SUEMENTARY INRMATIN - Nature · and HRMS on Bruker MicroTOF-Q, both with electrospray ionization. Elemental analysis was performed on ThermoFisher Scientific Flash 2000 with absolute

NATURE CHEMISTRY | www.nature.com/naturechemistry 1

SUPPLEMENTARY INFORMATIONDOI: 10.1038/NCHEM.2057

S1

Supplementary Information

Dynamic covalent chemistry of bisimines at the solid/liquid

interface monitored by scanning tunnelling microscopy

By

Artur Ciesielski, Mohamed El Garah, Sébastien Haar, Petr Kovaříček, Jean-Marie Lehn* and

Paolo Samorì*

ISIS & icFRC, Université de Strasbourg & CNRS, 8 allée Gaspard Monge, 67000 Strasbourg, France.

E-mail: [email protected], [email protected]

Table of content

1. Instrumentation S-2

2. Ex situ synthesis S-2

3. Adsorption end translational entropy calculations S-4

4. Scanning Tunnelling Microscopy experiments S-7

4.1 Experimental details S-7

4.2 Timescale of STM images S-9

4.3 Additional STM experiments S-10

4.3.1 Real-time bis-transimination S-10

4.3.2 Selective adsorption-induced pattern formation S-11

4.3.3 Adsorption-induced dynamic pattern selection S-12

5. NMR experiments S-13

5.1 A + B condensation S-13

5.2 A2B2 + B6 bis-transimination S-19

5.3 Selection in bis-imine A2Bx formation in solution S-22

6. HPLC experiments S-25

7. References S-26

S1

Supplementary Information

Dynamic covalent chemistry of bis-imines at the solid-liquid

interface monitored by scanning tunnelling microscopy

By

Artur Ciesielski, Mohamed El Garah, Sébastien Haar, Petr Kovaříček, Jean-Marie Lehn* and

Paolo Samorì*

ISIS & icFRC, Université de Strasbourg & CNRS, 8 allée Gaspard Monge, 67000 Strasbourg, France.

E-mail: [email protected], [email protected]

Table of content

1. Instrumentation S-2

2. Ex situ synthesis S-2

3. Adsorption end translational entropy calculations S-4

4. Scanning Tunnelling Microscopy experiments S-7

4.1 Experimental details S-7

4.2 Timescale of STM images S-9

4.3 Additional STM experiments S-10

4.3.1 Real-time bis-transimination S-10

4.3.2 Selective adsorption-induced pattern formation S-11

4.3.3 Adsorption-induced dynamic pattern selection S-12

5. NMR experiments S-13

5.1 A + B condensation S-13

5.2 A2B2 + B6 bis-transimination S-19

5.3 Selection in bis-imine A2Bx formation in solution S-22

6. HPLC experiments S-25

7. References S-26

© 2014 Macmillan Publishers Limited. All rights reserved.



S2

1. Instrumentation

NMR spectra were measured on Bruker Avance III (resonance frequencies 400.14

MHz for 1H and 100.62 MHZ for 13C) and Bruker Avance I (resonance frequencies

500.13 MHz for 1H and 125.76 MHZ for 13C). 600 MHz 1H-NMR spectra were acquired

on Bruker Avance III spectrometer (resonance frequency 600.13 MHz for 1H). The

spectra were referenced on residual solvent signal according to Nudelman et al.1

Deuterated solvents were purchased from Euriso-TOP and used without further

purification. Reagents and solvents were purchased from Sigma-Aldrich and Carlo Erba

and used without further purification. Mass spectra were obtained on Bruker MicroTOF

and HRMS on Bruker MicroTOF-Q, both with electrospray ionization. Elemental

analysis was performed on ThermoFisher Scientific Flash 2000 with absolute precision of

0.3 %. Melting points were measured on a Büchi Melting Point B-540 apparatus and

temperature data are uncorrected. HPLC analysis was performed on an Agilent 1220

Infinity HPLC instrument equipped with an Agilent Zorbax SB-Aq 5 um, 4.6x250 mm

column, using a water/acetonitrile gradient for elution (flow 1 mL/min, both solvents

with 0.01 % TFA, gradient program in Table). The analysis was repeated 5 times, run 1

was ignored and the signal area was averaged for runs 2-5 for calculation).

Time Water Acetonitrile

0 min 95 5

16 min 5 95

20 min 5 95

20.2 min 95 5

25 min 95 5

2. Ex situ synthesis

4-Hexadecyloxybenzaldehyde (A): In 100 mL of dry DMF 4-

hydroxybenzaldehyde (7.00 g, 57.3 mmol) was diluted and 2.50 g of sodium hydride (as

60 % dispersion in oil, 1.1 eq.) was added. When gas evolution ceased the mixture was

allowed to cool back to RT, then 19.25 g of n-hexadecylbromide was added via syringe

and reaction was stirred overnight at RT. Then 150 mL of water was added and mixture




