Complex Formation Research Articles

Seeing red: Light and temperature-dependent complex formation reveal new insights into phytochrome activity

Seeing red: Light and temperature-dependent complex formation reveal new insights into phytochrome activity

Complex Formation of Gold Nanoparticles with Collagen in Aqueous Media Studied by X-ray Scattering and Absorption Spectroscopy

Complex Formation of Gold Nanoparticles with Collagen in Aqueous Media Studied by X-ray Scattering and Absorption Spectroscopy

Exploring the Recognition Mechanism of Surfactant–Cyclodextrin Complex Formation: Insights from SPR Studies on Temperature and Ionic Liquid Influence

Exploring the Recognition Mechanism of Surfactant–Cyclodextrin Complex Formation: Insights from SPR Studies on Temperature and Ionic Liquid Influence

Detecting the dimensionality of genuine multiparticle entanglement

Complex forms of quantum entanglement can arise in two qualitatively different ways: either between many qubits or between two particles with higher-than-qubit dimension. While both the many-qubit frontier and the high-dimension frontier are well established, state-of-the-art quantum technology is becoming increasingly able to create and manipulate entangled states that simultaneously feature many particles and high dimension. Here, we investigate generic states that can be considered both genuinely high-dimensional and genuine multiparticle entangled. We consider a natural quantity that characterizes this key property. To detect it, we develop three different classes of criteria. These enable us both to probe the ultimate noise tolerance of this form of entanglement and to make detection schemes using sparse or even minimal measurement resources. The approach provides a simple way of benchmarking entanglement dimensionality in the multiparticle regime and general, platform-independent, detection methods that readily apply to experimental use.

Residue-Specific Epitope Mapping of the PD-1/Nivolumab Interaction Using X-ray Footprinting Mass Spectrometry

X-ray footprinting coupled with mass spectrometry (XFMS) presents a novel approach in structural biology, offering insights into protein conformation and dynamics in the solution state. The interaction of the cancer-immunotherapy monoclonal antibody nivolumab with its antigen target PD-1 was used to showcase the utility of XFMS against the previously published crystal structure of the complex. Changes in side-chain solvent accessibility, as determined by the oxidative footprint of free PD-1 versus PD-1 bound to nivolumab, agree with the binding interface side-chain interactions reported from the crystal structure of the complex. The N-linked glycosylation sites of PD-1 were confirmed through an LC-MS/MS-based deglycosylation analysis of asparagine deamidation. In addition, subtle changes in side-chain solvent accessibility were observed in the C′D loop region of PD-1 upon complex formation with nivolumab.

Advances of the Holographic Technique to Test the Basic Properties of the Thin-Film Organics: Refractivity Change and Novel Mechanism of the Nonlinear Attenuation Prediction

A large number of the thin-film organic structures (polyimides, 2-cyclooctylarnino-5-nitropyridine, N-(4-nitrophenyl)-(L)-prolinol, 2-(n-Prolinol)-5-nitropyridine) sensitized with the different types of the nano-objects (fullerenes, carbon nanotubes, quantum dots, shungites, reduced graphene oxides) are presented, which are studied using the holographic technique under the Raman–Nath diffraction conditions. Pulsed laser irradiation testing of these materials predicts a dramatic increase of the laser-induced refractive index, which is in several orders of the magnitude greater compared to pure materials. The estimated nonlinear refraction coefficients and the cubic nonlinearities for the materials studied are close to or larger than those known for volumetric inorganic crystals. The role of the intermolecular charge transfer complex formation is considered as the essential in the refractivity increase in nano-objects-doped organics. As a new idea, the shift of charge from the intramolecular donor fragment to the intermolecular acceptors can be proposed as the development of Janus particles. The energy losses via diffraction are considered as an additional mechanism to explain the nonlinear attenuation of the laser beam.

