MM PDF

Molecular Modeling Workshop
Molecular Modeling
Workshop
Laboratory for Molecular Simulation (LMS)
Manager: Dr. Lisa M. Prez

Director: Prof. Michael B. Hall
lms.chem.tamu.edu
mouse@chem.tamu.edu
Office: Rm. 2109 Chemistry (CHAN) phone: 845-9384
Please sign in and turn your cell phones to silent for the lecture
February 19, 2016
Introduction to Molecular Modeling

Visualization
Computational Chemistry Molecular Modeling
Quantum Mechanics
Ab initio Visualization Computational
Density-Functional Theory Chemistry
Semi-Empirical
Classical Mechanics Information

molecular mechanic (MM)
Science

molecular dynamics (MD)
Monte Carlo
Prediction of properties
Structural, chemical, physical, biological, etc.
Understand, explain, and possibly predict chemical processes
Tools to gain insight at the atomic and molecular level
Microscopic Macroscopic
February 19, 2016
Laboratory for Molecular Simulation, Texas A&M University 1

Microscopic Macroscopic
Time Grids
>min Continuum
Segments (FEA, CFD)
s
s Mesoscale
Atoms
ns Molecular
Electrons Dynamics
F=ma
ps Quantum
Mechanics
fs H=E

ngstroms nm m mm m Distance
February 19, 2016
Visualization
Building
Draw in 2-D
Convert to 3-D
Rotate
Rendering
Line
Stick
Ball and Stick
CPK Ball Maynard, D. and Vigh, G.
Dept. of Chemistry, Texas A&M University
Cartoon
Surfaces
Visualizing crystal structures
February 19, 2016

Visualization
Images generated in Chimera February 19, 2016
Software Purchases
The Laboratory for Molecular Simulation currently provides
a wide variety of academic licenses for commercial and
academic molecular modeling software for students and
researchers at Texas A&M University.
The LMS assists in the purchase of software that we currently

do not provide. $$$
The LMS also provides support in the use of Molecular

Modeling software through administration (ie. installation
and updates), training, and scripting.
February 19, 2016

Software Quantum Mechanics

Name Description Licensing Price
ADF Quantum Mechanics (QM) 8 CPU Floating License $$
ABINIT QM (Molecular and Periodic Systems) Site License* Free
AMPAC QM (Semi-empirical) Site License $
CRYSTAL QM for Periodic Systems Site License $
Dalton QM Specializing in magnetic/electric properties Site License* Free
Discovery Studio QM & MM/MD suite of software with a user-friendly Floating Licenses $$$
Interface for Life Sciences
GAMESS-US QM Site License* Free
Gaussian QM Site License $
Materials Studio MM/MD & QM suite of software with a user-friendly Floating Licenses $$$
GUI for Materials Sciences
MOLPRO QM (specializing in high-level calculations) Group Licenses $$
NWChem QM Site License* Free
ORCA QM specializing in spectroscopic properties Site License* Free
SIESTA QM specializing in electron transport and Solids Site License* Free
VASP QM specializing in QMD and ultra-soft ECPs Restricted Licenses $$
* Users need to register with the software provider at no charge.
February 19, 2016
Software Molecular Mechanics/Dynamics

AMBER Molecular Mechanics/Dynamics (MM/MD) Site License $
CHARMm MM/MD 8 Floating Licenses $$/$
Discovery Studio MM/MD & QM suite of software with a user-friendly Floating Licenses $$$
GUI for Life Sciences
GROMACS MM/MD specializing in speed and coarse-grained Site License* Free
simulations
GROMOS MM/MD Group License $
LAMMPS MM/MD Site License* Free
Materials Studio MM/MD & QM suite of software with a user-friendly Floating Licenses $$$
GUI for Materials Sciences
MOE MM/MD Drug discovery software Floating Licenses $$$
ICM MM/MD and more Floating or Node locked Free &

Licenses $$$
Schrdinger MM/MD and more Floating Licenses $$$
NAMD MM/MD Site License* Free
* Users need to register with the software provider at no charge.

