1,363 research outputs found

    Hidden in the dark:Seeking the vanished polycylic aromatic hydrocarbons in planet-forming discs

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    The origin of life is closely linked to the formation of planetary systems, and both are fundamental drivers of modern astronomical research. Especially carbon is of interest as it is the building block of life as we know.In the interstellar medium, about 15 % of carbon is locked in the form of polycyclic aromatic hydrocarbons (PAHs). The infrared signals of these complex molecules have been observed in numerous astrophysical environments. Their detection in planet-forming discs is of particular interest, as these are the birth-sites of exoplanets. By understanding the evolution of PAHs during planet formation, it is possible to trace a large fraction of carbon. Additionally, the signals of PAHs can reveal crucial information about planet-forming discs themselves to better understand planet formation.This thesis particularly focuses on the formation of molecular clusters of PAHs bound by van der Walls forces in planet forming discs. We analysed the stability of PAH clusters against stellar UV radiation from young stars and modelled their dissociation rates. Further, we model the evolution of clusters in the presence of dust grains, as they interact through freeze-out. Then, we investigate the depletion of observable gas-phase PAHs which has been observed in many discs. Next, we simulate observations and discuss the amount of retrievable information from spectra. Finally, we investigate the interaction of PAHs with stellar X-rays from T Tauri discs and their influence on the destruction of PAHs and PAH clusters

    Are we still chasing molecules that were never there? The role of quantum chemical simulations of NMR parameters in structural reassignment of natural products

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    Covering: 2019 to 2023. Even with the advent of modern and complementary spectroscopy techniques, comprehensive characterization of natural product continues to represent an onerous and time-consuming task, being far away to become rather “routine”. Mainly due to their highly complex structures and small amount of isolated sample, in milligram or sub-milligram quantities, structural misassignment of natural products are still a recurrence theme in the modern literature. Since the seminal paper from Nicolau and Snider, in 2005, evaluating the various cases of reassignment of natural products, from the present era, in which NMR parameters calculations play such an important role in the structural elucidation of natural products, helping to uncover and ultimately revise the structure of previously reported compounds, a pertinent question arises: are we still chasing molecules that were never there? In this minireview, we intent to discuss the current state of computational NMR parameter calculations, with a particular focus on their application in the structural determination of natural products. Additionally, we have conducted a comprehensive survey of the literature spanning the years 2019–2023, in order to select and discuss recent noteworthy cases of incorrectly assigned structures that were revised through NMR calculations. Therefore, our main goal is to show what can be done through computational simulations of NMR parameters, currently user-friendly and easily implemented by non-expert users with basic skills in computational chemistry, before venturing into complex and time-consuming total synthesis projects. In conclusion, we anticipate a promising future for NMR parameter calculations, fueled by the ongoing development of user-friendly tools and the integration of artificial intelligence. The emergence of these advancements is poised to broaden the applications of NMR simulations, offering a more accessible and reliable means to address the persistent challenge of structural misassignments in natural product chemistry

    Quantum computing and materials science: A practical guide to applying quantum annealing to the configurational analysis of materials

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    Using quantum computers for computational chemistry and materials science will enable us to tackle problems that are intractable on classical computers. In this paper, we show how the relative energy of defective graphene structures can be calculated by using a quantum annealer. This simple system is used to guide the reader through the steps needed to translate a chemical structure (a set of atoms) and energy model to a representation that can be implemented on quantum annealers (a set of qubits). We discuss in detail how different energy contributions can be included in the model and what their effect is on the final result. The code used to run the simulation on D-Wave quantum annealers is made available as a Jupyter Notebook. This Tutorial was designed to be a quick-start guide for the computational chemists interested in running their first quantum annealing simulations. The methodology outlined in this paper represents the foundation for simulating more complex systems, such as solid solutions and disordered systems