1H, 13C, 15N NMR, and DFT Studies on Complex Formation of Zinc(II) Ion with Ethylenediamine in Ionic Liquid [C2mIm][TFSA

¹H, ¹³C, ¹⁵N NMR, and DFT Studies on Complex Formation of Zinc(II) Ion with Ethylenediamine in Ionic Liquid [C₂mIm][TFSA

Microstructural evolution and formation of defect complexes in diamond films by nitrogen-containing plasma

Abstract The morphology and crystalline quality of polycrystalline diamond samples were studied by systematically varying the flowrate of nitrogen gas in the microwave plasma. A slight improvement in both crystallite size and crystalline quality is observed for a low concentration of 0.5 sccm nitrogen. With a further increase in nitrogen concentration, diamond switches from micro-crystalline (MCD) to nanocrystalline (NCD) with a nitrogen flow of 2.5 sccm (10% of methane concentration). The surface roughness of the sample is found to depend strongly on the crystallite size of the sample. Extensive spectroscopic studies have been done to understand the presence and formation of different defect complexes in diamond. The presence of nitrogen-containing defect complexes has been studied thoroughly and their concentration has been found to be limited by the solubility limit rather than the availability of reactants in the gas environment. In contrast, the effect these complexes have on the strain of the diamond film is found to be negligible. Optical emission spectroscopy (OES) of the plasma reveals the presence of C2 dimers as well as C-N radicals. However, they have little role in modifying diamond grain morphology or crystalline quality.

Photoinduced Electron Donor Acceptor Complex-Enabled α-C(sp3)-H Alkenylation of Amines.

Allylic amines are prevalent and vital structural components present in many bioactive compounds and natural products. Additionally, they serve as valuable intermediates and building blocks, with wide-ranging applications in organic synthesis. However, direct α-C(sp3)-H alkenylation of feedstock amines, particularly for the preparation of α-alkenylated cyclic amines, has posed a longstanding challenge. Herein, we present a general, mild, operationally simple, and transition-metal-free α-alkenylation of various readily available amines with alkenylborate esters in excellent E/Z - and diastereoselectivities. This method features good compatibility with water and oxygen, broad substrate scope, and excellent functional group tolerance, thereby enabling the late-stage modification of various complex molecules. Mechanistic studies suggest that the formation of a photoactive electron donor-acceptor complex between 2-iodobenzamide and the tetraalkoxyborate anion, which subsequently undergoes photoinduced single electron transfer and intramolecular 1,5-hydrogen atom transfer to generate the crucial α-amino radicals, is the key to success of this chemistry.

Design Optimization of a Novel Catalytic Approach for Transglucosylated Isomaltooligosaccharides into Dietary Polyols Structures by Leuconostoc mesenteroides Dextransucrase.

Polyols, or sugar alcohols, are widely used in the industry as sweeteners and food formulation ingredients, aiming to combat the incidence of diet-related Non-Communicable Diseases. Given the attractive use of Generally Regarded As Safe (GRAS) enzymes in both academia and industry, this study reports on an optimized process to achieve polyols transglucosylation using a dextransucrase enzyme derived from Leuconostoc mesenteroides. These enzyme modifications could lead to the creation of a new generation of glucosylated polyols with isomalto-oligosaccharides (IMOS) structures, potentially offering added functionalities such as prebiotic effects. These reactions were guided by a design of experiment framework, aimed at maximizing the yields of potential new sweeteners. Under the optimized conditions, dextransucrase first cleared the glycosidic bond of sucrose, releasing fructose with the formation of an enzyme-glucosyl covalent intermediate complex. Then, the acceptor substrate (i.e., polyols) is bound to the enzyme-glucosyl intermediate, resulting in the transfer of glucosyl unit to the tested polyols. Structural insights into the reaction products were obtained through nuclear maneic resonance (NMR) and matrix-assisted laser desorption/ionization time-of-flight (MALDI-TOF) analyses, which revealed the presence of linear α(1 → 6) glycosidic linkages attached to the polyols, yielding oligosaccharide structures containing from 4 to 10 glucose residues. These new polyols-based oligosaccharides hold promise as innovative prebiotic sweeteners, potentially offering valuable health benefits.

A DFT Mechanistic Study on the Aza-Aldol Reaction of Boron Aza-Enolates: Relative Stability of Six-Membered Transition State and Its Relevance to the Coordination Mode of the Leaving Group.

