Applications of Computational Chemistry

Do you have Real Problems to solve with Computational Chemistry

Approaches?

Dr. Nikhil Aggarwal

Ph.D. Chemistry (IIT Madras), [Link]. (DU), [Link]. (DU), India
Director, AIMs Institute , Delhi
Call or WhatsApp Us: +91-9790969349
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 1. Introduction: What is Computational Chemistry?
• Computational chemistry:
• Theoretical calculations of Molecular properties
• Presently: Important characterization tool in nanotechnology

• Computational chemistry is a rapidly growing field in chemistry.

• Computers are getting faster
• Algorithms and programs are maturing
• Is there anything a computational chemistry cannot deal with?
• From small molecules, to DNA/proteins, 3D crystals and surfaces
• From species in vacuum, to those in solvent at room temperature, and to those under
extreme conditions (high T/p)
• From structure, to properties, to spectra (UV, IR/Raman, NMR, VCD), to dynamics, to
reactivity
• All experiments done in labs can be done in silico
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Limited only by (super)computers not big/fast enough! 2
 2. Executing Computational Project: How to initiate Computing?
• These questions should be answered  Quantum Mechanical
• What do you want to know? i.e., via Schrödinger Equation
also called Quantum Chemistry
• How accurate does the prediction need to be?
• How much time can be devoted to the problem?  Molecular Mechanical
i.e., via Newton’s law F = ma
• What approximations are being made? also Molecular Dynamics

 Empirical/Statistical
e.g., QSAR, etc., clinical and medicinal chemistry

The answers to these questions will determine the type of calculation, model and basis set to be used

• Model: System of equations, or computations used to determine Molecule energetics

• Different models use different approximations (or levels of theory) to produce results of varying levels of
accuracy
• Trade off between accuracy and computational time. In general, “cost” of calculation increases with:
 Accuracy of calculation
 Size of the system.
• Two main types
04-May-21 9:23 PMof models: those that use Schrödinger's equation (or simplifications of it) and those that do
3 not
 3. Theory: What is the Basis of Computation-1?
• Schrödinger equation: Complete description of Molecule electronic structure
• If the equation could be fully solved all information pertaining to a molecule could be
determined.
Schrödinger’s Equation: 
 i   Hˆ 
t
Complex mathematical equation
Not solvable for systems with many atoms
Focus Today

• Schrödinger Equation can only be solved exactly for simple systems

• Rigid Rotor, Harmonic Oscillator, Particle in a Box, Hydrogen Atom
• For more complex systems (i.e. many electron atoms/molecules): Some simplifying
assumptions/approximations and solve it numerically
• Due to difficulty of equation computers are used in conjunction with simplifications and
parameterizations
• Still possible
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to get very accurate results (and also get very crummy results) 4
 3. Theory: What is the Basis of Computation-2?
Molecular Mechanics
• Simplest type of calculation
• Used when systems are very large and approaches that are more accurate become to costly
(in time and memory)

• Does not use any quantum mechanics instead uses parameters derived from experimental or
ab initio data
• Uses information like bond stretching, bond bending, torsions, electrostatic interactions, van
der Waals forces and hydrogen bonding to predict the energetics of a system
• The energy associated with a certain type of bond is applied throughout the molecule. This
leads to a great simplification of the equation

• It should be clarified that the energies obtained from molecular mechanics do not have any
physical meaning, but instead describe the difference between varying conformations (type of
isomer).
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 4. Types of Calculations: What can be Computed?
• A few basic types of calculations. From these calculations, other information can be determined/ derived
• Single-Point Energy • Predict stability, reaction mechanisms
• Geometry Optimization • Single-Point Energy, Geometry Optimization, Frequency
• Frequency
• Transition-state dipole and Quadrupole moments and
polarizabilities
• Solvent effect: Implicit model vs. explicit mode
• Emission Spectrum Simulation
What Else … ? • Potential Energy Diagrams (3D)
(To Count A Few) • Vibrational frequencies, IR and Raman Spectra
• NMR spectra
• Equilibrium and Transition state structures
• Excited states and UV spectra
• Temperature and Pressure effects
• Electron and Hole Density Distribution Maps.
04-May-21 9:23 PM • Thermochemical data 6
 Computational Cost
Method Scaling of Cost
HF M2 – M3
MP2 M5
CCSD M6
CCSD(T) M7

• Why not use best available correlation method with the largest available basis set?
• Increasing the molecule size 2x (say ethane  butane) would increase a
CCSD(T) calculation 128x (27).
• Tripling basis set size would increase MP2 calculation 243x (35).
• A MP2 calculation would be 100x more expensive than HF calculation with
same basis set.
• A CCSD(T) calculation would be 104x more expensive than HF calculation
with same basis set.
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 Size vs Accuracy: High Accuracy Possible
Assuming typical computing setup (number of CPUs, memory, disk space, etc.)

