of 9
S1
Supporting Information for
Methanol Formation in
1
Hyperthermal Oxygen Collisions with Methane
2
Clathrate Ice
3
Robert W. Grayson,
a
Konstantinos P. Giapis,
a
& William A. Goddard III
*b
.
4
a
Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena
5
CA 91135 USA.
b
Materials and Process Simulation Center, California Institute of Technology,
6
Pasadena CA 91135 USA
7
Figures
8
9
Figure S-1: Orthogonal views of the mixed CH
4
clathrate slab used in simulations. Visualized
10
with VESTA software.
1
11
12
S2
13
Figure S-2: Isolated 20-member cage structure of the CH
4
clathrate. Trapping of the CH
4
is
14
favorable by 0.3 eV. Visualized with VESTA software.
1
15
16
17
Figure S-3: Orthogonal views of the CH
4
ice slab used in simulations. Visualized with VESTA
18
software.
1
19
20
S3
21
Figure S-4: Start (A,C) and end (B,D) states for two consecutive impact cycles, illustrating the
22
simulation protocol. A) a projectile (atomic oxygen) is initialized in the “projectile plane” at
23
zmax + 10 Å with random XY coordinates and a velocity vector (fixed |
V
in
|,
θ
in
; randomized
).
24
B) When the simulation transitions from NVE to NVT dynamics, the “ice cluster basis” region is
25
used to differentiate between solid and vapor phases (highlighted in green), the latter of which is
26
not thermostatted. Between B and C, the vapor is translated upward 15 Å so as not to interfere
27
with the next projectile. Any molecules in the freeze region (blue) after this step are deleted. C)
28
A new projectile is initialized. D) Any molecules reaching the freeze region, like the red-
29
highlighted H
2
O, are omitted from time integration and pairwise interactions, until they are
30
removed at the end of the iteration. The visualization was created using the VESTA software.
1
31
S4
32
Figure S-5: Angular dependence for reactive scattering O on CH
4
clathrate. Left) Yield vs impact
33
angle (relative to the surface plane) for several species. Right) Total yield to C−O and O−O bond
34
formation (left axis) and, on the right axis, average final projectile z-position (Z
f
) relative to the
35
top of the slab (Z
max
). Here, the impact angle is measured from the surface plane, so 90
o
is
36
normal incidence. Note that this is the compliment of the angle of incidence, normally defined
37
with respect to the surface normal.
38
Forcefield parameters, from Rahaman et al. (2011)
2
39
Reactive MD-force field: Glycine November 21 Rahaman 2011 Glycine Tautomerization
40
39 ! Number of general parameters
41
50.0000 !Overcoordination parameter
42
9.5469 !Overcoordination parameter
43
1.6725 !Valency angle conjugation parameter
44
1.7224 !Triple bond stabilisation parameter
45
6.8702 !Triple bond stabilisation parameter
46
60.4850 !C2-correction
47
1.0588 !Undercoordination parameter
48
4.6000 !Triple bond stabilisation parameter
49
12.1176 !Undercoordination parameter
50
13.3056 !Undercoordination parameter
51
-40.0000 !Triple bond stabilization energy
52
0.0000 !Lower Taper-radius
53
10.0000 !Upper Taper-radius
54
2.8793 !Not used
55
33.8667 !Valency undercoordination
56
6.0891 !Valency angle/lone pair parameter
57
1.0563 !Valency angle
58
2.0384 !Valency angle parameter
59
S5
6.1431 !Not used
60
6.9290 !Double bond/angle parameter
61
0.3989 !Double bond/angle parameter: overcoord
62
3.9954 !Double bond/angle parameter: overcoord
63
-2.4837 !Not used
64
5.7796 !Torsion/BO parameter
65
10.0000 !Torsion overcoordination
66
1.9487 !Torsion overcoordination
67
-1.2327 !Conjugation 0 (not used)
68
2.1645 !Conjugation
69
1.5591 !vdWaals shielding
70
0.1000 !Cutoff for bond order (*100)
71
1.7602 !Valency angle conjugation parameter
72
0.6991 !Overcoordination parameter
73
50.0000 !Overcoordination parameter
74
1.8512 !Valency/lone pair parameter
75
0.5000 !Not used
76
20.0000 !Not used
77
5.0000 !Molecular energy (not used)
78
0.0000 !Molecular energy (not used)
79
0.7903 !Valency angle conjugation parameter
80
4 ! Nr of atoms; cov.r; valency;a.m;Rvdw;Evdw;gammaEEM;cov.r2;#
81
alfa;gammavdW;valency;Eunder;Eover;chiEEM;etaEEM;n.u.