S3

was extracted 3 x 200 mL of toluene, combined organic extracts were dried over

magnesium sulfate and evaporated on rotary evaporator. Pure product was obtained by

column chromatography on silica using petrolether / ethyl acetate (99:1 to 70: 30) as

eluent. Yield: 5.73 g (29 %). Analysis consistent with literature.2 1H-NMR (500 MHz, CDCl3): 10.12 (s, 1 H), 8.07 (d, J=8.70 Hz, 2 H), 7.23 (d, J=8.70

Hz, 2 H), 4.28 (t, J=6.58 Hz, 2 H), 2.05 (m, 2 H), 1.71 (m, 2 H), 1.50 (m, 24 H), 1.12 (t,

J=6.95 Hz, 3 H) 13C-NMR (125 MHz, CDCl3): 190.84, 164.28, 132.00, 129.72, 114.74, 68.43, 31.95,

29.73, 29.72, 29.72, 29.70, 29.69, 29.68, 29.61, 29.58, 29.40, 29.37, 29.07, 25.98, 22.72,

14.16

Elemental analysis: calc. C 79.71 %, H 11.05 %; found C 79.41 %, H 10.50 %.

MS: calc. 346.29, found 369.27 [M+Na]

N,N’-bis((4-hexadecyloxy)benzylidene)-α,ω-diamines

Compound A2B2, A2B6 and A2B12 were synthesized according to published protocol.3

Diamine (1.44 mmol) was mixed with two equivalents of 4-hexadecyloxybenzaldehyde

(A) (1.00 g, 2.89 mmol) in 100 mL of ethanol and refluxed for 2 hours. Reaction mixture

was then evaporated to dryness and pure product was obtained by recrystallization of the

crude from ethanol.

N,N’-bis((4-hexadecyloxy)benzylidene)-1,2-diaminoethane (A2B2)

Yield: 78 % 1H-NMR (400 MHz, CDCl3): 8.22 (s, 2H), 7.64 (d, J=8.73 Hz, 4 H), 6.90 (d, J=8.73 Hz,

4 H), 3.99 (t, J=6.61 Hz, 4 H), 3.93 (s, 4H), 1.80 (m, 4 H), 1.46 (m, 4 H), 1.27 (m, 48 H),

0.90 (t, J=6.81 Hz, 6 H) 13C-NMR (100 MHz, CDCl3): 162.14, 161.17, 129.64, 128.81, 114.40, 68.08, 61.80,

31.98, 29.76, 29.72, 29.66, 29.63, 29.44, 29.21, 29.08, 26.05, 26.00, 22.77, 14.23

Elemental analysis: calc. C 80.39 %, H 11.24 %, N 3.91 %; found C 80.51 %, H 11.14 %,

N 3.84 %.

MS: calc. 716.622, found 717.627 [M+H]

m.p.: 90 °C




S4

N,N’-bis((4-hexadecyloxy)benzylidene)-1,6-diaminohexane (A2B6)

Yield: 70 % 1H-NMR (500 MHz, CDCl3): 8.15 (s, 2 H), 7.61 (d, J=8.70 Hz, 4 H), 6.88 (d, J=8.70 Hz,

4 H), 3.95 (t, J=6.58 Hz, 4 H), 3.54 (t, J=6.88 Hz, 4 H), 1.76 (m, 4 H), 1.67 (m, 4 H), 1.23

(m, 56 H), 0.86 (t, J=6.90 Hz, 6 H) 13C-NMR (125 MHz, CDCl3): 161.08, 160.18, 129.52, 129.06, 114.47, 114.46, 68.09,

61.65, 31.96, 31.00, 29.74, 29.73, 29.71, 29.70, 29.66, 29.63, 29.60, 29.42, 29.40, 29.22,

27.19, 26.04, 22.73, 14.17


N 3.56 %.

MS: calc. 772.685, found 773.683 [M+H]

m.p.: 87 °C

N,N’-bis((4-hexadecyloxy)benzylidene)-1,12-diaminododecane (A2B12)

Yield: 85 % 1H-NMR (400 MHz, CDCl3): 8.20 (s, 2H), 7.67 (d, J=7.92 Hz, 4 H), 6.92 (d, J=8.64 Hz,

4 H), 3.99 (t, J=6.56 Hz, 4 H), 3.57 (t, J=6.98 Hz, 4 H), 1.80 (m, 4 H), 1.69 (m, 4 H), 1.46

(m, 4 H), 1.32 (m, 64 H), 0.89 (t, J=6.76 Hz, 6 H) 13C-NMR (100 MHz, CDCl3): 161.09, 160.09, 129.51, 114.48, 68.11, 61.72, 31.94,

31.06, 29.70, 29.67, 29.60, 29.57, 29.47, 29.40, 29.37, 29.21, 27.37, 26.02, 22.70, 14.13


N 3.24 %.

