Reconstructing the infrared spectrum of a peptide from representative conformers of the full canonical ensemble

Leucine enkephalin (LeuEnk), a biologically active endogenous opioid pentapeptide, has been under intense investigation because it is small enough to allow efficient use of sophisticated computational methods and large enough to provide insights into low-lying minima of its conformational space. Here, we reproduce and interpret experimental infrared (IR) spectra of this model peptide in gas phase using a combination of replica-exchange molecular dynamics simulations, machine learning, and ab initio calculations. In particular, we evaluate the possibility of averaging representative structural contributions to obtain an accurate computed spectrum that accounts for the corresponding canonical ensemble of the real experimental situation. Representative conformers are identified by partitioning the conformational phase space into subensembles of similar conformers. The IR contribution of each representative conformer is calculated from ab initio and weighted according to the population of each cluster. Convergence of the averaged IR signal is rationalized by merging contributions in a hierarchical clustering and the comparison to IR multiple photon dissociation experiments. The improvements achieved by decomposing clusters containing similar conformations into even smaller subensembles is strong evidence that a thorough assessment of the conformational landscape and the associated hydrogen bonding is a prerequisite for deciphering important fingerprints in experimental spectroscopic data.</p

From synchrotrons for XFELs : The soft x-ray near-edge spectrum of the ESCA molecule

A predictive understanding of soft x-ray near-edge absorption spectra of small molecules is an enduring theoretical challenge and of current interest for x-ray probes of molecular dynamics. We report the experimental absorption spectrum for the electron spectroscopy for chemical analysis (ESCA) molecule (ethyl trifluoroacetate) near the carbon 1s absorption edge between 285-300 eV. The ESCA molecule with four chemically distinct carbon sites has previously served as a theoretical benchmark for photoelectron spectra and now for photoabsorption spectra. We report a simple edge-specific approach for systematically expanding standard basis sets to properly describe diffuse Rydberg orbitals and the importance of triple excitations in equation-of-motion coupled-cluster calculations of the energy interval between valence and Rydberg excitations

Roadmap on dynamics of molecules and clusters in the gas phase

This roadmap article highlights recent advances, challenges and future prospects in studies of the dynamics of molecules and clusters in the gas phase. It comprises nineteen contributions by scientists with leading expertise in complementary experimental and theoretical techniques to probe the dynamics on timescales spanning twenty order of magnitudes, from attoseconds to minutes and beyond, and for systems ranging in complexity from the smallest (diatomic) molecules to clusters and nanoparticles. Combining some of these techniques opens up new avenues to unravel hitherto unexplored reaction pathways and mechanisms, and to establish their significance in, e.g. radiotherapy and radiation damage on the nanoscale, astrophysics, astrochemistry and atmospheric science

Regionale kosten en baten van alternatieve post-Kyoto klimaat regimes: Vergelijking van varianten van de &apos;Multi-stage&apos; en &apos;Per Capita Convergence&apos; regimes

Deze studie verkent de technische, economische en milieu implicaties van verschillende zogenaamde post-Kyoto regimes voor de verdeling van regionale reductie doelstellingen die leiden tot stabilisatie van de broeikasgasconcentratie in de atmosfeer op 550 en 650 ppmv CO2-equivalenten (het S550e en S650e profiel). Binnen deze profielen zijn de varianten van het 'Multi-stage' en 'Per Capita convergence' regime geevalueerd. Voor de Annex I landen zijn de reducties meer afhankelijk van het stabilisatieniveau dan van het type regime. In 2025 leiden de meeste regimes onder het S550e profiel tot een reductie van emissies van 25-50% ten opzichte van 1990 niveau (range afhankelijk van regio en regime). Voor de niet-Annex I landen zijn de reductiedoelstellingen meer gedifferentieerd, zowel wat betreft regiem als voor verschillende tijdsperiodes. Onder alle regimes is vroege toetreding van de (belangrijkste) niet-Annex I landen noodzakelijk. Vier groepen van regio's met vergelijkbare kostenniveaus ten opzichte van hun BNP kunnen worden geidentificeerd. De studie toont daarnaast dat klimaatbeleid kan leiden tot belangrijke nevenvoordelen, zoals een afname van de emissies van zwavel- en stikstofoxide. Samengevat, toont de studie aan dat in evaluatie van verdelingsregimes het niet voldoende is alleen naar de initiele allocatie te kijken, maar dat ook de bestrijdingkosten en consequenties voor energiehandel meegenomen moeten worden. De voordelen van het meedoen in emissiehandel en het reduceren van regionale luchtverontreiniging kunnen het mogelijk maken voor ontwikkelingslanden om deel te nemen aan het reduceren van mondiale broeikasgassen tegen lage kosten of zelfs opbrengsten. Echter, om de politieke haalbaarheid te vergroten zullen zowel het niveau als de vorm van de verplichtingen zo moeten worden gekozen dat economische risico's worden vermeden.The study documented here explores technical, economic and environmental implications of different post-Kyoto climate regimes for differentiation of future commitments that would lead to a stabilisation of greenhouse gas concentrations (Kyoto gases) in the atmosphere at 550 and 650 ppmv CO2-equivalents (S550e and S650e profile). Constrained by these two profiles, the implications of two different regimes, the Multi-stage and Per Capita Convergence approaches, are evaluated. For the Annex I regions, reduction targets are more dependent on the stabilisation level than on the type of regime chosen. In 2025, most regimes show emissions reductions for Annex I regions of 25-50% compared to their 1990 levels. For the non-Annex I regions, the results are generally more differentiated and differ strongly per regime and in time. Under all regimes, early participation of (major) non-Annex I regions is needed. Four groups of regions with similar efforts can be identified with respect to their abatement costs as percentage of GDP. The study also found that climate policies can induce significant co-benefits, such as a decrease in the sulphur and nitrogen oxide emissions. Overall, the analysis shows that in evaluating the implications of various regimes, it is not sufficient to evaluate only the allocation of the emissions compared to baseline. Abatement costs and changes in energy trade will also have to be assessed. The gains from participating in global-emissions trading and realising reduced air pollution damage and/or abatement costs can make early participation of (large) developing countries in global GHG control possible at low costs or even net gains. However, the level and form of commitment will have to be well chosen - and not be too strict - to balance economic risks and political viability.VROM-DGM EC-DG

