Browsing by Subject "MOLECULES"

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  • Beck, Janina; Fuhr, Olaf; Nieger, Martin; Bräse, Stefan (2020)
    The synthesis of highly substituted hydroanthraquinone derivatives with up to three stereogenic centres via a Diels-Alder reaction, starting from easily accessible 2-substituted naphthoquinones, is described. The [4+2]-cycloaddition is applicable for a broad range of substrates, runs under mild conditions and results in high yields. The highly regioselective outcome of the reactions is enabled by a benzoyl substituent at C2 of the dienophiles. The obtained hydroanthraquinones can be further modified and represent ideal substrates for follow-up intramolecular coupling reactions to create unique bicyclo[3.3.1] or -[3.2.2]nonane ring systems which are important natural product skeletons.
  • Serra, Angela; Önlü, Serli; Coretto, Pietro; Greco, Dario (2019)
    Traditional quantitative structure-activity relationship models usually neglect the molecular alterations happening in the exposed systems (the mechanism of action, MOA), that mediate between structural properties of compounds and phenotypic effects of an exposure.
  • Baryshnikov, Gleb V.; Valiev, Rashid R.; Karaush, Nataliya N.; Sundholm, Dage; Minaev, Boris F. (2016)
    Magnetically induced current densities and current pathways have been calculated for a series of fully annelated dicationic and dianionic tetraphenylenes, which are also named [8]circulenes. The gauge including magnetically induced current (GIMIC) method has been employed for calculating the current density susceptibilities. The aromatic character and current pathways are deduced from the calculated current density susceptibilities showing that the neutral [8]circulenes have two concentric pathways with aromatic and antiaromatic character, respectively. The inner octatetraene core (the hub) is found to sustain a paratropic (antiaromatic) ring current, whereas the ring current along the outer part of the macrocycle (the rim) is diatropic (aromatic). The neutral [8]circulenes can be considered nonaromatic, because the sum of the ring-current strengths of the hub and the rim almost vanishes. The aromatic character of the doubly charged [8]circulenes is completely different: the dianionic [8]circulenes and the OC-, CH-, CH2-, SiH-, GeH-, SiH2-, and GeH2-containing dicationic species sustain net diatropic ring currents i.e., they are aromatic, whereas the O-, S-, Se-, NH-, PH- and AsH-containing dicationic [8]circulenes are strongly antiaromatic. The present study also shows that GIMIC calculations on the [8]circulenes provide more accurate information about the aromatic character than that obtained using local indices such as nuclear-independent chemical shifts (NICSs) and H-1 NMR chemical shifts.
  • Greiner, Jonas; Sundholm, Dage (2020)
    A generating function method was used to simulate the vibrationally resolved absorption and emission spectra of perylene, terrylene and quaterrylene. This method operates on the basis of adiabatic excitation energies and electronic ground and excited state vibrational frequencies. These parameters were calculated using density functional theory with the PBE0 functional for perylene and terrylene and with the BH-LYP functional for quaterrylene. The vertical excitation energies of the lower excited states were calculated using functionals with differing amounts of Hartree-Fock exchange. The optimal functional for each molecule was chosen by comparing these energies to literature excitation energies. Using this technique the calculated absorption spectra and the calculated emission spectrum of perylene were found to be in excellent agreement with the literature experimental spectra after introducing a shift and a scaling factor. The most prominent bands of the absorption spectra were assigned to their respective vibronic transitions.
  • Valiev, Rashid R.; Fliegl, Heike; Sundholm, Dage (2017)
    Magnetizabilities and magnetically induced ring-current strength susceptibilities have been calculated at the Hartree-Fock, density functional theory and second order Moller-Plesset levels for a number of antiaromatic closed-shell carbaporphyrins, carbathia-porphyrins and isophlorins. The calculations yield a linear relation between magnetizabilities and ring-current strength susceptibilities. The calculations show that the porphyrinoids with the largest ring-current strength susceptibility are closed-shell paramagnetic molecules with positive magnetizabilities. The closed-shell paramagnetism is due to the large paramagnetic contribution to the magnetizability originating from the strong paratropic ring current in the antiaromatic porphyrinoids.
