Structure Of Such Species Research Articles

Glacial history of Saxifragawahlenbergii (Saxifragaceae) in the context of refugial areas in the Western Carpathians.

Despite the wealth of data available for mountain phylogeography, local-scale studies focused on narrow endemic species remain rare. Yet, knowledge of the genetic structure of such species biogeographically linked to a restricted area is of particular importance to understand the history of the local flora and its diversity patterns. Here, we aim to contribute to the phylogeographical overview of the Western Carpathians with a genetic study of Saxifragawahlenbergii, one of the most characteristic endemic species of this region. We sampled populations from all discrete parts of the species' distribution range to apply sequencing of selected non-coding cpDNA and nuclear ribosomal DNA (ITS) regions, as well as Amplified Fragment Length Polymorphism (AFLP) fingerprinting. First, while ITS sequences showed weak diversification, the genetic structure based on cpDNA sequences revealed two well-differentiated groups of haplotypes. One of them is restricted to the main center of the distribution range in the Tatra Mountains (Mts), while the second group included a series of closely related haplotypes, which in most cases were unique for particular isolated groups of populations in peripheral mountain ranges and in the south-eastern part of the Tatra Mts. AFLP fingerprinting also revealed a pattern of divergence among populations, while only partly corroborating the division observed in cpDNA. Taking into account all the data, the pattern of genetic structure, supported by the high levels of unique genetic markers in populations, may reflect the historical isolation of populations in several local refugia during the last glacial period. Not only the center of the range in the Tatra Mts, but also other, neighboring massifs (Malá Fatra, Nízke Tatry, Chočské vrchy, Muránska planina), where populations are characterized by separate plastid DNA haplotypes, could have acted as separate refugia.

Phylogeography of an insect inhabiting ‘Sky Islands’: the relationships among genetic structures and geographical characteristics, geohistorical characteristics, and cyclical climate changes

Abstract When gene flow has been restricted between populations, the genetic structure of such species often reflects geohistory and climate changes. Populations of species inhabiting high-altitude regions, known as ‘Sky Islands’, are isolated and exhibit restricted gene flow, so they often have habitat-specific genetic structures that correspond to their surrounding geographical structures. Here we focus on a limnephilid caddisfly, Rivulophilus sakaii, which inhabits the alpine zone of Japan. Phylogenetic analyses were conducted based on the mtDNA COI and 16S rRNA regions, and the nDNA 18S rRNA, 28S rRNA, CAD, EF1-α, and POL-II regions; the results indicated three phylogeographically differentiated intraspecific lineages. Haplotype network and demographic analyses based on the mtDNA COI region suggested the size of the respective isolated populations has stabilized. This suggests that mountain formation in the Japanese Archipelago due to volcanic activity has resulted in barriers to migration and dispersal between high-altitude aquatic insect populations. This was inferred to be an effect of Quaternary climate changes that caused vertical distributional shifts following mountain formation, resulting in repeated connection and fragmentation of the populations. This is important supporting information with regard to discussing the effects and functions of geohistory and climatic changes on the phylogenetic evolution of organisms presently inhabiting interglacial ‘Sky Islands’.

Spin–orbit effects in cluster chemistry: Considerations and applications for rationalization of their properties

Relativistic effects are usually taken into account in heavy-element-containing species, bringing to the scientific community stimulating cases of study. Scalar and spin–orbit effects are required to properly evaluate both the geometrical and electronic structures of such species, where, generally, scalar corrections are included. In order to take into account the spin–orbit term resulting from the interaction between the spatial and spin coordinates, double-valued point groups of symmetry are required, leading to total angular momenta (j) functions and atomic or molecular spinors, instead of pure orbital-angular momenta (l) and atomic or molecular orbitals. Here, we reviewed the role of spin–orbit coupling in bare and ligand-protected metallic clusters, from early to current works, leading to a more comprehensive relativistic quantum chemistry framework. As a result, the electronic structure is modified, leading to a variation in the calculated molecular properties, which usually improves the agreement between theory and experiment, allowing furthering rationalize of experimental results unexpected from a classical inorganic chemistry point of view. This review summarizes part of the modern application of spin–orbit coupling in heavy-elements cluster chemistry, where further treatment on an equal footing basis along with the periodic table is encouraged in order to incorporate such term in the general use vocabulary of both experimental and theoretical chemist and material scientist.

