Goldilock’s Conundrum

Which Rotaxane Macrocycle is Just Right?

A rotaxane is a mechanically-interlocked molecule that consists of one or more rings trapped on a linear unit, the thread, by two bulky constituents, the stoppers. Remarkably, the ring components are not covalently attached to the dumbell component, rather a mechanical bond is present that intrinsically links the components of the molecule and prevents their dissociation without the cleavage of one, or more, covalent bonds. The synthesis of these interlocked molecules is of much interest to chemists today as a means of not only synthetically mimicking molecular geometries found in nature, but also, and perhaps more interestingly, as a means of exploiting the emergent properties imparted as a result of the mechanical bond for function as catalysts, motors and sensors, to name but a few examples.

The synthesis of rotaxanes is analogous to Goldilock’s quest to find the perfect bowl of porridge or the bed that is just right – finding the correctly-sized macrocycle to thread a rotaxane dumbbell is also a game of too big, too small or just right. Historically speaking, many of the rotaxanes reported thus far achieve “just right” by providing a steric bulk to the dethreading of the two components by simply increasing the size of the rotaxane stoppers. This is a valid approach, however it would also be advantageous in terms of synthetic ease and the possibility of introducing diversity to the rotaxane library if we could move away from big macrocycles and the necessary bulky stoppers, to smaller stoppers that allow for much smaller macrocycles.

But – how small is too small? Sometimes a macrocycle is just not big enough. Steve Moratti and James Crowley of the University of Otago, and coincidentally where i began my foray into chemistry, have set out to study just this – what is the smallest macrocycle that can be incorporated into a [2]rotaxane synthesized using the highly efficient Cu(I)-catalyzed Huigsen 1,3-dipolar cycloaddition active metal template approach developed by the Leigh group( JACS, DOI:10.1021/JA056903F).

To date, the smallest macrocycle that has been utilized in the synthesis of such rotaxanes is a 26-membered ring that generates [2]rotaxanes in high yields (DOI; 10.002/ANIE.201100415). Moratti and Crowley took this exploration a step further and studied the possibility of rotaxanation using even smaller 22- and 24-membered rings. One of the biggest advantages of moving towards smaller rotaxanes is the greater ability with which they can be functionalized over their larger analogues. Smaller macrocycles and less chemically-complicated stopper groups can be functionalized much more readily, as demonstrated in this work by the incorporation of a free hydroxymethyl group into the macrocycle and the use of unfunctionalized phenyl groups in the stopper components.

This study determined that the limit for rotaxanation was the larger of the two rings, with a [2]rotaxane forming in 70% yield –  read the article in full for free* to find out more!

CuAAC “click” active-template synthesis of functionalised [2]rotaxanes using small exo-substituted macrocycles: how small is too small?
Asif Noor, Warrick K. C. Lo, Stephen C. Moratti and James D. Crowley
DOI: 10.1039/C4CC03077J

You may also like to have a look at this Feature Article by Edward Neal and Stephen Goldup* from Queen Mary University, which reviews some of the less discussed consequences of mechanical bonding for the chemical behaviour of rotaxanes, and their application in synthesis

*Access is free through a registered RSC account – click here to register

About the web writer

Anthea Blackburn is a guest web writer for Chemical Science. Anthea is a graduate student hailing from New Zealand, studying at Northwestern University in the US under the tutelage of Prof. Fraser Stoddart (a Scot), where she is exploiting supramolecular chemistry to develop multidimensional systems and study the emergent properties that arise in these superstructures. When time and money allow, she is ambitiously attempting to visit all 50 US states before graduation.

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Reviewing the synthesis of marine sponge metabolites

by webwriter Kate Montgomery, who is currently doing a PhD in drug delivery using polymer based nanoparticles, her project is a collaboration between Imperial College London and CSIRO in Melbourne. When she is not making extremely sticky polymers in the lab, Kate enjoys reading, running (very slowly) and deep sea diving.

This ChemComm Feature Article by Chuo Chen’s group, based at the Southwestern Medical Center, University of Texas focuses on biosynthesis and total synthesis of cyclic pyrrole-imidazole dimers. Pyrrole-imidazole alkaloids are secondary metabolites which are found exclusively in marine sponges. They have very unique structures and attractive biological properties. Part of what makes these molecules so interesting is the fact that they contain many functional groups and are highly populated with nitrogen atoms. Pyrrole-imidazole alkaloids often have polycyclic skeletons which make them ideal platforms to work on in the development of new synthetic ideas and methodologies.

