Synthesis of Levulinic Acids From Muconic Acids in Hot Water.

Levulinic acid is a key biorenewable platform molecule. Its current chemical production from sugars is plagued by limited yields, char formation and difficult separations. An alternative and selective route starting from muconic acid via simple heating in water at high temperature (180 °C) has been developed. Muconic acid can be obtained from sugars or catechol fermentation. Chemical oxidation of catechol is another possibility which advantageously can also be applied on substituted catechols, hereby providing substituted muconic acids. When applying the disclosed hydrothermal protocol on these substrates hitherto unknown substituted levulinic acids were accessed. In particular, 3-propyllevulinic acid has been synthesized from 4-propylcatechol, prepared from pine wood. This propylated derivative has been used for the synthesis of a 3-propyllevulinate diester, i.e. butane-1,4-diyl bis(4-oxo-3-propylpentanoate), via esterification with 1,4-butanediol. The diester showed superior performance as plasticizer in comparison to the corresponding levulinate diester in both PVC (polyvinyl chloride) and PLA (polylactic acid). It plasticizes equally effective as the notorious commercial phthalate-based benchmark DEHP (di-2-ethylhexyl phthalate) in PVC.

Selective Nickel-Catalyzed Hydrodeacetoxylation of Aryl Acetates.

Acetate serves as a renewable and easily installed leaving group for selective deoxygenation of phenolics (ArOH). Ni-catalyzed hydrodeacetoxylation of aryl acetates (Ar-OAc) with HBpin in a green carbonate solvent selectively delivers the corresponding deoxygenated arenes (ArH). The method is also applicable to highly challenging guaiacyl and syringyl acetates, leaving -OMe groups intact without arene reduction. Renewable 4-propylguaiacol obtained from pine can also be transformed without significant loss in yield versus oil derived feedstock. The observed chemoselectivity for Ar-OAc versus ArO-Ac bond cleavage was rationalized based on mechanistic experiments and DFT calculations. ArOH side-product formation is attributed to direct competitive Ni-catalyzed reduction of the C=O bond. Hydrodeacyloxylation of a set of aryl alkanoates featured interesting chemoselectivity with a dramatic influence of the length and structure of the alkyl chain on catalysis.

The Influence of the Amino Acid Side Chains on the Raman Optical Activity Spectra of Proteins.

The Raman optical activity (ROA) spectra of proteins show distinct patterns arising from the secondary structure. It is generally believed that the spectral contributions of the side-chains largely cancel out because of their flexibility and the occurrence of many side-chains with different conformations. Yet, the influence of the side-chains on the ROA patterns assigned to different secondary structures is unknown. Here, the first systematic study of the influence of all amino acid side-chains on the ROA patterns is presented based on density functional theory (DFT) calculations of an extensive collection of peptide models that include many different side-chain and secondary structure conformations. It was shown that the contributions of the side-chains to a large extent average out with conformational flexibility. However, specific side-chain conformations can have significant contributions to the ROA patterns. It was also shown that α-helical structure is very sensitive to both the exact backbone conformation and the side-chain conformation. Side-chains with χ1 ≈-60° generate ROA patterns alike those in experiment. Aromatic side-chains strongly influence the amide III ROA patterns. Because of the huge structural sensitivity of ROA, the spectral patterns of proteins arise from extensive conformational averaging of both the backbone and the side-chains. The averaging results in the fine spectral details and relative intensity differences observed in experimental spectra.

Solution Structure of Mannobioses Unravelled by Means of Raman Optical Activity.

Structural analysis of carbohydrates is a complicated endeavour, due to the complexity and diversity of the samples at hand. Herein, we apply a combined computational and experimental approach, employing molecular dynamics (MD) and density functional theory (DFT) calculations together with NMR and Raman optical activity (ROA) measurements, in the structural study of three mannobiose disaccharides, consisting of two mannoses with varying glycosidic linkages. The disaccharide structures make up the scaffold of high mannose glycans and are therefore important targets for structural analysis. Based on the MD population analysis and NMR, the major conformers of each mannobiose were identified and used as input for DFT analysis. By systematically varying the solvent models used to describe water interacting with the molecules and applying overlap integral analysis to the resulting calculational ROA spectra, we found that a full quantum mechanical/molecular mechanical approach is required for an optimal calculation of the ROA parameters. Subsequent normal mode analysis of the predicted vibrational modes was attempted in order to identify possible marker bands for glycosidic linkages. However, the normal mode vibrations of the mannobioses are completely delocalised, presumably due to conformational flexibility in these compounds, rendering the identification of isolated marker bands unfeasible.

The effect of protein backbone hydration on the amide vibrations in Raman and Raman optical activity spectra.