The mechanism of the aza-aldol reaction between boron aza-enolate and benzaldehyde is investigated by using density functional theory calculations. The result shows that the syn-E isomer is preferentially formed, consistent with experimental observations. The six-membered ring transition state (TS) with the boat form leads to the E isomer, while the more unstable chair TS does to the Z isomer. The preference of the syn isomer is determined by the interactions between the substituents of aza-enolate and benzaldehyde. Structural distortion and intrinsic reaction coordinate analyses of simplified model systems provide insights into the origin of the relative stability of the rate-determining TS with boat and chair forms. The boat TS is an early TS; thus, minimal structural distortions of the reactant are required to reach this TS. The Lewis pair interactions between the boron and imine groups during B-N elimination also influenced the relative stability of the TSs. This interaction involves the nitrogen lone pair in the boat TS, while the π(N═C) orbital is involved in the chair TS. The Lewis pair with the lone pair stabilizes the TS more than that with the π orbital. The boron aza-enolate with 9-BBN generates an ate complex and forms C-C bonds sequentially, whereas that with Bpin does not generate an ate complex and exhibits the concerted formation of B-O and C-C bonds. Thus, the higher electrophilicity of boron such as 9-BBN enhances the reactivity by facilitating the formation of the ate complex. A reaction design is proposed to reverse the syn/anti selectivity. Proof-of-concept DFT calculations suggested that the modification of the imine group would change the relative stability of the boat/chair TSs and give the anti-product.

Structural basis of human 20S proteasome biogenesis

New proteasomes are produced to accommodate increases in cellular catabolic demand and prevent the accumulation of cytotoxic proteins. Formation of the proteasomal 20S core complex relies on the function of the five chaperones PAC1-4 and POMP. Here, to understand how these chaperones facilitate proteasome assembly, we tagged the endogenous chaperones using CRISPR/Cas gene editing and examined the chaperone-bound complexes by cryo-EM. We observe an early α-ring intermediate subcomplex that is stabilized by PAC1-4, which transitions to β-ring assembly upon dissociation of PAC3/PAC4 and rearrangement of the PAC1 N-terminal tail. Completion of the β-ring and dimerization of half-proteasomes repositions critical lysine K33 to trigger cleavage of the β pro-peptides, leading to the concerted dissociation of POMP and PAC1/PAC2 to yield mature 20S proteasomes. This study reveals structural insights into critical points along the assembly pathway of the human proteasome and provides a molecular blueprint for 20S biogenesis.

Interactions of White Mugwort (Artemisia lactiflora Wall.) Extract with Food Ingredients during In Vitro Gastrointestinal Digestion and Their Impact on Bioaccessibility of Polyphenols in Various Model Systems

The bioaccessibility of phytochemicals is an important factor for new functional food design. The interaction of white mugwort extract (FE) and food ingredients (coconut oil, egg white albumen, brown rice powder, inulin, and mixtures thereof) was determined after in vitro digestion to inform the development of a functional soup for an aging population. Coconut oil exerted a protective effect on polyphenols, showing the highest bioaccessibility (62.9%) and antioxidant activity after intestinal digestion (DPPH 12.38 mg GAE/g DW, FRAP 0.88 mol Fe(ll)/g DW). In contrast, egg white albumen had the most significant negative effect on the polyphenol stability, resulting in the lowest bioaccessibility (12.49%). Moreover, FE promoted the emulsion stability and delayed starch digestion by inhibiting amylase activity via non-specific polyphenol–protein interactions, resulting in a decrease in the total reducing sugars (TRS) released during digestion. It also limited the protein digestion, probably due to the complex formation of polyphenols and proteins, consequently reducing the bioaccessibility of both amino acids and polyphenols. These findings provide useful information for designing functional food products that could promote the bioaccessibility and bioactivity of natural extracts.

Computational study of the supramolecular complexation of azocompounds with cucurbit[7]uril: effects on the production and release of free radicals.

