材料模拟与计算 Asignment5

完成下面两个练习，提交截图1.QM/MM calculation of the SW1 defect formation energy for a carbon Purpose: Introduces how to use the QMERA module in Materials Studio. Special attention is paid to preparing the system and which type of embedding scheme to use.Modules: Materials Visualizer, QMERATime:Prerequisites: NoneThe Stone-Wales (SW) defect is a common defect on carbon nanotubes that is thought to have important implications for their mechanical properties (see Andzelm et al., 2006). The 90° rotation of two carbon atoms around the midpoint of the C-C bond transforms four hexagons into two pentagons and two heptagons. This substructure is known as Stone-Wales defect. In this tutorial you will calculate the formation energy of a nonchiral SW defect (SW1).The following steps will be covered here:Getting startedQM region definitionQMERA calculationAnalysis of resultsNote: In order to ensure that you can follow this tutorial exactly as intended, you should use the1. Getting startedBegin by starting Materials Studio and creating a new project.Open the New Project dialog and enter Stone-Wales as the project name, click the OK button.The new project is created with Stone-Wales listed in the Project Explorer.2. Structure preparationThe first thing you need to do is prepare the structure of the single-walled nanotube (SWNT).Select Build | Build Nanostructure | Single-Wall Nanotube from the menu bar. Change the N and M indices to 8 and 0 respectively.This corresponds to a nanotube of 6.26 Å diameter.Uncheck the Periodic nanotube box and change the number of Repeat units to 7, this gives a nanotube length of 29.82 Å. Select Both ends from the Hydrogen termination dropdown list. Click the Build button and close the dialog.Now you have to create the defect in the middle of the nanotube.Right-click in the 3D Viewer and select Display Style from the shortcut menu to open the Display Style dialog. Click the Stick radio button and close the dialog.Press the LEFT arrow key twice to rotate the nanotube so that you can see its full length horizontally. The Z axis should be pointing to the left and the Y axis should be pointing up, on the axis orientation display, see Figure 1.Select two carbon atoms which are near the center of the nanotube wall and which are connected by a horizontal bond and then select the remainder of benzene rings at each end of the bond.Figure 1. SWNT with two central carbon atoms and their pendant benzene rings selected.Click on the arrow for the 3D Viewer Recenter from the toolbar and select View Onto fromthe dropdown list. Click anywhere in the 3D Viewer to deselect everything and reselect the central two carbon atoms.Figure 2. SWNT viewed from above, with two central carbon atoms selected.Select the Movement tools from the toolbar, change the Angle to 90.0 and click the Move Around Z button. Close the dialog.This creates the defect by rotating the two carbon atoms 90° around the screen Z axis.To view the appropriate connectivity select Build | Bonds from the menu bar to open the Bond Calculation dialog. Uncheck Calculate bond type, set the Convert representation to option to Resonant. Click the Calculate button and close the dialog.Rename the SWNT.xsd document to SW1.xsd.Figure 3. SW1 defect (highlighted here in blue) on an SWNT.3. QM region definitionThe next step is to define the QM region that you want to use in the simulation. It is necessary to include full rings in the calculation to avoid possible clashes between hydrogen link atoms, and to leave enough space between the defect and the boundary QM-MM atoms. In this case you will include the defect plus a crown of full rings around it in the QM region (see Figure 4).With the two carbon atoms central to the defect still selected, choose Edit | Atom Selection from the menu bar to open the Selection dialog. Select Connected from the Select by Property dropdown list and choose the Add to the existing selection radio button. Click the Select button four times and close the dialog. Hold down the SHIFT key and select the four carbons needed to complete the crown of six-membered rings.Select | Calculation from the modules toolbar to open the QMERA Calculation dialog. Click the Add button to add the selected atoms to the QuantumAtoms set.Click anywhere in the 3D Viewer, the atoms in the set will be highlighted in purple.Figure 4. SW1 defect with the QuantumAtoms set defined.If you want to visualize the hydrogen link atoms to be sure that there are no problems related to their position, you can use the View button on the QMERA Calculation dialog.On the Setup tab of the QMERA Calculation dialog click the View button. A new window will open, double-click on the LinkAtoms label. Check that the position of the hydrogen link atoms makes sense and close the window. Click the No button on the dialog asking whether to save the document.4. QMERA calculationYou are now ready to run the QMERA calculation. In this case the polarization effects are negligible and the charges of all atoms will be left as zero, which is compatible with the Dreiding forcefield. It is also sufficient to choose a mechanical embedding approach for the QM/MM calculation.There are two different models available for mechanical embedding: QM-Pot and additive. You will use the QM-Pot model which uses a subtractive