Analysis of intact ladderane phospholipids, originating from viable anammox bacteria, using RP-LC-ESI-MS

Since the discovery of the anaerobic ammonium oxidizing (anammox) bacteria, many attempts have been made in order to identify these environmentally important bacteria in natural environments. Anammox bacteria contain a unique class of lipids, called ladderane lipids and here we present a novel method to detect viable anammox bacteria in sediments and waste water treatment plants based on the use of a ladderane lipid biomarker. Intact ladderane phosphatidylcholine (PC) lipids are analyzed using reversed-phase liquid chromatography–electrospray ionization–mass spectrometry. Following extraction from the complex sediment matrix, reversed-phase LC is used to separate ladderane PC lipids based on their tail group hydrophobicity as well as their ether or ester link to the glycerol backbone in the sn-2 position. We investigate the presence of intact ladderane lipids in natural sediments displaying anammox activity and illustrate the use of a specific intact membrane forming PC lipid as a biomarker for viable anammox bacterial cells. The presented method can be used to elucidate the whereabouts of viable anammox bacteria, subsequently enabling an estimation of anammox activity. This will greatly increase the knowledge of anammox bacteria and their importance in the global nitrogen cycle.     

Improved analysis of ladderane lipids in biomass and sediments using high-performance liquid chromatography/atmospheric pressure chemical ionization tandem mass spectrometry

Ladderane lipids, containing three or five linearly concatenated cyclobutane moieties, are considered to be unique biomarkers for the process of anaerobic ammonium oxidation, an important link in the oceanic nitrogen cycle. Due to the thermal lability of the strained cyclobutane moieties, the ladderane lipids are difficult to analyze by gas chromatography. A method combining high-performance liquid chromatography coupled to positive ion atmospheric pressure chemical ionization tandem mass spectrometry (HPLC/APCI-MS/MS) was developed for the analysis of the most abundant ladderane lipids, occurring as fatty acids and ether-bound to glycerol. Detection was achieved by selective reaction monitoring of four specific fragmentations per ladderane lipid. Detection limits of 30-35 pg injected on-column and a linear response (r(2) > 0.99) over nearly 3 orders of magnitude were achieved for all compounds. Using this method, these unique ladderane lipids were for the first time identified in a surface sediment from the Gullmarsfjorden, in concentrations ranging from 1.1-5.5 ng/g for the ladderane fatty acids and of 0.7 ng/g for the monoether. It is foreseen that this method will allow the investigation of the occurrence of anaerobic ammonium oxidation in natural settings in much greater detail than before.     

Ladderane Natural Products: From the Ground Up

The ladderane family of natural products are well known for their linearly concatenated cyclobutane skeletal structure. Owing to their unique carbocyclic framework, several chemical syntheses have been reported since their discovery in 2002. The focus of this review is to showcase the novel tactics that have been used to generate the ladderane core and the challenges that are associated with the synthesis of these unusual and complex natural products.     

Photochemical studies on ladderane formation from conjugated esters in solution or solid phase

This letter describes a combined photochemical and X-ray crystallographic study of routes for the synthesis of cyclobutane or ladderane structures by a [2+2]-cycloaddition pathway and leads to a clearer definition of the 3-D structural requirements for such processes in the solid state.     

Ring strain in [n]ladderanes

The ring strain energies in a series of [ n]ladderanes (n = 3-8) have been calculated by using high-level ab initio method (G3MP2//B3LYP-6-31G*) and the series of isodesmic, homodesmotic, and protobranching compensated reactions. The results show that various four-member rings incorporated into the ladderane chain have different strain energies and that the total strain in a ladderane molecule is smaller than the corresponding sum of strain energies of the cyclobutane rings.     

