Letter Cite This: ACS Macro Lett. 2019, 8, 779−782
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About the Crystallization of Abiotic Coded Matter Benoît É ric Petit, Bernard Lotz,* and Jean-François Lutz* Université de Strasbourg, CNRS, Institut Charles Sadron, UPR22, 23 rue du Loess, 67034 Strasbourg, Cedex 2, France
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S Supporting Information *
ABSTRACT: The crystallization of digitally encoded polyurethanes was studied by electron diffraction. A series of oligomers with different primary structures was analyzed in this work. They all form hydrogen-bonding-directed lamellar single crystals with a base-centered orthorhombic unit cell. Although crystal morphology was the same in all cases, the digital coding of the oligomers has a small influence on the intersheet distance in the crystals. The crystal lattices allow calculation of the volume occupied by one basic information unit, which is in the range 148−188 Å3. Interestingly, this volume is about 3× smaller than that occupied by a coded nucleotide in a DNA double helix. Furthermore, crystallization of blends of oligourethanes with different coded primary structures was investigated. Oligomers with drastically different monomer compositions form structures that are not cocrystals but more probably segregated crystals containing distinct domains of different composition.
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lization21−27 and properties28−32 have been discussed in the literature. In this context, we describe in this communication the crystallization behavior of digitally encoded polyurethanes. In recent publications, we have reported the synthesis, sequencing and use as anticounterfeiting taggants of sequence-defined polyurethanes.33,34 In these structures, molecular coding is obtained using methylated and nonmethylated synthons that are defined as a binary alphabet.13 These coded polymers crystallize in organic solvents. Thus, the crystalline structure of polyurethanes with different primary structures was studied in this work by electron diffraction (ED). Chart 1 shows the general molecular structure of the coded polyurethanes examined in this work. The chains contain a
oded matter can be defined as an organized substance that contains molecularly encoded information. A typical example is a chromosome, which is the storage medium of genetic information. Inside chromosomes, information is stored in sequence-defined DNA chains and the volume occupied by one basic information unit (i.e., one nucleotide) is about 543 Å3.1 In general, the primary structure (i.e., tacticity and monomer sequence) of a polymer guides its structural organization.2 For instance, proteins, RNA, and man-made foldamers fold into complex organized structures, which are strongly sequence-dependent.3−5 It is different in DNA because coded monomers are confined in the interior of a double helix,1 whereas only the charged exterior is involved in higher chromosomal organization.6 Thus, the secondary structure of DNA is independent from the genome that it contains. In the emerging context of DNA data storage,7 it was recently reported that single-stranded DNA has a theoretical information density of 3.64 exabits·mm−3.8 To our knowledge, there is no example of man-made materials mimicking genetic coder matter. During the past decade, many examples of nonbiological sequence-defined polymers have been reported.9−11 In particular, recent significant progress deals with the development of so-called information-containing macromolecules,12−14 which are a promising new type of functional polymers with potential applications in data storage and anticounterfeiting technologies.15−19 However, most of the reported examples focus on the molecular encryption and decryption of these polymers. Very few studies describe the 2D or 3D organization of this new type of synthetic coded matter.20 For instance, the crystallization and cocrystallization of man-made informationcontaining macromolecules have not been reported so far, although interesting examples of precision polymers crystal© 2019 American Chemical Society
Chart 1. Molecular Structure of the Digital Polyurethanes
caproic acid end-group (α) that is a residual linker from solidphase synthesis and an OH group at the other extremity.33 They are coded using two different synthons: namely butyl carbamate (bit 0) and methyl-butyl carbamate (bit 1). The defined order of these units allows encryption of a digital Received: April 25, 2019 Accepted: June 6, 2019 Published: June 12, 2019 779
DOI: 10.1021/acsmacrolett.9b00307 ACS Macro Lett. 2019, 8, 779−782
Letter
ACS Macro Letters
Figure 1. Electron diffraction patterns and corresponding lattices obtained for homo-oligomers α000000 (a) and α111111 (b). The displayed molecular models include two repeat units per chain. Since the α111111 oligomer is not stereoregular, full and dashed gray spheres indicate areas potentially occupied by methyl groups. (c) Graph showing the evolution of intersheet distance as a function of the primary structure of the studied oligomer. The column on the right side of the graph denotes the number of 1-bits n that are included in the crystal lattice of a given oligomer. It differs from n′, which is the total number of 1-bits in the primary structure of a given oligomer. (d) Possible polymorphisms authorized by the antiparallel arrangement of the chain for oligomer α001000. Hydrogen bond are highlighted by blue dashes and lattice in the c axis limits are showed by dashed lines.