LMS does not currently hold a license February 19, 2016

Software Graphical User Interfaces (GUI)

AIM2000 Wavefunction Analysis (Bader Analysis) LMS License $
AGUI (Gaussview) GUI for AMPAC and Gaussian Site License $
AOMix MO analysis & spectra simulation Site License $
Avogadro Visualizer and GUI for many QM and MM codes Site License* Free
Chemmisian GUI for the analysis of electronic structure and spectra. Site License* $
Chimera Interactive Visualization and analysis of Molecular Site License* Free

Structures
Gabedit GUI for computational chemistry software Site License* Free
gOpenMol GUI for computational chemistry software Site License* Free
Jimp2 GUI for Fenske-Hall (QM) and more Site License* Free
Maestro GUI for Schrdinger Suite of Software Token Based Licnese $$$
Molden GUI to visualize results of modeling software Site License* Free
VMD GUI for NAMD and more Site License* Free
* Users need to register with the software provider at no charge. February 19, 2016
Materials Studio by BIOVIA

Bundle Name # of Licenses Modules Included in Bundle
Materials Studio 25 Visualizer MS Pipeline Pilot Collection
Base Conformers Reflex
Forcite Plus Parallel VAMP Parallel
Gaussian Interface VAMP Interface
QSAR+
Materials Studio 1 Adsorption Locator Mesocite
Classical & Amorphous Cell Mesodyn
Mesoscale Blends Mesodyn Interface
COMPASS Parallel Sorption
GULP Parallel Synthia
GULP Interface
Materials Studio 3 CASTEP Parallel GULP Parallel
Quantum CASTEP Interface GULP Interface
DFTB+ Parallel NMR CASTEP Parallel
DMOL3 Solid State Parallel ONETEP
DMOL3 Solid State Interface QMERA
QMERA Interface
1 Equilibria
February 19, 2016

Discovery Studio by BIOVIA

Bundle Name # of Licenses Modules Included in Bundle
Discovery Studio 18 Visualizer CHARMm
Base Analysis DMOL3 Molecular
Biopolymer MMFF (Force-Field)
Catalyst Conformation Protein Refine
Catalyst Score QUANTUMm (QM/MM)
CDOCKER
Discovery Studio 2 Catalyst DB Build De Novo Ligand Builder
Structure Based Catalyst DB Search Flexible Docking
Design Catalyst Hypothesis Libdock
Catalyst SBP LigandFit
Catalyst Shape LigandScore
CFF LUDI
De Novo Evolution MCSS
Discovery Studio 3 Modeler Protein Docking
Protein Protein Families Sequence Analysis
Protein Health X-ray analysis (CNX)
February 19, 2016
Schrdinger
Units Items
15 Tokens Glide (5 Tokens) QikProp (2 Tokens)
Liaison (4 Tokens) Canvas (1 Token)
Strike (1 Token) LigPrep (1 Token)
10 Licenses BioLuminate GUI
10 Tokens QSite (4 Tokens) pKa Predictor (3 Tokens)
MacroModel (2 Tokens) Epik (1 Token)
ConfGen (3 Tokens) SiteMap (1 Token)
Jaguar (2 Tokens) Prime (8 Tokens)
1 License PIPER
February 19, 2016

MOE Molecular Operating

Environment by Chemical Computing
Group
LMS holds a
3 Token License
With an option for

teaching licenses at no charge.
February 19, 2016
Computational Chemistry
Quantum Mechanics
Ab initio - based on first principles
Hartree-Fock Theory (HF)
Mller-Plesset Perturbation Theory (MPn ; n = 2, 3, 4, )
Configuration Interaction (CI ; CIS, CISD, CISDT, )
Coupled-Cluster (CC ; CCD, CCSD, CCSD(T), CCSD(TQ), )
Complete Active Space Self Consitent Field (CASSCF)
Multi-Reference Configuration Interaction (MRCI)
and many more
Density Functional Theory
B3LYP, BP86, B3PW91, mPW1PW91, PBE, M06, TPSS, B97x-D
and many more
Semi-empirical
AM1
PM3, PM5, PM7
and many more
February 19, 2016

Quantum Mechanics
Ab initio methods
Schrdinger Equation
H=E ; time-independent Schrdinger equation.
Applicable to any system, in principle.
Can model bond breaking and formation
Used for benchmark values
Can only be used for small system ( normally < 200 atoms )
Computationally expensive
Scaling: Nn n=2, 3, 4, 5, 6,
Commonly used codes
Gaussian 09, GAMESS-US, Spartan, NWChem
Q-Chem, MOLPRO, Dalton, GAMESS-UK, CRYSTAL
and many more
February 19, 2016
Quantum Mechanics
Density Functional Theory (DFT)
Total energy of a system depends only on the electron density
Etot= F[(x,y,z,s)]
Applicable to any system, in principle.
Can model bond breaking and formation
Includes electron correlation with little cost compared to ab initio
methods
Exact functional is not known
Commonly used software for DFT
Gaussian 09, Jaguar, DMol3, Turbomole, Amsterdam Density Functional
(ADF), GAMESS-US, NWChem, MOLPRO, Spartan, GAMESS-UK,
CRYSTAL, and many more
February 19, 2016

