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Can someone suggest me a method to generate a beta cristobalite structure with atoms less than 200.? I tried VMD's inorganic builder tool but so far unsuccessful.

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1 Answer 1

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This image was produced with VESTA using the CIF bellow. It has 74 atoms:

CIF file:

#(C) 2023 by FIZ Karlsruhe - Leibniz Institute for Information Infrastructure.  All rights reserved.
data_77458-ICSD
_database_code_ICSD 77458
_audit_creation_date 2003-04-01
_audit_update_record 2012-02-01
_chemical_name_common 'Silicon oxide'
_chemical_formula_structural 'Si O2'
_chemical_formula_sum 'O2 Si1'
_chemical_name_structure_type Cristobalite(high)#SiO2
_chemical_name_mineral "'Cristobalite beta'"
_exptl_crystal_density_diffrn 2.21
_diffrn_ambient_temperature 573.
_citation_title

;
Landau free energy and order parameter behaviour of the alpha/beta phase
transition in cristobalite
;
loop_
_citation_id
_citation_journal_full
_citation_year
_citation_journal_volume
_citation_page_first
_citation_page_last
_citation_journal_id_ASTM
primary 'Zeitschrift fuer Kristallographie' 1992 201 125 145 ZEKRDZ
loop_
_citation_author_citation_id
_citation_author_name
primary 'Schmahl, W.W.'
primary 'Swainson, I.P.'
primary 'Dove, M.T.'
primary 'Graeme-Barber, A.'
_cell_length_a 7.12637(1)
_cell_length_b 7.12637
_cell_length_c 7.12637
_cell_angle_alpha 90.
_cell_angle_beta 90.
_cell_angle_gamma 90.
_cell_volume 361.91
_cell_formula_units_Z 8
_space_group_name_H-M_alt 'F d -3 m S'
_space_group_IT_number 227
loop_
_space_group_symop_id
_space_group_symop_operation_xyz
1 'z+1/4, y+1/4, -x+1/4'
2 'y+1/4, x+1/4, -z+1/4'
3 'x+1/4, z+1/4, -y+1/4'
4 'z+1/4, x+1/4, -y+1/4'
5 'y+1/4, z+1/4, -x+1/4'
6 'x+1/4, y+1/4, -z+1/4'
7 'z+1/4, -y+1/4, x+1/4'
8 'y+1/4, -x+1/4, z+1/4'
9 'x+1/4, -z+1/4, y+1/4'
10 'z+1/4, -x+1/4, y+1/4'
11 'y+1/4, -z+1/4, x+1/4'
12 'x+1/4, -y+1/4, z+1/4'
13 '-z+1/4, y+1/4, x+1/4'
14 '-y+1/4, x+1/4, z+1/4'
15 '-x+1/4, z+1/4, y+1/4'
16 '-z+1/4, x+1/4, y+1/4'
17 '-y+1/4, z+1/4, x+1/4'
18 '-x+1/4, y+1/4, z+1/4'
19 '-z+1/4, -y+1/4, -x+1/4'
20 '-y+1/4, -x+1/4, -z+1/4'
21 '-x+1/4, -z+1/4, -y+1/4'
22 '-z+1/4, -x+1/4, -y+1/4'
23 '-y+1/4, -z+1/4, -x+1/4'
24 '-x+1/4, -y+1/4, -z+1/4'
25 '-z, -y, x'
26 '-y, -x, z'
27 '-x, -z, y'