82
cov r3;Elp;Heat inc.;n.u.;n.u.;n.u.;n.u.
83
ov/un;val1;n.u.;val3,vval4
84
C 1.3817 4.0000 12.0000 1.8903 0.1838 0.6544 1.1341 4.0000
85
9.7559 2.1346 4.0000 34.9350 79.5548 5.4088 6.0000 0.0000
86
1.2114 0.0000 202.2908 8.9539 34.9289 13.5366 0.8563 0.0000
87
-2.8983 2.5000 1.0564 4.0000 2.9663 0.0000 0.0000 0.0000
88
H 0.8930 1.0000 1.0080 1.3550 0.0930 0.8203 -0.1000 1.0000
89
8.2230 33.2894 1.0000 0.0000 121.1250 3.7248 9.6093 1.0000
90
-0.1000 0.0000 55.1878 3.0408 2.4197 0.0003 1.0698 0.0000
91
-19.4571 4.2733 1.0338 1.0000 2.8793 0.0000 0.0000 0.0000
92
O 1.2450 2.0000 15.9990 2.3890 0.1000 1.0898 1.0548 6.0000
93
9.7300 13.8449 4.0000 37.5000 116.0768 8.5000 8.3122 2.0000
94
0.9049 0.4056 68.0152 3.5027 0.7640 0.0021 0.9745 0.0000
95
-3.5500 2.9000 1.0493 4.0000 2.9225 0.0000 0.0000 0.0000
96
N 1.2333 3.0000 14.0000 2.2403 0.1102 0.9928 1.1748 5.0000
97
9.8276 12.0698 4.0000 30.2790 100.0000 6.1112 6.6645 2.0000
98
1.0433 0.1000 119.9837 0.7382 6.7108 2.7268 0.9745 0.0000
99
S6
-2.0000 4.0000 1.0183 4.0000 2.8793 0.0000 0.0000 0.0000
100
10 ! Nr of bonds; Edis1;LPpen;n.u.;pbe1;pbo5;13corr;pbo6
101
pbe2;pbo3;pbo4;Etrip;pbo1;pbo2;ovcorr
102
1 1 158.2004 99.1897 78.0000 -0.7738 -0.4550 1.0000 37.6117 0.4147
103
0.4590 -0.1000 9.1628 1.0000 -0.0777 6.7268 1.0000 0.0000
104
1 2 169.4760 0.0000 0.0000 -0.6083 0.0000 1.0000 6.0000 0.7652
105
5.2290 1.0000 0.0000 1.0000 -0.0553 6.9316 0.0000 0.0000
106
2 2 153.3934 0.0000 0.0000 -0.4600 0.0000 1.0000 6.0000 0.7300
107
6.2500 1.0000 0.0000 1.0000 -0.0790 6.0552 0.0000 0.0000
108
1 3 100.9167 136.3836 65.3877 0.3895 -0.3906 1.0000 18.8159 0.6674
109
1.1202 -0.3411 9.1099 1.0000 -0.1966 5.6975 0.0000 0.0000
110
3 3 142.2858 145.0000 50.8293 0.2506 -0.1000 1.0000 29.7503 0.6051
111
0.3451 -0.1055 9.0000 1.0000 -0.1225 5.5000 1.0000 0.0000
112
1 4 165.1874 148.6965 87.7249 -1.3237 -0.3504 1.0000 27.5446 0.1473
113
0.1449 -0.2871 7.2074 1.0000 -0.2565 4.4890 1.0000 0.0000
114
3 4 130.8596 169.4551 40.0000 0.3837 -0.1639 1.0000 35.0000 0.2000
115
1.0000 -0.3579 7.0004 1.0000 -0.1193 6.8773 1.0000 0.0000
116
4 4 157.9384 82.5526 152.5336 0.4010 -0.1034 1.0000 12.4261 0.5828
117
0.1578 -0.1509 11.9186 1.0000 -0.0861 5.4271 1.0000 0.0000
