Archive for the ‘Hot Articles’ Category

Customised peptides via nickel/photoredox-catalysed bioconjugation

Proteins have an expansive utility in the structure, function, replication and regulation of all cells, and developing tools to study each role is to the benefit of our continued health and wellbeing. One tool is protein bioconjugation, the covalent pairing of a molecule with a protein. Molecule-protein combinations are endless, provided there are efficient methods available to couple molecules with amino acids. Among bioconjugation methods, cysteine functionalisation is a popular choice because the primary thiol is highly nucleophilic thus aiding chemoselectivity. Furthermore, cysteine is rare, reducing the likelihood of many competing, reactive residues.

Transition metal catalysed transformations are uncommon in bioconjugations, despite prominence in other areas of synthetic chemistry. This is because only the most robust methods can overcome the challenges of this chemistry: the solubility of substrates in solvents other than aqueous media, the presence of other amino acids bearing reactive functional groups, and the requirement for low temperatures, low concentrations and mild pH to preserve protein structure.

Catalytic cycle for the nickel/phororedox catalysed synthesis of cysteine bioconjugates

Catalytic cycle for the nickel/phororedox catalysed synthesis of cysteine bioconjugates

A group of researchers from the University of Pennsylvania headed by Professor Gary Molander have developed a bioconjugation method in which aryl halides are cross-coupled with cysteine residues in peptides. Two complexes catalyse the reaction in two connected cycles: the photoredox cycle by a ruthenium-bipyridine complex, and the catalytic cycle by a nickel-bipyridine complex.

The reaction is efficient at room temperature and does not require prior functional group protection. The reaction can also be performed under dilute conditions (10 mM) and on gram scale (3.5 mmol). The scope table includes more than 35 reactions coupling a broad range of aryl halides with small peptides (4 and 9 amino acids) and biologically relevant molecules such as coenzyme A and sulphur-containing pharmaceuticals.

Protecting-group free functionalisation of small peptides under dilute conditions using nickel and ruthenium photoredox catalysis for cysteine functionalization

Protecting group free functionalisation of small peptides under dilute conditions

Included in the reaction scope are a number of substrates which highlight how this work can adapt to established techniques for studying proteins. Coupling of a coumarin generates a fluorescent molecule, which could be used to study the cellular localisation of a protein. Reaction with an aryl-bound biotin derivative demonstrates that affinity tags can be coupled, and utilising aryl-containing pharmaceutical agents is relevant to the synthesis of antibody-drug conjugates.

With this research the authors have contributed a robust catalytic system, which convincingly shows the value of combining a transition metal and photoredox catalyst to functionalise cysteine residues in biomolecules. A necessary next step for this chemistry, and no small task, is to further optimise the reaction conditions for whole proteins.

Read the research article:

Scalable thioarylation of unprotected peptides and biomolecules under Ni/photoredox catalysis

Chem. Sci., 2018, DOI: 10.1039/C7SC04292B

Brandon A. Vara, Xingpin Li, Simon Berritt, Christopher R. Walters, E. James Petersson, Gary A. Molander.


About the Author: 

Zoë Hearne is a PhD candidate in chemistry at McGill University in Montréal, Canada, under the supervision of Professor Chao-Jun Li. She hails from Canberra, Australia, where she completed her undergraduate degree. Her current research focuses on transition metal catalysis to effect novel transformations, and out of the lab she is an enthusiastic chemistry tutor and science communicator.

 

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Measuring the Strength of Hydrogen Bonds

For the first time, a group of scientists from University of California, San Diego in United States has quantitatively measured the strength of hydrogen bonds between two complex molecules. They also observed an abnormal trend regarding the bond strength in the absence and presence of electron transfer. This work contributes to the understanding of how the hydrogen bond strength changes, an important point that reveals the way biological systems function.

Hydrogen bonds are a type of electrostatic attraction between hydrogen atoms and certain highly electronegative atoms including N, O and F. These bonds help to bind individual water molecules together and keep water as liquid at room temperature, a critical condition for the origin of life.

