Volume 7 Issue 5, May 2015

Volume 7 Issue 5

The self-assembly of ordered molecular arrays on surfaces has received a lot of attention, but fractals are particularly challenging patterns to replicate. Now, a team of researchers led by Yongfeng Wang, Michael Gottfried and Kai Wu have shown how bent oligophenyls with a bromine atom at each end can selfassemble into Sierpinski triangle fractals on a silver surface (as shown on the cover). A combination of hydrogen bonding and halogen bonding between the adsorbed molecules guides the formation of the fractal structures, along with other factors such as molecule—substrate interactions and the temperature of the system.Article p389News & Views p370IMAGE: KAI WUCOVER DESIGN: KAREN MOORE

Feature

  • Feature |

    Quantum computers potentially offer a faster way to calculate chemical properties, but the exact implications of this speed-up have only become clear over the last year. The first quantum computers are likely to enable calculations that cannot be performed classically, which might reform quantum chemistry — but we should not expect a revolution.

    • Leonie Mueck

Thesis

  • Thesis |

    In the second of two essays looking at organic chemistry that can be found in the Solar System, Bruce C. Gibb focuses on the gas and ice giants as well as their satellites — concluding the tour on Saturn's fascinating moon Titan.

    • Bruce C. Gibb

Books and Arts

Research Highlights

Blogroll

News and Views

  • News & Views |

    Defect-free Sierpiński triangles can be self-assembled on a silver surface through a combination of molecular design and thermal annealing. Three-fold halogen-bonding arrays and precise surface epitaxy preclude structural errors, thus enabling the high-level complexity of these supramolecular fractal patterns.

    • Steven L. Tait
  • News & Views |

    Analysing post-translational modifications of histone proteins as they occur within chromatin is challenging due to their large number and chemical diversity. A major step forward has now been achieved by using split intein chemistry to engineer functionalized histones within cells.

    • Wolfgang Fischle
    • , Dirk Schwarzer
    •  & Henning D. Mootz
  • News & Views |

    In 1972, Baird showed theoretically that the electron counting rule for aromaticity and antiaromaticity in the lowest ππ* triplet state is opposite to that in the electronic ground state. A pair of compounds that manifests this reversal in character has now been identified and characterized experimentally for the first time.

    • Henrik Ottosson
    •  & K. Eszter Borbas
  • News & Views |

    Symbiotic bacteria synthesize many specialized small molecules; however, establishing the role these chemicals play in human health and disease has been difficult. Now, the chemical structure and mechanism of the Escherichia coli product colibactin provides insight into the link between this secondary metabolite and colorectal cancer.

    • Eric W. Schmidt
  • News & Views |

    Membranes are key components for the removal of greenhouse gases during fuel generation processes, such as hydrogen production, but simultaneous permeability and selectivity is difficult to obtain. This has now been achieved in ultrathin membranes that use the size-selective porosity of metal–organic frameworks to separate CO2 from H2.

    • Tina M. Nenoff
  • News & Views |

    Scaling relations between the molecular structures of reactive intermediates and the strength of the bonds they form with flat surfaces have now been extended to also predict how bonding strength is affected by surface topography. These relations can be applied to design more efficient nanoparticle catalysts.

    • J. Will Medlin
    •  & Matthew M. Montemore

Perspective

Articles

  • Article |

    A series of molecular fractals, specifically Sierpiński triangles, can be assembled on a Ag(111) surface from small, bent oligophenyls with a bromo group at each end. The self-assembly is driven by the formation of synergistic halogen and hydrogen bonds between the molecular building blocks, and defect-free structures with more than 100 individual components are observed.

    • Jian Shang
    • , Yongfeng Wang
    • , Min Chen
    • , Jingxin Dai
    • , Xiong Zhou
    • , Julian Kuttner
    • , Gerhard Hilt
    • , Xiang Shao
    • , J. Michael Gottfried
    •  & Kai Wu
  • Article |

    A method for engineering site-specific modifications of histone proteins within cellular chromatin has been developed using protein trans-splicing. This approach enabled a native histone modification, H2BK120 ubiquitination, to be incorporated in isolated nuclei, which was shown to trigger a downstream epigenetic effect.

    • Yael David
    • , Miquel Vila-Perelló
    • , Shivam Verma
    •  & Tom W. Muir
  • Article |

    Scaling relations between the adsorption energies of reaction intermediates facilitate the computational design of catalysts. However, these relations are restricted to low-index surfaces and how they differ from surface to surface cannot be predicted. Structural sensitivity has now been incorporated into scaling relations by elucidating how they are affected by the coordination number of an adsorption site.

