Ligands In Positions Research Articles

Molecular Binding of Cycloxydim to Acetyl-CoA Carboxylase in Cultivated Soybeans and Weed Plants

Acetyl-CoA carboxylase (ACC) is one of the main enzymes that play a regulatory role in the biosynthesis of fatty acids in plants. Cyclodime is one of the herbicides that is an inhibitor of this enzyme. Some weedy cereal plants, such as common hedgehog (Echinochloa crus-galli L.) and annual bluegrass (Poa annua L.), are resistant to cycloxyme. Other types of grass weeds – blood-red dewdrop (Digitaria sanguinalis (L.) Scop.) and green bristle (Setaria viridis (L.) P. Beauv.), on the contrary, are susceptible to the herbicide. The molecular mechanisms underlying ACC resistance are poorly understood. The explanation of the mechanism of resistance probably lies in the structure of ACC in different species. The use of bioinformatics methods will help to understand the mechanisms of adaptation based on the molecular properties of the enzyme, which will contribute to the creation of new herbicides. The purpose of this work was to study the specifics of the binding of cycloxydime to the ACC enzyme for each of these weed species, including soy (Glycine max (L.) Merr.). For weeds E. crus-galli and P. annua revealed from 6 to 7 possible complexes with different ligand positions relative to the receptor, which could potentially explain the mechanism of resistance. At the same time, a low binding energy was determined for the cycloxydime complex with G. max (up to –7.31 kcal/mol), which demonstrates the presence of other resistance mechanisms in the culture.

MAGPIE: An interactive tool for visualizing and analyzing protein-ligand interactions.

Quantitative tools to compile and analyze biomolecular interactions among chemically diverse binding partners would improve therapeutic design and aid in studying molecular evolution. Here we present Mapping Areas of Genetic Parsimony In Epitopes (MAGPIE), a publicly available software package for simultaneously visualizing and analyzing thousands of interactions between a single protein or small molecule ligand (the "target") and all of its protein binding partners ("binders"). MAGPIE generates an interactive three-dimensional visualization from a set of protein complex structures that share the target ligand, as well as sequence logo-style amino acid frequency graphs that show all the amino acids from the set of protein binders that interact with user-defined target ligand positions or chemical groups. MAGPIE highlights all the salt bridge and hydrogen bond interactions made by the target in the visualization and as separate amino acid frequency graphs. Finally, MAGPIE collates the most common target-binder interactions as a list of "hotspots," which can be used to analyze trends or guide the de novo design of protein binders. As an example of the utility of the program, we used MAGPIE to probe how different antibody fragments bind a viral antigen; how a common metabolite binds diverse protein partners; and how two ligands bind orthologs of a well-conserved glycolytic enzyme for a detailed understanding of evolutionarily conserved interactions involved in its activation and inhibition. MAGPIE is implemented in Python 3 and freely available at https://github.com/glasgowlab/MAGPIE, along with sample datasets, usage examples, and helper scripts to prepare input structures.

Molecular Docking of Nigella Sativa L. with PXR Receptors and the Effect of Thymoquinone on PXR Expression in HepG2 Cells

ABSTRACT. The interaction between herbal remedies and drugs is a fascinating phenomenon that might cause therapeutic complications in patients. Warfarin is an anticoagulant drug that provides anti-blood-clotting effects by inhibiting the formation of vitamin K-dependent coagulation factors, and warfarin interacts with the nuclear receptor PXR, subsequently modulating cytochrome P450 during the metabolism process. St. John's wort, an herbal medicine with antidepressant effects, can alter the pharmacokinetics of warfarin. Thymoquinone is one of the active compounds in N. sativa and has pharmacological activities such as anticoagulant, antidiabetic, diuretic, antidepressant, and anti-inflammatory effects. In this study, we investigated the compounds in Nigella sativa (N. sativa) against pregnane X receptor (PXR) and evaluated the impact of thymoquinone (TQ) administration on PXR expression in HepG2 cells. The molecular docking analysis was conducted utilizing the Molecular Operating Environment (MOE) with the PXR (PDB ID: 7AXJ). At the same time, the PXR gene expression was measured using RT-PCR instruments. The RMSD value in docking represents the deviation criteria between the native ligand position and the redocking position result, indicating the capability of MOE and PDB qualification for performing molecular docking. The docking analysis showed that warfarin had the strongest binding energy (7AXJ -6.0507) by forming hydrogen binding type on Arg410. Despite TQ being the major component, it also displayed a high affinity for the two PDB IDs (7AXJ -4.5962). Furthermore, the concurrent administration of warfarin and TQ (19.27 μM) in HepG2 cells showed a significant reduction in the relative mRNA expression of the PXR gene. Given the above-mentioned findings, our study adequately enables us to predict the mechanism behind herb-drug interactions (HDIs) implicating N. sativa, specifically the TQ compound to warfarin metabolism via the activation of the PXR receptor. Keywords: Thymoquinone, expression mRNA, PXR, molecular docking, HepG2 cells.

