Organic & Biomolecular Chemistry Blog

Multivalent scFvs, mitomycin C stereochemistry, peptide dendrimers and NET ligands in Issue 8

06 Feb 2012

On the cover of Issue 8 we have two cancer-related articles from Jacquelyn Gervay-Hague (University of California Davis) on multivalent single chain variable fragments with increased tumor-associated antigen affinity and from Federico Gago (Universidad de Alcalá) modelling the binding of mitomycin C and analogues to DNA.

A general chemical synthesis platform for crosslinking multivalent single chain variable fragments
Joan G. Schellinger, Avinash Kudupudi, Arutselvan Natarajan, Wenjun Du, Sally J. DeNardo and Jacquelyn Gervay-Hague
DOI: 10.1039/C0OB01259A

Rationale for the opposite stereochemistry of the major monoadducts and interstrand crosslinks formed by mitomycin C and its decarbamoylated analogue at CpG steps in DNA and the effect of cytosine modification on reactivity
Juan A. Bueren-Calabuig, Ana Negri, Antonio Morreale and Federico Gago
DOI: 10.1039/C1OB06675G

The issue also contains a review from Jean-Louis Reymond and Tamis Darbre on combinatorial libraries of peptide and glycopeptide dendrimers and hot papers on creating (D)-sugars from (L)-amino acids from Paul Clarke and stilbazolium dimers as NET ligands from James N. Wilson.

View the issue

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HOT article: (D)-sugars from (L)-amino acids – a step closer to understanding the origin of life

02 Feb 2012

By Francesca Burgoyne.

A conundrum for anyone studying the prebiotic world is how chirality first occurred, and why D-sugars are the natural isomers, whereas natural amino acids have the L-configuration. In this hot paper Paul Clarke and Christopher Hayes from the Universities of York and Nottingham have shown how carbohydrates could have formed in prebiotic conditions by producing (D)-erythrose and (D)-threose sugars with (L)-amino acid catalysts.

Having first used proline esters to catalyse the aldol reaction of TIPS-protected glycolaldehyde in water with good yields and moderate diastereo- and enantioselectivity, the group hypothesised that other proteinogenic amino acids (i.e. amino acids found in proteins) could also catalyse this reaction. Using N-methyl derivatives of the amino acid esters of (L)-alanine, (L)-leucine and (L)-valine they were able to produce the expected sugars, but were surprised to see that the (D)-enantiomer was the major product in all reactions. “This offers one potential explanation to account for the relationship between (L)-amino acids and (D)-sugars in nature” concludes Clarke.

This remarkable find has obviously generated a lot of interest in both scientific and the wider press: see articles in The Daily Mail, The Huffington Post, on Science Daily or the press release from University of York.

Asymmetric organocatalytic formation of protected and unprotected tetroses under potentially prebiotic conditions
Laurence Burroughs, Paul A. Clarke, Henrietta Forinto, James A. R. Gilks, Christopher J. Hayes, Matthew E. Vale , William Wade and Myriam Zbytniewski
DOI: 10.1039/C1OB06798B

This article is also part of our joint web theme issue with ChemComm on Organocatalysis and as with all our hot articles will be free to access for 4 weeks.

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Countdown to OBC 10th Anniversary continues

02 Feb 2012

By Marie Cote, Deputy Editor.

Now bringing you the top 10 most cited Full Papers ever – take a look!

As you know, we are celebrating the journal’s 10th Anniversary, and counting down the Top 10 most cited Organic & Biomolecular Chemistry research works from our different formats, according to ISI*. This week, find out which are our most cited ever Full Papers.

In addition all of these articles will be FREE for you to read until the end of next week.

