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iii, Materials Studio Online Help Tutorials.,. Accelrys Basic Training, Materials Studio,., Online Help,., Materials Studio,,.., Web http://accelrys.co.jp/.,,.,,,. : support-japan@accelrys.com : 03-5532-3860 : 03-5532-3802 ( : 10:00 17:00,, ), Web FAQ (http://accelrys.co.jp/customer-support/faq.html),,. FAQ. Username: faq Password: accelryskk Version 1.0 c 2010.,,.

v 1.................................. 1 1.1 Materials Studio................................... 1 1.2 Default Atom Style.................................. 2 1.3,.............................. 2 1.4....................... 8 2.................................... 13 2.1 Pt...................................... 13 2.2 Pt...................................... 14 2.3................................... 17 3..................................... 19 3.1....................................... 19 3.2..................................... 20 3.3..................................... 22 4..................................... 24 4.1..................................... 24 4.2.................................. 28 4.3.................................. 30 5........................................ 34 5.1........................................ 34 5.2............................... 35 5.3 Color Maps.................................... 37 5.4...................................... 39 5.5.......................................... 41 6.................................... 44 6.1.............................................. 45 6.2............................ 45 6.3..................... 47 6.4........................ 48 6.5............................... 49 6.6..................................... 50 7...................................... 51 7.1................... 51 7.2.............................. 53 8........................................... 56 8.1.............................................. 56 8.2 (Connolly).............................. 57 8.3 (Atom Volumes Field)......................... 60 8.4..................................... 64

vi A..................................... 67

1 1 :,, Visualizer. : Materials Visualizer : Materials Studio,,. Materials Studio,.,,,,,,.,..,.,,.. Materials Studio, 1.1 Materials Studio Materials Studio, Accelrys Materials Studio 5.5. Materials Studio,,.. Create a new project, OK. New Project.

2 Untitled ( ),. OK. Materials Studio, File New Project..... Note., OK.,,.. Online Help,, Help. Help Help Topics Materials Studio interface Toolbars Sketch toolbar., 1. View Explorers Job, Project, Properties. 2. View Toolbars. 3. Window. 4. Window Close All. 1.2 Default Atom Style, Line.,,,. Modify Default Atom Style, Display style, Ball and stick.,,,. 1.3,,.

3 File New, 3D Atomistic Document OK. 3D Atomistic Document. 3D Atomistic Document. Project Explorer 3D Atomistic Document, Rename, tut. (.xsd), tut.xsd.,., Undo. 1. 2. 3. Adjust Hydrogen, 4. Clean,,. tut.xsd 7 1. Esc.. 1: (, ).. Adjust Hydrogen, Clean, 3D.. 1,,,.

4 2:.. 1. 3D Viewer Rotation Mode., y, x., 3D Viewer, z. 2., 3D Viewer Zoom Mode,. 3D Viewer Translation Mode., 3.,, 3D Viewer Reset View, 3D Viewer Recenter, 3D Viewer Fit to View. 4.

5...xsd, Display Style. Display Style, Atom, Ball and Stick. 3: Display Style dialog ( ),..,. Ball radius,. 1. : Ctrl or Shift + 2. : 3. : :, : q,,

6, Atom Selection.,,. Atom Selection, Edit Atom Selection. 4: Atom Selection dialog,,.,.. Modify element Modify Modify element Oxygen., ( )., Properties Explore Element Symbol.. Adjust Hydrogen, Clean.,,.,,.,..

7 5:,.. Adjust Hydrogen, Clean,.. 1. Measure/Change.,,. 2.,., Properties Explore. 3. Measure/Change, Torsion. 4 (,,, ), (C O). 4..,.

8 ( ).,., O H. O H. 5., Properties Explorer Filter Torsion, Angle. OK. 6., Delete. 1.4,,., 3D Atomistic Document. File New 3D Atomistic Document, New 3D Atomistic Document.,,.,. 3D Atomistic Document 6. C C 2. 1 2. Clean. tut2.xsd. 2 1 2 3 1.

9,. 3. 6 Member, Alt,,.,. tut2.xsd, Copy, Cntl, c., Edit Copy. 3D Atomistic Document,, Paste. Cntl, v, Edit Paste.. 3D Atomistic Document naph, File Save,.,,.. 6:,.,., Delete., Modify Element. 3.