Experimental Evidence for the Involvement of Dinuclear Alkynylcopper(I) Complexes in Alkyne–Azide Chemistry

Dinuclear alkynylcopper(I) ladderane complexes are prepared by a robust and simple protocol involving the reduction of Cu₂(OH)₃OAc or Cu(OAc)₂ by easily oxidised alcohols in the presence of terminal alkynes; they function as efficient catalysts in copper‐catalysed alkyne–azide cycloaddition reactions as predicted by the Ahlquist–Fokin calculations. The same copper(I) catalysts are formed during reactions by using the Sharpless–Fokin protocol. The experimental results also provide evidence that sodium ascorbate functions as a base to deprotonate terminal alkynes and additionally give a convincing alternative explanation for the fact that the Cu^I‐catalysed reactions of certain 1,3‐diazides with phenylacetylene give bis(triazoles) as the major products. The same dinuclear alkynylcopper(I) complexes also function as catalysts in cycloaddition reactions of azides with 1‐iodoalkynes.     

Photoreactive 3D microporous lanthanide MOFs: formation of a strained ladderane in a partial single crystal-to-single crystal manner

The assembly of Er(3+) and Y(3+) cations with trans,trans-muconic acid affords a photoreactive 3D microporous MOF that, upon UV irradiation, undergoes a cycloaddition reaction (SCSC up to 55%), with in situ formation of a strained ladderane.     

Polyladderane Constructed from a Gemini Monomer through Photoreaction

Polyladderane, the first polymer to contain the ladderane functional group, was synthesized from a gemini monomer through photoreaction in the solid state. The modular design of the gemini monomers used to create polyladderane allowed specific structural modification, resulting in the formation of two distinct polymer products. Monomers were synthesized by connecting two photoreactive units, either sorbic acids (monomer I) or 2‐furanacrylic acids (monomer II), with a 1,4‐butanediol linker. Single‐crystal X‐ray diffraction analysis of the monomers confirmed that they packed in the desired head‐to‐tail orientation and within a viable distance for photoreaction by electronically complementary interaction. Pre‐organized gemini monomers were irradiated with UV light and monitored by FT‐IR. Two polyladderanes with cis ,anti ,cis ‐[3]‐ladderane as a characteristic functional group were constructed stereospecifically in 24–36 hours.     

Electrochemical reactions at the electrode/solution interface:Theory and applications to water electrolysis and oxygen reduction

Theoretical simulations on complex electrochemical processes have been developed on the basis of the understanding in electrochemistry,which has benefited from quantum mechanics calculations.This article reviews the recent progress on the theory and applications in electrocatalysis.Two representative reactions,namely water electrolysis and oxygen reduction,are selected to illustrate how the theoretical methods are applied to electrocatalytic reactions.The microscopic nature of these electrochemical reaction...     

Exotic biomodification of fatty acids

Many biotransformations of mid- to long chain fatty acyl derivatives are intrinsically interesting because of their high selectivity and novel mechanisms. These include one carbon transfer, hydration, isomerization, hydrogenation, ladderane and hydrocarbon formation, thiolation and various oxidative transformations such as epoxidation, hydroxylation and desaturation. In addition, hydroperoxidation of polyunsaturated fatty acids leads to a diverse array of bioactive compounds. The bioorganic aspects of selected reactions will be highlighted in this review; 210 references are cited.     

PBFC-PI量子动力学方法及应用

对多原子体系的量子动力学计算非常重要, 然而, 对含六原子以上的分子体系进行精确量子动力学计算仍具挑战性. 面向过程的基函数定制(PBFC)-并行迭代(PI)方法是一种高效的量子动力学方法, 已应用于对含九原子的丙二醛异构体系的氢迁移速率的精确量子计算. 本综述首先阐明了PBFC的基本思想, 之后重点回顾了PBFC-PI方法的具体内容、 该方法与其它方法的结合及其应用方面的新进展. 应用这些方法实现了对单氢迁移、 协同双氢迁移和分步双氢迁移3种类型基准体系的大规模并行计算, 有助于获得对氢迁移过程的新认识.     