10. Tandem oxidation processes for the preparation of nitrogen-containing heteroaromatic and heterocyclic compounds
Steven A. Raw, Cecilia D. Wilfred and Richard J. K. Taylor
Org. Biomol. Chem., 2004, 2, 788-796 DOI: 10.1039/B315689C

9. Novel molecular drug carrier: encapsulation of oxaliplatin in cucurbit[7]uril and its effects on stability and reactivity of the drug
Young Jin Jeon, Soo-Young Kim, Young Ho Ko, Shigeru Sakamoto, Kentaro Yamaguchi and Kimoon Kim
Org. Biomol. Chem., 2005, 3, 2122-2125 DOI: 10.1039/B504487A

8. Organocatalytic enantioselective indole alkylations of α,β-unsaturated ketones
Wei Chen, Wei Du, Lei Yue, Rui Li, Yong Wu, Li-Sheng Ding and Ying-Chun Chen
Org. Biomol. Chem., 2007, 5, 816-821 DOI: 10.1039/B616504D

7. Promoting laccase activity towards non-phenolic substrates: a mechanistic investigation with some laccase–mediator systems
Paola Baiocco, Anna Maria Barreca, Maura Fabbrini, Carlo Galli and Patrizia Gentili
Org. Biomol. Chem., 2003, 1, 191-197 DOI: 10.1039/B208951C

6. Synthesis and photophysical evaluation of charge neutral thiourea or urea based fluorescent PET sensors for bis-carboxylates and pyrophosphate
Thorfinnur Gunnlaugsson, Anthony P. Davis, John E. O’Brien and Mark Glynn
Org. Biomol. Chem., 2005, 3, 48-56 DOI: 10.1039/B409018G

5. Nitrophenyl derivatives of pyrrole 2,5-diamides: structural behaviour, anion binding and colour change signalled deprotonation
Salvatore Camiolo, Philip A. Gale, Michael B. Hursthouse and Mark E. Light
Org. Biomol. Chem., 2003, 1, 741-744 DOI: 10.1039/B210848H

4. Comparison of topological descriptors for similarity-based virtual screening using multiple bioactive reference structures
Jérôme Hert, Peter Willett, David J. Wilton, Pierre Acklin, Kamal Azzaoui, Edgar Jacoby and Ansgar Schuffenhauer
Org. Biomol. Chem., 2004, 2, 3256-3266 DOI: 10.1039/B409865J

3. Design, synthesis and photophysical studies of simple fluorescent anion PET sensors using charge neutral thiourea receptors
Thorfinnur Gunnlaugsson, Anthony P. Davis, Gillian M. Hussey, Juliann Tierney and Mark Glynn
Org. Biomol. Chem., 2004, 2, 1856-1863 DOI: 10.1039/B404706K

2. Urea vs. thiourea in anion recognition
David Esteban Gómez, Luigi Fabbrizzi, Maurizio Licchelli and Enrico Monzani
Org. Biomol. Chem., 2005, 3, 1495-1500 DOI: 10.1039/B500123D

1. Organocatalysis with proline derivatives: improved catalysts for the asymmetric Mannich, nitro-Michael and aldol reactions
Alexander J. A. Cobb, David M. Shaw, Deborah A. Longbottom, Johan B. Gold and Steven V. Ley
Org. Biomol. Chem., 2005, 3, 84-96 DOI: 10.1039/B414742A

Why do you think these papers have been so highly cited? Do you remember when these articles were first published? Perhaps they had an impact on your own research? We’d love to find out more – tell us by posting a comment on the blog in the box below……

Have you missed the Top 10 cited OBC communications? Find them in our earlier post here.

*Top cited articles according to ISI on the 1st of February 2012

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Have you seen our recent review articles? New routes to indoles, carbohydrates for drug discovery, artificial nucleobases & more

31 Jan 2012

By Francesca Burgoyne.

During 2011 we published a number of topical reviews on a wide range of topics by expert researchers in their fields. We’ve collected some of them below but take a look here for the whole list, we hope you’ll find something interesting in your area!

Sequential one-pot combination of multi-component and multi-catalysis cascade reactions: an emerging technology in organic synthesis
Dhevalapally B. Ramachary and Sangeeta Jain
DOI: 10.1039/C0OB00611D

Carbohydrate chemistry in drug discovery
M. Carmen Galan, David Benito-Alifonso and Gregory M. Watt
DOI: 10.1039/C0OB01017K

Recent advances in indole syntheses: New routes for a classic target
Rubén Vicente
DOI: 10.1039/C1OB05750B

Chiral separation by enantioselective liquid–liquid extraction
Boelo Schuur, Bastiaan J. V. Verkuijl, Adriaan J. Minnaard, Johannes G. de Vries, Hero J. Heeres and Ben L. Feringa
DOI: 10.1039/C0OB00610F

