Computational chemistry: Solving real-world chemical problems

Computational chemistry is a powerful tool for understanding real-world chemical problems. The gap between experiment and computational models is growing ever smaller. Calculated results for isolated molecules are becoming more relevant and reliable calculations for larger and larger molecular systems are becoming more accessible.

A computational study of enantioselective spiroacetalization catalyzed by phosphoric acids carried out by researchers at the Universidad de Salamanca and Oxford University effectively demonstrates the ability of advanced computational methods to elucidate key and often subtle factors that lead to different reaction outcomes.

The study uses a hybrid quantum mechanics (QM)/molecular mechanics (MM) method which makes computational simulations of large systems feasible by combining an accurate quantum mechanical description of the ‘interesting’ part of the system (i.e. the catalyst active site) with the computational efficiency of molecular mechanics applied to the surroundings. This way, one can assess the importance of environmental effects while avoiding a high computational cost. This is accomplished by partitioning the system’s total energy into inner (or active) and outer parts. The interactions within the inner part are then treated with the computationally higher quantum mechanics level and the outer parts are described using less expensive, lower level molecular mechanics methods.

The origin of greater enantioselectivity for the imidodiphosphoric acid (Figure, cat-II) over the binol phorophoric acid (Figure, cat-I) was determined through exhaustive analysis of transition state conformers using the QM/MM method. Ultimately,  it was determined that the source of chiral discrimination in catalyst II comes from a unique, bifunctional hydrogen bonding interaction between the catalyst and substrate. This confining interaction ends up limiting the accessible area to the imidodiphosphoric oxygen, resulting in an enantioselective outcome.

The significance of this work lies in the utility of theoretical models in explaining important empirical results. The ability to dissect a mechanism and identify the influential factors that determine a selective reaction outcome could not have been so easily accomplished without the use of computational analysis and will no doubt aid in the design of future organocatalysts for small, non-sterically demanding molecules.

To find out more see:

QM/MM study on the enantioselectivity of spiroacetalization catalysed by an imidodiphosphoric acid catalyst: how confinment works
Luis Simón and Robert S. Paton
DOI: 10.1039/C6OB00045B


Victoria Corless is currently completing her Ph.D. in organic chemistry with Prof. Andrei Yudin at The University of Toronto. Her research is centred on the synthesis of kinetically amphoteric molecules, which offer a versatile platform for the development of chemoselective transformations with particular emphasis on creating novel biologically active molecules.

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What are your colleagues reading in Organic & Biomolecular Chemistry?

The articles below are some of the most read Organic & Biomolecular Chemistry articles in January, February and March 2016.

Development of a stable phosphoarginine analog for producing phosphoarginine antibodies
Han Ouyang, Chuan Fu, Songsen Fu, Zhe Ji, Ying Sun, Peiran Deng and Yufen Zhao
DOI: 10.1039/C5OB02603B, Communication

Bifunctional primary amine-thioureas in asymmetric organocatalysis
Olga V. Serdyuk, Christina M. Heckel and Svetlana B. Tsogoeva
DOI: 10.1039/C3OB41403E, Perspective

Transition-metal catalyzed valorization of lignin: the key to a sustainable carbon-neutral future
Markus D. Kärkäs, Bryan S. Matsuura, Timothy M. Monos, Gabriel Magallanes and Corey R. J. Stephenson
DOI: 10.1039/C5OB02212F, Review Article

Design and synthesis of analogues of natural products
Martin E. Maier
DOI: 10.1039/C5OB00169B, Review Article

Organic synthetic transformations using organic dyes as photoredox catalysts
Shunichi Fukuzumi and Kei Ohkubo
DOI: 10.1039/C4OB00843J, Review Article

Biomineralization-inspired synthesis of functional organic/inorganic hybrid materials: organic molecular control of self-organization of hybrids
Atsushi Arakaki, Katsuhiko Shimizu, Mayumi Oda, Takeshi Sakamoto, Tatsuya Nishimura and Takashi Kato
DOI: 10.1039/C4OB01796J, Review Article