Reaction Mechanism Calculations
Cunxiang Zhao, T. Andrew Mitchell, Ravikrishna Vallakati, Lisa M. Prez, and Daniel Romo
J. Am. Chem. Soc., 2012, 134 (6), pp 30843094
DOI: 10.1021/ja209163w
February 19, 2016
February 19, 2016

February 19, 2016
3 + 6Acetonitrile 4 + 3Acetonitrile 5 + Naphthalene
2+
3
Ru c2v Ru
2+
5
Ru c2v Ru
N
N
N N N N
2+
4
Ru cs Ru
N
N N
February 19, 2016

NMR Calculations
Original
assignment for
spectra a)
Upfield
Downfield
(E)-2a is
lower in
energy than
(E)-2a-ZnCl2
February 19, 2016
Quantum Mechanics (ab initio, DFT, Semi-empirical)

Reaction Path Calculations
Thomson (Prez), L.M.; Hall, M.B. J. Am. Chem. Soc.2001, 123, 3995.
Calculating transition states is significantly more difficult than

minima.
Experimental data is needed to narrow reaction path possibilities to
be investigated computationally.
February 19, 2016

3 + 6Acetonitrile 4 + 3Acetonitrile 5 + Naphthalene
2+
4
2+ Ru Ru
cs
N
N N
3
Ru c2v Ru
2+
5
Ru c2v Ru
N
N
N N N N
February 19, 2016
UV/Vis spectra via TD-DFT

Experimental TD-DFT
February 19, 2016

UV/Vis spectra via TD-DFT

Experimental TD-DFT
February 19, 2016
Wavefunction Analysis
Atoms in Molecules (AIM)
A) Contour plot of the electron density of [1-F]+ showing the short and long C-F bonds. The
plane was selected to contain the C02, F, and C01 atoms. B) Contour plot of 1/4 2 (r) for
[1-F]+ illustrating the covalent nature of the short C-F bond and the dative nature of the long
C-F bond. Positive and negative values are shown with blue solid and red dashed lines,
respectively.
February 19, 2016

Quantum Mechanics
Semi-empirical Methods
AM1, PM3, PM5, PM7, PM7-TM, SAM1, etc.
Approximate solution to the Schrdinger equation
Replaces the expensive integrals with parameters
Applicability is limited by available parameterization
Mostly used for 1st row main group elements
Limited applicability to transition metals
Can model bond breaking/formation

Can model much larger systems than ab initio or DFT
Commonly used software
MOPAC 2012, Gaussian 09, Chem3d, AMPAC, VAMP, and many
more
February 19, 2016
Molecular Mechanics
Newtons equations
The potential is approximated by an empirical function
force field that is fitted to approximately reproduce
known interactions
Applicability is limited by the availability of
parameterization
Generally, the connectivity of atoms cannot change during
the simulation
Generally, not suitable for reaction mechanisms
Can predict relative energies of different conformational states of
material
And much more
February 19, 2016

Molecular Mechanics
The molecule is considered to be a collection of atoms held
together by simple elastic or harmonic forces.
Force Field - A mathematical expression that describes the

dependence of the energy of a molecule on the coordinates of the
atoms in the molecule.
Force Field Energy Expression:

E = Ebond + Eangle + Etorsion + Eoop(out-of-plane) + Enon-bond + Eother
February 19, 2016
Force Field Terms - Bond Term
February 19, 2016

Force Field Terms Angle Term
February 19, 2016
Force Field
Terms - Torsion,
Inversion &
Coulombic
Terms
February 19, 2016

Force
Field
Terms
Van der
Waals
Terms
February 19, 2016
Force Field
Terms
Cross Terms
February 19, 2016

Class II Bond stretching
forcefield Angle bending
(CFF91)
Torsion Out-of-plane
5-11 Cross Terms
Van der Waals

