Reference manuals - Avogadro -1Petr Kulhanek kulhanek@chemi.muni.cz National Center for Biomolecular Research, Faculty of Science Masaryk University, Kotlářská 2, CZ-61137 Brno Avogadro Reference manuals Reference manuals - Avogadro -2- Avogadro http://avogadro.openmolecules.net/wiki/Main_Page Program for construction and visualization of molecules. Freely available for MS Windows and Linux. Functionality overview: https://www.youtube.com/watch?v=xdmLoBlLmqs Reference manuals - Avogadro -3Building a model Reference manuals - Avogadro -4Building a model You can use the Avogadro program to build a 3D model of the reactant and the product. It is a freely distributed program that can be used both under the MS Windows operating system and under Linux clones (e.g., Ubuntu). Reference manuals - Avogadro -5Model draft When building a molecule, the bond lengths, angles and other parameters of the molecule are not optimal. This is due to the way structures are edited in the Avogadro program. The draft model must therefore be modified by optimizing the geometry before further use. Reference manuals - Avogadro -6Model optimization The program uses molecular mechanics (MM) methods to optimize geometry. For it to function properly, you must correctly define bond orders in the structure. Because MM is an empirical method, you must also choose the type of parameterization. In our case, we will use the force field MMFF94. Reference manuals - Avogadro -7Searching for the global minimum Reference manuals - Avogadro -8Finding the most stable geometry, I Default optimized geometry of the hexane has energy 2.5 kJ/mol (MMFF94). It is a local minimum on the ​​potential energy surface, which is not the lowest. Reference manuals - Avogadro -9Finding the most stable geometry, II Avogadro contains methods for finding the most stable conformer (structures). Reference manuals - Avogadro -10Finding the most stable geometry, III To find the most stable conformer we will use the systematic search method. Reference manuals - Avogadro -11Finding the most stable geometry, IV The most stable hexane conformer has energy -22.9 kJ/mol (MMFF94). The geometry of the found structure should be optimized again. Reference manuals - Avogadro -12Vibration visualization Reference manuals - Avogadro -13Vibration visualization Load soubor.log, containing results of vibration analysis, into Avogadro program. A summary of individual normal vibration frequencies can be found in the menu Extensions->Vibrations. vibration frequencyvibration visualization