expression to calculate the total energy. Forcefield parameters are therefore required for all atoms of the system.On the Setup tab of the QMERA Calculation dialog select Geometry Optimization as the Task and ensure that the Quality of the calculation is set to Medium.In order to complete the tutorial more quickly, you could use the Coarse quality setting.Click the More... button associated with the task, to open the QMERA Geometry Optimization dialog. Select HDLC as the Method and close the dialog.The HDLC minimizer combines the use of highly decoupled delocalized internal coordinates with the linear scaling BFGS update of the Hessian (L-BFGS) method. This usually achieves faster convergence than normal BFGS or conjugate gradient methods for covalent systems of this size.Click the More... button for the QM server to open the QMERA DMol3 Parameters dialog. Select GGA and PBE for the functional and close the dialog.Click the More... button for the MM server to open the QMERA GULP Parameters dialog. Ensure that Dreiding is selected as the Forcefield and Use current is selected for Charges, close the dialog. Select the Options tab of the QMERA Calculation dialog, ensure that Mechanical is selected as the Embedding scheme and Model is set to QM-Pot. Click the Run button.GGA functionals provide a good description of the electronic subsystem and the PBE exchangecorrelation functional has previously been identified as efficient for QM/MM calculations on nanotubes, see Andzelm et al., 2006 for similar calculations.Depending on your hardware, this calculation may take several hours to complete. If you wish to examine and analyze the results directly the output files are provided in theExamples/Projects/QMERA/Stone-Wales Files/Documents/ directory in the SW1 QMERA GeomOpt and SWNT QMERA GeomOpt folders.5. Analysis of resultsThe results of the calculation will be returned in a new folder called SW1 QMERA GeomOpt.Open the SW1.xsd file in the SW1 QMERA GeomOpt folder to see the optimized geometry.The final energy for this structure can be found in the SW1.csout file, the QM/MM Energy heading reports the corresponding energy in a.u., which is Hartree in this case.Double-click on SW1.csout to open the energy file, press the CTRL + F keys and enter Energy (subtractive) into the Find dialog.The end of the file is displayed. Scroll up a little and examine the QM/MM Energy.To examine the relationship between the energy and the structure you can compare the energy chart with the trajectory. You will need to analyze the results to obtain the trajectory and chart documents, even if you already have some charts with intermediate updates.Select Modules | QMERA | Analysis from the menu bar to open the QMERA Analysis dialog. Select Energy evolution and click the View button. Close the dialog.The energy evolution either creates or opens two chart documents, called SW1 Energies.xcd and SW1 Convergence.xcd.Make SW1.xtd the active document and, on the animation toolbar, click on the Play button.As the animation proceeds the seven-membered rings widen.Stop the animation and open SW1 Energies.xcd.Click on a point on the graph near the beginning of the optimization.The 3D Viewer displays the structure at the corresponding step in the calculation. In this way you can examine the structure at specific energies during the calculation.To obtain the formation energy for the SW1 defect you need to perform a QMERA calculation with the same settings for the defect free nanotube. To do this you should use a QM region of four fused C6 rings and a surrounding crown. The resultant QM region will be similar to the one shown in Figure 4, except that the central C-C bond of the QM region in Figure 4 will be horizontal rather than vertical. The output files for this calculation are provided in the Examples/Projects/QMERA/Stone-Wales Files/Documents/SWNT QMERA GeomOpt/ folder.Once you have both calculations you can calculate the formation energy of the SW1 defect as the difference in QM/MM Energy, converting from atomic units to eV according to: 1 a.u. (Hartree) =27.2113845 eV.You should obtain a value of around 2.1 eV.This is the end of this tutorial.ReferenceAndzelm, J., Govind, N., Maiti, A., Chem. Phys. Lett., 2006, (421), 58-62.2.QM/MM geometry optimization of a Ru(H)2(diphosphine)(diamine) Purpose: Introduces how to use the QMERA module in Materials Studio with special attention paidto which type of embedding scheme to use.Modules: Materials Visualizer, QMERATime:Prerequisites: NoneThe preparation of enantiomerically pure alcohols is of high importance in drug design. A breakthrough in this field was the discovery, by Noyori and co-workers, of highly efficient ruthenium catalysts for the enantioselective hydrogenation of ketones (R. Noyori, Angew. Chem., Int. Ed., 2002, 41, 2008). Among the best catalysts for carbonyl hydrogenation are octahedral complexes where Ru(II) is coordinated by a chiral diphosphine and a chiral diamine.Figure 1. Conversion of a ketone to a chiral secondary alcohol.In this tutorial you will use the QMERA module in Materials Studio to optimize the structure of a Ru(H)2 (diphosphine)(diamine) complex. You will use DMol3 to describe the QM region and the Dreiding forcefield to describe the MM region. The following steps will be covered here:Getting startedStructure