Oleg Borodin

Publication date: 6 September 2019

Source: Tetrahedron, Volume 75, Issue 36

Author(s): Ying-Chun He, Zhen-Xing Ren, Xue-Feng Zhao, Yong-Bin Zhang, Jun-Hong Wang, Jian-Bin Chao, Meng-Liang Wang

Graphical abstract

Using antimony‐activated iodine oxidation, an unusual trithioorthoformate‐capped disulfide cyclophane cage was synthesized. Sulfur extrusion was shown to be successful, providing the trithioether analogue. Additionally, yield optimization allowed for >58 % yield.

Abstract

An unusual trithioorthoformate‐capped cyclophane cage was assembled via antimony‐activated iodine oxidation of thiols as confirmed by ¹H‐NMR spectroscopy and X‐ray crystallography. The disulfide bridges can undergo desulfurization with hexamethylphosphorous triamide (HMPT) at ambient temperature to capture a trithioether cyclophane cage capped by the trithioorthoformate. In both cages a methine proton points directly into the small cavity. This unexpected structure is hypothesized to have formed as a result of haloform insertion during oxidation.

Jigsaw pieces: One of the major challenges for the creation of self‐replicating synthetic cells is the generation of membrane‐forming molecules by the cells themselves, which is required for cellular growth and ultimately cell division. Herein, different approaches and recent advances towards genetically encoded production of membranes are reviewed. Next to lipid membranes we discuss the potential production of membranes from amphiphilic peptides, and we address some of the challenges for the various approaches taken.

Abstract

The creation of self‐replicating cell‐mimicking systems – artificial cells – is one of the major goals of bottom‐up synthetic biology. An essential aspect of such systems is the realization of membranous compartments which can grow and divide in synchrony with the internal dynamics of the cells. Amphiphiles capable of forming membranes may be either externally provided to feed the growing compartments, or generated in situ through chemical processes. In the context of autonomously self‐replicating systems, genetically encoded membranes are of particular interest. Herein, we discuss typical approaches taken for the creation of cell‐like microcompartments via self‐assembly of amphiphiles. We specifically address some of the challenges associated with the generation of phospholipid or peptide‐based membranes via genetic and enzymatic processes.

A virtuous circle: Rain‐like precipitation, formed in a microfluidic implementation of the water cycle, creates local salt fluctuations at the gas–water interface, which separates DNA or RNA strands below their melting temperature. This salt‐dependent strand separation could have facilitated DNA or RNA replication on the early Earth.

Abstract

To understand the emergence of life, a better understanding of the physical chemistry of primordial non‐equilibrium conditions is essential. Significant salt concentrations are required for the catalytic function of RNA. The separation of oligonucleotides into single strands is a difficult problem as the hydrolysis of RNA becomes a limiting factor at high temperatures. Salt concentrations modulate the melting of DNA or RNA, and its periodic modulation would enable melting and annealing cycles at low temperatures. In our experiments, a moderate temperature difference created a miniaturized water cycle, resulting in fluctuations in salt concentration, leading to melting of oligonucleotides at temperatures 20 °C below the melting temperature. This would enable the reshuffling of duplex oligonucleotides, necessary for ligation chain replication. The findings suggest an autonomous route to overcome the strand‐separation problem of non‐enzymatic replication in early evolution.

Molecular communication is an important prerequisite for the realization of complex collective behaviors in a consortia of artificial cell‐scale systems.

Abstract

Communication between artificial cells is essential for the realization of complex dynamical behaviors at the multi‐cell level. It is also an important prerequisite for modular systems design, because it determines how spatially separated functional modules can coordinate their actions. Among others, molecular communication is required for artificial cell signaling, synchronization of cellular behaviors, computation, group‐level decision‐making processes and pattern formation in artificial tissues. In this review, an overview of various recent approaches to create communicating artificial cellular systems is provided. In this context, important physicochemical boundary conditions that have to be considered for the design of the communicating cells are also described, and a survey of the most striking emergent behaviors that may be achieved in such systems is given.

