1. Chemistry with Computers Yingbin Ge Iowa State University Central Washington University October 13, 2007

2. 2 Accuracy Computer time Hartree Fock (HF) Perturbation theory MP2 density functional theory (DFT) coupled- cluster CCSD(T) molecular mechanics

3. 3 What has been done? Global optimization of silicon nanoclusters. Chemical vapor deposition of silicon carbide. Si 14 H 20

4. 4 Global optimization of silicon nanoclusters Why Si nanoclusters? Si nanoclusters exhibit bright room- temperature photoluminescence which could be used in light-emitting devices. To model the excitation and emission of the Si nanoclusters, we need to know their thermodynamically stable structures. A. Meldrum group, Adv. Mater. 17, 845 (2005)

5. 5 Global vs. local optimization global minimum local minimum local optimization energy  Energy conformations

6. 6 Why is global optimization difficult? Ar 7 Ar 8 Ar 9 Ar 10 Ar 11 Ar 12 Ar 13 # LM4821641524641328 Tsai and Jordan, JPC 97, 11227 (1993)

7. 7 Global optimization strategies *Applications of evolutionary computation in chemistry, Structure and Bonding, Vol. 110 (2004) Exhaustive search: too many minima to sample. Random sampling:”But there’s one I always miss.” Genetic algorithm is based on “the fittest survive” principle. It has been proven efficient for the global optimization of clusters and molecules.*

8. 8 Genetic algorithm based global optimization Produce random structures as initial population. Evaluate energy (fitness) for each individual. Repeat following steps until convergence: Perform competitive selection. Apply genetic operators* to produce new clusters. Lower energy clusters replace higher-energy ones. *Genetic operators: crossover and mutation.

9. 9 Biological crossover and mutation Crossover of 2 DNA strings Mutation: 1 missing nucleotide missing nucleotide normal after mutation normal after crossover

10. 10 Crossover: silicon hydrides local opt. crossover

11. 11 Mutation methods Hydrogen shift Partial rotation

12. 12 Mutation methods SiH 2  SiH 3 a. initial geometryb. after mutationc. final structure SiH 2  SiH 3

13. 13 Si 10 H 16 Si 18 H 22 Si 14 H 1 8 Si 10 H 14 Si 14 H 20 Si 18 H 24 Diamond-lattice Si x H y global minima Si x H y-2 global minima MP2 & DFT

14. 14 Si x H y global minima Si x F y global minima Si 10 H 16 Si 10 H 14 Si 7 H 14 Si 8 H 14 Si 7 F 14 Si 8 F 14 Si 10 F 16 Si 10 F 14 MP2 & DFT DFT

15. 15 Ligand effect L= HCH 3 OHF L 2 Si=SiL 2 L 3 Si-SiL MP2 global minimum

16. 16 Ligand effect Si 10 (CH 3 ) 16 and Si 10 H 16 adopt the same diamond-lattice Si core. Si 10 (OH) 16 and Si 10 F 16 adopt same Si core with a 4-membered Si ring. Ligand electronegativity affects the Si core structures. -SiF 3 and -Si(OH) 3 are preferred at expenses of forming small 4-membered Si rings.

17. 17 What did we learn? GA is efficient, scaling O(N 4-5 ). Well H-passivated Si clusters adopt diamond-lattice Si cores. Si core can be tuned with # ligands. Si core can be tuned with ligand electronegativity. Si x Cl y and Si x Br y ? Further study the excitation and photon- emitting mechanism of Si nanoclusters. Questions and comments?

18. 18 Questions?

19. 19 May 18, 2007 HomeStead Road, Sunnyvale, CA http://www.opentravelinfo.com/north-america/gas-price-hike

20. 20 Nuclear Energy Additional energy source: less fight on oil. No SO 2 - less acid rains. No CO 2 - less global warming. Let’s try to keep New York & Shanghai above sea. http://globalwarming--awareness2007.com/globalwarming-awareness2007/

21. 21 What about the safety? Layer 3. Silicon carbide is impervious to fission products and serves as a pressure vessel. Layer 4. Pyrolytic carbon to protect SiC. Layer 2. Pyrolytic carbon to trap fission products. http://www.iaea.org/inis/aws/htgr/fulltext/xa54410.08.pdf Layer 1. Porous carbon to accommodate fission products and kernel swelling. UO 2 kernel

