X-ray crystallography of chemical compounds

Vibrational circular dichroism of plasmonic nanostructures embedding chiral drugs

We investigate the mid-infrared chiroptical response of plasmonic nanostructures based on Al-doped ZnO and layers of an aqueous solution of Ladarixin, a chiral pharmaceutical currently under clinical trial for the treatment of type 1 diabetes. We explore the possibilities offered by localised surface plasmon resonances (LSPRs) for the enhancement of vibrational circular dichroism (VCD) of the considered chiral drug solution. Focusing on diverse plasmonic nanoshell geometries, we find that LSPRs provide an amplification factor of VCD differential absorption cross-section ranging from [Formula: see text] to [Formula: see text] thanks to near-field intensity enhancement produced by LSPRs. Our results indicate that nanoshell LSPRs are promising for probing molecular chirality at the nanoscale.

Towards targeted cancer therapy: Synthesis, characterization, and biological activity of a new Cu(II)-ibuprofen-2,2'-dipyridylamine metal complex

This work reports the synthesis of a copper metal complex with the nonsteroidal anti-inflammatory drug (NSAID) ibuprofen, and 2,2'-dipyridylamine employing microwave-assisted synthesis (MWAS). To the best of authors knowledge, this is the first study reporting a NSAID-based complex achieved through MWAS. The coordination compound was characterised by elemental analysis, Fourier transform infrared spectroscopy, thermogravimetry, and ultraviolet-visible spectrophotometry. Additionally, the crystal structure of the copper metal complex was elucidated using single-crystal X-ray diffraction with synchrotron radiation. The compound's interaction with the biomolecules bovine serum albumin (BSA) and calf-thymus DNA (CT-DNA), was assessed through UV-Vis, circular dichroism, and fluorescence spectroscopy. Our findings demonstrate that the metal complex effectively binds to BSA, causing a reduction in its intrinsic fluorescence and α-helical content, and shows a capacity for intercalation between CT-DNA base pairs. Finally, the copper compound exhibited promising in vitro antitumoral activities against human breast cancer cell lines (MCF-7 and MDA-MB-231), as evaluated by MTT (3-[4,5-dimethylthiazol-2-yl]-2,5 diphenyl tetrazolium bromide) assay (although a similar cytotoxic effect against a non-tumoral epithelial cancer cell line, MCF-12A, was found), and increased oxidative stress levels as assessed by the TBARS (thiobarbituric acid reactive substances) assay and by evaluating glutathione levels. The results suggest that the metal complex promotes lipid peroxidation by increasing oxidative stress levels, leading to a reduction in viability of the two breast cancer cell lines.

Exploring the Significance, Extraction, and Characterization of Plant-Derived Secondary Metabolites in Complex Mixtures

Secondary metabolites are essential components for the survival of plants. Secondary metabolites in complex mixtures from plants have been adopted and documented by different traditional medicinal systems worldwide for the treatment of various human diseases. The extraction strategies are the key components for therapeutic development from natural sources. Polarity-dependent solvent-selective extraction, acidic and basic solution-based extraction, and microwave- and ultrasound-assisted extraction are some of the most important strategies for the extraction of natural products from plants. The method needs to be optimized to isolate a specific class of compounds. Therefore, to establish the mechanism of action, the characterization of the secondary metabolites, in a mixture or in their pure forms, is equally important. LC-MS, GC-MS, and extensive NMR spectroscopic strategies are established techniques for the profiling of metabolites in crude extracts. Various protocols for the extraction and characterization of a wide range of classes of compounds have been developed by various research groups and are described in this review. Additionally, the possible means of characterizing the compounds in the mixture and their uniqueness are also discussed. Hyphenated techniques are crucial for profiling because of their ability to analyze a vast range of compounds. In contrast, inherent chemical shifts make NMR an indispensable tool for structure elucidation in complex mixtures.