MS: calc. 856.778, found 857.793 [M+H]

m.p.: 92 °C

3. Adsorption and translational entropy calculations

In order to determine the enthalpic contribution to the adsorption energies of α,ω-

diamines, i.e. 1,2-diaminoethene (B2), 1,6-diaminohexane (B6) and 1,12-

diaminododecane (B12), as well as 4-hexadecyloxybenzaldehyde (A) and bis-imines

N,N’-bis((4-hexadecyloxy)benzylidene)-1,2-diaminoethane (A2B2), N,N’-bis((4-

hexadecyloxy)benzylidene)-1,6-diaminohexane (A2B6), and N,N’-bis((4-




S5

hexadecyloxy)benzylidene)-1,12-diaminododecane (A2B12) molecules, several all force-

field calculations were performed with the program CHARMM4, 5 using the

implementation in the c35b1 update. Parameterization of all investigated molecules was

done through the Merck molecular force field MMFF94,6 automatic module implemented

in CHARMM. Investigated molecules have been initially placed 6Å above the graphene.

The interaction energy between the molecules and graphene was calculated by

subtracting the energy upon displacement of the molecules 100Å away from the graphene

slab, and presented in Figure S1. In such a way desorption energies were obtained, which

are comparable (nearly equal) to adsorption energies.

Figure S1 | Comparison of adsorption energies. Adsorption energies of each molecule have been

compared with the length of corresponding molecule.

Noteworthy, the hereby MMFF calculated values are the enthalpy contribution to

the free energy of physisorption of an individual molecule, which is indeed known to

occupy a given surface area. When such adsorption energy is divided by the surface area

occupied by a single molecule on HOPG, the obtained value is not surprisingly constant

within the error bars for A2B2, A2B6 and A2B12 (see Table S1), which have a

comparable molecular conformation.




S6

In general, the total entropy for the system is the sum of four different entropies:

translational (Str), rotational (Srot), vibrational (Svib), and conformational (Sconf) entropy,

therefore the total entropy can be estimated as:

dStot = dSTr + dSrot + dSvib + dSconf (E1)

One could speculate that the molecules investigated in this manuscript are

relatively small and once physisorbed on graphite surface they would undergo minor

change in their conformations. In other words, the effect of the rotational, conformational

and vibrational entropy contribution can be expected to be modest at such interface.

Despite their contribution to the total entropy is limited, this may not be negligible. It is

however clear that an important contribution to the total entropy of the system comes

from the translational entropy.

By and large, the overall entropy estimation for molecular assemblies physisorbed

at a solid-liquid interface with the required precision cannot be attained making use of

state-of-the-art current computational methods.

Table S1 | Enthalpy of adsorption of A, A2B2, A2B6 and A2B12 molecules. In blue are indicated the

values of single molecules whereas it read is when such values are divided by the area occupied by the

molecules. The principal contribution to the error bar of the adsorption enthalpy per unit area is the error

associated with the dimensions of the unit cell of a given molecule. The latter, in STM studies done at the

solid-liquid interface using a commercial set-up, cannot be below 6%.

Molecule Area [nm2]

dH [kcal mol-1]

dH [eV]

dH/A [kcal mol-1 / nm2]

dH/A [eV / nm2]

A 1.36 ± 0.43 33.59 1.45 24.69 ± 5.92 1.06 ± 0.25 A2B2 2.84 ± 0.28 59.26 2.56 20.86 ± 1.86 0.90 ± 0.08 A2B6 3.53 ± 0.35 71.76 3.11 20.32 ± 1.82 0.88 ± 0.08

A2B12 3.91 ± 0.39 81.22 3.52 20.77 ± 1.88 0.90 ± 0.08

This finding confirms that the competitive physisorption at the solid liquid interface for

A2B2, A2B6 and A2B12 forming tightly packed monolayers, as a result of the

condensations and bis-transiminations reactions, is primarily governed by entropy

contributions to the free energy of physisorption at the solid-liquid interface.




S7

4. Scanning Tunneling Microscopy (STM) experiments

4.1. Experimental details

Scanning Tunneling Microscopy (STM) measurements were performed using a

Veeco scanning tunneling microscope (multimode Nanoscope III, Veeco) at the interface

between a highly oriented pyrolitic graphite (HOPG) substrate and a supernatant solution,

thereby mapping a maximum area of 1µm × 1µm. Solution of molecules were applied to

the basal plane of the surface. For STM measurements, the substrates were glued to a

magnetic disk and an electric contact was made with silver paint (Aldrich Chemicals).

The STM tips were mechanically cut from a Pt/Ir wire (90/10, diameter 0.25 mm). The

raw STM data were processed through the application of background flattening and the

drift was corrected using the underlying graphite lattice as a reference. The lattice was

visualized by lowering the bias voltage to 20 mV and raising the current up to 65 pA.

Aldehyde A was dissolved in chloroform and diluted with 1-phenyloctane to give 0.1

mM solution. STM imaging was carried out in constant height mode without turning off

the feedback loop, to avoid tip crashes. Monolayer pattern formation was achieved by

applying onto freshly cleaved HOPG 4µL of a solution. The STM images were recorded

at room temperature once achieving a negligible thermal drift. Solutions of α,ω-diamines

were prepared by dissolving the molecules in pyridine and diluting with 1-phenyloctane

to give 0.1 mM solution (solvent composition 99 % 1-phenyloctane + 1 % pyridine). To

allow for full solubilization of all compounds, the diamines B2, B6 and B12 were first

dissolved in pyridine (10 mM) and diluted with 1-phenyloctane to obtain the desired 0.1

mM stock solution (solvent composition 99 % 1-phenyloctane + 1 % pyridine). All of the

molecular models were minimized with MMFF and processed with QuteMol

visualization software (http://qutemol.sourceforge.net).