22. 22 Chemical vapor deposition CVD: gas phase molecules break down at high T; fragments deposit on a substrate to account for the solid growth. CH 4 CH2H2 inlets outlet substrate http://www.ieee-virtual-museum.org/collection/tech.php?taid=&id=2345958&lid=1 diamond growth

23. 23 Silicon carbide (SiC) coating process Coater Wall Deposition Zone Annealing Zone Uranium Particles precursors

24. 24 Why silicon carbide? High melting point: 2700  C. Mohs’ hardness: 9.3/10. Imperviousness to fission products. Lower reactivity at high temperature. Low cost. SiC made by chemical vapor deposition is ideal material for the protective layer of nuclear energy pellets.

25. 25 P: Defects in the SiC layer cause cracks on the surfaces of nuclear energy pellets. Q: How to reduce defects in SiC? A: Understand the mechanism of the SiC chemical vapor deposition. Propose ideal production condition.

26. 26 Detailed Reaction Kinetics for Modeling of Nuclear Fuel Pellet Coating for High Temperature Reactors. Drs. Gordon and Ge from the chemistry department. Drs. Fox and Gao from the chemical engineering department. Drs. Battaglia and Vedula from the mechanical engineering department.

27. 27 Chemical vapor deposition of SiC Precursors: CH 3 SiCl 3 (methyltrichlorosilane) Temperature: 1000-2000 K Pressure: ~1 atm Complex gas-phase and surface chemistry CH 3 SiCl 3  SiC (solid) + 3HCl 

28. 28 CH 3 SiCl 3 decomposition pathways  G =  H - T  S in kcal/mol at 0 K (left) and 1400 K (right)

29. 29 50 gas phase species Cl, Cl 2, H, H 2, HCl, C 2 H, C 2 H 2, C 2 H 3, C 2 H 3 Cl, C 2 H 4, C 2 H 5, C 2 H 5 Cl, C 2 H 6 (e), C 2 H 6, 1 CH 2, 3 CH 2, CH 2 C, CH 2 Cl, CH 2 Cl 2, CH 3, CH 3 CH(s), CH 3 Cl, CH 4, HCHC, Si 2 Cl 4, Si 2 Cl 5, Si 2 Cl 6, SiCl 2, SiCl 3, SiCl 4, SiH 2 Cl, SiH 2 Cl 2, SiH 3 Cl, SiHCl, SiHCl 2, SiHCl 3, CH 2 SiCl 2, CH 2 SiCl 3, CH 2 SiHCl, CH 2 SiHCl 2, CH 3 SiCl, CH 3 SiCl 2, CH 3 SiCl 2 Cl, CH 3 SiCl 3, CH 3 SiH 2 Cl, CH 3 SiHCl, CH 3 SiHCl 2, HC  SiCl, 1 CHSiCl 3, 3 CHSiCl 3

30. 30 41 reactions without a transition state To be continued …

31. 31 73 reactions with a transition state

32. 32 Reduced mechanism Our collaborators, including the chemical engineers and mechanical engineers, also complained about the long lists. How to reduce it? Remove the species whose concentration is very low at high temperatures. Keep important species such as 3 CH 2, CH 3, SiCl 2, and SiCl 3 as target molecules. Remove 1 species at a time and compare the reduced and full mechanisms. Reduced to 28 species and 29 reactions.

33. 33 Time (s) [C 2 H 3 ]

34. 34 Time (s) [SiHCl]

35. 35 Surface reactions: deposition Surface reactions involve thousands of atoms. Hybrid quantum mechanics/molecular mechanics (QM/MM) method. AccuracySystem size Quantum mechanics 1 kcal/moltens of atoms Molecular mechanics 10 kcal/mol millions of atoms

36. 36 (bulk)-C 3 SiCl QM + MM regions QM region C H Si Cl

37. 37 MM region H attacks Cl HCl leaving H 3 C attacks Si* Forming H 3 C-Si bond 1). Production of Si *. 2). Si-C growth. MM region

38. 38 What did we learn? A gas phase mechanism was proposed in the silicon carbide chemical vapor deposition. The gas phase mechanism was reduced to 28 species and 29 reactions. How temperature and precursor concentration affect gas phase chemistry. Surface chemistry under investigation. Questions and comments?