AgeliferinMany pyrrole-imidazole alkaloids have been tested and determined to have promising biological properties such as anticancer, antimicrobial, antiviral or immunosuppressive activities. Although this is the case, much work still needs to be carried out to determine the full biological profile of pyrrole-imidazole alkaloids.

Another aspect of pyrrole-imidazole alkaloids which still contains unknowns is the biosynthetic pathway; a range of biosynthetic pathways have been suggested but the complete route has not yet been fully determined. It is agreed that the main stages of the biosynthesis are catalysed by cyclases and oxidases but the exact enzymes have not been identified. A number of interesting hypotheses are highlighted and discussed in this review including work from Faulkner and Clardy who isolated the first dimeric pyrrole-imidazole alkaloid, sceptrin, in 1981.

As well as summarising different biosynthetic routes to these intriguing compounds the authors also discuss synthetic strategies. Numerous groups have successfully synthesised different pyrrole-imidazole dimers and highlights of this section include Baran’s work synthesising a number of different dimers and Chen’s own work which involves developing a biomimetic approach for the synthesis of ageliferins. Chen’s synthesis contains an oxidative radical cyclisation as the key step to give the ageliferin core skeleton. The group have successfully synthesised a range of ageliferins using this adaptable approach.

To download the full article for free* click the link below:

Dimeric pyrrole-imidazole alkaloids: synthetic approaches and biosynthetic hypotheses
Xiao Wang, Zhiqiang Ma, Xiaolei Wang, Saptarshi De, Yuyong Ma and Chuo Chen
DOI: 10.1039/c4cc02290d

*Access is free until the 12.07.14 through a registered RSC account – click here to register

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Dual warhead kills and disarms bacteria

Carla Pegoraro writes about a hot ChemComm article for Chemistry World

A compound that kills bacteria and cleaves their DNA to prevent them passing on drug-resistant genes has been designed by researchers in India.

The increasing ineffectiveness of antibiotics and the absence of suitable new ones are problems long recognised by the medical community. Bacteria can mutate and adapt to become resistant so the stock of effective antibiotics is diminishing. In a recent report, the UK’s Chief Medical Officer stated that increasingly resistant microbes represent a global threat that in the next 20 years could see many more deaths associated with what were routine and safe surgeries.


Read the full article in Chemistry World»

Read the original journal article in ChemComm – it’s free to download until 11th July:
A prospective antibacterial for drug-resistant pathogens: a dual warhead amphiphile designed to track interactions and kill pathogenic bacteria by membrane damage and cellular DNA cleavage
Durairaj Thiyagarajan, Sudeep Goswami, Chirantan Kar, Gopal Das and Aiyagari Ramesh
Chem. Commun., 2014, Advance Article, DOI: 10.1039/C4CC02354D, Communication

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ChemComm Emerging Investigator Lectureship Tours

Announcing the locations of our Emerging Investigator Lectureships tours for last year’s recipients

We are pleased to announce the locations of this summer’s ChemComm Emerging Investigator Lectureships tours. They will take place at conferences and universities across Europe, where our winners will showcase their latest research.

louiseProfessor Louise A. Berben (University of California Davis, USA)

26 June – 3 July 2014

Imperial College London, UK
University of Bristol, UK
Challenges in Inorganic and Materials Chemistry (ISACS13), Dublin, Ireland

Marina KuimovaDr Marina Kuimova (Imperial College London)

7 – 13 July 2014

Universidad del País Vasco-EHU, Bilbao, Spain
Donostia International Physics Center (DIPC), San Sebastian, Spain
25th IUPAC Symposium on Photochemistry, Bordeaux, France

Our annual lectureship recognises an emerging scientist in the early stages of their independent academic career.

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Printable Nanoscale Catalysts with Controlled Nano-morphologies

Iain Larmour is a guest web writer for ChemSci. He has researched a wide variety of topics during his years in the lab including nanostructured surfaces for water repellency and developing nanoparticle systems for bioanalysis by surface enhanced optical spectroscopies. He currently works in science management. In his spare time he enjoys reading, photography, art and inventing.

Nanoscale metal rings and dots could find potential use in a wide range of applications including catalysis. However, the impact the morphology differences have must be unambiguously ascertained before they can be used in practical applications. For this to be achieved there needs to be a simple and efficient fabrication process that can create arrays of nanoscale metal rings or dots for study.