The researchers, led by Prof. Kubiak, picked two ruthenium-based complexes joined by hydrogen bonds as their studying platform. As shown in Figure 1, the two-molecule system has three states depending on whether the ends are charged or not: the neutral state when both ends are not charged (left), the singly reduced state when only one end is negatively charged (middle), and the doubly reduced state when both ends are negatively charged (right). The group utilized infrared spectroscopy, UV-vis spectroscopy and electrochemical measurements to experimentally determine the strength of hydrogen bonds in these different redox states.

The results from the study found that the hydrogen bond energy of the neutral state and the doubly reduced state was in the range of 2.56-2.88 kcal/mol and 4.50-4.63 kcal/mol, respectively. Surprisingly, the hydrogen bond energy of the singly charged state did not lie between that of the neutral state and the doubly reduced state. It ranged from 7.78 kcal/mol to 8.31 kcal/mol, indicating the hydrogen bond is much stronger than for both the neutral and doubly-reduced states. The authors ascribed such an abnormality to the reinforcement brought by electron transfer i.e., the movement of the negative charge between the two ends.

This work is the first demonstration that hydrogen bond strength can be significantly enhanced by electron delocalization.

Figure 1. A schematic diagram showing the hydrogen bond strength of the singly reduced state (middle), the neutral state (left) and the doubly reduced states (right). [Note: In this figure, the lower the state lies, the stronger its hydrogen bond is. ET: electron transfer.]

To find out more please read:

Effects of Electron Transfer on the Stability of Hydrogen Bonds

Tyler M. Porter, Gavin P. Heim and Clifford P. Kubiak

Chem. Sci. DOI: 10.1039/c7sc03361c

About the blogger:

Tianyu Liu is a Ph.D. in chemistry graduated from University of California, Santa Cruz in United States. He is passionate about scientific communication to introduce cutting-edge researches to both the general public and the scientists with diverse research expertise. He is a web blogger for the Chem. Commun. and Chem. Sci. blog websites. More information about him can be found at http://liutianyuresearch.weebly.com/.

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Reductive power of hydrated electrons unleashed with green lasers


Source: © Royal Society of Chemistry
Laboratory-scale photoredox catalysis using hydrated electrons sustainably generated with a single green laser. Asc = ascorbate dianion, OER = one-electron reduced form, GS = ground state, MLCT = metal-to-ligand charge-transfer excited state

Solvated electrons are highly reductive so can force stubborn compounds to react where other reagents might fail. Now a team in Germany is generating them sustainably, using only a green laser and vitamin C. The group has used the technique to perform reactions previously impossible with a visible-light responsive catalyst.

Photons from the laser transform a ruthenium-based photocatalyst into an excited state, with a central oxidised ruthenium atom and a radical anion ligand. Vitamin C’s ascorbate dianion then quenches the excited species, producing a one-electron reduced form of the complex – where the ruthenium atom is no longer oxidised, but the ligand remains as a radical anion. Another photon can then eject the additional electron – generating the hydrated electron species that can induce reduction reactions of organic compounds, and simultaneously returns the catalyst to its ground state.

Read the full story by Jamie Durrani on Chemistry World.

 

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HOT Chemical Science articles for September

All of the referee-recommended articles below are free to access.