Figure S2 shows 50×50 nm2 STM images of A2B2, A2B6 and A2B12 supramolecular structures. In most of the cases the size of domains amounts to several

hundreds of nm2.




S8

Figure S2 | Comparison of 50×50 nm2 scale STM images of monolayers formed by bis-imines A2B2 (a),

A2B6 (b) and A2B12 (c).

In only a few cases, i.e. in ca. 5% of the cases, A2B6 and A2B12 molecules were

found to self-assemble into smaller domains, as displayed in Figure S3. Noteworthy, all

bis-transimination experiments have been carried out only if the size of single domains

was exceeding 100×100 nm2.

Figure S3 | Comparison of 50×50 nm2 scale STM images of monolayers formed by bis-imines A2B6 (a),

A2B12 (b), multiple domains are clearly visible.

4.2. Timescale of STM images

All STM imaged were recorded in constant current mode with a constant speed,

i.e. the scan rate fixed at 12.2 lines/sec. Therefore, all STM (512×512 pixel) images were

recorded in 41 seconds. Detailed scan parameters are presented in the Table S2.




S9

Table S2. Scanning parameters used during the STM characterization.

Size [nm2] Frequency [Hz] Tip velocity (µm/s) Time [s]

20

12.2

0.48 41

30 0.73 41

40 0.97 41

50 01.22 41

In order to estimate the time needed to bring the reactions to completion, i.e. the

time required to achieve the complete monolayer transformation upon addition of a drop

of α,ω-diamine solution on top of existing A monolayer (condensation), and/or upon

addition of a drop of α,ω-diamines on top of existing AB monolayers (bis-

transimination), the number of recorded pictures has been correlated with the time of the

reaction taking place at the solid-liquid interface.

The time-scale of in situ A + B condensation(s)

The time of the reactions has been calculated by counting the number of pictures

acquired starting immediately after addition of 0.5 eq of α,ω-diamines, i.e. B2, B6 or B12

on top of a pre-existing monolayer of A, until the surface was fully covered by bis-imine

architecture. 20 independent experiments have been performed in order to calculate the

average time of condensations taking place at the solid-liquid interface.

The time-scale of in situ bis-transimination(s)

The time of the in situ bis-transimination reactions taking place at the solid-liquid

interface has been calculated by counting the number of pictures acquired starting

immediately after addition of 1 eq of α,ω-diamines, i.e. B2, B6 or B12 on top of a pre-

existing monolayers of AB, until the surface was fully covered by bis-imine architecture

with different B units (bis-transimination product), as further analyzed by the unit cell

parameters. 20 independent experiments (for each bis-transimination) have been




S10

performed in order to calculate the average time of bis-transiminations taking place at the

solid-liquid interface.

It is important to note, that in both types of reactions, i.e. condensation and bis-

transimination, the drop of reagent (solution of B) was intentionally placed in different

positions on the HOPG surface with respect to STM tip. In such a way we could estimate

the average time needed to completely transform the supramolecular structures.

Additionally, we performed statistical analysis on experiments where the drop was placed

in fixed position, by scanning different areas of the sample.

4.3 Additional STM experiments

4.3.1 Real-time bis-transimination

In order to cast light onto dynamic process of in situ bis-transimination, several

consecutive images have been recorded after addition of 1 eq of B12 on top of a pre-

existing monolayer of A2B2, and are shown in Figure S4. Upon addition of B12 solution,

on top the A2B2 monolayer step-wise bis-transimination was visualized by STM. Figure

S4a shows the image taken immediately after depositing a drop of B12. As evident, the

reaction rate is much faster than the scan speed of the STM, therefore the bis-

transimination cannot be seen at the single molecule level. During the continuous scan

(Fig. S4b-f) over the same sample area, the area of A2B2 domain (indicated in red in Fig.

S4) decrease, indicating the progress of bis-transimination reaction, and formation of

A2B12 domains (in blue).




S11

Figure S4 | Series of STM images showing the direct exchange reaction at the solid-liquid interface

from the A2B2 structure (in red) to A2B12 (in blue). Tunneling parameters It= 15 pA, Vt = 550 mV. The

size of the STM images (a-f) amounts to 28 × 28 nm2.

4.3.2 Selective adsorption-induced pattern formation

In order to study selective nature of adsorption-induced pattern formation at the

solid-liquid interface several independent experiments have been performed, in which a 4

µL drop (pyridine:1-phenyloctane, 1:99 vol:vol) of a mixture of A2B2, A2B6 and A2B12

(equal molar concentration – 0.1 mM) was drop-cast on HOPG surface, revealed the

formation of A2B12 patterns exclusively, confirming the selective nature of adsorption-

induced pattern formation on a surface, under thermodynamic control. In order to confirm

the selective nature of pattern formation, experiment was reproduced 10 times and each

time 1 µm2 surface area (accessible with STM) has been monitored. For each set of

experiment, A2B12 patterns were formed within tens of seconds and covered the entire

surface of graphite.