    Strategies for Red-Light Photoswitching

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    Vuorovaikutteiset, muotoutuvat ja jopa älykkäät molekyylirakenteet ovat avain uuden sukupolven lääkeaineisiin ja toiminnallisiin materiaaleihin. Valokytkimet eli yhdisteet, jotka isomeroituvat reversiibelisti valon vaikutuksesta johtaen makroskooppisten ominaisuuksien muutoksiin, ovat erottamaton osa tätä tulevaisuutta. Mahdolliset sovelluskohteet ulottuvat lääketieteestä elektroniikkaan ja robotiikkaan. Valitettavasti useimmat valokytkinrakenteet, esimerkiksi laajalti käytetyt atsobentseenit, absorboivat ultraviolettivaloa, joka on vahingollista monille materiaaleille ja erityisesti eläville soluille. Jotta valokytkinten koko potentiaali voidaan hyödyntää, tarvitaan harmittomalla näkyvällä valolla toimivia yhdisteitä. Puna- tai infrapunavalo olisi ihanteellinen ärsyke biologian alalla käytettäville kytkimille. Sama pätee myös molekyylimoottoreihin eli yhdisteisiin, jotka pyörivät valon vaikutuksesta yksisuuntaisesti. Lisäksi sekä kytkinten että moottorien tulisi isomerisoitua valon vaikutuksesta tehokkaasti ja nopeasti, termisten isomerisaatioreaktioiden tulisi olla sovelluskohteesta riippuen hitaita tai nopeita ja yhdisteiden tulisi toimia hyvin erilaisissa ympäristöissä. Näiden ominaisuuksien hallitsemiseksi on tärkeää ymmärtää niiden taustalla olevat mekanismit. Tässä väitöskirjassa tutkimme kolmea keinoa toteuttaa valokytkentä punaisella valolla: (i) atsobentseenien absorptiospektrin siirtäminen rakennetta muokkaamalla, (ii) uusien, valmiiksi punaista valoa absorboivien rakenteiden hyödyntäminen ja (iii) epäsuora valokytkentä punavalolla aktivoitavia katalyyttejä hyödyntäen. Tarkastelemme strategioita teoreettiselta kannalta ja osoitamme, että niistä jokainen mahdollistaa valokytkennän punaista valoa käyttäen. Kullakin strategialla on etunsa ja haasteensa tehokkaan, nopean ja kestävän valokytkennän toteuttamiseksi. Tästä johtuen yksi ihanteellinen valokytkinmalli ei voi saavuttaa kaikkia eri sovelluksille asetettuja tavoitteita, vaan tulevaisuuden haaste on löytää kuhunkin käyttöön paras ratkaisu. Samoja periaatteita voidaan soveltaa myös molekyylimoottoreihin, jolloin molekulaarisen tason yksisuuntainen kiertoliike voidaan saada aikaan näkyvällä valolla. Lisäksi punaisella valolla toimivien valokytkinten rakenteita hyödyntämällä moottorien rotaatiota saadaan tehostettua.Responsive, adaptive and even intelligent molecular systems have been identified as the key to next-generation pharmaceuticals and functional materials. Photoswitches, compounds that isomerise reversibly between two distinct ground-state species upon excitation with light and consequently give rise to a macroscopic effect, are an integral part of this future. Their potential application areas range from photopharmacology to optoelectronics and soft robotics. However, most conventional photoswitch structures such as azobenzenes absorb ultraviolet light, high-energy photons that are detrimental to many artificial materials and especially to living systems. To harness their full potential, photoswitches should function efficiently with visible light that is benign to the environment. Red or near-infrared light would be the ideal stimulus for switches utilised in biological context, as these wavelengths are least absorbed by living tissue. The same applies to light-driven molecular motors, compounds that exhibit unidirectional rotation upon photoexcitation. In addition to absorption in the red part of the visible spectrum, both switches and motors should exhibit efficient and fast photoisomerisation, favourable thermal isomerisation kinetics and tolerance towards different environments in order to be useful in real-life applications. In this light, it is crucial to understand the underlying fundamental mechanisms that govern these attributes. In this thesis, we explore three different approaches to realise photoswitching with red light: (i) synthetic modifications of azobenzenes, (ii) utilisation of new photoswitch cores that inherently absorb low-energy photons, and (iii) indirect isomerisation with red-light photocatalysts. We study each strategy from a theoretical viewpoint and demonstrate that they all provide means to induce isomerisation with red light, each with unique advantages and challenges in terms of promoting efficient, fast and robust switching. As a result, a single optimal photoswitch system cannot be designed; instead, the challenge lies in identifying the best design for each application. The same principles can also be applied to molecular motors, giving rise to visible-light-powered unidirectional rotary motion on a molecular level. We show that drawing inspiration from red-light-absorbing photoswitches has repercussions not only on the visible-light absorption but also on enhanced rotation dynamics

