Towards an Understanding of the Carbon-Carbon Bond

In this essay, the classical question of “the influence of the number and kind of substituents on the strength of the C? C bond”, is pursued with the modern tools of contemporary physical organic chemistry. Based on the work of Karl Ziegler, the products and kinetics of thermolysis of a large number of highly branched aliphatic hydrocarbons and phenyl- or cyano-substituted derivatives were investigated. For each class of compounds, a linear relationship was found between the free enthalpy of activation of the homolytic cleavage of the weakest C? C bond and the strain energy in the ground state. These relationships permitted a quantitative separation of steric and electronic effects on the cleavage of C? C bonds. The influence of the size of the substituent groups on bond angles, bond lengths, and the conformational behavior of model compounds was studied by means of experimental structure determinations and force field calculations. C? C bond lengths up to 164 pm, bond angles at tetracoordinate carbon as large as 126°, and unusual eclipsed and gauche preferred conformations were found.     

Perspectives for Biotechnological Production and Utilization of Biopolymers: Metabolic Engineering of Polyhydroxyalkanoate Biosynthesis Pathways as a Successful Example

This article provides an overview of biopolymers, classed according to their chemical structures, function and occurrence, the principles of biosynthesis and metabolism in organisms. It will then focus on polyhydroxyalkanoates (PHA) for which technical applications in several areas are currently considered. PHAs represent a complex class of bacterial polyesters consisting of various hydroxyalkanoic acids that are synthesized by bacteria as storage compounds for energy and carbon if a carbon source is present in excess. Poly(3‐hydroxybutyrate), poly(3HB), is just one example. Most other PHAs are only synthesized if pathways exist which mediate between central intermediates of the metabolism or special precursor substrates on one side and coenzyme A thioesters of hydroxyalkanoic acids, which are the substrates of the PHA synthase catalyzing the polymerization, on the other side. During the last decade, basic and applied research have revealed much knowledge about the biochemical and molecular basis of the enzymatic processes for the synthesis of PHAs in microorganisms. The combination of detailed physiological studies, utilization of the overwhelming information provided by the numerous genome sequencing projects, application of recombinant DNA technology, engineering of metabolic pathways or enzymes and molecular breeding techniques applied to plants have provided new perspectives to produce these technically interesting biopolymers by novel or significantly improved biotechnological processes or by agriculture. Some examples for successful in vivo and in vitro engineering of pathways suitable for the synthesis and biotechnological production of PHAs consisting of medium‐chain‐length 3‐hydroxyalkanoic acids and short‐chain‐length hydroxyalkanoic acids will be provided.     

Understanding the Reactivity of Planar Polycyclic Aromatic Hydrocarbons: Towards the Graphene Limit

The Diels–Alder reactivity of maleic anhydride towards the bay regions of planar polycyclic aromatic hydrocarbons was explored computationally in the DFT framework. The process becomes more and more exothermic and the associated activation barriers become lower and lower when the size of the system increases. This enhanced reactivity follows an exponential behavior that reaches its maximum for systems having 18–20 benzenoid rings in their structures. This peculiar behavior was analyzed in detail by using the activation strain model of reactivity in combination with energy decomposition analysis. The influence of the change in the aromaticity of the polycyclic compound during the process on the respective activation barriers was also studied.     

Receptor-Based Screening Assays: New Perspectives in Anti-Doping Control

The so-called “growth promoters”, steroid hormones and β-agonists, are currently controlled by using hyphenated analytical methods (chromatography coupled to mass spectrometry) or, sometimes for screening purposes, on immunoassays. These methods are often too specific to allow an effective multianalyte control. To develop more efficient assays, the use of hormonal receptors as detection tools (receptor-based binding assays and cell-based assays) is proposed. Receptor-based assays represent useful tools in screening of hormonal residues in food, but they could also be applied in doping control (to detect “new” hormonal substances). Furthermore, these assays could be used to monitor the human exposure to endocrine disruptors.     