S12

4.3.3 Adsorption-induced dynamic pattern selection

Additional in situ bis-imination experiments have been performed to in order

explore the potential role of the adsorption energy (different for each A2B molecule),

acting as effector selecting/amplifying a number of a given A2B component adsorbed on

graphite surface. To this end, 4 µL drop containing a mixture of 2 eq of A and three α,ω-

diamines, i.e. B2 + B6 +B12 (1eq each) has been deposited on top of HOPG surface.

Statistical analysis of 10 independent experiments revealed that in majority of

experiments, deposition of a mixture on top of graphite surface, revealed the formation of

A2B12 patterns exclusively, however in 2 out of 10 experiments coexistence of two

structures was observed for relatively short period of time (1-3 min) as illustrated in

Figure S5.

Figure S5 | STM representative images of co-existing A2B structures. a) co-existing A2B6 and A2B12

domains, b) co-existing A2B2 and A2B12. The size of the STM images (a-b) amounts to 30 × 30 nm.

Interestingly, while the co-existence of A2B2/A2B12 and A2B6/A2B12 was

monitored in several sample areas, A2B2/A2B6 mixed structure was never observed

during STM pattern mapping, most likely related to the lowest adsorption energy given in

such system. Figure S5a shows co-existing A2B6 and A2B12 structures, which transforms

into uniform A2B12 patterns shortly after acquiring the STM image. Similar phenomenon




S13

occurs when A2B2 and A2B12 structures were investigated. Noteworthy, the highly

dynamic nature of adsorption/desorption/re-adsorption processes cannot be monitored at

the molecular-speed level; therefore intermediate states such as AB2, AB6 or AB12

cannot be observed with STM. It is important to note that such behaviour of mixed

solutions indicates that the interaction with the surface, i.e. adsorption energy, acts as

effector selecting/amplifying a given constituent of mixed solution on the surface and

also increases also its agonist in the supernatant solution.

5. NMR experiments

5.1 A + 2B condensation 1H-NMR experiments in 1-phenyloctane are rendered difficult by the poor

solubility of the bis-imines A2B2, A2B6 and A2B12 in this solvent and the formation of

gels, observable by the naked eye. On the other hand, aldehyde A is highly soluble in

phenyloctane, with a saturation concentration of 0.75 M, and remains in solution during

the entire experiment. Therefore, the decrease of the aldehyde concentration was

followed by NMR in the course of the A + B2 condensation in phenyloctane (with d3-

nitromethane as external standard in a sealed capillary), as compared to toluene, and the

conversion to imines is plotted in Graph S1. In all cases, precipitation of A2B2 was

observed when a critical concentration between 3.5 – 7 mM of A2B2 was reached. The

kinetic curves for the formation of A1B2 and the disappearance of A are consistent with a

second order kinetic model up to this point, beyond it, precipitation causes irreversible

removal of A2B2 from the reaction mixture (see Fig. S7).




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Figure S6 | 1H-NMR observation of the conversion of 4-hexadecyloxybenzaldehyde A to mono- and bis-

imines of B2. Comparison in toluene and phenyloctane at various concentrations. The curves show the

decrease of the –CHO aldehyde proton signal (8.53 ppm in phenyloctane and 9.70 ppm in toluene).

Figure S7 | 1H-NMR observation of the conversion of aldehyde A to mono-imine A1B2 and bis-imine

A2B2 in phenyloctane at 114 mM A and 57 mM B2 concentration. The red solid trace is experimental

observation of disappearance of the aldehyde CHO peak (8.53 ppm), the blue solid trace is the sum of the

emerging signals of the mono-imine A1B2 and the bis-imine A2B2 (6.86 and 6.89 ppm, respectively). Both

traces are compared with conversions calculated (dotted traces) from the second order kinetic model. The

mismatch between observed and calculated imines trace at times longer than 8x103 s is related to the

precipitation of bis-imine from the solution.




S15

Figure S8 | 1H-NMR spectra of the reaction A + B2 in phenyloctane (blue trace gives overview on the full

NMR spectrum, red trace is amplified to show the relevant reagent signals: aldehyde peak at 8.53 ppm,

mono-imine peak at 6.86 ppm, bis-imine peak at 6.89 ppm, in the aliphatic region the signal at 1.28 ppm

corresponds to free B2, two triplet at 1.69 and 2.29 ppm correspond to two methylene groups of the mono-

imine, and the singlet at 2.70 ppm corresponds to the bis-imine).

It is seen that the kinetics of condensation in toluene and phenyloctane are very

similar (slightly slower in phenyloctane). Thus, the rate of reaction in phenyloctane

cannot be higher than in toluene and the data obtained in d8-toluene are asymptotic limits

for the rate in phenyloctane. Taking into account the poor solubility in 1-phenyloctane,

the following kinetic data are therefore derived from 1H-NMR experiments in toluene.

