AND Logic Gates Based on Small Molecules with Chemical Inputs and Luminescence Output

AND logic gate behaviour can be recognized in chemical-responsive luminescence phenomena concerning small molecules. Though initial developments concerned separate and distinguishable chemical species as inputs, consideration of other types of input sets allows substantial expansion of the sub-field. Dissection of these molecular devices into modules, where possible, enables analysis of their logic behaviour according to supramolecular photochemical mechanisms.

2010: A Small Space Odyssey with Luminescent Molecules

The road to molecular logic and computation in Belfast, Northern Ireland started with chemical sensors in Colombo, Sri Lanka. This journey is mapped out with reference to design principles, such as those for luminescent PET (photoinduced electron transfer) sensing. Applications such as those for blood electrolyte diagnostics, "lab-on-a-molecule" systems, and molecular computational identification (MCID) are also met along the way.

Non-genetic mechanisms communicating antibiotic resistance:rethinking strategies for antimicrobial drug design

Introduction: Infections by multidrug-resistant bacteria are of great concern worldwide. In many cases, resistance is not due to the presence of specific antibiotic-modifying enzymes, but rather associated with a general impermeability of the bacterial cell envelope. The molecular bases of this intrinsic resistance are not completely understood. Moreover, horizontal gene transfers cannot solely explain the spread of intrinsic resistance among bacterial strains. Areas covered: This review focuses on the increased intrinsic antibiotic resistance mediated by small molecules. These small molecules can either be secreted from bacterial cells of the same or different species (e.g., indole, polyamines, ammonia, and the Pseudomonas quinolone signal) or be present in the bacterial cell milieu, whether in the environment, such as indole acetic acid and other plant hormones, or in human tissues and body fluids, such as polyamines. These molecules are metabolic byproducts that act as infochemicals and modulate bacterial responses toward antibiotics leading to increasing or decreasing resistance levels. Expert opinion: The non-genetic mechanisms of antibiotic response modulation and communication discussed in this review should reorient our thinking of the mechanisms of intrinsic resistance to antibiotics and its spread across bacterial cell populations. The identification of chemical signals mediating increased intrinsic antibiotic resistance will expose novel critical targets for the development of new antimicrobial strategies.

Enhancement of positron annihilation on molecules due to vibrational Feshbach resonances

The zero-range potential model is used to investigate positron collisions and annihilation with molecules. The Kr dimer is considered as an example. It is shown that (i) although positrons do not bind to individual Kr atoms, they do form bound states with Kr. (ii) A sequence of vibrationally excited states of the positron-molecule complex extends into the positron continuum, where it manifests as vibrational Feshbach resonances. (iii) These resonances give a very large contribution to the positron annihilation rate. Even after averaging over the thermal positron energy distribution, the contribution of the lowest Feshbach resonance exceeds that of the non-resonant background by an order of magnitude. © 2002 Elsevier Science B.V. All rights reserved.

Effect of positron-atom interactions on the annihilation gamma spectra of molecules

Calculations of ?-spectra for positron annihilation on a selection of molecules, including methane and its fluoro-substitutes, ethane, propane, butane and benzene are presented. The annihilation ?-spectra characterise the momentum distribution of the electron-positron pair at the instant of annihilation. The contribution to the ?-spectra from individual molecular orbitals is obtained from electron momentum densities calculated using modern computational quantum chemistry density functional theory tools. The calculation, in its simplest form, effectively treats the low-energy (thermalised, room-temperature) positron as a plane wave and gives annihilation ?-spectra that are about 40% broader than experiment, although the main chemical trends are reproduced. We show that this effective 'narrowing' of the experimental spectra is due to the action of the molecular potential on the positron, chiefly, due to the positron repulsion from the nuclei. It leads to a suppression of the contribution of small positron-nuclear separations where the electron momentum is large. To investigate the effect of the nuclear repulsion, as well as that of short-range electron-positron and positron-molecule correlations, a linear combination of atomic orbital description of the molecular orbitals is employed. It facilitates the incorporation of correction factors which can be calculated from atomic many-body theory and account for the repulsion and correlations. Their inclusion in the calculation gives -spectrum linewidths that are in much better agreement with experiment. Furthermore, it is shown that the effective distortion of the electron momentum density, when it is observed through positron annihilation -spectra, can be approximated by a relatively simple scaling factor. © IOP Publishing Ltd and Deutsche Physikalische Gesellschaft.

