10/15/2016 1 WebMO & Gaussian John Keller Department of Chemistry & Biochemistry University of Alaska Fairbanks Corrections and updates 9-5-2017 SCHEDULE 9-10 Intro and basic operation of WebMO and MOPAC 10-11 Basic Gaussian 11-12 Open
10/15/2016 2 Click here to log in (guest/webmo or yourusername/password) https://chem2.uaf.edu/facilities/webmo/ http://chem.uaf.edu/keller/workshop/
10/15/2016 3 How does the UAF WebMO installation work? world wide web Draw molecule & choose options User corsair2 webserver Secure Shell (ssh) network communication (encrypted) WebMO WebMO creates input file for MOPAC or Gaussian..and sends the job to a compute server. When the job is done, the output file is parsed and shown on Results page. The intermediate results can be visualized in the Job Manager. compute servers chemlinux1 chemlinux2 (& others) WebMO downloads the updated output file about every 5 sec.
10/15/2016 4 Comparison to UAF Research Computing Services (RCS, formerly ARSC) User Connect with PuTTY. Submit the job Upload 2 files with WinSCP Create a Gaussian input file and a command script on your local machine (manually or using GaussView or WebMO). Check progress with qstat -a command. Pacman Now: some Linux server Download output files View locally with GaussView or WebMO
10/15/2016 5 Levels of theory Molecular mechanics (MM+, OPLS, etc) Semi-empirical MO (PM3, PM6) Ab initio MO (Hartree-Fock HF) Density Functional Theory (DFT) (B3LYP ) Correlated ab initio MO (MP2 & others) Ball-and-spring model no orbitals no electronics 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. No. of parameters depends on the assigned basis set. Parameters derived from isolated atoms Some electron correlation No. of parameters depends on the assigned basis set. Parameters derived from isolated atoms More electron correlation Increasing accuracy (and calculation time) No. of parameters depends on the assigned basis set. Parameters derived from isolated atoms Includes excited state configurations Most electron correlation
10/15/2016 6 Basic WebMO and MOPAC 1) Build Example : FOOF 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
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10/15/2016 8 Exercise Log on as Guest or another user Build one of the following: F-O-O-F F-O-O-Cl H-O-O-H Cl-O-O-H (Draw it so that it looks trans ) Or similar
10/15/2016 9 109 47 109 47 WebMO s Cleanup function inserts each atom with its nominal hybridization bond angle.
10/15/2016 10 Optimize your molecule 1) Right Arrow 2) Engine: MOPAC 3) Select Server: First Available
10/15/2016 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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10/15/2016 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
10/15/2016 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. The Heat of Formation 3. Geometry Sequence Energies plot 4. Check symmetry elements 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 by clicking the right arrow
10/15/2016 15 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 optimized to a transition state. 5) Adjust - 6) MO surfaces
10/15/2016 16 For any molecule containing N atoms, there are 3N possible motions. Of these, 3 are whole-molecule translations (x, y, z directions). And 3 are whole-molecule rotations (around the x, y, z axes). The remaining 3N-6 are internal vibrations. Normal coordinate analysis by the software identifies the normal modes of the molecule, which are linear combinations of atomic motions. They correspond to the vibrational modes observed in the infrared and Raman spectra.
10/15/2016 17! Click here to animate the vibrational mode. The negative frequency is more properly an imaginary frequency.
Energy 10/15/2016 18 Surprisingly often, WebMO and HyperChem build molecules with imaginary vibrations. These are transition states, not stable states. Common in molecules with rotatable bonds. When these very symmetric structures are optimized, they 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
10/15/2016 19 A transition state is a fleeting state that occurs only when one stable form flips or twists into another stable form. Its lifetime is measured in femtoseconds. Conclusion: One should almost always carry out both geometry optimization and vibrations calculations - to prove that the optimized thing is a minimum on the Potential Energy Surface.
10/15/2016 20 Now you try it: 1) Select and adjust X-O-O-Y dihedral angle ~90 2) Re-optimize 3) Run another Vibrations job 4) Lowest frequency > 0?
10/15/2016 21 # * * = 90 FOOCl (and FOOF) actually have two different transition states, one anti (*) and one eclipsed (#).
10/15/2016 22 Basic WebMO and MOPAC 1) Build 2) Optimize 3) Symmetry 4) Vibrations 5) Adjust and re-optimize 6) MO surfaces
10/15/2016 23 break
10/15/2016 24 WebMO & Gaussian John Keller Department of Chemistry & Biochemistry University of Alaska Fairbanks SCHEDULE 9-10 Intro and basic operation of WebMO and MOPAC 10-11 Basic Gaussian 11-12 Open
10/15/2016 25 Gaussian software Review MOs Basis sets Performance comparison: system size and basis set choice Typical Gaussian jobs: Opt, Freq, MO, ESP, NBO, Transition metals
10/15/2016 26 1) Open your X-O-O-Y job 2) Click New Job Using This Geometry 3) Choose Molecular Orbitals 4) Change Job name; keep other settings 5) Right Arrow yes 6) Open Completed job 7) Find HOMO, LUMO etc. in MO Table Click here to display the MO surface.
