Natural Organic Molecules Research Articles

Chemisorption of polysulfides by keto groups modified Li4Ti5O12 nanofibers with 3D interwove network structure for LSBs

Lithium-sulfur batteries (LSBs) possess high energy density but suffer from severe capacity fading due to the dissolution of lithium polysulfide (LiPSs). Novel design and mechanisms to encapsulate LiPSs are greatly desired by high-performance LSBs towards practical applications. Herein, we report a strategy of preparing Lithium titanate (Li4Ti5O12, LTO) nanofibers using bacterial cellulose as excellent biomimetic mineralization template at room temperature. Natural abundant organic molecule of Anthraquinone (AQ) combine with the zero strain fast ionic conductor of LTO can inhibit the dissolution and diffusion of LiPSs through redox reactions during cycling. The keto groups (C = O) of AQ play a critical role in forming strong Lewis acid-based chemical bonding. The 3D interwove network structure of LTO nanofibers also hinders the shuttle effect of LiPSs. Polydopamine (PDA) coated on the outermost layer not only improves the conductivity of the whole electrode, but also enhances the wettability of the electrolyte. The long-term stability of S-based electrode is ensured by the synergistic effect of the three. This mechanism leads to a long cycling stability of S-based electrodes. With a high sulfur content of ∼ 70%, a low capacity decay of 0.042%, 0.063% and 0.061% per cycle for 500 cycles at the current densities of 1, 2 and 4C, respectively. The water-soluble binder was adopted, which was a solid step for the practical application of LSBs. This finding and understanding paves an alternative avenue for the future design of S-based cathodes toward the practical application of LSBs.

Interactions between model organic compounds and metal oxides

Because of their mechanical, thermal, and chemical resistance, ceramic materials are suitable for challenging water treatments, where different metal oxides (MeO) have been tested as active layers. However, organic fouling is a major drawback impacting its performance. Organics adsorb onto the membrane surface and into their pores during long-term operation, resulting in irreversible fouling. This investigation focussed on the interfacial interactions between model organic acids and MeO to obtain a fundamental understanding of the adsorption phenomena. Batch adsorption experiments of a series of small molecular weight, oxygenated, aromatic organic acids were performed with Al2O3, TiO2, and ZrO2 particles, at pH 4.2 and 7.6. The adsorption of simple acids was described by the Langmuir model and exhibited a strong dependence on the relative abundance of carboxyl groups, aliphaticity/aromaticity, alkyl chain length, and presence of hydroxyl groups. The adsorption of model compounds was higher at low pH and decreased with increasing pH. The difference in Al2O3, TiO2, and ZrO2 surface characteristics, as evidenced by TEM, XRD, and BET, led to differences in the adsorption density. The results obtained with these well-defined organic structures will assist in better understanding the interfacial interactions between complex natural organic matter molecules and MeO of different characteristics.

Surface Modulation of Iron-doped MoS2 Nanosheets by Phytic Acid for Enhanced Water Oxidation.

Surface modulation and heteroatom doping are important approaches for boosting the electrocatalytic performances of MoS2 nanosheets. As a molecular electrocatalyst, the natural organic phytic acid (PA) offer attractive intermediate for oxygen evolution reaction (OER). Here, a surface modulation strategy is demonstrated through the decoration of PA onto the basal plane of iron (Fe)-doped MoS2 nanosheets supported on nickel foam (NF) for boosted OER activity. Experimental results indicate that the PA modification and Fe doping could effectively boost the charge transfer and mass transport during the OER process. Specially, PA2-Fe-MoS2 grown on NF (PA2-Fe-MoS2 /NF) exhibits excellent OER activity (218 mV@20 mA cm-2 ) and durability, even superior to RuO2 and many other previously reported OER catalysts. This natural organic molecule modification provides a facile strategy to designing low-cost and efficient electrocatalytic materials.

Pd-Catalyzed C(sp2)-H olefination: synthesis of N-alkylated isoindolinone scaffolds from aryl amides of amino acid esters.

