1. BUILDING STRUCTURES, OPTIMIZATION, ADSORPTION LOCATOR TUTORIAL Day 3

2. Energy of adsorption Enthalpy of adsorption:
Isosteric heat of adsorption:
∆Hads - enthalpy of adsorption
P - pressure
qst - isosteric heat of adsorption
na – numer of moles of adsorbate
R – gas constant
T - temperature

3. Materials Studio – Adsorption Locator
Adsorption Locator simulates a substrate loaded with an adsorbate of a fixed composition. It allows you to find low energy adsorption sites.
Ujemna- endotermiczna, oddawanie energii,
Slajd z wytłumaczeniem energii adsorpcji (fizysorpcja)
Stable configuration –
Equilibrium pos – is in the min potential created by the surface,

4. Materials Studio – Adsorption Locator
Monte Carlo searches are carried out to obtain the adsorption configurations of the of the substrate-adsorbate system.
The simulated annealing schedule slowly decreases the temperature to find the lowest energy adsorption site.
Kilka slajdów
Czasteczka>pow en potencjalnej > czasteczka w roznych konfiguracjach>

5. B A C D POTENTIAL ENERGY SURFACE T
Zmienić rysunek!!!

6. BUILDING SiO2 CRYSTAL SURFACES
Materials Studio tutorial

7. Our goal – crystal surfaces of SiO2Ea Ea
3 KOŁO SIEBIE, STRZAŁKA W GORE, W DÓŁ, (LEPSZE GORSZE)
Jakosc!!!

8. BUILDING SiO2 CRYSTAL SURFACE WITH NH3+ FUNCTIONALIZATION
Materials studio tutorial

9. Always remember to save your project! Think how to name your files,
you must be well organized!
Do not create multilevel directories!

10. Open structure from yesterday – SiO2
Open the structure of the surface that we created yesterday.

11. Our goal – SiO2 surface with C3H6NH3 attached
ZMIENIĆ JAKOŚĆ!

12. New SiO2 crystal surface
Open new 3D Atomistic file. Then go to the Surface file and copy the surface using Ctrl+C combination.
Open the 3D Atomistic file and using Ctrl+V combination paste surface into the new file.

13. New SiO2 crystal surface
Highlight one hydrogen and change it to carbon atom.

14. Using the Sketch tool draw the C3H6NH3 Use the Adjust hydrogen button.
Then to the nitrogen attach one more hydrogen to get the NH3 group.
Save that 3D Atomistic as SiO2_surface_NH3
Additional hydrogen
SKETCH TOOL ,
ZAMIENIC NA WEGIEL,
IKONKI,
20min na rysowanie!

15. New SiO2 crystal surface
Open new 3D Atomistic file. Then go to the SiO2_surface_2NH3 file and copy the surface using Ctrl+C combination.
Open the 3D Atomistic file and using Ctrl+V combination paste surface into the new file.

16. New SiO2 crystal surface
Highlight one hydrogen and change it to carbon atom.

17. Repeat previous steps: Using the Sketch tool draw the second C3H6NH3
Use the Adjust hydrogen button.
Then to the nitrogen attach one more hydrogen to get the NH3 group.
Save that 3D Atomistic as SiO_surface_2NH3
Additional hydrogen

18. Check if both NH3 grups have all 3 hydrogens.

19. BUILDING SiO2 CRYSTAL SURFACE WITH COO – FUNCTIONALIZATION
Materials studio tutorial

20. Our goal – SiO2 surface with C2H4COO – attached

21. New SiO2 crystal surface – COO –
Open new 3D Atomistic file. Then go to the Surface file and copy the surface using Ctrl+C combination.
Open the 3D Atomistic file and using Ctrl+V combination paste surface into the new file.

22. New SiO2 crystal surface
Highlight one hydrogen and change it to carbon atom.

23. Using the Sketch tool draw one C2H4COO-.
Start with drawing 3 carbons [first carbon is attached to the Si atom] and two oxygens bonded to last carbon.

24. Highlight two oxygen-carbon bonds and change the Bond type by clicking on the Partial Double Bond button.

25. Use the Adjust hydrogen button
Save that 3D Atomistic as SiO2_surface_COO.

26. GLUCOSE Open new 3D Atomistic.
Using Sketch Atom Tool, draw glucose structure, which is positively charged. Which means leaving one of the oxygen atoms with free bond space.
Use Clean Structure button.
Optymalizacja przez forcite!!!!
FRONT VIEW
SIDE VIEW

27. GEOMETRY OPTIMIZATION TUTORIAL
Adsorption
GEOMETRY OPTIMIZATION TUTORIAL

28. Forcite Tools – Geometry Optimization
Open the glucose file

29. Forcite Tools – Geometry Optimization
Click on the Forcite Tools | Calculation

30. Forcite Tools – Geometry Optimization
Task: Geometry Optimization
Click More button. In the Setup tab choose in the Algorithm | Smart, Quality: Medium, Energy: 0,001 kcal/mol, Force: 0,5 kcal/mol/Å, Max.iterations: 500.
Uncheck the Optimize cell button.

31. Forcite Tools – Geometry Optimization
In the Energy tab choose in the Forcefield: COMPASSII, Charges: Forcefield assigned, Quality: Medium.
Summation method
Electrostatic: Atom based
Then click More button.