Host-guest system of a phosphorylated macrocycle assisting structure determination of oily molecules in single-crystal form

X-ray crystallography is the most reliable method for structure elucidation and absolute configuration determination of organic molecules based on their single-crystal forms. However, many analytes are hard to crystallize because of their low melting points (an oily state at room temperature) or conformational flexibility. Here, we report the crystallization of a macrocycle, CTX[P(O)Ph] (host), which is a cyclotrixylohydroquinoylene (CTX) derivative, with 26 oily organic molecules (guests), which is applied for the structural determination of the guest with X-ray crystallography. With the aid of the host, CTX[P(O)Ph], the guest molecules were well-ordered with full occupancy in crystal structures. In most cases, at least one guest structure without any disorder could be observed; solvent masking was not necessary for the single crystal X-ray structural analysis, and thus the structures of the guests could be successfully determined, and the absolute configuration could be assigned reliably for chiral guests with this method. The crystallization mechanism was further discussed from theoretical and experimental perspectives, suggesting that the negative electrostatic potential surface of CTX[P(O)Ph] and noncovalent interactions between the host and guest were crucial for the ordered arrangements of the guest.

Organotin (IV) Dithiocarbamate Compounds as Anticancer Agents: A Review of Syntheses and Cytotoxicity Studies

Organotin (IV) dithiocarbamate has recently received attention as a therapeutic agent among organotin (IV) compounds. The individual properties of the organotin (IV) and dithiocarbamate moieties in the hybrid complex form a synergy of action that stimulates increased biological activity. Organotin (IV) components have been shown to play a crucial role in cytotoxicity. The biological effects of organotin compounds are believed to be influenced by the number of Sn-C bonds and the number and nature of alkyl or aryl substituents within the organotin structure. Ligands target and react with molecules while preventing unwanted changes in the biomolecules. Organotin (IV) dithiocarbamate compounds have also been shown to have a broad range of cellular, biochemical, and molecular effects, with their toxicity largely determined by their structure. Continuing the investigation of the cytotoxicity of organotin (IV) dithiocarbamates, this mini-review delves into the appropriate method for synthesis and discusses the elemental and spectroscopic analyses and potential cytotoxic effects of these compounds from articles published since 2010.

Synthesis and application of methyl itaconate-anthracene adducts in configuration assignment of chiral secondary alcohols by 1H NMR

Novel chiral derivatising agents (CDAs) such as methyl itaconate-anthracene adducts (MIAs) were reported for the absolute configuration determination of chiral secondary alcohols by the ¹H NMR technique. These adducts were facilely prepared through well-known reactions, and furthermore, commercially available starting materials. According to these synthetic routes, the desired MIAs were afforded in 6 steps with 49% overall yield from dimethyl itaconate. Moreover, the represented MIAs provided significantly large differences of chemical shift values (Δδ^SR). No racemisation from the tertiary characteristics of the adjacent alpha carbon was observed.

Opportunities and Limitations for Assigning Relative Configurations of Antibacterial Bislactones using GIAO NMR Shift Calculations

Four new bislactones, dihydroacremonol (1), clonostachyone (2), acremodiol B (3), and acremodiol C (4), along with one known compound, hymeglusin (5), were isolated from cultures of two fungal strains (MSX59876 and MSX59260). Both strains were identified based on phylogenetic analysis of molecular data as Clonostachys spp.; yet, they biosynthesized a suite of related, but different, secondary metabolites. Given the challenges associated with elucidating the structures and configurations of bislactones, GIAO NMR calculations were tested as a complement to traditional NMR and HRESIMS experiments. Fortuitously, the enantiomer of the new natural product (4) was known as a synthetic compound, and the predicted configuration from GIAO NMR calculations (i.e., for the relative configuration) and optical rotation calculations (i.e., for the absolute configuration) matched those of the synthesis product. These results engendered confidence in using similar procedures, particularly the mixture of GIAO NMR shift calculations coupled with an orthogonal technique, to predict the configuration of 1-3; however, there were important limitations, which are discussed for each of these. The metabolites displayed antimicrobial activities, with compounds 1 and 4 being the most potent against Staphylococcus aureus with MICs of 1 and 4 μg/mL, respectively.

Feedback regulation of crystal growth by buffering monomer concentration

Crystallization is a ubiquitous means of self-assembly that can organize matter over length scales orders of magnitude larger than those of the monomer units. Yet crystallization is notoriously difficult to control because it is exquisitely sensitive to monomer concentration, which changes as monomers are depleted during growth. Living cells control crystallization using chemical reaction networks that offset depletion by synthesizing or activating monomers to regulate monomer concentration, stabilizing growth conditions even as depletion rates change, and thus reliably yielding desired products. Using DNA nanotubes as a model system, here we show that coupling a generic reversible bimolecular monomer buffering reaction to a crystallization process leads to reliable growth of large, uniformly sized crystals even when crystal growth rates change over time. Buffering could be applied broadly as a simple means to regulate and sustain batch crystallization and could facilitate the self-assembly of complex, hierarchical synthetic structures.