Synthesis of substituted pyrenes by indirect methods
Juan M. Casas-Solvas, Joshua D. Howgego and Anthony P. Davis
DOI: 10.1039/C3OB41993B, Review Article

Recent synthetic additions to the visible light photoredox catalysis toolbox
Ricardo A. Angnes, Zhou Li, Carlos Roque D. Correia and Gerald B. Hammond
DOI: 10.1039/C5OB01349F, Review Article

A protocol for amide bond formation with electron deficient amines and sterically hindered substrates
Maria E. Due-Hansen, Sunil K. Pandey, Elisabeth Christiansen, Rikke Andersen, Steffen V. F. Hansen and Trond Ulven
DOI: 10.1039/C5OB02129D, Communication

Metal catalyzed defunctionalization reactions
Atanu Modak and Debabrata Maiti
DOI: 10.1039/C5OB01949D, Review Article

Read more »

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Balticum Organicum Syntheticum (BOS) conference 2016

Balticum Organicum Syntheticum (BOS) conference 2016

3rd – 6th July 2016, Riga, Latvia

Organic & Biomolecular Chemistry and Natural Product Reports are pleased to support the 2016 BOS conference.  The conference aims to provide a forum for organic synthetic chemists to speak of their work and discuss important scientific problems and to promote discussion between academic and industrial scientists about the possibilities of mutual cooperation.

This international conference has a balanced program of academic and industrial speakers presenting fundamental and practical aspects of organic synthesis.  This year the speakers include:

  • Emily Balskus (Harvard University, USA) Chemical Discovery in the Microbial World
  • Inga Cikotiené (Vilnius University, Lithuania) From Curiosity to Development of New Synthetic Methods
  • Nuno Maulide (University of Vienna, Austria) Catalytic Rearrangements: Inspiration for Methods and Total Synthesis
  • Per-Ola Norrby (AstraZeneca, Sweden) Predictive Chemistry: Virtual Screening in Asymmetric Catalysis
  • Virgil Percec (University of Pennsylvania, USA) A Materials Genome Approach to Mimics of Biological Membranes and their Programmable Glycan Ligands
  • Stefan Schunk (Grünenthal GmbH, Germany) Cebranopadol, A Novel Analgesic – It’s Discovery from the MedChem Perspective
  • Ryan Shenvi (The Scripps Research Institute) Chemical Synthesis of Secondary Metabolites
  • John Sutherland (MRC Laboratory of Molecular Biology, Cambridge UK) Origins of Life Systems Chemistry
  • Māris Turks (Riga Technical University, Latvia) Sulfer Dioxide: Useful Reagent and Solvent in Organic Chemistry

For more information and to register please visit the website.

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XXVIII International Carbohydrate Symposium 2016

XXVIII International Carbohydrate Symposium 2016

17th – 21st July 2016, New Orleans, Louisiana USA

Organic & Biomolecular Chemistry are pleased to support the 28th International Carbohydrate Symposium.  The conference will feature an excellent range of speakers including:

  • Carolyn Bertozzi (Stanford University and Howard Hughes Medical Institute) – Glycocalyx engineering toward probing cancer glycome evolution
  • Vincent Bulone (University of Adelaide) – A journey into the world of Eukaryotic cell walls: structure and biosynthesis of essential polysaccharides
  • Bruce Hamaker (Purdue University) – Carbohydrate quality and how the concept may relate to healthier foods
  • Koichi Kato (Nagoya City University) – Structural views of glycen-dependent determination of glycoprotein fates in cells
  • Muthiah Manoharan (Alnylam Pharmaceuticals) – Carbohydrate Conjuated RNAi Therapeutics
  • James C Paulson (The Scripps Research Institute) – Sialic acids determinants of self
  • Soledad Penades (Centro de Investigacion Cooperativa en Biomateriales, CIC biomaGUNE) – Glycans and Glyconanotechnology
  • Stephen G Withers (University of British Columbia) – Accessing new and improved CAZymes through metagenomics and directed evolution

For more information and to book your place please visit the website.