  • Eskola, Arkke J.; Döntgen, Malte; Rotavera, Brandon; Caravan, Rebecca L.; Welz, Oliver; Savee, John D.; Osborn, David L.; Shallcross, Dudley E.; Percival, Carl J.; Taatjes, Craig A. (2018)
    Methyl vinyl ketone (MVK) and methacrolein (MACR) are important intermediate products in atmospheric degradation of volatile organic compounds, especially of isoprene. This work investigates the reactions of the smallest Criegee intermediate, CH2OO, with its co-products from isoprene ozonolysis, MVK and MACR, using multiplexed photoionization mass spectrometry (MPIMS), with either tunable synchrotron radiation from the Advanced Light Source or Lyman-alpha (10.2 eV) radiation for photoionization. CH2OO was produced via pulsed laser photolysis of CH(2)l(2) in the presence of excess O-2. Time-resolved measurements of reactant disappearance and of product formation were performed to monitor reaction progress; first order rate coefficients were obtained from exponential fits to the CH2OO decays. The bimolecular reaction rate coefficients at 300 K and 4 Torr are k(CH2OO + MVK) = (5.0 +/- 0.4) x 10(-13) cm(3) s(-1) and k(CH2OO + MACR) = (4.4 +/- 1.0) x 10(-13) cm(3) s(-1), where the stated +/- 2 sigma uncertainties are statistical uncertainties. Adduct formation is observed for both reactions and is attributed to the formation of a secondary ozonides (1,2,4-trioxolanes), supported by master equation calculations of the kinetics and the agreement between measured and calculated adiabatic ionization energies. Kinetics measurements were also performed for a possible bimolecular CH2OO + CO reaction and for the reaction of CH2OO with CF3CHCH2 at 300 K and 4 Torr. For CH2OO + CO, no reaction is observed and an upper limit is determined: k(CH2OO + CO) <2 x 10(-16) cm(3) s(-1). For CH2OO + CF3CHCH2, an upper limit of k(CH2OO + CF3CHCH2) <2 x 10(-14) cm(3) s(-1) is obtained.
  • Kim, Harold; Nguyen, Vicky P. K. H.; Petrova, Tatiana V.; Cruz, Maribelle; Alitalo, Kari; Dumont, Daniel J. (2010)
  • Leverentz, Hannah R.; Siepmann, J. Ilja; Truhlar, Donald G.; Loukonen, Ville; Vehkamäki, Hanna (2013)
  • Riva, Matthieu; Rantala, Pekka; Krechmer, Jordan E.; Peräkylä, Otso; Zhang, Yanjun; Heikkinen, Liine; Garmash, Olga; Yan, Chao; Kulmala, Markku; Worsnop, Douglas; Ehn, Mikael (2019)
    The impact of aerosols on climate and air quality remains poorly understood due to multiple factors. One of the current limitations is the incomplete understanding of the contribution of oxygenated products, generated from the gas-phase oxidation of volatile organic compounds (VOCs), to aerosol formation. Indeed, atmospheric gaseous chemical processes yield thousands of (highly) oxygenated species, spanning a wide range of chemical formulas, functional groups and, consequently, volatilities. While recent mass spectrometric developments have allowed extensive on-line detection of a myriad of oxygenated organic species, playing a central role in atmospheric chemistry, the detailed quantification and characterization of this diverse group of compounds remains extremely challenging. To address this challenge, we evaluated the capability of current state-of-the-art mass spectrometers equipped with different chemical ionization sources to detect the oxidation products formed from alpha-Pinene ozonolysis under various conditions. Five different mass spectrometers were deployed simultaneously for a chamber study. Two chemical ionization atmospheric pressure interface time-of-flight mass spectrometers (CI-APi-TOF) with nitrate and amine reagent ion chemistries and an iodide chemical ionization time-of-flight mass spectrometer (TOF-CIMS) were used. Additionally, a proton transfer reaction time-of-flight mass spectrometer (PTR-TOF 8000) and a new "vocus" PTR-TOF were also deployed. In the current study, we compared around 1000 different compounds between each of the five instruments, with the aim of determining which oxygenated VOCs (OVOCs) the different methods were sensitive to and identifying regions where two or more instruments were able to detect species with similar molecular formulae. We utilized a large variability in conditions (including different VOCs, ozone, NOx and OH scavenger concentrations) in our newly constructed atmospheric simulation chamber for a comprehensive correlation analysis between all instruments. This analysis, combined with estimated concentrations for identified molecules in each instrument, yielded both expected and surprising results. As anticipated based on earlier studies, the PTR instruments were the only ones able to measure the precursor VOC, the iodide TOF-CIMS efficiently detected many semi-volatile organic compounds (SVOCs) with three to five oxygen atoms, and the nitrate CI-APi-TOF was mainly sensitive to highly oxygenated organic (O > 