Molecular Information Storage Research Articles

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As classic molecular magnets with magnetic bistability, spin‐crossover (SCO) compounds have potentially important application value in molecular electronics, sensing, and information storage. Multistable control of SCO compounds is more difficult than bistability control. In this paper, we propose a strategy to control the number of spin‐transition steps to further understand the control of the multistability of SCO compounds. More details are discussed in the article by Li et al. on page 879—886.image

Design and characterization of Fe(II) complexes with tetradentate ligands exhibiting spin-crossover near room temperature.

Construction of spin-crossover (SCO) materials is very appealing for applications such as molecular switches and information storage. This study focuses on the design of Fe(II) complexes using N,N'-bis(2-pyridinylmethyl)-1,2-ethanediamine-based ligands with an N4 structure for SCO material development. By incorporating para-substituted benzene groups into the ligand's pyridine moiety, two polymorphs, α and β, were obtained, both exhibiting SCO activity. Notably, the β polymorph displayed a spin crossover temperature of 270 K, which is approaching room temperature. Structural analyses were conducted to compare the differences between the polymorphs, along with a literature review of related complexes, providing insights into the characteristics of SCO behavior.

Peptide-graphene logic sensing system for dual-mode detection of exosomes, molecular information processing and protection

Peptides with highly sequence-dependent recognition, assembly, and encoding abilities can perform functions similar to DNA or even better, such as biosensing, molecular information processing, coding, or storage. However, the combination of versatile peptides and 2D materials are rarely used for multipurpose integrated applications, including biosensing, information processing and security. Herein, peptide-graphene sensing system was comprehensively used for dual-signal sensing of tumor-derived exosomes (TDEs), logic computing, and information protection. The system used fluorescent-labeled CD63-binding peptide CP05 and graphene oxide (GO) to selectively detect CD63 and TDEs by fluorescence and resonance light scattering. From three levels such as matter, energy, and information analysis, the matter and energy changes in GO−CP05 peptide sensing system were transformed into valuable information, which achieve the dual-mode quantitative detection of TDEs and its marker CD63, and the actual serum analysis. This matter-energy interaction network was also informationized, and utilized for parallel and batch logic computing, two kinds of molecular crypto-steganography (based on peptide sequence and Boolean logic relationships), which facilitates development of intelligent sensing and advanced information technology. This work not only provides a new method for sensitive detection of important disease markers, but also provides ideas for integrating molecular sensing and informatization to open molecular digitization.

HS, an Ancient Molecular Recognition and Information Storage Glycosaminoglycan, Equips HS-Proteoglycans with Diverse Matrix and Cell-Interactive Properties Operative in Tissue Development and Tissue Function in Health and Disease.

Heparan sulfate is a ubiquitous, variably sulfated interactive glycosaminoglycan that consists of repeating disaccharides of glucuronic acid and glucosamine that are subject to a number of modifications (acetylation, de-acetylation, epimerization, sulfation). Variable heparan sulfate chain lengths and sequences within the heparan sulfate chains provide structural diversity generating interactive oligosaccharide binding motifs with a diverse range of extracellular ligands and cellular receptors providing instructional cues over cellular behaviour and tissue homeostasis through the regulation of essential physiological processes in development, health, and disease. heparan sulfate and heparan sulfate-PGs are integral components of the specialized glycocalyx surrounding cells. Heparan sulfate is the most heterogeneous glycosaminoglycan, in terms of its sequence and biosynthetic modifications making it a difficult molecule to fully characterize, multiple ligands also make an elucidation of heparan sulfate functional properties complicated. Spatio-temporal presentation of heparan sulfate sulfate groups is an important functional determinant in tissue development and in cellular control of wound healing and extracellular remodelling in pathological tissues. The regulatory properties of heparan sulfate are mediated via interactions with chemokines, chemokine receptors, growth factors and morphogens in cell proliferation, differentiation, development, tissue remodelling, wound healing, immune regulation, inflammation, and tumour development. A greater understanding of these HS interactive processes will improve therapeutic procedures and prognoses. Advances in glycosaminoglycan synthesis and sequencing, computational analytical carbohydrate algorithms and advanced software for the evaluation of molecular docking of heparan sulfate with its molecular partners are now available. These advanced analytic techniques and artificial intelligence offer predictive capability in the elucidation of heparan sulfate conformational effects on heparan sulfate-ligand interactions significantly aiding heparan sulfate therapeutics development.