    2007 GREAT Day Program

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    SUNY Geneseo’s First Annual G.R.E.A.T. Day.https://knightscholar.geneseo.edu/program-2007/1001/thumbnail.jp

    An aldehyde as a rapid source of secondary aerosol precursors: theoretical and experimental study of hexanal autoxidation

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    Aldehydes are common constituents of natural and polluted atmospheres, and their gas-phase oxidation has recently been reported to yield highly oxygenated organic molecules (HOMs) that are key players in the formation of atmospheric aerosol. However, insights into the molecular-level mechanism of this oxidation reaction have been scarce. While OH initiated oxidation of small aldehydes, with two to five carbon atoms, under high-NOx conditions generally leads to fragmentation products, longer-chain aldehydes involving an initial non-aldehydic hydrogen abstraction can be a path to molecular functionalization and growth. In this work, we conduct a joint theoretical–experimental analysis of the autoxidation chain reaction of a common aldehyde, hexanal. We computationally study the initial steps of OH oxidation at the RHF-RCCSD(T)-F12a/VDZ-F12//ωB97X-D/aug-cc-pVTZ level and show that both aldehydic (on C1) and non-aldehydic (on C4) H-abstraction channels contribute to HOMs via autoxidation. The oxidation products predominantly form through the H abstraction from C1 and C4, followed by fast unimolecular 1,6 H-shifts with rate coefficients of 1.7×10-1 and 8.6×10-1 s−1, respectively. Experimental flow reactor measurements at variable reaction times show that hexanal oxidation products including HOM monomers up to C6H11O7 and accretion products C12H22O9−10 form within 3 s reaction time. Kinetic modeling simulations including atmospherically relevant precursor concentrations agree with the experimental results and the expected timescales. Finally, we estimate the hexanal HOM yields up to seven O atoms with mechanistic details through both C1 and C4 channels.</p

    Precision mass measurements for the astrophysical rp-process and electron cooling of trapped ions

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    Precision mass measurements of rare isotopes with decay half-lives far below one second are of importance to a variety of applications including studies of nuclear structure and nuclear astrophysics as well as tests of fundamental symmetries. The first part of this thesis discusses mass measurements of neutron-deficient gallium isotopes in direct vicinity of the proton drip line. The reported measurements of 60-63Ga were performed with the MR-TOF-MS of TRIUMF's Ion Trap for Atomic and Nuclear Science (TITAN) in Vancouver, Canada. The measurements mark the first direct mass determination of 60Ga and yield a 61Ga mass value three times more precise than the literature value from AME2020. Our 60Ga mass value constrains the location of the proton dripline in the gallium isotope chain and extends the experimentally evaluated IMME for isospin triplets up to A=60. The improved precision of the 61Ga mass has important implications for the astrophysical rapid proton capture process (rp-process). Calculations in a single-zone model demonstrate that the improved mass data substantially reduces uncertainties in the predicted light curves of Type I X-ray bursts. TITAN has demonstrated that charge breeding provides a powerful means to increase the precision and resolving power of Penning trap mass measurements of radioactive ions. However, the charge breeding process deteriorates the ion beam quality, thus mitigating the benefits associated with Penning trap mass spectrometry of highly charged ions (HCI). As a potential remedy for the beam quality loss, a cooler Penning trap has been developed in order to investigate the prospects of electron cooling the HCI prior to the mass measurement. The second part of this thesis reports exploratory studies of electron cooling of singly charged ions in this cooler Penning trap. Comparison of measured ion energy evolutions to a cooling model provides a detailed understanding of the underlying cooling dynamics. Extrapolation of the model enables the deduction of tentative estimates of the expected cooling times for radioactive HCI