Rewired: A versatile rewiring mechanism leading to the emergence of constitutional dynamic networks is introduced (see picture). DNAzymes associated with the network constituents provide reporters to quantify the adaptive properties of the networks and guide emerging catalytic functions of the networks. The relevance of the study to the evolution of life is discussed.

Abstract

The evolution of networks is a fundamental unresolved issue in developing the area of systems chemistry. We introduce a versatile rewiring mechanism that leads to the emergence of nucleic‐acid‐based constitutional dynamic networks (CDNs). A two‐component constituent AA′ functionalized with a Mg²⁺‐ion‐dependent DNAzyme activator unit forms a complex with an intact hairpin H_BB′ composed of B and B′ sequences. Cleavage of H_BB′ leads to the two‐component constituent BB′, and its rewiring with AA′ yields CDN X composed of the equilibrated constituents AA′, AB′, BA′, and BB′. In analogy, subjecting AA′ to an intact hairpin H_CC′ leads to the formation of CDN Y consisting of AA′, AC′, CA′, and CC′. Subjecting AA′ to the mixture of H_BB′ and H_CC′ evolves the [3×3] CDN Z, composed of nine constituents, thus demonstrating hierarchical adaptive properties. Furthermore, the DNAzyme units associated with the constituents are applied to tailor emerging catalytic functions from the different CDNs.

Edible encryption: A new kind of encryption and decryption technique based on cellulose fiber/hydroxyapatite nanowire secret paper with white vinegar as an invisible security ink and fire as a decryption key has been developed (see figure).

Abstract

Security inks based on photoluminescent materials are mostly investigated for security applications, such as information encryption and decryption, anti‐counterfeiting, and data storage. Although they are invisible to the naked eye under ambient light, they can be detected under ultraviolet or near‐infrared light. Herein, a new kind of secret paper made from network‐structured ultralong hydroxyapatite nanowires and cellulose fibers has been developed. White vinegar, a common cooking ingredient, is used as an invisible security ink. Covert information on the secret paper written with white vinegar is totally invisible under natural light, but it can be decrypted and clearly read after exposure to fire; the response time to fire is short (<10 s). The ways of writing on the secret paper are diverse by using various pens loaded with white vinegar.

Carried away: The presented work describes impressive activation of electrogenic anion transport using artificial triazole quartet anion channels and the K⁺‐carrier valinomycin. The stacked protonated triazole quartets are stabilized by strong interactions with two anions, and hydrogen bonding/ion pairing of the anions are combined with anion–π recognition to produce columnar architectures.

Abstract

The self‐assembly of triazole amphiphiles was examined in solution, the solid state, and in bilayer membranes. Single‐crystal X‐ray diffraction experiments show that stacked protonated triazole quartets (T₄) are stabilized by multiple strong interactions with two anions. Hydrogen bonding/ion pairing of the anions are combined with anion–π recognition to produce columnar architectures. In bilayer membranes, low transport activity is observed when the T₄ channels are operated as H⁺/X⁻ translocators, but higher transport activity is observed for X⁻ in the presence of the K⁺‐carrier valinomycin. These self‐assembled superstructures, presenting intriguing structural behaviors such as directionality, and strong anion encapsulation by hydrogen bonding supported by vicinal anion–π interactions can serve as artificial supramolecular channels for transporting anions across lipid bilayer membranes.

Cellular uptake: The introduction of halogen, particularly iodine, atoms to small molecules and proteins is emerging as a novel and promising strategy not only for studying membrane activity and cellular functions, but also for improving the delivery of therapeutic agents. The strong halogen‐bond forming ability of iodine atoms plays a crucial role in membrane transport (see scheme).

Abstract

The plasma membrane regulates the transport of molecules into the cell. Small hydrophobic molecules can diffuse directly across the lipid bilayer. However, larger molecules require specific transporters for their entry into the cell. Regulating the cellular entry of small molecules and proteins is a challenging task. The introduction of halogen, particularly iodine, to small molecules and proteins is emerging to be a promising strategy to improve the cellular uptake. Recent studies reveal that a simple substitution of hydrogen atom with iodine not only increases the cellular uptake, but also regulates the membrane transport. The strong halogen‐bond‐forming ability of iodine atoms plays a crucial role in the transport and the introduction of iodine may provide an efficient strategy for studying membrane activity and cellular functions and improving the delivery of therapeutic agents. This Concept article does not provide a comprehensive picture of membrane transport but highlights halogen‐substitution as a novel strategy for understanding and regulating the cell‐membrane traffic.