Multi-Mode and Dynamic Persistent Luminescence from Metal Cytosine Halides through Balancing Excited-State Proton Transfer.

Persistent luminescence has attracted great attention due to the unique applications in molecular imaging, photodynamic therapy, and information storage, among many others. However, tuning the dynamic persistent luminescence through molecular design and materials engineering remains a challenge. In this work, the first example of excitation‐dependent persistent luminescence in a reverse mode for smart optical materials through tailoring the excited‐state proton transfer process of metal cytosine halide hybrids is reported. This approach enables ultralong phosphorescence and thermally activated delayed fluorescence emission colors highly tuned by modulation of excitation wavelength, time evolution, and temperature, which realize multi‐mode dynamic color adjustment from green to blue or cyan to yellow‐green. At the single crystal level, the 2D excitation/space/time‐resolved optical waveguides with triple color conversion have been constructed on the organic‐metal halide microsheets, which represent a new strategy for multi‐dimensional information encryption and optical logic gate applications.

Thermodriven, Acidity-Driven, and Photodriven Spin-State Switching in Pyridylacylhydrazoneiron(II) Complexes at or above Room Temperature.

The magnetic bistability of spin-crossover (SCO) materials is highly appealing for applications as molecular switches and information storage. However, switching of the spin state around room temperature remains challenging. In this work, we reported the successful manipulation of the spin states of two iron(II) complexes (1-Fe and 2-Fe) based on pyridylacylhydrazone ligands in manifold ways. Both complexes are stabilized in the low-spin (LS) state at room temperature because of the strong ligand-field strength imposed by the ligands. 2-Fe shows thermoinduced SCO above room temperature with a very large and reproducible hysteresis (>50 K), while 1-Fe remains in the LS state up to 400 K. Acidity-driven spin-state switching of the two complexes was achieved at room temperature as a result of the complex dissociation and release of iron(II) in its high-spin (HS) state. Recovery of the complex is feasible upon further alkalization treatment in the case of 1-Fe, allowing bidirectional modulation of the spin state of the metal center. Light-driven one-way switching from LS to HS is also achieved by virtue of E-to-Z isomerization at the C═N double bond, which results in dissociation of the complex because of the poor binding affinity in the Z configuration.

An object-oriented framework for evolutionary pangenome analysis

SummaryPangenome analysis is fundamental to explore molecular evolution occurring in bacterial populations. Here, we introduce Pagoo, an R framework that enables straightforward handling of pangenome data. The encapsulated nature of Pagoo allows the storage of complex molecular and phenotypic information using an object-oriented approach. This facilitates to go back and forward to the data using a single programming environment and saving any stage of analysis (including the raw data) in a single file, making it sharable and reproducible. Pagoo provides tools to query, subset, compare, visualize, and perform statistical analyses, in concert with other microbial genomics packages available in the R ecosystem. As working examples, we used 1,000 Escherichia coli genomes to show that Pagoo is scalable, and a global dataset of Campylobacter fetus genomes to identify evolutionary patterns and genomic markers of host-adaptation in this pathogen.

