Search

The selective hydrogenation of lignin-derived phenols under mild conditions is still a challenging work. In this study, 2.0 wt% Pd/γ-Al2O3 catalyst was found to show high catalytic performance for the selective hydrogenation of lignin-derived phenols, giving 100% conversion of substrate and 94.9% yield of cyclohexanols under optimized conditions. The excellent catalytic performance of the 2.0 wt% Pd/γ-Al2O3 catalyst could be possibly ascribed to its higher percentage (93.6%) of surface Pd0 species than other catalysts. The turnover number (TON) of substrate was 1363 with apparent activation energy (Ea) of 22.7 and 13.6 kJ mol−1 for the hydrogenation of 4-ethyl phenol to 4-ethyl cyclohexanone and subsequent hydrogenation for C=O bond over Pd/γ-Al2O3, respectively. The lower Ea could possibly explain the excellent catalytic activity for the full hydrogenation of 4-ethyl phenol to 4-ethyl cyclohexanol. Furthermore, this catalyst showed higher selectivity to hydrolysis and hydrogenation than to hydrogenolysis for the conversion of β-O-4, 4-O-5 and α-O-4 linked lignin-derived dimeric compounds with excellent substrate conversion and cyclohexanol product yield, offering great opportunity and potential for upgrading of lignin-derived phenols to well-defined end products. [ABSTRACT FROM AUTHOR]

Synthesis of W nanoparticles by magnetron sputtering combined with gas aggregation operated in Ar suffers from a continuous decrease of the synthesis rate, ceasing in a finite time interval, in the range of minutes to tens of minutes. Experimentally, we noticed that adding small amounts of H2 to Ar (5–20%) increases the synthesis rate, which remains constant over time, at a value dependent on the amount of injected hydrogen. Mass spectrometry investigations revealed, in the hydrogen presence, a dominance of the ArH+ ions over the Ar+ ones, associated also with an increased number of W+ and WH+ species in plasma, sustaining a substantial increase in the nucleation rate. [ABSTRACT FROM AUTHOR]

The selective hydrogenation of lignin-derived phenols under mild conditions is still a challenging work. In this study, 2.0 wt% Pd/γ-Al2O3 catalyst was found to show high catalytic performance for the selective hydrogenation of lignin-derived phenols, giving 100% conversion of substrate and 94.9% yield of cyclohexanols under optimized conditions. The excellent catalytic performance of the 2.0 wt% Pd/γ-Al2O3 catalyst could be possibly ascribed to its higher percentage (93.6%) of surface Pd0 species than other catalysts. The turnover number (TON) of substrate was 1363 with apparent activation energy (Ea) of 22.7 and 13.6 kJ mol−1 for the hydrogenation of 4-ethyl phenol to 4-ethyl cyclohexanone and subsequent hydrogenation for C=O bond over Pd/γ-Al2O3, respectively. The lower Ea could possibly explain the excellent catalytic activity for the full hydrogenation of 4-ethyl phenol to 4-ethyl cyclohexanol. Furthermore, this catalyst showed higher selectivity to hydrolysis and hydrogenation than to hydrogenolysis for the conversion of β-O-4, 4-O-5 and α-O-4 linked lignin-derived dimeric compounds with excellent substrate conversion and cyclohexanol product yield, offering great opportunity and potential for upgrading of lignin-derived phenols to well-defined end products. [ABSTRACT FROM AUTHOR]

The syntheses of the tripodal tetraamine ligands 2‐(pyridin‐2‐yl)‐N,N‐bis(quinolin‐2‐ylmethyl)ethan‐1‐amine (DQPEA), N‐(pyridin‐2‐ylmethyl)‐2‐(quinolin‐2‐yl)‐N‐(2‐(quinolin‐2‐yl)ethyl)ethan‐1‐amine (DQEPMA), 2‐(pyridin‐2‐yl)‐N,N‐bis(2‐(quinolin‐2‐yl)ethyl)ethan‐1‐amine (DQEPEA), N,N‐bis(pyridin‐2‐ylmethyl)‐2‐(quinolin‐2‐yl)ethan‐1‐amine (QEDPMA), and 2‐(pyridin‐2‐yl)‐N‐(2‐(pyridin‐2‐yl)ethyl)‐N‐(2‐(quinolin‐2‐yl)ethyl)ethan‐1‐amine (QEDPEA) containing mixed quinolyl and pyridyl moieties are reported, with 2‐vinylquinoline being used to attach quinolylethyl arms to the aliphatic N atom. X‐ray crystal structures of [(Mn(DQPEA))2O2](ClO4)2 ⋅ (CH3CN)2, [Cu(DQPEA)NCCH3](ClO4)2, [Zn(DQPEA)NCCH3](ClO4)2, [Pd(DQEPEA)Cl]Cl ⋅ 11H2O are detailed, with four, five, and six‐coordination observed. In addition, the dimeric complex [(DPEA)Co(μ‐OH)3Co(DPEA)](ClO4)3 ⋅ 0.5H2O ⋅ MeCN containing the tridentate DPEA ligand formed by N‐dealkylation of QEDPEA is reported. Calculations suggest that the very short Co…Co distance of 2.5946(6) Å in this complex is unlikely to be due to a Co−Co bond. [ABSTRACT FROM AUTHOR]

The energies of an electron in a one-dimensional crystal are studied with both the Schrödinger and Dirac equations using the plane wave expansion method. The crystalline potential sensed by the electron in a cell was calculated by accounting for the Coulombic (electrostatic) interaction between the electron and the surrounding cores (immobile positive ions at the center of the crystal cells). The energies and wave functions of the electron were calculated as a function of four parameters: the period a p of the lattice, the dimension n d i m of the matrix in the momentum space, the partition number l p a in which the unit cell is divided to calculate the potential and the number of cores n c o that affect the electron. It was found that 8000 cores (surrounding the electron) were needed to reach our convergence criterion. An analytical equation that accurately describes the behavior of the energies in function of the cores that affect the electron was also found. As case studies, the energies for pseudo-lithium and pseudo-graphene were obtained as a first approximation for one-dimensional lattices. Subsequently, the energies of an isolated dimer nanoparticle were also calculated using the supercell method. [ABSTRACT FROM AUTHOR]