Calculation of gamma spectra for positron annihilation on molecules

Calculations of gamma spectra for positron annihilation for a selection of molecules, including methane and its fluoro-substitutes, ethane, propane, butane and benzene are presented. The contribution to the ?-spectra from individual molecular orbitals is obtained from electron momentum distributions calculated using the density functional theory (DFT) based B3LYP/TZVP model. For positrons thermalised to room temperature, the calculation, in its simplest form, effectively treats the positron as a plane wave and gives positron annihilation ?-spectra linewidths that are broader (30-40%) than experiment, although the main chemical trends are reproduced. The main physical reason for this is the neglect of positron repulsion from the nuclei. We show that this effect can be incorporated through momentum-dependent correction factors, determined from positron-atom calculations, e.g., many-body perturbation theory. Inclusion of these factors in the calculation gives linewidths that are in improved agreement with experiment.

Imaging adiabatic control of charge transfer in molecules

Charge transfer is a subfemtosecond process in molecules that creates chemical and electronic structure changes. At the quantum level the process can be coherently controlled by ultrashort light pulses. We show how the charge transfer process can be manipulated using a combination of dynamic and static fields and predict how this can be observed experimentally by imaging with photoionization.

Elevated soluble cellular adhesion molecules are associated with increased mortality in a prospective cohort of renal transplant recipients

Increased plasma levels of cellular adhesion molecules (CAMs) have been shown to be predictors of all cause mortality in individuals with chronic renal failure 12 and patients with end-stage renal disease receiving haemodialysis 3. In renal transplant recipients the predictive value of CAMs has not been well characterised. The aim of this study was to assess the relationship between CAMs and all-cause mortality during prospective follow-up of a renal transplant cohort.

Defense peptides secreted by helminth pathogens: antimicrobial and/or immunomodulator molecules?

Host defense peptides (HDPs) are an evolutionarily conserved component of the innate immune response found in all living species. They possess antimicrobial activities against a broad range of organisms including bacteria, fungi, eukaryotic parasites, and viruses. HDPs also have the ability to enhance immune responses by acting as immunomodulators. We discovered a new family of HDPs derived from pathogenic helminth (worms) that cause enormous disease in animals and humans worldwide. The discovery of these peptides was based on their similar biochemical and functional characteristics to the human defense peptide LL-37. We propose that these new peptides modulate the immune response via molecular mimicry of mammalian HDPs thus providing a mechanism behind the anti-inflammatory properties of helminth infections.

Living is Information Processing: From Molecules to Global Systems

We extend the concept that life is an informational phenomenon, at every level of organisation, from molecules to the global ecological system. According to this thesis: (a) living is information processing, in which memory is maintained by both molecular states and ecological states as well as the more obvious nucleic acid coding; (b) this information processing has one overall function-to perpetuate itself; and (c) the processing method is filtration (cognition) of, and synthesis of, information at lower levels to appear at higher levels in complex systems (emergence). We show how information patterns, are united by the creation of mutual context, generating persistent consequences, to result in 'functional information'. This constructive process forms arbitrarily large complexes of information, the combined effects of which include the functions of life. Molecules and simple organisms have already been measured in terms of functional information content; we show how quantification may be extended to each level of organisation up to the ecological. In terms of a computer analogy, life is both the data and the program and its biochemical structure is the way the information is embodied. This idea supports the seamless integration of life at all scales with the physical universe. The innovation reported here is essentially to integrate these ideas, basing information on the 'general definition' of information, rather than simply the statistics of information, thereby explaining how functional information operates throughout life. © 2013 Springer Science+Business Media Dordrecht.

Adsorption properties of HKUST-1 toward hydrogen and other small molecules monitored by IR

Among microporous systems metal organic frameworks are considered promising materials for molecular adsorption. In this contribution infrared spectroscopy is successfully applied to highlight the positive role played by coordinatively unsaturated Cu2+ ions in HKUST-1, acting as specific interaction sites. A properly activated material, obtained after solvent removal, is characterized by a high fraction of coordinatively unsaturated Cu2+ ions acting as preferential adsorption sites that show specific activities towards some of the most common gaseous species (NO, CO2, CO, N-2 and H-2). From a temperature dependent IR study, it has been estimated that the H-2 adsorption energy is as high as 10 kJ mol(-1). A very complex spectral evolution has been observed upon lowering the temperature. A further peculiarity of this material is the fact that it promotes ortho-para conversion of the adsorbed H-2 species.