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Supplementary Material: Discovering chemistry with an ab initio nanoreactor
Lee-Ping Wang, Alexey Titov, Robert McGibbon, Fang Liu,
Vijay S. Pande and Todd J. Martínez
Supplementary Figure 1: Time trace of simulation
conditions in the first 20 picoseconds of the “Urey-
Miller” nanoreactor simulation. Top: Radius of the
spherical simulation boundary in Angstrom, showing
the time-dependent rectangular waveform. Middle:
Measured simulation temperature calculated from the
kinetic energy. The thermostat temperature is 2000
K. Bottom: Measured simulation pressure calculated
using the virial equation:
PV = NkBT +13
ri ⋅Fii∑ ,
where ri is the atomic position vector from the sphere
center, Fi is the force component arising from the
interatomic interactions, V is the sphere volume, and
T is the thermostat temperature. A Hanning window
of 51 time steps (25 fs) is used to smooth out high-
frequency artifacts in the pressure from bond
vibrations. The effect of the sphere radius on the
ideal gas part of the pressure is 0.8 GPa, which is
small compared to the temporal oscillations.
Supplementary Figure 2: Summary of reaction
statistics for the “Urey-Miller” nanoreactor
simulation.
Top: Three-dimensional representation; the bar
heights represent the number of distinct reactions,
binned by reaction energy and barrier height. The
bar colors represent the maximum number of
repetitions for any one reaction belonging to that bin.
Bottom: Two-dimensional representation; each
distinct reaction is represented by a circle. The circle
size and color corresponds to the number times each
distinct reaction was observed.
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Supplementary Figure 3: A selection of reaction
products discovered from the acetylene nanoreactor
simulation including linear and branched conjugated
chains, allenes, aromatic rings, and a smaller number
of highly strained rings.
Supplementary Figure 4: A selection of reaction
products that were discovered from the “Urey-
Miller” nanoreactor simulation including glycine,
several unnatural amino acids, and other compounds
discussed in the main text. The molecules were
chosen to represent the diversity of chemical bonding
in the collection of discovered products.
C C
H
cyclohexa-2,5-dien-1-ylium
buta-1,2,3-trieneC
(E)-5-(deca-5,8,9-trien-1-yn-1-yl)cyclopenta-1,3-diene
C
2-vinylbicyclo[5.2.0]nona-1(9),2,3,5,7-pentaene
5-methylcyclopenta-1,3-diene
(Z)-3-allylidene-6-(but-2-yn-1-yl)-1-vinylcyclohexa-1,4-diene
(R)-1-(but-3-en-2-yl)cyclopenta-1,3-diene
H
H
C
C
C
(3S,6s)-3-methyl-6-((1E,4S,6R,11E)-3-methylene-4-((1E,3E,5Z)-2-(propa-1,2-dien-1-yl)octa-1,3,5-trien-7-yn-1-yl)tetradeca-1,5,6,8,9,11-hexaen-13-yn-1-yl)cyclohexa-1,4-diene
benzeneNH C O
isocyanic acid
OH
HN
O
3-oxopropanimidic acid
H2N
NH2NH
O
NH2
1-(1,2-diaminoethyl)urea
NH2
NH2NH2
O NH2
1-(diaminomethoxy)ethane-1,2-diamine
O
HONH2
OH
2-amino-2-hydroxyacetic acid
OH
HO
NH2
2-aminopropane-1,1-diol
O
OH
(hydroxymethyl)carbamic acid
NH
OH
O
HONH2
NH2
2,2-diaminoacetic acid
O
HONH2
2-aminoacetic acid(glycine)
(α-hydroxyglycine)
(α-aminoglycine)
OHOH
ethane-1,2-diol(ethylene glycol)
NH2 NH2
O
urea
NH2
OH
1-aminopentan-2-ol
NH O O O
O
OH
(((hydroxymethoxy)carbonyl)oxy)methyl formimidate
H2N
OH
1-aminobutan-1-ol
O
HO NH
methylcarbamic acid
NH2O
O
N
HN
O
2-((aminooxy)carbonyl)pyrazolidin-3-one
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Supplementary Figure 5: Keto-enol isomerization
of 2-amino-2-hydroxyacetic acid to 2-aminoethene-
1,1,2-triol. This reaction is endothermic by 25
kcal/mol with a 38 kcal/mol barrier. The C-C bond
length is marked (Angstroms), showing that the
single bond has been transformed to a double bond
by the H transfer reaction. In an aqueous
environment, one expects that a similar reaction
could be catalyzed by a water molecule in place of
the ammonia molecule.
Supplementary Figure 6: Hydration reaction of
formaldehyde to methanediol with catalytic water
and ammonia molecules. Distances between reacting
pairs are labeled (in Angstrom).
Supplementary Figure 7: C-N to C-O bonding
rearrangement in 1-(1,2-diaminoethyl) urea.
Supplementary Figure 8: 2+2 addition of isocyanic
acid to ethanol, yielding a disubstituted oxetane
species.
Supplementary Figure 9: Carbonic acid-catalyzed
cleavage of one oxetane C-O bond from the product
in the reaction shown in Figure S6 to yield 3-
oxopropanimidic acid.
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Supplementary Video 1: Animation of nanoreactor
simulation on the acetylene system with automatic
recognition and highlighting of newly discovered
compounds.
Supplementary Video 2: Three-dimensional rotation
of Figure 2 showing reaction pyramid in higher
detail.
© 2014 Macmillan Publishers Limited. All rights reserved.