    Navigating chemical reaction space with a steering wheel

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    Autonomous reaction network exploration algorithms offer a systematic approach to explore mechanisms of complex chemical processes. However, the resulting reaction networks are so vast that an exploration of all potentially accessible intermediates is computationally too demanding. This renders brute-force explorations unfeasible, while explorations with completely pre-defined intermediates or hard-wired chemical constraints, such as element-specific coordination numbers, are not flexible enough for complex chemical systems. Here, we introduce a Steering Wheel to guide an otherwise unbiased automated exploration. The Steering Wheel algorithm is intuitive, generally applicable, and enables one to focus on specific regions of an emerging network. It also allows for guiding automated data generation in the context of mechanism exploration, catalyst design, and other chemical optimization challenges. The algorithm is demonstrated for reaction mechanism elucidation of transition metal catalysts. We highlight how to explore catalytic cycles in a systematic and reproducible way. The exploration objectives are fully adjustable, allowing one to harness the Steering Wheel for both structure-specific (accurate) calculations as well as for broad high-throughput screening of possible reaction intermediates.Comment: 40 pages, 10 figures, 1 tabl

    Computational development of models and tools for the kinetic study of astrochemical gas-phase reactions

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    This PhD thesis focuses on the application and development of computational tools and methodologies for the modeling of the kinetics of gas-phase reactions of astrophysical interest in the interstellar medium (ISM). The complexity related to the investigation of chemical reactivity in space is mostly due to the extreme physical conditions of temperature, pressure and exposure to high-energy radiation, which in turn also lead to the formation of exotic species, like radicals and ions. Nevertheless, there is still much to be understood about the formation of molecules, the major issue being the lack of sufficient laboratory (experimental and computational) studies. A more detailed and accurate study of all the chemical processes occurring in the ISM will allow us to obtain the data necessary to simulate the chemical evolution of an interstellar cloud over time using kinetic models including thousands of reactions that involve hundreds of species. The collection of the kinetic parameters required for the relevant reactions has led to the growth of different astrochemical databases, such as KIDA and UMIST. However, the data gathered in these catalogues are incomplete, and rely extensively on crude estimations and extrapolations. These rates are of paramount importance to get a better comprehension of the relative abundances of the chemical compounds extrapolated by the astronomers from the spectral data recorded through the radio telescopes and the in-orbit devices, like the satellites. Accurate state-of-the-art computational approaches play a fundamental role in analyzing feasible reaction mechanisms and in accurately predicting the associated kinetics. Such approaches usually rely on chemical intuition where a by-hand search of the most likely pathways is performed. Unfortunately, thisprocedure can lead to overlook significant mechanisms, especially when large molecular systems are investigated. Increasing the size of a molecule can also increase the number of its possible conformers which can show a different chemical reactivity with respect to the same chemical partner. This brings to get very complex chemical reaction networks in which hundreds of chemical species are involved and thousands of chemical reactions can occur.During the last decades, a lot of effort has been done to develop computational techniques able to perform extensive and thorough investigations of complex reaction mechanisms. Such approaches rely on automated computational protocols which drastically decrease the risk of making blunders during the search for significant reaction pathways.Furthermore, the accurate characterization of the potential energy surfaces (PESs) critical points, like reactants, intermediates, transition states and products involved in the reaction mechanism, is crucial in order to carry out a reliable kinetic investigation. The kinetic analysis of an erroneous potential energy surface, would lead to gross errors in the estimation of the rate constants of the chemical species involved in the reaction.In order to avoid such errors, the combination of high-level