Enantiomerization of Allylic Trifluoromethyl Sulfoxides Studied by HPLC Analysis and DFT Calculations

Enantiomerization of allylic trifluoromethyl sulfoxides occurs spontaneously at room temperature through the corresponding allylic trifluoromethanesulfenates via a [2,3]‐sigmatropic rearrangement. Dynamic enantioselective high‐performance liquid chromatography (HPLC) analysis revealed the stereodynamics of these sulfoxides ranging from chromatographic resolution to peak coalescence at temperatures between 5 and 53 °C. The rate constant of enantiomerization and activation parameters were determined and compared with Density Functional Theory (DFT) calculations. Chirality 28:136–142, 2016. © 2015 Wiley Periodicals, Inc.     

Local and long range potentials for heparin-protein systems for coarse-grained simulations

Heparin belongs to glycosaminoglycans (GAGs), a class of periodic linear anionic polysaccharides, which are functionally important components of the extracellular matrix owing to their interactions with various protein targets. Heparin is known to be involved in many cell signaling processes, while the experimental data available for heparin are significantly more abundant than for other GAGs. At the same time, the length and conformational flexibility of the heparin represent major challenges for its theoretical analysis. Coarse-grained (CG) approaches, which enable us to extend the size- and time-scale by orders of magnitude owing to reduction of system representation, appear, therefore, to be useful in simulating these systems. In this work, by using umbrella-sampling molecular dynamics simulations, we derived and parameterized the CG backbone-local potentials of heparin chains and the orientational potentials for the interactions of heparin with amino acid side chains to be further included in the physics-based Unified Coarse-Grained Model of biological macromolecules. With these potentials, simulations of extracellular matrix processes where both heparin and multiple proteins participate will be possible.     

The stereodynamics of 1,2‐dipropyldiaziridines

N‐alkylated trans‐diaziridines are an intriguing class of compounds with two stereogenic nitrogen atoms which easily interconvert. In the course of our investigations of the nature of the interconversion process via nitrogen inversion or electrocyclic ring opening ring closure, we synthesized and characterized the three constitutionally isomeric diaziridines 1,2‐di‐n‐propyldiaziridine 1 , 1‐isopropyl‐2‐n‐propyldiaziridine 2 , and 1,2‐diisopropyldiaziridine 3 to study the influence of the substituents on the interconversion barriers. Enantiomer separation was achieved by enantioselective gas chromatography on the chiral stationary phase Chirasil‐β‐Dex with high separation factors α (1‐isopropyl‐2‐n‐propyldiaziridine: 1.18; 1, 2‐diisopropyldiaziridine: 1.24; 100°C 50 kPa He) for the isopropyl substituted diaziridines. These compounds showed pronounced plateau formation between 100 and 150°C, and peak coalescence at elevated temperatures. The enantiomerization barriers ΔG? and activation parameters ΔH? and ΔS? were determined by enantioselective dynamic gas chromatography (DGC) and direct evaluation of the elution profiles using the unified equation implemented in the software DCXplorer. Interestingly, 1‐isopropyl‐2‐n‐propyldiaziridine and 1,2‐diisopropyldiaziridine exhibit similar high interconversion barriers ΔG? (100°C) of 128.3 ± 0.4 kJ mol^?1 and 129.8 ± 0.4 kJ mol^?1, respectively, which indicates that two sterically demanding substituents do not substantially increase the barrier as expected for a distinct nitrogen inversion process. Chirality, 2010. © 2009 Wiley‐Liss, Inc.     

Predicting community structure in snakes on Eastern Nearctic islands using ecological neutral theory and phylogenetic methods

Predicting species presence and richness on islands is important for understanding the origins of communities and how likely it is that species will disperse and resist extinction. The equilibrium theory of island biogeography (ETIB) and, as a simple model of sampling abundances, the unified neutral theory of biodiversity (UNTB), predict that in situations where mainland to island migration is high, species-abundance relationships explain the presence of taxa on islands. Thus, more abundant mainland species should have a higher probability of occurring on adjacent islands. In contrast to UNTB, if certain groups have traits that permit them to disperse to islands better than other taxa, then phylogeny may be more predictive of which taxa will occur on islands. Taking surveys of 54 island snake communities in the Eastern Nearctic along with mainland communities that have abundance data for each species, we use phylogenetic assembly methods and UNTB estimates to predict island communities. Species richness is predicted by island area, whereas turnover from the mainland to island communities is random with respect to phylogeny. Community structure appears to be ecologically neutral and abundance on the mainland is the best predictor of presence on islands. With regard to young and proximate islands, where allopatric or cladogenetic speciation is not a factor, we find that simple neutral models following UNTB and ETIB predict the structure of island communities.     

