Jalokaasumolekyylien vuorovaikutukset niiden ympäristön kanssa

The importance of intermolecular interactions to chemistry, physics, and biology is difficult to overestimate. Without intermolecular forces, condensed phase matter could not form. The simplest way to categorize different types of intermolecular interactions is to describe them using van der Waals and hydrogen bonded (H-bonded) interactions. In the H-bond, the intermolecular interaction appears between a positively charged hydrogen atom and electronegative fragments and it originates from strong electrostatic interactions. H-bonding is important when considering the properties of condensed phase water and in many biological systems including the structure of DNA and proteins. Vibrational spectroscopy is a useful tool for studying complexes and the solvation of molecules. Vibrational frequency shift has been used to characterize complex formation. In an H-bonded system A∙∙∙H-X (A and X are acceptor and donor species, respectively), the vibrational frequency of the H-X stretching vibration usually decreases from its value in free H-X (red-shift). This frequency shift has been used as evidence for H-bond formation and the magnitude of the shift has been used as an indicator of the H-bonding strength. In contrast to this normal behavior are the blue-shifting H-bonds, in which the H-X vibrational frequency increases upon complex formation. In the last decade, there has been active discussion regarding these blue-shifting H-bonds. Noble-gases have been considered inert due to their limited reactivity with other elements. In the early 1930 s, Pauling predicted the stable noble-gas compounds XeF6 and KrF6. It was not until three decades later Neil Bartlett synthesized the first noble-gas compound, XePtF6, in 1962. A renaissance of noble-gas chemistry began in 1995 with the discovery of noble-gas hydride molecules at the University of Helsinki. The first hydrides were HXeCl, HXeBr, HXeI, HKrCl, and HXeH. These molecules have the general formula of HNgY, where H is a hydrogen atom, Ng is a noble-gas atom (Ar, Kr, or Xe), and Y is an electronegative fragment. At present, this class of molecules comprises 23 members including both inorganic and organic compounds. The first and only argon-containing neutral chemical compound HArF was synthesized in 2000 and its properties have since been investigated in a number of studies. A helium-containing chemical compound, HHeF, was predicted computationally, but its lifetime has been predicted to be severely limited by hydrogen tunneling. Helium and neon are the only elements in the periodic table that do not form neutral, ground state molecules. A noble-gas matrix is a useful medium in which to study unstable and reactive species including ions. A solvated proton forms a centrosymmetric NgHNg+ (Ng = Ar, Kr, and Xe) structure in a noble-gas matrix and this is probably the simplest example of a solvated proton. Interestingly, the hypothetical NeHNe+ cation is isoelectronic with the water-solvated proton H5O2+ (Zundel-ion). In addition to the NgHNg+ cations, the isoelectronic YHY- (Y = halogen atom or pseudohalogen fragment) anions have been studied with the matrix-isolation technique. These species have been known to exist in alkali metal salts (YHY)-M+ (M = alkali metal e.g. K or Na) for more than 80 years. Hydrated HF forms the FHF- structure in aqueous solutions, and these ions participate in several important chemical processes. In this thesis, studies of the intermolecular interactions of HNgY molecules and centrosymmetric ions with various species are presented. The HNgY complexes show unusual spectral features, e.g. large blue-shifts of the H-Ng stretching vibration upon complexation. It is suggested that the blue-shift is a normal effect for these