Won Bae Kim and team, from the School of Materials Science and Engineering at the Gwangju Institute of Science and Technology, report such a method in their new ChemComm paper. They make use of the powerful transfer printing technique, but importantly have created suitable stamps that can generate ring or dot arrays. These stamps use one dimensional carbon nanostructures that are supported within the hexagonal pores of anodic aluminium oxide, the tip shapes being controlled by ion milling conditions. After loading with a suitable catalytic metal they are then used in transfer printing onto indium tin oxide substrates.

SEM images of nanoring and nanodot stamps showing the supported one dimensional carbon structures within the AAO pores.


The team demonstrate the catalytic ability of the printed metal ring and dot arrays by studying methanol oxidation in acidic solution with platinum structures and carbon monoxide electrooxidation in alkaline solution with gold structures. With this approach they were able to study the effect of morphology on the catalytic activity – to find out which was better, rings or dots, you will have to read the ChemComm article today!

To read the details for free* check out the Chem Comm article in full:

Transfer printing of metal nanoring and nanodot arrays for use in catalytic reactions

Sang Ho Lee, Sung Mook Choi, Seungha Yoon, Huisu Jeong, Gun Young Jung, Beong Ki Cho and Won Bae Kim

DOI: 10.1039/C4CC02939A

*Access is free untill Friday 4th July through a registered RSC account – click here to register

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Top 25 most downloaded ChemComm articles Jan–Mar 2014

Read on to find out which ChemComm articles your colleagues were downloading most in the first quarter of 2014

Nanoporous metal formates for krypton/xenon separation
Keith V. Lawler, Zeric Hulvey and Paul M. Forster
DOI: 10.1039/C3CC44374D

MoS2–MWCNT hybrids as a superior anode in lithium-ion batteries
Kartick Bindumadhavan, Suneel Kumar Srivastava and Sourindra Mahanty
DOI: 10.1039/C3CC38598A

Fe-Catalysed oxidative C–H/N–H coupling between aldehydes and simple amides
Jing Wang, Chao Liu, Jiwen Yuan and Aiwen Lei
DOI: 10.1039/C4CC01447B

Kinetic trapping of the host–guest association intermediate and its transformation into a thermodynamic inclusion complex

Oksana Danylyuk, Vladimir P. Fedin and Volodymyr Sashuk
DOI: 10.1039/C3CC37868C

A turn-on fluorescent Fe3+ sensor derived from an anthracene-bearing bisdiene macrocycle and its intracellular imaging application
Lin Qiu, Chengcheng Zhu, Huachao Chen, Ming Hu, Weijiang He and Zijian Guo
DOI: 10.1039/C3CC49482A

A one-step low temperature processing route for organolead halide perovskite solar cells

Matthew J. Carnie, Cecile Charbonneau, Matthew L. Davies, Joel Troughton, Trystan M. Watson, Konrad Wojciechowski, Henry Snaith and David A. Worsley
DOI: 10.1039/C3CC44177F

Preparation of conjugated 1,3-enynes by Rh(III)-catalysed alkynylation of alkenes via C–H activation
Karl D. Collins, Fabian Lied and Frank Glorius
DOI: 10.1039/C4CC01141D

A robust, catalytic metal–organic framework with open 2,2′-bipyridine sites
Honghan Fei and Seth M. Cohen
DOI: 10.1039/C4CC01607F

Copper-catalysed oxidative C–H/C–H coupling between olefins and simple ethers
Dong Liu, Chao Liu, Heng Li and Aiwen Lei
DOI: 10.1039/C4CC00867G

Graphene quantum dots: emergent nanolights for bioimaging, sensors, catalysis and photovoltaic devices

Jianhua Shen, Yihua Zhu, Xiaoling Yang and Chunzhong Li
DOI: 10.1039/C2CC00110A

Flexible, low-temperature, solution processed ZnO-based perovskite solid state solar cells

Mulmudi Hemant Kumar, Natalia Yantara, Sabba Dharani, Michael Graetzel, Subodh Mhaisalkar, Pablo P. Boix and Nripan Mathews
DOI: 10.1039/C3CC46534A

A sensitive colorimetric and fluorescent sensor based on imidazolium-functionalized squaraines for the detection of GTP and alkaline phosphatase in aqueous solution
Ningjie Wu, Jingbo Lan, Lipeng Yan and Jingsong You
DOI: 10.1039/C4CC00752B

Copper-mediated S–N formation via an oxygen-activated radical process: a new synthesis method for sulfonamides

Xin Huang, Jichao Wang, Zhangqin Ni, Sichang Wang and Yuanjiang Pan
DOI: 10.1039/C4CC01353K