(Invited) Tailoring of Single-Walled Carbon Nanotube Luminescence as Photoswitchable Near-Infrared Emitters

Single-molecule localization microscopy (SMLM) has set a new paradigm in the field of optical imaging by delivering super-resolution images i.e. with resolution much better than the diffraction limit. We demonstrated over the last years that such approaches can be designed to understand basic excitonic processes in carbon nanotubes [1-2]. In the field of bioimaging, SMLM is currently limited to the visible or far-red range, missing the near-infrared region where biological tissues are however the most transparent. One reason for this is that single-molecule emitter optical properties still need to be tailored in the near-infrared, including photoswitching capabilities which is a basic ingredient to achieve single-molecule SMLM. To fill this gap, optical imaging of single-wall carbon nanotubes can first be greatly facilitated in brain tissues by covalent functionalization of luminescent defects, reducing the required excitation light intensity by one order of magnitude [3]. In addition, we have introduced a novel type of hybrid nanomaterials consisting of single-wall carbon nanotubes covalently functionalized with photo-switching molecules that are used to control the intrinsic luminescence of the single nanotubes in the near-infrared (beyond 1 µm) [4]. Through the control of photoswitching, we demonstrate super-localization imaging of nanotubes unresolved by diffraction limited microscopy opening the route toward SMLM in the near-infrared for biological applications. Photocontrol of individual near-infrared emitters will also be highly desirable for elementary optical molecular switches or information storage elements since most communication data transfer protocols are established in this spectral range.

Single crystals of mechanically entwined helical covalent polymers.

Double helical conformation of polymer chains is widely observed in biomacromolecules and plays an essential role in exerting their biological functions, such as molecular recognition and information storage. It has remained challenging, however, to prepare synthetic helical polymers, and those that exist have mainly been limited to single-stranded polymers or short oligomeric double helices. Here, we report the synthesis of covalent helical polymers, with a high molecular weight, from the achiral monomer hexahydroxytriphenylene through to spiroborate formation. Polymerization and crystallization occurred simultaneously under solvothermal conditions to form single crystals of the resulting helical covalent polymers. Characterization by single-crystal X-ray diffraction showed that each crystal consisted of pairs of mechanically entwined polymers. No strong non-covalent interactions were observed between the two helical polymers that formed a pair; instead, each strand interacted with neighbouring pairs through hydrogen bonding. Each individual crystal was made up of helical polymers of the same handedness, but the crystallization process produced a racemic conglomerate, with equal amounts of right-handed and left-handed crystals.

Stimuli-responsive discriminative detection of Cu2+ and Hg2+ with concurrent sensing of S2- from aqueous medium and bio-fluids by C N fused azophenine functionalized “smart” hydrogel assay @A potential biomarker sensor for Wilson’s disease

• Azophenine based colorimetric chemosensor, CN-1 is synthesized by solvent-free FeCl 3 mediated C N bond fusion pathway. • CN-1 can selectively and discriminatively detect aqueous Cu 2+ , Hg 2+ with LOD of 30 and 480 ppb respectively. • The reversible sensing by S 2− could formulate “Write-Read-Erase-Read” memory element and 4-input complex logic circuitry. • CN-1 can successfully detect Cu 2+ & Hg 2+ in real water samples with qualified recoveries by functionalized hydrogel assay. • The detection ability of unbound Cu 2+ from bio-fluids made it a potential diagnostic tool for monitoring Wilson’s disease. A multi-functional azophenine based colorimetric chemosensor, CN-1 has been reported by catalytic FeCl 3 mediated facile oxidative C N bond fusion of o -anisidine. The chemosensor, characterized by single crystal X-ray crystallography, can be exploited towards ‘naked-eye’ discriminative detection of Cu 2+ and Hg 2+ (LOD = 30 and 480 ppb respectively) from purely aqueous medium through colorimetric and electrochemical (CV) readouts. It is equally responsive towards intoxicated real water specimen, like river water, industrial sewage water, demonstrating its practical applicability. Along with detection, CN-1 exhibited metal ion sequestration capability, leading to the removal of ∼74 % and ∼40 % removal of Cu 2+ and Hg 2+ respectively from contaminated water bodies. Moreover, the unprecedented uniqueness of the synthesized azophenine based chemosensor levies in its capability towards ppb level Cu 2+ detection colorimetrically from target-specific bio-fluids to monitor aberrant unbound copper levels, thereby highlighting it as a potential biomarker sensor as well as a pathological non-invasive diagnostic tool of Wilson’s disease , which has been explored for the first time in the domain of azophenine based host-guest chemistry. The reversible spectrochemical response in presence of aqueous S 2− could efficiently formulate “ Write-Read-Erase-Read ” nature of a memory element and four-input complex logic circuitry for molecular level information storage, which is also hitherto unexplored in the azophenine family. One step ahead, fabrication of functionalized “smart” hydrogel assay escalates the reliability and practical applicability of the present work through simple ‘naked eye’ colorimetric-optical readouts.