molecules, and that originates from the enhanced (HNg)+Y- ion-pair character upon complexation. It is also found that the HNgY molecules are energetically stabilized in the complexed form, and this effect is computationally demonstrated for the HHeF molecule. The NgHNg+ and YHY- ions also show blue-shifts in their asymmetric stretching vibration upon complexation with nitrogen. Additionally, the matrix site structure and hindered rotation (libration) of the HNgY molecules were studied. The librational motion is a much-discussed solid state phenomenon, and the HNgY molecules embedded in noble-gas matrices are good model systems to study this effect. The formation mechanisms of the HNgY molecules and the decay mechanism of NgHNg+ cations are discussed. A new electron tunneling model for the decay of NgHNg+ absorptions in noble-gas matrices is proposed. Studies of the NgHNg+∙∙∙N2 complexes support this electron tunneling mechanism.Molekyylien välisten vuorovaikutusten merkitystä biologisiin-, kemiallisiin- ja fysikaalisiin prosesseihin on hyvin vaikea yliarvioida. Ilman näitä vuorovaikutuksia ei aine esiintyisi kiinteässä eikä nestemäisessä olomuodossa, eikä näin koko tuntemaamme ympäristöä olisi olemassa. Tämän vuoksi molekyylien välisten vuorovaikutuksien ymmärtäminen on ensiarvoisen tärkeätä mm. materiaali-, lääke-, ilmakehä- ja nanotieteille sekä monille tekniikan sovelluksille. Vetysidokset ovat eräs molekyylien välisten vuorovaikutusten erityisjoukko, mikä näyttelee suurta osaa esimerkiksi veden ja jään rakenteessa sekä monissa biologisissa systeemeissä, kuten proteiinien ja DNA:n rakenteessa ja toiminnassa. Vetysitoutumista tutkitaan pääasiassa infrapunaspektroskopian avulla, missä vetysitoutuminen todetaan molekyylien sormenjäljessä, spektrissä, tapahtuneissa muutoksissa. Tässä tutkimuksessa on nähty kokeellisesti ensimmäiset jalokaasua sisältävien yhdisteiden vuorovaikutukset toisten molekyylien kanssa ja näiden vuorovaikutuksien luonne todetaan hyvin poikkeukselliseksi tunnettuihin systeemeihin nähden. Jalokaasujen reaktiokyvyttömyys on herättänyt mielenkiintoa jo yli sadan vuoden ajan, ja tunnetuista alkuaineista ainoastaan helium ja neon eivät muodosta kemiallisia yhdisteitä. Näiden kahden viimeisen vapaan alkuaineen yhdisteiden valmistaminen on suuri tieteelinen haaste ja onnistuessaan tieteellinen läpimurto. Teoreettisesti on ehdotettu heliumin yhdisteen, HHeF:n, olemassaolo, mutta sen kokeellisen havaitsen uskotaan olevan lähes mahdotonta. Tässä työssä on esitetty tämän yhdisteen valmistusmenetelmä, jossa käytetään apuna molekyylien ympäristön vuorovaikutuksista johtuvaa vakauttavaa tekijää. Suuri osa molekyylien välisistä reaktioista tapahtuu nestemäisessä ja kiinteässä olomuodossa. Esimerkiksi lähes kaikki elämän kannalta tärkeät reaktiot tapahtuvat nestemmäisen veden sisällä. Fysikaalis-kemiallisten tapahtumien ymmärtäminen näissä olomuodoissa on erityisen merkityksellistä ja moniin näistä reaktiosta osallistuvat sähköisesti varatut atomit ja molekyylit. Tässä tutkimuksessa ehdotettiin uusi malli jalokaasukiteeseen eristettyjen protonien neutraloitumisreaktiolle. Tämä ilmiö mahdollisesti tapahtuu myös veteen liuenneille protonille ja voi näin selittää vedessä tapahtuvia protoninsiirtoreaktiota, mitkä ovat tärkeitä erityisesti solun sisällä tapahtuville ilmiöille. Tästä tutkimuksesta saatuja tuoksia voidaan käyttää apuna rakennettaessa uusia malleja kuinka molekyylit muodostavat yhdessä suurempia kokonaisuuksia ja aiheuttavat toisissaan toiminnallisia muutoksia. Tutkimukessa tarkastellaan myös laajemmin molekyylien käyttäytymistä kiinteässä väliaineessa ja luodaan edellytkset paremmalle kiinteän olomuodon ilmiöiden ymmärtämiselle. Tutkimus kuuluu tieteellisen perustutimuksen piiriin, mutta sillä voi olla merkitystä myös soveltaville tieteille

