Transcript Presentation Title - Information Technology Services

Gaussian & GaussView
Shubin Liu, Ph.D.
Research Computing Center, ITS
University of North Carolina at Chapel Hill
Agenda
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Introduction
Capabilities
Input File Preparation
Gaussian GUI – GaussView
Run G03 Jobs @ UNC-CH
Some Advanced Topics
Hands-on Experiments – next hour
The PPT format of this presentation is available here:
http://its2.unc.edu/divisions/rc/training/scientific/
/afs/isis/depts/its/public_html/divisions/rc/training/scientific/short_courses/
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Course Goal
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What Gaussian/GaussView packages are
How to prepare input files via GaussView
How to run G03 jobs on UNC-CH servers
How to view G03 results
Learn selected advanced topics
Hands-on experiments
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Pre-requisites
 Basic UNIX knowledge
 Introduction to Scientific Computing
 An account on Emerald
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About Us
 ITS – Information Technology Services
• http://its.unc.edu
• http://help.unc.edu
• Physical locations:
 401 West Franklin St.
 211 Manning Drive
• 10 Divisions/Departments
 Information Security
 Research Computing Center
 User Support and Engagement
 Communication Technologies
 Enterprise Applications
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IT Infrastructure and Operations
Teaching and Learning
Office of the CIO
Communications
Finance and Administration
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Research Computing
Center
 Where and who are we and what do we do?
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ITS Manning: 211 Manning Drive
Website
http://its.unc.edu/research-computing.html
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Groups
 Infrastructure -- Hardware
 User Support -- Software
 Engagement -- Collaboration
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About Myself
 Ph.D. from Chemistry, UNC-CH
 Currently Senior Computational Scientist @ Research Computing Center, UNC-CH
 Responsibilities:
• Support Computational Chemistry/Physics/Material Science software
• Support Programming (FORTRAN/C/C++) tools, code porting, parallel computing, etc.
• Training, Workshops/Short Courses – currently 4, one more to come soon
• Conduct research and engagement projects in Computational Chemistry
 Development of DFT theory and concept tools
 Applications in biological and material science systems
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About You
 Name, department, group, interest?
 Any experience before with Gaussian or
GaussView?
 What do you expect to use them? What
kind of systems?
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Gaussian & GaussView
 Gaussian is a general purpose electronic structure
package for use in computational chemistry.
Current version 03 E01.
 Most widely used computational chemistry
package. The latest release is version 2009.
 GaussView is a graphical user interface (GUI)
designed to be used with Gaussian to make
calculation preparation and output analysis
easier, quicker and more efficient. Current
version 4.1.2.
 Vendor’s website: http://www.gaussian.com
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Gaussian 98/03 Functionality
 Energies
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MM: AMBER, Dreiding, UFF force field
Semiempirical: CNDO, INDO, MINDO/3, MNDO, AM1, PM3
HF: closed-shell, restricted/unrestricted open-shell
DFT: many local/nonlocal functionals to choose
MP: 2nd-5th order; direct and semi-direct methods
CI: single and double
CC: single, double, triples contribution
High accuracy methods: G1, G2, CBS, etc.
MCSCF: including CASSCF
GVB
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Gaussian 98/03 Functionality
 Gradients/Geometry optimizations
 Frequencies (IR/Raman, NMR, etc.)
 Other properties
• Populations analyses
• Electrostatic potentials
• NMR tensors
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Several solvation models (PCM, COSMOS)
Two and three layer ONIOM – E, grad, freq
Transition state search
IRC for reaction path
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New in Gaussian 03/09
 Molecular Dynamics
• BOMD – Born-Oppenheimer MD
• ADMP – Atom-Centered Density Matrix Propagation
 Periodic Boundary Conditions (PBC) – HF and DFT energies and
gradients
 Properties with ONIOM models
 Spin-spin coupling and other additions to spectroscopic
properties
 Also – improved algorithms for initial guesses in DFT and faster
SCF convergence
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Gaussian Input File
Structure
 .com,.inp, or .gjf (Windows version)
 Free format, case insensitive
 Spaces, commas, tabs, forward slash as delimiters between
keywords
 ! as comment line/section
 Divided into sections (in order)
• Link 0 commands (%)
• Route section – what calculation is to do
• Title
• Molecular specification
• Optional additional sections
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Input File – Example 1
# HF/6-31G(d)
!Route section
!Blank line
water energy
!Title section
!Blank line
0 1
!Charge & multiplicity
O -0.464 0.177 0.0
Coordinate
!Geometry in Cartesian
H -0.464 1.137 0.0
H 0.441 -0.143 0.0
!Blank line
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Input File – Example 2
%nproc=2
%chk=water.chk
#b3lyp/6-311+G(3df,2p) opt freq
Calcn Title: test
0 1
O
h 1 r
h 1 r 2 a
variables
r=0.98
a=109.