Isoindolinone is a constituent of various natural products and synthetic biologically active compounds. The classical multi-step synthetic methods used to prepare various indolinone derivatives are tedious and challenging. One-pot synthetic methods are attractive and economical. Transition-metal-catalyzed C-H activation is an emerging tool for synthesizing natural products and small organic molecules via reducing the number of synthetic steps necessary. This paper describes the synthesis of N-alkyl-3-methenyl chiral isoindolinone derivatives from aryl amides of L-amino acids and non-activated alkene via Pd-catalyzed C(sp2)-H olefination. Herein, the amino acid residue acts as a directing group for olefination at the aryl ring, and then cyclization occurs at the amide NH. Hence, this methodology could be helpful to transform standard amino acids into respective chiral isoindolinone derivatives.

Online Counter Gradient LC-FT-ICR-MS Enables Detection of Highly Polar Natural Organic Matter Fractions.

Natural organic matter (NOM) is a highly complex mixture of natural organic molecules. The recent developments in NOM molecular characterization methods have shown that ESI-FT-ICR hyphenated with liquid chromatography (LC) is a promising approach to also obtain chemical information (such as polarity and molecular size) about NOM molecules. However, due to changing solvent composition during gradient elution in LC-FT-ICR-MS, ionization conditions also change throughout the chromatographic separation process. In this study, we applied a post-LC column counter gradient (CG) to ensure stable solvent conditions for transient ESI-MS signals. Suwanee River Fulvic Acid (SRFA) standard and a peat pore water were used as representative dissolved NOM samples for method development and validation. Our results show that in polar NOM fractions (which elute with <50% methanol) the TIC intensity and number of assigned molecular formulas were increased by 48% and 20%, as compared to the standard gradient (SG) method. Further application of a Q-isolation and selective ion accumulation for low abundance fractions revealed over 3 times more molecular formulas (especially for CHNO, CHOS, CHNOS formula classes) than in full scan mode. The number of detected highly polar NOM compounds (with elemental ratios H/C < 1, O/C > 0.6) were more than 20 times larger for CG-LC mode as compared to direct infusion (DI) (5715 vs 266 MF). We conclude that the application of a postcolumn counter gradient in LC-FT-ICR-MS analyses of NOM offers novel insight into the most polar fractions of NOM which are inaccessible in conventional DI measurements.

Abundant Natural Dye-Based Organic Molecule As Sole Redox Active Material for Symmetric Aqueous Redox Flow Battery

Organic redox flow batteries (ORFBs) are considered potential substitutes to their traditional metal-based counterparts for application as large scale energy storage device[1] . This is in consideration to the merits offered by organic redox active materials i.e. inexpensive, environment friendly, high solubility and existence in diverse molecular structures that facilitates synthetic tunability to design molecules with the desired physicochemical properties[2] . However, capacity fade as result of cross-contamination has been one of the main challenges hindering development of this energy storage technology[3] . Symmetric redox flow batteries that employs a single redox active material in both electrolytes have the potential to address this challenge making them very attractive[4] .In this work, a low-cost organic dye is coupled with a radical organic molecule to form a sole bifunctional redox active material that can be used as both negoyte (-0.71V) and posolyte (0.52V versus Hg/Hg2SO4) in an organic symmetric aqueous redox flow battery. Cyclic voltammetry studies of the combined bifunctional molecule reveal reversible redox reactions of the redox couples leading to a theoretical cell voltage of 1.23V. A symmetric pumped cell testing demonstrated over 100 consecutive charge/discharge cycles with nearly 85% coulombic efficiency at current density of 2.5 mAcm-2. The battery utilizes a pH neutral supporting electrolyte (NaCl in water) which is inexpensive, non-corrosive and non-flammable resulting to a low-cost, durable, safe and environmental-friendly redox flow battery.

Azaindole therapeutic agents

Azaindole structural framework is an integral part of several biologically active natural and synthetic organic molecules; and several FDA approved drugs for various diseases. In the last decade, quite a number of literature reports appeared describing the pharmacology, biological activity and therapeutic applications of a variety of azaindole molecules. This prompted the organic and medicinal chemistry community to develop novel synthetic methods for various azaindoles and test them for a bioactivity against a variety of biological targets. Herein, we have summarized the biological activity of therapeutically advanced clinical candidates and several preclinical candidate drugs that contain azaindole structural moiety.

Computational and Biological Investigations on Abl1 Tyrosine Kinase: A Review.