• Ab initio method: ~100 atoms

• DFT method: ~1000 atoms
• Semi-empirical method: ~10,000 atoms
• MM/MD: ~100,000 atoms
 Despite all these approximations highly
accurate results are still possible.

Molecule CBS De EZPVE ECV ESR Atomic Theoretical Experimental

SO D0 (0K) D0 (0K)
NH2 (2B1) 181.8 -12.0 0.4 -0.2 0.0 170.0 170.00.3
H3CSH (1A) 473.5 -28.6 1.5 -0.6 -0.6 445.2 445.1
CCSD(T) Atomization
SO2 (1A1) 257.6 -3.9 1.0 -0.9 -1.0 253.7 254.00.2 Energies for
Na2 (1g+) 16.8 -0.2 0.3 0.0 0.0 16.9 16.80.3 Various Molecules
BrCl (1+) 56.6 -0.6 0.4 -0.4 -4.4 51.6 51.50.3
CH3I (1+) 372.3 -22.4 3.7 -0.9 -7.3 345.4 344.80.3
1
SiPM
04-May-21 9:23 2H6 ( A1g) 536.1 -30.5 0.0 -1.1 -0.9 503.6 500.1 8
 Example 1: Yttrium Catalyzed Rearrangement of Acetylene

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Example 2: Computed vs. Experimental Enthalpy
Changes He in kJ/mol
Exptl. CCSD(T) SCF G2 DFT

CH4  CH2 + H2 544(2) 542 492 534 543

C2H4  C2H2 + H2 203(2) 204 214 202 208

H2CO  CO + H2 21(1) 22 3 17 34

2 NH3  N2 + 3 H2 164(1) 162 149 147 166

2 H2O  H2O2 + H2 365(2) 365 391 360 346

2 HF  F2 + H2 563(1) 562 619 564 540

Gaussian-2 (G2) method of Pople and co-workers is a combination of MP2 and QCISD(T)
 Glimpse of My Research Interest

Head-to-Tail stacking
(0o ≤  ≤ 54.7o)

α Cofacial stacking
 (54.7o ≤  ≤ 90.0o)
r

r – Distance b/n molecular centers

 - Molecular Slippage angle : angle subtended by Monomeric transition
dipole moment (TDM) and line connecting molecular centers
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α – Polarization angle : angle subtended b/n monomeric TDMs
 Emission Characteristics: Excited State Equilibrium Structures
Excited State (ES) Structures (Emission characteristics):
 Excited state structure computation in solution: distinction b/n
equilibrium & non-equilibrium methods

 Solvent responds in two different ways to solute state changes:

I. it polarizes its electron distribution, very rapid
II. solvent molecules reorient themselves via rotation, much
slower
 Equilibrium computation: solvent fully respond to solute in
both ways
 Non-equilibrium calculation: too rapid for solvent to fully
respond

Excited state equilibrium structures & Emission maxima:

Step 1: Excited state structures for electronic excitations were first computed at TD-DFT/M062X/6-31G+(d,p) level with IEFPCM
in Water: Non-equilibrium solvation
Emission occur from vibrationally relaxed excited state in an equilibrium solvent reaction field
Step 2: Minimum energy point on excited state potential energy surface: TD-DFT geometry optimizations on obtained excited
state structures: Equilibrium solvation
𝝂=𝒑
Step 3: Finally emission
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maximum: Difference b/n energies of Vibrationally excited ground state (𝑬𝟏 ) & Equilibrium12electronic
excited state (𝑬𝝂=𝟏
𝒏 )
 Excited States Electron (𝜌𝑒𝑙𝑒 𝑟 ) & Hole (𝜌ℎ𝑜𝑙𝑒 𝑟 ) Density Distribution Maps
 Monomeric & Dimeric Singlet Excitation: Multimolecular orbital
 Single orbital pair excitation model Non-applicability: Conceptualizing multimolecular orbital excitations in terms of Electron
& Hole density distribution maps (EDD and HDD)
 EDD ( ρ𝑒𝑙𝑒 𝑟 ) & HDD ( ρℎ𝑜𝑙𝑒 𝑟 ): Linear combination of MO wavefunction ( 𝚽 ) & configuration coefficient (w)
corresponding to electron transition from several occupied (i) – to – virtual (l) MO

ρ𝑒𝑙𝑒 𝑟 = ෍(𝑤𝑖𝑙 )2 Φ𝑙 𝑟 Φ𝑙 𝑟 + ෍ ෍ 𝑤𝑖𝑙 𝑤𝑖𝑚 Φ𝑙 𝑟 Φ𝑚 𝑟 ρℎ𝑜𝑙𝑒 𝑟 = ෍(𝑤𝑖𝑙 )2 Φ𝑖 𝑟 Φ𝑖 𝑟 + ෍ ෍ 𝑤𝑖𝑙 𝑤𝑗𝑙 Φ𝑖 𝑟 Φ𝑗 𝑟