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Continuous Flow Processes as an Enabling Technology in Synthesis

Recent advancements in reaction control and method development strategies have significantly impacted the way in which synthetic chemistry is performed. Arguably, one of the most widely amenable and enabling technologies is continuous flow chemistry, which can offer advantages over batch in terms of cost, reaction efficiency and safety. Its implementation is changing the way in which we think about and conduct chemistry and in some areas has expanded our synthetic capabilities.

As a result, numerous syntheses of commercially and pharmaceutically relevant compounds are being redesigned around flow processes in order to improve efficiency and reproducibility. In addition, the flow reactor configuration can be readily customized to meet specific reaction demands.

These changes are most evident within the pharmaceutical industry where increasing pressure to continually identify and optimize lead compounds has renewed interest in the development of sustainable and cost effective processes for both research and production purposes.1

A direct example of this comes from Prof. Ian Baxendale’s laboratory at Durham University.2 Heterocyclic motifs are prevalent in pharmaceuticals and have constituted one of the largest areas of research in organic chemistry. Through a convenient telescope continuous flow process, ethyl isocyanoacetate—a highly sensitive and reactive compound frequently used as a key building block in heterocycle synthesis—was generated in situ and used to synthesize diverse heterocyclic structures in a convergent manner.

General reaction scheme for the muti-step flow synthesis of 1,2,4-triazole and pyrrole[1,2-c]pyrimidine-based heterocycles.

Continuous flow limits issues related to hazardous exothermic processes, reaction scale-up and handling of highly reactive or toxic intermediates, overcoming numerous safety concerns inherent in batch chemistry. Furthermore, flow chemistries have also been combined with additional features such as microwave irradiation, solid-supported reagents or catalysts, photochemistry, inductive heating and electrochemistry, which greatly increase its application in synthetic organic chemistry.3,4

Significant developments within the last decade indicate that the full potential of flow chemistry has yet to be realized. As with any new up-and-coming technology, there exist limitations that more and more researchers are willing to tackle. This is evident in the prevalence of flow systems now being utilized not only within academic laboratories but also in industrial institutions.

Interesting and innovative examples of synthetic reactions translated to flow systems have recently been published in Organic and Biomolecular Chemistry and can also be found in the joint OBC/ChemComm collection ‘Recent Advances in Flow Synthesis and Continuous Processing’. Select examples are discussed below.


Establishing a multistep continuous flow process is a logical step forward in the development of flow technology. However, genuine applications remain limited due to inherent challenges such as solvent incompatibility, intermediate work-up and dilution effects. Prof. Floris Rutjes and his coworkers at Radboud University have provided a solution to this problem.5 They effectively integrated a two-step chemoenzymatic flow synthesis of incompatible reaction steps through the use of an inline liquid-liquid separation module.

Two step synthesis of cyanohydrins and schematic representation of the flow set up with integrated liquid-liquid phase separation module.

Homogenous metal catalysis has seen limited use in industrial processes due to difficult separation from product material and troublesome recovery of precious metals. To remedy this, an immobilised iridium hydrogen transfer catalyst was developed by Prof. Ian Baxendale and coworkers for use in flow based systems by incorporation of a ligand to a porous polymeric monolithic flow reactor, which limits metal leaching and catalyst deactivation.6

A monolith reactor testing configuration using immobilized iridium hydrogen transfer catalyst.

Finally, Prof. Bradely Pentelute and his group at the Massachusetts Institute of Technology very recently reported an efficient continuous-flow system for the challenging synthesis of peptides containing perfluoroaromatic molecules in place of labile disulfide bonds.7 Application of a rapid flow-based solid-phase peptide synthesis allowed the researchers to circumvent previously encountered problems associated with this chemistry and has resulted in an overall improvement in quality and isolated yield of the peptides.