!Link 0 section
!Route/Keywords
!Blank line
!Title
!Ban line
!Charge & multiplicity
!Geometry in Z-matrix
!Blank line
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Input File – Link 0 Commands
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First “Link 0” options (Examples)
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%chk
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%chk=myjob.chk
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%mem=12MW
%mem
%nproc
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$nproc=4
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%rwf=1,1999mb,b,1999mb
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%sc=e,1999mb,f,1999mb
%rwf
%scr
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Input File – Keyword Specification
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Keyword line(s) – specify calculation type and other job options
Start with # symbol
Can be multiple lines
Terminate with a blank line
Format
• keyword=option
• keyword(option)
• keyword(option1,option2,…)
• keyword=(option1,option2,…)
 User’s guide provides list of keywords, options, and basis set notion
http://www.gaussian.com/g_ur/keywords.htm
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Basis Set
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Minimal basis set (e.g., STO-3G)
Double zeta basis set (DZ)
Split valence basis Set (e.g., 6-31G)
Polarization and diffuse functions (6-31+G*)
Correlation-consistent basis functions (e.g., aug-cc-pvTZ)
Pseudopotentials, effective core potentials
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Input File – Title Specification
 Brief description of calculation – for
users benefit
 Terminate with a blank line
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Input File – Molecular Geometry
 1st line charge and multiplicity
 Element label and location
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Cartesian coordinate
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Label x y z
Z-matrix
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Label atoms bond length atom2 angle atm3 dihedral
 If parameters used instead of numerical values then variables
section follows
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 Again end in blank line
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A More Complicated Example
%chk=/scr/APPS_SCRDIR/f33em5p77c.chk
%mem=4096MB
%NProc=4
#B3LYP/6-31G* opt geom=Checkpoint Guess=read nosymm scf=tight
Geometry optimization of a sample molecule
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--Link1-%chk=/scr/APPS_SCRDIR/f33em5p77c.chk
%mem=4096MB
%NProc=2
# B3LYP/6-311++G** sp pop=nbo nosymm guess=read geom=checkpoint
Single Point Energy for the "reference state" of molecule with one more
electron.
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Other Gaussian Utilities
 formchk – formats checkpoint file so it can be used by other programs
 cubgen – generate cube file to look at MOs, densities, gradients, NMR in
GaussView
 freqchk – retrieves frequency/thermochemsitry data from chk file
 newzmat – converting molecular specs between formats (zmat, cart,
chk, cache, frac coord, MOPAC, pdb, and others)
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GaussView
GaussView 4.1.2 makes using Gaussian 03 simple and straightforward:
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Sketch in molecules using its advanced 3D Structure Builder, or
load in molecules from standard files.
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Set up and submit Gaussian 03 jobs right from the interface, and
monitor their progress as they run.
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Examine calculation results graphically via state-of-the-art
visualization features: display molecular orbitals and other
surfaces, view spectra, animate normal modes, geometry
optimizations and reaction paths.
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Online help: http://www.gaussian.com/g_gv/gvtop.htm
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GaussView Availability
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Support platforms:
– IBM RS6000 (AIX 5.1) (Happy/yatta/p575)
– LINUX 32-bit OS (Emeraldtest)
– LINUX 64-bit OS (Emerald, Topsail, Cedar/Cypress)
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GaussView: Build
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Build structures by atom, functional group, ring, amino acid (central fragment, amino-terminated and
carboxyl-terminated forms) or nucleoside (central fragment, C3’-terminated, C5’-terminated and free
nucleoside forms).