Coulombic February 19, 2016
Molecular Mechanics
Force Fields differ in their parameters, terms and the method of
development
Class I - simple functional form with data fitted to quantum mechanical
calculations and/or experiment (AMBER, CHARMM, etc)
Class II - more complicated functional form using cross terms and data
fitted to quantum mechanical calculations and/or experiment (CFF, PCFF,
etc)
Class III - new generation force fields that incorporate polarizability
(AMOEBA, AMBER ff02, CHARMM Drude, etc)
Rules Based - covers most of the periodic table UFF, DREIDING, etc
Fundamental quantities are derived for each atom type: electronegativity, hardness,
atomic radius, etc.
Forcefield parameters are derived at runtime using a series of theoretically or
empirically derived rules
Specialist - developed for a particular family of compounds flourinated
polymers, zeolites, etc.
Reaction Forcefields - ReaxFF
February 19, 2016

Common Force Fields

MM2/MM3/MM4: Molecular Mechanic Force field for
small organic molecules
CHARMM: Chemistry at Harvard Macromolecular
Mechanics
AMBER: Assisted Model Building with Energy Refinement
OPLS: Optimized Parameters for Liquid Simulation
CFF: Consistent Force Field
CVFF: Valence Consistent Force Field
MMFF94: Merck Molecular Force Field 94
DREIDING: Generic rules based force field
UFF: Universal Force Field
ReaxFF: Speciality force-field to allow bond breaking
February 19, 2016
UFF Universal Force-Field

The Universal forcefield's atom types are denoted by an element name of one or two
characters followed by up to three other characters:
The first two characters are the element symbol (i.e., N_ for nitrogen ).
The third character (if present) represents the hybridization state
1 = linear
2 = trigonal
R = an atom involved in resonance
3 = tetrahedral
4 = square planar
5 = trigonal bipyramidal
6 = octahedral
The fourth and fifth characters (if present) indicate characteristics such as
the oxidation state (i.e., Rh6+3 represents octahedral Rh in the +3 formal oxidation
state
H___b indicates a diborane bridging hydrogen type
O_3_z is a framework oxygen type suitable for zeolites).
A. K. Rappe; C. J. Casewit; K. S. Colwell; W. A. Goddard III; W. M. Skiff J. Am. Chem. Soc. 114, 10024-10035
(1992).
February 19, 2016

Force Field Atom Types

CFF/ CFF91/ PCFF
carbonyl functional groups C and O
c_0 carbonyl carbon of aldehydes, ketones
c_1 carbonyl carbon of acid, ester, amide
c_2 carbonyl carbon of carbamate, urea
cz carbonyl carbon of carbonate
o= oxygen double bonded to O, C, S, N, P
o_1 oxygen in carbonyl group
o_2 ester oxygen
oo oxygen in carbonyl group, carbonate only
oz ester oxygen in carbonate
February 19, 2016
Atom Types o=
hn
Sf
Cp
nb
s1
PCFF force field - PCFF was developed based on CFF91 and is intended for
application to polymers and organic materials. It is useful for polycarbonates, melamine
resins, polysaccharides, other polymers, organic and inorganic materials, about 20
inorganic metals, as well as for carbohydrates, lipids, and nucleic acids and also cohesive
energies, mechanical properties, compressibility's, heat capacities, elastic constants. It
handles electron delocalization in aromatic rings by means of a charge library rather than
bond increments.
February 19, 2016

Minimization
Minimize the potential energy
E = Ebond + Eangle + Etorsion + Eoop + Enonbond + Eother
Local
Energy
Minima
Local
Minima
Local
Global Minima
Minimum
February 19, 2016
Minimization Strategies
Cascade Approach - Smart Minimizer
Steepest decent
Max gradient > 100
Conjugate Gradient
Max gradient < 100
Newton
iterative (pure) Newton-Raphson.
BFGS (Broyden-Fletcher-Goldfarb-Shanno)
DFP (Davidon-Fletcher-Powell)
truncated Newton-Raphson
Final Convergence
Many software programs will perform these steps for you,

but some programs you will need to perform this manually.
February 19, 2016

Mutations and Minimization
Native
February 19, 2016
Molecular Dynamics
Minimization methods will only optimize your molecule to
the closest local minimum
Methods to find the global minimum
Systematic conformational search
Very time consuming and essentially impossible for anything but the
smallest of molecules
CH3(CH2)n+1CH3
n=1 3 possible configurations <1 sec
n=2 243 1 min
n=10 59,049 2 hour
n=15 14,348,907 100 days
Molecular Dynamics, Random Sampling, Monte Carlo, Hybrid
Monte Carlo/Dynamics methods
Samples the potential energy surface by perturbing the geometry
February 19, 2016

