Biologically active molecules with a "light switch"

Biologically active compounds which are light-responsive offer experimental possibilities which are otherwise very difficult to achieve. Since light can be manipulated very precisely, for example, with lasers and microscopes rapid jumps in concentration of the active form of molecules are possible with exact control of the area, time, and dosage. The development of such strategies started in the 1970s. This review summarizes new developments of the last five years and deals with "small molecules", proteins, and nucleic acids which can either be irreversibly activated with light (these compounds are referred to as "caged compounds") or reversibly switched between an active and an inactive state.     

Addressable DNA–Myoglobin Photocatalysis

In the spotlight : A hybrid myoglobin, containing a single‐stranded DNA anchor and a redox‐active ruthenium moiety tethered to the heme center can be used as a photocatalyst. The catalyst can be selectively immobilized on a surface‐bound complementary DNA molecule and thus readily recycled from complex reaction mixtures. This principle may be applied to a range of heme‐dependent enzymes allowing the generation of novel light‐triggered photocatalysts.

     

Photoinduced Bioorthogonal 1,3‐Dipolar Poly‐cycloaddition Promoted by Oxyanionic Substrates for Spatiotemporal Operation of Molecular Glues

PGlue^PZ, a pyrazoline (PZ)‐based fluorescent adhesive which can be generated spatiotemporally in living systems, was developed. Since PGlue^PZ carries many guanidinium ion (Gu⁺) pendants, it strongly adheres to various oxyanionic substrates through a multivalent salt‐bridge interaction. PGlue^PZ is given by bioorthogonal photopolymerization of a Gu⁺‐appended monomer (Glue^TZ), bearing tetrazole (TZ) and olefinic termini. Upon exposure to UV light, Glue^TZ transforms into a nitrileimine (NI) intermediate (Glue^NI), which is eligible for 1,3‐dipolar polycycloaddition. However, Glue^NI in aqueous media can concomitantly be deactivated into Glue^WA by the addition of water, and the polymerization hardly occurs unless Glue^NI is concentrated. We found that, even under high dilution, Glue^NI is concentrated on oxyanionic substrates to a sufficient level for the polymerization, so that their surfaces can be point‐specifically functionalized with PGlue^PZ by the use of a focused beam of UV light.     

Quantum chemical methods for the investigation of photoinitiated processes in biological systems: theory and applications.

With the advent of modern computers and advances in the development of efficient quantum chemical computer codes, the meaningful computation of large molecular systems at a quantum mechanical level became feasible. Recent experimental effort to understand photoinitiated processes in biological systems, for instance photosynthesis or vision, at a molecular level also triggered theoretical investigations in this field. In this Minireview, standard quantum chemical methods are presented that are applicable and recently used for the calculation of excited states of photoinitiated processes in biological molecular systems. These methods comprise configuration interaction singles, the complete active space self-consistent field method, and time-dependent density functional theory and its variants. Semiempirical approaches are also covered. Their basic theoretical concepts and mathematical equations are briefly outlined, and their properties and limitations are discussed. Recent successful applications of the methods to photoinitiated processes in biological systems are described and theoretical tools for the analysis of excited states are presented.     

Light-controlled tools

Spatial and temporal control over chemical and biological processes plays a key role in life, where the whole is often much more than the sum of its parts. Quite trivially, the molecules of a cell do not form a living system if they are only arranged in a random fashion. If we want to understand these relationships and especially the problems arising from malfunction, tools are necessary that allow us to design sophisticated experiments that address these questions. Highly valuable in this respect are external triggers that enable us to precisely determine where, when, and to what extent a process is started or stopped. Light is an ideal external trigger: It is highly selective and if applied correctly also harmless. It can be generated and manipulated with well-established techniques, and many ways exist to apply light to living systems-from cells to higher organisms. This Review will focus on developments over the last six years and includes discussions on the underlying technologies as well as their applications.     

Meeting the sustainable development goals in a tropical climate

This article reflects on the Federation of Asian Chemical Societies (FACS) Citation Award Lecture delivered in the Industrial Technology Research Institute Symposium on CO₂ Utilization and Green Technology during the 18th Asian Chemical Congress held in Taipei, December 12, 2019. Malaysia produces sizable amounts of palm oil and palm kernel oil, with palm fronds and tree trunks as the main waste. At the Malaysia Japan International Institute of Technology, the biomass was decomposed to produce fine chemicals, used as substrate for mushroom growth, and converted to bio-coke for heat energy. A notable difference has been found regarding the emission of greenhouse gases from a natural peat forest and those from the oil palm plantation converted from peatlands, where in the palm plantation, water table is lowered and aerobic processes occurs, resulting in more CO₂ being released compared to CH₄. The introduction of fertilizers to the plantation resulted in more N₂O being released. The team has also pioneered a project to plant temperate vegetables. Cooling pipes (16–18°C with circulating water cooled by chiller) were embedded within each thermal conditioning soil plot. Lettuce and radish, the experimental plants, showed good growth in the thermal conditioning soil due to nitrogen-fixing bacteria, which were destroyed at a higher temperature.     

Effect of Photoinduced Size Changes on Protein Refolding and Transport Abilities of Soft Nanotubes

Self‐assembly of azobenzene‐modified amphiphiles (Gly_nAzo, n=1–3) in water at room temperature in the presence of a protein produced nanotubes with the protein encapsulated in the channels. The Gly₂Azo nanotubes (7 nm internal diameter [i.d.]) promoted refolding of some encapsulated proteins, whereas the Gly₃Azo nanotubes (13 nm i.d.) promoted protein aggregation. Although the 20 nm i.d. channels of the Gly₁Azo nanotubes were too large to influence the encapsulated proteins, narrowing of the i.d. to 1 nm by trans‐to‐cis photoisomerization of the azobenzene units of the Gly₁Azo monomers packed in the solid bilayer membranes led to a squeezing out of the proteins into the bulk solution and simultaneously enhanced their refolding ratios. In contrast, photoinduced transformation of the Gly₂Azo nanotubes to short nanorings (<40 nm) with a large i.d. (28 nm) provided no further refolding assistance. We thus demonstrate that pertubation by the solid bilayer membrane wall of the nanotubes is important to accelerate refolding of the denatured proteins during their transport in the narrow nanotube channels.