Raman and specifically Raman optical activity (ROA) spectroscopy are very sensitive to the solution structure and conformation of biomolecules. Because of this strong conformational sensitivity, density functional theory (DFT) calculations are often used to get a better understanding of the experimentally observed spectral patterns. While e.g. for carbohydrate structure the water molecules that surround the solute have been demonstrated to be of vital importance to get accurate modelled ROA spectra, the effect of explicit water molecules on the calculated ROA patterns of peptides and proteins is less well studied. Here, the effect of protein backbone hydration was studied using DFT calculations of HCO-(l-Ala)5-NH2 in specific secondary structure conformations with different treatments of the solvation. The effect of the explicit water molecules on the calculated spectra mainly arises from the formation of hydrogen bonds with the amide C[double bond, length as m-dash]O and N-H groups. Hydrogen bonding of water with the C[double bond, length as m-dash]O group determines the shape and position of the amide I band. The C[double bond, length as m-dash]O bond length increases upon formation of C[double bond, length as m-dash]OH2O hydrogen bonds. The effect of the explicit water molecules on the amide III vibrations arises from hydrogen bonding of the solvent with both the C[double bond, length as m-dash]O and N-H group, but their contributions to this spectral region differ: geometrically, the formation of a C[double bond, length as m-dash]OH2O bond decreases the C-N bond length, while upon forming a N-HH2O hydrogen bond, the N-H bond length increases.

Is Raman Optical Activity Spectroscopy Sensitive to ß-Turns in Proteins? Secondary Structure and Side-Chain Dependence.

ß-turns are essential for the structure and function of proteins. The spectroscopic technique Raman optical activity (ROA) has been suggested to be sensitive to such structural elements of proteins in solution. Three spectral features have been reported to mark ß-turns in protein ROA spectra: being a negative band at 1220 cm-1 , positive intensity around 1290 cm-1 and negative intensity around 1340-1380 cm-1 . In this work, density functional theory calculations demonstrated that these assignments are inaccurate as these spectral regions are not robust and sense the exact secondary structure surrounding the ß-turn as well. Furthermore, it was demonstrated that the amino acid side-chains affect the exact ROA patterns which can direct future research to perform a systematic analysis of the contributions of the side-chains.

Ramachandran mapping of peptide conformation using a large database of computed Raman and Raman optical activity spectra.

In the past few decades, Raman optical activity (ROA) spectroscopy has been shown to be very sensitive to the solution structure of peptides and proteins. A major and urgent challenge remains the need to make detailed assignments of experimental ROA patterns and relate those to the solution structure adopted by the protein. In the past few years, theoretical developments and implementations of ROA theory have made it possible to use quantum chemical methods to compute the ROA spectra of peptides. In this work, a large database of ROA spectra of peptide model structures describing the allowed backbone conformations of proteins was systematically calculated and used to make unprecedented detailed assignments of experimental ROA patterns to the conformational elements of the peptide in solution. By using a similarity index to compare an experimental spectrum to the database spectra (2902 theoretical spectra), the conformational preference of the peptide in solution can be assigned to a very specific region in the Ramachandran space. For six (poly)peptides this approach was validated and gives excellent agreement between experiment and theory. Additionally, hydrogen/deuterium exchanged structures and the conformational dependence of the amide modes in Raman spectra can be analysed using the new database. The excellent agreement between experiment and theory demonstrates the power of the newly developed database as a tool to study Raman and ROA patterns of peptides and proteins. The interpretation of experimental ROA patterns of different proteins published in the scientific literature is discussed based on the spectral trends observed in the database.

Base metal-catalyzed benzylic oxidation of (aryl)(heteroaryl)methanes with molecular oxygen.

The methylene group of various substituted 2- and 4-benzylpyridines, benzyldiazines and benzyl(iso)quinolines was successfully oxidized to the corresponding benzylic ketones using a copper or iron catalyst and molecular oxygen as the stoichiometric oxidant. Application of the protocol in API synthesis is exemplified by the alternative synthesis of a precursor to the antimalarial drug Mefloquine. The oxidation method can also be used to prepare metabolites of APIs which is illustrated for the natural product papaverine. ICP-MS analysis of the purified reaction products revealed that the base metal impurity was well below the regulatory limit.

Studying the glycan moiety of RNase B by means of Raman and Raman optical activity.

Raman and Raman optical activity (ROA) spectroscopy are used to study the solution-phase structure of the glycan moiety of the protein ribonuclease B (RNase B). Spectral data of the intact glycan moiety of RNase B is obtained by subtracting high-quality spectral data of RNase A, the non-glycosylated form of the RNase, from the spectra of the glycoprotein. The remaining difference spectra are compared to spectra generated from Raman and ROA data of the constituent disaccharides of the RNase glycan, achieving convincing spectral overlap. The results show that ROA spectroscopy is able to extract detailed spectral data of the glycan moieties of proteins, provided that the non-glycosylated isoform is available. Furthermore, good comparison between the full glycan spectrum and the regenerated spectra based on the disaccharide data lends great promise to ROA as a tool for the solution-phase structural analysis of this structurally elusive class of biomolecules.