5) molecules (HOMs). In addition, the vocus showed good agreement with the iodide TOF-CIMS for the SVOC, including a range of organonitrates. The amine CI-APi-TOF agreed well with the nitrate CI-APi-TOF for HOM dimers. However, the loadings in our experiments caused the amine reagent ion to be considerably depleted, causing nonlinear responses for monomers. This study explores and highlights both benefits and limitations of currently available chemical ionization mass spectrometry instrumentation for characterizing the wide variety of OVOCs in the atmosphere. While specifically shown for the case of alpha-Pinene ozonolysis, we expect our general findings to also be valid for a wide range of other VOC-oxidant systems. As discussed in this study, no single instrument configuration can be deemed better or worse than the others, as the optimal instrument for a particular study ultimately depends on the specific target of the study.
  • Valiev, R. R.; Cherepanov, V. N.; Baryshnikov, G. V.; Sundholm, D. (2018)
    A method for calculating the rate constants for internal-conversion (k(IC)) and intersystem-crossing (k(ISC)) processes within the adiabatic and Franck-Condon (FC) approximations is proposed. The applicability of the method is demonstrated by calculation of k(IC) and k(ISC) for a set of organic and organometallic compounds with experimentally known spectroscopic properties. The studied molecules were pyrromethene-567 dye, psoralene, hetero[8]circulenes, free-base porphyrin, naphthalene, and larger polyacenes. We also studied fac-Alq(3) and fac-Ir(ppy)(3), which are important molecules in organic light emitting diodes (OLEDs). The excitation energies were calculated at the multi-configuration quasi-degenerate second-order perturbation theory (XMC-QDPT2) level, which is found to yield excitation energies in good agreement with experimental data. Spin-orbit coupling matrix elements, non-adiabatic coupling matrix elements, Huang-Rhys factors, and vibrational energies were calculated at the time-dependent density functional theory (TDDFT) and complete active space self-consistent field (CASSCF) levels. The computed fluorescence quantum yields for the pyrromethene-567 dye, psoralene, hetero[8]circulenes, fac-Alq(3) and fac-Ir(ppy)(3) agree well with experimental data, whereas for the free-base porphyrin, naphthalene, and the polyacenes, the obtained quantum yields significantly differ from the experimental values, because the FC and adiabatic approximations are not accurate for these molecules.
  • Rojalin, Tatu; Kurki, Lauri; Laaksonen, Timo; Viitala, Tapani; Kostamovaara, Juha; Gordon, Keith C.; Galvis, Leonardo; Wachsmann-Hogiu, Sebastian; Strachan, Clare J.; Yliperttula, Marjo (2016)
    In this work, we utilize a short-wavelength, 532-nm picosecond pulsed laser coupled with a time-gated complementary metal-oxide semiconductor (CMOS) single-photon avalanche diode (SPAD) detector to acquire Raman spectra of several drugs of interest. With this approach, we are able to reveal previously unseen Raman features and suppress the fluorescence background of these drugs. Compared to traditional Raman setups, the present time-resolved technique has two major improvements. First, it is possible to overcome the strong fluorescence background that usually interferes with the much weaker Raman spectra. Second, using the high photon energy excitation light source, we are able to generate a stronger Raman signal compared to traditional instruments. In addition, observations in the time domain can be performed, thus enabling new capabilities in the field of Raman and fluorescence spectroscopy. With this system, we demonstrate for the first time the possibility of recording fluorescence-suppressed Raman spectra of solid, amorphous and crystalline, and non-photoluminescent and photoluminescent drugs such as caffeine, ranitidine hydrochloride, and indomethacin (amorphous and crystalline forms). The raw data acquired by utilizing only the picosecond pulsed laser and a CMOS SPAD detector could be used for identifying the compounds directly without any data processing. Moreover, to validate the accuracy of this time-resolved technique, we present density functional theory (DFT) calculations for a widely used gastric acid inhibitor, ranitidine hydrochloride. The obtained time-resolved Raman peaks were identified based on the calculations and existing literature. Raman spectra using non-time-resolved setups with continuous-wave 785- and 532-nm excitation lasers were used as reference data. Overall, this demonstration of time-resolved Raman and fluorescence measurements with a CMOS SPAD detector shows promise in diverse areas, including fundamental chemical research, the pharmaceutical setting, process analytical technology (PAT), and the life sciences.
