Infrared Spectroscopic and Theoretical Characterization of a Selection of Biologically Relevant Gaseous Ionic Complexes

The structures of gaseous sodiated poly(alanines), Ala8−12 Na+ , were studied using infrared multiple photon dissociation (IRMPD) spectroscopy complimentarily to molecular dynamics and quantum chemical methods. Experimental results were obtained in both the 3000-3600 cm−1 region and the 1000-1800 cm−1 fingerprint region. Replica-exchange molecular dynamics (REMD) simulations using the multipolar-based polarizable AMOEBA force field were used to explore the conformational potential energy surface. A selection of resulting structures was extensively treated with a wide range of sequentially higher-order quantum chemical methods (from the RI-B3LYP-D/def2-SVP level to the RI-CC2/def2-TZVPP//RI-MP2/def2-SVP level). Calculated results suggest an α-helical conformation to be the lowest-energy for all Ala8−12 Na+ peptides, and that only for Ala8 Na+ does an accessible low energy structure exist that is also likely to contribute to the room temperature experiments. Experimental results confirmed these suggestions. All Ala8−12 Na+ peptides have a free C-OH band in the 3575 cm−1 region resulting from the free C-terminal C-OH of the α-helical conformation, a necessary observation for α-helical poly(alanine) peptides. As well, bound N-H bands were found to create somewhat of an α-helical signature in the 3315-3435 cm−1 region. For a given peptide, the order of vibrational modes follows the order of N-H· · ·O=C hydrogen bond lengths (longer bond length gives higher frequency N-H vibration). Additionally for α-helical conformations, calculated N-H· · ·O=C hydrogen bond lengths consistently decrease from the N-terminus (≈2.15 Ang.) to the C-terminus (≈1.90 Ang.). This results in a consistent and similar N-H stretching band between 3315-3425 cm−1 of ordered N-H modes. Proton-bound and sodium-bound-dimer ions (Ala6)2 H+, (Ala6)2Na+, (Ala12Ala6)H+, (Ala12Ala6)Na+, (Ala12)2Na+ were considered under similar experimental and computational methodologies; however, IRMPD results were obtained only for (Ala6)2H+. Computations indicate that in these sodium-bound and proton-bound dimers, α-helical type conformations are dominant for all but the smallest dimers ((Ala6)2H+, (Ala6)2Na+), suggesting that the interaction of Ala6H+ or Ala6Na+ with neutral Ala6 is not sufficiently stabilizing to the helical conformation. In the globular conformations, intermolecular and intramolecular hydrogen bonds and coordination of the Na+ are favoured at the expense of a more extensive intramolecular helical-type hydrogen bond network. The lowest-energy globular conformation of Ala6Na+ has both C-terminal COOH groups, one N-terminal NH2 group and an additional two C=O groups interacting with Na+. Such a coordination of the Na+ would not be possible if either or both peptides were helical, where instead, a low-coordination with three or four C=O groups would result. The relative stability of the α-helical conformation was found to be largely related to the stabilization of the macrodipole of the helix. Interaction of two peptides was, in some cases, found to favour formation of α-helical structure even where the isolated peptides would be globular, for example Ala12H+. Interaction of the protonated NH3+ groups with the C-terminal C=O of the neutral peptide places the positive charge somewhat on the exterior of the structure, apparently limiting the unfavourable electrostatic interaction of the positive charge with the dipole (positive) of the helix. (Ala12)2Na+ is a somewhat obvious case, where both monomer units of the dimer are calculated to be independently helical. Although when isolated, Ala12Na+ is calculated to be completely helical through all 12 residues, more complete coordination of the sodium by C=O groups (disrupting, to a small extent, the helix) is calculated to occur. This is likely a result of the interaction of the macrodipole of the helix and the sodium cation being weaker as a result of the interaction between the N-terminus of Ala12Na+ and the C-terminus of the neutral Ala12. Additionally, a series of gaseous ionic clusters formed from guanidinium chloride, [GuanxCl(x−1)]+ and [GuanxCl(x+1)]−, were studied under a similar computational methodology. IRMPD spectra were obtained in both the 3000-3600 cm−1 region and the 1000- 1800 cm−1 fingerprint region. REMD simulations were found to be necessary for locating conformational minima in clusters containing more than four guanidinium ions (x≥4). Experimental spectra were found to be well modelled at the B3LYP-D/def2-SVP level, in most cases. M06/6-311+G(d,p) vibrational analysis was found to be an improvement over B3LYP-D/def2-SVP analysis, at only a moderate increase in computational cost, while the significantly more costly MP2/6-31G(d) results did not offer improvement to the M06/6-311+G(d,p) results over a limited test set. Although only practically possible for the smallest clusters, consideration of anharmonic vibrational frequencies at the B3LYP/6-311+G(d,p) level offered significant improvement over harmonically calculated modes. Generally, smaller clusters were noted to largely adopt high-symmetry conformations, while larger clusters formed cage-like structures with a small number of guanidinium ions contained in the interior