Abl1 tyrosine kinase is a validated target for the treatment of chronic myeloid leukemia. It is a form of cancer that is difficult to treat and much research is being done to identify new molecular entities and to tackle drug resistance issues. In recent years, drug resistance of Abl1 tyrosine kinase has become a major healthcare concern. Second and third-generation TKI reported better responses against the resistant forms; still they had no impact on long-term survival prolongation. New compounds derived from natural products and organic small molecule inhibitors can lay the foundation for better clinical therapies in the future. Computational methods, experimental and biological studies can help us understand the mechanism of drug resistance and identify novel molecule inhibitors. ADMET parameters analysis of reported drugs and novel small molecule inhibitors can also provide valuable insights. In this review, available therapies, point mutations, structure-activity relationship and ADMET parameters of reported series of Abl1 tyrosine kinase inhibitors and drugs are summarised. We summarise in detail recent computational and molecular biology studies that focus on designing drug molecules, investigation of natural product compounds and organic new chemical entities. Current ongoing research suggests that selective targeting of Abl1 tyrosine kinase at the molecular level to combat drug resistance in chronic myeloid leukemia is promising.

Deuterium Residual Quadrupolar Couplings: Crossing the Current Frontiers in the Relative Configuration Analysis of Natural Products.

The determination of the 3D structure (configuration and preferred conformation) of complex natural and synthetic organic molecules is a long-standing but still challenging task for chemists, with various implications in pharmaceutical sciences whether or not these substances have specific bioactivities. Nuclear magnetic resonance (NMR) in aligning media, either lyotropic liquid crystals (LLCs) or polymer gels, in combination with molecular modeling is a unique framework for solving complex structural problems whose analytical wealth lies in the establishment of nonlocal structural correlations. As an alternative to the already well-established anisotropic NMR parameters, such as RDCs (residual dipolar couplings) and RCSAs (residual chemical shift anisotropies), it is shown here that deuterium residual quadrupolar couplings (2H-RQCs) can be extracted from 2H 2D-NMR spectra recorded at the natural abundance level in samples oriented in a homopolypeptide LLCs (poly-γ-benzyl-l-glutamate (PBLG)). These 2H-RQCs were successfully used to address nontrivial structural problems in organic molecules. The performance and scope of this new tool is examined for two natural chiral compounds of pharmaceutical interest (strychnine and artemisinin). This is the first report in which the 3D structure/relative configuration of complex bioactive molecules is unambiguously determined using only 2H-RQCs, which, in this case, are at 2H natural abundance.

Well-defined poly(ethylene glycol) polymers as non-conventional reactive tracers of colloidal transport in porous media

HypothesisA prominent fraction of mobile organic matter in natural aqueous soil solutions is formed by molecules in sizes that seamlessly exceed the lower end of what is defined as a colloid. The hydrodynamics and the functional diversity of these molecules result in a transport behavior that is fundamentally different from smaller compounds. However, there is a lack of “reactive tracers” that allow for the study of colloidal transport phenomena appropriately. We hypothesize that tailor-made and well-defined synthetic polymers can overcome this limitation. ExperimentsWe prepared and characterized the hydrodynamic properties of water-soluble poly(ethylene glycol)s (PEG) and studied their adsorption to mixtures of quartz, illite, and goethite in batch and column experiments. FindingsWe used this information to independently predict the transport of PEG with striking agreement to the observed mean breakthrough times in all porous media. As PEG transport can be comprehensively and quantitatively reconstructed, we conclude that functionalized PEGs are promising candidates to be used as tailorable and non-toxic tracers available in the size range of natural organic (macro-)molecules.

Chemistry and Bioactivities of Secondary Metabolites from the Genus Talaromyces.

Fungi have especially captured the interest and fascination of natural product chemists in that they produce a dizzying array of natural organic molecules with many unique functional groups and atom arrangements. In this review, we focus on the genus Talaromyces (Trichocomaceae) which has been a hot spot of natural product studies over the last three decades. This review summarized the discovery, structures, and bioactivities of various classes of 151 compounds isolated from both terrestrial and marine derived fungal strains of the genus Talaromyces reported from 1994 to 2019.