  • Hyttinen, Noora; Wolf, Matthieu; Rissanen, Matti; Ehn, Mikael; Peräkylä, Otso; Kurten, Theo; Prisle, Nønne L. (2021)
    Oxidized organic compounds are expected to contribute to secondary organic aerosol (SOA) if they have sufficiently low volatilities. We estimated saturation vapor pressures and activity coefficients (at infinite dilution in water and a model water-insoluble organic phase) of cyclohexene- and alpha-pinene-derived accretion products, "dimers", using the COSMOtherm19 program. We found that these two property estimates correlate with the number of hydrogen bond-donating functional groups and oxygen atoms in the compound. In contrast, when the number of H-bond donors is fixed, no clear differences are seen either between functional group types (e.g., OH or OOH as H-bond donors) or the formation mechanisms (e.g., gas-phase radical recombination vs liquid-phase closed-shell esterification). For the cyclohexene-derived dimers studied here, COSMOtherm19 predicts lower vapor pressures than the SIMPOL.1 group-contribution method in contrast to previous COSMOtherm estimates using older parameterizations and nonsystematic conformer sampling. The studied dimers can be classified as low, extremely low, or ultra-low-volatility organic compounds based on their estimated saturation mass concentrations. In the presence of aqueous and organic aerosol particles, all of the studied dimers are likely to partition into the particle phase and thereby contribute to SOA formation.
  • Wannarit, Nanthawat; Pakawatchai, Chaveng; Mutikainen, Ilpo; Costa, Ramon; Moreira, Iberio de P. R.; Youngme, Sujittra; Illas, Francesc (2013)
  • Toropainen, Antti Elia; Kangasluoma, Juha; Kurten, Theo; Vehkamäki, Hanna; Keshavarz, Fatemeh; Kubecka, Jakub (2021)
    Using a combination of quantum chemistry and cluster size distribution dynamics, we study the heterogeneous nucleation of n-butanol and water onto sodium chloride (NaCl)(10) seeds at different butanol saturation ratios and relative humidities. We also investigate how the heterogeneous nucleation of butanol is affected by the seed size through comparing (NaCl)(5), (NaCl)(10), and ( NaCl)(25) seeds and by seed electrical charge through comparing (Na10Cl9)(+), (NaCl)(10), and (Na9Cl10)(-) seeds. Butanol is a common working fluid for condensation particle counters used in atmospheric aerosol studies, and NaCl seeds are frequently used for calibration purposes and as model systems, for example, sea spray aerosol. In general, our simulations reproduce the experimentally observed trends for the NaCl-BuOH-H2O system, such as the increase of nucleation rate with relative humidity and with temperature (at constant supersaturation of butanol). Our results also provide molecular-level insights into the vapor-seed interactions driving the first steps of the heterogeneous nucleation process. The main purpose of this work is to show that theoretical studies can provide molecular understanding of initial steps of heterogeneous nucleation and that it is possible to find cost-effective yet accurate-enough combinations of methods for configurational sampling and energy evaluation to successfully model heterogeneous nucleation of multicomponent systems. In the future, we anticipate that such simulations can also be extended to chemically more complex seeds.