Molecular Dynamics
Methods to find the global minimum
High temperature dynamics
Simulated annealing
Quench dynamics
Energy supplied to the minimized
structure at the start of the simulation
T(K)
Energy
minimize
Time ps Time ps
Simulated Annealing Quench Dynamics
February 19, 2016
Molecular Dynamics
Molecular Dynamics Variations
Constant Volume - Constant Temperature (NVT)
Constant Volume - Constant Energy (NVE)
Constant Pressure Constant Temperature (NPT)
construct a set of velocities based on the ensemble being used
Velocities satisfy the Maxwell-Boltzmann distribution

Each run will start with a different random seed
Allow atoms to move for one time step 1

r (t + t ) = r (t )+ t v(t )+ t 2 a (t )
2
Calculate the force on the atoms - forcefield
Calculate the acceleration F=ma

1
v(t + t ) = v(t )+ t (a (t )+ a(t + t ))
Calculate the new velocity 2
1
Calculate the new position r (t + t ) = r (t )+ t v(t )+ t 2 a (t )
2
Repeat for as many time steps as desired
February 19, 2016

Molecular Dynamics
Choosing a time step
Your time step should be a factor of 10 smaller that the fastest process
in your system.
Molecular motions such as rotations and vibrations are on the order of 10-11 -
10-14 s
Therefore, a time step of 1 fs (10-15 s) or less must be used for most
systems.
You can increase your time step by restricting the fastest processes
SHAKE or RATTLE algorithms restrict the vibrational motion of the
molecule of interest
Therefore, a time step of 2-3 fs can be used with the SHAKE or RATTLE
algorithm
There are some modified shake algorithms that claim they are stable up to
time steps of 8 fs
Most simulations are on the order of picoseconds (10-12 s) or
nanoseconds (10-9 s)
Protein folding tripzip2 (12-residue protein) folds on the order of
2.5 s (10-6 s)
February 19, 2016
Molecular Simulation of ab Initio Protein Folding

for a Millisecond Folder NTL9(139)
Vincent A. Voelz, Gregory R. Bowman, Kyle Beauchamp, Vijay S. Pande Journal of the
American Chemical Society 2010 132 (5), 1526-1528
http://folding.stanford.edu/English/Papers#ntoc6
Gromacs(GPU version) and Folding@Home were used for the simulations with implicit
solvation
http://youtu.be/gFcp2Xpd29I
February 19, 2016

Conformational Searches
Ion mobility-mass spectrometry
peptide map of bovine
hemoglobin. Two low-energy
MD calculated structures are
assigned to peptide signals within
the plot: (1) LLGNVLVVVLAR
and (2) LLVVYPWTQR. The
two peptide projections shown
are 15 (top) and 10 (bottom).
Brandon T. Ruotolo, Guido F. Verbeck, Lisa M.
Prez (Thomson), Kent J. Gillig, and David H.
Russell J. Am. Chem. Soc., 124, 4214, 2002.
Ion mobility-mass
spectrometry peptide map of
horse heart myoglobin. Two
low-energy MD calculated
structures are assignaed to
peptide signals within the plot:
(1) HGTVVLTALGGILK and
(2) VEADIAGHGQEVLIR.
The two peptide projections
shown are 10 (top) and 15
(bottom).
February 19, 2016
Monte Carlo RIS Metropolis Monte Carlo

In outline, an RMMC simulation proceeds as follows:
Perform an energy minimization on the molecule
Randomly select a rotatable backbone bond.
Select a random torsion value for this bond between -180 and
+180 degrees.
Rotate the bond to its new torsion value and compute the new
energy of the chain.
Generate a random number, R, between 0 and 1. If
exp[-(Enew -Eold)/kT] > R, keep the new torsion value. Otherwise,
restore the old value.
Repeat until the desired number of iterations has been
performed
February 19, 2016

Molecular Dynamics Steps

Prepare the Molecule
Minimization
Required!!!!!!
Heating
Raise the temperature of the system from 0oC to the desired
temperature.
Many programs/researchers skip this step
Equilibration
Ensure that the system is stable (NVE)
Production
Run simulation to collect pertinent data
NVT, NVE, NPT, etc
February 19, 2016
Solvation
Explicit Solvation
Very expensive
Solvent molecules tend to boil off Non-Periodic water simulation
Need to use a periodic system to prevent loss of solvent

molecules Periodic water simulation
Solvent Dielectric Models

Treat the solvent as a bulk property
Vacuum = 1.0
Water = 78.39
Proteins = 4.0
Constant dielectric constant
Distance Dependent Dielectric Models
Dielectric constant varies with the distance between the charged
species
Generally used for large systems and proteins
February 19, 2016