Synthesis of Alfaprostol Key Intermediate Ynol via Br/Mg Exchange

Prostaglandins (PGs) are natural organic molecules that effect a wide range of biological processes, which is why they are often used in clinical and veterinary practice.1–3 The most well-known syn...

An Effective and Environmentally Friendly Synthesis of 1,3-Keto-alcohols

The 1,3-hydroxycarbonyl group is an essential synthon for natural products and bioactive organic molecules. In order to obtain this structure, a number of reaction methods have been developed and, ...

Thiols in Natural Organic Matter: Molecular Forms, Acidity, and Reactivity with Mercury(II) from First-Principles Calculations and High Energy-Resolution X-ray Absorption Near-Edge Structure Spectroscopy

Thiol functional groups in natural organic matter form strong complexes with Hg(II) and other soft metal cations and therefore are an important component of sulfur and metal cycling in the environment. However, characterizing thiol reactivity is difficult because natural organic molecules are complex both in composition and molecular structure. Here, reactivity was assessed by calculating the Gibbs free energies of thiolation and thiol deprotonation reactions for model structures considered to form during abiotic sulfurization of natural organic matter. Gaussian calculations were performed at the CCSD(T) level of theory. Thiol addition is predicted to be faster by as much as 8 orders of magnitude on unsaturated cyclic structures rich in ketone and ether linkages than on open-chain carbonyl structures. The pKa values of thiols added to carboxyl-rich alicyclic molecules are predicted to be above 10, whereas pKa values of thiols bonded to lignin-derived polyhydroxyphenols are predicted to be between 2 and 6....

Recent Advances and Sensing Applications of Carbon Dots

AbstractCarbon dots (C dots) with biocompatibility, brightness, stability against photoirradiation and salt, and ease in preparation have become important materials for sensing and imaging. They can be prepared from natural materials and small organic molecules through hydrothermal, microwave‐assistant, and electrochemical methods, with advantages of simplicity and low cost. To enhance the quantum yields of C dots in the red and near‐infrared regions, doping of C dots with heteroatoms such as nitrogen and sulfur has been suggested. C dots both with and without being functionalized recognition elements such as antibodies and aptamers are selective and sensitive for sensing of analytes, including metal ions (e.g., Fe3+, Hg2+, Cu2+), small molecules (e.g., H2O2, cysteine, glutathione), and biopolymers like proteins, as well as for in vitro and in vivo imaging. Depending on the size, charge, and surface ligands of C dots used to label cells, fluorescence images of different organelles are shown. Multicolor images of bacteria, mammalian cells, and plant tissues incubated with C dots are realized when excited at different wavelengths. In this review, many excellent sensing and imaging examples of C dots are presented to highlight their features and to show their challenges for analytical applications.

A Strong Link Between Organic Chemistry and Chemical Crystallography Started a Century Ago

The article sheds light on some historical crossings of organic chemistry and chemical crystallography. It connects past and present bringing into the focus Prof. Kata Mlinarić-Majerski’s research. An impact of structural chemistry on organic synthesis and reactivity is shown. X-ray structure analysis was established as a unique method to determine the composition and architecture of synthetic and natural organic molecules, already in the second decade of the last century; some of historical and scientific milestones are shown. Numerous controversies were solved, when intriguing molecular structures had been determined and the nature of chemical bond was clarified. An absolute structure (chirality) determination using an anomalous dispersion of X-rays was an important step forward, particularly in pharmaceutical industry. Structural data provided by X-ray crystallography, stored by Cambridge Structural Data Centre have been of great impact on many areas of science. They are closely related to intra- and intermolecular forces and structure/function correlations directing us to synthesis of compounds with designed properties. The developments of supramolecular chemistry, crystal engineering, materials science, and most of all of molecular machines have been assisted by chemical crystallography. The essay does not aim to review the complete scientific opus of Prof. K. Mlinarić-Majerski but it is focused on some of the highlights of her research. The interdisciplinary approach in her research is related to the use of X-ray structural analysis to define molecular architecture, conformational chirality, conformational isomerism, and get insight into reaction paths, interactions governing molecular assembling, and to recognise chemical properties of new compounds. In these researches the X-ray crystallographers were involved.

Osmolyte-Induced Folding and Stability of Proteins: Concepts and Characterization.