Effect of 6,6'-Substituents on Bipyridine-Ligated Ni Catalysts for Cross-Electrophile Coupling.

A family of 4,4'-tBu2-2,2'-bipyridine (tBubpy) ligands with substituents in either the 6-position, 4,4'-tBu2-6-Me-bpy (tBubpyMe), or 6 and 6'-positions, 4,4'-tBu2-6,6'-R2-bpy (tBubpyR2; R = Me, iPr, sBu, Ph, or Mes), was synthesized. These ligands were used to prepare Ni complexes in the 0, I, and II oxidation states. We observed that the substituents in the 6 and 6'-positions of the tBubpy ligand impact the properties of the Ni complexes. For example, bulkier substituents in the 6,6'-positions of tBubpy better stabilized (tBubpyR2)NiICl species and resulted in cleaner reduction from (tBubpyR2)NiIICl2. However, bulkier substituents hindered or prevented coordination of tBubpyR2 ligands to Ni0(cod)2. In addition, by using complexes of the type (tBubpyMe)NiCl2 and (tBubpyR2)NiCl2 as precatalysts for different XEC reactions, we demonstrated that the 6 or 6,6' substituents lead to major differences in catalytic performance. Specifically, while (tBubpyMe)NiIICl2 is one of the most active catalysts reported to date for XEC and can facilitate XEC reactions at room temperature, lower turnover frequencies were observed for catalysts containing tBubpyR2 ligands. A detailed study on the catalytic intermediates (tBubpy)Ni(Ar)I and (tBubpyMe2)Ni(Ar)I revealed several factors that likely contributed to the differences in catalytic activity. For example, whereas complexes of the type (tBubpy)Ni(Ar)I are low spin and relatively stable, complexes of the type (tBubpyMe2)Ni(Ar)I are high-spin and less stable. Further, (tBubpyMe2)Ni(Ar)I captures primary and benzylic alkyl radicals more slowly than (tBubpy)Ni(Ar)I, consistent with the lower activity of the former in catalysis. Our findings will assist in the design of tailor-made ligands for Ni-catalyzed transformations.

Iso-mukaadial acetate and ursolic acid acetate bind to Plasmodium Falciparum heat shock protein 70: towards targeting parasite protein folding pathway.

Plasmodium falciparum is the most lethal malaria parasite. P. falciparum Hsp70 (PfHsp70) is an essential molecular chaperone (facilitates protein folding) and is deemed a prospective antimalarial drug target. The present study investigates the binding capabilities of select plant derivatives, iso-mukaadial acetate (IMA) and ursolic acid acetate (UAA), against P. falciparum using an in silico docking approach. The interaction between the ligands and PfHsp70 was evaluated using plasmon resonance (SPR) analysis. Molecular docking, binding free energy analysis and molecular dynamics simulations were conducted towards understanding the mechanisms by which the compounds bind to PfHsp70. The molecular docking results revealed ligand flexibilities, conformations and positions of key amino acid residues and protein-ligand interactions as crucial factors accounting for selective inhibition of Hsp70. The simulation results also suggest protein-ligand van der Waals forces as the driving force guiding the interaction of these compounds with PfHsp70. Of the two compounds, UAA and IMA bound to PfHsp70 within the micromolar range based on surface plasmon resonance (SPR) based binding assay. Our findings pave way for future rational design of new selective compounds targeting PfHsp70.