10 6 4,., Clean., Fragment Browser.. 3D Atomistic Document, Adjust Hydrogen., Define., Define fragment, Fragment Library User. Fragment Name Pyrrole, Add.,. Window Close All.,. 3D Atomistic Document, Browser User Pyrrole,., Fragment. Alt, Delete. 4., Copy, Paste. 3..

11 7: 4,.,.,,, Select Fragment..,. Shift Alt,., Shift,.. 8:,.,.,. Clean.,.

12 9:.

13 2 :. : Materials Visualizer : Materials Studio,., Materials Studio.,.. Pt ( ) Pt ( ),,, 2D-3D Note. Materials Studio,. 2.1 Pt Pt, Materials Studio,., Pt, Find Symmetry,.. Pt File Import, Import, Example Documents 3D Model Pt.xsd,. Example C:\Program Files\Accelrys\Materials Studio 5.5\share.,,.

14 ( ). Build Symmetry Find Symmetry Find Symmetry, Find, Find Symmetry. Symmetry Group.,, Properties Explorer Filter Lattice 3D, Properties Explorer. 10: Find Symmetry dialog 2.2 Pt 3D Atomistic Document. File New 3D Atomistic Document, OK.,. Build Crystal Build Crystal Build Crystal, Space Group, Enter Group 225 FM-3M. Lattice Parameter, Length a: 3.9239 Build. Build Add Atoms, Add Atoms. Atoms, Element:, Pt OK. Options, Test for bond as atoms are created. Coordinate system: Fractional. Add.

15 11: Add Atoms dialog Pt,. 12: Pt bulk structure Build Surface Cleave Surface, Cleave Surface. Surface Box, Cleave plane (h k l): 1 1 1 Tab. Top Thickness Fractional 1.0 3.0, Cleave.

16 13: Cleave Surface dialog 14: Pt (1 1 1) structure (2D) Super Cell Build Symmetry Super Cell, Supercell. Supercell range: U V 3. 3D Build Crystal Build Vacuum slab..., Build Vacuum Slab Crystal. Vacuum thickness 20Å, Build.

17 15: Pt (1 1 1) structure (3D), Display Style Lattice Style: Original. 2.3,... 3D Atomistic Document, Hydrogen,. Esc,., Copy., Paste.. Fragment,. Fragment. Fragment, Fragment, Select Fragment.

18 : Shift Alt. : Shift.,,. 16: H2 on Pt (1 1 1) structure.

19 3 : 2,, 3. : Materials Visualizer, Amorphous Cell :,., 2. Materials Studio,. Builder Layers. Builder Layers, - -.. Note. Amorphous Cell. 3.1 / /.,. Import, Fe.xsd. Ball and Stick., Display Style, Ball and Stick. Supercell. Build Symmetry Supercell, Supercell. A, B, C 7, 3, 2, Create Supercell. Supercell.

20 17: Fe 7x3x2 supercell,., Lattice Parameters. Lattice Parameters, a b. 3.2 Amorphous Cell,., Build Build Polymers Homopolymer. 4., Chain length. Tacticity. 18: Homopolymer dialog Chain length: 4, Build.

21 19:,., Amorphous Cell, Calculation, Module Amorphous Cell Calculation. Amorphous Cell Calculation. 20: Amorphous Cell Calculation dialog Task Confined layer. Composition Molecule 1 polyethylene.xsd, Loading 5.,.

22 Density 1 0.7.,. More..., Amorphous Cell Confined Layer. Lattice type Orthorhombic, a b Fe Supercell.. Run. Project Explorer Polyethylene AC Constr. polyethylene.xtd. 21: polyethylene.xtd,.. 3.3,, 2. Build Build Layers, Build Layers. Build Layers.

23 22: Build Layers dialog Define Layers, Layer1 Fe.xsd, Layer2 polyethylene.xtd, Layer3 Fe.xsd. Layer Details,. Options, Configure for confined shear use. Build. Layer.xsd. 23:.

24 4 :,, Polymer Builder. : Materials Visualizer :.,, tacticity( ),,,., Materials Studio.. 4.1,,.,. 3D Atomistic Document. New, 3D Atomistic Document. p- (p-phenylene vinylene), PPV. 24: p- 25: p-

25,. Sketch Ring.. Alt, 3D Atomistic Document 3D Atomistic Document.,.. Sketch Atom..,.., 2. Esc. 2. Sketch Atom 1.. 2, 2..,. Adjust Hydrogen Clean. 26: p-, 3D Viewer Selection Mode. Repeat Unit. Build Build Polymers Repeat Unit. Repeat Unit.