The TSH receptor (TSHR) and its many forms are the primary antigens of Graves' disease as evidenced by the presence of TSHR antibodies of differing biological activity. The TSH holoreceptor undergoes complex posttranslational changes including cleavage of its ectodomain and oligomer formation. We have previously shown that the TSHR exists in both monomeric and dimeric structures in the thyroid cell membrane and have demonstrated, by modeling, that the transmembrane domains (TMD) can form stable dimeric structures. Based on these earlier simulations of the TSHR-TMD structure and our most recent model of the full-length TSHR, we have now built models of full-length TSHR multimers with and without TSH ligand in addition to multimers of the extracellular leucine-rich domain, the site of TSH and autoantibody binding. Starting from these models we ran molecular dynamics simulations of the receptor oligomers solvated with water and counterions; the full-length oligomers also were embedded in a dipalmitoylphosphatidylcholine bilayer. The full-length TSHR dimer and trimer models stayed in the same relative orientation and distance during 2000 ns (or longer) molecular dynamics simulation in keeping with our earlier report of TMD dimerization. Simulations were also performed to model oligomers of the leucine-rich domain alone; we found a trimeric complex to be even more stable than the dimers. These data provide further evidence that different forms of the TSHR add to the complexity of the immune response to this antigen that, in patients with autoimmune thyroid disease, generate an autoantibody reactome with multiple types of autoantibody to the TSHR. [ABSTRACT FROM AUTHOR]

The translational diffusivity of covalent open‐[60]fullerene dimers in an organic solvent was found to be well describable by a prolate ellipsoid model while a monomeric open‐[60]fullerene behaves like a sphere model. The water association dynamics were examined for two open‐[60]fullerene dimers, showing a higher water affinity for the sp3‐linked dimer relative to sp2‐linked dimer owing to an effective orbital–orbital overlap identified by π(fullerene)→σ*(H2O) interactions as suggested by theoretical calculations. [ABSTRACT FROM AUTHOR]

Ultrafast reaction processes take place when resonant features of nonlinear model systems are taken into account. In the targeted energy or electron transfer dimer model this is accomplished through the implementation of nonlinear oscillators with opposing types of nonlinearities, one attractive while the second repulsive. In the present work, we show that this resonant behavior survives if we take into account the vibrational degrees of freedom as well. After giving a summary of the basic formalism of chemical reactions we show that resonant electron transfer can be assisted by vibrations. We find the condition for this efficient transfer and show that in the case of additional interaction with noise, a distinct non-Arrhenius behavior develops that is markedly different from the usual Kramers-like activated transfer. [ABSTRACT FROM AUTHOR]

This study utilized density functional theory (DFT) in quantum chemistry to investigate the gas-phase parasitic reaction mechanism between diethylzinc (DEZn) and tert-butanol (t-BuOH) during the metal-organic chemical vapor deposition (MOCVD) growth process of ZnO thin films. By calculating the Gibbs free energy changes along various reaction pathways at different temperatures, a comprehensive thermodynamic evaluation of key intermediates (HOZnOBut, H(ZnO)2 But, HZnOH), as well as the formation of dimers (Zn2 O2 H4, Zn2 O4 H4, Zn4 O4 H4), and trimers (Zn3 O6 H6) was performed. The main objective was to identify potential pathways and products that could lead to the formation of nanoparticles, which might impede ZnO thin film growth. Research has shown that under high-temperature deposition conditions (673.15 K

We previously found that chronic adenosine A1 receptor stimulation with N6-Cyclopentyladenosine increased α-synuclein misfolding and neurodegeneration in a novel α-synucleinopathy model, a hallmark of Parkinson's disease. Here, we aimed to synthesize a dimer caffeine-indan linked by a 6-carbon chain to cross the blood–brain barrier and tested its ability to bind α-synuclein, reducing misfolding, behavioral abnormalities, and neurodegeneration in our rodent model. Behavioral tests and histological stains assessed neuroprotective effects of the dimer compound. A rapid synthesis of the 18F-labeled analogue enabled Positron Emission Tomography and Computed Tomography imaging for biodistribution measurement. Molecular docking analysis showed that the dimer binds to α-synuclein N- and C-termini and the non-amyloid-β-component (NAC) domain, similar to 1-aminoindan, and this binding promotes a neuroprotective α-synuclein "loop" conformation. The dimer also binds to the orthosteric binding site for adenosine within the adenosine A1 receptor. Immunohistochemistry and confocal imaging showed the dimer abolished α-synuclein upregulation and aggregation in the substantia nigra and hippocampus, and the dimer mitigated cognitive deficits, anxiety, despair, and motor abnormalities. The 18F-labeled dimer remained stable post-injection and distributed in various organs, notably in the brain, suggesting its potential as a Positron Emission Tomography tracer for α-synuclein and adenosine A1 receptor in Parkinson's disease therapy. [ABSTRACT FROM AUTHOR]

The study of localized surface plasmons (LSPs) in nanoscale structures is an essential step towards identifying optimal plasmonic modes that can facilitate robust optomechanical coupling and deepen our understanding of light–matter interactions at the nanoscale. This paper investigates, numerically, using the finite element method, LSP modes in a design comprising two coupled nano-ridges deposited on a gold layer with an interposing polymer spacer layer. Such a structure, usually referred to as a particle-on-mirror structure, shows exquisite optical properties at the nanoscale. We first examine the LSP modes of a single nano-ridge through the analysis of its scattering cross-section in the visible and infrared ranges. To enhance the plasmonic response, a thin polymer layer is placed at the middle of the ridge, which introduces additional LSP modes confined within the former. Then, we extend the analysis to the dimer configuration, which exhibits more complex and enhanced plasmonic behavior compared to a single nano-ridge. In particular, the dimer configuration yields LSP resonances with a quality factor enhancement of approximately threefold relative to a single nano-ridge. Furthermore, the presence of the polymer layer within the ridges significantly improves plasmon field localization and the quality factor. These findings underscore the potential of nano-ridge-based structures in advancing optomechanical coupling and offering valuable insights for the development of high-performance acousto-plasmonic devices. In particular, the proposed device could help significantly improve the design of nano-acousto-optic modulators, operating in the visible or in the near-infrared ranges, that require an enhanced light–phonon coupling rate. [ABSTRACT FROM AUTHOR]