and QM/MM setupQMERA calculationNote: In order to ensure that you can follow this tutorial exactly as intended, you should use the1. Getting startedBegin by starting Materials Studio and creating a new project.Open the New Project dialog and enter Ru_complex as the project name, click the OK button.The new project is created with Ru_complex listed in the Project Explorer.2. Structure and QM/MM setupThe structure you will use is shown below:Figure 2. Ru(II) complex used as an asymmetric hydrogenation catalyst for ketones.Select File | Import... from the menu bar and browse to Examples\Projects\QMERA\Ru_complex Files\Documents\Ru_start.xsd. Click the Open button.Once you have the structure of the complex you can prepare the QMERA calculation. For this system you will include the polarization of the QM region due to the MM region. To this end, you will include the MM point charges in the SCF part of the QM calculation. This type of approach is called electrostatic embedding and it does not require forcefield parameters for the QM region, for either atom types or charges, because an additive expression is used to calculate the total energy of the system.You need to define the QM region first. The atoms to include in the QM region are shown in Figure 3. The QM region includes the Ru center, the two hydrides (H), the two P atoms and the H2NCHCHNH2 diamine backbone.Figure 3. Ru(II) complex with the QM region indicated using stick representation.Use the selection tool to select the QM region indicated above. Select the QMERA modulefrom the Modules toolbar and choose Calculation to open the QMERA Calculation dialog. Click the Add button to add the selected atoms to the QuantumAtoms set.Click anywhere in the 3D Viewer, the atoms in the set will be highlighted in purple.If you want to visualize the hydrogen link atoms to be sure that there are no problems related to their position, you can use the View button in the QMERA Calculation dialog.On the Setup tab of the QMERA Calculation dialog click the View button. A new window will open with the LinkAtoms selected. Check that the position of the hydrogen link atoms makes sense and close the window. Click the No button on the dialog which asks if you want to save this document. You need to setup and modify the ligand charges. In electronic embedding methods, the basic requirement for the choice of charges is that net charge of the MM atoms must be integer. In this case this is achieved by using the QEq method to calculate separately the charges of each ligand bound to the QM region, under the constraint that the net charge must be zero.Select Modify | Charges from the menu bar to open the Charges dialog. On the Calculate tab choose QEq as the Method. Select one of the MM ligand residues (for example a phenyl ring) and click the Calculate button. The ligand charges have been determined now. Repeat this procedure for all the other MM ligands.Close the Charges dialog.Note that the atoms in the QM region do not need to have charges assigned.The prepared structure can also be imported from Examples\Projects\QMERA\Ru_complex Files\Documents\Ru_complex.xsd.You can now run the QMERA calculation.3. QMERA calculationOn the Setup tab of the QMERA Calculation dialog, select Geometry Optimization as the Task and Medium for the Quality of the calculation. Click the More... button for the Task to open the QMERA Geometry Optimization dialog.Select HDLC as the Method and close the dialog.Click the More... button for the QM server to open QMERA DMol3 Parameters dialog. Select GGA and PBE for the Functional and close the dialog.This Ru(II) complex has a zero net QM charge, the two hydride ligands act as electron donors (2 × -1) to compensate for the metal's 2+ charge and no other QM atoms contribute charges (all other ligands coordinate the Ru center through dative bonding). So the DMol3 charge can remain at a value of zero for this system.For the MM server click the More... button to open the QMERA GULP Parameters dialog. Select Dreiding as the Forcefield and Use current for the Charges, close the dialog.On the QMERA Calculation dialog, click on the Options tab and select Electronic as the Embedding scheme and Disperse boundary charge as the Model. Click the Run button.Depending on your hardware, this calculation may take several hours to complete. If you wish to examine and analyze the results directly the output files are provided in theExamples\Projects\QMERA\Ru_complex Files\Documents\ directory in the Ru_complex QMERA GeomOpt folder.After performing the calculation for the Ru(II) complex you can proceed to include the substrate (ketone) in the calculation. The ketone will belong to the QM region and as a consequence you do not need charges or atom types for that structure. You can draw the ketone in the same document as the Ru(II) complex and add it to the QM region using the Add button on the QMERA Calculation dialog.The prepared structure for the complex and substrate can be found atExamples\Projects\QMERA\Ru_complex Files\Documents\Ru_complex+ketone_2.xsd. If you wish to examine and analyze the results of the QM/MM calculation on the ketone system directly, the output files from the QMERA run can be found in the Examples\Projects\QMERA\Ru_ complex Files\Documents\Ru_complex+ketone_2 QMERA GeomOpt folder.。