Flow system for the synthesis of H2 relaxin fragment analogues using modified solid-phase peptide synthesis

To find out more see:

1 Flash chemistry: flow chemistry that cannot be done in batch. J. Yoshida, Y. Takahashi, A. Nagaki, Chem. Commun., 2013, 49, 9896. DOI: 10.1039/C3CC44709J

2 Flow synthesis of ethyl isocyanoacetate enabling the telescoped synthesis of 1,2,4-triazoles and pyrrolo-[1,2-c]pyrimidines. M. Baumann. A. M. Rodriguez Garcia, I. R. Baxendale, Org. Biomol. Chem., 2015, 13, 4231. DOI: 10.1039/C5OB00245A

3 Liquid phase oxidation chemistry in continuous-flow microreactors. H. P. L. Gemoets, Y. Su, M. Shang, V. Hessel, R. Luque, T. Noël, Chem. Soc. Rev.201645, 83. DOI: 10.1039/C5CS00447K

4 Flow chemistry syntheses of natural products. J. C. Pastre, D. L. Browne, S. V. Ley, Chem. Soc. Rev.201342, 8849. DOI: 10.1039/C3CS60246J

5 Chemoenzymatic flow cascade for the synthesis of protected mandelonitrile derivatives. M.M. Delville, K. Koch, J.C.M. van Hest, F.P.J.T. Ruties, Org. Biomol. Chem., 2015, 13, 1634. DOI: 10.1039/C4OB02128B

6 A monolith immobilised iridium Cp* catalyst for hydrogen transfer reactions under flow conditions. M. V. Rojo, L. Guetzoyan, I. R. Baxendale, Org. Biomol. Chem., 2015, 13, 1768. DOI: 10.1039/C4OB02376E

7 A perfluoroaromatic abiotic analog of H2 relaxin enabled by rapid flow-based peptide synthesis. T. Luhmann, S. K. Mong, M. D. Smino, L. Meinel, B. L. Pentelute, Org. Biomol. Chem., 2016, 14, 3345. DOI: 10.1039/C6OB00208K


Victoria Corless is currently completing her Ph.D. in organic chemistry with Prof. Andrei Yudin at The University of Toronto. Her research is centred on the synthesis of kinetically amphoteric molecules, which offer a versatile platform for the development of chemoselective transformations with particular emphasis on creating novel biologically active molecules.

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16th French-American Chemical Society meeting

French-American Chemical Society
16th Meeting

19-23 June 2016  -  Santa Barbara, California, USA

Organic & Biomolecular Chemistry and Catalysis Science & Technology are delighted to support the 16th French-American Chemical Society meeting. The conference will feature an excellent range of speakers including:

  • Dennis Hall (University of Alberta) – Studies Towards the Synthesis of Polycyclic Alkaloids
  • Bastien Nay (Muséum National d’Histoire Naturelle) – Bio-inspired Strategies for the Total Synthesis of Polycyclic Chalasins and Related PKS-NRPS Natural Products
  • Surya Prakash (USC) – Our Recent Studies on Fluoroalkylations
  • David Williams (Indiana University) - Studies Towards the Synthesis of Polycyclic Alkaloids, and 
  • Françoise Colobert (Université de Strasbourg) – Enantiopure Sulfoxide, an Efficient Chiral Directing Group for Stereoselective C-H Bond Activation.

Register now to secure your place and take part in this great five day symposium with 20 speakers comprising established and emerging researchers from both academia and industry. The meeting is organised by Professor Bruce Lipshutz (University of California Santa Barbara), Dr Robert Dodd (Institut de Chimie des Substances Naturelles) and Dr Jean Suffert (Université de Strasbourg) this year.

For more information and to book your place please visit the event page.

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Poster Prize winner at the University of California Symposium for Chemical Sciences

Congratulations to the Poster Prize winner at the University of California Symposium for the Chemical Sciences.

Poster Prize winner Bryn Taylor

Bryn Taylor (right) with Jennifer Griffiths from the RSC (photo courtesy of Beverly Chou from the Shea group)

The winner is Bryn Taylor of UC San Diego who is currently working as a graduate student in the group of Rob Knight and co-advised by Rommie Amaro. Her research encompasses computational chemistry and biophysics, focusing on microbial proteomes and the function of the microbiome.