IL37 plays important roles in the regulation of innate immunity and its oligomeric status is critical to these roles. In its monomeric state, IL37 can effectively inhibit the inflammatory response of IL18 by binding to IL18Rα, a capacity lost in its dimeric form, underlining the pivotal role of the oligomeric status of IL37 in its anti-inflammatory action. Until now, two IL37 dimer structures have been deposited in PDB, reflecting a substantial difference in their dimer interfaces. Given this discrepancy, we analyzed the PDB structures of the IL37 dimer (PDB IDs: 6ncu, 5hn1) along with a AF2-multimer prediction by molecular dynamics (MD) simulations. Results showed that the 5hn1 and AF2-predicted dimers have the same interface and stably maintained their conformations throughout simulations, while the recent IL37 dimer (PDB ID: 6ncu) with a different interface did not, proposing a possible issue with the recent IL37 dimer structure (6ncu). Next, focusing on the stable dimer structures, we have identified five critical positions of V71/Y85/I86/E89/S114, three new positions compared to the literature, that would reduce dimer stability without affecting the monomer structure. Two quintuple mutants were tested by MD simulations and showed partial or complete dissociation of the dimer. Overall, the insights gained from this study reinforce the validity of the 5hn1 and AF2 multimer structures, while also advancing our understanding of the IL37 dimer interface through the generation of monomer-locked IL37 variants.

In the present study, we have confined the smallest water clusters namely, monomer and dimer under various carbon nanotubes and fullerenes using quantum mechanics/molecular mechanics methods. We observed the change in their structural, vibrational, optical and electronic properties as compared to each other as well as against the free monomer and dimer. For monomer, the confinement effect was found to be the greatest for carbon nanotube CNT(7,0) followed by C-60 and then by C-78. However, in the case of the dimer, there was a change in its structure, thus exhibiting different confining effects in each geometry. We also note that, as the diameter of the CNT goes on increasing, the confining effects over the monomer and the dimer go on decreasing. We have also confined a monomer by placing it over one C-60 fullerene, and between two and three C-60 fullerenes at various sites—the hexagon, pentagon and the vertex at different distances from the surface, and compared the extent of confinement. In the vibrational spectra, for short-range interactions, a redshift was observed, whereas a blueshift was seen in the case of long-range interactions as we went from hexagon to pentagon to vertex sites. We have also confirmed the results obtained by studying their structural, vibrational, electronic and optical properties. [ABSTRACT FROM AUTHOR]

Recently, an ever‐growing interest has been paid on organic single‐molecule white light‐emitting materials for effective white organic light‐emitting diodes (WOLEDs). However, subject to Kasha's rule, photons can only be emitted from the lowest excited state and thus panchromatic or dual emissions are extremely forbidden, which results in a certain challenge in achieving white emission. Herein, a strategy of synergetic carbonyl and heptagonal structure is proposed for organic single‐molecule white light emission and demonstrated by TAO/TABO/TA2O organic luminescent materials that are modified on aryl ketones/amine fragments. Among them, due to the robust intermolecular interactions triggered by synergetic carbonyl and heptagonal structure, TA2O exhibits vibrant monomer and dimer photoluminescence with dual thermally activated delayed fluorescence (TADF) characteristics. As a result, the first single‐molecule dual‐TADF WOLED based on the synergetic system is successfully fabricated with an external quantum efficiency of 7.2%. This study not only expands the scope of carbonyl and heptagonal structure for novel optoelectronic properties and applications but also opens new avenues for the development of efficient single‐molecule WOLEDs with dual TADF mechanisms. [ABSTRACT FROM AUTHOR]

Mitochondrial uncoupling by small molecule protonophores is a promising strategy for developing novel anticancer agents. Recently, aryl urea substituted fatty acids (aryl ureas) were identified as a new class of protonophoric anticancer agents. To mediate proton transport these molecules self‐assemble into membrane‐permeable anionic dimers in which intermolecular hydrogen bonds between the carboxylate and aryl‐urea anion receptor delocalise the negative charge across the aromatic π‐system. In this work, we extend the aromatic π‐system by introducing a second phenyl substituent to the aryl urea scaffold and compare the proton transport mechanisms and mitochondrial uncoupling actions of these compounds to their monoaryl analogues. It was found that incorporation of meta‐linked phenyl substituents into the aryl urea scaffold enhanced proton transport in vesicles and demonstrated superior capacity to depolarise mitochondria, inhibit ATP production and reduce the viability of MDA‐MB‐231 breast cancer cells. In contrast, diphenyl ureas linked through a 1,4‐distribution across the phenyl ring displayed diminished proton transport activity, despite both diphenyl urea isomers possessing similar binding affinities for carboxylates. Mechanistic studies suggest that inclusion of a second aryl ring changes the proton transport mechanism, presumably due to steric factors that impose higher energy penalties for dimer formation. [ABSTRACT FROM AUTHOR]

An automated pipeline for comprehensive calculation of intermolecular interaction energies based on molecular force-fields using the Tinker molecular modelling package is presented. Starting with non-optimized chemically intuitive monomer structures, the pipeline allows the approximation of global minimum energy monomers and dimers, configuration sampling for various monomer–monomer distances, estimation of coordination numbers by molecular dynamics simulations, and the evaluation of differential pair interaction energies. The latter are used to derive Flory–Huggins parameters and isotropic particle–particle repulsions for Dissipative Particle Dynamics (DPD). The computational results for force fields MM3, MMFF94, OPLS-AA and AMOEBA09 are analyzed with Density Functional Theory (DFT) calculations and DPD simulations for a mixture of the non-ionic polyoxyethylene alkyl ether surfactant C10E4 with water to demonstrate the usefulness of the approach. Scientific Contribution To our knowledge, there is currently no open computational pipeline for differential pair interaction energies at all. This work aims to contribute an (at least academically available, open) approach based on molecular force fields that provides a robust and efficient computational scheme for their automated calculation for small to medium-sized (organic) molecular dimers. The usefulness of the proposed new calculation scheme is demonstrated for the generation of mesoscopic particles with their mutual repulsive interactions. [ABSTRACT FROM AUTHOR]