Towards a Quantitative Understanding of Protein Hydration and Volumetric Properties

Herein, we probe by pressure perturbation calorimetry (PPC) the coefficient of thermal expansion, the volumetric and the hydration properties of variants of a hyperstable variant of staphylococcal nuclease (SNase), Δ+PHS. The temperature‐dependent volumetric properties of the folded and unfolded states of the wild‐type protein are calculated with previously published data. The present PPC results are used to interpret the volume diagram and expansivity at a molecular level. We conclude that the expansivity of the unfolded state is, to a first approximation, temperature independent, while that of the folded state decreases with increasing temperature. Our data suggest that at low temperature the defining contribution to ΔV comes mainly from excluded volume differences and ΔV for unfolding is negative. In contrast, at high temperatures, differential solvation due to the increased exposed surface area of the unfolded state and, in particular, its larger thermal volume linked to the increased conformational dynamics of the unfolded state ensemble takes over and ΔV for unfolding eventually becomes positive.     

Towards a Fundamental Understanding of Urea and Thiourea inclusion Compounds

This article reviews some of the fundamental scientific issues associated with solid inclusion compounds, and describes the approaches and strategies that may be used to investigate the structural, dynamic and chemical properties of these systems. Two particular families of solid organic inclusion compounds - the urea and thiourea inclusion compounds - are highlighted. In order to understand the fundamental nature of these solids, it has been necessary to apply a wide range of experimental, computational and theoretical approaches. Each technique provides information on a different aspect of the solid, and the combined information obtained from these complementary approaches allows a comprehensive understanding to be established. Several issues of contemporary interest for urea and thiourea inclusion compounds are described, and the approaches that have been taken towards a fundamental understanding of these systems are explained.     

Engineering a Metabolic Pathway for Isobutanol Biosynthesis in Bacillus subtilis

Isobutanol can be biosynthesized via ??-ketoisovalerate catalyzed by heterologous keto acid decarboxylase (KDC) and alcohol dehydrogenase (ADH). In this work, isobutanol biosynthesis pathway was designed in Bacillus subtilis, a notable solvent-tolerant host. In order to do that, a plasmid pPKA expressing KDC and ADH under the control of a B. subtilis strong promoter P₄₃ was constructed. Isobutanol was detected in the products of the recombinant B. subtilis harboring pPKA plasmid, whereas none was detected by the wild-type strain. Effects of the medium ingredients such as glucose concentration and valine addition, and operating parameters such as initial pH, inoculation volume, and medium work volume on isobutanol production were also investigated. Isobutanol production reached to the maximum of 0.607?g/L after 35-h cultivation under the conditions: glucose concentration of 3%, valine addition of 2%, initial pH of 7.0, inoculum of 1%, and work volume of 50?mL/250?mL. Though the isobutanol production by the recombinant was low, it was the first successful attempt to produce isobutanol in engineered B. subtilis, and the results showed its great potential as an isobutanol-producing cell factory.     

Towards a Molecular Understanding of Asymmetric Heterogeneous Catalysis: Hydrogenation of 1-Phenyl-1,2-Propanedione1

The present work comprises a detailed investigation of a complex reaction system, revealing features of reaction mechanisms that are general for asymmetric heterogeneous catalysis. Heterogeneous enantioselective hydrogenation of 1-phenyl-1,2-propanedione was studied over cinchonidine modified Pt catalysts producing (R)-1-hydroxy-1-phenylpropanone as the main product with an enantiomeric excess (ee) of 65% at maximum yield, which could be further increased above 90% due to kinetic resolution. The results of kinetic studies in batch and continuous reactors, catalyst screening and characterization results, as well as quantum chemical calculations, are summarized, and pertinent mechanistic aspects are discussed.     

Multiferroic Domain Boundaries as Active Memory Devices: Trajectories Towards Domain Boundary Engineering

Twin boundaries in ferroelastics and curved interfaces between crystalline and amorphous zircon can, in principle, act as multiferroic structural elements and lead the way to the discovery of novel multiferroic devices which are based on structurally heterogeneous materials. While this paradigm has not yet been explored in full, this review shows that physical and chemical properties can vary dramatically inside twin boundaries and interfaces. Properties that have been already been explored include electric dipoles in a non‐polar matrix, the appearance of superconductivity in twin boundaries and the catalytic reaction of hydrous species in interfaces of radiation damaged material. Some of the fundamental physical and chemical properties of twin boundaries and related interfaces are described and possible applications are outlined.     