Designing And Testing An Air-PCM Heat Exchanger For Building Ventilation Application Coupled To Energy Storage

Due to the increase of energy costs, buildings energy consumption has tended to decrease in the past decades. This gives an opportunity for developing innovative renewable technologies that are more adapted to recent buildings with low energy demand. In this context, one main challenge is to manage non-simultaneous availability of heat source or sink and the energy demand of buildings. Hence, different technologies dedicated to energy storage have been developed recently; one of them is the use of Phase Change Materials (PCM). These materials are considered because they exhibit a high latent energy and a tunable phase change temperature according to their composition. This paper studies a PCM heat exchanger coupled to a building ventilation system. This PCM module can either store heat during the day (e.g. by cooling solar PV panels) and restore it to the building during the night for space heating purposes or store coolness during the night and give it back during the day and thus act as a free cooling system. This project aims to develop a performing air-PCM heat exchanger providing latent energy storage of 0.5 kWh, this energy is delivered between 15 and 30°C. This heat exchanger is based on corrugated cells that can be easily filled, lined up and then locked in a box, letting the air pass between the cells. The PCM used for the prototype is mainly composed of paraffin. In order to develop an efficient PCM ventilation module, two different ways of investigation were followed and used in parallel. The first one used CFD simulations and the second one, a semi-empirical model based on correlations. The CFD simulations were able to predict the convection coefficient on the air side and also show the flow repartition between the different channels whereas the semi-empirical model allowed a parametrical study in order to identify the best possible geometry. Once the heat exchanger geometry was optimized, a test bench was built and a prototype of air-PCM heat exchanger was manufactured in order to measure its thermal and hydraulic performances. The tests consist in either a complete solidification or liquefaction of the PCM starting from respectively liquid PCM at 30°C or solid PCM at 15°C. The airflow rate was set to 45m³/h, which corresponds barely to the ventilation rate of a traditional room in a residential building. A comparison between the models and the measurements was carried out in order to calibrate the semi-empirical model. Finally, the investigation of a free-cooling application in buildings was performed to calculate the annual performance of the system in different types of climates

Information and Design: Book Symposium on Luciano Floridi’s The Logic of Information

Purpose – To review and discuss Luciano Floridi’s 2019 book The Logic of Information: A Theory of Philosophy as Conceptual Design, the latest instalment in his philosophy of information (PI) tetralogy, particularly with respect to its implications for library and information studies (LIS). Design/methodology/approach – Nine scholars with research interests in philosophy and LIS read and responded to the book, raising critical and heuristic questions in the spirit of scholarly dialogue. Floridi responded to these questions. Findings – Floridi’s PI, including this latest publication, is of interest to LIS scholars, and much insight can be gained by exploring this connection. It seems also that LIS has the potential to contribute to PI’s further development in some respects. Research implications – Floridi’s PI work is technical philosophy for which many LIS scholars do not have the training or patience to engage with, yet doing so is rewarding. This suggests a role for translational work between philosophy and LIS. Originality/value – The book symposium format, not yet seen in LIS, provides forum for sustained, multifaceted and generative dialogue around ideas