AbstractCanagliflozin, Dapagliflozin, and Empagliflozin, glucagon-like peptide-1 receptor agonists, are indicated for managing type II diabetes. Although the genotoxicity profiles of these drugs are well-explored, limited information exists regarding the genotoxic potential of their impurities. In this investigation, the dimer impurities of Canagliflozin, Dapagliflozin, and Empagliflozin underwent both in silico and in vitro assessments for mutagenic potential. Tester strains of Salmonella typhimurium and Escherichia coli were subjected to the Ames test, utilizing concentrations of up to 1 µg per plate, with and without the presence of metabolic activation. Evaluation of micronucleus induction in TK6 cells was conducted through a micronucleus test, exploring concentrations up to 500 µg/mL, with or without the presence of exogenous metabolic activation. Under the specific test conditions, the dimer impurities of Canagliflozin, Dapagliflozin, and Empagliflozin showed no evidence of mutagenicity or clastrogenicity, establishing their in vitro classification as nonmutagenic. These findings align with negative in silico predictions from quantitative structure–activity relationship (QSAR) analyses for mutagenicity and genotoxicity of the dimer impurities. Collectively, these studies contribute clinically relevant safety information by confirming that the dimer impurities of Canagliflozin, Dapagliflozin, and Empagliflozin are nonmutagenic and nongenotoxic, emphasizing the consistency between in silico and in vitro data. [ABSTRACT FROM AUTHOR]

CRTAM (Class-I MHC restricted T cell-associated molecule) is a member of the Nectin-like family, composed of two extracellular domains, one constant domain (IgC) and another variable domain (IgV), expressed in activated CD8 T cells, epithelial cells, natural killer (NK) cells, and in a subpopulation of CD4 T cells. CRTAM recognizes the ligand Nectin-like 2 (Necl2) through the IgV domain. However, the role of the IgC domain during this ligand recognition has yet to be understood. In this study, we show the purification of soluble-folded Ig domains of CRTAM, and we demonstrate that the IgC domain forms a homodimer in solution via hydrophobic interactions. By surface plasmon resonance (SPR) analysis, we also demonstrate that CRTAM binds to Necl2 with an affinity of 2.16 nM. In conclusion, CRTAM's IgC is essential for a high-affinity interaction with Necl-2.

Estradiol dimers (EDs) possess significant anticancer activity by targeting tubulin dynamics. In this study, we synthesised 12 EDs variants via copper-catalysed azide-alkyne cycloaddition (CuAAC) reaction, focusing on structural modifications within the aromatic bridge connecting two estradiol moieties. In vitro testing of these EDs revealed a marked improvement in selectivity towards cancerous cells, particularly for ED1–8. The most active compounds, ED3 (IC50 = 0.38 μM in CCRF-CEM) and ED5 (IC50 = 0.71 μM in CCRF-CEM) demonstrated cytotoxic effects superior to 2-methoxyestradiol (IC50 = 1.61 μM in CCRF-CEM) and exhibited anti-angiogenic properties in an endothelial cell tube-formation model. Cell-based experiments and in vitro assays revealed that EDs interfere with mitotic spindle assembly. Additionally, we proposed an in silico model illustrating the probable binding modes of ED3 and ED5, suggesting that dimers with a simple linker and a single substituent on the aromatic central ring possess enhanced characteristics compared to more complex dimers.

Alloying Pt catalysts with transition metal elements is an effective pathway to enhance the performance of oxygen reduction reaction (ORR), but often accompanied with severe metal dissolution issue, resulting in poor stability of alloy catalysts. Here, instead of forming traditional alloy structure, we modify Pt surface with a novel Ni−W dimer structure by the atomic layer deposition (ALD) technique. The obtained NiW@PtC catalyst exhibits superior ORR performance both in liquid half‐cell and practical fuel cell compared with initial Pt/C. It is discovered that strong synergistic Ni−W dimer structure arising from short atomic distance induced a stable compressive strain on the Pt surface, thus boosting Pt catalytic performance. This surface modification by synergistic dimer sites offers an effective strategy in tailoring Pt with excellent activity and stability, which provides a significant perspective in boosting the performance of commercial Pt catalyst modified with polymetallic atom sites. [ABSTRACT FROM AUTHOR]

The addition of Na[BArF24] (BArF24 = tetrakis(3,5-bis(trifluoromethyl)phenyl)borate) to [Pd(PP)Cl2] (PP = 1,1′-bis(phosphino)ferrocene ligands) compounds results in the loss of a chloride ligand and the formation of the dimeric species [Pd2(PP)2(μ-Cl)2][BArF24]2. In most cases, the addition of a monodentate phosphine, PR3, to these dimeric species leads to cleaving of the dimer and formation of [Pd(PP)(PR3)Cl][BArF24]. While these reactions are readily observed via a significant color change, the 31P{1H} NMR spectra offer more significant support, as the singlet for the dimer is replaced with three doublets of doublets. The reaction seems to take place for a wide range of PR3 ligands, although there do appear to be steric limitations to the reaction. The compounds were thoroughly characterized by NMR, and X-ray crystal structures of several of the compounds were obtained. In addition, the ferrocenyl backbone of the 1,1′-bis(phosphino)ferrocene ligands provides an opportunity to examine the oxidative electrochemistry of these compounds. In general, the potential at which oxidations of these compounds occurs shows a dependence on the phosphine substituents. [ABSTRACT FROM AUTHOR]

In this work, in order to investigate the short-range interactions between molecules, the spin-magnetic unit nitronyl nitroxide (NN) was introduced to synthesize self-assembly single radical molecules with hydrogen bond donors and acceptors. The structures and magnetic properties were extensively investigated and characterized by UV-Vis absorption spectroscopy, electron paramagnetic resonance (EPR), and superconducting quantum interference devices (SQUIDs). Interestingly, it was observed that the single molecules can form two different dimers (ring-closed dimer and "L"-type dimer) in different solvents, due to hydrogen bonding, when using EPR to track the molecular spin interactions. Both dimers exhibit ferromagnetic properties (for ring-closed dimer, J/kB = 0.18 K and ΔES−T = 0.0071 kcal/mol; for "L"-type dimer, the values were J/kB = 9.26 K and ΔES−T = 0.037 kcal/mol). In addition, the morphologies of the fibers formed by the two dimers were characterized by transmission electron microscopy (TEM) and atomic force microscopy (AFM). [ABSTRACT FROM AUTHOR]