28 '-z, -x, y'
29 '-y, -z, x'
30 '-x, -y, z'
31 '-z, y, -x'
32 '-y, x, -z'
33 '-x, z, -y'
34 '-z, x, -y'
35 '-y, z, -x'
36 '-x, y, -z'
37 'z, -y, -x'
38 'y, -x, -z'
39 'x, -z, -y'
40 'z, -x, -y'
41 'y, -z, -x'
42 'x, -y, -z'
43 'z, y, x'
44 'y, x, z'
45 'x, z, y'
46 'z, x, y'
47 'y, z, x'
48 'x, y, z'
49 'z+1/4, y+3/4, -x+3/4'
50 'y+1/4, x+3/4, -z+3/4'
51 'x+1/4, z+3/4, -y+3/4'
52 'z+1/4, x+3/4, -y+3/4'
53 'y+1/4, z+3/4, -x+3/4'
54 'x+1/4, y+3/4, -z+3/4'
55 'z+1/4, -y+3/4, x+3/4'
56 'y+1/4, -x+3/4, z+3/4'
57 'x+1/4, -z+3/4, y+3/4'
58 'z+1/4, -x+3/4, y+3/4'
59 'y+1/4, -z+3/4, x+3/4'
60 'x+1/4, -y+3/4, z+3/4'
61 '-z+1/4, y+3/4, x+3/4'
62 '-y+1/4, x+3/4, z+3/4'
63 '-x+1/4, z+3/4, y+3/4'
64 '-z+1/4, x+3/4, y+3/4'
65 '-y+1/4, z+3/4, x+3/4'
66 '-x+1/4, y+3/4, z+3/4'
67 '-z+1/4, -y+3/4, -x+3/4'
68 '-y+1/4, -x+3/4, -z+3/4'
69 '-x+1/4, -z+3/4, -y+3/4'
70 '-z+1/4, -x+3/4, -y+3/4'
71 '-y+1/4, -z+3/4, -x+3/4'
72 '-x+1/4, -y+3/4, -z+3/4'
73 '-z, -y+1/2, x+1/2'
74 '-y, -x+1/2, z+1/2'
75 '-x, -z+1/2, y+1/2'
76 '-z, -x+1/2, y+1/2'
77 '-y, -z+1/2, x+1/2'
78 '-x, -y+1/2, z+1/2'
79 '-z, y+1/2, -x+1/2'
80 '-y, x+1/2, -z+1/2'
81 '-x, z+1/2, -y+1/2'
82 '-z, x+1/2, -y+1/2'
83 '-y, z+1/2, -x+1/2'
84 '-x, y+1/2, -z+1/2'
85 'z, -y+1/2, -x+1/2'
86 'y, -x+1/2, -z+1/2'
87 'x, -z+1/2, -y+1/2'
88 'z, -x+1/2, -y+1/2'
89 'y, -z+1/2, -x+1/2'
90 'x, -y+1/2, -z+1/2'
91 'z, y+1/2, x+1/2'
92 'y, x+1/2, z+1/2'
93 'x, z+1/2, y+1/2'
94 'z, x+1/2, y+1/2'
95 'y, z+1/2, x+1/2'
96 'x, y+1/2, z+1/2'
97 'z+3/4, y+1/4, -x+3/4'
98 'y+3/4, x+1/4, -z+3/4'
99 'x+3/4, z+1/4, -y+3/4'
100 'z+3/4, x+1/4, -y+3/4'
101 'y+3/4, z+1/4, -x+3/4'
102 'x+3/4, y+1/4, -z+3/4'
103 'z+3/4, -y+1/4, x+3/4'
104 'y+3/4, -x+1/4, z+3/4'
105 'x+3/4, -z+1/4, y+3/4'
106 'z+3/4, -x+1/4, y+3/4'
107 'y+3/4, -z+1/4, x+3/4'
108 'x+3/4, -y+1/4, z+3/4'
109 '-z+3/4, y+1/4, x+3/4'
110 '-y+3/4, x+1/4, z+3/4'
111 '-x+3/4, z+1/4, y+3/4'
112 '-z+3/4, x+1/4, y+3/4'
113 '-y+3/4, z+1/4, x+3/4'
114 '-x+3/4, y+1/4, z+3/4'
115 '-z+3/4, -y+1/4, -x+3/4'
116 '-y+3/4, -x+1/4, -z+3/4'
117 '-x+3/4, -z+1/4, -y+3/4'
118 '-z+3/4, -x+1/4, -y+3/4'
119 '-y+3/4, -z+1/4, -x+3/4'
120 '-x+3/4, -y+1/4, -z+3/4'
121 '-z+1/2, -y, x+1/2'
122 '-y+1/2, -x, z+1/2'
123 '-x+1/2, -z, y+1/2'
124 '-z+1/2, -x, y+1/2'
125 '-y+1/2, -z, x+1/2'
126 '-x+1/2, -y, z+1/2'
127 '-z+1/2, y, -x+1/2'
128 '-y+1/2, x, -z+1/2'
129 '-x+1/2, z, -y+1/2'
130 '-z+1/2, x, -y+1/2'