39. 39 Research plan Atomic layer deposition of Al 2 O 3, TiO 2, and SiO 2. Global optimization of protein structures. Astrochemistry in ice. Chemical vapor deposition of diamond C, pyrolytic C, and bulk Si. Fast global optimization of large silicon clusters.

40. 40 Atomic layer deposition ALD is based on sequential, self-limiting surface chemical reactions. Precise atomic layer control: no defects! http://www.colorado.edu/chemistry/GeorgeResearchGroup/intro/aldcartoon.GIF repeat A B

41. 41 Vanadium oxide (V x O y ) catalyzed oxidative dehydrogenation Experimental energy barrier: 20-30 kcal/mol. Theoretical energy barrier: 45-80 kcal/mol. What’s wrong? Vanadium oxide is supported by the ALD produced Al 2 O 3, SiO 2, or TiO 2 surfaces. How to model an ALD surface? How does the ALD surface help lower the energy barrier of C 3 H 8 + 1/2O 2  C 3 H 6 + H 2 O?

42. 42 Global optimization of protein structures: important for drug design primary structure secondary structure quaternary structure tertiary structure

43. 43 Global optimization methods Random sampling: 30 dihedral angles each with 5 possible values. 5 30 (~1 billion trillion) conformations. Molecular dynamics: some proteins fold in minutes; energy and force need to be evaluated 10 18 times (  t=10 -15 s). Genetic algorithm + Tabu + In situ adaptive tabulation.

44. 44 Genetic algorithm. crossover mutation dihedral angles a). E new  E old b). E new   w i E i old c). compute E new 11 22 Tabu (taboo): to penalize the moves to previously visited conformations. In situ adaptive tabulation. {  1 …  N } -> E

45. 45 Astrochemistry in ice Europa Ganymede Callisto ?

46. 46 Jupiter’s Magnetic Field

47. 47 Potential energy surface of 1 H 2 O 2 CCSD(T) (kcal/mol)

48. 48 Probable Reaction Paths to HOOH 1 O + H 2 O  1 H 2 O-O  HOOH 1 O 2 + H 2  1 H 2 O-O  HOOH 1 O ( 3 O) + H 2 O  2 OH + 2 OH  HOOH

49. 49 Future work Study the reaction paths at higher level of theories. Study the potential energy surfaces that involves cations such as 2 O +. Reaction rate constant calculations. Molecular dynamics calculations. Elucidation of H 2 O 2 formation mechanism. Study of H 2 O 2 reaction paths in a biological environment.

50. 50 Acknowledgements Prof. John D. Head at University of Hawaii Prof. Mark S. Gordon at Iowa State University Department of Energy Grant # DE-FC07-05ID14661

51. 51 Questions and comments are welcome.

53. 53 Crossover and mutation: Si only cluster Deaven and Ho, PRL 75, 288 (1995) A B a b a B A b crossover mutation local opt. local opt.

54. 54 Reaction rate constant k B -- Boltzmann constant T -- temperature h -- Planck constant R -- Gas constant -- Free energy barrier (some times hard to obtain)

55. 55 GTS T (K) R=3.0 Å at 2000 K Free Energy Profile of CH 4  H + CH 3 R=3.6 Å at 400 K R=3.4 Å at 1200 K

56. 56 Molecular dynamics approximations for A + B  A-B Elec. degeneracy Collision area Reaction probability Relative velocity  : reduced mass.  : symmetry factor.

57. 57 Predict k: from CH 3 + H  H-CH 3 to CX 3 + Y  Y-CX 3 CH 3 +F CH 3 +Cl CF 3 +F CCl 3 +Cl

58. 58 Predict k k 1 ( 2 CH 3 + 2 H  1 CH 4 ) k 2 ( 3 CH 2 + 2 H  2 CH 3 ) Free energy barrier is hard to get.

59. 59 + + + + + + + + + (0.0) (19.3) (7.9) (47.7) (16.9) (75.9) (59.8) (69.7) (64.6) (34.2) PES of SiCl 3 + H 2 Si: blue Cl: green H: light grey  G at 0 K (kcal/mol)

60. 60 Predict k: from CH3 + CH3  CH3-CH3 to CX3 + CY3  CX3-CY3 CH 3 +CCl 3 CCl 3 +CCl 3 CH 3 +SiH 3

61. 61 Potential energy surface of 3 H 2 O 2 CCSD(T)//CASSCF (kcal/mol)