10/15/2016 27 Use Files, Preferences to adjust the appearance of MOs
10/15/2016 28 Click here to log in https://chem2.uaf.edu/facilities/webmo/ http://chem.uaf.edu/keller/workshop/
10/15/2016 29 Gaussian User s Reference is available on-line, and in printed format. https://chem2.uaf.edu/facilities/webmo/g09ur/index.htm
10/15/2016 30 Website and book are excellent! www.expchem3.com
10/15/2016 31 Levels of theory Molecular mechanics (MM+, OPLS, etc) Semi-empirical MO (PM3, PM6) Ab initio MO (Hartree-Fock HF) Density Functional Theory (DFT) (B3LYP ) Correlated ab initio MO (MP2 & others) Ball-and-spring model no orbitals no electronics 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. No. of parameters depends on the assigned basis set. Parameters derived from isolated atoms Some electron correlation No. of parameters depends on the assigned basis set. Parameters derived from isolated atoms 3 to 25 parameters for mixing HF & DF expressions. More electron correlation Increasing accuracy (and calculation time) No. of parameters depends on the assigned basis set. Parameters derived from isolated atoms Includes excited state configurations Most electron correlation
10/15/2016 32 MOs are formed by linear combination of atomic orbitals. Electron density (0.008 e/å 3 ) node node anti-bonding MO antibond = c AO - c AO H atom H atom bonding MO 1s AO 1s AO bond = c AO + c AO d = 0.76 Å d = 2.8 Å d =
10/15/2016 33 In semi-empirical MO theory (PM6 and others), molecular orbitals are formed by linear combinations of s, p x, p y, and p z AOs. H atoms use only s; heavy atoms use s + 3 p s. s p x p y p z The orbital functions on the constituent atoms are the basis set.
10/15/2016 34 Gaussian and other QM programs use larger basis sets. The most common are the split-valence basis sets. 1 st row atoms have a set of six d-type orbitals. These are also called Pople basis sets after John Pople, Nobel laureate, split-valence basis set inventor, and founder of Gaussian, Inc. Basis orbital for core electrons of 1 st row atom contains 6 Gaussian terms. 6-31G(d) 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 ) + sixd H: 1s + (1s) H: 1s + (1s) Inner valence shell functions contain 3 Gaussian terms. Outer valence shell functions contain 1 Gaussian term.
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30 kcal/mol Energy /Hartrees 10/15/2016 36-75.98 H 2 O Hartree-Fock Single Point -75.99-76.00 6-31G(d) -76.01 6-311G(d) -76.02 6-311++G(2d,p) -76.03 6-311++G(3df,3pd) -76.04 10 20 30 40 50 60 70 80 # basis functions Molecular energy approaches a minimum value - the infinite basis set limit - as the basis set gets larger.
No. of heavy atoms 10/15/2016 37 Total No. of Basis Functions and Wall Clock Time for One Energy Calculation α-cyclodextrin 66 710 1290 1.6 15 Tetracycline 32 336 600 1030 0.3 2.2 48 Vitamin B-6 15 168 5 s 294 500 812 0.4 3.4 22 SO 2 -formic acid 6 62 104 184 278 0.5 s 3 s 0.2 0.7 3-21G 6-31G(d,p) 6-311++G(2d,p) 6-311++G(3df,3pd) Basis set size Hartree-Fock; Antec12; 12 processors
10/15/2016 38 Gaussian input (.com) file format - energy (single point) - optimization - vibrations - molecular orbital Name the checkpoint file theory/basisset jobtype charge multiplicity Molecular description
10/15/2016 39 Gaussian input (.com) file format - energy (single point) - optimization - opt + freq - molecular orbital You may wish to add terms to modify the default optimization.
10/15/2016 40 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 so important to prove that the final structure is an energy minimum.
10/15/2016 41 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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10/15/2016 43 The electron density at the outer surface of molecules is about 0.025 electrons/å 3. In a crystal containing tightly packed organic compounds, this is the density at the intermolecular contact points. 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.
10/15/2016 Electrostatic potential mapped onto the electron density surface 44 Color at each point on the surface reflects work needed to bring a +1 electron unit of charge (i.e. a proton) from infinity to that point. = sum of potential due to the nuclei (+) and potential due to the electron density (-).
10/15/2016 45 Natural Bond Orbitals (NBO) Gaussian contains the NBO program v 3.0. 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) 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
10/15/2016 46 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.
10/15/2016 47 Here are several YouTube videos showing how to use Jmol or JSmol to illustrate molecules and orbitals: Torture-Testing Teropyrene: Alt-Tab to Jmol MO Display Jmol Applet Molecules for PowerPoint Avoid the Java Security Prompt by Adding a JSmol Wrapper to Jmol Webpage A Jmol webpage showing two NBOs in the SO 2 -pyridine complex (J.W. Keller, J. Phys. Chem. A 2015, 119, 10390-10398.)
10/15/2016 48 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
10/15/2016 49 %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
10/15/2016 50 Your questions