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!

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, …

ICSD: Inorganic Crystal Structure Database

Coordinates: Cartesian / Fractional / Internal

############################################################################### # Noreus, D.Werner, P.-E. (1982) # Acta Chemica Scandinavica, Series A: (28,1974-) 36, 847-851 # Structural studies of hexagonal Mg2 Ni Hx # # CIF by ICSD-for-WWW, Copyright 2003 FIZ-Karlsruhe & A.W.Hewat (hewat@ill.fr) # NOT TO BE PUBLISHED IN ANY FORM. See http://icsd.ill.fr/icsd/conditions.html data_104839-ICSD _database_code_ICSD 104839 _audit_creation_date 2004-10-01 _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' 1982 36 847 851 ACAPCT _publ_author_name Noreus, D.Werner, P.-E. _cell_length_a 5.2107(2) _cell_length_b 5.2107 _cell_length_c 13.2437(5) _cell_angle_alpha 90. _cell_angle_beta 90. _cell_angle_gamma 120. _cell_volume 311.411 _cell_formula_units_Z 6 _symmetry_space_group_name_H-M 'P 62 2 2' _symmetry_Int_Tables_number 180 _refine_ls_R_factor_all 0.0316 _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 Mg0+ 0. Ni0+ 0. _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 0.5 0 0.1158(2) 0.0 1. Mg2 Mg0+ 6 i 0.1626(6) 0.3252 0 0.0 1. Ni1 Ni0+ 3 b 0 0 0.5 0.0 1. Ni2 Ni0+ 3 d 0.5 0 0.5 0.0 1. _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 Mg0+ 0.69(5) 0.69(5) 0.69(5) 0 0 0 Mg2 Mg0+ 0.53(5) 0.53(5) 0.53(5) 0 0 0 Ni1 Ni0+ 0.73(4) 0.73(4) 0.73(4) 0 0 0 Ni2 Ni0+ 0.82(4) 0.82(4) 0.82(4) 0 0 0 #End of data_104839-ICSD cif file

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}

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

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

Carbon Nanotube (CNT)

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).

(110) (111) (211)

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

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

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

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

Si(100)-(2x1) reconstruction

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)

Si(111)-(7x7) reconstruction

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

fcc (100) face

fcc (110) face

fcc (111) face

Surface Overlayer: Matrix notation

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)

CH3S/Au(111)

A variety of imperfections can also afflict single crystals Point defects

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

Interstitials accommodate other species: FCC

Interstitials accommodate other species: HCP

Interstitials accommodate other species: BCC