One-dimensional and two-dimensional liquid chromatography of sulphonated lignins

One- and two-dimensional separation methods have been developed for the analysis of lignosulphonates and sulphonated kraft lignins. The evaluated sulphonated lignins are all used as dispersants in agrochemical formulations, where some give rise to physical instabilities of formulations. It is of interest to identify the properties of the sulphonated lignins that determine the formulation characteristics. Tetrapentylammonium bromide has been used as an ion-pair reagent in a gradient-elution reversed-phase liquid-chromatographic (IP-RPLC) method, as well as in aqueous size-exclusion chromatography (SEC). Clear differences in the size distribution were observed between different batches of sulphonated lignins. The RPLC and SEC methods were combined in a comprehensive two-dimensional liquid chromatography system. The retention times in the two dimensions were highly correlated. Therefore, the full potential of comprehensive two-dimensional liquid chromatography was not yet realized. However, the results did reveal that retention in IP-RPLC was not determined by the degree of sulphonation of similar-size molecules. Rather, molecules were separated according to size and the degree of sulphonation appears to be approximately constant. The information obtained in this study represents a significant step towards meaningful correlations between the requirements of surfactants within an agrochemical formulation and structural parameters, such as the size and the degree of sulphonation of lignin oligomers.     

Polymer characterization by interaction chromatography

Liquid chromatography (LC) is a powerful tool for the characterization of synthetic polymers, that are inherently heterogeneous in molecular weight, chain architecture, chemical composition, and microstructure. Of different versions of the LC methods, size exclusion chromatography (SEC) is most commonly used for the molecular weight distribution analysis. SEC separates the polymer molecules according to the size of a polymer chain, a well‐defined function of molecular weight for linear homopolymers. The same, however, cannot be said of nonlinear polymers or copolymers. Hence, SEC is ill suited for and inefficient in separating the molecules in terms of chemical heterogeneity, such as differences in chemical composition of copolymers, tacticity, and functionality. For these purposes, another chromatographic method called interaction chromatography (IC) is found as a better tool because its separation mechanism is sensitive to the chemical nature of the molecules. The IC separation utilizes the enthalpic interactions to vary adsorption or partition of solute molecules to the stationary phase. Thus, it is used to separate polymers in terms of their chemical composition distribution or functionality. Further, the IC method has been shown to give rise to much higher resolution over SEC in separating polymers by molecular weight. We present here our recent progress in polymer characterization with this method. © 2005 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 43: 1591‐1607, 2005     

Chemical,Thermal and Antioxidant Properties of Lignins Solubilized during Soda/AQ Pulping of Orange and Olive Tree Pruning Residues

Some agroforestry residues such as orange and olive tree pruning have been extensively evaluated for their valorization due to its high carbohydrates content. However, lignin-enriched residues generated during carbohydrates valorization are normally incinerated to produce energy. In order to find alternative high added-value applications for these lignins, a depth characterization of them is required. In this study, lignins isolated from the black liquors produced during soda/anthraquinone (soda/AQ) pulping of orange and olive tree pruning residues were analyzed by analytical standard methods and Fourier-transform infrared spectroscopy (FTIR), nuclear magnetic resonance (solid state ¹³C NMR and 2D NMR) and size exclusion chromatography (SEC). Thermal analysis (thermogravimetric analysis (TGA), differential scanning calorimetry (DSC)) and antioxidant capacity (Trolox equivalent antioxidant capacity) were also evaluated. Both lignins showed a high OH phenolic content as consequence of a wide breakdown of β-aryl ether linkages. This extensive degradation yielded lignins with low molecular weights and polydispersity values. Moreover, both lignins exhibited an enrichment of syringyl units together with different native as well as soda/AQ lignin derived units. Based on these chemical properties, orange and olive lignins showed relatively high thermal stability and good antioxidant activities. These results make them potential additives to enhance the thermo-oxidation stability of synthetic polymers.     

