Chem545

Introduction to IQmol
 Computational chemistry

Learn what kind of question one can ask computational chemistry

and
what tools are available for non-experts

2
Quantum mechanics + computers -> properties of molecules
 Vibrations and rotations.
Born-Oppenheimer approximation
When Born-Oppenheimer
so-called electronic approximation
3. Whenwavefunctions is valid?
to beapproximation
solutions of the el
(idea)
Born-Oppenheimer is vali
224309-6 Mozhayskiy, Babikov, and Krylov

What can4.happen when

What can BOwhen
happen breaks?
BO breaks?
Hel i (r; R) = Ui (R) i (r; R)
How to H 5. How
solve thetofull
solve the full problem
problem (using (using
as a as a b
elbasis)
el ⌘ Te + Ven + Vee + Vnn el

equation1.3.4
at each Potential
fixed geometry of nuclei,
energy and resulting
surfaces: conce
.4 parametrically
pend Potential on energy surfaces:
nuclear geometry (we use concepts
’;’ instead
Consider a solution of electronic Schrödinger equatio
U(R) is called
en parametric andPotential
explicitEnergy Surface (PES)
dependence on R). Calculated a
siderThis
a solution
nuclear
is ofthat
electronic
motion
potential Schrödinger
(in adiabatic
determines equation:
approximation)
nuclear motions and E(
is
urves Ui (R) of O2 molecule are shown in Fig. 1.2. We will
FIG. 6. !Color" PESs of the ground !X" and the first eight excited states
cyclic N+3 . Coordinates are as in Fig. 5. Three out of four states in ea

ear motion(PES).
(in adiabatic approximation)
multiplicity are almost degenerate at D3h geometry, two being exact

and
degenerate.
is —called
tential which governs
DefinitionGradient
nuclear
of the gradient:
motion (bound states
(vector): gradR = rR = @R1 , . . . , @R3n
CYCLIC N3+ @ vib
V. THE ANALYSIS OF THE „E + A + B… ‹ E PROBLEM IN
@
S).
states — dissociation, etc). At each internuclear @distance, th
The electronic Hamiltonian H = Te + U!r , Q" can be e
panded as Taylor series with respect to small nuclear di
2
Gradient Hessian
(vector): (matrix):
grad H=Rir
,Rj == rR@i r,R.j .=. ,@Ri@@Rj
placements Q! from a reference high symmetry configur
tion !Q! = 0",

Definition ofSE
the electronic thegives
2nd derivative
ground
R (Hessian)
state
R energy.
@R1 Higher
# 3n# energy s
@R
H = H0 +
!H
!Q!
Q! +
!2H
!," ! Q !! Q "
Q!Q" + ¼ = H0 + V.

cally excited Stationary

states. Notepoints
thatof PES
some ⌘
of gradient
@
the
2
states vanishes
are
!

in a
unbou !3

ian (matrix): HRi ,Rj = rRi rRj = @Ri @Rj We truncate this expansion at linear terms and start b
solving the Schrödinger equation for Hamiltonian H0. Th

ted to one of such states, it dissociates to two oxygen atom

perturbation V thus includes linear vibronic coupling term
#!!!H / !Q!"Q!.1,2
 Chemistry and Potential Energy
Surfaces
Transition State

Reaction Barrier
Reaction Energy

Reactant Product

Reaction energy -> Thermodynamics

Reaction barrier -> Kinetics
Cyclobutane (C8H8) ring opening: Transition state versus an
intermediate
 How the calculations are done?

There are many software packages:

Gamess, Firefly, Molcas, Molpro, Gaussian, Psi4, CFOUR, Dalton,
Dirac, Bagel, Orca, Turbomole, NWChem, TeraChem, Q-Chem,
etc.

And many visualizers:

GaussView, Gabedit, Jmol, ChemCraft, Molden, Avogadro,
Chimera, VMD, IQmol, etc.

This class is designed primarily for Q-Chem and IQmol.