CBe2 H5 - : Unprecedented 2σ/2π Double Aromaticity and Dynamic Structural Fluxionality in a Planar Tetracoordinate Carbon Cluster.

A 14-electron ternary anionic CBe2 H5 - cluster containing a planar tetracoordinate carbon (ptC) atom is designed herein. Remarkably, it can be stabilized by only two beryllium atoms with both π-acceptor/σ-donor properties and two hydrogen atoms, which means that the conversion from planar methane (transition state) to ptC species (global minimum) requires the substitution of only two hydrogen atoms. Moreover, two ligand H atoms exhibit alternate rotation, giving rise to interesting dynamic fluxionality in this cluster. The electronic structure analysis reveals the flexible bonding positions of ligand H atoms due to C-H localized bonds, highlighting the rotational fluxionality in the cluster, and two CBe2 3c-2e delocalized bonds endow its rare 2σ/2π double aromaticity. Unprecedentedly, the fluxional process exhibits a conversion in the type of bonding (σ bond↔π bond), which is an uncommon fluxional mechanism. The cluster can be seen as an attempt to apply planar hypercoordinate carbon species to molecular motors.

Interfacial rheology of lanthanide binding peptide surfactants at the air-water interface.

Peptide surfactants (PEPS) are studied to capture and retain rare earth elements (REEs) at air-water interfaces to enable REE separations. Peptide sequences, designed to selectively bind REEs, depend crucially on the position of ligands within their binding loop domain. These ligands form a coordination sphere that wraps and retains the cation. We study variants of lanthanide binding tags (LBTs) designed to complex strongly with Tb3+. The peptide LBT5- (with net charge -5) is known to bind Tb3+ and adsorb with more REE cations than peptide molecules, suggesting that undesired non-specific coulombic interactions occur. Rheological characterization of interfaces of LBT5- and Tb3+ solutions reveal the formation of an interfacial gel. To probe whether this gelation reflects chelation among intact adsorbed LBT5-:Tb3+ complexes or destruction of the binding loop, we study a variant, LBT3-, designed to form net neutral LBT3-:Tb3+ complexes. Solutions of LBT3- and Tb3+ form purely viscous layers in the presence of excess Tb3+, indicating that each peptide binds a single REE in an intact coordination sphere. We introduce the variant RR-LBT3- with net charge -3 and anionic ligands outside of the coordination sphere. We find that such exposed ligands promote interfacial gelation. Thus, a nuanced requirement for interfacial selectivity of PEPS is proposed: that anionic ligands outside of the coordination sphere must be avoided to prevent the non-selective recruitment of REE cations. This view is supported by simulation, including interfacial molecular dynamics simulations, and interfacial metadynamics simulations of the free energy landscape of the binding loop conformational space.

In silico study of inhibition activity of boceprevir drug against 2019-nCoV main protease.

Boceprevir drug is a ketoamide serine protease inhibitor with a linear peptidomimetic structure that exhibits inhibition activity against 2019-nCoV main protease. This paper reports electronic properties of boceprevir and its molecular docking as well as molecular dynamics simulation analysis with protein receptor. For this, the equilibrium structure of boceprevir has been obtained by DFT at B3LYP and ωB97XD levels with 6-311+G(d,p) basis set in gas and water mediums. HOMO-LUMO and absorption spectrum analysis have been used to evaluate the boceprevir's toxicity and photosensitivity, respectively. Molecular docking simulation has been performed to test the binding affinity of boceprevir with 2019-nCoV MPRO; which rendered a variety of desirable binding locations between the ligand and target protein's residue positions. The optimum binding location has been considered for molecular dynamics simulation. The findings have been addressed to clarify the boceprevir drug efficacy against the 2019-nCoV MPRO.

In silico simulation of hyperoside, isoquercetin, quercetin, and quercitrin as potential antivirals against the pNP868R protein of African swine fever virus.

