Spin Simulator provides you with a variety of tools to help you create accurate spin simulations by adding, manipulating and removing spin definitions and coupling constants, grouping spin definitions into spin systems, and viewing summary details about your current simulation.
Spin simulation is a computationally intensive process, and takes more time as the simulation you are creating becomes more complex. Generally, the amount of time required to recalculate a simulation increases more or less linearly with the number of spin definitions (protons) in the simulation, and exponentially with the number of distinct J-couplings. Spin Simulator monitors the overall complexity of your simulation as you work, and if you attempt to take an action that would result in unusable simulation times, the action is cancelled, and you see a warning dialog indicating that the resulting simulation would be too complex.
| Menu Location | File > New Simulation... |
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New Simulation creates a new spin simulation with the default simulation frequency of 800 MHz.
Tips and Tricks
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The new simulation does not have a spectrum overlay by default. Add a spectrum overlay before you continue editing the simulation.
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You can overlay only one spectrum at a time in Spin Simulator.
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You need to save your simulation to an
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Spectrum overlays are not retained in the saved files.
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If you need to model distinct structures in a single simulation, such as different enantiomers in solution, you may want to use spin systems to organize them. A spin system in Spin Simulator is a set of spin definitions that you have defined as only interacting with each other. These spin systems can have their own abundance in solution.
| Menu Location | Simulation > Add New Spin System... |
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How do I add a new spin system?
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Click Add New Spin System.
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If this is the first spin system you have added, a new dropdown list appears above the Spin Definition list, showing the available spin systems. Additional spin systems also appear in this dropdown list.
How do I select a different spin system?
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In the Spin Definition list, select the spin system to which you would like to switch from the drop-down list.
Alternately, click on a spin definition belonging to the other spin system in the Spectrum Graph.
| Menu Location | Simulation > Delete Current Spin System... |
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How do I delete a spin system?
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Select a spin system from the drop-down list above the spin definition list.
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Click Delete Current Spin System.
Tips and Tricks
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Deleting a spin system deletes all spin definitions and J-modifiers associated with the spin system as well.
Spin Simulator creates computer models of the interactions among the members of a spin system. Within Spin Simulator, you may consider a member of a spin system as equivalent to a single proton, or a group of protons that are both chemical shift equivalent and magnetic-equivalent. Spin definitons describe the members of spin systems, and are the basic building blocks of the models created by Spin Simulator.
A spin definition consists of three basic pieces of information: The number of protons represented by the spin definition, the center of the spin definition in ppm (equivalent to a chemical shift in an NMR spectrum), and a width in sw (analogous to a linewidth at half-height in an NMR spectrum).
You can organize spin definitions into spin systems, as described elsewhere in this chapter (see “Spin Systems”).
| Menu Location | Simulation > Add Spin Definitions |
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How do I add a new spin definition?
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Click the Add Spin Definitions button on the toolbar, or from the menu under Simulation > Add Spin Definitions.
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Click on the screen the ppm location where you want the new spin definition. A single proton spin definition will be added to the simulation. You can change the number of protons and add J-Modifiers later.
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Click on the Stop Adding Spin Definitions button on the toolbar (or press ESC) to leave spin definition addition mode.
How do I edit a spin definition?
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Select the spin definition by clicking on it in the Spectrum Graph, or by selecting it in the Spin Definition list in the Simulation Details panel.
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Do any of the following:
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Click and drag the blue triangle on the horizontal axis to change the center of the spin definition.
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Click and drag the blue triangle on the vertical axis to change the height of the simulation.
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Click and drag the spin definition directly in the Spectrum View to change its center and the simulation height simultaneously.
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Click and drag the blue triangles on either edge of the spin definition (at around half the height of the tallest peak) to change the width of the spin definition.
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Use the W and S keys or the up and down arrow keys to adjust the height of the whole simulation up and down.
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Use the A and D keys or the left and right arrow keys to adjust the position of the selected spin definitions left and right.
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Use the Q and E keys to display the next or previous spin definition.
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| Menu Location | Simulation > Reassign Selected Spin Definitions... |
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How do I reassign a spin definition from one spin system to another?
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Select a spin definition in the Spectrum Graph or by selecting it in the Spin Definition list in the information panel.
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Click Reassign Selected Spin Definitions....
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Select either a target spin system, or select a new spin system.
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All spin definitions coupled to the current selected spin definitions will also be reassigned. Uncheck the check box if you want to uncouple the selected spin definitions and move only the selected spin definitions instead.
| Menu Location | Simulation > Delete Selected Spin Definition |
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How do I delete a spin definition?
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Select a spin definition in the Spectrum Graph or by selecting it in the Spin Definition list in the information panel.
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Click Delete Selected Spin Definition.