118
2 3 160.0000 0.0000 0.0000 -0.5725 0.0000 1.0000 6.0000 0.5626
119
1.1150 1.0000 0.0000 0.0000 -0.0920 4.2790 0.0000 0.0000
120
2 4 208.1369 0.0000 0.0000 -0.3949 0.0000 1.0000 6.0000 0.3340
121
6.0174 1.0000 0.0000 1.0000 -0.1026 5.5235 0.0000 0.0000
122
6 ! Nr of off-diagonal terms; Ediss;Ro;gamma;rsigma;rpi;rpi2
123
1 2 0.1239 1.4004 9.8467 1.1210 -1.0000 -1.0000
124
2 3 0.0283 1.2885 10.9190 0.9215 -1.0000 -1.0000
125
2 4 0.1275 1.3000 9.8924 1.0418 -1.0000 -1.0000
126
1 3 0.0647 2.0109 10.0105 1.3177 1.2052 1.0682
127
1 4 0.1952 1.8813 9.7734 1.3434 1.2545 1.1533
128
3 4 0.1201 2.4775 9.0171 1.5285 1.0682 1.2716
129
42 ! Nr of angles;at1;at2;at3;Thetao,o;ka;kb;pv1;pv2
130
1 1 1 59.0573 30.7029 0.7606 0.0000 0.7180 6.2933 1.1244
131
1 1 2 65.7758 14.5234 6.2481 0.0000 0.5665 0.0000 1.6255
132
2 1 2 70.2607 25.2202 3.7312 0.0000 0.0050 0.0000 2.7500
133
1 2 2 0.0000 0.0000 6.0000 0.0000 0.0000 0.0000 1.0400
134
1 2 1 0.0000 3.4110 7.7350 0.0000 0.0000 0.0000 1.0400
135
2 2 2 0.0000 27.9213 5.8635 0.0000 0.0000 0.0000 1.0400
136
1 1 3 66.0686 28.5756 1.4793 0.0000 2.9950 58.6562 1.0000
137
3 1 3 84.3310 21.5172 5.4724 -1.0000 1.5183 0.0000 2.9776
138
1 1 4 66.8437 45.0000 1.2491 0.0000 1.1834 0.0000 3.0000
139
S7
3 1 4 82.7022 45.0000 0.5769 0.0000 1.1019 0.0000 1.0000
140
4 1 4 90.0000 43.1792 0.5055 0.0000 1.1155 0.0000 1.0204
141
2 1 3 64.3088 32.5434 2.1997 0.0000 0.1000 0.0000 1.2995
142
2 1 4 63.9629 41.6246 1.4921 0.0000 0.2000 0.0000 2.8070
143
1 2 4 0.0000 0.0019 6.3000 0.0000 0.0000 0.0000 1.0400
144
1 3 1 68.4903 45.0000 1.3617 0.0000 2.8294 0.0000 1.0000
145
1 3 3 80.6161 45.0000 1.4073 0.0000 1.0572 68.1072 1.4451
146
1 3 4 69.5983 45.0000 1.4248 0.0000 2.9000 0.0000 2.3286
147
3 3 3 89.9934 17.9465 1.7798 0.0000 2.9881 0.0000 1.0538
148
3 3 4 83.5202 33.7933 1.0337 0.0000 2.9000 0.0000 1.3398
149
4 3 4 67.1317 42.3748 1.7873 0.0000 3.0072 0.0000 1.5832
150
1 3 2 90.0000 7.1513 7.5000 0.0000 1.3111 0.0000 3.0000
151
2 3 3 75.6935 50.0000 2.0000 0.0000 1.0000 0.0000 1.1680
152
2 3 4 72.7348 20.1071 7.5000 0.0000 0.1000 0.0000 1.0746
153
2 3 2 85.8000 9.8453 2.2720 0.0000 2.8635 0.0000 1.5800
154
1 4 1 70.6778 12.3495 3.0486 0.0000 2.8702 0.0000 1.0000