Mechanical properties and inhomogeneous nanostructures of dicyandiamide-cured epoxy resins

Dicyandiamide (DICY)-cured epoxy resins are important materials for structural adhesives and matrix resins for fiber reinforced prepregs. The objective of this study was to examine the mechanical and physical properties as well as the gel structures of the cured resins and discuss the relationships among them. Diglycidyl ether of bisphenol-A (DGEBA) oligomers were chosen as the common chemical structure of the epoxy resins. Four kinds of resin mixtures were formulated using the seven types of DGEBA oligomers having different molecular weight distributions. Three resin formulations having bimodal-type molecular weight distributions were designed to have almost identical rubbery plateau values of the storage modulus in dynamic mechanical analyses after curing, means that they had almost equivalent average crosslink density and basic chemical structure. However, the toughness, ductility, and environmental (heat and solvent) resistance of these three formulations were different. Atomic force microscopy revealed the existence of inhomogeneous nanoscale gel structures in these cured resins. The morphological differences in the gel structures in terms of their size, the connectivity, and the relative magnitude of the heterogeneity would cause the difference in several properties of the DICY-cured epoxy resins. © 2007 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 45: 1425–1434, 2007     

A critique on the structural analysis of lignins and application of novel tandem mass spectrometric strategies to determine lignin sequencing

This review is devoted to the application of MS using soft ionization methods with a special emphasis on electrospray ionization, atmospheric pressure photoionization and matrix‐assisted laser desorption/ionization MS and tandem MS (MS/MS) for the elucidation of the chemical structure of native and modified lignins. We describe and critically evaluate how these soft ionization methods have contributed to the present‐day knowledge of the structure of lignins. Herein, we will introduce new nomenclature concerning the chemical state of lignins, namely, virgin released lignins (VRLs) and processed modified lignins (PML). VRLs are obtained by liberation of lignins through degradation of vegetable matter by either chemical hydrolysis and/or enzymatic hydrolysis. PMLs are produced by subjecting the VRL to a series of further chemical transformations and purifications that are likely to alter their original chemical structures. We are proposing that native lignin polymers, present in the lignocellulosic biomass, are not made of macromolecules linked to cellulose fibres as has been frequently reported. Instead, we propose that the lignins are composed of vast series of linear related oligomers, having different lengths that are covalently linked in a criss‐cross pattern to cellulose and hemicellulose fibres forming the network of vegetal matter. Consequently, structural elucidation of VRLs, which presumably have not been purified and processed by any other type of additional chemical treatment and purification, may reflect the structure of the native lignin. In this review, we present an introduction to a MS/MS top–down concept of lignin sequencing and how this technique may be used to address the challenge of characterizing the structure of VRLs. Finally, we offer the case that although lignins have been reported to have very high or high molecular weights, they might not exist on the basis that such polymers have never been identified by the mild ionizing techniques used in modern MS. Copyright © 2015 John Wiley & Sons, Ltd.     

Characterization of the water-insoluble fraction from fast pyrolysis liquids (pyrolytic lignin). Part IV: Structure elucidation of oligomeric molecules

Various wet chemical and spectroscopic methods used in lignin chemistry as well as pyrolysis-gas chromatography/mass spectrometry were applied to elucidate the structure of pyrolytic lignins (PLs) with the help of previously obtained data on molecular weight distribution and laser desorption ionization-time of flight-mass spectrometry. PL from beech wood (Fagus sylvatica L.) was used as reference and in addition results from elemental analysis of carbon and hydrogen were used as basis for proposing five chemical structures, ranging from a tetramer to an octamer. The oligomers are typically characterized by biphenyl, phenyl coumaran, diphenyl ethers, stilbene and resinol structures. The results were used to speculate the formation of the pyrolytic lignin. It is concluded that pyrolytic lignin emerges as result of both recombination reactions and thermal ejection of intact lignin fragments.     

Reinforcement of metal-ceramic coatings in the course of their partial fusion

Factors and mechanisms responsible for the appearance of layered structures of variable cross section in protective coatings based on self-fluxing alloys were studied. A number of structural fragments of composite coatings based on safe-fluxing PG-10K-01 and PG-SR3 alloys (initial formulations and those reinforced with oxide ceramic particles), formed by sputtering in a plasma flux and then partially fused in a furnace, by a gas-oxygen flame, and with laser and electron beams, were revealed and studied. The relationships of the element distribution across the coating layer as a whole and in separate phases were determined. The effect exerted on the chemical composition and microhardness of coatings by the size, structure, and arrangement of inclusions in the coating cross section was demonstrated.     