Tips and Tricks
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A spin definition can describe no more than ten protons. However, given that a spin definition typically describes chemically and magnetically equivalent protons, a value greater than three (a methyl group) is often not necessary.
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A spin system can contain any number of protons and spin definitions, as long as the total number of transitions is less than 2000. If you need to create a simulation requiring more than 2000 transitions, you will need to use multiple spin systems.
The total number of transitions in the current simulation appears in the simulation details (see “Simulation Details”).
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Height adjustments always affect the whole spin system, not just the currently selected spin definition. If you need to adjust the heights more than is possible in Spin Simulator, finish the simulation, save it and import it in Compound Builder, then make your adjustments there.
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Deleting a spin definition also deletes any J-modifiers that you have associated with that spin definition.
The Spin Navigator lets you quickly move among the spin definitions that you have created in the current simulation. It appears in the top left corner of the Spectrum Graph as an ordered list of the approximate positions of all the spin definitions of the simulation, in ppm. When you click on a spin definition's position, the view zooms to provide an optimal view of the spin definition. You can also use the Spin Navigator to move sequentially through the list of spin definitions in either direction.
How do I display the spin definitions of a simulation in the Spectrum Graph?
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Make sure that the Spin Navigator is visible.
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Click a spin definition's position to zoom directly to that spin definition. Click the left or right arrow to move sequentially through the list of spin definitions.
Tips and Tricks
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Click on a spin definition and drag along the Spin Navigator to include adjacent spin definitions in the Spectrum Graph.
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Use the Q and E keys to display the next or previous cluster.
When you create a new spin definition, it appears on the Spectrum View as a single, unsplit peak. J-modifiers let you split a spin definition into more complex shapes, to fit the shape of real spectra. J-modifiers can be uncoupled, affecting only one spin definition, or coupled, linking the spin definition to another one via its coupling constant. Coupled J-modifiers result in more accurate simulations, as Spin Simulator can use them to calculate higher-order coupling effects, accounting for tenting and other complex behaviour.
| Menu Location | Compound > Add New J-Modifier... |
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How do I add an uncoupled J-modifier to a spin definition?
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Select the spin definition to which you would like to add a J-modifier.
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Open the Add New J-Modifier... dialog.
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Enter a J-value for the new J-modifier, in Hz.
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Select Uncoupled Split, and specify a split count for the new J-modifier.
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Click OK.
How do I add a coupled J-modifier to a spin definition?
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Select one of the two spin definitions that you would like to link with a coupled J-modifier.
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Open the Add New J-Modifier... dialog.
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Enter a J-value for the new J-modifier, in Hz.
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Select Coupled, and select the spin definition to which you would like to link.
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Click OK.
| Menu Location | Compound > Edit Selected J-Modifier... |
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How do I edit an existing J-modifier?
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Select a spin definition.
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Select a J-modifier that you would like to edit.
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Open the Edit Selected J-Modifier... dialog.
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Make your desired changes.
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Click OK.
How do I couple two spin definitions using splits that I have already defined?
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Select one of the two spin definitions that you would like to link, and select the uncoupled split that will link it to the other spin definition.
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Open the Edit Selected J-Modifier... dialog.
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Select Coupled, and select the spin definition to which you would like to link.
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Select the uncoupled split from the second spin definition that you would like to link to.
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Click OK.
| Menu Location | Compound > Delete Selected J-Modifier |
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How do I delete a J-modifier?
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Select a spin definition.
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Select a J-modifier that you would like to delete.
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Click Delete Selected J-Modifier.
| Menu Location | Compound > Uncouple |
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How do I uncouple a J-modifier?
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Select a spin definition.
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Select a J-modifier that you would like to uncouple.
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Click Uncouple.
| Menu Location | Compound > Ungroup Selected Splits |
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| Menu Location | Compound > Group Selected Splits |
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How do I ungroup J-modifiers?
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Select a spin definition.
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Select an uncoupled split with a split count greater than 1.
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Click Ungroup Selected Splits..
How do I group several J-modifiers?
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Select a spin definition.
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Select several uncoupled splits that you would like to combine. Hold down Ctrl or Cmd to multi-select J-modifiers.
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Click Group Selected Splits..
Tips and Tricks
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J-Modifiers can only link two spin definitions that are in the same spin system.
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When coupling two spin definitions, uncoupled splits are only shown if the degree of splitting in the second spin definition makes theoretical sense according to the number of protons in the first spin definition.
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When you delete a coupled J-modifier, you will delete it from both spin definitions to which it applies. If you only want to delete the J-modifier from one spin definition, uncouple it first.
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Uncoupling a coupled J-modifier will result in an uncoupled split on each of the two previously coupled spin definitions, each split having the same J-value as the original coupled J-value.
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Most operations involving J-modifiers are available by right-clicking on a J-modifier in the Simulation view.
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