Informatics
Storage and retrieval of information
Databases
Structures
Properties
Activities
Combinatorial Chemistry
Protein Bioinformatics
Drug Design
Catalysis
QSAR Quantitative Structure Activity Relationships
February 19, 2016
Quantitative Structure Activity Relationship (QSAR)

Multi-variant mathematical relationship between a set of
physico-chemical properties (descriptors) and a property of
interest
Biological activity
Solubility
Mechanical behavior
February 19, 2016

Homology
Utilizes structure and sequence similarities for predicting unknown
protein structures.
Database comparison
Molecular mechanics/
dynamics
NMR constraints
Web resource: http://zhanglab.ccmb.med.umich.edu/I-TASSER/
February 19, 2016
Drug Design
Generate a pharmacophore based on a set of known
biologically active molecules.
Use the pharmacophore to search a database for other
potentially active molecules.
February 19, 2016

Drug Design
de Novo drug design analog based drug design
Design ligands to interact with a know receptor
February 19, 2016
Useful Web Sites

Laboratory for Molecular Simulation
http://lms.chem.tamu.edu/
Listing of Hardware and Software available through the LMS
BIOVIA, Inc.
http://www.accelrys.com/
Chemical Computing Group, Inc.
http://www.chemcomp.com/software.htm
MOE Molecular Operating Environment
Schrdinger Inc.
http://www.schrodinger.com/
http://www.schrodinger.com/videos
Support videos
Gaussian, Inc.
http://www.gaussian.com/
February 19, 2016

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Molecular Modeling Workshop

Manager: Dr. Lisa M. Prez

February 19, 2016

Introduction to Molecular Modeling

February 19, 2016

Laboratory for Molecular Simulation, Texas A&M University 1

February 19, 2016

Laboratory for Molecular Simulation, Texas A&M University 2

Images generated in Chimera February 19, 2016

The LMS assists in the purchase of software that we currently

The LMS also provides support in the use of Molecular

February 19, 2016

Laboratory for Molecular Simulation, Texas A&M University 3

Software Quantum Mechanics

Software Molecular Mechanics/Dynamics

AMBER Molecular Mechanics/Dynamics (MM/MD) Site License $

CHARMm MM/MD 8 Floating Licenses $$/$

LAMMPS MM/MD Site License* Free

ICM MM/MD and more Floating or Node locked Free &

NAMD MM/MD Site License* Free

* Users need to register with the software provider at no charge.

Laboratory for Molecular Simulation, Texas A&M University 4

Software Graphical User Interfaces (GUI)

AIM2000 Wavefunction Analysis (Bader Analysis) LMS License $

AGUI (Gaussview) GUI for AMPAC and Gaussian Site License $

AOMix MO analysis & spectra simulation Site License $

Chimera Interactive Visualization and analysis of Molecular Site License* Free

gOpenMol GUI for computational chemistry software Site License* Free

Molden GUI to visualize results of modeling software Site License* Free

VMD GUI for NAMD and more Site License* Free

Materials Studio by BIOVIA

Laboratory for Molecular Simulation, Texas A&M University 5

Discovery Studio by BIOVIA

February 19, 2016

February 19, 2016

Laboratory for Molecular Simulation, Texas A&M University 6

MOE Molecular Operating

With an option for

February 19, 2016

Laboratory for Molecular Simulation, Texas A&M University 7

February 19, 2016

February 19, 2016

Laboratory for Molecular Simulation, Texas A&M University 8

Reaction Mechanism Calculations

February 19, 2016

Reaction Mechanism Calculations

February 19, 2016

Laboratory for Molecular Simulation, Texas A&M University 9

Reaction Mechanism Calculations

February 19, 2016

3 + 6Acetonitrile 4 + 3Acetonitrile 5 + Naphthalene

February 19, 2016

Laboratory for Molecular Simulation, Texas A&M University 10

February 19, 2016

Quantum Mechanics (ab initio, DFT, Semi-empirical)

Calculating transition states is significantly more difficult than

Laboratory for Molecular Simulation, Texas A&M University 11

3 + 6Acetonitrile 4 + 3Acetonitrile 5 + Naphthalene

February 19, 2016

UV/Vis spectra via TD-DFT

February 19, 2016

Laboratory for Molecular Simulation, Texas A&M University 12

UV/Vis spectra via TD-DFT