Sirtuin 2 (SIRT2) is a class III histone deacetylase that is highly conserved from bacteria to mammals. We prepared and characterized the wild‐type (WT) and mutant forms of the histone deacetylase (HDAC) domain of human SIRT2 (hSIRT2) using various biophysical methods and evaluated their deacetylation activity. We found that WT hSIRT2 HDAC (residues 52–357) forms a homodimer in a concentration‐dependent manner with a dimer–monomer dissociation constant of 8.3 ± 0.5 μM, which was determined by mass spectrometry. The dimer was disrupted into two monomers by binding to the HDAC inhibitors SirReal1 and SirReal2. We also confirmed dimer formation of hSIRT2 HDAC in living cells using a NanoLuc complementation reporter system. Examination of the relationship between dimer formation and deacetylation activity using several mutants of hSIRT2 HDAC revealed that some non‐dimerizing mutants exhibited deacetylation activity for the N‐terminal peptide of histone H3, similar to the wild type. The hSIRT2 HDAC mutant Δ292–306, which lacks a SIRT2‐specific disordered loop region, was identified to exist as a monomer with slightly reduced deacetylation activity; the X‐ray structure of the mutant Δ292–306 was almost identical to that of the WT hSIRT2 HDAC bound to an inhibitor. These results indicate that hSIRT2 HDAC forms a dimer, but this is independent of deacetylation activity. Herein, we discuss insights into the dimer formation of hSIRT2 based on our biophysical experimental results. [ABSTRACT FROM AUTHOR]

The Ebola virus (EBOV) is a lipid‐enveloped virus with a negative sense RNA genome that can cause severe and often fatal viral hemorrhagic fever. The assembly and budding of EBOV is regulated by the matrix protein, VP40, which is a peripheral protein that associates with anionic lipids at the inner leaflet of the plasma membrane. VP40 is sufficient to form virus‐like particles (VLPs) from cells, which are nearly indistinguishable from authentic virions. Due to the restrictions of studying EBOV in BSL‐4 facilities, VP40 has served as a surrogate in cellular studies to examine the EBOV assembly and budding process from the host cell plasma membrane. VP40 is a dimer where inhibition of dimer formation halts budding and formation of new VLPs as well as VP40 localization to the plasma membrane inner leaflet. To better understand VP40 dimer stability and critical amino acids to VP40 dimer formation, we integrated computational approaches with experimental validation. Site saturation/alanine scanning calculation, combined with molecular mechanics‐based generalized Born with Poisson‐Boltzmann surface area (MM‐GB/PBSA) method and molecular dynamics simulations were used to predict the energetic contribution of amino acids to VP40 dimer stability and the hydrogen bonding network across the dimer interface. These studies revealed several previously unknown interactions and critical residues predicted to impact VP40 dimer formation. In vitro and cellular studies were then pursued for a subset of VP40 mutations demonstrating reduction in dimer formation (in vitro) or plasma membrane localization (in cells). Together, the computational and experimental approaches revealed critical residues for VP40 dimer stability in an alpha‐helical interface (between residues 106–117) as well as in a loop region (between residues 52–61) below this alpha‐helical region. This study sheds light on the structural origins of VP40 dimer formation and may inform the design of a small molecule that can disrupt VP40 dimer stability. [ABSTRACT FROM AUTHOR]

Throughout its lifecycle, Entamoeba histolytica encounters a variety of stressful conditions. This parasite possesses Heat Shock Response Elements (HSEs) which are crucial for regulating the expression of various genes, aiding in its adaptation and survival. These HSEs are regulated by Heat Shock Transcription Factors (EhHSTFs). Our research has identified seven such factors in the parasite, designated as EhHSTF1 through to EhHSTF7. Significantly, under heat shock conditions and in the presence of the antiamoebic compound emetine, EhHSTF5, EhHSTF6, and EhHSTF7 show overexpression, highlighting their essential role in gene response to these stressors. Currently, only EhHSTF7 has been confirmed to recognize the HSE as a promoter of the EhPgp5 gene (HSE_EhPgp5), leaving the binding potential of the other EhHSTFs to HSEs yet to be explored. Consequently, our study aimed to examine, both in vitro and in silico, the oligomerization, and binding capabilities of the recombinant EhHSTF5 protein (rEhHSTF5) to HSE_EhPgp5. The in vitro results indicate that the oligomerization of rEhHSTF5 is concentration-dependent, with its dimeric conformation showing a higher affinity for HSE_EhPgp5 than its monomeric state. In silico analysis suggests that the alpha 3 α-helix (α3-helix) of the DNA-binding domain (DBD5) of EhHSTF5 is crucial in binding to the major groove of HSE, primarily through hydrogen bonding and salt-bridge interactions. In summary, our results highlight the importance of oligomerization in enhancing the affinity of rEhHSTF5 for HSE_EhPgp5 and demonstrate its ability to specifically recognize structural motifs within HSE_EhPgp5. These insights significantly contribute to our understanding of one of the potential molecular mechanisms employed by this parasite to efficiently respond to various stressors, thereby enabling successful adaptation and survival within its host environment. [ABSTRACT FROM AUTHOR]