The condensation reaction of a diamine B with the aldehyde A to form first the

mono-imine and consequently the bis-imine is described by the following general

scheme.

Figure S9 | General scheme for the condensation of aldehyde A with a diamine.




S16

As the diamine B possesses two functional groups, the actual concentration of

amino-groups B is twice as high as the diamine concentration. Taking into account the

reversibility of the reaction and the fact that the observed rate is the sum of the forward

and backward reaction ( 𝑘𝑘𝑘𝑘! = (𝑘𝑘𝑘𝑘!,! + 𝑘𝑘𝑘𝑘!,! ) connected by the equilibrium constant

(𝐾𝐾𝐾𝐾! =!!,!!!,!

), one obtains a set of differential equations:

! !!"

= −k! A− A!" B− B!" − k! A− A!" A!B− A!B!" (E2)

![!!!]!"

= k! A− A!" B− B!" − k![A− A!"][A!B− A!B!"] (E3)

![!!!]!"

= k![A− A!"][A!B− A!B!"] (E4)

The initial and boundary conditions are the initial 𝐴𝐴𝐴𝐴!,𝐵𝐵𝐵𝐵!,𝐴𝐴𝐴𝐴!𝐵𝐵𝐵𝐵!,𝐴𝐴𝐴𝐴!𝐵𝐵𝐵𝐵! and the

equilibrium concentration values 𝐴𝐴𝐴𝐴!" ,𝐵𝐵𝐵𝐵!"and 𝐴𝐴𝐴𝐴!𝐵𝐵𝐵𝐵!" which are experimentally available

by 1H-NMR. This set of differential equations can then be solved iteratively in Excel to

obtain the second order rate constants.

When aldehyde A (2 eq., 36.4 mM) is mixed with B2 diamine (1 eq., 18.2 mM) a

slow formation first of mono-imine and subsequently of bis-imine is observed in the

CH=N imine proton region (peak at 8.02 ppm for the mono-imine and at 8.10 ppm for the

bis-imine) and in the aliphatic region (peak 2.38 ppm for free ethylenediamine, triplet at

2. 89 ppm and 3.48 ppm for mono-imine, and peak 3.99 ppm for bis-imine, for NMR

traces see Figure S11).

Noteworthy, the equilibrium takes place approximately after 48 hours and

contains 80 % bis-imine, 10 % mono-imine and 10 % unreacted aldehyde. The solutions

are homogenous, even at a concentration as high as 180 mM. Kinetic experiments were

performed in d8-toluene at concentration 36.4 mM for aldehyde A and 18.2 mM for

diamine B2 (ratio aldehyde:amino-group 1:1). By plotting the integral intensity of the

corresponding signals (aldehyde 9.70 ppm, mono-imine 8.02 ppm and bis-imine 8.10

ppm) the rate constants can be determined by iteratively solving the equations E2-E4.

The values obtained for the second order rate constants (as defined in Fig. S9) are k1 =




S17

2.0 x 10-3 s-1 M-1 and k2 = 2.7 x 10-3 s-1 M-1 with very good coefficient of determination

R2 = 0.9999 (see Fig. S10).

Figure S10 | 1H-NMR observation of species formation in the reaction of two equivalents of A with 1 eq.

of B2 in d8-toluene (R2=0.9999); average of four runs; data based on the integration of the signals of

aldehyde 9.70 ppm, mono-imine 8.02 ppm and 8.10 ppm).

With the rate constants in hand, one can estimate the kinetics of the imine

formation process in the drop on the HOPG surface in the STM measurement. To fully

cover the STM surface (1 cm2) a total amount of 3.5 x 1013 of A2B2 molecules is needed

to be produced by the condensation reactions (2.5 x 1013 of A2B12), based on the area of

a unit cell. By mixing 4 µL of 0.1 mM solution of aldehyde A with 2 µL of 0.1 mM

solution of diamine B one gets 6 µL of the solution with the concentration of 6.67 x 10-5

M of aldehyde and 3.33 x 10-5 M of the diamine. This means that the required

concentration of the bis-imine A2B2 in the supernatant solution is 9.7 x 10-6 M (6.9 x 10-6

M for A2B12). From the known rate constants and initial concentrations the model given

by equations E2-E4 indicates that the reaction time needed to reach this concentration of

A2B2 is approximately 1.25 x 107 s. The fact that full surface coverage is achieved in less

than 600 seconds gives the rate acceleration by a factor of about 2 x 104.




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Figure S11 | 1H-NMR spectra of the reaction of two equivalents of A with 1 eq. of B2 in d8-toluene

(aldehyde peak at 9.70 ppm, mono-imine peak at 8.02 ppm, bis-imine peak at 8.10 ppm; in the aliphatic

region the signal at 2.38 ppm corresponds to the methylene groups of free B2, the two triplets at 2.89 and

3.48 ppm correspond to the two methylene groups of the mono-imine, and the singlet at 3.99 ppm

corresponds to the bis-imine).

