suementary inrmatindiaminomethoxy)ethane-1,2-diamine o ho nh2 oh 2-amino-2-hydroxyacetic acid oh ho...

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NATURE CHEMISTRY | www.nature.com/naturechemistry 1 SUPPLEMENTARY INFORMATION DOI: 10.1038/NCHEM.2099 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 = Nk B T + 1 3 r i F i i , where r i is the atomic position vector from the sphere center, F i 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.

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Page 1: SUEMENTARY INRMATINdiaminomethoxy)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

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. 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.

© 2014 Macmillan Publishers Limited. All rights reserved.

Page 2: SUEMENTARY INRMATINdiaminomethoxy)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

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)

(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

© 2014 Macmillan Publishers Limited. All rights reserved.

Page 3: SUEMENTARY INRMATINdiaminomethoxy)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

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.

Page 4: SUEMENTARY INRMATINdiaminomethoxy)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

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.