Nature, Published online: 06 June 2019; doi:10.1038/d41586-019-01763-w

Nature, Published online: 24 May 2019; doi:10.1038/d41586-019-01651-3

Nature, Published online: 22 May 2019; doi:10.1038/d41586-019-01562-3

Who is the best? Owing to the suitable electronegativity provided by P and synergistic effects of the carbon nanotubes, the RuP₂/CNT composite achieved high catalytic performance as a hydrogen evolution reaction (HER) electrocatalyst. This may result from the modulation effect of the electronic properties and the depressed adsorption free energy of RuP₂ (see scheme).

Abstract

The utilization of noble‐metal catalysts for the hydrogen evolution reaction (HER) provides an efficient strategy for hydrogen acquisition. However, exploring catalysts with suitable hydrogen binding strength for the HER process is always of great importance, but extremely challenging. In this work, sulfur and phosphor as electron‐withdrawing elements were incorporated into carbon nanotube (CNT)‐supported Ru catalysts, which were prepared through a facile solution reduction reaction and post thermo treatment. Owing to the suitable electronegativity provided by P and synergistic effects of the carbon nanotubes, the RuP₂/CNT achieved a high catalytic performance as a HER electrocatalyst. This may result from the modulation effect of the electronic properties and the depressed adsorption free energy of RuP₂. Electrochemical tests present that the RuP₂/CNT composite exhibit a small overpotential of 58 mV at 10 mA cm⁻² in acidic electrolyte. In a neutral or alkaline environment, the overpotential is 82 and 40 mV, respectively. The RuP₂/CNT electrode also possesses stable durability for long‐time cycling, suggesting its remarkable property as promising all‐pH HER catalyst.

Insights into the supramolecular polymerisation mechanism of an acid‐sensitive photoresponsive gelator (L1) are reported in this work. Addition of trifluoacetic acid (TFA) leads to the transformation of the anti‐parallel H‐bonded fibrillar assembly of L1 into unique superhelical braid‐like fibers stabilized by H‐bonding of parallel stacked L1:TFA dimers. Light irradiation causes the disassembly of the superhelical fibres and their reconstruction into thin fibres via a different pathway associated with a rapid cis–trans isomerisation under isothermal conditions. More information can be found in the Full Paper by G. Fernández et al. on https://doi.org/10.1002/chem.201900775page 9230.

Sweet surface Employing electrospray ion beam deposition, nonvolatile sucrose can be deposited on clean surfaces. In their Communication on https://doi.org/10.1002/anie.201901340page 8336 ff., S. Abb et al. present the 2D crystalline assembly of sucrose on a Cu(100) surface. By combining scanning tunneling microscopy images and multi‐stage modelling, the conformation and assembly pattern of sucrose is revealed.

Cutting the Gordian knot: Collision‐induced dissociation and travelling‐wave ion‐mobility mass spectrometry together provide a fast screening method to identify the topology of molecular Hopf and Solomon links, a [3]catenate, and a trefoil knot, even when they coexist in quickly equilibrating dynamic combinatorial libraries.

Abstract

A rapid screening method based on traveling‐wave ion‐mobility spectrometry (TWIMS) combined with tandem mass spectrometry provides insight into the topology of interlocked and knotted molecules, even when they exist in complex mixtures, such as interconverting dynamic combinatorial libraries. A TWIMS characterization of structure‐indicative fragments generated by collision‐induced dissociation (CID) together with a floppiness parameter defined based on parent‐ and fragment‐ion arrival times provide a straightforward topology identification. To demonstrate its broad applicability, this approach is applied here to six Hopf and two Solomon links, a trefoil knot, and a [3]catenate.