Tidying up the conformational ensemble of a disordered peptide by computational prediction of spectroscopic fingerprints.

The most advanced structure prediction methods are powerless in exploring the conformational ensemble of disordered peptides and proteins and for this reason the "protein folding problem" remains unsolved. We present a novel methodology that enables the accurate prediction of spectroscopic fingerprints (circular dichroism, infrared, Raman, and Raman optical activity), and by this allows for "tidying up" the conformational ensembles of disordered peptides and disordered regions in proteins. This concept is elaborated for and applied to a dodecapeptide, whose spectroscopic fingerprint is measured and theoretically predicted by means of enhanced-sampling molecular dynamics coupled with quantum mechanical calculations. Following this approach, we demonstrate that peptides lacking a clear propensity for ordered secondary-structure motifs are not randomly, but only conditionally disordered. This means that their conformational landscape, or phase-space, can be well represented by a basis-set of conformers including about 10 to 100 structures. The implications of this finding have profound consequences both for the interpretation of experimental electronic and vibrational spectral features of peptides in solution and for the theoretical prediction of these features using accurate and computationally expensive techniques. The here-derived methods and conclusions are expected to fundamentally impact the rationalization of so-far elusive structure-spectra relationships for disordered peptides and proteins, towards improved and versatile structure prediction methods.

HPC+ in the medical field: Overview and current examples.

BACKGROUND: To say data is revolutionising the medical sector would be a vast understatement. The amount of medical data available today is unprecedented and has the potential to enable to date unseen forms of healthcare. To process this huge amount of data, an equally huge amount of computing power is required, which cannot be provided by regular desktop computers. These areas can be (and already are) supported by High-Performance-Computing (HPC), High-Performance Data Analytics (HPDA), and AI (together "HPC+"). OBJECTIVE: This overview article aims to show state-of-the-art examples of studies supported by the National Competence Centres (NCCs) in HPC+ within the EuroCC project, employing HPC, HPDA and AI for medical applications. METHOD: The included studies on different applications of HPC in the medical sector were sourced from the National Competence Centres in HPC and compiled into an overview article. Methods include the application of HPC+ for medical image processing, high-performance medical and pharmaceutical data analytics, an application for pediatric dosimetry, and a cloud-based HPC platform to support systemic pulmonary shunting procedures. RESULTS: This article showcases state-of-the-art applications and large-scale data analytics in the medical sector employing HPC+ within surgery, medical image processing in diagnostics, nutritional support of patients in hospitals, treating congenital heart diseases in children, and within basic research. CONCLUSION: HPC+ support scientific fields from research to industrial applications in the medical area, enabling researchers to run faster and more complex calculations, simulations and data analyses for the direct benefit of patients, doctors, clinicians and as an accelerator for medical research.

Metal ions shape α-synuclein.

α-Synuclein is an intrinsically disordered protein that can self-aggregate and plays a major role in Parkinson's disease (PD). Elevated levels of certain metal ions are found in protein aggregates in neurons of people suffering from PD, and environmental exposure has also been linked with neurodegeneration. Importantly, cellular interactions with metal ions, particularly Ca2+, have recently been reported as key for α-synuclein's physiological function at the pre-synapse. Here we study effects of metal ion interaction with α-synuclein at the molecular level, observing changes in the conformational behaviour of monomers, with a possible link to aggregation pathways and toxicity. Using native nano-electrospray ionisation ion mobility-mass spectrometry (nESI-IM-MS), we characterize the heterogeneous interactions of alkali, alkaline earth, transition and other metal ions and their global structural effects on α-synuclein. Different binding stoichiometries found upon titration with metal ions correlate with their specific binding affinity and capacity. Subtle conformational effects seen for singly charged metals differ profoundly from binding of multiply charged ions, often leading to overall compaction of the protein depending on the preferred binding sites. This study illustrates specific effects of metal coordination, and the associated electrostatic charge patterns, on the complex structural space of the intrinsically disordered protein α-synuclein.

Carbamate Synthesis Using a Shelf-Stable and Renewable C1 Reactant.

4-Propylcatechol carbonate is a shelf-stable, renewable C1 reactant. It is easily prepared from renewable 4-propylcatechol (derived from wood) and dimethyl carbonate (derived from CO2 ) using a reactive distillation system. In this work, the 4-propylcatechol carbonate is used for the two-step synthesis of carbamates under mild reaction conditions. In the first step, 4-propylcatechol carbonate is treated with an alcohol at 50-80 °C in the presence of a Lewis acid catalyst, such as Zn(OAc)2 ⋅2 H2 O. With liquid alcohols, no solvent is used and with solid alcohols 2-methyltetrahydrofuran is used as solvent. In the second step, the alkyl 2-hydroxy-propylphenyl carbonate intermediates obtained react with amines at room temperature in 2-methyltetrahydrofuran, forming the target carbamates and the byproduct 4-propylcatechol, which can be recycled into a carbonate reactant.

