periodic model build-up outline learn about crystals… (hw) learn about materials studio… search...
TRANSCRIPT
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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!
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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, …
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ICSD: Inorganic Crystal
Structure Database
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• Coordinates: Cartesian / Fractional / Internal
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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studies of hexagonal Mg2 Ni Hx# # CIF by ICSD-for-WWW, Copyright 2003 FIZ-Karlsruhe & A.W.Hewat ([email protected])# NOT TO BE PUBLISHED IN ANY FORM.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
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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}
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Crystal (Periodic Structure w Translational Symmetry)
1
m3m
4/mmm
mmm
6/mmm 3m
2/m
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Au, Ag, Pt, Cu, Ni, Pd, etc.
Fe, V, K, Bi, etc.
Ru, Be, La, etc.
Im3m
Fm3m
P63/mmc
Crystal Structure
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Carbon Nanotube (CNT)
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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)
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(110)(111)
(211)
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fcc unit cell (100) face
fcc unit cell (110) face
fcc unit cell (111) face
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bcc unit cell (100) face
bcc unit cell (110) face
hcp unit cell (0001) face
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High Miller Index surfaces: most likely terraces + steps
fcc(775)
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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
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Si(100)-(2x1) reconstruction
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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)
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Si(111)-(7x7) reconstruction
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Adsorption Coverage (Packing)
Surface Overlayer: Wood’s notation
fcc (100) face fcc (110) face fcc (111) face
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fcc (100) face
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fcc (110) face
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fcc (111) face
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Surface Overlayer: Matrix notation
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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
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CH3S/Au(111)
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A variety of imperfectionscan also afflict single crystals
Point defects
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A variety of imperfectionscan also afflict single crystals
Line defects
Edge dislocation Screw dislocation
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Interstitials accommodate other species: FCC
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Interstitials accommodate other species: HCP
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Interstitials accommodate other species: BCC