Regionale kosten en baten van alternatieve post-Kyoto klimaat regimes: Vergelijking van varianten van de 'Multi-stage' en 'Per Capita Convergence' regimes

The study documented here explores technical, economic and environmental implications of different post-Kyoto climate regimes for differentiation of future commitments that would lead to a stabilisation of greenhouse gas concentrations (Kyoto gases) in the atmosphere at 550 and 650 ppmv CO2-equivalents (S550e and S650e profile). Constrained by these two profiles, the implications of two different regimes, the Multi-stage and Per Capita Convergence approaches, are evaluated. For the Annex I regions, reduction targets are more dependent on the stabilisation level than on the type of regime chosen. In 2025, most regimes show emissions reductions for Annex I regions of 25-50% compared to their 1990 levels. For the non-Annex I regions, the results are generally more differentiated and differ strongly per regime and in time. Under all regimes, early participation of (major) non-Annex I regions is needed. Four groups of regions with similar efforts can be identified with respect to their abatement costs as percentage of GDP. The study also found that climate policies can induce significant co-benefits, such as a decrease in the sulphur and nitrogen oxide emissions. Overall, the analysis shows that in evaluating the implications of various regimes, it is not sufficient to evaluate only the allocation of the emissions compared to baseline. Abatement costs and changes in energy trade will also have to be assessed. The gains from participating in global-emissions trading and realising reduced air pollution damage and/or abatement costs can make early participation of (large) developing countries in global GHG control possible at low costs or even net gains. However, the level and form of commitment will have to be well chosen - and not be too strict - to balance economic risks and political viability.Deze studie verkent de technische, economische en milieu implicaties van verschillende zogenaamde post-Kyoto regimes voor de verdeling van regionale reductie doelstellingen die leiden tot stabilisatie van de broeikasgasconcentratie in de atmosfeer op 550 en 650 ppmv CO2-equivalenten (het S550e en S650e profiel). Binnen deze profielen zijn de varianten van het 'Multi-stage' en 'Per Capita convergence' regime geevalueerd. Voor de Annex I landen zijn de reducties meer afhankelijk van het stabilisatieniveau dan van het type regime. In 2025 leiden de meeste regimes onder het S550e profiel tot een reductie van emissies van 25-50% ten opzichte van 1990 niveau (range afhankelijk van regio en regime). Voor de niet-Annex I landen zijn de reductiedoelstellingen meer gedifferentieerd, zowel wat betreft regiem als voor verschillende tijdsperiodes. Onder alle regimes is vroege toetreding van de (belangrijkste) niet-Annex I landen noodzakelijk. Vier groepen van regio's met vergelijkbare kostenniveaus ten opzichte van hun BNP kunnen worden geidentificeerd. De studie toont daarnaast dat klimaatbeleid kan leiden tot belangrijke nevenvoordelen, zoals een afname van de emissies van zwavel- en stikstofoxide. Samengevat, toont de studie aan dat in evaluatie van verdelingsregimes het niet voldoende is alleen naar de initiele allocatie te kijken, maar dat ook de bestrijdingkosten en consequenties voor energiehandel meegenomen moeten worden. De voordelen van het meedoen in emissiehandel en het reduceren van regionale luchtverontreiniging kunnen het mogelijk maken voor ontwikkelingslanden om deel te nemen aan het reduceren van mondiale broeikasgassen tegen lage kosten of zelfs opbrengsten. Echter, om de politieke haalbaarheid te vergroten zullen zowel het niveau als de vorm van de verplichtingen zo moeten worden gekozen dat economische risico's worden vermeden

Deepening into the nucleation and fission processes of nano-hydrated ammonia clusters - A combined theoretical and experimental study

While largely studied in the macroscopic scale, the dynamics leading to the nucleation and fission of atmospheric aerosols are very poorly understood at the nano or molecular scale. A model system consisting on ionized hydrogen-bonded ammonia and water molecules have been studied experimentally using mass- and 3D momentum spectroscopy and theoretically using ab initio molecular dynamics simulations