    • Federico Calle-Vallejo
    • , David Loffreda
    • , Marc T. M. Koper
    •  & Philippe Sautet
  • Article |

    Genotoxic small molecules from the bacterial colibactin pathway — a gut-associated non-ribosomal peptide synthetase–polyketide synthase hybrid gene cluster linked to colorectal cancer — have remained elusive due to their instability. Now, one of these, the colibactin warhead, an unprecedented substituted spirobicyclic structure, has been characterized and shown to crosslink duplex DNA in vitro.

    • Maria I. Vizcaino
    •  & Jason M. Crawford
  • Article |

    In the ground state, aromatic rings contain [4n + 2] π electrons whereas antiaromatic systems have [4n] π-electrons. Baird's rule states that this situation is reversed in the lowest triplet excited state. It has now been shown using a combination of spectroscopy and quantum chemical calculations that two closely related bis-rhodium hexaphyrins exhibit properties consistent with Baird's rule.

    • Young Mo Sung
    • , Min-Chul Yoon
    • , Jong Min Lim
    • , Harapriya Rath
    • , Koji Naoda
    • , Atsuhiro Osuka
    •  & Dongho Kim
  • Article |

    Photoswitching of phytochromes is based on the isomerization of the tetrapyrrole chromophore, and eventually leads to the (de)activation of an enzymatic output module. Now it has been shown that both the structural changes associated with photoswitching and the thermal decay of the light-activated state are coupled to proton translocations in the chromophore pocket.

    • Francisco Velazquez Escobar
    • , Patrick Piwowarski
    • , Johannes Salewski
    • , Norbert Michael
    • , Maria Fernandez Lopez
    • , Anna Rupp
    • , Bilal Muhammad Qureshi
    • , Patrick Scheerer
    • , Franz Bartl
    • , Nicole Frankenberg-Dinkel
    • , Friedrich Siebert
    • , Maria Andrea Mroginski
    •  & Peter Hildebrandt
  • Article |

    Structural elucidation of a peptide natural product has revealed an unprecedented post-translational modification involving formation of a carbon–carbon bond between the side-chains of lysine and tryptophan. This motif defines a new family of cyclic peptides. Biochemical studies reveal that this C-C bond is generated by a radical SAM enzyme, and delineate its catalytic mechanism.

    • Kelsey R. Schramma
    • , Leah B. Bushin
    •  & Mohammad R. Seyedsayamdost
  • Article |

    Lipid bilayers containing porphyin-phospholipid that is chelated with cobalt have been shown to capture his-tagged proteins and peptides. This method offers a simple route for functionalizing pre-formed lipid bilayers without disrupting their integrity. Using this approach homing peptides were attached to cargo-loaded liposomes to enable tumour targeting, and an HIV-derived protein fragment elicited antibodies following binding to immunogenic liposomes.

    • Shuai Shao
    • , Jumin Geng
    • , Hyun Ah Yi
    • , Shobhit Gogia
    • , Sriram Neelamegham
    • , Amy Jacobs
    •  & Jonathan F. Lovell
  • Article |

    The extraction of (bio)molecules from fluid mixtures is vital for applications ranging from biomedical diagnostics to environmental analysis. Now a robust chemomechanical sorting system for the extraction of thrombin is described in which pH-dependent binding of the analyte to a specific aptamer is combined with volume changes of the pH-responsive hydrogel in a biphasic microfluidic regime, resulting in a catch-and-release system.

    • Ankita Shastri
    • , Lynn M. McGregor
    • , Ya Liu
    • , Valerie Harris
    • , Hanqing Nan
    • , Maritza Mujica
    • , Yolanda Vasquez
    • , Amitabh Bhattacharya
    • , Yongting Ma
    • , Michael Aizenberg
    • , Olga Kuksenok
    • , Anna C. Balazs
    • , Joanna Aizenberg
    •  & Ximin He
  • Article |

    It is difficult to develop a selective ligand for point mutations in proteins that are not found in easily addressable locations. Now, an all-chemical, epitope-targeting strategy has been reported, and was used to discover an inhibitory peptide with selectivity for the E17K point mutation in the PH Domain of the Akt1 oncoprotein.

    • Kaycie M. Deyle
    • , Blake Farrow
    • , Ying Qiao Hee
    • , Jeremy Work
    • , Michelle Wong
    • , Bert Lai
    • , Aiko Umeda
    • , Steven W. Millward
    • , Arundhati Nag
    • , Samir Das
    •  & James R. Heath

Addenda

In Your Element

  • In Your Element |

    Lars Öhrström ponders the importance of potassium in matters of life and death.

    • Lars Öhrström

Correction

Addenda