Metabolic Engineering of Biosynthetic Pathway for Production of Renewable Biofuels

Metabolic engineering is an important area of research that involves editing genetic networks to overproduce a certain substance by the cells. Using a combination of genetic, metabolic, and modeling methods, useful substances have been synthesized in the past at industrial scale and in a cost-effective manner. Currently, metabolic engineering is being used to produce sufficient, economical, and eco-friendly biofuels. In the recent past, a number of efforts have been made towards engineering biosynthetic pathways for large scale and efficient production of biofuels from biomass. Given the adoption of metabolic engineering approaches by the biofuel industry, this paper reviews various approaches towards the production and enhancement of renewable biofuels such as ethanol, butanol, isopropanol, hydrogen, and biodiesel. We have also identified specific areas where more work needs to be done in the future.     

Modulation of Triterpene Saponin Production: In Vitro Cultures,Elicitation, and Metabolic Engineering

Saponins are secondary metabolites that are widely distributed in the plant kingdom and are often the active components in medicinal herbs. Hence, saponins have a potential for the pharmaceutical industry as antibacterial, virucidal, anti-inflammatory, and anti-leishmanial drugs. However, their commercial application is often hindered because of practical problems, such as low and variable yields and limited availability of natural resources. In vitro cultures provide an alternative to avoid problems associated with field production; they offer a system in which plants are clonally propagated and yield is not affected by environmental changes. Additionally, treatment of in vitro cultures with elicitors such as methyl jasmonate may increase the production of saponins up to six times. In vitro cultures are amenable to metabolic engineering by targeting specific genes to enhance saponin production or drive production towards one specific class of saponins. Hitherto, this approach is not yet fully explored because only a limited number of saponin biosynthesis genes are identified. In this paper, we review recent studies on in vitro cultures of saponin-producing plants. The effect of elicitation on saponin production and saponin biosynthesis genes is discussed. Finally, recent research efforts on metabolic engineering of saponins will also be presented.     

The Effects of Sulphate and Tartrate Ions on the Molecular Organization of Water: Towards Understanding the Hofmeister Series (VI)

Using the 1-propanol (1P) probing methodology we have developed earlier, we characterized the effects of sulphate and tartrate anions on the molecular organization of H₂O. The results indicate that these two large anions belong to a new class of ??hydrophobe-like hydration center??. That is, sulphate and tartrate ions act as ??hydration centers?? with the hydration number 14±3 for both, and leave the bulk H₂O, away from hydration shells, unperturbed in the absence of the probing 1-propanol. As the mole fraction of the probe increases, however, the hydrogen bond probability of bulk H₂O away from hydration shells appears to decrease smoothly, as occurs with ??hydrophobes?? in H₂O. We plot the negative hydration number against the power to reduce the hydrogen bond probability of bulk H₂O for the two large anions. We also plotted the characteristic indices for ??hydrophiles?? and ??hydration centers?? whose characteristics we determined in the same manner earlier. H₂O defines the origin on this map. We found that a typical Hofmeister ranking for each anion matches reasonably well with that of the distance from the origin for each ion, in decreasing order starting from ions plotted in the north-west quadrant (representing the ??hydrophobe-like?? behavior) of the map and then in increasing order from the origin towards the south on the ordinate, the ??hydrophile-like?? behavior. These findings could be useful in understanding the Hofmeister series, pointing to the importance of the contribution made by the effect of each ion on H₂O, in addition to helping understand direct ion-protein interactions.     

Monomer-Dimer Control and Crystal Engineering in TASPs

We have reported a template assembled synthetic protein (cavitein?Q4) as an unexpected dimer in the solid state and as a monomer-dimer equilibrium in solution. We have since reported an ability to bias a cavitein's monomer-dimer equilibrium in solution by sequence design involving histidine metal chelation or disulfide incorporation. However, little remains known about the forces contributing to dimeric cavitein crystal nucleation and lattice stabilization. We, therefore, designed glutamine variants to probe factors involved in dimeric cavitein crystallization. It was found that a key glutamate hydrogen-bonding interaction between dimers is integral to crystal formation and stabilization. Additionally, we obtained a crystal structure of a cavitein (Q4-E3H) designed to bias the dimeric structure via histidine metal coordination. The resolved structure indicates a histidine cluster interaction that likely accounts for the biased dimeric form observed in solution.     