Pagoo: An Encapsulated and Object-Oriented Framework for Evolutionary Analysis of Bacterial Pangenomes

Pangenome analysis is fundamental to explore molecular evolution occurring in bacterial populations. Despite the extensive availability of software for pangenome reconstruction, there is a lack of tools that allow customization of downstream data analysis in a simple and standardized way. To fill this gap, we introduce Pagoo, a new framework that enables straightforward handling of pangenome data. The encapsulated nature of Pagoo allows the storage of complex molecular and phenotypic information using an object-oriented approach that includes built-in methods, allowing the user going back and forward to the data using a single programming environment. Also, this design allows to save any analysis along with the unaltered pangenome data in a single file, making it sharable and reproducible. Pagoo acts as an API between the pangenome data and the user through the R console, providing tools to query, subset, compare, visualize and perform statistical analyses, which can be also used in concert with other microbial genomics packages available in the R ecosystem. As working examples, we used 1,000 Escherichia coli genomes to show that Pagoo is scalable, and a global dataset of Campylobacter fetus genomes to identify evolutionary patterns and genomic markers of host-adaptation in this pathogen. Pagoo represents an integrative and extensible approach to make pangenome analysis simple and reproducible.

Low-Noise Solid-State Nanopore Enhancing Direct Label-Free Analysis for Small Dimensional Assemblies Induced by Specific Molecular Binding.

Solid-state nanopores show special potential as a new single-molecular characterization for nucleic acid assemblies and molecular machines. However, direct recognition of small dimensional species is still quite difficult due the lower resolution compared with biological pores. We recently reported a very efficient noise-reduction and resolution-enhancement mechanism via introducing high-dielectric additives (e.g., formamide) into conical glass nanopore (CGN) test buffer. Based on this advance, here, for the first time, we apply a bare CGN to directly recognize small dimensional assemblies induced by small molecules. Cocaine and its split aptamer (Capt assembly) are chosen as the model set. By introducing 20% formamide into CGN test buffer, high cocaine-specific distinguishing of the 113 nt Capt assembly has been realized without any covalent label or additional signaling strategies. The signal-to-background discrimination is much enhanced compared with control characterizations such as gel electrophoresis and fluorescence resonance energy transfer (FRET). As a further innovation, we verify that low-noise CGN can also enhance the resolution of small conformational/size changes happening on the side chain of large dimensional substrates. Long duplex concatamers generated from the hybridization chain reaction (HCR) are selected as the model substrates. In the presence of cocaine, low-noise CGN has sensitively captured the current changes when the 26 nt aptamer segment is assembled on the side chain of HCR duplexes. This paper proves that the introduction of the low-noise mechanism has significantly improved the resolution of the solid-state nanopore at smaller and finer scales and thus may direct extensive and deeper research in the field of CGN-based analysis at both single-molecular and statistical levels, such as molecular recognition, assembly characterization, structure identification, information storage, and target index.

(Invited) Photoswitchable Near-Infrared Emitters Based on Single-Walled Carbon Nanotube Hybrids

Super-resolution microscopy (SRM) has set a new paradigm in the field of optical imaging by delivering images with resolution much better than the diffraction limit. We demonstrated over the last years that such approaches can be designed to understand basic excitonic processes in carbon nanotubes [1-2]. In the field of bioimaging, SRM is currently limited to the visible range, missing the near-infrared region where biological tissues are however the most transparent. One reason for this is that single-molecule photoswitchable emitters, which are the basic ingredients to achieve single-molecule SRM, have not yet been developed in the near-infrared. To fill this gap, we have recently introduced a novel type of hybrid nanomaterials consisting of single-wall carbon nanotubes covalently functionalized with photo-switching molecules that are used to control the intrinsic luminescence of the single nanotubes in the near-infrared (beyond 1 µm) [3]. Through the control of photoswitching, we demonstrate super-localization imaging of nanotubes unresolved by diffraction limited microscopy opening the route toward SRM in the near-infrared for biological applications. Photocontrol of individual near-infrared emitters will also be highly desirable for elementary optical molecular switches or information storage elements since most communication data transfer protocols are established in this spectral range.