sequence, as previously described.33 It must be noted that the polymers are not stereoregular. In order to understand the structure of polyurethane crystals, a series of nine oligomers with similar chain length (i.e., six coded units) but containing different monomer sequences was examined in this work (Table S1). Single crystals suitable for ED analysis were obtained by crystallization of the oligomers in a 1:1 (v/v) mixture of dimethyl sulfoxide and water (1.25−2.5 mg·mL−1). The morphology of the crystals depends on both crystallization conditions and sample type. Single crystals with a length of several micrometers and a width of about one micrometer could be obtained in all cases (Figure S1). Figure 1a,b shows the ED patterns recorded for the crystals of the homo-oligomers α000000 and α111111 (i.e., the composition extremes of the oligomer series). They are characterized by a 2 mm symmetry with sharp 110 and 020 reflections. For example, pattern resolution of the α111111 crystal allowed determination of a base-centered orthorhombic unit cell with a and b dimensions of 4.88 and 9.06 Å, respectively. This suggests a hydrogenbonding driven lamellar organization of the oligourethane chains with an intermolecular H-bond distance a (in the a axis) and an intersheet distance b (in the b axis), as shown in the crystal lattice sketch of Figure 1b. It must be noted that the fact that α111111 is atactic does not prevent crystallization, as observed for other types of polymers.35,36 By comparing the crystal lattices of α000000 and α111111, it is observed that the a dimension, defined by the hydrogen bonds, remains nearly constant, whereas the presence of methyl side-chains affects the interlayer distance b. Indeed, intersheet distance b is about 1.2× larger in α111111 crystals (4.53 Å, Figure 1b) than in α000000 crystals (3.66 Å, Figure 1a). In between these two extremes, the crystal
structure of oligomers with intermediate 0/1 comonomer compositions was investigated. All co-oligomers of the series exhibited the same orthorhombic symmetry (Figures S2) as the one observed for the homo-oligomers and for other linear polyurethanes.37 Figure 1c shows the evolution of the intersheet distance b with the primary structure of the oligomers. Between the extreme values of the homo-oligomers, b is influenced by comonomer composition but also by the position of the methyl coded units in the co-oligomer sequences. For instance, b was found to be similar in α000000 and α000001 (3.67 Å) crystals, but larger in crystals of α001000 (3.88 Å). In other words, the presence of a methyl side chain on the terminal position of the oligomer does not increase intersheet distance, while a methyl positioned inside the chain does. This suggests that the terminal monomer unit is not included in the crystal lattice. This hypothesis was confirmed by other observations. For example, the intersheet distance b measured for α111111 (4.53 Å) is similar to the one of α111110 (4.47 Å) but larger than the one of α011111 (4.36 Å). Hence, as indicated by the colored lines in Figure 1c, b increases with n, which is the number of 1-bits that are included in the lattice. This number can be calculated using the simple formula n = n′ − n′′, where n′ is the total number of 1bits in the primary structure of a given oligomer and n′′ is the number of 1-bits located at the terminal position of the sequence. Moreover, the antiparallel arrangement of the chains in c axis allows the α end-group to be either inside or outside the crystal lattice. Both polymorphisms allow the formation of six hydrogen bonds between each oligomer (Figure 1d). Yet, if the α end-groups were outside the lattice, the methyl side chains of two molecules may face each other in some specific sequences (e.g., α001000, Figure 1d) and not in others (e.g., α010000, Figure S3a). The fact that b was found to be slightly 780
DOI: 10.1021/acsmacrolett.9b00307 ACS Macro Lett. 2019, 8, 779−782
Letter