Parity conservation and polarization of differential cross sections in complex-forming chemical reactions

For complex-forming chemical reactions, such as atom-diatom insertion reactions, quantum scattering and quantum statistical calculations usually predict sharp forward/backward peaks in the Differential Cross Sections (DCS). Conversely, the corresponding classical calculations are unable to reproduce these peaks. We show here that the basic reason for such an intriguing failure is that parity conservation is ignored in classical mechanics. A by-product of the analysis is a simple parity-restoring approximation that might significantly increase the ability of classical mechanics to describe DCSs over the whole angular range for the title processes.     

Enthalpy of mixing of porous nanocluster polyoxometalates of keplerate-type Mo<Subscript>72</Subscript>Fe<Subscript>30</Subscript> with polyvinyl alcohol and polyethylene glycol

The interaction between porous spherical nanocluster polyoxometalate and water-soluble nonionic polymers (polyvinyl alcohol and polyethylene glycol) in the compositions of film is studied via calorimetry. The concentration dependences of the enthalpies of these processes are obtained using calculations based on the thermodynamic cycle.     

Interplay between aromaticity and strain in double group transfer reactions to 1,2‐benzyne

Density Functional Theory calculations are used to explore the double hydrogen atom transfer from different alkanes to 1,2‐benzyne. State‐of‐the‐art calculations including the Activation Strain Model of reactivity, Energy Decomposition Analysis, and Valence Bond methods, reveal the origins of the relatively low activation barriers computed for these processes compared to the analogous reaction involving acetylene. In addition, the interplay between the in‐plane aromaticity of the corresponding transition states and the variation of the π‐aromaticity associated with the benzyne moiety as well as their influence on the barrier heights of the transformations are analyzed in detail. © 2016 Wiley Periodicals, Inc.     

Calculating zeros: Non-equilibrium free energy calculations

Free energy calculations on three model processes with theoretically known free energy changes have been performed using short simulation times. A comparison between equilibrium (thermodynamic integration) and non-equilibrium (fast growth) methods has been made in order to assess the accuracy and precision of these methods. The three processes have been chosen to represent processes often observed in biomolecular free energy calculations. They involve a redistribution of charges, the creation and annihilation of neutral particles and conformational changes. At very short overall simulation times, the thermodynamic integration approach using discrete steps is most accurate. More importantly, reasonable accuracy can be obtained using this method which seems independent of the overall simulation time. In cases where slow conformational changes play a role, fast growth simulations might have an advantage over discrete thermodynamic integration where sufficient sampling needs to be obtained at every λ-point, but only if the initial conformations do properly represent an equilibrium ensemble. From these three test cases practical lessons can be learned that will be applicable to biomolecular free energy calculations.     

Molecular symmetry and ab initio calculations: IV. Symmetry-matrix and symmetry-supermatrix in calculations of two-electron repulsion integrals

The product of two Gaussians having different centers is itself a one-center Gaussian, thus multicenter integrals with a Cartesian Gaussian basis can be reduced to one-center integrals. Recurrence relations for overlap integrals and electron repulsion integrals (ERIs) are derived at these centers. The calculations of overlap integrals and ERIs are carried out step by step from the highest symmetry case (one center) to required cases (different centers) by using the translation of Cartesian Gaussians. Full exploitation of symmetry in calculation processes can result in optimal use of these recurrence relations. Compared with the recently published algorithms, based on the recurrence relations derived by Obara and Saika [J. Chem. Phys., 84 , 3963 (1986)], the floating point operations (FLOPs) for ERI calculations (having four different centers) can be reduced by a factor of ca. 2. A significant extra saving in calculations and storage can be obtained if atoms, linear, or planar molecules are discussed. © 1997 John Wiley & Sons, Inc.     