The microdetection of organoparticulates from diazonium compounds

The thermal decompositions of a series of diazonium compounds have been investigated using the new technique of organic particulate analyses (OPA). This extremely sensitive technique makes possible the detection of particulates emitted from the diazonium compounds during thermal decomposition. The submicron particulates derived in this fashion are readily detectable by their influence on the output current of an ion chamber detector or by their effect on the cloud chamber of a condensation nuclei monitor.Of the 14 diazonium compounds evaluated, 11 were found to exhibit particulation behavior below 190 °C. In some cases, very strong particulation was detectable. No apparent correlation between the organic particulation temperature range (OPTR) and their literature thermal decomposition temperatures was evident. Efforts were made to characterize the nature of the particulates using mass spectrometry but this was hampered by the extreme complexities of the spectral patterns.In terms of their abilities to produce particulates, the diazonium compounds can be placed in four main groups reflecting their chemical composition, molecular size, and degree of substitution. Vapor phase association of the molecular fragments formed during thermal decomposition might be occurring to produce the required particulate size detectable by the present instrumentation.     

Characteristic Spectral Patterns in the Carbon‐13 Nuclear Magnetic Resonance Spectra of Hexagonal and Crenellated Graphene Fragments

Nuclear magnetic resonance (NMR) spectroscopy is an important molecular characterisation method that may aid the synthesis and production of graphenes, especially the molecular‐scale graphene nanoislands that have gathered significant attention due to their potential electronic and optical applications. Herein, carbon‐13 NMR chemical shifts were calculated using density functional theory methods for finite, increasing‐size fragments of graphene, hydrogenated graphene (graphane) and fluorinated graphene (fluorographene). Both concentric hexagon‐shaped (zigzag boundary) and crenellated (armchair) fragments were investigated to gain information on the effect of different types of flake boundaries. Convergence trends of the ¹³C chemical shift with respect to increasing fragment size and the boundary effects were found and rationalised in terms of low‐lying electronically excited states. The results predict characteristic behaviour in the ¹³C NMR spectra. Particular attention was paid to the features of the signals arising from the central carbon atoms of the fragments, for graphene and crenellated graphene on the one hand and graphane and fluorographene on the other hand, to aid the interpretation of the overall spectral characteristics. In graphene, the central nuclei become more shielded as the system size increases whereas the opposite behaviour is observed for graphane and fluorographene. The ¹³C signals from some of the perimeter nuclei of the crenellated fragments obtain smaller and larger chemical shift values than central nuclei for graphene and graphane/fluorographene, respectively. The diameter of the graphenic quantum dots with zigzag boundary correlates well with the predicted carbon‐13 chemical shift range, thus enabling estimation of the size of the system by NMR spectroscopy. The results provide data of predictive quality for future NMR analysis of the graphene nanoflake materials.     

Impact of landuse change on the molecular composition of soil organic matter

The conversion of grassland into cultivated land is a common agricultural practice, generally leading to the decrease of the soil organic matter (SOM) content. In this study, we analysed quantitative changes in carbon content. Additionally qualitative changes occurring in the soil organic matter composition on a molecular basis were assessed using Curiepoint pyrolysis coupled to gas chromatography and mass spectrometry (pyrolysis GC/MS). The aim of the study was to follow the development of SOM in grassland soil, after conversion into arable soil.Soil was sampled before the conversion (0 month) as well as 3 months, and 1 year after the conversion. The samples were treated with 10% HF to remove mineral material before being subjected to analysis of the bulk chemical composition by pyrolysis GC/MS. The relative contributions of single molecules were obtained by the integration of the total ion chromatogram.Pyrolysis products derived from lignins, proteins and polysaccharides were identified in all samples. SOM under grassland, arable land and converted grassland released similar pyrolysis products. Three months after the conversion, lignin-derived pyrolysis products were found at lower concentrations in the converted grassland soil. Principal component analysis showed that arable land, grassland and the converted grassland could be distinguished using the score plot of the 2nd and 3rd principal components. The differences induced by grassland conversion are only transitory and 1 year after the conversion, SOM has a similar composition as SOM of the initial grassland soil.     

New insights into the molecular architecture of hardwood lignins by chemical degradative methods

Lignins are composed of phenylpropane units interconnected by labile and resistant bonds. A two-step degradation, thioacidolysis, provides detailed information on these network polymers. The first step involves lignin depolymerization with ethanethiol and BF₃ etherate. The determination of the recovered thioethylated monomers provides an estimation of lignin units only involved in labile ether bonds. The ligninderived dimers, representative of resistant interunit bonds, are determined after a further desulfurization step. Results obtained for native and industrial hardwood lignins underline their structural differences. Native hardwood lignins are typified by a high proportion of linear fragments linked bifunctionally by β-O-4 bonds.     