Cascade polycyclisations in natural product synthesis
Edward A. Anderson
DOI: 10.1039/C1OB05212H

Targeting DNA base pair mismatch with artificial nucleobases. Advances and perspectives in triple helix strategy
Vincent Malnuit, Maria Duca and Rachid Benhida
DOI: 10.1039/C0OB00418A

Unlocked nucleic acid – an RNA modification with broad potential
Anna Pasternak and Jesper Wengel
DOI: 10.1039/C0OB01085E

Nitrogen cation–π interactions in asymmetric organocatalytic synthesis
Shinji Yamada and John S. Fossey
DOI: 10.1039/C1OB05228D

If you have an idea for a review article that hasn’t been covered and you would like to see included, contact the Editorial Office – we’d love to hear from you.

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Synthesising ureas from CO2, recognition of oxoanions and cross-metathesis for heterocycles in Issue 7

30 Jan 2012

By Francesca Burgoyne.

The cool images on this week’s cover are from Giuseppe Resnati, NFMLab, and James C. Anderson, UCL.

Resnati and colleagues have conducted an NMR study of phosphate oxoanion binding of a 2-iodo-imidazolium receptor with charge assisted halogen bonding, finding a surprisingly strong binding constant for phosphate anions, their work is highlighted on the outside front cover.

2-Iodo-imidazolium receptor binds oxoanions via charge-assisted halogen bonding
Massimo Cametti, Kari Raatikainen, Pierangelo Metrangolo, Tullio Pilati, Giancarlo Terraneo and Giuseppe Resnati
DOI: 10.1039/C1OB06524F

On a completely different topic, Anderson and Moreno have been using CO₂ to produce ureas at ambient conditions, using 12- and 14- electron titanium imido complexes:

Synthesis of ureas from titanium imido complexes using CO2 as a C-1 reagent at ambient temperature and pressure
James C. Anderson and Rafael Bou Moreno
DOI: 10.1039/C1OB06576A

As well as these the issue also contains a review from Tim Donohoe on olefin cross-metathesis for heterocycle synthesis and plenty of other hot articles, take a look…

Hot articles in this issue:

Some cyclization reactions of 1,3-diphenylbenzo[e][1,2,4]triazin-7(1H)-one: preparation and computational analysis of non symmetrical zwitterionic biscyanines
Theodosia A. Ioannou, Panayiotis A. Koutentis, Harry Krassos, Georgia Loizou and Daniele Lo Re
DOI: 10.1039/C1OB06622F

Oxidative Prins and Prins/Friedel–Crafts cyclizations for the stereoselective synthesis of dioxabicycles and hexahydro-1H-benzo[f]isochromenes via the benzylic C–H activation
B. V. Subba Reddy, Prashant Borkar, J. S. Yadav, P. Purushotham Reddy, A. C. Kunwar, B. Sridhar and René Grée
DOI: 10.1039/C1OB06489D

Chemoenzymatic synthesis of a mixed phosphine–phosphine oxide catalyst and its application to asymmetric allylation of aldehydes and hydrogenation of alkenes
Derek R. Boyd, Mark Bell, Katherine S. Dunne, Brian Kelly, Paul J. Stevenson, John F. Malone and Christopher C. R. Allen
DOI: 10.1039/C1OB06599H

James C. Anderson and Rafael Bou Moreno

Org. Biomol. Chem., 2012, 10, 1334-1338
DOI: 10.1039/C1OB06576A

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Certain 12- and 14- electron titanium imido complexes

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Imaging Norepinephrine transporters (NET) with self-reporting dyes

23 Jan 2012

By Marie Cote, Deputy Editor.

One area of research developed in Dr James N. Wilson‘s lab at the University of Miami (Florida, USA) is aimed at elucidating the complex molecular mechanisms of intercellular communication, via the development of fluorescent analogues of neuroactive compounds.

In their latest OBC communication, Wilson et al. describe the synthesis, characterization and interaction of cell lines with novel dimeric stilbazolium-based dyes that probe the functional limit of norepinephrine transport (NET) in cells. Upon exposure to different NET proteins, these environmentally sensitive dyes turn on the fluorescence and their binding to NET can be monitored using fluorescence microscopy

This article will be FREE to access for the next 4 weeks.
Why not read it now and let us know what you think by posting a comment below!