Pride-asap: Automatic fragment ion annotation of identified PRIDE spectra

We present an open source software application and library written in Java that provides a uniform annotation of identified spectra stored in the PRIDE database. Pride-asap can be ran in a command line mode for automated processing of multiple PRIDE experiments, but also has a graphical user interface that allows end users to annotate the spectra in PRIDE experiments and to inspect the results in detail. Pride-asap binaries, source code and additional information can be downloaded from http://pride-asa-pipeline.googlecode.com.This article is part of a Special Issue entitled: Standardization and Quality Control in Proteomics.Howard Hughes Medical Institute (International Student Research Fellowship

A comparison of collision cross section values obtained via travelling wave ion mobility-mass spectrometry and ultra high performance liquid chromatography-ion mobility-mass spectrometry : application to the characterisation of metabolites in rat urine

A comprehensive Collision Cross Section (CCS) library was obtained via Travelling Wave Ion Guide mobility measurements through direct infusion (DI). The library consists of CCS and Mass Spectral (MS) data in negative and positive ElectroSpray Ionisation (ESI) mode for 463 and 479 endogenous metabolites, respectively. For both ionisation modes combined, TWCCSN2 data were obtained for 542 non-redundant metabolites. These data were acquired on two different ion mobility enabled orthogonal acceleration QToF MS systems in two different laboratories, with the majority of the resulting TWCCSN2 values (from detected compounds) found to be within 1% of one another. Validation of these results against two independent, external TWCCSN2 data sources and predicted TWCCSN2 values indicated to be within 1-2% of these other values. The same metabolites were then analysed using a rapid reversed-phase ultra (high) performance liquid chromatographic (U(H)PLC) separation combined with IM and MS (IM-MS) thus providing retention time (tr), m/z and TWCCSN2 values (with the latter compared with the DI-IM-MS data). Analytes for which TWCCSN2 values were obtained by U(H)PLC-IM-MS showed good agreement with the results obtained from DI-IM-MS. The repeatability of the TWCCSN2 values obtained for these metabolites on the different ion mobility QToF systems, using either DI or LC, encouraged the further evaluation of the U(H)PLC-IM-MS approach via the analysis of samples of rat urine, from control and methotrexate-treated animals, in order to assess the potential of the approach for metabolite identification and profiling in metabolic phenotyping studies. Based on the database derived from the standards 63 metabolites were identified in rat urine, using positive ESI, based on the combination of tr, TWCCSN2 and MS data.</p

Carrier-envelope phase stability of hollow-fibers used for high-energy, few-cycle pulse generation

We investigated the carrier-envelope phase (CEP) stability of a hollow-fiber setup used for high-energy, few-cycle pulse generation. Saturation of the output pulse energy is observed at 0.6 mJ for a 260 um inner-diameter, 1 m long fiber, statically filled with neon, with the pressure adjusted to achieve an output spectrum capable of supporting sub-4fs pulses. The maximum output pulse energy can be increased to 0.8mJ by using either differential pumping, or circularly polarized input pulses. We observe the onset of an ionization-induced CEP instability, which does not increase beyond an input pulse energy of 1.25 mJ due to losses in the fiber caused by ionization. There is no significant difference in the CEP stability with differential pumping compared to static-fill, demonstrating that gas flow in differentially pumped fibers does not degrade the CEP stabilization.Comment: 4 pages, 4 figure

