2/7/2017 1 Computational Chemistry Using the University of Alaska WebMO Site John Keller Department of Chemistry & Biochemistry University of Alaska Fairbanks Intro and operation of WebMO and MOPAC Basic Gaussian
2/7/2017 2 Click here to log in (guest/webmo or yourusername/password) https://chem2.uaf.edu/facilities/webmo/ http://chem.uaf.edu/keller/workshop/
2/7/2017 3 How does a WebMO job work? webserver world wide web User Draw molecule & choose options WebMO creates input file for MOPAC or Gaussian When the job is done, the output file is parsed and shown on Results page. The updated, intermediate results can be visualized in the Job Manager. compute servers chemlinux1 chemlinux2 (& others). Running Gaussian, MOPAC, and NWChem
2/7/2017 4 User Accounts MOPAC NWChem Gaussian CPU time limit (h) guest 4 Non-UAF unlimited UAF unlimited Machines Server Cores Procs Mem (GB) CPU Gaussian NWChem MOPAC Chemlinux1 8 8 16 Xeon (2) (6.3) Chemlinux2 8 8 32 Xeon (2) Chemlinux3 8 8 32 Xeon (2) (6.3) Antec12 6 12 32 Core i7 5820K (6.6) Corsair3 10 20 64 Core i7 6950X (6.6) Corsair2 4 8 24 Core i7 930 (WebMO)
2/7/2017 5 Levels of theory Correlated ab initio MO (MP2 & others) Molecular mechanics (MM+, OPLS, etc) Ball-andspring model no orbitals no electronics Semi-empirical MO (PM3, PM6) Uses 27 orbital parameters for each element Parameters derived from stable molecules Electron correlation implicit, since the parameters are fr real molecules, where actual electron correlation occurs. Ab initio MO (Hartree-Fock HF) MOs = linear combination of basis orbitals. Parameters derived from isolated atoms Some electron correlation Density Functional Theory (DFT) (B3LYP ) MOs = linear combination of basis orbitals. 3-25 Parameters derived from atoms and molecular databases More electron correlation MOs = linear combination of basis orbitals. Parameters derived from isolated atoms Includes excited state configurations Most electron correlation
2/7/2017 6 Basic WebMO and MOPAC 1) Build Example : ClOOF or similar, starting with trans conformation. 2) Optimize Use MOPAC PM3 or PM6. 3) Symmetry 4) Vibrations 5) Adjust and re-optimize. 6) MO surfaces
2/7/2017 7 Log in
2/7/2017 8 Begin with New Job, Create New Job
2/7/2017 9 Choose atom type ( F key for fluorine, O key for oxygens.. Use the Build tool to add atoms and bonds. Then do Cleanup, Comprehensive- Idealized. 109 47 Cleanup adjusts angles and bond lengths to their nominal values. 109 47
2/7/2017 10 Optimize your molecule 1) Right Arrow 2) Engine: MOPAC 3) Select Server: First Available
2/7/2017 11 Enter an informative Job Name Type of calculation Geometry Optimization Theory: PM6 (a recent version of PM3 semi-empirical) Charge: (0 for molecule) Multiplicity: generally singlet (unless odd # of valence e - )
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2/7/2017 13 Generate on the Preview tab shows the input file automatically created by WebMO. It can be modified manually. Submit job by clicking the right arrow
2/7/2017 14 When the job is Complete, click the job name or icon to see the Results View Job: 1) The symmetry elements in your optimized molecule (Show Symmetry Elements button 4 th from top left) 2) Heat of Formation 3) Geometry Sequence Energies plot Now click New Job Using This Geometry 1) Job Name: JK-FOOF-PM6-Freq 2) Calculation: Vibrational Frequencies 3) Theory: PM6 4) Charge: 0 5) Multiplicity: Singlet Submit job
2/7/2017 15! Click here to animate the vibrational mode. The negative frequency is just a symbol for an imaginary frequency.