131 '-y+1/2, z, -x+1/2'
132 '-x+1/2, y, -z+1/2'
133 'z+1/2, -y, -x+1/2'
134 'y+1/2, -x, -z+1/2'
135 'x+1/2, -z, -y+1/2'
136 'z+1/2, -x, -y+1/2'
137 'y+1/2, -z, -x+1/2'
138 'x+1/2, -y, -z+1/2'
139 'z+1/2, y, x+1/2'
140 'y+1/2, x, z+1/2'
141 'x+1/2, z, y+1/2'
142 'z+1/2, x, y+1/2'
143 'y+1/2, z, x+1/2'
144 'x+1/2, y, z+1/2'
145 'z+3/4, y+3/4, -x+1/4'
146 'y+3/4, x+3/4, -z+1/4'
147 'x+3/4, z+3/4, -y+1/4'
148 'z+3/4, x+3/4, -y+1/4'
149 'y+3/4, z+3/4, -x+1/4'
150 'x+3/4, y+3/4, -z+1/4'
151 'z+3/4, -y+3/4, x+1/4'
152 'y+3/4, -x+3/4, z+1/4'
153 'x+3/4, -z+3/4, y+1/4'
154 'z+3/4, -x+3/4, y+1/4'
155 'y+3/4, -z+3/4, x+1/4'
156 'x+3/4, -y+3/4, z+1/4'
157 '-z+3/4, y+3/4, x+1/4'
158 '-y+3/4, x+3/4, z+1/4'
159 '-x+3/4, z+3/4, y+1/4'
160 '-z+3/4, x+3/4, y+1/4'
161 '-y+3/4, z+3/4, x+1/4'
162 '-x+3/4, y+3/4, z+1/4'
163 '-z+3/4, -y+3/4, -x+1/4'
164 '-y+3/4, -x+3/4, -z+1/4'
165 '-x+3/4, -z+3/4, -y+1/4'
166 '-z+3/4, -x+3/4, -y+1/4'
167 '-y+3/4, -z+3/4, -x+1/4'
168 '-x+3/4, -y+3/4, -z+1/4'
169 '-z+1/2, -y+1/2, x'
170 '-y+1/2, -x+1/2, z'
171 '-x+1/2, -z+1/2, y'
172 '-z+1/2, -x+1/2, y'
173 '-y+1/2, -z+1/2, x'
174 '-x+1/2, -y+1/2, z'
175 '-z+1/2, y+1/2, -x'
176 '-y+1/2, x+1/2, -z'
177 '-x+1/2, z+1/2, -y'
178 '-z+1/2, x+1/2, -y'
179 '-y+1/2, z+1/2, -x'
180 '-x+1/2, y+1/2, -z'
181 'z+1/2, -y+1/2, -x'
182 'y+1/2, -x+1/2, -z'
183 'x+1/2, -z+1/2, -y'
184 'z+1/2, -x+1/2, -y'
185 'y+1/2, -z+1/2, -x'
186 'x+1/2, -y+1/2, -z'
187 'z+1/2, y+1/2, x'
188 'y+1/2, x+1/2, z'
189 'x+1/2, z+1/2, y'
190 'z+1/2, x+1/2, y'
191 'y+1/2, z+1/2, x'
192 'x+1/2, y+1/2, z'
loop_
_atom_type_symbol
_atom_type_oxidation_number
Si4+ 4
O2- -2
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_occupancy
Si1 Si4+ 8 a 0 0 0 2.61(10) 1.
O1 O2- 16 c 0.125 0.125 0.125 . 1.
loop_
_atom_site_aniso_label
_atom_site_aniso_type_symbol
_atom_site_aniso_B_11
_atom_site_aniso_B_22
_atom_site_aniso_B_33
_atom_site_aniso_B_12
_atom_site_aniso_B_13
_atom_site_aniso_B_23
O1 O2- 9.64(9) 9.64 9.64 -4.34(3) -4.34 -4.34
#End of TTdata_77458-ICSD
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1
  • $\begingroup$ Do you know if there's a way to get a single dangling O bond on a surface silicon? because if i am to functionalize a surface like this, I could be getting only geminal silanols at the surface $\endgroup$
    – Xdrake
    Jul 4 at 17:05

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