Random Computer Generation of 3D Molecular Structures: Theoretical and Statistical Analysis

Summary: A computer program has been developed to generate three‐dimensional molecular structures randomly from a given collection of elementary chemical functional groups: the so‐called fragment database. The gradual assembly of the various fragments present in the database is performed according to a “self‐generation algorithm” (SGA). The latter is based on the covalent binding, step by step, between the unoccupied electronic valencies associated with the fragments of the database, and those of the growing molecular structure. When the number of electronic valencies of the molecular structure is zero, the growth process for this particular molecule is completed. It is shown that SGA is able to reproduce the asymmetric mass distributions of some natural colloids, like humic substances. In this article, particular attention is given to the analysis of the relationship existing between the fragment composition of the database and that of the collection of molecules generated. Mathematical expressions are derived and discussed, to understand the relationship between the proportions of the different types of fragments and the final composition of the generated molecular ensembles. For that purpose, a “pathway” formalism is proposed to describe exhaustively the whole set of generated molecules by specifying the distribution function of all of the fragments therein integrated. A statistical analysis that satisfactorily reproduces the predictions of the pathway model is extensively discussed.

Example of a three‐dimensional structure obtained with the “self‐generation algorithm” (SGA).     

Conformation Design of Open-Chain Compounds

At the brink of the 21st century, chemistry is increasingly concerned with the function that molecules fulfil as drugs, receptors, or-as ensemble of molecules-as materials. The capability of compounds to fulfil such functions cannot sufficiently be described by using only the terms composition and configuration. A decisive role is played in addition by the conformation of the molecules, which serves as the link between molecular composition and molecular function. Expressions such as "active conformation" or "competent conformation" allude to this aspect. Chemists have to develop an understanding how a flexible molecule adopts the conformation (a distinct shape) which is optimal for the function in question and how this process can be controlled. On the outset of such considerations, we may ask how nature succeeded in the process of evolution to endow flexible molecules with a preference to adopt the conformation which is optimal for the function it has to serve. In this review, I report on how we have reached a crude level of understanding of conformation design in nature with reference to the class of polyketide natural products, how we developed these insights into a conformation design of open-chain compounds, and which applications are already in sight.     

Molecular Organization of Various Collagen Fragments as Revealed by Atomic Force Microscopy and Diffusion‐Ordered NMR Spectroscopy

Heterogeneous mixtures of collagen fragments can be used as nutrition supplement or as key ingredients for ointments with therapeutic relevance in wound healing. Some mixtures of collagen fragments are referred to as collagen hydrolysates owing to the production process with hydrolytic enzymes. Since the precise composition of collagen hydrolysates is generally unknown, it is of interest to analyze samples containing various collagen fragments with appropriate biophysical methods. Any product optimization without a profound knowledge concerning the size and the molecular weight distribution of its components is nearly impossible. It turned out that a combination of AFM methods with NMR techniques is exceptionally suited to examine the size range and the aggregation behavior of the collagen fragments in the hydrolysates of fish, jellyfish, chicken, porcine and bovine collagen. Supported by molecular modeling calculations, the AFM and NMR experiments provide a detailed knowledge about the composition of collagen hydrolysates and collagen ointments. Furthermore, the data allow a correlation between the size of the fragments and their potential bioactivity.     

Towards formation of buckminsterfullerene C60 in quantum chemical molecular dynamics

We present follow-up studies on the formation mechanism of fullerene molecules from random ensembles of C2 molecules using quantum chemical molecular dynamics. Two possible roadmaps are investigated as to how buckminsterfullerene C60 and higher fullerenes could be formed. In a "size-up" scenario, fullerenes of the cage size of C72-C96 were found to form directly from high concentrations of C2 molecules at 2000 K with periodic supply of batches of additional C2's. In a "size-down" approach, smaller fullerenes are sometimes formed by losing carbon fragments in "fall-off" or "pop-out" annealing processes under prolonged heating of giant fullerenes, which were self-assembled at initial stages from C2's with lower concentrations. Both roadmaps are found to provide explanations for the appearance of C60 and larger fullerenes in combustion and carbon arc experiments.     