The meeting took place for the first time and was supported by eight UC departments (UC Davis, UCLA, UC San Diego, UC Berkeley, UC Riverside, UC Santa Cruz, UC Irvine, UC Santa Barbara). All areas of chemistry, including biological, organic, inorganic, analytical and physical chemistry were represented and the symposium provided an excellent opportunity for graduate students and postdocs to not only present their work in a multidisciplinary environment, but also take part in different workshops to further their career and establish connections with professionals from industry, government and alternative science jobs.

The prize was presented by the RSC Editorial Development Manager, North America, Dr Jennifer Griffiths.

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Developing a fragment-based design-friendly methodology

Posted on behalf of Victoria Corless, guest web writer for Organic & Biomolecular Chemistry

Target-based approaches to drug discovery have dominated pharmaceutical research since the early 1990s because they allow for increased screening capacity and rational drug design. Advances in combinatorial chemistry, high-throughput screening and gene expression profiling have been effective in the development of novel treatments for validated targets; however, a link between the downward trend in the number of new chemical entities reaching commercialization and the predominance of target-based drug discovery methods in the pharmaceutical industry has been suggested.

To address these issues, new technologies are constantly being developed and fragment-based drug design (FBDD) has emerged as a way to improve the quality and (most importantly) the efficiency of the drug discovery process. FBDD identifies the binding of low molecular weight ligands using techniques such as X-ray crystallography or NMR spectroscopy, and the binding information is then used to assemble potent lead compounds with drug-like properties.

In a recent publication, researchers at Astex Pharmaceuticals have noted that the success of FBDD often relies on the development of new synthetic methodologies for ligand elaboration. Despite the simplicity of fragment-like compounds, challenges lie in their design and synthesis as well as in developing the methodology to combine and grow fragments into high affinity leads. It is therefore important to identify compounds with attractive ‘fragment properties’ which are used as part of a selection process for adding new fragments into the Astex screening library. These include incorporation of diverse polar groups, multiple synthetically accessible positions for fragment growth in three dimensions and synthetic tractability among others.

Dihydroisoquinolone and some of its derivatives were identified in this study as ideal fragment-like compounds for the development of a FBDD-friendly synthetic methodology.

Schematic representation of synthetic elaboration of fragment 1. Growth positions are shown as blue arrows and the incorporation of aromatic heteroatoms and polar binding groups are indicated.

As proof of concept, the previously reported synthesis of dihydroisoquinolone-based compounds using Rh(III)-catalyzed C-H bond activation1 was modified to incorporate additional potential binding groups as well as synthetic handles for efficient fragment-to-lead elaboration.

Their results illustrate an excellent example of how the application of FBDD-friendly synthetic methodology can be used to expand upon published methodologies to increase their utility in developing useful templates for fragment-based drug discovery. Although inventive ideas, such as this work, are making small contributions in pharmaceutical research, there is a need for more organic chemists to engage in these synthetic challenges if drug discovery techniques are to be fruitful in the long-run.

1 N. Guimond et al. J. Am. Chem. Soc., 2011, 133(16), 6449–6457


To find out more see:

Design and synthesis of dihydroisoquinolones for fragment-based drug discovery (FBDD)
Nick Palmer, Torren M. Peakman, David Norton and David C. Rees
DOI: 10.1039/C5OB02461G


Victoria Corless is currently completing her Ph.D. in organic chemistry with Prof. Andrei Yudin at The University of Toronto. Her research is centred on the synthesis of kinetically amphoteric molecules, which offer a versatile platform for the development of chemoselective transformations with particular emphasis on creating novel biologically active molecules.

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Revitalizing palladium-catalyzed α-arylation of enolates to generate diverse isoquinoline-based compounds

Posted on behalf of Victoria Corless, guest web writer for Organic & Biomolecular Chemistry

Research efforts carried out by Professor Timothy Donohoe of Oxford University have been focussed on connecting new methodologies in organic synthesis and catalysis with impactful applications to the fields of medicinal chemistry and natural product synthesis.

One of the group’s most recent endeavors includes the development of a generalized strategy to access highly functionalized and diverse isoquinoline cores without the use of expensive and highly-specialized starting materials.