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The neural crest is an embryonic population of multipotent stem cells that form numerous defining features of vertebrates. Due to lack of reliable techniques to perform transcriptional profiling in intact tissues, it remains controversial whether the neural crest is a heterogeneous or homogeneous population. By coupling multiplex single molecule fluorescence in situ hybridization with machine learning algorithm based cell segmentation, we examine expression of 35 genes at single cell resolution in vivo. Unbiased hierarchical clustering reveals five spatially distinct subpopulations within the chick dorsal neural tube. Here we identify a neural crest stem cell niche that centers around the dorsal midline with high expression of neural crest genes, pluripotency factors, and lineage markers. Interestingly, neural and neural crest stem cells express distinct pluripotency signatures. This Spatial Genomic Analysis toolkit provides a straightforward approach to study quantitative multiplex gene expression in numerous biological systems, while offering insights into gene regulatory networks via synexpression analysis

Three-dimensional imaging for the quantification of spatial patterns in microbiota of the intestinal mucosa

Improving our understanding of host-microbe relationships in the gut requires the ability to both visualize and quantify the spatial organization of microbial communities in their native orientation with the host tissue. We developed a systematic procedure to quantify the three-dimensional (3D) spatial structure of the native mucosal microbiota in any part of the intestines with taxonomic and high spatial resolution. We performed a 3D biogeographical analysis of the microbiota of mouse cecal crypts at different stages of antibiotic exposure. By tracking eubacteria and four dominant bacterial taxa, we found that the colonization of crypts by native bacteria is a dynamic and spatially organized process. Ciprofloxacin treatment drastically reduced bacterial loads and eliminated Muribaculaceae (or all Bacteroidetes entirely) even 10 d after recovery when overall bacterial loads returned to preantibiotic levels. Our 3D quantitative imaging approach revealed that the bacterial colonization of crypts is organized in a spatial pattern that consists of clusters of adjacent colonized crypts that are surrounded by unoccupied crypts, and that this spatial pattern is resistant to the elimination of Muribaculaceae or of all Bacteroidetes by ciprofloxacin. Our approach also revealed that the composition of cecal crypt communities is diverse and that Lactobacilli were found closer to the lumen than Bacteroidetes, Ruminococcaceae, and Lachnospiraceae, regardless of antibiotic exposure. Finally, we found that crypts communities with similar taxonomic composition were physically closer to each other than communities that were taxonomically different.Peer reviewe

Kr–Cl stretching vibration of HKrCl: Matrix-isolation and anharmonic ab initio study

The Kr–Cl stretching vibration of HKrCl molecule is studied. The absorption shows ³⁵Cl and ³⁷Cl isotopic splitting due to natural abundance of the Cl isotopes. The observed Kr–Cl stretching vibrations of the HKrCl are at 253.1 (³⁵Cl) and 248.3 cm–¹ (³⁷Cl). Deuteration of the HKrCl does not cause experimentally a shift of the Kr–Cl stretching frequency. In addition to the Kr–Cl stretching mode, the bending mode of DKrCl is observed at 397.7 cm–¹. The vibrational analysis suggests that the Kr–Cl bond show, in addition to ionic, some covalent character. Anharmonic ab initio calculations are employed to verify vibrational properties of various isotopologues of HKrCl

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The neural crest is an embryonic population of multipotent stem cells that form numerous defining features of vertebrates. Due to lack of reliable techniques to perform transcriptional profiling in intact tissues, it remains controversial whether the neural crest is a heterogeneous or homogeneous population. By coupling multiplex single molecule fluorescence in situ hybridization with machine learning algorithm based cell segmentation, we examine expression of 35 genes at single cell resolution in vivo. Unbiased hierarchical clustering reveals five spatially distinct subpopulations within the chick dorsal neural tube. Here we identify a neural crest stem cell niche that centers around the dorsal midline with high expression of neural crest genes, pluripotency factors, and lineage markers. Interestingly, neural and neural crest stem cells express distinct pluripotency signatures. This Spatial Genomic Analysis toolkit provides a straightforward approach to study quantitative multiplex gene expression in numerous biological systems, while offering insights into gene regulatory networks via synexpression analysis

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