  • Wang, Linping; Pogue, Sylvain; Laamanen, Karoliina; Saarela, Jani; Poso, Antti; Laitinen, Tuomo; Valkonen, Jari P. T. (2021)
    Sweet potato virus disease (SPVD), caused by synergistic infection of Sweet potato chlorotic stunt virus (SPCSV) and Sweet potato feathery mottle virus (SPFMV), is responsible for substantial yield losses all over the world. However, there are currently no approved treatments for this severe disease. The crucial role played by RNase III of SPCSV (CSR3) as an RNA silencing suppressor during the viruses' synergistic interaction in sweetpotato makes it an ideal drug target for developing antiviral treatment. In this study, high-throughput screening (HTS) of small molecular libraries targeting CSR3 was initiated by a virtual screen using Glide docking, allowing the selection of 6,400 compounds out of 136,353. We subsequently developed and carried out kinetic-based HTS using fluorescence resonance energy transfer technology, which isolated 112 compounds. These compounds were validated with dose-response assays including kinetic-based HTS and binding affinity assays using surface plasmon resonance and microscale thermophoresis. Finally, the interference of the selected compounds with viral accumulation was verified in planta. In summary, we identified five compounds belonging to two structural classes that inhibited CSR3 activity and reduced viral accumulation in plants. These results provide the foundation for developing antiviral agents targeting CSR3 to provide new strategies for controlling sweetpotato virus diseases. IMPORTANCE We report here a high-throughput inhibitor identification method that targets a severe sweetpotato virus disease caused by coinfection with two viruses (SPCSV and SPFMV). The disease is responsible for up to 90% yield losses. Specifically, we targeted the RNase III enzyme encoded by SPCSV, which plays an important role in suppressing the RNA silencing defense system of sweetpotato plants. Based on virtual screening, laboratory assays, and confirmation in planta, we identified five compounds that could be used to develop antiviral drugs to combat the most severe sweetpotato virus disease.
  • Yau, Anthony C. Y.; Globisch, Maria Ascencion; Onyeogaziri, Favour Chinyere; Conze, Lei L.; Smith, Ross; Jauhiainen, Suvi; Corada, Monica; Orsenigo, Fabrizio; Huang, Hua; Herre, Melanie; Olsson, Anna-Karin; Malinverno, Matteo; Sundell, Veronica; Jahromi, Behnam Rezai; Niemelä, Mika; Laakso, Aki; Garlanda, Cecilia; Mantovani, Alberto; Lampugnani, Maria Grazia; Dejana, Elisabetta; Magnusson, Peetra U. (2022)
    Cerebral Cavernous Malformation (CCM) is a brain vascular disease with various neurological symptoms. In this study, we describe the inflammatory profile in CCM and show for the first time the formation of neutrophil extracellular traps (NETs) in rodents and humans with CCM. Through RNA-seq analysis of cerebellum endothelial cells from wild-type mice and mice with an endothelial cell-specific ablation of the Ccm3 gene (Ccm3(iECKO)), we show that endothelial cells from Ccm3(iECKO) mice have an increased expression of inflammation-related genes. These genes encode proinflammatory cytokines and chemokines, as well as adhesion molecules, which promote recruitment of inflammatory and immune cells. Similarly, immunoassays showed elevated levels of these cytokines and chemokines in the cerebellum of the Ccm3(iECKO) mice. Consistently, both flow cytometry and immunofluorescence analysis showed infiltration of different subsets of leukocytes into the CCM lesions. Neutrophils, which are known to fight against infection through different strategies, including the formation of NETs, represented the leukocyte subset within the most pronounced increase in CCM. Here, we detected elevated levels of NETs in the blood and the deposition of NETs in the cerebral cavernomas of Ccm3(iECKO) mice. Degradation of NETs by DNase I treatment improved the vascular barrier. The deposition of NETs in the cavernomas of patients with CCM confirms the clinical relevance of NETs in CCM.
  • Benkyi, Isaac; Staszewska-Krajewska, Olga; Gryko, Daniel T.; Jaszuński, Michał; Stanger, Amnon; Sundholm, Dage (2020)
    The aromaticity of three nonplanar, fully conjugated aza-nanographenes built around a pyrrolo[3,2-b]pyrrole core is assessed through the application of two different computational procedures—GIMIC and NICS. We examine the calculated magnetically induced current densities (GIMIC) and nucleus-independent chemical shifts (NICS). The structural differences between these three apparently similar molecules lead to significantly different aromatic properties. GIMIC analysis indicates that the peripheral diatropic ring current of 3.9 nA/T for the studied bowl-shaped diaza-nanographene is the strongest, followed by the double [6]helicene which lacks seven-membered rings, and is practically nonexistent for the double [5]helicene possessing seven-membered rings. The biggest difference however is that in the two not-fully-fused molecules, the central pyrrole rings possess a significant diatropic current of about 4.1 nA/T, whereas there is no such current in the diaza-nanographene. Moreover, the antiaromaticity of the seven-membered rings is increasing while moving from double [5]helicene to diaza-nanographene (from −2.4 to −6.0 nA/T). The induced currents derived from NICSπ,zz-XY-scan analysis for all of the studied systems are in qualitative agreement with the GIMIC results. Subtle differences may originate from σ-electron currents in GIMIC or inaccuracy of NICSπ,zz values due to the nonplanarity of the systems, but the general picture is similar.