The Search for Chiral Asymmetry as a Potential Biosignature in our Solar System.

The search for evidence of extraterrestrial life in our Solar System is currently guided by our understanding of terrestrial biology and its associated biosignatures. The observed homochirality in all life on Earth, that is, the predominance of "left-handed" or l-amino acids and "right-handed" or d-sugars, is a unique property of life that is crucial for molecular recognition, enzymatic function, information storage and structure and is thought to be a prerequisite for the origin or early evolution of life. Therefore, the detection of l- or d-enantiomeric excesses (ee) of chiral amino acids and sugars could be a powerful indicator for extant or extinct life on another world. However, studies of primitive meteorites have revealed they contain extraterrestrial amino acids and sugar acids (aldonic acids) with large enantiomeric excesses of the same chirality as terrestrial biology resulting from nonbiological processes, complicating the use of chiral asymmetry by itself as a definitive biosignature. Here we review our current knowledge of the distributions and enantiomeric and isotopic compositions of amino acids and polyols found in meteorites compared to terrestrial biology and propose a set of criteria for future life detection missions that can be used to help establish the origin of chiral asymmetry.

Modulation of transversal conductivity of europium(III) bisphthalocyaninate ultrathin films by peripheral substitution

In the present work, we demonstrate that transversal conductivity and, consequently, electrochemical activity of ultrathin solid films of two structurally similar octa-butoxy and tetra-crown-ether substituted europium bisphthalocyaninates are quite different. It is shown that presence of the crown moieties allows excellent transfer of charge through monomolecular ultrathin films of respectively substituted complex. This enables their redox-multistability, which can be utilized in molecular logic and information storage devices. On the other hand, transversal charge transfer is inhibited in the films of octa-butoxy-substituted bisphthalocyaninate, which might be promising for organic field-effect transistor applications.

One Among Millions: The Chemical Space of Nucleic Acid-Like Molecules.

Biology encodes hereditary information in DNA and RNA, which are finely tuned to their biological functions and modes of biological production. The central role of nucleic acids in biological information flow makes them key targets of pharmaceutical research. Indeed, other nucleic acid-like polymers can play similar roles to natural nucleic acids both in vivo and in vitro; yet despite remarkable advances over the last few decades, much remains unknown regarding which structures are compatible with molecular information storage. Chemical space describes the structures and properties of molecules that could exist within a given molecular formula or other classification system. Using structure generation methods, we explore nucleic acid analogues within the formula ranges BC3-7H5-15O2-4 and BC3-6H5-15N1-2O0-4, where B is a recognition element (e.g., a nucleobase). Other restrictions included two obligatory points of attachment for inclusion into a linear polymer and substructures predicting chemical stability. These sets contain 86,007 (CHO) and 75,309 (CHNO) compositionally isomeric structures, representing 706,568 CHO and 454,422 CHNO stereoisomers, that diversely and densely occupy this space. These libraries point toward there being large spaces of unexplored chemistry relevant to pharmacology and biochemistry and efforts to understand the origins of life.

Small Janus dimer as electric field manipulated molecular clam switch and electric information storage unit

AbstractA small Janus molecular dimer, as external electric field (Fz) manipulated both a molecular clam switch and a novel electric information storage unit, is found by quantum chemical computations for the first time. The molecular clam switching is intriguing and reversible. A critical Fz value of 95 × 10−4 au causes a dramatically open change in conformation from Closed form to Open form. And a small reversed electric field of Fz = −10 × 10−4 au performs a close change from Open form to Closed form. In the switching process, owing to the existence of a great electric dipole moment (μ) contrast between 0 and 22.13 D, the molecular clam switch may serve as an electric information storage unit. Gratifyingly, the reading, writing, and erasing of binary information on the electric information storage unit are easy. And further calculations show that Janus graphene fragment dimer can also serve as a molecular clam switch. Thus, this work proposes a new molecular switch prototype in the invention of artificial molecular machines, and a novel electric information storage unit in the field of molecular electronics.