ACS Macro Letters larger for α001000 (3.88 Å) than for α010000 (3.82 Å) probably reflects such a sequence-specific steric hindrance. The comparison of b in the crystals of α010101 (4.08 Å), in which some methyl groups face each other (Figure S3), and α010010 (4.04 Å) also consolidates the hypothesis that the lattice does not include the α end-group. The determination of the crystal structure of the sequence-coded polyurethanes allows calculation of the volume occupied by one basic information unit, which is in the range 148−188 Å3 (Table S1). This is calculated using a and b values extracted from ED patterns and the length between two repeating units c (8.5 Å) that is estimated by molecular modeling. This volume is about three times smaller than the one occupied by a coded nucleotide in DNA. It suggests an ultrahigh theoretical information density of about 5.3−6.8 exabits·mm−3. The crystal lattices obtained for different digitally encoded polyurethanes indicate that 0/1 molecular coding has an effect on b dimension but does not change drastically the crystalline morphology. Thus, it was tempting to examine if oligomers with different primary structures can be cocrystallized. Indeed, the possibility to confine different coded primary structures inside the same organized material would be an exciting feature for molecular data storage. As a proof-of-principle, we examined the most extreme situation that is the crystallization of blends of composition extremes α000000 and α111111. Joint crystallization was performed using the same experimental conditions as described above. Electron diffraction experiments performed on crystals obtained from 1:1, 3:1, and 1:3 (w/w) mixtures of α111111 and α000000 oligomers led to comparable patterns (Figure S2). They are characterized by 110 symmetrical reflections and two clearly distinguishable 4.51 and 3.63 Å reflections on the b* axis (Figure 2). The
demonstrated that oligomers with different primary structures can be jointly crystallized into segregated monocrystals, thus, opening the possibility to store different fragments of aperiodic sequence information inside a single piece of organized coded matter. Still, it must be pointed out that these proof-ofconcepts have only been obtained with minimal information sequences. Nevertheless, the results of this communication suggest that abiotic coded crystals could be interesting storage materials for ultradense, and possibly long-term, preservation of molecular information.
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ASSOCIATED CONTENT
* Supporting Information S
The Supporting Information is available free of charge on the ACS Publications website at DOI: 10.1021/acsmacrolett.9b00307. Full experimental part: detailed experimental procedures; Table S1 and Figures S1−S3 (PDF)
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AUTHOR INFORMATION
Corresponding Authors
*E-mail: jfl
[email protected]. *E-mail:
[email protected]. ORCID
Bernard Lotz: 0000-0001-8091-9014 Jean-François Lutz: 0000-0002-3893-2458 Notes
The authors declare no competing financial interest.
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ACKNOWLEDGMENTS J.F.L. thanks the excellence network Chemistry of Complex Systems (LabEx CSC), the University of Strasbourg and the CNRS for financial support. The authors also thank Laurence Charles (ICR, Aix-Marseille Université) for accurate mass measurement of the oligourethanes by electrospray high resolution mass spectrometry.
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REFERENCES
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Figure 2. ED pattern obtained from a crystal resulting of the recrystallization of a 1:1 mixture of α111111 and α000000 (b). Dashed lines highlight the similarity between this pattern and those obtained for the corresponding homo-oligomers crystals (a, c).
distances are similar to those observed for the single crystals ED patterns of α111111 and α000000 oligomers, which suggests that both oligomers coexist in the same crystal, but they are constituents of different lattices, which suggests segregated regions, or possibly lamellas, of different composition. In summary, it was shown that sequence-coded atactic oligourethanes self-organize into H-bond-stabilized lamellar crystals with a base-centered orthorhombic unit cell. The observed crystal lattices do not significantly depend on the coded primary structure of the oligourethanes. Only the intersheet distance was found to be influenced by the presence of coded methyl groups. Furthermore, the volume occupied by one basic coded unit in these oligourethane crystals was found to be significantly smaller than the one of a nucleotide, thus, evidencing that the information storage density of these materials is higher than in DNA. Furthermore, it was 781
DOI: 10.1021/acsmacrolett.9b00307 ACS Macro Lett. 2019, 8, 779−782
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DOI: 10.1021/acsmacrolett.9b00307 ACS Macro Lett. 2019, 8, 779−782