155
1 4 3 73.9745 21.1329 2.3337 0.0000 2.8701 0.0000 1.7170
156
1 4 4 71.4579 14.0942 2.8540 0.0000 2.8701 0.0000 1.0631
157
3 4 3 74.2613 20.9008 2.8607 -18.0069 3.0701 0.0000 1.3874
158
3 4 4 74.2615 27.8669 1.6736 -0.9193 3.0117 0.0000 1.4381
159
4 4 4 73.3189 24.9685 2.2561 0.0000 2.9983 0.0000 2.1573
160
1 4 2 70.2498 13.6111 2.6311 0.0000 0.2025 0.0000 1.0000
161
2 4 3 74.5739 45.0000 1.4078 0.0000 0.3956 0.0000 3.0000
162
2 4 4 79.7136 45.0000 0.5316 0.0000 0.5437 0.0000 1.0000
163
2 4 2 80.2201 6.8385 7.5000 0.0000 0.1000 0.0000 1.0000
164
1 2 3 0.0000 8.9481 0.5983 0.0000 0.0000 0.0000 1.0000
165
1 2 4 0.0000 0.2694 2.1363 0.0000 0.0000 0.0000 1.8036
166
1 2 5 0.0000 15.0000 3.0000 0.0000 0.0000 0.0000 1.0400
167
3 2 3 0.0000 15.0000 2.8900 0.0000 0.0000 0.0000 2.8774
168
3 2 4 0.0000 1.0574 0.1000 0.0000 0.0000 0.0000 2.7676
169
4 2 4 0.0000 0.0100 1.0929 0.0000 0.0000 0.0000 2.1728
170
2 2 3 0.0000 8.5744 3.0000 0.0000 0.0000 0.0000 1.0421
171
2 2 4 0.0000 0.0019 6.0000 0.0000 0.0000 0.0000 1.0400
172
41 ! Nr of torsions;at1;at2;at3;at4;;V1;V2;V3;V2(BO);vconj;n.u;n
173
1 1 1 1 -0.2500 34.7453 0.0288 -6.3507 -1.6000 0.0000 0.0000
174
1 1 1 2 -0.2500 29.2131 0.2945 -4.9581 -2.1802 0.0000 0.0000
175
2 1 1 2 -0.2500 31.2081 0.4539 -4.8923 -2.2677 0.0000 0.0000
176
1 1 1 3 -0.5740 22.4215 0.8787 -2.7603 -1.1000 0.0000 0.0000
177
2 1 1 3 1.8164 18.8479 0.5134 -7.0513 -1.0978 0.0000 0.0000
178
3 1 1 3 -2.5000 56.1599 -1.0000 -4.3607 -0.8614 0.0000 0.0000
179
S8
1 1 3 1 2.5000 14.6490 1.0000 -2.5209 -0.9000 0.0000 0.0000
180
1 1 3 2 -2.2946 11.6826 -1.0000 -2.5000 -0.9000 0.0000 0.0000
181
2 1 3 1 -1.0402 26.8401 0.6384 -2.5000 -0.9000 0.0000 0.0000
182
2 1 3 2 -1.0000 66.0304 0.7580 -5.4593 -1.1000 0.0000 0.0000
183
1 1 3 3 1.0182 5.3409 0.1292 -4.3356 -2.0544 0.0000 0.0000
184
2 1 3 3 2.1531 45.9655 1.0000 -2.5000 -2.8274 0.0000 0.0000
185
3 1 3 1 0.6706 80.0000 -0.2443 -4.7181 -3.0437 0.0000 0.0000
186
3 1 3 2 -1.0000 91.6742 -0.5000 -3.9849 -3.0476 0.0000 0.0000
187
3 1 3 3 -1.9346 5.0000 0.6401 -3.3416 -2.7174 0.0000 0.0000
188
1 3 3 1 1.0469 4.3827 0.8149 -3.4434 -2.7536 0.0000 0.0000
189
1 3 3 2 -2.5000 -0.5181 0.0268 -5.4085 -2.9498 0.0000 0.0000