𝑖→𝑙 𝑖→𝑙 𝑖→𝑚≠𝑙 𝑖→𝑙 𝑖→𝑙 𝑗≠𝑖→𝑙

Figure: Example illustrating the linear combination of ground state MOs according to their weighing contributions & thus computed EDD and HDD maps for 𝑺𝑵 state
𝐒𝑵 𝐄𝐱𝐜𝐢𝐭𝐞𝐝 𝐬𝐭𝐚𝐭𝐞 𝐜𝐡𝐚𝐫𝐚𝐜𝐭𝐞𝐫𝐢𝐬𝐭𝐢𝐜𝐬: 𝜆𝑵 , f

EDD
LUMO LUMO LUMO+1 Visual
w = 16 % w = 36 % w = 35 % CT
Extent

HDD
HOMO
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 Accurate TDM Computation: Dimeric Geometric Parameters
 Electron (C-(r)) & Hole (C+) Density Distribution Centroids:
2 2 2 2 2 2
𝑥 − 𝑥+ 𝑦 − 𝑦+ 𝑧 − 𝑧+ 𝑥 − 𝑥− 𝑦 − 𝑦− 𝑧 − 𝑧−
𝐶+ 𝑟 = 𝐴+ 𝑒 − 2 − 2 − 2 𝐶− 𝑟 = 𝐴− 𝑒 − 2 − 2 − 2
2𝜎+𝑥 2𝜎+𝑦 2𝜎+𝑧 2𝜎−𝑥 2𝜎−𝑦 2𝜎−𝑧

 Monomeric TDM Direction: Line passing through EDD and HDD centroids for associated electronic transition

𝑀𝑚𝑜𝑛 𝐶−
𝐶− 𝐶−
𝐶+ 𝐶− 𝐶+ 𝐶+
𝐶+ 𝑀𝜆𝑚𝑜𝑛
𝑀𝑚𝑜𝑛
PNA 𝑀𝑚𝑜𝑛 TC NT RB

 Dimeric Geometric Parameters (⍺, θ and r)

O-
04-May-21 9:23 PM O- J- J-
14
 Quantifying Locally Excited vs. Charge Transfer Characteristics
CT Direction & Magnitude: Bahers et al. defined CT spatial extent associated with 𝜑𝐶 + 𝐶 − and t Å indexes 1, 2
𝐶+ 𝑟 𝐶− 𝑟
C- and C+ Overlap integral (𝝋𝑪+ 𝑪− ) = ‫׬‬ 𝐴+ 𝐴−
𝑑𝑟 ; t Å = 𝐷𝑐𝑡 Å − 𝐻 Å

Figure: Example depicting the predominant Charge Transfer & Locally Excited molecular dimer (TC) singlet states quantified with 𝜑 & t-indexes

CDD CDD
ty = 3.37 Å ty = - 1.30 Å

tz = - 1.00 Å
tz = - 0.64 Å tx = - 3.04 Å tx = - 3.64 Å

φ = 0.156 Charge Transfer φ = 0.968 Locally Excited

1. Le Bahers, T.; Adamo, C.; Ciofini, I., J. Chem. Theo. Comput. 2011, 7, 2498-2506.
04-May-21 9:23 PM 15
2. Ciofini, I.; Le Bahers, T.; Adamo, C.; Odobel, F.; Jacquemin, D., J. Phys. Chem. C 2012, 116, 11946-11955.
 Published Research Publications

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 A New Class of Nitroanilinic Dimer, the PNA O−Dimer: Electronic
Structure and Emission Characteristics of O−Dimeric Aggregates
P-nitroaniline (PNA) monomer P-nitroaniline oblique dimer

Aggregation
(Aprotic solvent, THF )

Non-fluorescent Aggregation Induced Emission (AIE)

Excited
State 2

Twisted
Excited State 1

PNA O-Dimer

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 Novel Non-fluorescent J-Aggregates of Tetracenes: A Rare Violation

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 Popular QM codes
Gaussian (Ab Initio, Semi-empirical, DFT)
Gamess-US/UK (Ab Initio, DFT)
Spartan (Ab Initio, Semi-empirical, DFT)
NWChem (Ab Initio, DFT, MD, QM/MM)
MOPAC/2000 (Semi-Empirical)
DMol3/CASTEP (DFT)
Molpro (Ab initio)
ADF (DFT)
ORCA (DFT)
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 Caution or Conclusion!
• Different choices of methods and basis sets can yield large variation in results
• Important to know: Errors associated with and limitations of different computational approaches
• This is important when doing your own calculations, and when evaluating the calculations of
others.

Don’t just accept the numbers the computer spits!

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 Thank you !!!

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