An inclusion complex between 2,2'-azobis(2-methylpropionamidine) dihydrochloride (AAPH), a widely employed azocompound, and cucurbit[7]util (CB[7]), has shown an increased yield of radicals derived from the homolytic cleavage of the azo bond. Aimed to get insights about the formation of complexes and their effect on the yield of radicals production, complexes of CB[7] with seven azocompounds were studied by computational methods. Molecular electrostatic surfaces and structural analysis showed that the inclusion of symmetrical azocompounds inside of CB[7] depends mainly on the charge density and position of the functional groups at the main chain of the azoderivative. Analysis of non-covalent interactions and thermodynamic outcomes revealed that positively charged azocompounds with amidinium or imidazolium groups presented strong favorable interactions (multiple hydrogen bonds) with the oxygens of CB[7] portals. Additionally, carbon-centered radicals generated from the complexes (azocompounds@CB[7]) were corroborated using the electron localization function (ELF). Results evidenced that the strength of the interactions and the level of inclusion (partial or complete) between the azocompound and CB[7] determined the final orientation of the radicals (located out- or inside of the CB[7] cavity). Obtained results could be employed to design new supramolecular systems based on the properties of azocomplound@CB[7] complexes for new scientific or industrial applications. First-principles calculations at B3LYP-D3BJ/6-311g(d,p) level theory in the gas phase and in solvent (PCM, water) were performed in Gaussian 16 software package. The dispersion energy correction was included through the Grimme's dispersion with Becke-Johnson damping D3(BJ). Thermodynamical data and the minimum character of all structures were obtained from vibrational frequency calculations. NBO, Multiwfn, Chemcraft, and NCIPLOT software were used to perform population analysis, analyze outcomes, visualize data, and display non-covalent interactions respectively.

Mouse polyomavirus infection induces lamin reorganisation.

The nuclear lamina is a dense network of intermediate filaments beneath the inner nuclear membrane. Composed of A-type lamins (lamin A/C) and B-type lamins (lamins B1 and B2), the nuclear lamina provides a scaffold for the nuclear envelope and chromatin, thereby maintaining the structural integrity of the nucleus. A-type lamins are also found inside the nucleus where they interact with chromatin and participate in gene regulation. Viruses replicating in the cell nucleus have to overcome the nuclear envelope during the initial phase of infection and during the nuclear egress of viral progeny. Here, we focused on the role of lamins in the replication cycle of a dsDNA virus, mouse polyomavirus. We detected accumulation of the major capsid protein VP1 at the nuclear periphery, defects in nuclear lamina staining and different lamin A/C phosphorylation patterns in the late phase of mouse polyomavirus infection, but the nuclear envelope remained intact. An absence of lamin A/C did not affect the formation of replication complexes but did slow virus propagation. Based on our findings, we propose that the nuclear lamina is a scaffold for replication complex formation and that lamin A/C has a crucial role in the early phases of infection with mouse polyomavirus.

Ligand-Directed Synthesis of a Self-Organized Chloro-Bridged Cubic Pd(II) Cage Showing Selective Encapsulation of Phenols.

The synthesis and guest recognition properties of a neutral Pd24-cubic cage, [{Pd3(NiPr)3PO}8(μ2-Cl)24] 1 are reported. The formation of the cubical assembly takes place by an exclusive one-pot ligand-assisted pathway directed by an oximido linker. The initial coordination of the oximido ligand pre-organizes the [Pd3(NiPr)3PO]3+ polyhedral building units into a tetrameric intermediate, which then transforms into an oximido-tethered tetrahedral assembly and to the cubical cage 1 in the presence of chloride ions. In the absence of the directing oximido linker, no cage formation was observed, and the Pd6-precursor was found to undergo self-condensation, giving rise to a new pentameric polyhedral cluster, [Pd5{(NiPr)3PO}2(OAc)2(OH)2] 2. The central cavity of the cube has been probed for guest encapsulation studies, which shows a high binding with phenolic guest molecules with association constants of the order of 104-105 M-1. The favorable formation of host-guest complexes was attributed to the strong hydrogen bonding interactions between the host and guest functional groups.

Data access arrangements in genomic research consortia

One of the most common terms that is used to describe entities responsible for sharing genomic data for research purposes is ‘genomic research consortium’. However, there is a lack of clarity around the language used by consortia to describe their data sharing arrangements. Calls have been made for more uniform terminology. This article reports on a review of the genomic research consortium literature illustrating a wide diversity in the language that has been used over time to describe the access arrangements of these entities. The second component of this research involved an examination of publicly available information from a dataset of 98 consortia. This analysis further illustrates the wide diversity in the access arrangements adopted by genomic research consortia. A total of 12 different access arrangements were identified, including four simple forms (open, consortium, managed and registered access) and eight more complex tiered forms (for example, a combination of consortium, managed and open access). The majority of consortia utilised some form of tiered access, often following the policy requirements of funders like the US National Institutes of Health and the UK Wellcome Trust. It was not always easy to precisely identify the access arrangements of individual consortia. Greater consistency, clarity and transparency is likely to be of benefit to donors, depositors and accessors alike. More work needs to be done to achieve this end.