Multiple adaptation of constitutional dynamic networks and information storage in constitutional distributions of acylhydrazones.

We report a study of the behavior of four dynamic covalent libraries (DCLs) based on acylhydrazones aAbB and of the corresponding square constitutional dynamic networks (CDNs) NA-ND under the effect of three agents, namely, metal cations, base + metal cations and light irradiation; in particular, the successful switching of the CDN NB between two orthogonal distributions results, respectively, from metallo-selection and photo-selection. The four DCLs undergo triple adaptation when subjected to the three agents with the generation of specific CDN distributions characteristic of each of the four DCLs. The ternary outputs displayed by the DCLs present three states (-1, 0 and 1) related to three different constitutional distributions expressed in response to the triple inputs applied. This latter process amounts to the storage of molecular information in dynamic distributions rather than in selective interactions between complementary entities undergoing molecular recognition.

Chiral Light Design and Detection Inspired by Optical Antenna Theory.

Chiral metallic nanostructures can generate evanescent fields which are more highly twisted than circularly polarized light. However, it remains unclear how best to exploit this phenomenon, hindering the optimal utilization of chiral electromagnetic fields. Here, inspired by optical antenna theory, we address this challenge by introducing chiral antenna parameters: the chirality flux efficiency and the chiral antenna aperture. These quantities, which are based on chirality conservation, quantify the generation and dissipation of chiral light. We then present a label-free experimental technique, chirality flux spectroscopy, which measures the chirality flux efficiency, providing valuable information on chiral near fields in the far field. This principle is verified theoretically and experimentally with two-dimensionally chiral coupled nanorod antennas, for which we show that chiral near and far fields are linearly dependent on the magnetoelectric polarizability. This elementary system confirms our concept to quantify chiral electromagnetic fields and paves the way toward broadly tunable chiral optical applications including ultrasensitive detection of molecular chirality or optical information storage and transfer.

Synthesis and Mass Spectrometry Analysis of Oligo-peptoids.

Peptoids are sequence-controlled peptide-mimicking oligomers consisting of N-alkylated glycine units. Among many potential applications, peptoids have been thought of as a type of molecular information storage. Mass spectrometry analysis has been considered the method of choice for sequencing peptoids. Peptoids can be synthesized via solid phase chemistry using a repeating two-step reaction cycle. Here we present a method to manually synthesize oligo-peptoids and to analyze the sequence of the peptoids using tandem mass spectrometry (MS/MS) techniques. The sample peptoid is a nonamer consisting of alternating N-(2-methyloxyethyl)glycine (Nme) and N-(2-phenylethyl)glycine (Npe), as well as an N-(2-aminoethyl)glycine (Nae) at the N-terminus. The sequence formula of the peptoid is Ac-Nae-(Npe-Nme)4-NH2, where Ac is the acetyl group. The synthesis takes place in a commercially available solid-phase reaction vessel. The rink amide resin is used as the solid support to yield the peptoid with an amide group at the C-terminus. The resulting peptoid product is subjected to sequence analysis using a triple-quadrupole mass spectrometer coupled to an electrospray ionization source. The MS/MS measurement produces a spectrum of fragment ions resulting from the dissociation of charged peptoid. The fragment ions are sorted out based on the values of their mass-to-charge ratio (m/z). The m/z values of the fragment ions are compared against the nominal masses of theoretically predicted fragment ions, according to the scheme of peptoid fragmentation. The analysis generates a fragmentation pattern of the charged peptoid. The fragmentation pattern is correlated to the monomer sequence of the neutral peptoid. In this regard, MS analysis reads out the sequence information of the peptoids.