Finding the sweet spot: The combination of preparative mass spectrometry with scanning tunneling microscopy has enabled the imaging of the disaccharide sucrose on a Cu(100) surface with subunit‐level resolution. By employing a multistage modeling approach, the conformation of the disaccharide on the surface as well as the interactions between the sucrose molecules can be deduced.

Abstract

Saccharides are ubiquitous biomolecules, but little is known about their interaction with, and assembly at, surfaces. By combining preparative mass spectrometry with scanning tunneling microscopy, we have been able to address the conformation and self‐assembly of the disaccharide sucrose on a Cu(100) surface with subunit‐level imaging. By employing a multistage modeling approach in combination with the experimental data, we can rationalize the conformation on the surface as well as the interactions between the sucrose molecules, thereby yielding models of the observed self‐assembled patterns on the surface.

Side‐chain immiscibility allows full control over the formation of a highly stable, discrete anti‐cooperative assembly that is in competition with the formation of cooperative supramolecular polymers, which may open up new strategies for pathway control in self‐assembly.

Abstract

Controlling the nanoscale morphology in assemblies of π‐conjugated molecules is key to developing supramolecular functional materials. Here, we report an unsymmetrically substituted amphiphilic Pt^II complex 1 that shows unique self‐assembly behavior in nonpolar media, providing two competing anti‐cooperative and cooperative pathways with distinct molecular arrangement (long‐ vs. medium‐slipped, respectively) and nanoscale morphology (discs vs. fibers, respectively). With a thermodynamic model, we unravel the competition between the anti‐cooperative and cooperative pathways: buffering of monomers into small‐sized, anti‐cooperative species affects the formation of elongated assemblies, which might open up new strategies for pathway control in self‐assembly. Our findings reveal that side‐chain immiscibility is an efficient method to control anti‐cooperative assemblies and pathway complexity in general.

Molecular gripping: The emergence of nanoscale machines has inspired the quest for molecular grippers, and the effort has been expedited by the development of redox‐active, quinone‐based resorcin[4]arene cavitands. This Concept article describes the breakthroughs in the design and control of resorcin[4]arenes by electronic and electromagnetic stimuli using various electroanalytical, spectroscopic, and spectroelectrochemical methods. It outlines the current state and future perspectives of molecular grippers.

Abstract

The quest for nanoscale molecular machines has inspired the search for their close relatives, molecular grippers. This path was paved by the development of resorcin[4]arene cavitands and their quinone‐based redox‐active congeners. In this Concept article, the efforts to design and establish the control of quinone‐functionalized resorcin[4]arenes by electronic and electromagnetic stimuli is described. This was achieved by relying on paramagnetic semiquinone radical anions formed electrochemically or by photoredox catalysis. The gripper‐like motion of such species could not be studied by conventional NMR spectroscopy. Instead, an entirely different approach had to be developed that included various electroanalytical and spectroelectrochemical methods, including UV/Vis/NIR spectroelectrochemistry, pulsed EPR and Davies ¹H ENDOR spectroscopy, transient absorption spectroscopy, and time‐resolved luminescence measurements, besides density functional theory calculations and X‐ray crystallography. The conceptual breakthroughs are reviewed as well as the current state and future perspectives of photoredox‐switchable molecular grippers.

Catalytic reactions can be challenging to develop and implement because of unforeseen interactions between reaction components. As a consequence, chemists rely on laborious screening. This review describes strategies to improve the way that catalytic experiments are designed, implemented, analyzed, and interpreted.

Abstract

Homogeneous catalysis has provided chemists with numerous transformations to enable rapid construction of organic molecules. However, these reactions are complex, requiring multiple substrate‐dependent mechanistic steps to operate in harmony under a single set of experimental conditions. As a consequence, synthetic chemists often carry out laborious, empirical screening to identify suitable catalysts, solvents, and additives to achieve high yields and selectivity. In this Minireview, recently developed tools, technologies, and strategies will be described that improve this development process. In particular, the application of high throughput techniques to run more experiments, experimental design principles to access better data, and statistical tools to provide predictive models will be discussed.