26 27: Repeat Unit dialog Head Tail 28: Head 3D Atomistic Document. Repeat Unit Head Atom.,. Tail 3D Atomistic Document. Repeat Unit Tail Atom. Repeat Unit.,. 29: p-,,. Project Explorer 3D Atomistic Document. Rename. p-phenylene vinylene.

27,. Homopolymer. Build Build Polymers Homopolymer. Homopolymer. 30: Homopolymer dialog Polymerize,. Current project. Library: Current project., Repeat unit.,. Repeat unit: p-phenylene vinylene. 20. 10. Chain length, 10 20.. Build. 3D Atomistic Document. 31: p-,.

28 File Save Project.. Window Close All. 4.2, Materials Studio 3D Atomistic Document., Block Copolymer. Build Build Polymers Block Copolymer. Block Copolymer. 32: Block Copolymer dialog Block Copolymer 3. Polymerize, Advanced, Branches. Advanced Branches. Polymerize. Block Copolymer,.,,. 5, 10, 5. Polymerize. Add Block Definition.

29 33: Add Block Definition dialog, Block Copolymer Add Block Definition. Library., oxides. Library: oxides. Repeat unit. Repeat unit., oxyethylene Add. Add Block Definiation Repeat unit, oxypropylene. Add. 2 Polymerizer Repeat unit., 5. Repeat unit oxyethylene. Add, Close. Close Add Block Definition.. Block Copolymer. 34: Block Copolymer dialog

30. Build. 35: 3D Atomistic Document., 2. 1. Select Repeat Unit. 1... Window Close All. 4.3. Random Copolymer Build Build Polymers. Block Copolymer. Build Build Polymers Random Copolymrer. Random Copolymer.

31 36: Random Copolymer dialog,. Random Copolymer. Add Repeat Unit. 37: Add Repeat dialog Library., dienes. Repeat unit. c-butadiene. Add. acrylates. Library acrylates. Repeat unit acrylonitrile. Add. Close, Add Repeat Unit. Random Copolymer Chain length, 10 20.

32 38: Random Copolymer dialog, Probabilities tab Probabilities Reactivity Ratios 2. Probabilities ( ):. Reactivity Ratios ( ):.. Random Copolymer Probabilities. 20:80.. 1 ( ) 2 ( ), 2. Random Copolymer Probabilities. 1,1 matrix cell. Edit Probabilities Matrix. Probability matrix cell value, 0.5 0.8. 1, 0.8. 1,, 1 2 0.2. 1,2 matrix cell. Edit Probabilities Matrix 0.5 0.2. 2.

33 39: Random Copolymer dialog, Probabilities tab 20:80.. Build. 40:,. 20:80, Polymerize Force concentrations. Force concentrations. Build.,,...

34 5 : Materials Visuallizer,. : Materials Visualizer : Materials Visualizer,,. Materials Studio,,...., DMol 3.. Color Maps Tip.,. Project Explorer, Project Explorer. 5.1. Import, Examples/Documents/3D Model/benzene.xsd. Volume Visualization.

35 View Toolbars Volume Visualization. Create Isosurfaces.,. DMol3 total electron density, OK.. 41: 5.2 Display Style. 3D Atomistic Document, Display Style. Isosurface. Isosurface. 42: Display Style dialog, Isosurface tab

36. Display Style, Dots. Dot size 3.,., solid. Display Style, Solid.,., ball and stick.. Atom, Ball and Stick. Isosurface, transparency 2... Transparency.,..,,. Display Style Isosurface, Isovalue ( ).,.. Note.,.. Color. Custom color selector. OK.. Note.,.,..,,. Mapped Field DMol3 electrostatic potential. Display Style.

37 43:. Display Style, Banded.,,. 5.3 Color Maps Color Maps. 3D Atomistic Document, Color Maps. 44: Color Maps dialog Color Maps. From To. Spectrum Blue-White-Red., From,., To,., (Color Chooser). Color Maps Color Chooser ( ).

38.. Color Chooser. Color Chooser 3.. 45: Color Maps dialog Tip.,. 3, 3.. 0.12496.. Color Chooser. 2, 2.... Bands 128.., From To,.,. From To. From.

