Oleg Borodin

Towards exact molecular dynamics simulations with machine-learned force fields

Towards exact molecular dynamics simulations with machine-learned force fields, Published online: 24 September 2018; doi:10.1038/s41467-018-06169-2

Energy consumption in chemical fuel-driven self-assembly

Energy consumption in chemical fuel-driven self-assembly, Published online: 17 September 2018; doi:10.1038/s41565-018-0250-8

Preparation of asymmetric phospholipid vesicles for use as cell membrane models

Preparation of asymmetric phospholipid vesicles for use as cell membrane models, Published online: 06 September 2018; doi:10.1038/s41596-018-0033-6

Folding one-dimensional polymer chains into well-defined topologies represents an important organization process for proteins, but replicating this process for supramolecular polymers remains a challenging task. We report supramolecular polymers that can fold into protein-like topologies. Our approach is based on curvature-forming supramolecular rosettes, which affords kinetic control over the extent of helical folding in the resulting supramolecular fibers by changing the cooling rate for polymerization. When using a slow cooling rate, we obtained misfolded fibers containing a minor amount of helical domains that folded on a time scale of days into unique topologies reminiscent of the protein tertiary structures. Thermodynamic analysis of fibers with varying degrees of folding revealed that the folding is accompanied by a large enthalpic gain. The self-folding proceeds via ordering of misfolded domains in the main chain using helical domains as templates, as fully misfolded fibers prepared by a fast cooling rate do not self-fold.

Gas-phase sugar formation using hydroxymethylene as the reactive formaldehyde isomer

Gas-phase sugar formation using hydroxymethylene as the reactive formaldehyde isomer, Published online: 10 September 2018; doi:10.1038/s41557-018-0128-2

Multi‐electron storage: A new photo‐charge separator (PCS) consisting of a [Ru(bpy)₃]²⁺ chromophore and multiple methylviologen (MV²⁺) electron acceptors [Ru(bpyMV2)₃]¹⁴⁺ is developed. In the presence of an electron donor, it shows consecutive photo‐driven electron transfer events leading to multi‐electron storage over the PCS. When coupled with colloidal Pt as a catalyst, photocatalytic H₂ evolution is promoted (see figure).

Abstract

A new photo‐charge separator (PCS) consisting of a [Ru(bpy)₃]²⁺ (bpy=2,2′‐bipyridine) chromophore and six viologen (MV²⁺) acceptors, [Ru(bpyMV2)₃]¹⁴⁺, is synthesized and its application in the photocatalytic H₂ evolution reaction is reported. The present PCS possesses shorter linkers for connecting the Ru chromophore and the MV²⁺ acceptors in comparison with our previous PCSs (Inorg. Chem. Front., 2016, 3, 671–680) and shows a consecutive photo‐driven electron transfer in the presence of a sacrificial electron donor [ethylenediaminetetraacetic acid (EDTA)], leading to a multi‐electron storage over the PCS. This behavior can also be coupled with the catalytic H₂ evolution by the presence of a colloidal Pt catalyst. More importantly, the present PCS exhibits a much higher durability during the photolysis, which is attributed to the higher rate in the catalytic process. The high durability is also attributed to its bulky framework preventing undesirable side reactions.

Sea power: Producing hydrogen from water in an efficient manner could significantly reduce consumption of fossil fuels. The abundant presence of water in oceans offers an important alternative approach for water splitting using seawater. Herein various ways are reported to efficiently reduce seawater to hydrogen.

Abstract

Producing hydrogen from water in an efficient manner could significantly reduce consumption of fossil fuels. In this regard the abundant presence of water in oceans offers an important alternative approach for water splitting using seawater. Direct use of seawater for the generation of hydrogen is a difficult and complex process due to the presence of various ions in seawater, which affect the activity of the catalysts and makes the selectivity towards efficient water splitting a challenging task. Herein various ways are reported to efficiently reduce seawater to hydrogen under visible light irradiation by various catalysts already reported by this group. A better performance than pure water was observed in some cases, and in a few cases the opposite was observed, implying that with a proper approach seawater can be efficiently reduced to generate hydrogen.

Bridge size matters! Structural analysis of a series of bis‐bipyridinium gemini surfactants uncovered structure–property relationships that are crucial in determining both their ability to form donor–acceptor supramolecular helical‐fiber‐based hydrogels and the hydrogel strength. These relationships were also correlated to the versatile processability and tunable functionality of their solid‐state aerogel, xerogel film, and ink‐jet printed thermochromes.

Abstract

The processability and functional performance of stimuli‐responsive supramolecular materials are key factors in determining their utility and potential for mass adoption, usage, and profitability. However, it is difficult to predict how structural changes to the molecular components of these systems will impact their operation. Here, a series of π‐electron‐deficient bis‐bipyridinium gemini surfactants were synthesized and evaluated to elucidate the structure–property relationships that govern their ability to form helical‐fiber‐based donor–acceptor hydrogels, impact hydrogel strength, and influence their solid‐state thermochromism. When combined with the π‐electron‐rich donor melatonin, the helical‐fiber‐ and hydrogel‐forming ability of the gemini surfactants was largely influenced by the dimensions of the rigid bridging group that connects the two bis‐bipyridinium units. Dynamic viscoelastic rheology and linear sweep voltammetric analysis revealed a positive correlation between the length of the gemini‐surfactant bridging group and both the hydrogel strength and the magnitude of the charge‐transfer interaction between the donor–acceptor pair. Solid‐state thermochromic transition temperatures of processed aerogels, xerogel films, and inkjet‐printed patterns were positively correlated with the strength of the charge transfer interaction between the donor–acceptor pair and, thus, also with the length of the gemini surfactant bridging group. The results provide impactful insights that will enable the development of new donor–acceptor‐based thermochromes with versatile processability and tunable functionality.