Origin of the Distinctive Electronic Structure of Co- and Fe-Porphyrin-Nitrene and Its Effect on Their Nitrene Transfer Reactivity

Metal-bound nitrene species are the crucial intermediate in catalytic nitrene transfer reactions exhibited by engineered enzymes and molecular catalysts. The electronic structure of such species and its correlation with nitrene transfer reactivity have not been fully understood yet. This work presents an in-depth electronic structure analysis and nitrene transfer reactivity of two prototypical metal-nitrene species derived from CoII(TPP) and FeII(TPP) (TPP = meso-tetraphenylporphyrin) complexes and tosyl azide nitrene precursor. Parallel to the well-known "cobalt(III)-imidyl" electronic structure of the Co-porphyrin-nitrene species, the formation mechanism and electronic structure of the elusive Fe-porphyrin-nitrene have been established using density functional theory (DFT) and multiconfigurational complete active-space self-consistent field (CASSCF) calculations. Electronic structure evolution analysis for the metal-nitrene formation step and CASSCF-derived natural orbitals advocates that the electronic nature of the metal-nitrene (M-N) core of Fe(TPP) is strikingly different from that of the Co(TPP). Specifically, the "imidyl" nature of the Co-porphyrin-nitrene [(TPP)CoIII-•NTos] (Tos = tosyl) (I1Co) is contrasted by the "imido-like" character of the Fe-porphyrin-nitrene [(TPP)FeIV[Formula: see text]NTos] (I1Fe). This difference between Co- and Fe-nitrene has been attributed to the additional interactions between Fe-dπ and N-pπ orbitals in Fe-nitrene, which is further complemented by the shortened Fe-N bond length of 1.71 Å. This stronger M-N bond in Fe-nitrene compared to the Co-nitrene is also reflected in the higher exothermicity (ΔΔH = 16 kcal/mol) of the Fe-nitrene formation step. The "imido-like" character renders a relatively lower spin population on the nitrene nitrogen (+0.42) in the Fe-nitrene complex I1Fe, which undergoes the nitrene transfer to the C═C bond of styrene with a considerably higher enthalpy barrier (ΔH‡ = 10.0 kcal/mol) compared to the Co congener I1Co (ΔH‡ = 5.6 kcal/mol) possessing a higher nitrogen spin population (+0.88) and a relatively weaker M-N bond (Co-N = 1.80 Å).

Unexpected Gene-Flow in Urban Environments: The Example of the European Hedgehog.

Simple SummaryAn urban environment holds many barriers for mammals with limited mobility such as hedgehogs. These barriers appear often unsurmountable (e.g., rivers, highways, fences) and thus hinder contact between hedgehogs, leading to genetic isolation. In our study we tested whether these barriers affect the hedgehog population of urban Berlin, Germany. As Berlin has many of these barriers, we were expecting a strong genetic differentiation among hedgehog populations. However, when we looked at unrelated individuals, we did not see genetic differentiation among populations. The latter was only detected when we included related individuals too, a ‘family clan’ structure that is referred to as gamodemes. We conclude that the high percentage of greenery in Berlin provides sufficient habitat for hedgehogs to maintain connectivity across the city.We use the European hedgehog (Erinaceus europaeus), a mammal with limited mobility, as a model species to study whether the structural matrix of the urban environment has an influence on population genetic structure of such species in the city of Berlin (Germany). Using ten established microsatellite loci we genotyped 143 hedgehogs from numerous sites throughout Berlin. Inclusion of all individuals in the cluster analysis yielded three genetic clusters, likely reflecting spatial associations of kin (larger family groups, known as gamodemes). To examine the potential bias in the cluster analysis caused by closely related individuals, we determined all pairwise relationships and excluded close relatives before repeating the cluster analysis. For this data subset (N = 65) both clustering algorithms applied (Structure, Baps) indicated the presence of a single genetic cluster. These results suggest that the high proportion of green patches in the city of Berlin provides numerous steppingstone habitats potentially linking local subpopulations. Alternatively, translocation of individuals across the city by hedgehog rescue facilities may also explain the existence of only a single cluster. We therefore propose that information about management activities such as releases by animal rescue centres should include location data (as exactly as possible) regarding both the collection and the release site, which can then be used in population genetic studies.