To increase the solubility of the diamines (most importantly B12), 1 % of pyridine

was added to the 1-phenyloctane solvent. The kinetic experiment for the condensation of

the aldehyde A with the diamine B2 was performed in d8-toluene containing 1 % of

pyridine and compared to the experiment without pyridine. The rates of the aldehyde

conversion to imines (both mono- and bis-imines) are almost identical (see Fig. S12),

thus showing that a pyridine content up to 1 % does not affect the kinetics of the

processes discussed above.




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Figure S12 | The conversion of the aldehyde A (36.4 mM) to imines in reaction with B2 (18.2 mM),

comparison of the reaction rates in d8-toluene without and with 1 % of pyridine.

5.2 A2B2 + B6 bis-transimination

The bis-transimination, i.e. the A2B2 + B6 exchange reaction, was investigated in

toluene and followed by 1H-NMR at 600 MHz. The higher field led to partial separation

of the A1B6 and A2B6 signals, therefore, they can be deconvoluted. To the equilibrated

reaction mixtures from the imine formation experiments (see above), 1 eq of 18.2 mM

solution of B6 in d8-toluene was added (reagent ratio A:B2:B6 = 2:1:1, theoretical

concentrations 33.1 : 16.5 : 16.5 mM). The evolution of the 1H-NMR signals is shown

in Figure S13. The signals for AxB6 and B6 have not been normalized since they are due

to multiple products; they are plotted with respect to the right ordinate axis.




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Figure S13 | Signal evolution in exchange experiments followed by 600 MHz 1H-NMR. The

NMR signals are normalized for the number of protons, i.e. the signal for A2Bx is divided by two that for

B2 divided by 4 etc., so that they correspond to relative concentrations in solution. Mixed signals (B6

amine and AxB6 imine signals), due to the overlap of the signals from several species, cannot be

normalized and are plotted with respect to the right ordinate axis.

The re-equilibration of the reaction mixtures proceeds through several reactions

Figure S14 | General scheme for imine exchange processes in the A2B2 + B6 reaction.

As a result of this complex reaction network, it is difficult to establish a kinetic

model. To fully cover the 1 cm2 of HOPG surface with A2B6, 2.8 x 1013 molecules are




S21

needed (calculated from the unit cell area of a single A2B6 molecule as reported in the

main text – Table 1), which corresponds to 5.6 x 1013 of aldehyde residues. The total

amount of aldehyde molecules added is 2.4 x 1014 and thus about 23 % of the aldehyde

needs to be transformed to A2B6 to achieve full surface coverage, as observed by STM in

less than 200 seconds. The time needed to achieve this conversion in solution at 16.5 mM

concentration of B6 as followed by NMR is about 4000 s, indicating again kinetic

enhancement.

Figure S15 | 1H-NMR (at 600 MHz, aromatic region) of the signal evolution during the A2B2 + B6 imine

exchange reaction (the peaks assignment: A2B2 8.10 ppm, A1B6 8.09 ppm, A2B6 8.08 ppm, A1B2 8.02

ppm).




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Figure S16 | 1H-NMR (at 600 MHz, aliphatic region) of the signal evolution during the A2B2 + B6 imine

exchange reaction (the peaks assignment: A2B2 3.99 ppm, A1B6 3.55 ppm, A2B6 3.58 ppm, A1B2 3.48 and

2.90 ppm, B2 2.38 ppm, signal around 2.50 ppm is a mixture of the –CH2NH2 signals of B6 and A1B6).

5.3 Selection in bis-imine A2Bx formation in solution

The strong selection observed by STM on the HOPG surface was compared to

experiments in solution. In d8-toluene, the aldehyde A (4 eq.) was mixed with B2 (1 eq.,

20 mM) and B12 (1 eq., 20 mM) to favour the formation of the corresponding bis-imines

A2B2 and A2B12 over the mono-imines described in previous exchange kinetic

experiments. The mixture was heated at 60 °C overnight to reach the equilibrium. Since

precipitation of some bis-imines was observed at room temperature, the NMR spectra

were recorded at 50 °C when the solutions were homogenous. In the equilibrated mixture

the bis-imines are formed almost quantitatively, approximately 10 % of the aldehyde

remains unreacted which is reflected by approximately 10 % of the A1B2 mono-imine

formation, while the A1B12 mono-imine is present in less than 2 %. This can be due to

the proximity of sterically demanding aldehyde groups in case of the bis-imine A2B2.

The bis-imines are formed in the same amounts, thus indicating that there is no selection

for either of the bis-imines formed.




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Figure S17 | The 400 MHz 1H-NMR spectrum of the mixture of 4 eq. of aldehyde A with B2 and B12

diamines (1 eq. each, both 20 mM in d8-toluene), aliphatic part. The singlet at 3.4 ppm corresponds to the

methylene signals of the A2B2, pseudotriplet at 3.0 ppm contains =N-CH2-signals of both A1B12 and

A2B12, triplets at 2.9 and 2.3 ppm correspond to the methylene signals of the A1B2, multiplet at 1.95 ppm

correspond to the -CH2-NH2 proton of the A1B12.

