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Periodic Model Build-up

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Presentation on theme: "Periodic Model Build-up"— Presentation transcript:

1 Periodic Model Build-up
Outline Learn about crystals… (HW) Learn about Materials Studio… Search ICSD/CSD/PDB if necessary… Import several crystals using Materials Studio… Build CNT using Materials Studio… Move to Room #310 & Do It Yourself!

2 Lab examples Pure crystal [Si, Ag, Au] Alloy [Co/Tb, Fe/Si]
Oxide [TiOx] Boride [TmB4, TmAlB4] CNT, C60, diamond & their derivatives [PCBM] Organic & Polymer [P3HT, PQT, PSS, PEDOT] & their surfaces, interfaces, composites, defects, …

3 ICSD: Inorganic Crystal Structure Database

4

5 Coordinates: Cartesian / Fractional / Internal

6 ###############################################################################
# Noreus, D.Werner, P.-E. (1982) # Acta Chemica Scandinavica, Series A: (28,1974-) 36, # Structural studies of hexagonal Mg2 Ni Hx # # CIF by ICSD-for-WWW, Copyright 2003 FIZ-Karlsruhe & A.W.Hewat # NOT TO BE PUBLISHED IN ANY FORM. See data_ ICSD _database_code_ICSD _audit_creation_date _chemical_name_systematic 'Magnesium nickel (2/1)' _chemical_formula_structural 'Mg2 Ni' _chemical_formula_sum 'Mg2 Ni1' _publ_section_title loop_ _citation_id _citation_journal_abbrev _citation_year _citation_journal_volume _citation_page_first _citation_page_last _citation_journal_id_ASTM primary 'Acta Chemica Scandinavica, Series A: (28' ACAPCT _publ_author_name Noreus, D.Werner, P.-E. _cell_length_a (2) _cell_length_b _cell_length_c (5) _cell_angle_alpha _cell_angle_beta _cell_angle_gamma _cell_volume _cell_formula_units_Z _symmetry_space_group_name_H-M 'P ' _symmetry_Int_Tables_number _refine_ls_R_factor_all _symmetry_equiv_pos_site_id _symmetry_equiv_pos_as_xyz 1 'x, x-y, -z+1/3' 2 '-x+y, y, -z' 3 '-y, -x, -z+2/3' 4 '-x, -x+y, -z+1/3' 5 'x-y, -y, -z' 6 'y, x, -z+2/3' 7 'x-y, x, z+1/3' 8 'y, -x+y, z+2/3' 9 '-x, -y, z' 10 '-x+y, -x, z+1/3' 11 '-y, x-y, z+2/3' 12 'x, y, z' loop_ _atom_type_symbol _atom_type_oxidation_number Mg Ni _atom_site_label _atom_site_type_symbol _atom_site_symmetry_multiplicity _atom_site_Wyckoff_symbol _atom_site_fract_x _atom_site_fract_y _atom_site_fract_z _atom_site_B_iso_or_equiv _atom_site_occupancy Mg1 Mg0+ 6 f (2) Mg2 Mg0+ 6 i (6) Ni1 Ni0+ 3 b Ni2 Ni0+ 3 d _atom_site_aniso_label _atom_site_aniso_type_symbol _atom_site_aniso_U_11 _atom_site_aniso_U_22 _atom_site_aniso_U_33 _atom_site_aniso_U_12 _atom_site_aniso_U_13 _atom_site_aniso_U_23 Mg1 Mg (5) 0.69(5) 0.69(5) 0 0 0 Mg2 Mg (5) 0.53(5) 0.53(5) 0 0 0 Ni1 Ni (4) 0.73(4) 0.73(4) 0 0 0 Ni2 Ni (4) 0.82(4) 0.82(4) 0 0 0 #End of data_ ICSD cif file

7 Geometry or Nuclear Coordinates {RA}
Cartesian coordinates {xA, yA, zA} Z-matrix (internal coordinates) {rA, A, A} Fractional coordinates (in crystals) {xA/a, yA/b, zA/c}

8

9

10 Crystal (Periodic Structure w Translational Symmetry)
4/mmm mmm 6/mmm 3m 2/m 1

11 Crystal Structure Im3m Fe, V, K, Bi, etc. Fm3m
Au, Ag, Pt, Cu, Ni, Pd, etc. P63/mmc Ru, Be, La, etc.

12 Carbon Nanotube (CNT)

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14

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19

20 Miller Index (Uniquely identifies planes or surfaces)
Practive with a simple cubic crystal (100) Step 1 : Identify the intercepts on the x- , y- and z- axes. Intercepts: a,, Step 2 : Specify the intercepts in fractional coordinates. Fractional intercepts: 1,, Step 3 : Take the reciprocals of the fractional intercepts. Reciprocals: 1,0,0 Coordinates are converted to fractional coordinates by dividing by the respective cell-dimension. (Example) A point (x,y,z) in a unit cell of dimensions a x b x c  has fractional coordinates of (x/a, y/b, z/c).

21 (110) (111) (211)

22 fcc unit cell (100) face fcc unit cell (110) face fcc unit cell (111) face

23 bcc unit cell (100) face bcc unit cell (110) face hcp unit cell (0001) face

24 High Miller Index surfaces:
most likely terraces + steps fcc(775)

25 Surface Reconstruction
Even single crystal surfaces will not exhibit the ideal geometry of atoms to be expected by truncating the bulk structure of the solid parallel to a particular plane. Difference between the real structure and the ideal structure may be imperceptibly small (surface relaxation ) may be much more marked and involve a change in the surface periodicity (surface reconstruction ) * Adsorbate-induced reconstruction

26 Si(100)-(2x1) reconstruction

27

28 Si(100) c(2x4) imaged at T = 120 K. At temperatures < 150 K the dimer row reconstruction of Si(100) is replaced by the honeycomb pattern of the c(2x4)-reconstruction (2nd order phase transition (2x1)c(2x4)). (20 nm x 20 nm)

29 Si(111)-(7x7) reconstruction

30

31 Adsorption Coverage (Packing) Surface Overlayer: Wood’s notation
fcc (100) face fcc (110) face fcc (111) face

32 fcc (100) face

33 fcc (110) face

34 fcc (111) face

35 Surface Overlayer: Matrix notation

36 Adsorption Sites fcc (100) face fcc (111) face hcp (0001) face
H(4-fold) fcc H(3-fold) O(1-fold) hcp H(3-fold) O(1-fold) B(2-fold) B(2-fold)

37 CH3S/Au(111)

38 A variety of imperfections can also afflict single crystals
Point defects

39 A variety of imperfections can also afflict single crystals
Line defects Edge dislocation Screw dislocation

40 Interstitials accommodate other species: FCC

41 Interstitials accommodate other species: HCP

42 Interstitials accommodate other species: BCC

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