It is well-known that the typical protein’s three-dimensional structure is relatively unstable in harsh conditions. A practical approach to maintain the folded state and thus improve the stability and activity of proteins in unusual circumstances is to directly apply stabilizing substances such as osmolytes to the protein-containing solutions. Osmolytes as natural occurring organic molecules typically called “compatible” solutes, based on the concept that they do not perturb cellular components. However, urea and guanidine hydrochloride (GuHCl) as denaturing osmolytes destabilize many macromolecular structures and inhibit functions. Several studies have been so far performed to explain the actual interaction of an osmolyte with a protein. The present review is aimed to achieve a collective knowledge of the progress arise in the field of osmolyte-protein interactions. The following is also an overview of the main techniques to measure protein stability in the presence of osmolytes.

Gallic Acid-Promoted SET Process for Cyclobutanone Oximes Activation and (Carbonylative-)Alkylation of Olefins

Despite the general success of metal catalysts in modern organic chemistry, the exploration of natural available organic molecules as catalysts still has a strong appeal to scientists because of their green and sustainable advantages. Herein an intermolecular coupling reaction of cyclobutanone oximes with olefins promoted by biowaste gallic acid is reported. Both alkylation and carbonylative alkylation reactions proceeded well in this system. Various cyclobutanone oximes and olefins can be transformed into the corresponding products in moderate to good yields. Detailed EPR investigations and control experiments are consistent with a single-electron transfer mechanism.

Advances in Spirocyclic Hybrids: Chemistry and Medicinal Actions.

The present review deals with the progress in medicinal chemistry of spirocyclic compounds, a wider class of natural and synthetic organic molecules, defined as a hybrid of two molecular entities covalently linked via a unique tetrahedral carbon. This spiro central carbon confers to the molecules a tridimensional structurally oriented framework, which is found in many medicinally relevant compounds, a well-known example is the antihypertensive spironolactone. Various bioactive natural products possess the privileged spiro linkage and different chemo-types thereof become synthetically accessible since the 20th century. Actually, there has been a growing interest in the synthesis of heterocyclic hybrids gathered via a spiro carbon. Most of these combinations are two moieties in one scaffold being able to interfere with biological systems through sequential mechanisms. Spirocyclic hybrids containing indole or oxindole units are compounds exhibiting higher interaction with biological receptors by protein inhibition or enzymatic pathways and their recognition as promising anticancer agents in targeted chemotherapy is foreseen. These specific, low-weight and noncomplex spirocyclic hybrids are potent inhibitors of SIRT1, Mdm2-p53 and PLK4, showing affinity for anaplastic lymphoma kinase (ALK) receptor. They are also known as excellent DNA binders, acting on cellular division by arresting the cell cycle at different phases and inducing apoptotic cell death. A structural diversity of spirocyclic hybrids has proved neuroprotective effects, anti-HIV, antiviral and antibacterial activities. Hundred of papers are mentioned in this review underlying chemical issues and pharmacological potencies of spiro compounds, which render them impressive synthetic hits for innovative drug conception.

Computational Tools for Calculating log β Values of Geochemically Relevant Uranium Organometallic Complexes.

Uranium (UVI) interacts with organic ligands, subsequently controlling its aqueous chemistry. It is therefore imperative to assess the binding ability of natural organic molecules. We evidence that density functional theory (DFT) can be used as a practical protocol for predicting the stability of UVI organic ligand complexes, allowing for the development of a relative stability series for organic complexes with limited experimental data. Solvation methods and DFT settings were benchmarked to suggest a suitable off-the-shelf solution. The results indicate that the IEFPCM solvation method should be employed. A mixed solvation approach improves the accuracy of the calculated stability constant (log β); however, the calculated log β are approximately five times more favorable than experimental data. Different basis sets, functionals, and effective core potentials were tested to check that there were no major changes in molecular geometries and Δr G. The recommended method employed is the B3LYP functional, aug-cc-pVDZ basis set for ligands, MDF60 ECP and basis set for UVI, and the IEFPCM solvation model. Using the fitting approach employed in the literature with these updated DFT settings allows fitting of 1:1 UVI complexes with root-mean-square deviation of 1.38 log β units. Fitting multiple bound carboxylate ligands indicates a second, separate fitting for 1:2 and 1:3 complexes.