electronic structure calculations via composite scheme can be helpful to get a more precise estimation of the energy barriers involved in the reaction mechanism. It has been proven that "cheap"[1] composite schemes can achieve subchemical accuracy without any empirical parameters and with convenient computation times, making them perfect for the purpose of this thesis.In recent decades, many efforts have been made to develop theoretical and computational methodologies to perform accurate numerical simulations of the kinetics of such complex reaction mechanisms in a wide range of thermodynamic conditions that mimic extreme reaction environmentsas for combustion systems, the atmosphere and the ISM. Such methodologies are based on the ab initio-transition-state-theory-based master equation approach, which allows the determination of rate coefficients and branching ratios of chemical species involved in complex chemical reactions. This methodology allows to make accurate predictions of the relative abundances of the reaction products for complex reactions even under conditions of temperature and pressure not experimentally accessible, such as those that characterize the ISM. Based on these premises, this dissertation has been focused on the application of a computational protocol for the ab initio-based computational modeling and kinetic investigation of gas-phase reactions which can occur in the ISM.This protocol is based on the application of validated methodologies for the automated discovery of complex reaction mechanisms by means of the AutoMeKin[2] program, the accurate calculation of the energetic of the potential energy surfaces (PESs) through the junChS and junChS-F12a "cheap" composite schemes and the kinetic investigation using the StarRate computer program specifically designed to study gas-phase reactions of astrochemical interest in conjunction with the MESS program. Furthermore, this dissertation has been also focused on the development and implementation of StarRate, a computer program for the accurate calculation of kinetics through a chemical master equation approach of multi-step chemical reactions. StarRate is an object-based program written in the so-called F language. It is structured in three main modules, namely molecules, steps and reactions, which extract the properties needed to calculate the kinetics for the single-step reactions partecipating in the overall reaction. Another module, in_out, handles program&rsquo;s input and output operations. The main program,starrate, controls the sequences of the calling of the procedures contained in each of the three main modules.Through these modular structure, StarRate[3] can compute canonical and microcanonical rate coefficients taking into account for the tunneling effect and the energy-dependent and time-dependent evolution of the species concentrations involved in the reaction mechanism. Such protocol has been applied to investigate the formation reaction mechanisms of some complex interstellar polyatomic molecules, named interstellar complex organic molecules (iCOMs). More specifically, the formation of prebiotic iCOMs in space has raised considerable interest in the scientific community, because they are considered as precursors of more complex biological systems involved in the origin of life in the Universe. Debate on the origins of these biomolecular building blocks has been further stimulated by the discovery of nucleobases and amino acids in meteorites and other extraterrestrial sources. However, few insights on the chemistry which brings to the formation of such compounds is known.&nbsp;&nbsp;References:&nbsp;[1] Jacopo Lupi,Silvia Alessandrini,Cristina Puzzarini,and Vincenzo Barone.junchs and junchs-F12 models:Parameter-free efficient yet accurate compositeschemes for energies and structures of noncovalent complexes. Journal of Chem-ical Theory and Computation, 17(11):6974&ndash;6992, 2021. PMID: 34677974.[2] Emilio Mart&iacute;nez-N&uacute;&ntilde;ez, George L. Barnes, David R. Glowacki, Sabine Kopec,Daniel Pel&aacute;ez, Aurelio Rodr&iacute;guez, Roberto Rodr&iacute;guez-Fern&aacute;ndez, Robin J. Shan-non, James J. P. Stewart, Pablo G. Tahoces, and Saulo A. Vazquez.Au-tomekin2021: An open-source program for automated reaction discovery. Journalof Computational Chemistry, 42(28):2036&ndash;2048, 2021.[3] Surajit Nandi, Bernardo Ballotta, Sergio Rampino, and Vincenzo Barone.Ageneral user-friendly tool for kinetic calculations of multi-step reactions withinthe virtual multifrequency spectrometer project. Applied Sciences, 10(5), 2020

    Towards quantitative physics-informed device level models for organic light-emitting diodes

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