The isoquinoline motif and its derivatives are ubiquitous in a number of natural products, pharmaceutical agents, and chiral catalyst ligands. However, classical syntheses are often centered on electrophilic aromatic substitution of electron-rich systems, resulting in limited chemical diversity in accessible products. New routes are still highly desirable and a resurgence in synthetic efforts has resulted in a number of notable contributions using modern synthetic methodology.

In 2012, Prof. Donohoe and coworkers reported a sequential palladium-catalyzed α-arylation of enolates and cyclization to access isoquinolines based on chemistry originally and independently reported by Buckwald, Hartwig and Miura in 1997. Though a powerful reaction, it remained underutilized in the assembly of complex aromatic compounds. Using clever reaction engineering, Donohoe and coworkers envisioned synthesizing a psuedo-1,5-dicarbonyl accessible through α-arylation of enolizable ketones with aryl halides possessing a protected aldehyde or ketone in the ortho-position. In addition, trapping with reactive electrophiles resulted in functionalization at the C4 position. This methodology can be carried out in one pot, tolerates a wide range of substituents and most notably, provides a route to synthetically challenging electron-deficient isoquinoline scaffolds.

Palladium-catalyzed enolate arylation as a key C–C bond-forming reaction for the synthesis of isoquinolines

Their current study presents significant extensions of this earlier work and further demonstrates the innovation possible through transition metal catalysis in enabling the construction of complex architectures in interesting ways. The three- and four-component coupling procedures involve multiple bond formations in one pot from largely commercially available starting materials. Reaction versatility is demonstrated through the use of ketone, ester or nitrile enolates as well as electron-rich, electron-deficient or even sterically hindered aryl halides and in situ functionalization of intermediates to directly access a number of highly functionalized isoquinoline based compounds.

In addition to rejuvenating interesting and underexplored chemistry, Prof. Donohoe and coworkers have appreciably impacted the areas of natural product synthesis and medicinal chemistry through their innovative and streamlined synthesis of isoquinoline-based compounds and it will be interesting to see where their future endeavours will lead.


To find out more see:

Palladium-catalyzed enolate arylation as a key C–C bond-forming reaction for the synthesis of isoquinolines
Ben S. Pilgrim, Alice E. Gatland, Carlos H. A. Esteves, Charlie T. McTernan, Geraint R. Jones, Matthew R. Tatton, Panayiotis A. Procopiou and Timothy J. Donohoe
DOI: 10.1039/C5OB02320C


Victoria Corless is currently completing her Ph.D. in organic chemistry with Prof. Andrei Yudin at The University of Toronto. Her research is centred on the synthesis of kinetically amphoteric molecules, which offer a versatile platform for the development of chemoselective transformations with particular emphasis on creating novel biologically active molecules.

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E-WiSPOC 16

European-Winter School on Physical Organic Chemistry (E-WiSPOC)

31st January – 5th February 2016, Bressanone, Italy


OBC is pleased to support the European-Winter School on Physical Organic Chemistry (E-WiSPOC) 2016.

The topic for 2016 is – Functional Surfaces in Chemistry and Biology.

Lectures will be speaking on a variety of subjects, including:

  • Francesco Zerbetto – Theoretical and computational chemistry (University of Bologna)
  • Maria Ramos – Computational biochemistry (University of Porto)
  • Maria Minunni – Surface plasmon resonance (University of Firenze)
  • Chris Hunter – Physical organic chemistry and biomolecular interactions (University of Cambridge)
  • Bart Ravoo – Biological and supramolecular system (University of Muenster )
  • Jurrian Huskens – Biomolecular adhesion and tissue engineering (University of Twente)
  • Alessandro Casnati – Bioorganic and supramolecular chemistry (University of Parma)
  • Zoltan Takats – Ambient mass spectrometry (Imperial College London)

The school,which is part of the cultural initiatives of the Organic Division of the Italian Chemical Society, is open to PhD students and post-docs.

For information visit the e-wispoc website: www.chimica.unipd.it/wispoc or write to: wispoc.chimica@unipd.it

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