Engineering functional materials by halogen bonding

Engineering functional materials endowed with unprecedented properties require the exploitation of new intermolecular interactions, which can determine the characteristics of the bulk materials. The great potential of Halogen Bonding (XB), namely any noncovalent interaction involving halogens as electron acceptors, in the design of new and high‐value functional materials is now emerging clearly. This Highlight will give a detailed overview on the energetic and geometric features of XB, showing how some of them are quite constant in most of the formed supramolecular complexes (e.g., the angle formed by the covalent and the noncovalent bonds around the halogen atom), while some others depend strictly on the nature of the interacting partners. Then, several specific examples of halogen‐bonded supramolecular architectures, whose structural aspects as well as applications in fields as diverse as enantiomers' separation, crystal engineering, liquid crystals, natural, and synthetic receptors, will be fully described. © 2006 Wiley Periodicals, Inc. J Polym Sci Part A: PolymChem 45: 1–15, 2007     

Protocell Communication through the Eyes of Synthetic Organic Chemists

The bottom-up fabrication of synthetic cells (protocells) from molecules and materials, is a major challenge of modern chemistry. A significant breakthrough has been the engineering of protocells capable of chemical communication using bio-derived molecules and ex situ stabilised cell machineries. These, however, suffer from short shelf-lives, high costs, and require mild aqueous conditions. In this Concept Article we analyse the chemistry at the heart of protocell communication to highlight new opportunities for synthetic chemists in protocell engineering. Specifically, we (i) categorise the main bio-derived chemical communication machineries in enzyme cascades, DNA strand displacement, and gene-mediated communication; (ii) review the chemistries of these signal transduction machineries; and (iii) introduce new types of bio-inspired, fully synthetic artificial enzymes to replace their natural counterparts. Developing protocells that incorporate synthetic analogues of bio-derived signal transduction machineries will improve the robustness, stability, and versatility of protocells, and broaden their applications to highly strategic fields such as photocatalysis and fine chemicals production.     

Perfluorocarbon-Hydrocarbon Discrete Intermolecular Aggregates: An Exceptionally Short N⋯I Contact

1-Iodoperfluoroheptane ( 1a ) and tetramethylethylenediamine ( 2 , TMEDA) form the 2:1 ratio stable aggregate 3a and a similar behaviour is shown by 1-iodoperfluoroalkanes 1b-e and iodopentafluorobenzene 1f . These aggregates have been characterised in solution by 1 H/ 19 F-NMR spectroscopy and in the solid state through IR and single crystal X-ray diffraction. The determined structure of 3a (triclinic, a =6.2283(10), b =9.250(2), c =15.098(3) Å, f =81.369(5), g =81.397(5), n = 86.010(5), V =849.3(3) A m 3 , T =175(3) K, space group P-1 (No. 2), Z =1; d (calc)=2.167 g cm m 3 ; 4121 independent reflections, 3665 with I o >2( I o ); final refinement gave R1=0.0400, wR2=0.0901) showed the second shortest N > I interaction found in the crystallographic literature [2.762(3) Å] and the interdigitation of perfluorocarbon and hydrocarbon modules due to co-operative -C-H > F-C- interactions. Calculations to quantify these latter interactions have been also performed.     

The fluorous effect in biomolecular applications

From being a niche area only a few decades ago, fluorous chemistry has gained momentum and is, nowadays, a fervent area of research. It has brought forth, in fact, numerous applicative innovations that stretch among different fields: from catalysis to separation science, from supramolecular to materials and analytical chemistry. Recently, the unique features of perfluorinated compounds have reached the attention of the biochemists' audience. This tutorial review introduces the basic concepts of fluorous chemistry and illustrates its main biomolecular applications. Special attention has been given to fluorous microarrays and their combination with Mass-Spectroscopy (MS) techniques, to protein properties modification by the introduction of local fluorous domains, and to the most recent applications of (19)F-Magnetic Resonance Imaging ((19)F-MRI).     