African swine fever (ASF) causes disease in pigs with up to 100% mortality rates. There is no effective vaccine to protect against it. This study aimed to perform in silico docking of ASF virus (ASFV) pNP868R protein with potential flavonoid ligands to identify ligands that interfere with mRNA cap formation. The ASFV pNP868R protein was tested with hyperoside, isoquercetin, quercetin, and quercitrin in this in silico simulation. ASFV pNP868R protein was extracted from the Research Collaboration for Structural Bioinformatics Protein Data Bank (RCSB PDB) database with PDB ID 7D8U (https://www.rcsb.org/structure/7D8U). Standard ligands were separated from proteins using UCSF Chimera 1.13. The standard ligand was redocked to protein using AutoDockTools 1.5.6 with the AutoDock4 method for validation. In the docking process, the grid box size was 40 × 40 × 40 Å3 with x, y, and z coordinates of 16.433, -43.826, and -9.496, respectively. The molecular docking process of the proposed ligand-protein complex can proceed if the standard ligand position is not significantly different from its original position in the viral protein's pocket. The root mean square deviation (RMSD), root mean square fluctuation (RMSF), and radius of gyration (RoG) of the hyperoside with the lowest energy binding need to be analyzed with molecular dynamics using Groningen machine for chemical simulation 5.1.1. Molecular docking and dynamic simulation revealed that hyperoside had the most stable and compact binding to the pNP868R protein. Hyperoside binds to the protein at the minimum energy of -9.07 KJ/mol. The RMSD, RMSF, and RoG values of 0.281 nm, 0.2 nm, and 2.175 nm, respectively, indicate the stability and compactness of this binding. Hyperoside is the most likely antiviral candidate to bind to the pNP868R protein in silico. Therefore, it is necessary to test whether this flavonoid can inhibit mRNA capping in vitro and elicit the host immune response against uncapped viral mRNA.

Effect of β-Substitution and β,β'-Fusion on the Formation of Boron Complexes of Porphycenes.

Boron(III) complexation was investigated in a series of β-substituted porphycenes. Unlike meso-arylporphycenes, these macrocycles undergo a facile complexation reaction. Upon fusion of the β,β'-positions of the porphycene ligand, the complexation resulted in fast insertion of boron, forming the cisoid-B2OF2 complex. However, in the case of the other β-substituted porphycenes, only bis-BF2 complexes formed. The effect of these substituents on the core geometry and photophysical properties are elaborated here.

The cooperative effects of ligand substituent positions and solvents on spin crossover in Mn(III) complexes based on hexadentate Schiff-base ligands

Spin crossover (SCO), as a molecular bistable phenomenon, has attracted extensive interest. In this paper, the syntheses, crystal structures and magnetic properties of three Mn(III) hexadentate Schiff-base complexes [Mn(3-OMe-sal-N-1,5,8,12)]AsF6·H2O (1), [Mn(4-OMe-sal-N-1,5,8,12)]AsF6·H2O (2) and [Mn(5-OMe-sal-N-1,5,8,12)]AsF6(3) have been reported. The substituent positions of ligands and solvent molecules have a cooperative effect on SCO behavior. Complex 1 shows a complete SCO between the high-spin (HS, S = 2) and low-spin (LS, S = 1) states without thermal hysteresis, and complex 2 shows a gradual incomplete SCO behavior. The transition temperatures of 2 (T1/2 = 241 K) is 98 K higher than that of 1 (T1/2 = 143 K), which indicates that the ligand field strength of (4-OMe-sal-N-1,5,8,12)2– is stronger than that of (3-OMe-sal-N-1,5,8,12)2–. Due to the absence of crystallizing solvent water molecule, complex 3 maintains a HS state in the test temperature range.