Covalent Probes To Capture Legionella pneumophila Dup Effector Enzymes.

Upon infection of host cells, Legionella pneumophila releases a multitude of effector enzymes into the cell's cytoplasm that hijack a plethora of cellular activities, including the host ubiquitination pathways. Effectors belonging to the SidE-family are involved in noncanonical serine phosphoribosyl ubiquitination of host substrate proteins contributing to the formation of a Legionella-containing vacuole that is crucial in the onset of Legionnaires' disease. This dynamic process is reversed by effectors called Dups that hydrolyze the phosphodiester in the phosphoribosyl ubiquitinated protein. We installed reactive warheads on chemically prepared ribosylated ubiquitin to generate a set of probes targeting these Legionella enzymes. In vitro tests on recombinant DupA revealed that a vinyl sulfonate warhead was most efficient in covalent complex formation. Mutagenesis and X-ray crystallography approaches were used to identify the site of covalent cross-linking to be an allosteric cysteine residue. The subsequent application of this probe highlights the potential to selectively enrich the Dup enzymes from Legionella-infected cell lysates.

Design redistribution: the role and involvement of craftsmen in the embodiment of design in the Indonesian rattan furniture industry

ABSTRACT This article explores the roles and positions of craftsmen in the design development within the Indonesian rattan furniture industry. Positioned as subcontractors, craftsmen play an essential role in the design development process, particularly in the exploration and interpretation of sketch drawings into prototypes that meet buyers’ specifications and gain their approval. This research utilised a phenomenological approach to explore the experiences of craftsmen in creating prototypes conveyed solely through sketch drawings. Rattan furniture design is generally dynamic and organic, characterised by numerous curves and complex forms that are challenging to depict accurately. Sketch drawings are rough and often lack proper proportions, scalability, standardisation, and intricate details, leading to varying interpretations of the prototype sketch drawings. Based on their experience and creativity, the craftsmen create prototypes solely by referring to sketch drawings. Consequently, there has been a significant collaboration between contractors and craftsmen as subcontractors in the design process. This research is part of an initiative aimed at recognising craftsmen as marginalised participants in small business entities, highlighting their contributions and rights within the collaborative design process.

Preparation, characterization and heat release behavior of inclusion complexes formed between carvone or limonene and acyclic cucurbit[n]urils.

Carvone and limonene are naturally occurring monoterpenoids with unique aromas, making them valuable substances in synthetic fragrance production. However, their application is limited due to low stability and rapid volatilization. To address this challenge, host-guest complexes offer a promising solution. In this study, two acyclic cucurbit[n]urils were synthesized to form inclusion complexes with carvone and limonene, aiming to enhance their thermal stability and achieve excellent heat release properties. The binding behavior of the complexes was investigated using NMR, X-ray diffraction (XRD), Fourier transform infrared (FTIR) and molecular bonding analyses, confirming the formation of host-guest inclusion complexes. Our study successfully prepared four inclusion complexes (M1/CA, M2/CA, M1/LI, M2/LI) and characterized them using NMR, XRD and FTIR techniques. These complexes exhibited a 1:1 stoichiometric ratio, and their binding constants were determined through fluorescence titration. The thermal controlled release experiment shows that the degree of carvone and limonene release is different with a change of temperature, indicating that the inclusion complexes have good thermally controlled release performance, and the thermal release retention rate has a certain correlation with KS value. The larger the KS value, the higher the thermal release retention rate of the inclusion complexes, the lower the volatilization of the inclusion complexes, the longer the retention time and the better the thermal stability. This study presents a novel approach for developing carvone- and limonene-based fragrances, expanding their application potential in various industries. © 2024 Society of Chemical Industry.