Surface chirality of CuO thin films

We present X-ray photoelectron spectroscopy (XPS) and X-ray photoelectron diffraction (XPD) investigations of CuO thin films electrochemically deposited on an Au(001) single-crystal surface from a solution containing chiral tartaric acid (TA). The presence of enantiopure TA in the deposition process results in a homochiral CuO surface, as revealed by XPD. On the other hand, XPD patterns of films deposited with racemic tartaric acid or the "achiral" meso-tartaric acid are completely symmetric. A detailed analysis of the experimental data using single scattering cluster calculations reveals that the films grown with l(+)-TA exhibit a CuO(1) orientation, whereas growth in the presence of d(-)-TA results in a CuO(11) surface orientation. A simple bulk-truncated model structure with two terminating oxygen layers reproduces the experimental XPD data. Deposition with alternating enantiomers of tartaric acid leads to CuO films of alternating chirality. Enantiospecifity of the chiral CuO surfaces is demonstrated by further deposition of CuO from a solution containing racemic tartaric acid. The pre-deposited homochiral films exhibit selectivity toward the same enantiomeric deposition pathway.     

A molecular dynamics study of human endostatin and its synthetic fragments with antiangiogenic properties

Human endostatin is one of the better characterized endogenous angiogenesis inhibitors, and its ability to modulate vascularization of tumours could be of great therapeutic interest. These properties are not exclusive to the full-length protein, but are shared by some of its synthetic fragments. A number of research groups have partitioned human endostatin in different peptides and have investigated their activity, in order to collect a body of experimental data which could be important in shedding new light on their structure-activity relationships. It was also reported that a small active fragment can become inactive when contained in a larger fragment, revealing an apparent discrepancy in the experimental results. Very few studies have been devoted to the computational analysis of these systems and to the rationalization of their properties using molecular modelling. Through molecular dynamics simulations of human endostatin and of four synthetic fragments, we have been able to rationalize the experimental findings. In particular, we have identified a pattern consisting of six amino acids, namely R-R(G)-A-D-R-A, which appears to be an active epitope if it is properly exposed to the solvent. Interestingly, this pattern can be already present in sequential order in the primary structure, or it can be generated by the spatial approach of two groups of residues, far apart in the primary structure, as an effect of the peptide folding. Comparing the structural features and the time evolution of all the simulated peptides we provide a coherent explanation of their activity or inactivity.     

Supramolecular Hierarchy among Halogen‐Bond Donors

Through a combination of structural chemistry, vibrational spectroscopy, and theory, we have systematically examined the relative structure‐directing importance of a series of ditopic halogen‐bond (XB) donors. The molecular electrostatic potential surfaces of six XB donors were evaluated, which allowed for a charge‐based ranking. Each molecule was then co‐crystallized with 21 XB acceptors and the results have made it possible to map out the supramolecular landscape describing the competition between I/Br–ethynyl donors, perfluorinated I/Br donors, and I/Br–phenyl based donors. The results offer practical guidelines for synthetic crystal engineering driven by robust and directional halogen bonds.     

4,4′-Dibromo-2,2′,3,3′,5,5′,6,6′-octafluorobiphenyl

The mol­ecule of the title compound, C₁₂Br₂F₈, shows approximate D₂ symmetry. The dihedral angle formed by the two rings is 60.2 (1)°.     

Multibody dynamics analysis of the human upper body for rotorcraft–pilot interaction

The study of the biodynamic response of helicopter passengers and pilots, when excited by rotorcraft vibrations that are transmitted through the seat and, for the latter, the control inceptors, is of great importance in different areas of aircraft design. Handling qualities are affected by the proneness of the aircraft to give rise to adverse interactions, an unwanted quality that can be captured by the so-called biodynamic feedthrough. On the other hand, the transmissibility of vibrations, especially from the seat to the head, affects the comfort of pilots and passengers during flight. Detailed and parametrised multibody modelling of the human upper body can provide a strong base to support design decisions justified by a first-principles approach. In this work, a multibody model of the upper body is formed by connecting a previously developed detailed model of the arms to a similarly detailed model of the spine. The whole model can be adapted to a specific subject, identified by age, gender, weight and height. The spine model and the scaling procedure have been validated using the experimental results for seat to head transmissibility. The coupled spine-arms model is used to evaluate the biodynamic response in terms of involuntary motion induced on the control inceptors, including the related nonlinearities.