Fragment-based drug design: computational & experimental state of the art

Fragment-based screening is an emerging technology which is used as an alternative to high-throughput screening (HTS), and often in parallel. Fragment screening focuses on very small compounds. Because of their small size and simplicity, fragments exhibit a low to medium binding affinity (mM to μM) and must therefore be screened at high concentration in order to detect binding events. Since some issues are associated with high-concentration screening in biochemical assays, biophysical methods are generally employed in fragment screening campaigns. Moreover, these techniques are very sensitive and some of them can give precise information about the binding mode of fragments, which facilitates the mandatory hit-to-lead optimization. One of the main advantages of fragment-based screening is that fragment hits generally exhibit a strong binding with respect to their size, and their subsequent optimization should lead to compounds with better pharmacokinetic properties compared to molecules evolved from HTS hits. In other words, fragments are interesting starting points for drug discovery projects. Besides, the chemical space of low-complexity compounds is very limited in comparison to that of drug-like molecules, and thus easier to explore with a screening library of limited size. Furthermore, the "combinatorial explosion" effect ensures that the resulting combinations of interlinked binding fragments may cover a significant part of "drug-like" chemical space. In parallel to experimental screening, virtual screening techniques, dedicated to fragments or wider compounds, are gaining momentum in order to further reduce the number of compounds to test. This article is a review of the latest news in both experimental and in silico virtual screening in the fragment-based discovery field. Given the specificity of this journal, special attention will be given to fragment library design.     

Syntheses of O-antigen polysaccharide fragments of nitrogen-fixing rhizobacteria of the genus <Emphasis Type="Italic">Azospirillum</Emphasis>

Fragments of O-antigen polysaccharides of nitrogen-fixing rhizobacteria of the genus Azospirillum isolated from natural sources may greatly vary in the monosaccharide composition, molecular weight, as well as in the presence of side chains and branching sites along the main chain. These variations, along with the differences in purity and homogeneity of the samples, hamper investigations of the role of individual components of O-antigen polysaccharides of the rhizobacteria Azospirillum in interactions with plants, including important cereal crops. Therefore, synthetic oligosaccharides, which correspond to O-antigen polysaccharide fragments of rhizobacteria of the genus Azospirillum and have a strictly defined structure and high purity, are highly demanded. The review summarizes the data on the synthesis of these oligosaccharide fragments as promising tools for investigation of the mechanism of formation of a symbiotic association with plants.     

Pressure-Dependent Structure of Methanol–Water Mixtures up to 1.2 GPa: Neutron Diffraction Experiments and Molecular Dynamics Simulations

Total scattering structure factors of per-deuterated methanol and heavy water, CD₃OD and D₂O, have been determined across the entire composition range as a function of pressure up to 1.2 GPa, by neutron diffraction. The largest variations due to increasing pressure were observed below a scattering variable value of 5 Å⁻¹, mostly as shifts in terms of the positions of the first and second maxima. Molecular dynamics computer simulations, using combinations of all-atom potentials for methanol and various water force fields, were conducted at the experimental pressures with the aim of interpreting neutron diffraction results. The peak-position shifts mentioned above could be qualitatively reproduced by simulations, although in terms of peak intensities, the accord between neutron diffraction and molecular dynamics was much less satisfactory. However, bearing in mind that increasing pressure must have a profound effect on repulsive forces between neighboring molecules, the agreement between experiment and computer simulation can certainly be termed as satisfactory. In order to reveal the influence of changing pressure on local intermolecular structure in these “simplest of complex” hydrogen-bonded liquid mixtures, simulated structures were analyzed in terms of hydrogen bond-related partial radial distribution functions and size distributions of hydrogen-bonded cyclic entities. Distinct differences between pressure-dependent structures of water-rich and methanol-rich composition regions were revealed.     

Robust Atomistic Modeling of Materials,Organometallic, and Biochemical Systems

Modern chemistry seems to be unlimited in molecular size and elemental composition. Metal‐organic frameworks or biological macromolecules involve complex architectures and a large variety of elements. Yet, a general and broadly applicable theoretical method to describe the structures and interactions of molecules beyond the 1000‐atom size regime semi‐quantitatively is not self‐evident. For this purpose, a generic force field named GFN‐FF is presented, which is completely newly developed to enable fast structure optimizations and molecular‐dynamics simulations for basically any chemical structure consisting of elements up to radon. The freely available computer program requires only starting coordinates and elemental composition as input from which, fully automatically, all potential‐energy terms are constructed. GFN‐FF outperforms other force fields in terms of generality and accuracy, approaching the performance of much more elaborate quantum‐mechanical methods in many cases.