and optimize its geometry using molecular
mechanics.
2) Optimize the geometry of the water molecule using the HF/cc-pVDZ
3) Measure significant geometric parameters of the optimized geometry and compare
them with the initial model.
4) Employing vibrational analysis, verify that the found geometry corresponds to the local
minimum on the PES.
5) Perform energy and property calculation at the HF/cc-pVDZ level of theory and extract:
• total energy
• dipole moment
• Mulliken and MK (Merz-Singh-Kollman) atomic charges
6) Repeat the calculation described in the point 5 on the same geometry for the following
basis sets:
• cc-pVTZ
• cc-pVQZ
• cc-pV5Z
C7800 Introduction to molecular modelling - seminar -7-
Solution
1) Create an initial geometry of water molecule in Nemesis (Project: Build Structure).
Pre-optimize model geometry using molecular mechanics. Select such a force field
(Geometry->Optimizer Setup), which in your opinion best describes its geometry.
2) Save pre-optimized model geometry in the xyz format under the name water.xyz to a
folder 00.input (File->Export Structure as…->OpenBabel). Next, save the input file for
the program Gaussian (HF/cc-pVDZ, Geometry Optimization) with name opt.com to a
folder 01.opt (File->Export Structure as…->Gaussian).
3) Run the calculation in the program Gaussian in the directory 01.opt using the Infinity
environment.
Data organization
00.input
01.opt
02.freq
03.props
01.cc-pVDZ
02.cc-pVTZ
03.cc-pVQZ
04.cc-pV5Z
C7800 Introduction to molecular modelling - seminar -8Solution,
cont.
4) In the directory 01.opt, open the file opt.log in the Nemesis program (Project:
Trajectory, File->Import Trajectory from…-> Gaussian-> Geometry Optimization File).
Analyze the course of optimization and the geometry of the optimized model.
5) Save the optimized geometry as an input file for Gaussian (HF/cc-pVDZ, Frequencies)
with name freq.com to a folder 02.freq (File->Export Structure as…->Gaussian). In the
directory, run the calculation in the program Gaussian using the Infinity environment.
6) In the directory 02.freq, open the file opt.log in the Nemesis program (Project:
Trajectory, File->Import Trajectory from…-> Gaussian->Vibrations File). Does the
geometry correspond to a local minima?
7) If so, successively save the optimized geometry in the directories 03.props/01.ccpVDZ,…
When creating the input file props.com for Gaussian select “MK Charges“ and
the correct basis set. Run the calculations in Gaussian using the Infinity environment
(All jobs can be submitted at once).
8) Analyze the calculated data and put them in the following tables.
C7800 Introduction to molecular modelling - seminar -9Results
I
Geometry of water molecule
fill in the used force field
Method MM HF/cc-pVDZ Difference
d(HO) [Å]
Q(HOH) [˚]
C7800 Introduction to molecular modelling - seminar -10Results
II
Water molecule
result of the calculation
absolute energy (E(RHF))
relative energy with respect to cc-pVDZ basis
Basis set
Cardinal
number
E Er
[au] [kcal/mol]
cc-pVDZ 2 0.0
cc-pVTZ 3
cc-pVQZ 4
cc-pV5Z 5
CBS
C7800 Introduction to molecular modelling - seminar -11Results
III
Water molecule
Basis
set
Cardinal
number
Mulliken ESP m
q(H) q(O) q(H) q(O) [D]
cc-pVDZ 2
cc-pVTZ 3
cc-pVQZ 4
cc-pV5Z 5
CBS
C7800 Introduction to molecular modelling - seminar -12Water
molecule dimer
Individual project
➢ Reference manuals
➢ Gaussian (QM calculations)
➢ Nemesis (preparation, visualization)
➢ CBS - Extrapolation to a complete basis
➢ VMD (volumetric data visualization)
➢ Infinity (submitting jobs)
C7800 Introduction to molecular modelling - seminar -13-
Tasks
1) Create model of the water molecule dimer and optimize its geometry using molecular
mechanics.
2) Optimize the geometry of the water molecule dimer using the HF/cc-pVDZ.
3) Measure significant geometric parameters of the optimized geometry and compare
them with the initial model. Try to justify the observed differences.
4) Verify that the found geometry corresponds to the local minimum on the PES, using
vibrational analysis.
5) With optimized geometry, perform the energy calculation for the bases:
• cc-pVDZ
• cc-pVTZ
• cc-pVQZ
• cc-pV5Z
6) For each base, determine the interaction energy between water molecules.
7) Determine the interaction energy extrapolated to CBS.
8) Display the electrostatic potential mapped to electron density calculated by the HF/ccpVDZ.
Compare the potential with a water molecule.
C7800 Introduction to molecular modelling - seminar -14-
Solution
The procedure is analogous to that of water monomer.
Data organization
00.input
01.opt
02.freq
03.props
01.cc-pVDZ
02.cc-pVTZ
03.cc-pVQZ
04.cc-pV5Z
C7800 Introduction to molecular modelling - seminar -15Results
I
Geometry of water molecule dimer
fill in the used force field
hydrogen bond
At your discretion, list other geometric parameters that best capture the difference
between the two geometries.
Method MM HF/cc-pVDZ Difference
d(HO) [Å]
Q(HOH) [˚]
d(H...O) [Å]
C7800 Introduction to molecular modelling - seminar -16Basis
set
Cardinal
number
E Er Ei
[au] [kcal/mol] [kcal/mol]
cc-pVDZ 2 0.0
cc-pVTZ 3
cc-pVQZ 4
cc-pV5Z 5
CBS
Results II
result of the calculation
relative energy with respect to cc-pVDZ basis
interaction energy between
two water molecules
Water molecule dimer
monomereri EEE *2dim −=