Chemoenzymatic synthesis of heparan sulfate and heparin oligosaccharides and NMR analysis: paving the way to a diverse library for glycobiologists
Xing Zhang, Vijayakanth Pagadala, Hannah M. Jester, Andrew M. Lim, Truong Quang Pham, Anna Marie P. Goulas, Jian Liu and  Robert J. Linhardt
Chem. Sci., 2017, Advance Article
DOI: 10.1039/C7SC03541A, Edge Article

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Displacement and hybridization reactions in aptamer-functionalized hydrogels for biomimetic protein release and signal transduction
Jinping Lai, Shihui Li, Xuechen Shi, James Coyne, Nan Zhao, Fengping Dong, Yingwei Mao and  Yong Wang
Chem. Sci., 2017, Advance Article
DOI: 10.1039/C7SC03023A, Edge Article

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Effects of electron transfer on the stability of hydrogen bonds
Tyler M. Porter, Gavin P. Heim and Clifford P. Kubiak
Chem. Sci., 2017, Advance Article
DOI: 10.1039/C7SC03361C, Edge Article

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Drilling Holes on Metal Organic Framework Crystals with Phosphoric Acid

Synthesis of porous materials with tunable pore size remains a long-standing challenge for materials research. These materials, particularly hierarchical porous materials with copious different sized pores, are attractive candidates as catalysts, battery electrodes, and guest molecule hosts etc. An ideal synthesis protocol of hierarchical porous materials should be easy and capable of fine tuning pore size within a wide size range as well as able to preserve structural integrity. Unfortunately, it is extremely challenging for the currently developed methods to achieve the aforementioned three characteristics simultaneously.

Recently, this challenge has been addressed by Kimoon Kim and co-workers from the Institute of Basic Science and the Pohang University of Science and Technology in Republic of Korea. Their strategy targeted at metal organic frameworks (MOFs), a family of highly porous crystalline materials built by interconnected metal-organic complexes, as the starting materials. Phosphoric acid was chosen to selectively break down the building blocks and create pores with tunable diameters (Figure 1). Detailed synthesis procedures are published in Chemical Science.

Figure 1. Schematic illustration of the major steps of the demonstrated strategy.

The authors specifically chose the octahedral-shaped MIL-100(Fe) MOF crystals as an example, and demonstrated that their method could readily turn the original smooth crystals into highly porous ones merely by phosphoric acid aqueous solutions. Moreover, simply changing the concentration of phosphoric acid was able to tune the diameter of the created pores from 2.4 nm to 18.4 nm (Figure 2).

Figure 2. Scanning electron microscopy images and pore diameter distributions (showing pores larger than 2 nm only) of different MOFs: (a) the untreated MIL-100(Fe) and the acid treated MIL-100(Fe) with phosphoric acid concentration of (b) 20 mM, (c) 40 mM, (d) 60 mM and (e) 80 mM. All scale bars represent 200 nm.

Structural evolution analysis revealed that the etching process initiated preferably by cleaving the coordination bonds between metal cores and organic ligands around the hexagonal windows on (2 2 0) crystal planes. It further propagated to dig out the inner part of MIL-100(Fe), forming pores on surface.

This method is expected to be applicable to other MOFs coupled with properly selected etchants, thus making the hierarchical porous crystals with tailorable porous structures readily available to worldwide materials researchers.

To find out more please read:

Hollowing Out MOFs: Hierarchical Micro- and Mesoporous MOFs with Tailorable Porosity via Selective Acid Etching

Jaehyoung Koo, In-Chul Hwang, Xiujun Yu, Subhadeep Saha, Yonghwi Kim and Kimoon Kim

DOI: 10.1039/c7sc02886e

About the blogger:

Tianyu Liu is a Ph.D. in chemistry graduated from University of California-Santa Cruz. He is passionate about scientific communication to introduce cutting-edge researches to both the general public and the scientists with diverse research expertise. He is a web writer for the Chem. Commun. and Chem. Sci. blog websites. More information about him can be found at http://liutianyuresearch.weebly.com/.

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HOT Chemical Science articles for August

All of the referee-recommended articles below are free to access.