Energy 2/7/2017 16 Surprisingly often, WebMO and HyperChem build molecules with imaginary vibrations. These are transition states, not stable states. Common in organic molecules with rotatable bonds. When these very symmetric structures are optimized, they sometimes remain symmetric! Why? The geometry optimization algorithm tests the E vs coordinate slope, which = 0 at both maxima and minima. How do you know if this has happened? A vibration frequency calculation will show a negative (imaginary) frequency. The cure? Manually nudge the system off the maximum, and restart the optimization. Geometry coordinate
2/7/2017 17 Basic WebMO and MOPAC 1) Build 2) Optimize 3) Symmetry 4) Vibrations For stable conformation, all frequencies must be > 0. If one frequency is < 0, you have arrived at a transition state, not a stable molecule. 5) Adjust - 6) MO surfaces A frequency calculation is valid only if it uses the same theoretical method and basis set as the geometry optimization.
2/7/2017 18 # * * = 90 FOOCl has two different transition states: one anti (*) and one eclipsed (#).
2/7/2017 19 Basic WebMO and MOPAC 1) Build 2) Optimize 3) Symmetry 4) Vibrations 5) Adjust and re-optimize 6) MO surfaces
2/7/2017 20 Open X-O-O-Y job 1) Click New Job Using This Geometry 2) Choose Molecular Orbitals 3) Change Job name; keep other settings 4) Right Arrow yes 5) Open Completed job 6) Find HOMO, LUMO etc. in MO Table
2/7/2017 21 Use File, Preferences to adjust the appearance of MOs
2/7/2017 22 Basic Gaussian
2/7/2017 23 Gaussian software Review MOs Basis sets Performance comparison: system size and basis set choice Typical Gaussian jobs: Opt, Freq, MO, ESP, NBO, Transition metals
2/7/2017 24 On-line Gaussian 09 User s Reference https://chem2.uaf.edu/facilities/webmo/g09ur/index.htm
2/7/2017 25 Excellent website and book! www.expchem3.com
Increased accuracy (and calculation time) 2/7/2017 26 Levels of theory- Gaussian Correlated ab initio MO (MP2 & others) Density Functional Theory (DFT) (B3LYP ) Ab initio MO (Hartree-Fock HF) Semi-empirical MO (PM3, PM6) Molecular mechanics (MM+, OPLS, UFF, etc)
H 2 MOs: formed by linear combination of 1s atomic orbitals. 27 Electron density (0.008 e/å 3 ) node node anti-bonding MO H atom H atom bonding MO 1s AO 1s AO d = 0.76 Å d = 2.8 Å d =
28 In semi-empirical MO theory (PM6 and others), molecular orbitals are formed by linear combinations of s, (and on heavy atoms) p x, p y, and p z AOs. s p x p y p z The orbital functions on the constituent atoms are the basis set.
2/7/2017 29 Gaussian and other QM programs use larger basis sets. The most common are split-valence basis sets. Basis orbital for core electrons of 2 nd row atom contains 6 Gaussian terms. 6-31G(d) 2 nd row atoms have an additional set of six d-type orbitals. Inner valence shell orbital contains 3 Gaussian terms. Outer valence shell orbital contains 1 Gaussian. H 2 O has 19 orbitals in the 6-31G(d) basis. O: 1s + 2s,2p x,2p y,2p z + (2s,2p x,2p y,2p z ) + six d H: - 1s + (1s) H: - 1s + (1s)
2/7/2017 30 r e - n
Wall clock time 2/7/2017 31 Assuming optimized in ~20 iterations, these would require ~10 min using 12 proc s on Antec12 Tetracycline C 22 H 24 O 8 N 2 HF/3-21G: 336 basis orbs Optimization required 26 iterations in 10 min Hartree-Fock; Antec12; 12 processors
2/7/2017 32 Gaussian input (.com) file format - energy (single point) - optimization - vibrations - molecular orbital name the checkpoint file theory/basisset jobtype charge multiplicity molecular description
2/7/2017 33 Gaussian input (.com) file format - energy (single point) - optimization - opt + freq - molecular orbital You may wish to add terms to modify the default optimization.
2/7/2017 34 Gaussian input (.com) file format - energy (single point) - optimization - opt + freq - molecular orbital Optimization + Vibrations jobs run sequentially In Gaussian, these are often run together because it is important to prove that the final structure is an energy minimum.
