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Tmolex Tutorial TmoleX A Graphical User Interface to the TURBOMOLE Quantum Chemistry Program Package User manual COSMOlogic GmbH & Co. KG Imbacher Weg 46 51379 Leverkusen, Germany Phone +49-2171-363-668 Fax +49-2171-731-689 E-mail turbomole @cosmologic.de Web http://www.cosmologic.de Version 4.4 July 2018 Page 2 / 97 Table of contents 1. Installation..................................................................................................................................................... 5 1.1. Windows............................................................................................................................................... 5 1.2. Linux..................................................................................................................................................... 6 1.3. Mac OS................................................................................................................................................. 7 1.4. Online Updates..................................................................................................................................... 8 2. A quick tour.................................................................................................................................................. 9 2.1. Starting the program............................................................................................................................. 9 2.2. An illustrative example: Part 1............................................................................................................11 2.3. The tool bar......................................................................................................................................... 12 2.4. The sections....................................................................................................................................... 13 2.5. An illustrative example: Part 2............................................................................................................15 2.5.1 Geometry panel..............................................................................................................................15 2.5.2 Basis set panel............................................................................................................................... 16 2.5.3 Molecular start orbitals panel..........................................................................................................18 2.5.4 Level of theory: Select method.......................................................................................................20 2.5.5 Start Job: Select kind of job and start it...........................................................................................22 2.5.6 Results............................................................................................................................................ 24 2.6. Job Administration..............................................................................................................................25 3. The 3D visualization.................................................................................................................................... 27 3.1. The 3D builder.................................................................................................................................... 27 3.1.1 Navigation....................................................................................................................................... 28 3.2. Building blocks: Pre-stored structures.................................................................................................29 3.2.1 Generate and store your own building blocks.................................................................................29 3.3. Import structure................................................................................................................................... 30 3.4. Use SMILES code.............................................................................................................................. 31 3.5. The 2D Builder.................................................................................................................................... 32 3.6. Easy building: Paint tool...................................................................................................................... 33 3.7. Build complex molecules by merging fragments.................................................................................34 The trick to set a bond length to zero works only in cases where the selected bond is not part of a ring! 37 3.7.1 Building step by step 1....................................................................................................................38 3.7.2 Change bond length........................................................................................................................40 3.7.3 Change torsion............................................................................................................................... 41 3.7.4 Change bond angle.........................................................................................................................42 3.7.5 Building step by step 2....................................................................................................................43 3.8. Pre-optimization.................................................................................................................................. 45 3.9. Labels and Measurements..................................................................................................................46 3.10. Moving, Rotating, Scaling.................................................................................................................49 3.11. The gradient viewer..........................................................................................................................52 3.12. Surface plots..................................................................................................................................... 54 4. Properties................................................................................................................................................... 60 4.1. Vibrational frequencies....................................................................................................................... 60 4.2. IR spectrum........................................................................................................................................ 62 4.3. Nuclear magnetic shielding.................................................................................................................63 4.4. UV/Vis and CD spectra (TD-DFT).......................................................................................................64 5. Constrained optimization and Scan jobs....................................................................................................65 5.1. Defining fixed internal coordinates...........................................................................................................65 5.2. Use internal coordinates..........................................................................................................................67 5.3. Start constrained optimization.............................................................................................................67 5.4. Scan along an internal coordinate......................................................................................................68 Page 3 / 97 5.5. Scan along several internal coordinates.............................................................................................69 6. Periodic boundary conditions...................................................................................................................... 70 6.1. Import of cif files.................................................................................................................................. 72 7. Job Templates............................................................................................................................................ 73 7.1. Define job templates...........................................................................................................................73 7.2. Apply job templates............................................................................................................................74 7.3. Results of job templates...................................................................................................................... 75 8. Batch processing........................................................................................................................................ 76 8.1. Read in and use several molecules....................................................................................................76 Generate batch jobs from existing jobs.....................................................................................................78 8.2. Apply templates for batch jobs............................................................................................................79 8.3. Run local or remote batch jobs...........................................................................................................80 8.4. Visualize and export results of batch jobs...........................................................................................84
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