In Silico Design, Synthesis and Evaluation of Novel Series of Benzothiazole- Based Pyrazolidinediones as Potent Hypoglycemic Agents

Background:

The discovery of novel ligand binding domain (LBD) of peroxisome proliferator- activated receptor γ (PPARγ) has recently attracted attention to few research groups in order to develop more potent and safer antidiabetic agents.

Objective:

This study is focused on docking-based design and synthesis of novel compounds combining benzothiazole and pyrazolidinedione scaffold as potential antidiabetic agents.

Methods:

Several benzothiazole-pyrazolidinedione hybrids were synthesized and tested for their in vivo anti-hyperglycemic activity. Interactions profile of title compounds against PPARγ was examined through molecular modelling approach.

Results:

All tested compounds exhibited anti-hyperglycemic activity similar or superior to the reference drug Rosiglitazone. Introducing chlorine atom and alkyl group at position-6 and -5 respectively on benzothiazole core resulted in enhancing the anti-hyperglycemic effect. Docking study revealed that such groups demonstrated favorable hydrophobic interactions with novel LBD Ω- pocket of PPARγ protein.

Conclusion:

Among the tested compounds, N-(6-chloro-5-methylbenzo[d]thiazol-2-yl-4-(4((3,5- dioxopyrazolidin-4-ylidene)methyl)phenoxy)butanamide 5b was found to be the most potent compound and provided valuable insights to further develop novel hybrids as anti-hyperglycemic agents.

Supramolecular Chirality in Azobenzene-Containing Polymer System: Traditional Postpolymerization Self-Assembly Versus In Situ Supramolecular Self-Assembly Strategy

Recently, the design of novel supramolecular chiral materials has received a great deal of attention due to rapid developments in the fields of supramolecular chemistry and molecular self-assembly. Supramolecular chirality has been widely introduced to polymers containing photoresponsive azobenzene groups. On the one hand, supramolecular chiral structures of azobenzene-containing polymers (Azo-polymers) can be produced by nonsymmetric arrangement of Azo units through noncovalent interactions. On the other hand, the reversibility of the photoisomerization also allows for the control of the supramolecular organization of the Azo moieties within polymer structures. The construction of supramolecular chirality in Azo-polymeric self-assembled system is highly important for further developments in this field from both academic and practical points of view. The postpolymerization self-assembly strategy is one of the traditional strategies for mainly constructing supramolecular chirality in Azo-polymers. The in situ supramolecular self-assembly mediated by polymerization-induced self-assembly (PISA) is a facile one-pot approach for the construction of well-defined supramolecular chirality during polymerization process. In this review, we focus on a discussion of supramolecular chirality of Azo-polymer systems constructed by traditional postpolymerization self-assembly and PISA-mediated in situ supramolecular self-assembly. Furthermore, we will also summarize the basic concepts, seminal studies, recent trends, and perspectives in the constructions and applications of supramolecular chirality based on Azo-polymers with the hope to advance the development of supramolecular chirality in chemistry.

Synthesis, characterization, and computational study of a new heteroaryl chalcone

This work presents the synthesis of the chalcone (E)-3-(2,6-difluorophenyl)-1-(furan-2-yl)-prop-2-en-1-one molecule through the equimolar reaction between 1-(furan-2-yl)-ethenone and 2,6-difluorobenzaldehyde. The crystallographic characterization and the extensive theoretical study regarding electronic properties were obtained. The supramolecular arrangement was described by X-ray diffraction and Hirshfeld surfaces. Optimized geometrical structure was obtained by density functional theory, and the electronic study for differences between the solid and gas phases was carried out with M062-X at 6-311++G(2d,2p) basis set. Natural bond orbital, frontier molecular orbitals (HOMO-LUMO), and molecular electrostatic potential map were determined to elucidate the information related to the charge transfer in the molecule. The theoretical and experimental vibrational spectra were plotted, which included the IR intensities, the calculated and experimental vibrational frequencies, and the assigned vibrational modes for the main groups of DTP.