ABSTRACT The cAMP receptor proteins (CRPs) play a critical role in bacterial environmental adaptation by regulating global gene expression levels via cAMP binding. Here, we report the structure of DdrI, a CRP family protein from Deinococcus radiodurans. Combined with biochemical, kinetic, and molecular dynamics simulations analyses, our results indicate that DdrI adopts a DNA-binding conformation in the absence of cAMP and can form stable complexes with the target DNA sequence of classical CRPs. Further analysis revealed that the high-affinity cAMP binding pocket of DdrI is partially filled with Tyr113-Arg55-Glu65 sidechains, mimicking the anti-cAMP-mediated allosteric transition. Moreover, the second syn-cAMP binding site of DdrI at the protein-DNA interface is more negatively charged compared to that of classical CRPs, and manganese ions can enhance its DNA binding affinity. DdrI can also bind to a target sequence that mimics another transcription factor, DdrO, suggesting potential cross-talk between these two transcription factors. These findings reveal a class of CRPs that are independent of cAMP activation and provide valuable insights into the environmental adaptation mechanisms of D. radiodurans.IMPORTANCEBacteria need to respond to environmental changes at the gene transcriptional level, which is critical for their evolution, virulence, and industrial applications. The cAMP receptor protein (CRP) of Escherichia coli (ecCRP) senses changes in intracellular cAMP levels and is a classic example of allosteric effects in textbooks. However, the structures and biochemical activities of CRPs are not generally conserved and there exist different mechanisms. In this study, we found that the proposed CRP from Deinococcus radiodurans, DdrI, exhibited DNA binding ability independent of cAMP binding and adopted an apo structure resembling the activated CRP. Manganese can enhance the DNA binding of DdrI while allowing some degree of freedom for its target sequence. These results suggest that CRPs can evolve to become a class of cAMP-independent global regulators, enabling bacteria to adapt to different environments according to their characteristics. The first-discovered CRP family member, ecCRP (or CAP) may well not be typical of the family and be very different to the ancestral CRP-family transcription factor.

The systematization of possible ways to form C28 and C30 fullerene isomers has been completed in this work. An additional confirmation was obtained that fullerenes created by incorporating dimers into the initial structure had a minimum energy. Two other methods for the formation of new fullerenes were also considered, namely, the connection of two domes with the same symmetry and that of fullerenes with compatible symmetry. The symmetry order of the studied fullerenes varied from the second to the seventh ones. A collaboration analysis of the formation energy values and geometric simulation results allowed us to draw conclusions about the structural changes in the resulting fullerenes.

Despite the availability of high resolution crystal structure of the catalytic domain of human carbonic anhydrase IX (denoted as HCA IX-c), its solution structure and functional dynamics are mostly unknown. In this article, we report classical molecular dynamics (MD) simulation studies on the structure and non-reactive dynamics of dimeric HCA IX-c (d-HCA IX-c, with chains A and B) in water and compare them to each chain simulated in water as a monomeric solute (mA/mB). While the average solution structures appear to be largely similar in all systems, d-HCA IX-c shows significant deviations from mA and mB in terms of non-reactive reorganization of the active site needed to initiate the rate determining proton transfer step between a zinc-bound water and one of the sidechain N-atoms of a distal histidine residue (His-64). First, 2−6 water molecules are found to form fluctuating hydrogen bonded networks that would serve as proton paths across the active site. A minimally frustrated core of each monomer in the dimeric protein is found to be associated with a significantly higher likelihood of forming complete proton transfer pathways mediated by 2 water molecules synchronously at the two active sites hosted by the monomeric chains. The relative stability and kinetics of transition between two major sidechain rotamers of His-64 are also affected by dimerization. The sidechain rotation of His-64 is found to involve at least one transition as slow as 105s−1 in chain A of d-HCA IX-c thereby rendering it slower than the actual rate determining proton transfer step. This observation indicates an important deviation from the widely accepted mechanism of catalysis by HCAs.

Enhanced optical and infrared activity of subwavelength metal nanoparticles is key to their use in optoelectronics, spectroscopy, and sensing. The present work compared spectra of nanosphere dimers merged by centrifuging gold nanospheres with corresponding simulated nanoscale dimers. Geometric features of the nanosphere dimers were related to corresponding optical and near-infrared activity through simulation. Differences in optical and infrared activity of the nanosphere dimers were largely attributable to changes in the radius of the nanosphere and the radius of the conductive junction between merged nanospheres. The features observed in the experimental spectra were attributed to a select number of dimers exhibiting predominantly optical and infrared activity, consistent with observations made in the corresponding transmission electron microscope image. The preparation and simulation methods in the present work appear useful to guide design, fabrication, and implementation of sustainably-synthesized nanosphere dimers with desired optical features for optoelectronic, spectroscopic, and sensing applications.

Parity-Time Symmetry, or abbreviated as -Symmetry, can be explained as the propagation of an optical beam in two bound waveguides, where one waveguide experiences strengthening and the other waveguide experiences weakening, with each intensity having the same value. Then, the two waveguides are known as dimers, so the phenomenon is called dimer -Symmetry. Furthermore, the -Symmetry dimer is expanded into a system consisting of a collection of -Symmetry Dimers, where each dimer is bound by a binding constant. The result of this expansion is called the multi dimer -Symmetry system. Research on the propagation of optical rays in waveguides plays an important role in the development of optical-based communication technology in the future

The review highlights the relationship between the molecular organization of the light-harvesting complex of photosystem II (LHCII) and sunlight utilization by higher plants. The molecular form of LHCII switches rapidly and reversibly during diurnal changes of light intensity, from low (ca. 10) to high [ca. 1,000 µmol(photon) m-2 s-1], so the sensitivity of LHCII to light may control the balance between light harvesting and photoprotection state. Our understanding and concept of this mechanism are based on the knowledge of the structure and photophysics of different LHCII molecular forms: monomer, dimer, trimer, and aggregate. It is proposed that LHCII monomers, dimers, and lateral aggregates are fundamental blocks of excess light-dissipation machinery. Trimer is exceptionally well suited to play a physiological role of an antenna complex. A correlation between the LHCII molecular form and the presence of xanthophyll cycle pigment violaxanthin and zeaxanthin in the complex structure is also shown. Moreover, the role of LHCII protein phosphorylation in thylakoid membrane architecture is also discussed. The dual function of LHCII has been studied in the natural thylakoid membranes of chloroplasts, in the artificial lipid-LHCII model membranes, and by suspension of LHCII in a detergent solution.