39,,,.,.,.,. 3D Atomistic Document, Display Style. Isosurface, Isovalue.. Color Maps, From.,. From Mapped Minimum. To, Mapped Maximum..,.,,. 5.4,...,. Create Slices Best Fit.,. DMol3 electrostatic potential, OK.

40 46:.., Color Maps..,,. 3D Atomistic Document, Color Maps. From Mapped Minimum, To Mapped Mean.,,.. Volumetric Selection.. DMol3 electron density DMol3 elecgtrostatic potential DMol3 electron density, DMol3 electrostatic potential.. Isosurface1.,. Color Maps. Color Maps, Color Chooser 2.,. Display Style. 3D Atomistic Document, Display Style. Show Frame..

41 3D Viewer Reset View. Create Slices, Parallel to 1st and 3rd axis. DMol3 electrostatic potential, OK. 47: 2 X-Z. 1. Note.,.,. C-C. Create Slices. DMol3 electrostatic potential, OK... Tip.. 5.5,. View Display Options, Fast render on move.. Shift Alt,.,. Shift,.. Tip. 3, Shift, Shift,.

42 Note., Properties Explorer. Volumetric Selection. Volumetric Selection. DMol3 electrostatic potential. Volumetric Selection. 48: Volumetric Selection dialog Delete.. Volumetric Selection, Slice2. Delete. 2. Volumetric Selection, DMol3 total electron density, Isosurface1.. 49:

. 43

44 6 : Materials Visualizer Movement Move To mode. : Materials Visualizer :,.,,. Materials Visualizer,,, Movement., ( ),., best fit line/plane,,.,,,.,.. Tip.,. Project Explorer, Project Explorer.

45 6.1 Materials Studo,. Materials Studo, Materials Studio, Windows, Accelrys Materials Studio 5.5. Materials Studio,,. Create a new project OK.. Zeolite. Zeolite, OK. 6.2,. File Import..., Import. Import Document, Structures zeolites MOR.msi, Import..,, P1. Build Symmetry Make P1.,..,., Ball and Stick,.

46 50: Centroid,. Shift q.,,.. Create Centroid, Centroid. 3D Atomistic document,.,. 51: Centroid Tip. Properties Explorer,.,, IsWeighted..

47 6.3. Cl H C H H 52: Structure of chloromethane New, 3D Atomistic Document. Project Explorer 3D Atomistic.xsd, Rename chloromethane.xsd. Sketch Sketch,. Sketch, 3D Viewer, 1. Adjust Hydrogen., Clean. chloromethane.xsd, Ctrl c. Project Explorer MOR.xsd, Ctrl v.. 53: Edit Copy and Edit Paste,.

48, -. Shift,. Create Centroid, Best Fit Line. Best Fit Line.. Home 3D Viewer Reset View Fit Line, Align Onto View Align In/Out.. Best, 54: Best Fit Line. Best Fit Line. Best Fit Line, Delete. 6.4, Move To.. Note..,. Move To.,.,,.

49 55:,. Tip.., Alt, Move To,. 3D Viewer Selection Mode. MOR.xsd, Display Style. Lattice, Style In-Cell.,.. Centroid, Delete. 6.5,.,,.. Create Centroid Centroid.,. Properties Explorer, View Explorers Property Explorer. Properties Explorer.,.

50 Property Explorer Filter Centroid. Properties Explorer, CentroidXYZ. Z 0.00. OK. 3D Viewer, x, y z,,,. Z=0. 6.6 Materials Visualizer,. 3D Viewer Reset View,.,., Movement. Movement.. Movement Translation Distance. Move Right, Move Left., 0.5 Å. Note., 3D Atomistic document, x, y z. 0.5 Å,,..

51 7 :,. : Materials Visualizer : Polymorph Prediction,,. Materials Visualizer 3D Atomistic Collection,.,,.. Tip.,. Project Explorer, Project Explorer. 7.1. QSAR,. New, Study Table Document,. Insert From File Insert Into Active Document, Examples QSAR Structures, Corrosion.xsd. Corossion.

52 56: 3D Atomistic Collection document (.xod ). A 1 7., Extract To Collection., Extracted From Study Table.xod. 57: xod Note. 3D Atomistic,., 3D Atomistic Collection, Project Explorer,, Insert Into. 3D Atomistic Trajectory,,,., 3D Atomistic ( ).,,..xsd.xod,.xod,,. 3D Atomistic.

