SUEMENTARY INRMATIN diaminomethoxy)ethane-1,2-diamine O HO NH2 OH 2-amino-2-hydroxyacetic acid OH HO NH2 2-aminopropane-1,1-diol O OH (hydroxymethyl)carbamic acid N H OH O HO NH2 NH2
SUEMENTARY INRMATIN diaminomethoxy)ethane-1,2-diamine O HO NH2 OH 2-amino-2-hydroxyacetic acid OH HO NH2 2-aminopropane-1,1-diol O OH (hydroxymethyl)carbamic acid N H OH O HO NH2 NH2
SUEMENTARY INRMATIN diaminomethoxy)ethane-1,2-diamine O HO NH2 OH 2-amino-2-hydroxyacetic acid OH HO NH2 2-aminopropane-1,1-diol O OH (hydroxymethyl)carbamic acid N H OH O HO NH2 NH2
SUEMENTARY INRMATIN diaminomethoxy)ethane-1,2-diamine O HO NH2 OH 2-amino-2-hydroxyacetic acid OH HO NH2 2-aminopropane-1,1-diol O OH (hydroxymethyl)carbamic acid N H OH O HO NH2 NH2

SUEMENTARY INRMATIN diaminomethoxy)ethane-1,2-diamine O HO NH2 OH 2-amino-2-hydroxyacetic acid OH HO NH2 2-aminopropane-1,1-diol O OH (hydroxymethyl)carbamic acid N H OH O HO NH2 NH2

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  • NATURE CHEMISTRY | www.nature.com/naturechemistry 1

    SUPPLEMENTARY INFORMATIONDOI: 10.1038/NCHEM.2099

    Wang, et al. Nanoreactor Page 1

    Supplementary Material: Discovering chemistry with an ab initio nanoreactor

    Lee-Ping Wang, Alexey Titov, Robert McGibbon, Fang Liu,

    Vijay S. Pande and Todd J. Martnez

    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.

    2014 Macmillan Publishers Limited. All rights reserved.

  • NATURE CHEMISTRY | www.nature.com/naturechemistry 2

    SUPPLEMENTARY INFORMATIONDOI: 10.1038/NCHEM.2099

    Wang, et al. Nanoreactor Page 2

    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)

    (-hydroxyglycine)

    (-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

    2014 Macmillan Publishers Limited. All rights reserved.

  • NATURE CHEMISTRY | www.nature.com/naturechemistry 3

    SUPPLEMENTARY INFORMATIONDOI: 10.1038/NCHEM.2099

    Wang, et al. Nanoreactor Page 3

    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.

    2014 Macmillan Publishers Limited. All rights reserved.

  • NATURE CHEMISTRY | www.nature.com/naturechemistry 4

    SUPPLEMENTARY INFORMATIONDOI: 10.1038/NCHEM.2099

    Wang, et al. Nanoreactor Page 4

    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.

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