32. COMPASSII forcefield bond stretching deflection out of the surface
angle bending
electrostatic interactions
torsion
Van der Waals interactions

33. COMPASSII forcefield
COMPASSII forcefield is optimized with both quantum mechanics and experimental data to reach good accuracy in describing the system such as: common organics molecules, small inorganic molecules, polymers or metals, metal halides, metal oxides, silica or ionic liquids.
Polymers
Crystals (metal oxides)
Organic
Molecules

34. Forcite Tools – Geometry Optimization
Check the Calculate automatically box.
Dodatkowy slajd job control -

35. Forcite Tools – Geometry Optimization
Go to Job control Tab and check your settings
Click Run.

36. Forcite Tools – Geometry Optimization
Open file Surface

37. Constraints Highlight atoms below the first layer of the surface.
Go to Modify | Constraints and check the boxes Fix Cartesian position

38. Forcite Tools – Geometry Optimization
Click on the Forcite Tools | Calculation

39. Forcite Tools – Geometry Optimization
Task: Geometry Optimization
Click More button. In the Setup tab choose in the Algorithm | Smart, Quality: Medium, Energy: 0,001 kcal/mol, Force: 0,5 kcal/mol/Å, Max.iterations: 500.
Uncheck the Optimize cell button.

40. Forcite Tools – Geometry Optimization
In the Energy tab choose in the Forcefield: COMPASSII, Charges: Forcefield assigned, Quality: Medium.
Summation method
Electrostatic: Ewald
Then click More button.

41. Forcite Tools – Geometry Optimization
Check the Calculate automatically box.
Dodatkowy slajd job control -

42. Forcite Tools – Geometry Optimization
Go to Job control Tab and check your settings
Click Run.

43. Deformation energy

44. Rigid adsorption energy

45. Deformation energy

46. Adsorption energy

47. Adsorption energy
Or simply

48. Forcite Tools – Geometry Optimization
Open file SiO2_surface_NH3

49. Constraints Go to Modify | Constraints
Higlight all atoms in the box that form the crystal surface.
Go to Modify | Constraints
Check Fix Cartesian position box.

50. Constraints
Molecule itself should not be constrained.

51. Forcite Tools – Geometry Optimization
Click on the Forcite Tools | Calculation

52. Forcite Tools – Geometry Optimization
Task: Geometry Optimization
Click More button. In the Setup tab choose in the Algorithm | Smart, Quality: Medium, Energy: 0,001 kcal/mol, Force: 0,5 kcal/mol/Å, Max.iterations: 500.
Uncheck the Optimize cell button.

53. Forcite Tools – Geometry Optimization
In the Energy tab choose in the Forcefield: COMPASSII, Charges: Forcefield assigned, Quality: Medium.
Summation method
Electrostatic: Ewald
Then click More button.

54. Forcite Tools – Geometry Optimization
Check the Calculate automatically box.
Dodatkowy slajd job control -

55. Forcite Tools – Geometry Optimization
Go to Job control Tab and check your settings
Click Run.

56. Forcite Tools – Geometry Optimization
Open file SiO2_surface_2NH3

57. Constraints Go to Modify | Constraints
Higlight all atoms in the box that form the crystal surface.
Go to Modify | Constraints
Check Fix Cartesian position box.

58. Constraints
Molecules itself should not be constrained.

59. Forcite Tools – Geometry Optimization
Click on the Forcite Tools | Calculation

60. Forcite Tools – Geometry Optimization
Choose on the Task | Geometry Optimization

61. Forcite Tools – Geometry Optimization
Task: Geometry Optimization
Click More button. In the Setup tab choose in the Algorithm | Smart, Quality: Medium, Energy: 0,001 kcal/mol, Force: 0,5 kcal/mol/Å, Max.iterations: 1000.
Uncheck the Optimize cell button.
1000

62. Forcite Tools – Geometry Optimization
In the Energy tab choose in the Forcefield: COMPASSII, Charges: Forcefield assigned, Quality: Medium.
Summation method
Electrostatic: Ewald
Then click More button.

63. Forcite Tools – Geometry Optimization
Check the Calculate automatically box.

64. Forcite Tools – Geometry Optimization
Go to Job control Tab and check your settings
Click Run.

65. Forcite Tools – Geometry Optimization
Open file SiO2_surface_COO

66. Constraints Go to Modify | Constraints
Higlight all atoms in the box that form the crystal surface.
Go to Modify | Constraints
Check Fix Cartesian position box.

67. Constraints
Molecule itself should not be constrained.

68. Forcite Tools – Geometry Optimization
Click on the Forcite Tools | Calculation

69. Forcite Tools – Geometry Optimization
In the Energy tab choose in the Forcefield: COMPASSII, Charges: Forcefield assigned, Quality: Medium.
Summation method
Electrostatic: Ewald
Then click More button.

70. Forcite Tools – Geometry Optimization
Check the Calculate automatically box.

71. Forcite Tools – Geometry Optimization
Go to Job control Tab and check your settings
Click Run.

72. TRY USING DIFFERENT FUNCTIONALIZATION GROUPS AND CHECK
CHALLENGE YOURSELF!
TRY USING DIFFERENT FUNCTIONALIZATION
GROUPS AND CHECK
STUDY GLUCOSE ADSORBTION?