Effects of Electron Transfer on the Stability of Hydrogen Bonds
Tyler M. Porter,  Gavin P, Heim and Clifford P. Kubiak
Chem. Sci., 2017, Accepted Manuscript
10.1039/C7SC03361C, Edge Article

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Magnetic Control of Cellular Processes using Biofunctional Nanoparticles
Cornelia Monzel, Chiara Vicario, Jacob Piehler, Mathieu Coppey and Maxime Dahan
Chem. Sci., 2017, Accepted Manuscript
10.1039/C7SC01462G, Minireview

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Hollowing out MOFs: hierarchical micro- and mesoporous MOFs with tailorable porosity via selective acid etching
Jaehyoung Koo, In-Chul Hwang, Xiujun Yu, Subhadeep Saha, Yonghwi Kima and Kimoon Kim
Chem. Sci., 2017, Advance Article
10.1039/C7SC02886E, Edge Article

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Biosynthesis of methyl-proline containing griselimycins, natural products with anti-tuberculosis activity
Peer Lukat, Yohei Katsuyama, Silke C. Wenzel, Tina Binz, Claudia König, Wulf Blankenfeldt, Mark Brönstrup and Rolf Müller
Chem. Sci., 2017, Accepted Manuscript
10.1039/C7SC02622F, Edge Article

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Mimicking Biological Systems with Supramolecular Assemblies: A Step Closer

Biological systems, such as circadian rhythms and ion pumps, are generally able to respond autonomously to chemical stimuli. Such ability is at the root of certain amphiphilic molecules (i.e. molecules containing both hydrophilic and hydrophobic parts) that can change their configurations temporally at the presence of the stimulants. In recent decades, building artificial biological systems with active, adaptive and autonomous behaviours similar to natural biological systems has become a hot topic.

Supramolecular assemblies are among the most extensively explored building materials. A supramolecular assembly is a system consisting of complex molecules held together by non-covalent bonds, such as DNA. One of the major technological hurdles for developing artificial biological systems using supramolecular assemblies is to acquire assemblies with an amphiphilic nature and the ability to undergo a transient change of configuration when stimulated. The change should also be highly reversible and durable. Currently, extensive research efforts are committed to finding candidates that address the aforementioned challenge.

A research group from Jawaharlal Nehru Centre for Advanced Scientific Research in India recently made a step forward and published their work in Chemical Science. They developed an amphiphilic supramolecular motif, coined PN-VN foldamer, which could switch its conformation upon contact with oxidizing and reducing agents. As shown in Figure 1a, the skeleton of the supramolecular motif is composed of three sections. The green head is an electron donor pyranine (PN), the red tail is an electron acceptor called viologen (VN) rendering the hydrophobic nature, and the blue body is a flexible hydrophilic hexaethylene glycol that connects the electron donor and acceptor.

Figure 1. (a) The structure of the amphiphilic PN-VN foldamer. (b) Unfolded and folded states of the PN-VN foldamer correspond to sheet and vesicle morphologies, respectively.

The researchers demonstrated the assembly pattern of PN-VN foldamers (Figure 1b) by using two chemical fuels, sodium dithionite and glucose, as the stimulants. The transformation process is depicted in Figure 2a. When undisturbed, the negatively charged PN (PN3-) and the positively charged VN (VN2+) can attract each other via a charge transfer interaction, folding the entire molecular chains to vesicles. When placed in a solution containing sodium dithionite and glucose, the VN2+ terminal can be instantaneously reduced by sodium dithionite to its radical cation form (VN•+). The reduction weakens the charge transfer interaction, and subsequently unfolds PN-VN vesicles to sheets. Meanwhile, catalyzed by glucose oxidase (an enzyme), the excess glucose in the same solution can oxidize VN•+ back to its original state, resulting in the folded state that recovers vesicles. The transition is directly confirmed by transmission electron microscopy as shown in Figure 2b. Since the reduction process proceeds much faster than the oxidation process, it is observed that PN-VN vesicles first extend to sheets momentarily and gradually but automatically fold back to vesicles within minutes. The rate of the transition can be well tuned by varying the concentration of glucose oxidase.