Acceleration Workspace of Cooperating Multi-Finger Robot Systems

We present a mathematical method for acceleration workspace analysis of cooperating multi-finger robot systems using a model of point-contact with friction. A new unified formulation from dynamic equations of cooperating multi-finger robots is derived considering the force and acceleration relationships between the fingers and the object to be handled. From the dynamic equation, maximum translational and rotational acceleration bounds of an object are calculated under given constraints of contact conditions, configurations of fingers, and bounds on the torques of joint actuators for each finger. Here, the rotational acceleration bounds can be applied as an important manipulability index when the multi-finger robot grasps an object. To verify the proposed method, we used a set of case studies with a simple multi-finger mechanism system. The achievable acceleration boundary in task space can be obtained successfully with the proposed method and the acceleration boundary depends on the configurations of fingers.     

Linking dispersal, immigration and scale in the neutral theory of biodiversity

In the classic spatially implicit formulation of Hubbell's neutral theory of biodiversity a local community receives immigrants from a metacommunity operating on a relatively slow timescale, and dispersal into the local community is governed by an immigration parameter m . A current problem with neutral theory is that m lacks a clear biological interpretation. Here, we derive analytical expressions that relate the immigration parameter m to the geometry of the plot defining the local community and the parameters of a dispersal kernel. Our results facilitate more rigorous and extensive tests of the neutral theory: we conduct a test of neutral theory by comparing estimates of m derived from fits to empirical species abundance distributions to those derived from dispersal kernels and find acceptable correspondence; and we generate a new prediction of neutral theory by investigating how the shapes of species abundance distributions change theoretically as the spatial scale of observation changes. We also discuss how our main analytical results can be used to assess the error in the mean-field approximations associated with spatially implicit formulations of neutral theory.     

Ultrastructure of the tegument of the cestode Paraechinophallus japonicus (Bothriocephalidea: Echinophallidae), a parasite of the bathypelagic fish Psenopsis anomala

Abstract. The ultrastructure of the tegument in Paraechinophallus japonicus (Bothriocephalidea: Echinophallidae), a cestode parasite of the bathypelagic fish Psenopsis anomala , was studied using scanning and transmission electron microscopy. Paraechinophallus japonicus lacks a true scolex. Four different types of microtriches have been observed on the tegumental surface of P. japonicus. Capilliform (∼2.3-μm long) and blade-like spiniform (∼1.4-μm long) microtriches are intermingled on the surface of the pseudoscolex. Capilliform microtriches are distinct in possessing a short base and a long electron-lucent cap. The strobila is covered with two types of microtriches, namely filiform (∼2.1-μm long) and tusk-shaped microtriches (≤4.5-μm long). Tusk-shaped microtriches are limited to the posterior border of each proglottid and are characterized by a short and narrow base, and a large and wide, sharply pointed, electron-dense cap. Similar tusk-shaped microtriches were previously found in members of the family Echinophallidae and may represent an autapomorphy of echinophallid cestodes, all of them being parasitic in centrolophid fish. A unified terminology of microthrix parts is proposed.     

Molecular Mechanisms of Stress Adaptation in Plant Natural Populations

Recent advances in studies of genetic variation at protein and DNA levels in plant natural populations and its relationship with environmental changes were reviewed with special reference to the works on the wild barley ( Hordeum spontaneum C. Koch.). On one side, adaptation was shown in statistic data, on the other side, the fact that a considerable part of genetic variation does exist within populations (subpopulations) under same ecological condition indicated its maintainability of neutral or near-neutral mutations in natural populations. The researches on adaptive populations of plants, especially on wild soybean ( Glycine soja Sieb. et Zucc.) mainly conducted in author's laboratory, have shown that the most part of molecular variation within and among populations can not be explained by selection particularly as far as the individual uniqueness was concerned. There are some data shown that adaptation may be caused by accumulation of a few near-neutral mutations. Recent publications on molecular mechanisms of morphological evolution has been received special attention to elucidate the discrepancy between molecular evolution and morphological adaptive evolution. A frame on the unified evolution theory has been built. Finally some related viewpoints of philosophy were discussed.     

Revisiting the use of the invasive species concept: An empirical approach

Invasion science has not been developed without controversies. Two questions that are still unsolved are: what is an invasive species?, and are invasive species an inherent conservation problem? These questions have led to discussions about effects versus origins. In contrast to the definitional problems, a unified framework describing invasion as a step‐by‐step process has been widely accepted. I conducted a bibliographic search with two separate databases searching for (i) evidence of less use of controversial terms over time; (ii) how many articles defined ‘invasive species’; (iii) the criteria used to define a species as invasive; and (iv) in which stage of the invasion continuum were species labelled as invasive located. My results show that controversial terms are widely used, that authors rarely define ‘invasive species’ and, often, it is very complicated to determine which criterion they used. In addition, only a fraction of the species labelled as invasive could be classified as such according to the unified framework of invasion stages. This is not a merely semantic issue, because invasive is a strong and value‐laden term that is used to guide environmental agendas. The uncritical use of a key concept could hamper research, complicate communication among peers and produce mixed results.