53 Physical Systems,., Physical Systems. Physical Systems. 58: Physical Systems,. Physical Systems, Corrosion-1, Corrosion-7. Physical Systems,. Tip. Shift Ctrl,. Physical Systems,. Corrosion-7, Physical Systems Corrosion-3. Corrosion -3,.. Physical Systems Corrosion-1, Delete., Physical Systems. 7.2 Materials Visualizer,., Superpose Structures

54.,. Physical Systems, Corrosion-2. Create Centroid, Principal Axes.,. 59: Corrosion-2 with principal axes Create Centroid averaged geometry objects. Corrosion-3 Corrosion-7. Close, Physical Systems.,. Extracted From Study Table.xod,. Alt. Materials Visualizer,,. x, y z,.. 3D Viewer Reset View, Align Onto View. x, y z,.,, 3D Atomistic. Extracted From Study Table.xod, Return To Study Table.

55,. Models,.,,, Extract To Atomistic Documents. 3D Atomistic, Project Explorer. Physical Systems, Extract To Atomistic Documents,.xsd..

56 8 :. : Materials Visualizer : Materials Visualizer 3, Sorption,, 3.,., ( ),,. 1,., ( ).,,,. (Field segregation), Materials Visualizer,, Sorption., (Connolly surface). (Atom Volumes Field: ),.. Connolly (Atom Volumes Field) (Segregates) Tip.,. Project Explorer, Project Explorer. 8.1 Materials Studio, Segreate.

57, Materials Studio, Materials Studio Accelrys Materials Studio 5.5., Materials Studio,,.. Create a new project, OK. New Project. Untitled ( ),. OK. Materials Studio, File New Project..... Note., Setting Organizer. Creating a project. 8.2 (Connolly),. Connolly.,. Import, Import Document. Examples Documents 3D Model TON.msi. Atom Volumes & Surfaces Connolly. Tools Atom Volumes & Surfaces. Atoms Volumes & Surfaces. Connolly. Solvent, Connolly. Create. 3D Atomistic, Analysis.

58 60: Atom Volumes & Surfaces dialog, Analysis tab 61:,., Connolly. Atom Volumes Field. Atom Volumes Field.

59 62: Atom Volumes & Surfaces dialog, Analysis tab 63:,.. Atom Volumes Field. Connolly,.

60 Connolly radius. Connolly,,,.,,. Connolly radius 0.90. Atom Volumes & Surfaces. 64: 8.3 (Atom Volumes Field), 1,.. 1. (. ) (segregation),.. Volume Visualization. 65: Volume Visualization Toolbar

61 3D Viewer,. View Toolbars Volume Visualization. Create Segregates..,. 66: Properties Explorer, 1. Properties Explorer Filter Segregate., FieldVolume SegregateXYZ. 3D Atomistic,. Volume Visualization Volumetric Selection,. Volume Visualization Volumetric Selection. Volumetric Selection,. Connolly. Connolly Surfaces. Segregator @0 Segregator. @0 0. +,.

62 +, Segregator @0.. Volumetric Selection..,. 14. 67: Volumetric Selection dialog Properties Explorer Display Style,. 3D Viewer, Display Stule, Display Style. Segregagte. Display Style Coloring. Constraints,.,. Isovalue. 0.,. Tip.,,.,.,,.

63 Values Low. 68: Low High.,. All,. Values High. Connectivities.,.,. Connectivities Isolated. 12. Connectivities Accessible. 2. Tip., Sorption. Connectivities All. Note. Properties Explorer Matrials API., MaterialsScript,.

64,,. Volumetric Selection, Shift. Create Isosurfaces.,. 8.4 Create Segregates,. Create Segregates, Analyze Segregated Field. Segregate Analysis.. Analyze.., 140, 2 2. 69: Tip. MaterialsScript,,. TON.xsd. Segregate Analysis Segregate major axis, Analyze.,.

65 TON.xsd, Segregate Analysis Segregate radius (best-fit sphere), Analyze.,. TON.xsd, Segregate Analysis, Segregate separation, Analyze.. 70: 71:

66 72: Tip.,..

67 A Materials Studio 3D Viewer 3D Viewer, Seletion, Rotation, Zoom, Translation.,. Chart Viewer..,.,. Tip.,,.