• Show or hide as many builder panels as desired.
• Define custom fragment libraries.
Open PDB files and other standard molecule file formats.
Optionally add hydrogen atoms to structures automatically, with excellent accuracy.
Graphically examine & modify all structural parameters.
Rotate even large molecules in 3 dimension: translation, 3D rotation and zooming are all accomplished
via simple mouse operations.
• Move multiple molecules in the same window individually or as a group.
• Adjust the orientation of any molecule display.
View molecules in several display modes: wire frame, tubes, ball and stick or space fill style.
• Display multiple views of the same structure.
• Customize element colors and window backgrounds.
Use the advanced Clean function to rationalize sketched-in structures
Constrain molecular structure to a specific symmetry (point group).
Recompute bonding on demand.
Build unit cells for 1, 2 and 3 dimensional periodic boundary conditions calculations (including
constraining to a specific space group symmetry).
Specify ONIOM layer assignments in several simple, intuitive ways: by clicking on the desired atoms, by
bond attachment proximity to a specified atom, by absolute distance from a specified atom, and by PDB
file residue.
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GaussView: Build
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GaussView: Build
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GuassView: Setup
 Molecule specification input is set up automatically.
 Specify additional redundant internal coordinates by clicking on the
appropriate atoms and optionally setting the value.
 Specify the input for any Gaussian 03 calculation type.
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Select the job from a pop-up menu. Related options automatically appear in the
dialog.
Select any method and basis set from pop-up menus.
Set up calculations for systems in solution. Select the desired solvent from a
pop-up menu.
Set up calculations for solids using the periodic boundary conditions method.
GaussView specifies the translation vectors automatically.
Set up molecule specifications for QST2 and QST3 transition state searches using
the Builder’s molecule group feature to transform one structure into the
reactants, products and/or transition state guess.
Select orbitals for CASSCF calculations using a graphical MO editor, rearranging
the order and occupations with the mouse.
 Start and monitor local Gaussian jobs.
 Start remote jobs via a custom script.
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GaussView: Setup
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GuassView: Showing Results
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Show calculation results summary.
Examine atomic changes: display numerical values or color atoms by charge (optionally
selecting custom colors).
Create surfaces for molecular orbitals, electron density, electrostatic potential, spin
density, or NMR shielding density from Gaussian job results.
• Display as solid, translucent or wire mesh.
• Color surfaces by a separate property.
• Load and display any cube created by Gaussian 03.
Animate normal modes associated with vibrational frequencies (or indicate the motion
with vectors).
Display spectra: IR, Raman, NMR, VCD.
• Display absolute NMR results or results with respect to an available reference
compound.
Animate geometry optimizations, IRC reaction path following, potential energy surface
scans, and BOMD and ADMP trajectories.
Produce web graphics and publication quality graphics files and printouts.
• Save/print images at arbitrary size and resolution.
• Create TIFF, JPEG, PNG, BMP and vector graphics EPS files.
• Customize element, surface, charge and background colors, or select high quality
gray scale output.
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GuassView: Showing Results
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Surfaces
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Reflection-Absorption Infrared Spectrum of AlQ3
N
O
Al
O
N
N
O
Wavenumbers (cm-1)
752
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1000
1386
1338
1116
800
1473
1200
1580 1605
1400
1600
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GaussView: VCD
(Vibrational Circular Dichroism)
Spectra
GaussView can display a variety of computed spectra, including IR, Raman, NMR and VCD. Here we see the
VCD spectra for two conformations of spiropentyl acetate, a chiral derivative of spiropentane. See F. J. Devlin,
P. J. Stephens, C. Österle, K. B. Wiberg, J. R. Cheeseman, and M. J. Frisch, J. Org. Chem. 67, 8090 (2002).
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GaussView: ONIOM
Bacteriorhodopsin, set up for an ONIOM calculation (stylized). See T. Vreven and K. Morokuma,
“Investigation of the S0->S1 excitation in bacteriorhodopsin with the ONIOM(MO:MM) hybrid
method,” Theor. Chem. Acc. (2003).