Selective oxidation of methane with H2O2 over Fe-silicalite-1: An investigation of the influence of crystal sizes, calcination temperatures and acidities

Selective oxidation of methane to hydrocarbon oxygenates using H2O2 as oxidant over Fe-silicalite-1 catalysts was conducted in a micro fixed-bed reactor. The influence of different crystal sizes, different calcination temperatures and different acidities of the catalysts on the reaction was investigated. A sub-micrometer crystal size around 400 nm was preferable because diffusion limitations occur also in the secondary particle having a size of 200 μm when primary particle size is below 400 nm. After calcination, framework Fe species were found partially migrated to extra-framework positions. By increasing calcination temperatures, a growing fraction of extra-framework Fe species and concurrently a growing variety of types and structures of such species was observed. These newly formed extra-framework Fe species seem to be just responsible for the decomposition of H2O2 and over-oxidation of the oxygenates. Similarly, Brønsted acid sites also seem only to enhance the decomposition of H2O2 and over-oxidation of oxygenates. The formation of Fe sites responsible for selective methane oxidation were already completed upon removal of the template at a calcination temperature of 370 °C.

How diverse can rare species be on the margins of genera distribution?

Different genetic patterns have been demonstrated for narrowly distributed taxa, many of them linking rarity to evolutionary history. Quite a few species in young genera are endemics and have several populations that present low variability, sometimes attributed to geographical isolation or dispersion processes. Assessing the genetic diversity and structure of such species may be important for protecting them and understanding their diversification history. In this study, we used microsatellite markers and plastid sequences to characterize the levels of genetic variation and population structure of two endemic and restricted species that grow in isolated areas on the margin of the distribution of their respective genera. Plastid and nuclear diversities were very low and weakly structured in their populations. Evolutionary scenarios for both species are compatible with open-field expansions during the Pleistocene interglacial periods and genetic variability supports founder effects to explain diversification. At present, both species are suffering from habitat loss and changes in the environment can lead these species towards extinction.

Long‐distance dispersal and barriers shape genetic structure of peatmosses (Sphagnum) across the Northern Hemisphere

AbstractAimDisjunctly distributed peatmosses (Sphagnum) have been found to exhibit little genetic structure over regional and intercontinental scales, mainly caused by high ability for transoceanic long‐distance dispersal. Although, most Northern Hemisphere peatmoss species have wide circumboreal/nemoral ranges, little is known about the magnitude and effects of long‐distance dispersal and barriers in shaping the genetic structure of such species. We investigate whether high dispersal capacity has caused genetic homogeneity across broad areas of the Northern Hemisphere, or whether barriers act to shape genetic structure across different species with similar distributional ranges.LocationNorthern Hemisphere.MethodsWe studied genetic variation and structure in six Sphagnum species using 19 microsatellite loci.ResultsFour out of six species were genetically structured in similar ways; with mainly one Beringian and one Atlantic group. Overall, both the North American and Eurasian continents seemed to act as a barrier to gene flow in several species. However, the most abrupt breakpoint between genetic groups was found in south‐east Alaska.Main conclusionsWe found evidence for extensive gene flow between regions across the Northern Hemisphere among peatmosses, with oceans seemingly acting as weaker barriers to gene flow than landmasses. Plants from the amphi‐Atlantic and amphi‐Beringian regions of several species were genetically differentiated. Similar genetic structuring across several species, indicate that spore‐producing species do not disperse freely across their entire distributional range, but are likely limited by wind directions, landmass barriers and/or habitat availability.

Properties of reactive oxygen species by quantum Monte Carlo.