2/7/2017 35 What to do in case of a Failed Gaussian job. ***Check the.log output file**** The most common reason is a typo when you manually edit the input file. opt-vtight instead of opt=vtight Another fairly common error is adding an extra H when building. Optimization (Opt) jobs fail most often because of slow convergence of the energy, where the default maximum number of iterations is reached. - in this case use opt=(maxcycle=50) Other tactics for failed optimizations: - optimize at lower level of theory, then re-start. - for DFT methods, use ultrafine grid. - if you encounter small oscillations, test vibrations of one structure it usually is a minimum w/o imaginary frequency
2/7/2017 36 Gaussian input (.com) file format - energy (single point) - optimization - opt + freq - molecular orbital Pop is population analysis, which gives the electron populations of all orbitals. MOs and electron density graphics require orbital densities.
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38 The electron density at a molecule s outer surface is about 0.025 electrons/å 3. The outer surface is sometimes defined as the density at intermolecular contacts within a crystal. 0.2 electrons/å 3 0.1 electrons/å 3 0.02 electrons/å 3 Electron density ~ 0.025 electrons/å 3 Electron density increases closer to nuclei, and gradually goes to zero at greater distances.
Electrostatic potential mapped onto the electron density surface 39 Nuc: Color at each point on the surface reflects work required to bring +1 unit of electric charge from infinity to that point. = sum of potential due to the nuclei (+) and potential due to the electron density (-). H +
2/7/2017 40 Natural Bond Orbitals (NBO) NBO re-mixes the calculated MOs into linear combinations, making localized orbitals similar to, *,, * orbitals. Do CH 3 NH 2 example. %NProcShared=2 %CHK=CH3NH2-631Gss-B3LYP-NBO.chk #N B3LYP/6-31G(d,p) SP GFINPUT POP=(FULL,NBORead)formcheck CH3NH2-631Gss-B3LYP-NBO 0 1 C 0.00000000 0.00000000 0.00000000 N 0.00000000-1.46441000 0.00000000 H -0.50842300-1.80749900 0.81152600 H -0.50842300-1.80749900-0.81152600 H 0.54198500 0.36067300-0.88027600 H -0.99297500 0.48137700 0.00000000 H 0.54198500 0.36067300 0.88027600 $NBO FILE=NBODATA AOPNAO=W32 AOPNHO=W34 AOPNBO=W36 DMNAO=W82 DMNHO=W84 DMNBO=W86 FNAO=W92 FNHO=W94 FNBO=W96 $END
2/7/2017 41 Lone pair on N. This is the donor in the intramolecular donor-acceptor interaction. Or, in other words, hyperconjugation between N and CH 3 group. C-H* anti-bond. This is the acceptor orbital.
2/7/2017 42 Natural Bond Orbitals (NBOs) in GaussView
2/7/2017 43 Transition metals (and other larger atoms): Effective Core Potentials The issue: The high nuclear charge of a larger atoms pulls in inner core electrons and increases their speed to near speed of light. Hence this is a relativistic effect on the core electrons. Especially important for 2 nd and 3 rd row transition metals. This relativistic effect changes the energy and shape of inner orbitals, which in turn affects the valence shell electrons. Inner electrons are represented by pseudo potential functions, or effective core potentials. Mo(CO) 4 (CS) 2 /Sally/7235
2/7/2017 44 %NProcShared=8 %CHK=MoC6O4S2trans-lan2dz-B3-Opt.chk #N B3LYP/gen pseudo=read OPT MoC6O4S2trans-lan2dz-B3-Opt Gen keyword says describe basis sets down here. 0 1 Mo 0.00000000 0.00000000 0.00000000 C 2.11646714-0.12233914-0.00000000 O 3.28451739-0.18985650-0.00000000 C -0.12233914-2.11646714-0.00000000 O -0.18985650-3.28451739-0.00000000 C -0.00000000-0.00000000-2.12000000 S -0.00000000-0.00000000-3.51620000 C -2.11646714 0.12233914-0.00000001 O -3.51034044 0.20290985-0.00000001 C 0.00000000-0.00000000 2.12000000 S 0.00000000-0.00000000 3.29000000 C 0.12233914 2.11646714 0.00000000 O 0.18985650 3.28451739 0.00000000 Pseudo=read keyword says check at end for the type of ECP basis to used for heavy atom Mo. Blank lines required here. C O S 0 6-31G(d,p) **** Mo 0 lanl2dz **** Mo 0 lanl2dz zero
2/7/2017 45 Your questions