Particle formation and surface processes on atmospheric aerosols: A review of applied quantum chemical calculations

Aerosols significantly influence atmospheric processes such as cloud nucleation, heterogeneous chemistry, and heavy-metal transport in the troposphere. The chemical and physical complexity of atmospheric aerosols results in large uncertainties in their climate and health effects. In this article, we review recent advances in scientific understanding of aerosol processes achieved by the application of quantum chemical calculations. In particular, we emphasize recent work in two areas: new particle formation and heterogeneous processes. Details in quantum chemical methods are provided, elaborating on computational models for prenucleation, secondary organic aerosol formation, and aerosol interface phenomena. Modeling of relative humidity effects, aerosol surfaces, and chemical kinetics of reaction pathways is discussed. Because of their relevance, quantum chemical calculations and field and laboratory experiments are compared. In addition to describing the atmospheric relevance of the computational models, this article also presents future challenges in quantum chemical calculations applied to aerosols.     

Amphoteric doping of carbon nanotubes by encapsulation of organic molecules: electronic properties and quantum conductance

In order to investigate and optimize the electronic transport processes in carbon nanotubes doped with organic molecules, we have performed large-scale quantum electronic structure calculations coupled with a Green's function formulation for determining the quantum conductance. Our approach is based on an original scheme where quantum chemistry calculations on finite systems are recast to infinite, non-periodic (i.e., open) systems, therefore mimicking actual working devices. Results from these calculations clearly suggest that the electronic structure of a carbon nanotube can be easily manipulated by encapsulating appropriate organic molecules. Charge transfer processes induced by encapsulated organic molecules lead to efficient n- and p-type doping of the carbon nanotube. Even though a molecule can induce p and n doping, it is shown to have a minor effect on the transport properties of the nanotube as compared to a pristine tube. This type of doping therefore preserves the intrinsic properties of the pristine tube as a ballistic conductor. In addition, the efficient process of charge transfer between the organic molecules and the nanotube is shown to substantially reduce the susceptibility of the pi electrons of the nanotube to modification by oxygen while maintaining stable doping (i.e., no dedoping) at room temperature.     

Thermodynamics of reversible gas adsorption on alkali-metal exchanged zeolites--the interplay of infrared spectroscopy and theoretical calculations

Detailed understanding of weak solid-gas interactions giving rise to reversible gas adsorption on zeolites and related materials is relevant to both, fundamental studies on gas adsorption and potential improvement on a number of (adsorption based) technological processes. Combination of variable-temperature infrared spectroscopy with theoretical calculations constitutes a fruitful approach towards both of these aims. Such an approach is demonstrated here (mainly) by reviewing recent studies on hydrogen and carbon monoxide adsorption (at a low temperature) on alkali-metal exchanged ferrierite. However, the methodology discussed, which involves the interplay of experimental measurements and theoretical calculations at the periodic DFT level, should be equally valid for many other gas-solid systems. Specific aspects considered are the identification of gas adsorption complexes and thermodynamic studies related to standard adsorption enthalpy and entropy.     

Computational study on the 1,2-rearrangement in beta-(nitroxy)vinyl and beta-(acetoxy)vinyl radicals

The 1,2-nitroxyl and 1,2-acetoxyl rearrangement in beta-(nitroxy)vinyl and beta-(acetoxy)vinyl radicals 13a and 13b, respectively, has been studied for the gas phase with various ab initio and density functional methods. The energetically most favorable pathway for 13a is calculated to proceed via reversible fragmentation/radical addition through transition state I-19a. In the case of 13b, rearrangement through a five-membered ring transition state III-16b and the fragmentation/radical addition pathway via transition state I-19b are competing processes. Mulliken and natural population analysis reveal a certain degree of charge separation in III-16a/b that may indicate a potential solvent effect on the rearrangement rate. A stepwise group migration through a cyclic radical intermediate V-18a/b or rearrangement through a three-membered ring transition state II-15a/b can be ruled out for both vinyl radicals. A comparison of the results of the calculations with experimental findings provides important insights into the kinetics of "self-terminating radical oxygenations". A significant method dependence on the outcome of the calculations was observed, which revealed the unsuitability of the UHF, MP2, B3LYP, and mPW1PW91 methods for computing these radical rearrangement processes. The results from BHandHLYP/cc-pVDZ calculations showed the best agreement with single-point energy calculations performed at the QCISD and CCSD(T) levels of theory.