Optical bleaching of perovskite (CH3NH3)PbI3 through room-temperature phase transformation induced by ammonia
Yixin Zhao and Kai Zhu
DOI: 10.1039/C3CC48522F

Direct N-acylation of azoles via a metal-free catalyzed oxidative cross-coupling strategy

Jingjing Zhao, Pan Li, Chungu Xia and Fuwei Li
DOI: 10.1039/C4CC01587H

“Click”-extended nitrogen-rich metal–organic frameworks and their high performance in CO2-selective capture
Pei-Zhou Li, Xiao-Jun Wang, Kang Zhang, Anjaiah Nalaparaju, Ruyi Zou, Ruqiang Zou, Jianwen Jiang and Yanli Zhao
DOI: 10.1039/C3CC49457H

Efficient photocatalytic hydrogen generation from water by a cationic cobalt(II) porphyrin
Mirco Natali, Alessandra Luisa, Elisabetta Iengo and Franco Scandola
DOI: 10.1039/C3CC48882A

ZnCl2-catalyzed chemoselective cascade reactions of enaminones with 2-furylcarbinols: a versatile process for the synthesis of cyclopenta[b]pyrrole derivatives
Chengyu Wang, Chunyi Dong, Lingkai Kong, Yanli Li and Yanzhong Li
DOI: 10.1039/C3CC49191A

Manganese-catalyzed intermolecular C–H/C–H coupling of carbonyls and heteroarenes
Keika Hattori, Asraa Ziadi, Kenichiro Itami and Junichiro Yamaguchi
DOI: 10.1039/C4CC01376J

A copper(I)/copper(II)–salen coordination polymer as a bimetallic catalyst for three-component Strecker reactions and degradation of organic dyes
Yun-Long Hou, Raymond Wai-Yin Sun, Xiao-Ping Zhou, Jun-Hao Wang and Dan Li
DOI: 10.1039/C3CC47996J

Aerobic oxidation catalysis with stable radicals
Qun Cao, Laura M. Dornan, Luke Rogan, N. Louise Hughes and Mark J. Muldoon
DOI: 10.1039/C3CC47081D

Reduction of graphene oxide viaL-ascorbic acid
Jiali Zhang, Haijun Yang, Guangxia Shen, Ping Cheng, Jingyan Zhang and Shouwu Guo
DOI: 10.1039/B917705A

Versatile ruthenium(II)-catalyzed C–H cyanations of benzamides

Weiping Liu and Lutz Ackermann
DOI: 10.1039/C3CC49502G

Revealing the metal-like behavior of iodine: an iodide-catalysed radical oxidative alkenylation
Shan Tang, Yong Wu, Wenqing Liao, Ruopeng Bai, Chao Liu and Aiwen Lei
DOI: 10.1039/C4CC00644E

Iodine-catalyzed three-component oxysulfenylation of alkenes with sulfonyl hydrazides and alcohols
Fu-Lai Yang, Fu-Xiang Wang, Ting-Ting Wang, Yi-Jie Wang and Shi-Kai Tian
DOI: 10.1039/C3CC48961B


ChemComm is the home of urgent high quality communications from across the chemical sciences. With a world renowned reputation for quality and fast times to publication (average of 40 days), ChemComm is the ideal place to publish your research. 

Submit your urgent research to ChemComm today! 

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International Symposia on Advancing the Chemical Sciences 7-10 August 2014

Don’t miss your chance to showcase your work – there are only 2 weeks left until the poster abstract deadline

ISACS 14 Challenges in Organic Chemistry will bring together world leading experts in the field of organic chemistry and synthesis.

The best contribution will be awarded a fantastic prize from Chemistry World so don’t delay, be sure to submit your poster abstract by 2 June 2014.

Themes for the ISACS 14, Shanghai China are:

  • Organic and metal based catalysis
  • Total Synthesis
  • New Synthetic methodologies
  • Physical organic chemistry
  • Bioorganic and medicinal chemistry
  • For more information on how to submit your poster abstract please visit our conferences and events homepage.

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    Erwin Reisner 2014 RSC Award winner

    Please join us in congratulating Erwin Reisner on his achievement

    Harrison-Meldola Memorial PrizeHarrison-Meldola Memorial Prize

    ChemComm Advisory Board member Erwin Reisner is a Harrison-Meldona Memorial Prize winner. Erwin was awarded this prize for his work in combining molecular synthesis, chemical biology and materials chemistry to develop artificial photosynthesis.