The relationship between Hirshfeld potential and cytotoxic activity: a study along a series of flavonoid and chromanone derivatives

The present study examines a series of six biologically-active flavonoid and chromanone derivatives by X-ray crystal structure analysis: (E)-3-benzylidene-2-phenylchroman-4-one, C₂₂H₁₆O₂, I, (E)-3-(4-methylbenzylidene)-2-phenylchroman-4-one, C₂₃H₁₈O₂, II, (E)-3-(3-methylbenzylidene)-2-phenylchroman-4-one, C₂₃H₁₈O₂, III, (E)-3-(4-methoxybenzylidene)-2-phenylchroman-4-one, C₂₃H₁₈O₃, IV, (E)-3-benzylidenechroman-4-one, C₁₆H₁₂O₂, V, and (E)-3-(4-methoxybenzylidene)chroman-4-one, C₁₇H₁₄O₃, VI. The cytotoxic activities of the presented crystal structures have been determined, together with their intermolecular interaction preferences and Hirshfeld surface characteristics. An inverse relationship was found between the contribution of C...C close contacts to the Hirshfeld surface and cytotoxic activity against the WM-115 cancer line. Dependence was also observed between the logP value and the percentage contribution of C...H contacts to the Hirshfeld surface.

Biologically active fungal depsidones: Chemistry, biosynthesis, structural characterization, and bioactivities

Fungi produce a wide range of structurally unique metabolites. Depsidones represent one of the most interesting classes of metabolites, consisting of two 2,4-dihydroxybenzoic acid rings linked together by both ether and ester bonds. Naturally occurring depsidones are produced by lichen, fungi, and plants. They possessed a wide array of bioactivities, including antioxidant, antiproliferative, antimalarial, cytotoxic, antibacterial, radical scavenging, antihypertensive, anti-inflammatory, antifungal, and aromatase and protein kinase inhibitory. In order to point out the potential of this class of compounds, the present review focuses only on the depsidones that have been isolated from fungal source and published from 1978 to 2018. This review outlined the research on the biosynthesis, source, isolation, spectral and physical data, and bioactivities of the naturally occurring fungal depsidones. On the basis of 88 references, > 80 compounds have been described.

Palladium(II)-Catalyzed Mono- and Bis-alkenylation of N-Acetyl-2-aminobiaryls through Regioselective C-H Bond Activation

We developed palladium-catalyzed oxidative coupling of olefins with N-acyl 2-aminobiaryls through a sequence of ortho C-H bond activation/alkene insertion/reductive elimination. Furthermore, we controlled the selectivity of mono- and bis-alkenylation products with the solvent effect. The developed protocol was promising for a broad substrate scope ranging from activated olefins with a wide variety of functional groups to unactivated olefins.

A publicly available crystallisation data set and its application in machine learning

A publicly available crystallisation database for clusters of highly similar compounds is used to build machine learning models.

Determination of absolute configuration using single crystal X-ray diffraction

Single crystal X-ray crystallography is the most powerful structural method for the determination of the 3D structures of molecules. While the results of a routine diffraction experiment readily provide unambiguous determination of the relative configuration of all stereogenic centers in the molecule, determination of absolute configuration is more challenging. This chapter provides some helpful tips towards increasing the chances of success in the determination of the absolute configuration of a chiral, enantiomerically pure natural product using X-ray crystallography.

Non-robotic high-throughput setup for manual assembly of nanolitre vapour-diffusion protein crystallization screens

Nanolitre-sized drops are characteristic of high-throughput protein crystallization screening. Traditionally, reliable nanolitre drop dispensing has required the use of robotics. This work describes the design and development of a protocol for the reproducible manual assembly of nanolitre-sized protein vapour-diffusion crystallization trials in a 96/192-drop format. The protocol exploits the repetitive-pipetting mode of handheld motorized pipettes together with simple tools available in standard laboratories. The method saves precious protein material without sacrificing the effectiveness of the screening process. To verify the approach, two monoclonal antibody Fab fragments were crystallized alone and in a complex with tau peptide antigens in 0.2–0.5 µl drops. Crystals grown directly from the screen conditions in sitting drops on 96-well plates diffracted up to 1.6 Å resolution on a synchrotron source. The results proved that successful crystallization in nanolitre high-throughput format is affordable even in the absence of expensive robotic instrumentation.