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

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_numberMg0+ 0.Ni0+ 0. loop__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_occupancyMg1 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.loop__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_23Mg1 Mg0+ 0.69(5) 0.69(5) 0.69(5) 0 0 0Mg2 Mg0+ 0.53(5) 0.53(5) 0.53(5) 0 0 0Ni1 Ni0+ 0.73(4) 0.73(4) 0.73(4) 0 0 0Ni2 Ni0+ 0.82(4) 0.82(4) 0.82(4) 0 0 0#End of data_104839-ICSD

################################################################################ 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studies of hexagonal Mg2 Ni Hx# # CIF by ICSD-for-WWW, Copyright 2003 FIZ-Karlsruhe & A.W.Hewat (hewat@ill.fr)# NOT TO BE PUBLISHED IN ANY FORM.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 'Mg2 Ni1'loop__citation_id_citation_journal_abbrev_citation_year_citation_journal_volume_citation_page_first_citation_page_last_citation_journal_id_ASTMprimary 'Acta Chemica Scandinavica, Series A: (28' 1982 36 847 851 ACAPCTloop__publ_author_nameNoreus, 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 0.0316loop__symmetry_equiv_pos_site_id_symmetry_equiv_pos_as_xyz

cif file

Geometry or Nuclear Coordinates {RA}

• Fractional coordinates (in crystals) {xA/a, yA/b, zA/c}

• Cartesian coordinates {xA, yA, zA}

• Z-matrix (internal coordinates) {rA, A, A}

Crystal (Periodic Structure w Translational Symmetry)

1

m3m

4/mmm

mmm

6/mmm 3m

2/m

Au, Ag, Pt, Cu, Ni, Pd, etc.

Fe, V, K, Bi, etc.

Ru, Be, La, etc.

Im3m

Fm3m

P63/mmc

Crystal Structure

Carbon Nanotube (CNT)

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

Miller Index (Uniquely identifies planes or surfaces)Practive with a simple cubic crystal

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).

(100)

(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)

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

Surface 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

fcc (100) face fcc (111) face

O(1-fold) O(1-fold)B(2-fold) B(2-fold)

fcc H(3-fold)

hcp H(3-fold)

H(4-fold)

hcp (0001) face

Adsorption Sites

CH3S/Au(111)

A variety of imperfectionscan also afflict single crystals

Point defects

A variety of imperfectionscan 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