In the title compound, C22H19NO5S·C2D6OS, the central six-membered ring has a slightly distorted boat conformation, while the fused pyrrolidine ring adopts an envelope conformation. These conformations are stabilized by O—H...O hydrogen bonds between the main compound and solvent molecules. In addition, intramolecular C—H...O hydrogen bonds in the main molecule form two S(6) rings. Molecules are connected by pairs of intermolecular C—H...O hydrogen bonds, forming dimers with a R22(8) motif. These dimers form a three-dimensional network through O—H...O, O—H...S and C—H...O hydrogen bonds with each other directly and through solvent molecules. In addition, weak π–π stacking interactions [centroid-to-centroid distances = 3.9937 (10) and 3.9936 (10) Å, slippages of 2.034 and 1.681 Å] are observed. The intermolecular contacts were quantified using Hirshfeld surface analysis and two-dimensional fingerprint plots, revealing the relative contributions of the contacts to the crystal packing to be H...H 41.7%, O...H/H...O 27.7%, C...H/H...C 17.0%, and S...H/H...S 7.5%.

The energies of an electron in a one-dimensional crystal are studied with both the Schrödinger and Dirac equations using the plane wave expansion method. The crystalline potential sensed by the electron in a cell was calculated by accounting for the Coulombic (electrostatic) interaction between the electron and the surrounding cores (immobile positive ions at the center of the crystal cells). The energies and wave functions of the electron were calculated as a function of four parameters: the period ap of the lattice, the dimension ndim of the matrix in the momentum space, the partition number lpa in which the unit cell is divided to calculate the potential and the number of cores nco that affect the electron. It was found that 8000 cores (surrounding the electron) were needed to reach our convergence criterion. An analytical equation that accurately describes the behavior of the energies in function of the cores that affect the electron was also found. As case studies, the energies for pseudo-lithium and pseudo-graphene were obtained as a first approximation for one-dimensional lattices. Subsequently, the energies of an isolated dimer nanoparticle were also calculated using the supercell method.

Ultrafast reaction processes take place when resonant features of nonlinear model systems are taken into account. In the targeted energy or electron transfer dimer model this is accomplished through the implementation of nonlinear oscillators with opposing types of nonlinearities, one attractive while the second repulsive. In the present work, we show that this resonant behavior survives if we take into account the vibrational degrees of freedom as well. After giving a summary of the basic formalism of chemical reactions we show that resonant electron transfer can be assisted by vibrations. We find the condition for this efficient transfer and show that in the case of additional interaction with noise, a distinct non-Arrhenius behavior develops that is markedly different from the usual Kramers-like activated transfer.

The current research presents simple synthesis, single crystal X-ray structure determination, Hirshfeld surface (HS) analysis, crystal voids studies, and density function theory (DFT) calculations of N-carbamothioylbenzamide and 1,3,5-triazinane-2,4,6-trithione co-crystal. Consequently, single crystal X-ray analysis revealed that the synthesized compounds are co-crystallized in a monoclinic crystal system with space group of P21/c and Z = 4. HS analysis visualized, explored, and subsequently quantified intermolecular interactions present in the crystal lattices of the co-crystallized compounds. HS analysis indicated close contacts associated with molecular interactions in greater depth and augments the significance of hydrogen atom contacts in crystal packing. Similarly, void studies assessed mechanical stability, and indicated the absence of any large cavity within the packed co-crystal. Moreover, the optimized molecular structures, using DFT at B3LYP/6–311G(d,p) level, were compared with the experimentally determined ones. HOMO–LUMO energy gap was determined and the frequencies as well as the molecular electrostatic potential surface were calculated at the B3LYP/6–311 G level. The DFT computed geometry was found to be in good agreement with the crystal data geometry. [ABSTRACT FROM AUTHOR]

Construction of functional synthetic systems that can reversibly bind and transport the most biologically important gaseous molecules, oxygen and nitric oxide (NO), remains a contemporary challenge. Myoglobin and nitrophorin perform these respective tasks employing a protein‐embedded heme center where one axial iron site is occupied by a histidine residue and the other is available for small molecule ligation, structural features that are extremely difficult to mimic in protein‐free environments. Indeed, the hitherto reported designs rely on sophisticated multistep syntheses for limiting access to one of the two axial coordination sites in small molecules. We have shown previously that binuclear Ga(III) and Al(III) corroles have available axial sites, and now report a redox‐active binuclear Fe(III) corrole, (1‐Fe)2, in which each (corrolato)Fe(III) center is 5‐coordinate, with one axial site occupied by an imidazole from the other corrole. The binuclear structure is further stabilized by attractive forces between the corrole π systems. Reaction of NO with (1‐Fe)2 affords mononuclear iron nitrosyls, and of functional relevance, the reaction is reversible: nitric oxide is released upon purging the nitrosyls with inert gases, thereby restoring (1‐Fe)2 in solutions or films. [ABSTRACT FROM AUTHOR]

Cholesteric liquid crystal (CLC) is anticipated to have applications such as blue light and ultraviolet (UV) light blocking for human skin owing to its selective wavelength reflection against incident sunlight through several hundred nanometres of a periodic helical twist structure. In this study, we investigated short chiral pitch control and enlargement of the blue phase (BP) temperature range by adding an achiral constituent of 4-n-octylbenzoic acid (8 BA) into CLC mixtures composed of three kinds of cholesteryl compounds: cholesteryl chloride, cholesteryl pelargonate and cholesteryl palmitate. Hydrogen bonding dependence of chiral pitch and BP temperature range were also investigated for achiral dopant (8 BA) and CLC mixture through temperature-dependent Fourier-transform infrared analysis. It was found that 40 wt% of 8 BA within the CLC mixture selectively reflected UV and blue light over 360–400 nm with a decrease of chiral pitch. It was also found that the BP temperature range increased by 15.6°C owing to hydrogen bond dimers composed of 8 BA molecules in the CLC mixture. [ABSTRACT FROM AUTHOR]

Phenyl-bis-(4,5-dihydroxy-2,7-disulfonato-3-naphthyl)methane, tetrasodium salt, self-assembles into a dimer in water. This dimer host forms complexes with a 1:1 host to guest stoichiometry with cyclodextrins (α, β and γ) in aqueous solution. The inclusion geometry of the cyclodextrins in the cavity of the dimer host is found to vary due to different sizes of the cyclodextrins. The complexation studies indicated that there is no distinction between host and guest for the cyclodextrin (α, β and γ) and the dimer. The stability constants of the dimer host with α-, β- and γ-cyclodextrins were 622, 2450 and 963 M−1, respectively. [ABSTRACT FROM AUTHOR]