Introduction to IQmol
Purpose:
Build molecules
Set up QC calculations
Analyze results
IQmol)
http://iqmol.org
Calculations: Q-Chem
•  WriOen)by)Dr.)Andrew)Gilbert)
IQmol author: Dr. Andrew Gilbert
•  Molecular)builder)
•  Hierarchical)input)generator)
•  Job)manager:)local/remote)submission)
Lets fire it and see what we get:
Build Mode Add Hydrogens Minimize Energy (classical forcefield)

Build Elements Add Fragments

(periodic table) (pre-built molecules)
 Stationary points on PES and relation
to chemistry Excited states:
Beyond Born-Oppenheimer
Ground state

To find stationary points on PES we need to start from some trial

structure and follow gradients
Playing with IQmol (DEMO):
1. Build molecules
Options (from elements, from fragments, import XYZ)
Minimize function and force fields (crude!); switch to MMFF94
Different view options

2. Learn how to use ‘Manipulate’ mode

Right click and drag (translate)
Left click and drag: rotate
Two fingers drag up or down: Zoom

3. How to use ‘Select’ function

Select: Left click, deselect: right click. Can select/deselect several
atoms by left/right click and drag selection window
Selected atoms: CNRL or Command: + right click and drag
Use molecule from the Gallery of fragments: Look at fullerene
Save image (how to get rid of background)
Exercise I: Building molecules

1. Build water molecule from atoms and measure structural

parameters
2. Build methanol molecule
3. From methanol make formaldehyde by deleting atoms
4. Get molecule from the gallery and modify it:
Take ethylene and substitute two Hs by F
Convert cis to trans isomers by rotating selected atoms

Keep brief summary of what is done (word doc with images and
numbers)
IQmol: Setting up Q-Chem calculations
DEMO:
Optimize water molecule

Type of calculation: SP, OPT, …..

Method for solving SE: HF/6-31: very simple
Show how to submit simple optimization
Look at dipole moment
Measure structural parameters
Total energies: shows in geometries (scroll), how to see output
- You can use ‘Job Monitor’ to see what happens with the
submitted job
- When job is finished, IQmol asks for permission to move files
from the server to your laptop — you need to allow and specify
which directory to put them in

Important: When you submit, IQmol asks to name the job.

This name will be used to name the output files. So if you use
the same name and the same directory, you will overwrite your
results from previous jobs. Good practice is to give meaningful
and different names to your jobs and to keep things organized.

IQmol remembers history of the operations. Use reset option to

clear it.
Exercise 2: Optimizing molecules

Build a molecule: Ethylene

Optimize with HF/6-31G
Measure and report structural parameters
Optimize with wB97X-D/6-31+G*
Measure and report structural parameters
Exercise 3: Computing energy differences

Build and optimize 2 isomers CHFCClH (doubly

substituted ethylene)
Collect structures and respective energies
Total energies: Find in the output
Compare relative energies of the isomers
Compare dipole moments

use wB97X-D/6-31G*
DEMO:

Optimize water molecule and compute frequencies (using + option

in IQmol)
Look at the frequencies: Static and dynamic picture
Look at the spectrum: Double-click on frequencies
Definition and meaning of ZPE and where to find it
Thermodynamic quantities (from electronic energies to free
energies)
Exercise 4: Computing frequencies

Build methanol and formaldehyde

Do OPT+FREQ calculation
Analyze frequencies and structures
How does CO bondlength changes between
formaldehyde and methanol?
How does CO frequency change?

use wB97X-D/6-31G*

To see the spectrum: Double-click on ‘Frequencies’ word

in the Model View window
Advanced concepts:

Notes on symmetry in optimization

Optimization with constraints
PES scans
Transition state search and rxn coordinate
 1.1 Energy units
Atomic energy units:
In electronic structure calculations we use ato
Electron charge e=1
Electron mass electron
m=1 charge, electron mass, and Plank cons
1.2 Energy range 9
Plank constant & h̄=1 =1 (Plank constant) & m=1 (electron m
atomic units?
Table 1.1: Atomic units: Important constants to remember.
Quantity Atomic units Value
Length ao , or bohr 0.52918 Å
• Equations assume simpler form, e.g., t
Dipole moment 2 unit charges separated by ao 2.5418 Debyes (D)
Energy hydrogen atom in atomic units is:
hartree 27.211 eV
627.51 kcal/mole
4.36·10 18 J
1
1.042·10 18 cal
2 1 2 1
( ⌅
2.195·105 cm 1
r ⌅R
2
6.58·1015 Hz 2M |R
3.158·105 K
C-C bond ~90 kcal/mol
as compared to the SE in the SI units:
Electronic transitions: 0.5-6 eV
Vibrations: 100-3000 2
cm-1 2
ΔZPE: ~0.5 kcal/mol
(
h̄ 2
⌅r
h̄
⌅2R
e