The electronic properties of the oxygen molecule, in its singlet and triplet states, and of many small oxygen-containing radicals and anions have important roles in different fields of chemistry, biology, and atmospheric science. Nevertheless, the electronic structure of such species is a challenge for ab initio computational approaches because of the difficulties to correctly describe the statical and dynamical correlation effects in presence of one or more unpaired electrons. Only the highest-level quantum chemical approaches can yield reliable characterizations of their molecular properties, such as binding energies, equilibrium structures, molecular vibrations, charge distribution, and polarizabilities. In this work we use the variational Monte Carlo (VMC) and the lattice regularized Monte Carlo (LRDMC) methods to investigate the equilibrium geometries and molecular properties of oxygen and oxygen reactive species. Quantum Monte Carlo methods are used in combination with the Jastrow Antisymmetrized Geminal Power (JAGP) wave function ansatz, which has been recently shown to effectively describe the statical and dynamical correlation of different molecular systems. In particular, we have studied the oxygen molecule, the superoxide anion, the nitric oxide radical and anion, the hydroxyl and hydroperoxyl radicals and their corresponding anions, and the hydrotrioxyl radical. Overall, the methodology was able to correctly describe the geometrical and electronic properties of these systems, through compact but fully-optimised basis sets and with a computational cost which scales as N(3) - N(4), where N is the number of electrons. This work is therefore opening the way to the accurate study of the energetics and of the reactivity of large and complex oxygen species by first principles.

Landscape genetics of an early successional specialist in a disturbance‐prone environment

Species that specialize in disturbed habitats may have considerably different dispersal strategies than those adapted to more stable environments. However, little is known of the dispersal patterns and population structure of such species. This information is important for conservation because many postfire specialists are at risk from anthropogenic changes to natural disturbance regimes. We used microsatellite markers to assess the effect of landscape variation and recent disturbance history on dispersal by a small mammal species that occupies the early seral stage of vegetation regeneration in burnt environments. We predicted that a postfire specialist would be able to disperse over multiple habitat types (generalist) and not exhibit sex-biased dispersal, as such strategies should enable effective colonization of spatially and temporally variable habitat. We found significant differentiation between sites that fitted an isolation-by-distance pattern and spatial autocorrelation of multilocus genotypes to a distance of 2-3 km. There was no consistent genetic evidence for sex-biased dispersal. We tested the influence of different habitat- and fire-specific landscape resistance scenarios on genetic distance between individuals and found a significant effect of fire. Our genetic data supported recently burned vegetation having greater conductance for gene flow than unburnt habitat, but variation in habitat quality between vegetation types and occupied patches had no effect on gene flow. Postfire specialists must evolve an effective dispersal ability to move over distances that would ensure access to early successional stage vegetation. Natural disturbance and natural heterogeneity may therefore not influence population genetic structure as negatively as expected.

Electronic structure analysis of small gold clusters Au m (m ≤ 16) by density functional theory

Small gold clusters Au m (m ≤ 16) were analyzed step by step using the density functional theory at B3LYP level with a Lanl2DZ pseudopotential to understand the rules governing the structures obtained for the most stable clusters. After a characterization by means of the NBO population analysis and spin densities, the particular electronic structure of such species was confronted to their structural parameters and stability. It appears that the most stable structures can be described in an original way through resonance structures resulting from an analysis of Aum clusters into dimeric Au2 subunits. These are arranged so as to promote: 1. A good overlap between bonding σ and anti-bonding σ* areas belonging to different Au2 units. 2. A cyclic flow of electrons over the whole cluster. This model uses relatively simple chemical concepts in order to justify most of the structures already found in the literature as well as to establish a new approach explaining the structural transition from two- to threedimensional configurations.

Binuclear cyclopentadienylrhodium halides and cyanides in the +2 to +3 oxidation states