Conformational Disorder and Dynamics of Proteins Sensed by Raman Optical Activity.

Raman optical activity (ROA) spectra of proteins hold a lot of information about their structure in solution. To create a better understanding of the ROA spectra of, among others, the intrinsically disordered proteins (IDPs), involved in neurodegenerative diseases, the effect of conformational disorder and dynamics on the ROA spectra was studied. Density functional theory (DFT) calculations of small ensembles of model peptides with increasing disorder show that the ROA patterns of α-helical and polyproline II (PPII) structure reflect the average backbone angles in the ensemble. The amide III region in the ROA spectra of the α-helical peptides is shown to retain its typical -/+/+ pattern, while the amide III region of PPII secondary structure diminishes in intensity with increasing structural disorder. The results show that the ROA spectra of IDPs hence more likely stem from short stretches of well-defined PPII helices rather than a very flexible chain. Further DFT calculations support that mixing of PPII with helical secondary structure is consistent with experimental spectra of IDPs, while mixing with ß-strand results in spectral patterns that are not observed experimentally. The detailed information obtained from these results contributes to a better understanding of the spectrum-structure relation.

The effect of reactive oxygen and nitrogen species on the structure of cytoglobin: A potential tumor suppressor.

Many current anti-cancer therapies rely on increasing the intracellular reactive oxygen and nitrogen species (RONS) contents with the aim to induce irreparable damage, which subsequently results in tumor cell death. A novel tool in cancer therapy is the use of cold atmospheric plasma (CAP), which has been found to be very effective in the treatment of many different cancer cell types in vitro as well as in vivo, mainly through the vast generation of RONS. One of the key determinants of the cell's fate will be the interaction of RONS, generated by CAP, with important proteins, i.e. redox-regulatory proteins. One such protein is cytoglobin (CYGB), a recently discovered globin proposed to be involved in the protection of the cell against oxidative stress. In this study, the effect of plasma-produced RONS on CYGB was investigated through the treatment of CYGB with CAP for different treatment times. Spectroscopic analysis of CYGB showed that although chemical modifications occur, its secondary structure remains intact. Mass spectrometry experiments identified these modifications as oxidations of mainly sulfur-containing and aromatic amino acids. With longer treatment time, the treatment was also found to induce nitration of the heme. Furthermore, the two surface-exposed cysteine residues of CYGB were oxidized upon treatment, leading to the formation of intermolecular disulfide bridges, and potentially also intramolecular disulfide bridges. In addition, molecular dynamics and docking simulations confirmed, and further show, that the formation of an intramolecular disulfide bond, due to oxidative conditions, affects the CYGB 3D structure, thereby opening the access to the heme group, through gate functioning of His117. Altogether, the results obtained in this study (1) show that plasma-produced RONS can extensively oxidize proteins and (2) that the oxidation status of two redox-active cysteines lead to different conformations of CYGB.

Direct Measurements of the Crowding Effect in Proteins by Means of Raman Optical Activity.

The effect of crowding interactions on the structure of dephosphorylated α-casein was studied with Raman optical activity (ROA). It was found that ROA is sensitive to the structural changes in the protein, induced by the presence of crowding agents. This effect depends on the employed crowding agent and its concentration.

Mechanism of the CuII-catalyzed benzylic oxygenation of (aryl)(heteroaryl)methanes with oxygen.

A mechanistic study of the copper-catalyzed oxidation of the methylene group of aryl(di)azinylmethanes was performed. Initial reaction rates were measured making use of in situ IR reaction monitoring and a kinetic analysis of the reaction was executed. The reaction proved to be first order in oxygen concentration. For substrate and acid concentration, saturation kinetics due to O2 mass transfer limitation were observed. The occurrence of mass transfer limitation was further confirmed by examining the effect of the stirring rate on the initial reaction rate. Interestingly, the effect of the concentration of the catalyst on the rate shows that higher loadings result in a maximal initial rate, followed initially by a steady decrease and subsequently a rate plateau when the concentration is increased further. Mass transfer limitation and increased concentration of dinuclear catalytically active species rationalizes this hitherto unprecedented rate behavior. Continuous-wave and pulsed electron paramagnetic resonance methods were used to characterize the catalytic species present in the solution during the reaction and confirmed the presence of both mono- and dinuclear copper species. Analysis of a diverse substrate scope points towards imine-enamine tautomerization as a crucial process in the oxidation reaction. DFT calculations of these equilibrium constants (pKeq) provided us with a qualitative tool to predict whether or not a substrate is viable for oxidation under the reaction conditions developed.