Figure 2. (a) Schematic of the transient configuration change between vesicles and sheets. SDT: sodium dithionite; GOx: glucose oxidase. (b) Transmission electron microscopic images of the vesicles (left) and the sheets (right). Inset in the left panel shows the distribution of the wall thickness of the vesicles. Inset in the right panel is a confocal fluorescence microscopy image of a selected sheet (scale bar: 2 μm).

To find out more please read:

Temporal Switching of an Amphiphilic Self-assembly By a Chemical Fuel-driven Conformational Response

Krishnendu Jalani, Shikha Dhiman, Ankit Jain, and Subi J. George

DOI: 10.1039/c7sc01730h

About the author:

Tianyu Liu is a Ph.D. in chemistry graduated from University of California-Santa Cruz. He is passionate about scientific communication to introduce cutting-edge researches to both the general public and the scientists with diverse research expertise. He is a web writer for the Chem. Commun. and Chem. Sci. blog websites. More information about him can be found at http://liutianyuresearch.weebly.com/.

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HOT Chemical Science articles for July

All of the referee-recommended articles below are free to access.

Solid–State Molecular Organometallic Chemistry. Single–Crystal to Single–Crystal Reactivity and Catalysis with Light Hydrocarbon Substrates
F. Mark Chadwick, Alasdair I. McKay, Antonio J. Martinez-Martinez, Nicholas H. Rees, Tobias Krämer, Stuart A. Macgregor and Andrew S. Weller
Chem. Sci., 2017, Advance Article
DOI: 10.1039/C7SC01491K, Edge Article

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Efficient stabilisation of a dihydrogenphosphate tetramer and a dihydrogenpyrophosphate dimer by a cyclic pseudopeptide containing 1,4-disubstituted 1,2,3-triazole moieties
Disha Mungalpara, Arto Valkonen, Kari Rissanen and Stefan Kubik
Chem. Sci., 2017, Advance Article
DOI: 10.1039/C7SC02700A, Edge Article

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Dual targeting of the cancer antioxidant network with 1,4-naphthoquinone fused Gold(I) N-heterocyclic carbene complexes
R. McCall, M. Miles, P. Lascuna, B. Burney, Z. Patel, K. J. Sidoran, V. Sittaramane, J. Kocerha, D. A. Grossie, J. L. Sessler, K. Arumugam and J. F. Arambula
Chem. Sci., 2017, Advance Article
DOI: 10.1039/C7SC02153D, Edge Article

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Remote C–H insertion of vinyl cations leading to cyclopentenones
Sarah E. Cleary, Magenta J. Hensinger and Matthias Brewer
Chem. Sci., 2017, Advance Article
DOI: 10.1039/C7SC02768K, Edge Article

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HOT Chemical Science articles for June

The referee-recommended articles below are free to access until 5th August 2017.

Formation and decay of negative ion states up to 11 eV above the ionization energy of the nanofabrication precursor HFeCo3(CO)12
Ragesh Kumar T P, Ragnar Bjornsson, Sven Barth and Oddur Ingólfsson
Chem. Sci., 2017, Advance Article
DOI: 10.1039/C7SC01927K, Edge Article

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Structural-functional analysis of engineered protein-nanoparticle assemblies using graphene microelectrodes
Jinglei Ping, Katherine W. Pulsipher, Ramya Vishnubhotla, Jose A. Villegas, Tacey L. Hicks, Stephanie Honig, Jeffery G. Saven, Ivan J. Dmochowski and A. T. Charlie Johnson
Chem. Sci., 2017, Advance Article
DOI: 10.1039/C7SC01565H, Edge Article

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Light-driven catalytic process offers greener route to organic alcohols

Researchers in Spain have developed a light-driven catalytic process that offers a greener way to produce organic alcohols – important compounds used to manufacture pharmaceuticals and pesticides.

Researchers have developed a catalytic system to reduce aromatic ketones and both aliphatic and aromatic aldehydes that uses earth-abundant metals and light.

Read the full story by Jamie Durrani on Chemistry World.

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