Figure S18 | The aldehyde and imine section of the 400 MHz 1H-NMR spectrum of the mixture of 4 eq. of

aldehyde A with diamines B2 and B12 (1 eq. and 20 mM each). Approximately 10 % of the aldehyde

remains unreacted (9.12 ppm). The imine signals overlap and only the signal of A1B2 is separated at 7.45

ppm. Indicated integral values are correlated to the aliphatic part of the spectrum in Figure S17.




S24

In the next experiment, all three diamines B2, B6 and B12 (1 eq. and 20 mM

each) were reacted in the NMR tube with 6 eq. of aldehyde A. Again, the NMR spectra

were recorded at 50 °C to dissolve the precipitate formed in the course of the reaction.

Equilibrium was reached by heating at 60 °C overnight. In the equilibrated mixture, the

bis-imines are formed almost quantitatively, only 8 % of the aldehyde remains unreacted

which results in approximately 10 % formation of the A1B2 mono-imine while other

mono-imines are present only in < 4 % amounts. This can be due to the proximity of

sterically demanding aldehyde groups in case of the bis-imine A2B2. The bis-imines are

formed in the same amounts, thus indicating that there is no selection for either of the bis-

imines formed.

Figure S19 | The aliphatic section of the 400 MHz 1H-NMR spectrum of the mixture of 6 eq. of the

aldehyde A with diamines B2, B6 and B12 (1 eq. and 20 mM each). The singlet at 3.4 ppm corresponds to

the methylene signals of the A2B2, the multiplet at 3.0 ppm contains =N-CH2-combined signals of A1B6,

A2B6, A1B12 and A2B12, triplets at 2.9 and 2.3 ppm correspond to the methylene signals of the A1B2, the

multiplet at 1.95 ppm correspond to -CH2-NH2 protons of the A1B6 and A1B12.




S25

Figure S20 | The aldehyde and imine section of the 400 MHz 1H-NMR spectrum of the mixture of 6 eq. of

the aldehyde A with diamines B2, B6 and B12 (1 eq. and 20 mM each). Approximately 8 % of the

aldehyde (9.12 ppm) remains unreacted. The signals partially overlap: separated single at 7.45 ppm

correspond to mono-imine A1B2, the singlet at 7.50 ppm corresponds to A2B6, the singlet at 7.55 ppm

contains both A2B2 and A2B12 signals (corrected integrals obtained by signal deconvolution gives integral

intensity of 2.0 for the A2B6 at 7.50 ppm and 4.0 for the mixed A2B2 and A2B12 signal at 7.55 ppm).

Indicated integral values are correlated to the aliphatic part of the spectrum in Figure S19. The ratio of bis-

imines A2B2 : A2B6 : A2B12 is 1:1:1.

6. High-performance liquid chromatography (HPLC) experiments

HPLC was used to gain quantitative information on the distribution of the species

in a mixture of 2 eq of A and three α,ω-diamines, i.e. B2 + B6 + B12 (1 eq each). To this

end, NMR samples were reduced by Bu4NBH4 (to freeze imine exchange), acidified by

methanolic HCl, evaporated, dissolved in 0.2 mL of methanol and finally injected into the

HPLC apparatus (10 µL per run). The mixture of amines obtained from the reduction of

an equilibrated mixture of 40 mM of aldehyde A and three α,ω-diamines B2, B6 and B12

(each 20 mM) contained: 24 % A1B2, 32 % A1B6, 33 % A1B12, 1 % A2B2, 4 % A2B6




S26

and 5 % A2B12, as shown in Figure S21. The eluted fractions were collected and the

compounds were confirmed by MS analysis.

Figure S21 | HPLC chromatogram showing the distribution of species obtained from the reduction of an

equilibrated mixture of A + B2 + B6 + B12.

7. References 1. Gottlieb, H. E., Kotlyar, V., Nudelman, A. NMR Chemical Shifts of Common

Laboratory Solvents as Trace Impurities. J. Org. Chem. 62, 7512-7515 (1997). 2. Gray, G. W., Jones, B. Mesomorphism and chemical constitution. Part II. The

trans-p-n-alkoxycinnamic acids. J. Chem. Soc. Resumed 1467–1470 (1954). 3. Senapati, S., Mishra, B. K., Behera, G. B., Mahendroo, P. P. Synthesis and

Spectral Analysis of Some Schiff Bases Containing Long Alkyl Chains. Bull. Chem. Soc. Jpn. 62, 321-324 (1989).

4. Brooks, B. R., et al. Charmm - a Program for Macromolecular Energy, Minimization, and Dynamics Calculations. J. Comput. Chem. 4, 187-217 (1983).

5. Brooks, B. R., Yang, W., York, D. M., Karplus, M. CHARMM: The Biomolecular Simulation Program. et al., J. Comput. Chem. 30, 1545-1614 (2009).

6. Halgren, T. A. Merck molecular force field .1. Basis, form, scope, parameterization, and performance of MMFF94. J. Comput. Chem. 17, 490-519 (1996).


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SUEMENTARY INRMATIN - Nature · and HRMS on Bruker MicroTOF-Q, both with electrospray ionization. Elemental analysis was performed on ThermoFisher Scientific Flash 2000 with absolute