1 Maestro Tutorial and Exercises Per-Ola Norrby, 2003 Introduction This tutorial is intended to teach the basics of the program Maestro. This is a graphical structure manipulation package that can interface with several computational engines. Here, we will only cover how to start molecular mechanics calculations in the application MacroModel. Exercises will be interspersed with tutorial sections and tips (in boxes). If you're already familiar with modeling, you may want to skip the latter. Text in bold are names of menus, windows, buttons etc. You start Maestro by typing "maestro" in a Unix/Linux window (note: case sensitive!). This brings up the main structure manipulation window, with a row of pull-down menus on top and a settings panel to the right. Selecting a menu item will generally bring up a window with settings. You can keep any number of windows open simultaneously, but keep track of which windows and options are active. For example, if Delete option is on, clicking on the structure will delete something even if your eyes happen to be on the Build window. You can always make a window inactive by clicking on the Hide button. Do this whenever you're finished temporarily with a window (you can always bring it back using the menu selection). For the computational tasks described here, you should select MacroModel from the Applications menu. Note that the calculation will always be performed on everything currently visible in the window. If you have two molecules in your window, you will calculate a supramolecular complex, not two separate tasks. After you have selected a task in a window (eg., building, deleting, inverting, measuring), you perform the task on your current structure by clicking with the left mouse button on an atom in your structure. The effect of a click is controled by the settings panel to the right. Usually, you perform an action on a single atom or bond, but you can change the setting here to, for example, add hydrogens to or delete an entire molecule. Your current structure can be rotated or translated using the middle and right mouse buttons. The default is a track-ball rotation using the middle mouse button, but you can change this using the settings in the panel to the right. Using the Advanced… settings, you can also rotate or translate single molecules. In general, you can trust most default settings in the program. Only change the settings if you know what you are doing, or want to experiment. If you start to get "strange" results, you may have changed a setting somewhere. Closing down and restarting the program will restore the default settings. 2 Basic structure building, saving, and energy minimization Selecting Build… from the Edit menu will bring up a window that allows you to add atoms and fragments to your molecule. Fragments are always added with filled valencies. Clicking in an empty space will add a new molecule, whereas clicking on an atom will change it to the selected fragments. On the Atoms & Bonds card, you will find tools for setting an existing atom to any element, and for inverting an atom. The latter is accomplished by clicking on the atom to be inverted, then on two non-moving substituents.1 The moving substituents should not be part of a ring. If you want to save and retrieve a structure, this can be accomplished with Import Structures or Export under the Project menu. You can either type a filename, or select an existing file with Read From… or Write To…. Note that the lists of existing files are not automatically updated, you may have to use the Filter button for this. Your filenames should usually be of the type "jobname.mae". If you start any type of calculation with the name "jobname", the program will automatically generate files starting with "jobname" for the result. Molecular mechanics tasks are available under the MacroModel menu. In the Minimization window, you find a load of settings. For now, you only need to select the force field under Potential and minimization method (TNCG or PRCG) under Mini, then start the job. If you give it a name (without periods, field Job:), the results will be automatically stored on disk. Starting the job brings up the Monitor window where you soon see the final energy. Exercise 1.1 The difference in energy between axial and equatorial methyl cyclohexane is one of the basic numbers in conformational analysis. Calculate the energy difference between the axial and equatorial chair conformers of methyl cyclohexane: Me Me Compare the results obtained by using different force fields with the experimentally determined gas phase value ∆H(axial - equatorial) = 7.3 kJ/mol. Build the molecule from Cyclohexyl and Methyl fragments in the Build window. You can either build it twice in two different conformations, or invert the methyl substituted carbon. You find the invert tool on the Atoms card in Build. You click once on the methyl-substituted ring carbon, then once each on the two adjacent ring carbons. Minimize the axial and equatorial conformers by using all available force- fields. MM2* MM3* AMBER* OPLS AMBER94 MMFF MMFFS OPLS-AA Eax Eeq ∆E To discuss: How many of these comparisons would you need to rank the accuracy of the force fields? How accurate would your experimental data need to be? 1 Bug warning. If this fails, try clicking the non-moving substituents in the opposite order. 3 More on building and measuring. On the Atoms card in the Build window, you can select Draw to allow freehand drawing of an arbitrary skeleton. Clicking in an empty region will add an atom, with a bond to the last atom selected. A second click will de-select it so that you can start a new sequence of bonds. You can click on existing atoms to form bonds to it. Adding a bond between already bonded atoms will cycle the bond order (singleÆdoubleÆtripleÆsingle). When the skeleton is finished, you can fill out the valencies using the Hydrogen Treatment card. Using the default scheme, select Apply current treatment to all atoms. Under the Analysis menu, the Measurements window has tools for measuring distances and angles. Select the appropriate tool, then select atoms to add a label with the measurement. For angles and torsions, you select first a terminal atom, then the central atom(s), then the second terminal atom. There are also buttons for clearing all labels, or deleting a specific label. Exercise 1.2 The H..H distance (R) in the molecule below is very short, 1.748 Å , according to accurate neutron diffraction data. R H H H H You can create this molecule using Draw. First create the decaline skeleton by clicking in the order shown below, click once more on the last atom to terminate drawing. Rotate the molecule so that you see it from the side, move the central atoms down by selecting MoveXY, clicking the atom once, and clicking the new position (to ensure a cis fusion). After reselecting Draw, add the bridges by clicking in the order shown (don’t forget the extra click after the first bridge to terminate that chain). Finish by adding hydrogens, then minimize. 2 8 move 1 2 down 6 3 9 7 1 7 6 12,13 4 10 3,4 5 5 11 This provides a good test of the repulsive part of the vdW potential in force-fields. Minimize the molecule using all available force fields. Make sure you have a cis ring fusion. Measure the H··H distance. MM2* MM3* AMBER* OPLS AMBER94 MMFF MMFFS OPLS-AA H ··H Discussion: One of the force fields was parameterized to reproduce this molecule. Can you identify it? 4 Charged molecules and energy minimizations in solvent To create charged molecules, you can set atomic formal charges using Build>Atoms&Bonds>Properties (a subcard on a card in the Build window). You should only use integer formal charges. For example, a carboxylate anion should be built with a charge of –1 on the carboxylate oxygen, no charge on the carbonyl (the force field will, in that specific situation, use a formal charge of –0.5 on each oxygen). To get the correct valence, you should set the charge before adding hydrogens. If you want to display your atom type and formal charge, you find the Atom Labels window under the Display menu. Charged molecules are strongly affected by solvent. Settings for a continuum simulation of water or chloroform solvent are found on the Potential card in the Minimization window. Exercise 2.1 Build the equatorial and axial chair conformers of the cyclohexyl ammonium ion: H3N NH3 Energy minimize the conformers in gas phase and in water and compare the energy differences between the two conformers in gas phase and in water. Use the MM3* force field. Try to explain the results! Why does solvation favor one isomer more than the other? gas phase aqueous phase Eax Eeq ∆E Exercise 2.2 Build the equatorial and axial chair conformers of a-bromo cyclohexanone: O Br O Br Energy minimize the conformers in gas phase and in CDCl3 and compare the energy differences between the two conformers for the two cases. Use the MM3* force field. Try to explain the results! Compare with experimental data: ∆G(gas phase) = -4.3 kJ/mol, ∆G(CDCl3) = -3.0 kJ/mol gas phase CDCl3 Eax Eeq ∆E 5 Conformational Searching - comparisons of conformational analysis in gas phase and in water. The Monte Carlo technique in Macromodel will generate new structures by rotation around single bonds. For ring systems, a bond must be broken and reformed in the generation step.