190
2 3 3 2 -2.1995 -25.0000 -1.0000 -2.6000 -0.9921 0.0000 0.0000
191
1 3 3 3 2.4118 -24.8219 0.9706 -2.5004 -0.9972 0.0000 0.0000
192
2 3 3 3 -2.5000 43.1840 -0.6826 -6.6539 -1.2407 0.0000 0.0000
193
3 3 3 3 -2.5000 -25.0000 1.0000 -2.5000 -0.9000 0.0000 0.0000
194
1 1 4 2 -1.0000 71.4280 -0.5000 -8.0000 -1.9825 0.0000 0.0000
195
2 1 4 2 -1.0000 63.9914 0.7449 -8.0000 -2.1051 0.0000 0.0000
196
3 1 4 2 -1.0000 24.9527 1.0000 -4.6063 -2.5261 0.0000 0.0000
197
3 1 1 4 1.0000 25.3373 1.0000 -4.1453 -0.9511 0.0000 0.0000
198
4 1 1 4 -1.0000 21.8427 1.0000 -4.0686 -1.7241 0.0000 0.0000
199
1 1 4 1 1.0000 83.8750 1.0000 -6.5279 -1.6589 0.0000 0.0000
200
3 1 4 1 -1.0000 48.6477 1.0000 -8.0000 -1.8038 0.0000 0.0000
201
2 1 1 4 1.0000 98.8297 -0.2745 -4.9954 -1.9000 0.0000 0.0000
202
4 1 4 2 0.5000 2.8273 -0.1650 -7.9605 -2.0202 0.0000 0.0000
203
2 1 4 1 -1.0000 92.9120 -0.4541 -7.7688 -1.5996 0.0000 0.0000
204
0 1 2 0 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000
205
0 2 2 0 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000 0.0000
206
0 2 3 0 0.0000 0.1000 0.0200 -2.5415 0.0000 0.0000 0.0000
207
0 1 1 0 0.0000 50.0000 0.3000 -4.0000 -2.0000 0.0000 0.0000
208
0 3 3 0 0.5511 25.4150 1.1330 -5.1903 -1.0000 0.0000 0.0000
209
0 1 4 0 0.2176 40.4126 0.3535 -3.9875 -2.0051 0.0000 0.0000
210
0 2 4 0 0.0000 0.1032 0.3000 -5.0965 0.0000 0.0000 0.0000
211
0 3 4 0 1.1397 61.3225 0.5139 -3.8507 -2.7831 0.0000 0.0000
212
0 4 4 0 0.7265 44.3155 1.0000 -4.4046 -2.0000 0.0000 0.0000
213
4 1 4 4 -0.0949 8.7582 0.3310 -7.9430 -2.0000 0.0000 0.0000
214
4 ! Nr of hydrogen bonds;at1;at2;at3;Rhb;Dehb;vhb1
215
3 2 3 2.1200 -3.5800 1.4500 19.5000
216
3 2 4 2.1215 -7.5000 1.4500 19.5000
217
4 2 3 1.7500 -4.3286 1.4500 19.5000
218
4 2 4 2.4000 -2.3575 1.4500 19.5000
219
S9
References
220
1. Momma, K. & Izumi, F.
VESTA 3
for three-dimensional visualization of crystal, volumetric and
221
morphology data.
J Appl Crystallogr
44
, 1272–1276 (2011).
222
2. Rahaman, O., van Duin, A. C. T., Goddard, W. A. & Doren, D. J. Development of a ReaxFF
223
Reactive Force Field for Glycine and Application to Solvent Effect and Tautomerization.
J.
224
Phys. Chem. B
115
, 249–261 (2011).
225
226