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Gaussian/GaussView @ UNC
 Installed in AFS ISIS package space /afs/isis/pkg/gaussian
• Package name: gaussian
• Versions: 03D02, 03E01 (default version)
• Type “ipm add gaussian” to subscribe the service
 Availability
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SGI Altix 3700, cedar/cypress
IBM P690, happy/yatta
LINUX cluster, emerald.isis.unc.edu
LINUX Cluster, topsail.unc.edu
 Package information available at:
http://help.unc.edu/6082
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Access GaussView
 From UNIX workstation
• Login to emerald, cedar, topsail, or happy
ssh –X emerlad.isis.unc.edu
• Invoke gaussview or gview via LSF interactive queue
 From PC desktop via X-Win32 or SecureCRT
• Detailed document available at:
http://its2.unc.edu/divisions/rc/training/scientific/g03_gv_instructions.doc
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Submit G03 Jobs to Servers
 To submit single-CPU G03 jobs to computing servers via LSF:
bsub -q qname
-m mname
g03 input.inp
where “qname” stands for a queue name, e.g., week, month,
etc., “mname” represents a machine name, e.g., cypress,
yatta, etc., and “input.inp” denotes the input file prepared
manually or via GaussView.
For example:
bsub -q week -m cypress g03 input.inp
bsub -q month -m p575-n02 g03 input.inp
bsub -q idle -R blade g03 input.inp
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Submit G03 Jobs to Servers
 To submit multiple-CPU G03 jobs via LSF:
-- G03 is parallelized via OpenMP
bsub -q qname
-n ncpu -m mname
g03 input.inp
where “qname” stands for a queue name, e.g., week, idle, etc., “ncpu” is the
number of CPUs requested, e.g., 2 or 4 or 8, “mname” represents a machine name,
e.g., yatta, cypress, etc., and “input.inp” denotes the input file prepared
manually or via GaussView.
For example
bsub -q week -n 4 -m cypress g03 input.inp
To submit multiple CPU g03 jobs on Emerald, make sure only all CPUs are from the
same node because G03 is parallelized via OpenMP (for share-memory SMP
machines)
bsub -q week -n 4 –R “blade span[ptile=4]” g03 input.inp
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Default Settings
 Temporary files
• P575/Yatta/cypress:
• Emerald:
/scr/APPS_SCRDIR
/tmp
 Memory
• P575/Yatta/cypress:
• Emerald:
1GB
512MB
 MAXDISK
• P575/Yatta/cypress:
• Emerald:
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4GB
2GB
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Advanced Topics
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Potential energy surfaces
Transition state optimization
Thermochemistry
NMR, VCD, IR/Raman spectra
NBO analysis
Excited states (UV/visible spectra)
Solvent effect
PBC
ONIOM model
ABMD, BOMD, etc.
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Potential Energy
Surfaces
 Many aspects of chemistry can be reduced to questions about
potential energy surfaces (PES)
 A PES displays the energy of a molecule as a function of its
geometry
 Energy is plotted on the vertical axis, geometric coordinates
(e.g bond lengths, valence angles, etc.) are plotted on the
horizontal axes
 A PES can be thought of it as a hilly landscape, with valleys,
mountain passes and peaks
 Real PES have many dimensions, but key feature can be
represented by a 3 dimensional PES
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Model Potential Energy Surface
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Calculating PES in
Gaussian/GaussView
 Use the keyword “scan”
 Then change
input file properly
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Transition State Search
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Calculating Transition
States
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Locating Transition
States
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TS Search in Gaussian
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TS Search in
Gaussian/GaussView
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TS Search in
Gaussian/GaussView
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Animation of Imaginary
Frequency
 Check that the imaginary
frequency corresponds to
the TS you search for.
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Intrinsic Reaction Coordinate Scans
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Input for IRC Calculation
StepSize=N
Step size along the reaction path, in units of 0.01 amu-1/2-Bohr. The
default is 10.
RCFC
Specifies that the computed force constants in Cartesian coordinates
from a frequency calculation are to be read from the checkpoint file.
ReadCartesianFC is a synonym for RCFC.