Improvement of Adenosylcobalamin Production by Metabolic Control Strategy in Propionibacterium freudenreichii

An efficient metabolic control approach was developed to improve the industrial anaerobic fermentation of adenosylcobalamin (ado-cbl) by Propionibacterium freudenreichii. The effects of 5,6-dimethylbenzimidazole (DMB) on cell growth and ado-cbl biosynthesis were investigated. Subsequently, the results obtained from the batch culture showed that an important intermediate of ado-cbl separated from the cell extract was identified as adenosylcobinamide (ado-cbi) by high-performance liquid chromatography coupled to an ultraviolet diode array detector and ESI mass spectrometry analysis. Ado-cbi can be converted to ado-cbl when linked to DMB, which is an essential compound for ado-cbi bioconversion. This key ado-cbi is useful not only in determining ado-cbl concentration in the fermentation process but also in serving as an effective compound to guide DMB incorporation for the harvest of the maximum ado-cbl concentration. Accordingly, with scaling up to 100?L fermentation, the experimental results showed that the discrepancy was less than 1?% using the developed prediction technique. Overall, the findings show that the method is efficient in evaluating the fermentation of ado-cbl by propionibacteria.     

Towards Green Routes for Polymer Synthesis: Polymerization of Cyclodextrin Host‐Guest Complexed Diethyl Fumarate and Copolymerization with Complexed Styrene in Homogenous Aqueous Solution

Summary: The radical homo‐ and copolymerization of styrene ( 1 ) and diethyl fumarate (DEF, 2 ) in the presence of methylated β‐cyclodextrin (β‐CD) in water is described. It has been shown for the first time that homopolymerization of CD‐complexed DEF and its copolymerization with CD‐complexed styrene occur readily in aqueous solution. In the absence of CD, or in organic solvents, the homopolymerization of DEF is strongly retarded.

     

Cellular Cations Control Conformational Switching of Inositol Pyrophosphate Analogues

The inositol pyrophosphate messengers (PP‐InsPs) are emerging as an important class of cellular regulators. These molecules have been linked to numerous biological processes, including insulin secretion and cancer cell migration, but how they trigger such a wide range of cellular responses has remained unanswered in many cases. Here, we show that the PP‐InsPs exhibit complex speciation behaviour and propose that a unique conformational switching mechanism could contribute to their multifunctional effects. We synthesised non‐hydrolysable bisphosphonate analogues and crystallised the analogues in complex with mammalian PPIP5K2 kinase. Subsequently, the bisphosphonate analogues were used to investigate the protonation sequence, metal‐coordination properties, and conformation in solution. Remarkably, the presence of potassium and magnesium ions enabled the analogues to adopt two different conformations near physiological pH. Understanding how the intrinsic chemical properties of the PP‐InsPs can contribute to their complex signalling outputs will be essential to elucidate their regulatory functions.     

Understanding Interactions between Cellular Matrices and Metal Complexes: Methods To Improve Silver Nanodot‐Specific Staining

Metal complexes are frequently used for biological applications due to their special photophysical and chemical characteristics. Due to strong interactions between metals and biomacromolecules, a random staining of cytoplasm or nucleoplasm by the complexes results in a low signal‐to‐background ratio. In this study, we used luminescent silver nanodots as a model to investigate the major driving force for non‐specific staining in cellular matrices. Even though some silver nanodot emitters exhibited excellent specific staining of nucleoli, labeling with nanodots was problematic owing to severe non‐specific staining. Binding between silver and sulfhydryl group of proteins appeared to be the major factor that enforced the silver staining. The oxidation of thiol groups in cells with hexacyanoferrate(III) dramatically weakened the silver‐cell interaction and consequently significantly improved the efficiency of targeted staining.     

Metabolic Engineering of Escherichia coli Cells for Ethanol Production under Aerobic Conditions

The ethanol production by recombinant Escherichia coli introducing of pyruvate decarboxylase (pdc) and alcohol dehydrogenase (adhB) from Zymomonas mobilis was investigated under aerobic conditions. In aerobic culture (K_La = 1.5 min^-1), the cells expressing pdc and adhB produced 0.4 g l^-1 ethanol when cultured for 18 h. This value was improved in BW25113Δpta/pHfdh/pTadhB-pdc following 4 g l^-1 formate feeding at 0.8 g l^-1 ethanol. In higher oxygenation level (K_La = 6.1 min^-1), the production of ethanol was further enhanced at 1.79 g l^-1 ± 0.37 g l^-1 after 24 h cultivation. Formate was found not detectable at the end of culture, indicating complete degradation this organic acid to regenerate NADH from NAD⁺. The culture strategy was effective to inactivate lactate dehydrogenase, which is major competitor for ethanol production in utilizing NADH.