  • Wirz, Lukas N.; Dimitrova, Maria; Fliegl, Heike; Sundholm, Dage (2018)
    The topology of twisted molecular rings is characterized by the linking number, which is equal to the sum of the twist-a local property of the molecular frame-and the writhe-a global parameter, which represents the bending of the molecular ring. In this work, we investigate a number of cyclic all-trans C40H40 annulenes with varying twisting numbers for a given linking number and their dications. The aromatic character is assessed by calculating ring-current strength susceptibilities using the gauge-including magnetically induced currents (GIMIC) method, which makes it possible to conduct a systematic study of the relation between the topology and aromaticity of twisted molecules. We found that the aromatic properties of the investigated Mobius twisted molecules are not only dependent on the linking number as previously suggested but also depend strongly on the partitioning of the linking number into the twist and writhe contributions.
  • Willmann, Knut; Vent-Schmidt, Thomas; Rasanen, Markku; Riedel, Sebastian; Khriachtchev, Leonid (2015)
    The HKrCCH center dot center dot center dot HCCH complex is identified in a Kr matrix with the H-Kr stretching bands at 1316.5 and 1305 cm(-1). The monomer-to-complex shift of the H-Kr stretching mode is about +60 cm(-1), which is significantly larger than that reported previously for the HXeCCH center dot center dot center dot HCCH complex in a Xe matrix (about +25 cm(-1)). The HKrCCH center dot center dot center dot HCCH complex in a Kr matrix is formed at similar to 40 K via the attachment of mobile acetylene molecules to the HKrCCH monomers formed at somewhat lower annealing temperatures upon thermally-induced mobility of H atoms (similar to 30 K). The same mechanism was previously proposed for the formation of the HXeCCH center dot center dot center dot HCCH complex in a Xe matrix. The assignment of the HKrCCH center dot center dot center dot HCCH complex is fully supported by the quantum chemical calculations. The experimental shift of the H-Kr stretching mode is comparable with the computational predictions (+46.6, +66.0, and +83.2 cm(-1) at the B3LYP, MP2, and CCSD(T) levels of theory, respectively), which are also bigger that the calculated shift in the HXeCCH center dot center dot center dot HCCH complex. These results confirm that the complexation effect is bigger for less stable noble-gas hydrides.
  • Rose, Clémence; Zha, Qiaozhi; Dada, Lubna; Yan, Chao; Lehtipalo, Katrianne; Junninen, Heikki; Mazon, Stephany Buenrostro; Jokinen, Tuija; Sarnela, Nina; Sipilä, Mikko; Petäjä, Tuukka; Kerminen, Veli-Matti; Bianchi, Federico; Kulmala, Markku (2018)
    A substantial fraction of aerosols, which affect air quality and climate, is formed from gaseous precursors. Highly oxygenated organic molecules (HOMs) are essential to grow the newly formed particles and have been evidenced to initiate ion-induced nucleation in chamber experiments in the absence of sulfuric acid. We investigate this phenomenon in the real atmosphere using an extensive set of state-of-the-art ion and mass spectrometers deployed in a boreal forest environment. We show that within a few hours around sunset, HOMs resulting from the oxidation of monoterpenes are capable of forming and growing ion clusters even under low sulfuric acid levels. In these conditions, we hypothesize that the lack of photochemistry and essential vapors prevents the organic clusters from growing past 6 nm. However, this phenomenon might have been a major source of particles in the preindustrial atmosphere and might also contribute to particle formation in the future and consequently affect the climate.