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IRC Calculation in
GaussView
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Reaction Pathway Graph
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Thermochemistry
from ab initio Calculations
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Thermochemistry
from ab initio Calculations
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Thermochemistry from frequency
calculation
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Modeling System in Solution
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Calculating Solvent Effect
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Calculating Solvent Effect
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Solvent Effect: Menshutkin Model
Reaction Transition State
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Solvent Effect: Menshutkin Model
Reaction Transition State
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NMR Shielding Tensors
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NMR Example Input
%chk=ethynenmr
#p hf/6-311+g(2d,p) nmr
nmr ethyne
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C
C,1,r1
H,1,r2,2,a2
H,2,r3,1,a3,3,d3,0
Variables
R1=1.20756258
R2=1.06759666
R3=1.06759666
A2=180.0
A3=180.0
D3=0.0
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Comparison of Calculated and
Experimental Chemical Shifts
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QM/MM: ONIOM Model
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QM/MM: ONIOM Model
From GaussView menu: Edit -> Select Layer
Low Layer
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Medium Layer
High Layer
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QM/MM: ONIOM Setup
From GaussView menu: Calculate ->Gaussian->Method
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QM/MM: ONIOM Setup
 For the medium and low layers:
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QM/MM: ONIOM Setup
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What Is NBO?
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Natural Bond Orbitals (NBOs) are localized few-center orbitals ("few" meaning
typically 1 or 2, but occasionally more) that describe the Lewis-like molecular
bonding pattern of electron pairs (or of individual electrons in the open-shell
case) in optimally compact form. More precisely, NBOs are an orthonormal set
of localized "maximum occupancy" orbitals whose leading N/2 members (or N
members in the open-shell case) give the most accurate possible Lewis-like
description of the total N-electron density.
C-C Bond
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C-H Bond
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NBO Analysis
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NBO in GaussView
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Natural Population Analysis
#rhf/3-21g pop=nbo
RHF/3-21G for formamide (H2NCHO)
0 1
H
H
N
C
O
H
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-1.908544
-1.188060
-1.084526
0.163001
1.196265
0.140159
0.420906
-1.161135
-0.157315
0.386691
-0.246372
1.492269
0.000111
0.000063
0.000032
-0.000154
0.000051
0.000126
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NPA
Output
Sample
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Further Readings
 Computational Chemistry (Oxford Chemistry Primer) G. H. Grant and
W. G. Richards (Oxford University Press)
 Molecular Modeling – Principles and Applications, A. R. Leach (Addison
Wesley Longman)
 Introduction to Computational Chemistry, F. Jensen (Wiley)
 Essentials of Computational Chemistry – Theories and Models, C. J.
Cramer (Wiley)
 Exploring Chemistry with Electronic Structure Methods, J. B. Foresman
and A. Frisch (Gaussian Inc.)
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Comments & Questions???
Please direct comments/questions about
Gaussian/GaussView to
E-mail: [email protected]
Please direct comments/questions pertaining to this
presentation to
E-Mail: [email protected]
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Hands-on: Part I
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Access GaussView to Emerald cluster from PC desktop
If not done so before, type “ipm add gaussian”
Check if Gaussian is subscribed by typing “ipm q”
Get to know GaussView GUI
Build a simple molecular model
Generate an input file for G03 called, for example, input.com
View and modify the G03 input file
Submit G03 job to emerald compute nodes using the week or now
queue:
bsub –R blade –q now g03 input.com
The WORD .doc format of this hands-on exercises is available here:
http://its2.unc.edu/divisions/rc/training/scientific/
/afs/isis/depts/its/public_html/divisions/rc/training/scientific/short_courses/labDirections_gaussian_2009.doc
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Hands-on: Part II
 Calculate/View Molecular Orbitals with GaussView
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http://educ.gaussian.com/visual/Orbs/html/OrbsGaussView.htm
Calculate/View Electrostatic Potential with GaussView
• http://educ.gaussian.com/visual/ESP/html/ESPGaussView.htm
Calculate/View Vibrational Frequencies in GaussView
• http://educ.gaussian.com/visual/Vibs/html/VibsGaussview.htm
Calculate/View NMR Tensors with GaussView
• http://educ.gaussian.com/visual/NMR/html/NMRGausview.htm
Calculate/View a Reaction Path with GaussView
• http://educ.gaussian.com/visual/RPath/html/RPathGaussView.ht
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