The pentamethylcyclopentadienylrhodium chlorides (η5-Me5C5)2Rh2(μ-Cl)2 and (η5-Me5C5)2Rh2(μ-Cl)2Cl2 have been synthesized, structurally characterized by X-ray crystallography, and shown to be useful precursors for the synthesis of a variety of organorhodium derivatives, including intermediates for catalytic reactions. We now report density functional theory studies on related Cp2Rh2Xn (X=Cl, F, CN; n=2, 3, 4) derivatives of the unsubstituted cyclopentadienyl ligand. The lowest energy structures of such species are found to be Cp2Rh2(μ-X)2Xn−2 with terminal Cp ligands and two bridging X ligands. Such predicted structures for Cp2Rh2Cl2 and Cp2Rh2Cl4 are close to the experimental structures for the permethylated derivatives (η5-Me5C5)2Rh2Cln (n=2, 4). For Cp2Rh2Cl2 the relatively small singlet–triplet separation may relate to the experimentally observed high reactivity of the Rh–Rh bond in (η5-Me5C5)2Rh2(μ-Cl)2. For the rhodium(III) derivatives Cp2Rh2X4 (X=Cl, F, CN), the doubly bridged structures with trans configurations of the two Rh–X bonds to the terminal X groups have lower energies than the corresponding cis isomers. The lowest energy Cp2Rh2(μ-CN)2(CN)n−2 structures have the bridging cyano groups bonded to one rhodium atom through the carbon atom and to the other rhodium atom through the nitrogen atom. Such structures with the bridging cyano groups oriented in the same or opposite directions have similar energies. The Rh(II,III) mixed valence Cp2Rh2X3 structures are predicted to be disfavored relative to disproportionation into Cp2Rh2X2+Cp2Rh2X4.

Collisional Activation of Protein Complexes: Picking Up the Pieces

Mass spectrometry is fast becoming a vital approach not only for the identification and quantification of proteins, but also for the study of the noncovalent assemblies they form. Approaches for ionizing, transmitting, and detecting protein complexes intact in the mass spectrometer are now well established. The challenge has therefore shifted to developing and applying mass spectrometry approaches to elucidate the structure of such species. A crucial aspect to this goal is inducing their disassembly in the gas phase to mine information as to their composition and organization. Here the consequences of collisionally activating protein complexes are illustrated through ion mobility mass spectrometry measurements and discussed in the context of the current literature. Although a consensus view of the mechanism of dissociation is starting to emerge, it is also clear that a number of aspects remain unresolved. These outstanding questions and frontier challenges must be addressed if gas-phase dissociative approaches are to reach their full potential in the study of protein assemblies.

Molecular structures of the 1,6-disubstituted triptycenes Sb2(C6F4)3and Bi2(C6F4)3using gas-phase electron diffraction and ab initio and DFT calculations

The structures of the D(3h)-symmetric molecules dodecafluoro-1,6-distibatriptycene and dodecafluoro-1,6-dibismatriptycene [Z2(C6F4)3 (Z = Sb, Bi)] have been determined in the gas phase by electron diffraction, using the SARACEN method, with restraints obtained from quantum chemical calculations. Several methods of ab initio and density functional theory geometry calculations have been performed and recommendations made as to their relative suitabilities for determining the structures of such species. Calculations using the MP2 method with a small-core pseudopotential (aug-cc-pVQZ-PP) on the Sb and Bi atoms and the 6-311G* basis set on the light atoms were found to give the closest correlation with the experimental results for both molecules. Differences in structure were found depending on whether a large-core or small-core pseudopotential was used on the heavy atoms.

Tetrahedral Intermediates in Reactions of Carboxylic Acid Derivatives with Nucleophiles

AbstractFor Abstract see ChemInform Abstract in Full Text.

Linking Monte-Carlo simulation and target transformation factor analysis: a novel tool for the EXAFS analysis of mixtures

Aqueous metal complexes are important chemical species in the geosphere, since they often determine the mobility of metals in the environment. While EXAFS spectroscopy is the method of choice to determine the structure of such species in environmental matrices, it often fails when several complexes coexist. In this case, all present complexes contribute to the EXAFS signal, and the deconvolution into single contributions is difficult. We have developed a new algorithm to determine the spectral contributions of the single in mixtures of species, based on a combination of Monte-Carlo Simulation and Target Transformation Factor Analysis (MCTFA). This novel approach requires solely the structure of the interacting ligand as input data, enabling the determination of complexes even in “messy” environmental samples.