In the title compound, C22H19NO5S·C2D6OS, the central six-membered ring has a slightly distorted boat conformation, while the fused pyrrolidine ring adopts an envelope conformation. These conformations are stabilized by O—HO hydrogen bonds between the main compound and solvent mol­ecules. In addition, intra­molecular C—HO hydrogen bonds in the main mol­ecule form two S(6) rings. Mol­ecules are connected by pairs of inter­molecular C—HO hydrogen bonds, forming dimers with a R²2(8) motif. These dimers form a three-dimensional network through O—HO, O—HS and C—HO hydrogen bonds with each other directly and through solvent mol­ecules. In addition, weak π–π stacking inter­actions [centroid-to-centroid distances = 3.9937 (10) and 3.9936 (10) Å, slippages of 2.034 and 1.681 Å] are observed. The inter­molecular contacts were qu­anti­fied using Hirshfeld surface analysis and two-dimensional fingerprint plots, revealing the relative contributions of the contacts to the crystal packing to be HH 41.7%, OH/HO 27.7%, CH/HC 17.0%, and SH/HS 7.5%. [ABSTRACT FROM AUTHOR]

We prove a quantitative Russo–Seymour–Welsh (RSW)-type result for random walks on two natural examples of random planar graphs: the supercritical percolation cluster in Z 2 and the Poisson Voronoi triangulation in R 2 . More precisely, we prove that the probability that a simple random walk crosses a rectangle in the hard direction with uniformly positive probability is stretched exponentially likely in the size of the rectangle. As an application, we prove a near optimal decorrelation result for uniform spanning trees for such graphs. This is the key missing step in the application of the proof strategy of Berestycki et al. (Ann Probab 48(1):1–52, 2020) for such graphs [in Berestycki et al. (2020), random walk RSW was assumed to hold with probability 1]. Applications to almost sure Gaussian-free field scaling limit for dimers on Temperleyan-type modification on such graphs are also discussed. [ABSTRACT FROM AUTHOR]

Spider dragline silk has attracted great interest due to its outstanding mechanical properties, which exceed those of man-made synthetic materials. Dragline silk, which is composed of at least major ampullate spider silk protein 1 and 2 (MaSp1 and MaSp2), contains a long repetitive domain flanked by N-terminal and C-terminal domains (NTD and CTD). Despite the small size of the CTD, this domain plays a crucial role as a molecular switch that regulates and directs spider silk self-assembly. In this study, we report the 1H, 13C, and 15N chemical shift assignments of the Latrodectus hesperus MaSp2 CTD in dimeric form at pH 7. Our solution NMR data demonstrated that this protein contains five helix regions connected by a flexible linker. [ABSTRACT FROM AUTHOR]

The crystal structure of a bis-urea derivative based on A1/A2-functionalized pillar[5]arene (DUP) that encapsulates dimethyl formamide (DMF) inside the macrocyclic cavity is reported. The crystal structure of DUP·DMF, C63H70N4O12·C3H7NO, reveals that out of two urea functionalized spacers, one arm is oriented above the macrocyclic cavity with strong hydrogen-bonding interactions between the urea H atoms and DMF guest, whereas, the other arm is positioned away from the macrocycle, leading to intermolecular hydrogen-bonding interactions between the urea H atoms of two adjacent pillar[5]arene macrocycles, resulting in the formation of a supramolecular dimer.

The study of localized surface plasmons (LSPs) in nanoscale structures is an essential step towards identifying optimal plasmonic modes that can facilitate robust optomechanical coupling and deepen our understanding of light–matter interactions at the nanoscale. This paper investigates, numerically, using the finite element method, LSP modes in a design comprising two coupled nano-ridges deposited on a gold layer with an interposing polymer spacer layer. Such a structure, usually referred to as a particle-on-mirror structure, shows exquisite optical properties at the nanoscale. We first examine the LSP modes of a single nano-ridge through the analysis of its scattering cross-section in the visible and infrared ranges. To enhance the plasmonic response, a thin polymer layer is placed at the middle of the ridge, which introduces additional LSP modes confined within the former. Then, we extend the analysis to the dimer configuration, which exhibits more complex and enhanced plasmonic behavior compared to a single nano-ridge. In particular, the dimer configuration yields LSP resonances with a quality factor enhancement of approximately threefold relative to a single nano-ridge. Furthermore, the presence of the polymer layer within the ridges significantly improves plasmon field localization and the quality factor. These findings underscore the potential of nano-ridge-based structures in advancing optomechanical coupling and offering valuable insights for the development of high-performance acousto-plasmonic devices. In particular, the proposed device could help significantly improve the design of nano-acousto-optic modulators, operating in the visible or in the near-infrared ranges, that require an enhanced light–phonon coupling rate.

We previously found that chronic adenosine A1 receptor stimulation with N6-Cyclopentyladenosine increased α-synuclein misfolding and neurodegeneration in a novel α-synucleinopathy model, a hallmark of Parkinson’s disease. Here, we aimed to synthesize a dimer caffeine-indan linked by a 6-carbon chain to cross the blood–brain barrier and tested its ability to bind α-synuclein, reducing misfolding, behavioral abnormalities, and neurodegeneration in our rodent model. Behavioral tests and histological stains assessed neuroprotective effects of the dimer compound. A rapid synthesis of the 18F-labeled analogue enabled Positron Emission Tomography and Computed Tomography imaging for biodistribution measurement. Molecular docking analysis showed that the dimer binds to α-synuclein N- and C-termini and the non-amyloid-β-component (NAC) domain, similar to 1-aminoindan, and this binding promotes a neuroprotective α-synuclein “loop” conformation. The dimer also binds to the orthosteric binding site for adenosine within the adenosine A1 receptor. Immunohistochemistry and confocal imaging showed the dimer abolished α-synuclein upregulation and aggregation in the substantia nigra and hippocampus, and the dimer mitigated cognitive deficits, anxiety, despair, and motor abnormalities. The 18F-labeled dimer remained stable post-injection and distributed in various organs, notably in the brain, suggesting its potential as a Positron Emission Tomography tracer for α-synuclein and adenosine A1 receptor in Parkinson’s disease therapy.