Activating evolution: Carboxylic C=O bonds need to be activated for the nucleophilic attack by a −N: group. In metabolic processes such as purine and pyrimidine synthesis, this activation is carried out by ATP. It is proposed that at the onset of life, similar reactions took place on mineral surfaces where Lewis acids played the role of C−O activators.

Abstract

The origin of life is mostly divided into “genetics first” and “metabolism first” hypotheses. The former is based on spark‐tube tests and organic species from meteorites and comets, and proposes a heterotrophic origin of life also consistent with the “RNA World” concept. The “metabolism first” hypothesis posits that life began autotrophically on minerals and/or hydrothermal vents. The lack of direct evidence means it is not possible to lend solid support to either hypothesis but the “metabolism first” option can be explored if a continuous geochemical, catalytically dynamic process is assumed. Using this approach, it is speculated that purine and pyrimidine synthesis originated on a mineral surface, which was later replaced by ATP. The same applies to redox processes where metal‐bound hydrides could have been replaced by NAD.

Publication date: 17 October 2018

Source: Tetrahedron Letters, Volume 59, Issue 42

Author(s): Agnes Kütt, Sigrid Selberg, Ivari Kaljurand, Sofja Tshepelevitsh, Agnes Heering, Astrid Darnell, Karl Kaupmees, Mare Piirsalu, Ivo Leito

Graphical abstract

Half-metallic carbon nitride nanosheets with micro grid mode resonance structure for efficient photocatalytic hydrogen evolution

Half-metallic carbon nitride nanosheets with micro grid mode resonance structure for efficient photocatalytic hydrogen evolution, Published online: 22 August 2018; doi:10.1038/s41467-018-05590-x

Intrigued by the potential of nanoscale machines, scientists have long attempted to control molecular motion. We monitored the individual 0.7-nanometer steps of a single molecular hopper as it moved in an electric field along a track in a nanopore controlled by a chemical ratchet. The hopper demonstrated characteristics desired in a moving molecule: defined start and end points, processivity, no chemical fuel requirement, directional motion, and external control. The hopper was readily functionalized to carry cargos. For example, a DNA molecule could be ratcheted along the track in either direction, a prerequisite for nanopore sequencing.

Designing electrochemically reversible H₂ oxidation and production catalysts

Designing electrochemically reversible H₂ oxidation and production catalysts, Published online: 29 August 2018; doi:10.1038/s41570-018-0032-8

Liquid crystalline (LC) elastomers (LCEs) enable large-scale reversible shape changes in polymeric materials; however, they require intensive, irreversible programming approaches in order to facilitate controllable actuation. We have implemented photoinduced dynamic covalent chemistry (DCC) that chemically anneals the LCE toward an applied equilibrium only when and where the light-activated DCC is on. By using light as the stimulus that enables programming, the dynamic bond exchange is orthogonal to LC phase behavior, enabling the LCE to be annealed in any LC phase or in the isotropic phase with various manifestations of this capability explored here. In a photopolymerizable LCE network, we report the synthesis, characterization, and exploitation of readily shape-programmable DCC-functional LCEs to create predictable, complex, and fully reversible shape changes, thus enabling the literal square peg to fit into a round hole.

Modelling polymerization: A new analytical model of coupled cooperative supramolecular polymerizations is proposed to describe the biphasic aggregation of an amphiphilic BF₂‐azadipyrromethene (BODIPY) dye.

Abstract

Based on our studies on biphasic self‐assembly behavior of an amphiphilic BF₂‐azadipyrromethene (aza‐BODIPY) dye 1, a new analytical model to quantitatively describe the thermodynamic properties of the aggregation involving two competing supramolecular polymerization processes is proposed. In this model, the formation of the metastable as well as the thermodynamically stable aggregates was considered to follow a nucleated polymerization mechanism. The numerical calculation based on the new model gives insight into the formation of different species in such complicate aggregate systems. Moreover, the aggregation of the biphasic self‐assembly processes for dye 1 was investigated by concentration‐dependent UV/Vis spectroscopy. The experimental data were analyzed by using the new model to evaluate the thermodynamic parameters including aggregation constants, the size of nuclei, and the cooperativity the two types of aggregates.

TORC about: The utilization of tunable orthogonal reversible covalent (TORC) bonds is highlighted in this Minireview. The focus lies in the variety of different applications that are possible, including controlling molecular assembly, operating complex molecular machines, and designing dynamic, self‐healable polymer networks.

Abstract

Dynamic assembly of macromolecules in biological systems is one of the fundamental processes that facilitates life. Although such assembly most commonly uses noncovalent interactions, a set of dynamic reactions involving reversible covalent bonding is actively being exploited for the design of functional materials, bottom‐up assembly, and molecular machines. This Minireview highlights recent implementations and advancements in the area of tunable orthogonal reversible covalent (TORC) bonds for these purposes, and provides an outlook for their expansion, including the development of synthetically encoded polynucleotide mimics.

Understanding the practical limitations of chemical reactions is critically important for efficiently planning the synthesis of compounds in pharmaceutical, agrochemical, and specialty chemical research and development. However, literature reports of the scope of new reactions are often cursory and biased toward successful results, severely limiting the ability to predict reaction outcomes for untested substrates. We herein illustrate strategies for carrying out large-scale surveys of chemical reactivity by using a material-sparing nanomole-scale automated synthesis platform with greatly expanded synthetic scope combined with ultrahigh-throughput matrix-assisted laser desorption/ionization–time-of-flight mass spectrometry (MALDI-TOF MS).