Tetrahedral intermediates in reactions of carboxylic acid derivatives with nucleophiles

AbstractTransacylation reactions of carboxylic acids, carboxylic acid esters, carboxylic acid amides and other carboxylic acid derivatives are among the most widespread and most important reactions in chemistry and biochemistry. Already in 1887, Claisen suggested a tetrahedral intermediate in transformations of carboxylic acid derivatives with nucleophiles. A historical overview gives insight into the studies to detect possible tetrahedral intermediates in such reactions. However, only in recent years has detailed information concerning the structures of such species become available. In this review, neutral, cationic and anionic tetrahedral intermediates are described which serve as models for transacylations under neutral, acid‐catalysed or basic conditions. The characteristically different structures correspond nicely with experimental experience with reactions of carboxylic acid derivatives and with quantum chemical model calculations on tetrahedral intermediates. Finally, by means of model calculations, an explanation is given for the fast reactions of Weinreb amides, RC(O)N(CH3)OCH3, with organolithium and even with Grignard reagents: the reactions are determined by comparatively stable chelate transition states. Copyright © 2004 John Wiley & Sons, Ltd.

Chemistry of Vibronic Coupling. 3. How One Might Maximize Off-Diagonal Dynamic Vibronic Coupling Constants for Intervalence Charge-Transfer (IVCT) States in an ABA• System (A, B = Alkali Metal, H, Halogen)?

We investigate computationally the vibronic coupling constant in a large group of simple uncharged ABA• systems (A, B = H, Li, Na, K, Rb, Cs, F, Cl, Br, I), which may be formally mixed-valence or intermediate-valence ones. These open-shell species belong to three chemically quite distinct groups: intermetallic, interhalogen, and salt-like triatomics. Constraining these systems to a linear symmetric geometry, we optimize the A−B bond length at a certain level of theory and determine the electronic and vibrational structure of such species. At this common geometry we calculate a vibronic stability parameter for the antisymmetric mode (G), defined as the ratio of force constants for the antisymmetric to the symmetric stretching mode. G is a sensitive indicator of the magnitude of vibronic coupling. Values of G smaller than 1 (asymmetric mode softening) indicate large values of the off-diagonal vibronic coupling constant. Negative G indicate very large values of that constant, leading to vibronic instability. The smallest values of G are obtained for interhalogen species (most of them are vibronically unstable). Salt-like ABA and BAB molecules, as well as intermetallic species are vibronically stable. Two further interesting correlations evolve: the calculated force constants for the symmetric stretching mode correlate well with f, a parameter defined as the sum of the electronegativities of the A and B elements divided by the AB bond length. Large values of f also indicate strong vibronic coupling.

The Phenomenon of Conglomerate Crystallization. XVII. Clavic Dissymmetry in Coordination Compounds. XV. The Effect of the Charge Compensating Ions on the Phenomenon of Conglomerate Crystallization

Abstract In this report, we discuss the effect of the counter ion on the crystallization behaviour of chiral ions which may produce racemic or conglomerate crystals. We demonstrate that the counter ion is often capable of influencing the crystallization pathway and provide examples of substances in which the same chiral ion produces enantiomorphic crystals or racemic crystals depending on the nature of the counter ion. Moreover, we demonstrate that the crystal structures of such species amply demonstrate the reasons for such differences in crystallization pathway. In the species selected for the illustrations, the underlying phenomenon being influenced by the choice of counter ion is hydrogen bonding. This summary provides examples of counter ion pairs as varied as halides vs NO3 −, halides vs NO2 −, K+1 vs Ag+, etc., influencing the choice of crystallization pathway. Also, we illustrate the fact that the same ion (i.e., NO3 −) can play either a positive or a negative role in such a selection.

Reactions of molybdenum and tungsten halides with acetylenic hydrocarbons: an approach to the structure and pathways of formation of metathesis catalysts

A number of acetylene and mixed acetylene-nitrile complexes of tungsten and molybdenum halides have been prepared and investigated. Depending on the acetylene and the reaction conditions, one or more acetylene molecules may be coordinated to the metal. In the latter case acetylenes are coordinated not as single molecules but in systems of conjugated non-aromatic double bonds. On the basis of the supposed structure of such species and on their pyrolysis products a decomposition scheme is proposed, which consider the formation of apparent metathesis products as a side reaction of the cyclotrimerization of acetylenes to aromatic hydrocarbons.