    Erwin’s communication ‘Al-doped ZnO inverse opal networks as efficient electron collectors in BiVO4 photoanodes for solar water oxidation’ (C3EE44031A) is part of the ‘Celebrating the 2014 RCS Prize and Award Winners’ themed collection and is free* to access for a limited time only.

    You can access papers by other 2014 RSC Prize and Award Winners for free* for a limited time. A full list of winners and more information about RSC Prizes and Awards can be found at: www.rsc.org/awards.

    *Access is free until 06.06.14 through a registered RSC account – click here to register

    Erwin recent tutorial review describes an emerging technique which allows for the light-dependent activity of Photosystem II adsorbed onto an electrode surface to be studied. This fascinating review can be accessed by clicking the link below.

    Protein film photoelectrochemistry of the water oxidation enzyme photosystem II
    Masaru Kato, Jenny Z. ZhangNicholas Paul and Erwin Reisner
    DOI: 10.1039/C4CS00031E

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    Congratulations to the Poster Prize winners at the Spring 2014 RSC Carbohydrate Group Meeting!

    The Royal Society of Chemistry Carbohydrate Group held a successful meeting at the University of Bath from Wednesday 30 April–Thursday 1 May.

    Three of our journals – ChemComm, Chemical Science and Organic & Biomolecular Chemistry – were delighted to sponsor a poster prize each and we would like to join in congratulating the winners. Jerry Turnbull, Chair of the RSC Carbohydrate Group, presented the prizes as follows:

    ChemComm Poster Prize
    ‘Lactose as a ‘Trojan Horse’ for QD Cell Transport’
    David Benito-Alifonso
    University of Bristol

    Chemical Science Poster Prize
    The Biosynthesis of and Synthetic Approaches to Double C-glycosides’
    Kevin Mahone
    University of St. Andrews

    Organic & Biomolecular Chemistry Poster Prize
    ‘L-glucose and D-idose from D-glucose’
    Zilei Liu
    Oxford University

    Left to Right: David Benito-Alifonso; Kevin Mahoney; Zilei Liu; Jerry Turnbull

      For more details about the meeting, visit the RSC Carbohydrate 2014 website.

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    Betaine Bistriflimide: F-block chemistry enabled by a stabilizing Ionic Liquid

    Kevin Murnaghan is a guest web-writer for Chemical Communications. He is currently a Research Chemist in the Adhesive Technologies Business Sector of Henkel AG & Co. KGaA, based in Düsseldorf, Germany. His research interests focus primarily on enabling chemistries and technologies for next generation adhesives and surface treatments. Any views expressed here are his personal ones and not those of Henkel AG & Co. KGaA.

    Due to their low volatility, favourable solvent properties and tunable phase behaviour, ionic liquid (IL) technology continues to attract interest in a wide variety of applications. Over the last few decades, the term ‘task specific ionic liquid’ (TSIL) has appeared, the meaning of which is that the application has been considered more carefully in the design and structure of one or both of the constituent IL ions.

    In this ChemComm communciation, researchers from the Los Alamos National Laboratory, New Mexico, USA, describe advances in the application of ILs in the area of nuclear fuel reprocessing. The authors describe how neptunium may exist in solution in +III, +IV, +V and + VI oxidation states. The pentavalent state is the most stable and common, but interestingly, usually the most reluctant to coordinate with ligands, or take part in ion exchange processes.

    Ionic liquid molecular structure and stabilizing behaviour towards Np(V) in aqueous solution


    In aqeuous solution, in the presence of the ionic liquid betaine bistriflimide, the lifetime of the Np(IV) solution species is significantly increased. This is followed by the presence of a characteristic electronic adsorption at 970nm. Without the IL, an anti-oxidant is required to keep the metal from converting to its +V form. Np(V) has a rich and complex coordination chemistry at room temperature, so the authors repeated experiments with sources of  Np(V) at 60oC. After 3 days, 90% of the starting neptunium compound had been converted to the betaine complexed form, compared with a 15% conversion at room temperature. Again the material was stable in solution, not resulting in Np(IV) species unless a reducing agent such as hydrazine was deliberately added.

    With this detailed study, the authors significantly add to the body of knowledge of competitive coordination chemistry of actinides in aqueous solutions of ionic liquids. This should, in turn, enable new separation technology R&D for the important task of nuclear fuel reprocessing.

    Read this ChemComm communication for free* today!

    Unusual redox stability of neptunium in the ionic liquid [Hbet][Tf2N]
    Kristy Long, George Goff and Wolfgang Runde
    DOI: 10.1039/C4CC01835D

    *Access is free untill Friday 6th June through a registered RSC account – click here to register


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