Aden Murphy

From reactants to products via simple hydrogen-bonding networks: Information transmission in chemical reactions

The transmission of information is ubiquitous in nature and often occurs through supramolecular hydrogen bonding processes. Here we report that there is a remarkable correlation during synthesis between the efficiency of the hydrogen-bond-directed assembly of peptide-based [2]rotaxanes and the symmetry distortion of the macrocycle in the structure of the final product. It transpires that the ability of the flexible macrocycle-precursor to wrap around an unsymmetrical hydrogen bonding template affects both the reaction yield and a quantifiable measure of the symmetry distortion of the macrocycle in the product. When the yields of peptide rotaxane-forming reactions are high, so is the symmetry distortion in the macrocycle; when the yields are low, indicating a poor fit between the components, the macrocycle symmetry is relatively unaffected by the thread. Thus during a synthetic sequence, as in complex biological assembly processes, hydrogen bonding can code and transmit “information”—in this case a distortion from symmetry—between chemical entities by means of a supramolecularly driven multicomponent assembly process. If this phenomenon is general, it could have far reaching consequences for the use of supramolecular-directed reactions in organic chemistry.

High-frequency vibrations of the simplest benzylic amide [2]catenane

Infrared and Raman spectroscopies along with molecular orbital calculations are used to studyfor the first timethe vibrational motions of a topologically complicated chemical system, namely a [2]catenane of the benzylic amide type. Because of the intrinsic line width of the spectra, comparison of experiments and theory is only partially successful. The insight given by the simulationswhich show that the CO normal modes are delocalized while the N−H modes are localizedis, however, useful and makes us propose a simple model that explains both the larger line width of the spectra of the catenane with respect to those of the parent macrocycle and the great sensitivity of the infrared spectrum of the catenane to the environment. Examples of such sensitivity are the frequency shifts observed upon going from KBr to CsI, features not present in the case of the macrocycle.

STM investigation of flexible supramolecules: Benzylic amide [2] catenanes

Abstract Benzylic amide [2] catenane (CAT1) deposited from a methanol solution onto highly oriented pyrolitic graphite (HOPG) has been investigated by ambient scanning tunneling microscopy (STM). Submolecular features are resolved which suggest that the adsorption of CAT1 is driven by the electrostatic attraction of carbonyl groups and HOPG. Our evidence shows that CAT1 is mobile at RT on HOPG surface. A statistical analysis of the observed features reveals a bimodal distribution of the lateral size which correlates with the expected diameter of a single macrocycle and the catenane respectively.

Inelastic neutron scattering of large molecular systems: The case of the original benzylic amide [2]catenane

The inelastic neutron scattering (INS) spectrum of the original benzylic amide [2]catenane is recorded and simulated by a semiempirical quantum chemical procedure coupled with the most comprehensive approach available to date, the CLIMAX program. The successful simulation of the spectrum indicates that the modified neglect of differential overlap (MNDO) model can reproduce the intramolecular vibrations of a molecular system as large as a catenane (136 atoms). Because of the computational costs involved and some numerical instabilities, a less expensive approach is attempted which involves the molecular mechanics-based calculation of the INS response in terms of the most basic formulation for the scattering activity. The encouraging results obtained validate the less computationally intensive procedure and allow its extension to the calculation of the INS spectrum for a second, theoretical, co-conformer, which, although structurally and energetically reasonable, is not, in fact, found in the solid state. T...

Experimental and theoretical studies of the low-lying electronic states of the simplest benzylic amide [2]catenane

The lowest electronically excited states of the simplest benzylic amide [2]catenane (1) have been studied by a combination of experimental and theoretical techniques. Experimentally, steady-state and transient absorption spectra, emission spectra, and the optoacoustic response in solution have been recorded for the catenane and a model compound (N,N′-dibenzylisophthalic diamide (2)), as well as the electron energy loss spectrum of the catenane deposited on the Au(111) surface. The theoretical picture builds on the results of semiempirical quantum chemical calculations and shows that partial delocalisation of the electronic states over the many chromophores of the catenanes can occur.

Nonlinear Optical Properties of Benzylic Amide [2] Catenanes: A Novel Versatile Photonic Material

Abstract Benzylic amide catenanes are a class of synthetically-accessible interlocked molecular rings which can rotate one through the other depending on the nature of the local environment. The rings contain four phenyl units each and interlocking also affords their packing in novel, highly interacting ways that may lead to unexpected properties thus opening up the possibility of developing new materials. Third harmonic generation in benzylic amide catenane solutions was measured at a wavelength of γ = 1064 nm, with the fundamental and the harmonic wavelengths in the region of transparency of the material. The thoroughly non resonant value of the hyperpolarisability γ(-3ω; ω, ω, ω) was found to be (6.5 ± 0.7) × 10−35 esu with a negligible imaginary part, in agreement with the value of (6.8 ± 0.9) × 10−35 esu calculated from a bond-additivity model of hyperpolarisability. The static second order hyperpolarisability predicted by a Molecular Orbital model was about a factor four less than the experimental value. Second hyperpolarizability values of several solvents were also measured at the fundamental wavelength of γ = 1064 nm.

Raman and far infrared characterization of the simplest benzylic amide [2] catenane

Abstract The Benzylic Amide [2] Catenane (CAT1) is the simplest member of a family of supramolecules prepared by self-assembly synthesis and discovered at UMIST. The molecular system consists of 136 atoms forming two identical macrocycles mechanically interlocked. This unique structural property allows novel mechanical and electronic interactions that modify the properties of the Catenane with respect to the macrocycle monomer. In particular, a circumrotational motion of the two interlocked rings has been found in solution of CAT1 by NMR spectroscopy. In this work we report on Raman and Far Infrared experiments on polycrystalline CAT1 with the aim of contributing to the understanding of the basic mechanism of the intra-ring rotation of Catenanes.