The Proteomics Identifications database: 2010 update

The Proteomics Identifications database (PRIDE, http://www.ebi.ac.uk/pride) at the European Bioinformatics Institute has become one of the main repositories of mass spectrometry-derived proteomics data. For the last 2 years, PRIDE data holdings have grown substantially, comprising 60 different species, more than 2.5 million protein identifications, 11.5 million peptides and over 50 million spectra by September 2009. We here describe several new and improved features in PRIDE, including the revised submission process, which now includes direct submission of fragment ion annotations. Correspondingly, it is now possible to visualize spectrum fragmentation annotations on tandem mass spectra, a key feature for compliance with journal data submission requirements. We also describe recent developments in the PRIDE BioMart interface, which now allows integrative queries that can join PRIDE data to a growing number of biological resources such as Reactome, Ensembl, InterPro and UniProt. This ability to perform extremely powerful across-domain queries will certainly be a cornerstone of future bioinformatics analyses. Finally, we highlight the importance of data sharing in the proteomics field, and the corresponding integration of PRIDE with other databases in the ProteomExchange consortium.European Union (ProDaC grant LSHG-CT-2006-036814)Burroughs Wellcome Fund (Grant WT085949MA

Localisation and Mislocalisation of the Interferon-Inducible Immunity-Related GTPase, Irgm1 (LRG-47) in Mouse Cells

Irgm1 (LRG-47) is an interferon-inducible Golgi membrane associated GTPase of the mouse whose disruption causes susceptibility to many different intracellular pathogens. Irgm1 has been variously interpreted as a regulator of homologous effector GTPases of the IRG family, a regulator of phagosome maturation and as an initiator of autophagy in interferon-induced cells. We find that endogenous Irgm1 localises to late endosomal and lysosomal compartments in addition to the Golgi membranes. The targeting motif known to be required for Golgi localisation is surprisingly also required for endolysosomal localisation. However, unlike Golgi localisation, localisation to the endolysosomal system also requires the functional integrity of the nucleotide binding site, and thus probably reflects transient activation. Golgi localisation is lost when Irgm1 is tagged at either N- or C-termini with EGFP, while localisation to the endolysosomal system is relatively favoured. N-terminally tagged Irgm1 localises predominantly to early endosomes, while C-terminally tagged Irgm1 localises to late endosomes and lysosomes. Both these anomalous distributions are reversed by inactivation of the nucleotide binding site, and the tagged proteins both revert to Golgi membrane localisation. Irgm1 is the first IRG protein to be found associated with the endolysosomal membrane system in addition to either Golgi (Irgm1 and Irgm2) or ER (Irgm3) membranes, and we interpret the result to be in favour of a regulatory function of IRGM proteins at cellular membrane systems. In future analyses it should be borne in mind that tagging of Irgm1 leads to loss of Golgi localisation and enhanced localisation on endolysosomal membranes, probably as a result of constitutive activation

Infrared Multiple-Photon Dissociation Action Spectroscopy of the b(2)(+) Ion from PPG: Evidence of Third Residue Affecting b(2)(+) Fragment Structure

Infrared multiple-photon dissociation (IRMPD) action spectroscopy was performed on the b2 + fragment ion from the protonated PPG tripeptide. Comparison of the experimental infrared spectrum with computed spectra for both oxazolone and diketopiperazine structures indicates that the majority of the fragment ion population has an oxazolone structure with the remainder having a diketopiperazine structure. This result is in contrast with a recent study of the IRMPD action spectrum of the PP b2 + fragment ion from PPP, which was found to be nearly 100% diketopiperazine (Martens et al. Int. J. Mass Spectrom. 2015, 377, 179). The diketopiperazine b2 + ion is thermodynamically more stable than the oxazolone but normally requires a trans/cis peptide bond isomerization in the dissociating peptide. Martens et al. showed through IRMPD action spectroscopy that the PPP precursor ion was in a conformation in which the first peptide bond is already in the cis conformation and thus it was energetically favorable to form the thermodynamically-favored diketopiperazine b2 + ion. In the present case, solution-phase NMR spectroscopy and gas-phase IRMPD action spectroscopy show that the PPGprecursor ion has its first amide bond in a trans configuration suggesting that the third residue is playing an important role in both the structure of the peptide and the associated ring-closure barriers for oxazolone and diketopiperazine formation