Probing the functional limits of the norepinephrine transporter with self-reporting, fluorescent stilbazolium dimers
Erika L. Smith, Adrienne S. Brown, Edward Adjaye-Mensah and James N. Wilson
Org. Biomol. Chem., 2012, Advance Article
DOI: 10.1039/C2OB06796J, Communication

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Cyclocondensation reactions of the heterocyclic scaffold benzotriazinone lead to several highly coloured acenes

23 Jan 2012

By Marie Cote, Deputy Editor.

In this OBC Hot Article, Panayiotis Koutentis and co-workers at the University of Cyprus show how 1,3-Diphenylbenzo[e][1,2,4]triazin-7(1H)-one reacts with various bisnucleophiles to give a variety of deeply coloured polyazaacenes, including two zwitterionic analogues.

Read the article to find out more about the preparation, mechanistic considerations and photophysical studies of these new heterocyclic ring systems derived from benzo[1,2,4]triazin-7-ones.

FREE to access for a period of 4 weeks!

Some cyclization reactions of 1,3-diphenylbenzo[e][1,2,4]triazin-7(1H)-one: preparation and computational analysis of non symmetrical zwitterionic biscyanines
Theodosia A. Ioannou, Panayiotis A. Koutentis, Harry Krassos, Georgia Loizou and Daniele Lo Re
Org. Biomol. Chem., 2012, Advance Article
DOI: 10.1039/C1OB06622F, Paper

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Issue 6 online – including water-binding aquafoldamers, fluorinated probes and glycosylated 5-hydroxylysine

23 Jan 2012

By Francesca Burgoyne.

On the outside front cover of this week’s issue is a hot article from Huaiqing Zhao, National University of Singapore, et al. on a series of water-binding aquafoldamers with potential use in recognizing topologically diverse larger water clusters and as synthetic water channels. This article is part of our forthcoming themed issue on Foldamer Chemistry.

Synthesis, structural investigation and computational modelling of water-binding aquafoldamers
Huaiqing Zhao, Wei Qiang Ong, Xiao Fang, Feng Zhou, Meng Ni Hii, Sam Fong Yau Li, Haibin Su and Huaqiang Zeng
DOI: 10.1039/C1OB06609A

The inside front cover is work from Jonathan Guimond-Tremblay, Université Laval, et al. on the synthesis of three monofluorinated dimyristoylphosphatidylcholine derivatives for use as probes in ¹⁹F NMR studies to study the effects of drugs and peptides on model membranes.

Synthesis and properties of monofluorinated dimyristoylphosphatidylcholine derivatives: Potential fluorinated probes for the study of membrane topology
Jonathan Guimond-Tremblay, Marie-Claude Gagnon, Jozy-Ann Pineault-Maltais, Vanessa Turcotte, Michèle Auger and Jean-François Paquin
DOI: 10.1039/C2OB06570C

The issue also includes a review on the synthesis of glycosylated (2S,5R)-hydroxylysine from Margaret Brimble and coworkers and a hot article from Valentina Cerulli et al., on a highly diastereoselective Ugi multicomponent reaction

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Organic & Biomolecular Chemistry Blog

Multivalent scFvs, mitomycin C stereochemistry, peptide dendrimers and NET ligands in Issue 8

HOT article: (D)-sugars from (L)-amino acids – a step closer to understanding the origin of life

Countdown to OBC 10th Anniversary continues

Have you seen our recent review articles? New routes to indoles, carbohydrates for drug discovery, artificial nucleobases & more

Synthesising ureas from CO2, recognition of oxoanions and cross-metathesis for heterocycles in Issue 7

Top 10 Communication articles from Organic & Biomolecular Chemistry

Imaging Norepinephrine transporters (NET) with self-reporting dyes

Cyclocondensation reactions of the heterocyclic scaffold benzotriazinone lead to several highly coloured acenes

Issue 6 online – including water-binding aquafoldamers, fluorinated probes and glycosylated 5-hydroxylysine

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