Identification of Favorable Silica Surface Sites for Single‐Molecule Magnets

AbstractIndustrial data storage application based on single‐molecule magnets (SMMs) necessitates not only strong magnetic remanence at high temperatures but also requires the implementation of SMMs into a solid material to increase their durability and addressability. While the understanding of the relationship between the local structure of the metal and the resulting magnetic behavior is well understood in molecular systems, it remains challenging to establish a similar understanding for magnetic materials, especially for isolated lanthanide sites on surfaces. For instance, dispersed Dy(III) ions on silica prepared via surface organometallic chemistry exhibit slow magnetic relaxation at low temperatures, but the origin of these properties remains unclear. In this work, we modelled ten neutral complexes with coordination numbers (CN) between three and six ([Dy(OSiF3)3(O(SiF3)2)CN‐3]) representing possible surface sites for dispersed Dy(III) ions and investigated their SMM potential via ab initio CASSCF/RASSI‐SO calculations. Detailed analysis of the data shows the strong influence of the spatial position of the anionic ligands while the neutral ligands only play a minor role for the magnetic properties. In particular, a T‐shape like orientation of the anionic ligands is predicted to exhibit good SMM properties making it a promising targeted coordination environment for molecular and surface‐based SMMs.

Zn-based Metal-Organic Frameworks Using Triptycene Hexacarboxylate Ligands: Synthesis, Structure, and Gas-Sorption Properties.

A series of metal-organic frameworks (MOFs) based on zinc ions and two triptycene ligands of different size were synthesized under solvothermal conditions. The structural analyses revealed that these are isostructural three-dimensional-network MOFs. The high porosity and thermal stability of these MOFs can be attributed to the highly rigid triptycene-based ligands. Their BET specific surface areas depend on the size of the triptycene ligands. In contrast to these surface-area data, the H2 and CO2 adsorption of these MOFs is larger for MOFs with small pores. Consequently, we introduced functional groups to the bridge-head position of the triptycene ligands and investigated their effect on the gas-sorption properties. The corresponding results unveiled the role of the functional groups in the specific CO2 binding via an induced interaction between adsorbates and the functional groups. Excellent H2 and CO-2 properties in these MOFs were achieved in the absence of open metal sites.

Heteroleptic dirhodium(II,II) acetato-bipyridyl complexes: Evaluation as catalyst precursors for hydroformylation reactions

The synthesis of cationic bimetallic ‘pseudo-paddlewheel’ dirhodium(II,II) acetato-bipyridyl complexes of the type [Rh2(OAc)2(bis-4,4′-R-bipy)2]2+ containing either acetate (AcO-) or hexafluorophosphate (PF6-) counter ions is described. In both series, the 4 and 4′ positions of each bipyridyl ligand are substituted such that R = H, CF3 or OMe (complexes 1-3 for AcO- and 4-6 for PF6- derivatives). As catalyst precursors for the hydroformylation reaction, the complexes were initially evaluated using 1-octene as a substrate. The complex which displayed the greatest chemoselectivity toward aldehydes was evaluated further as a catalyst precursor for the hydroformylation of styrene, cyclohexene and 7-tetradecene as substrates. A correlation between product distributions in terms of chemo- and regioselectivity in the hydroformylation reaction versus axial site interaction is delineated. Recyclability was achieved through suitable modification of the substituent and counter ion, culminating in a simplistic method of post-catalytic precursor collection with minimal reduction of the catalytic activity over 5 cycles.

In-silico Assessment of Potent Immunomodulators from Pimpinella anisum and its Antioxidant Potential

New targets, effective substances, and safety in pharmacological models are highlighted by recent drug development. The study’s primary goal is to use an in-silico technique to determine the immunomodulatory potential of phytoconstituents from Pimpinella anisum. Several computer aided tool were utilized for in-silico. autodock vina is major free tool utilized to examine a drug discovery strategy based on the atomic-level screening of small compounds and proteins and protein-ligand interactions. Basic docking phases include ligand position, orientation, and binding affinities. The current methodology includes ligand choice, protein prep, target, ligand optimisation, target active binding site analysis, and binding affinity. SwissADME was used to assess the pharmacokinetic parameters, and Lipinski’s “rules” were used to assess drug similarity. In the current research paper six ligands such as P-anisaldehyde, trans-anethole, cis-anethole, estragole, and linalool were dock against two proteins 1M48 and 1P9M. Molecular docking studies suggest strong binding affinity between -6.9 to -4.2 in case on 1M48 and -6.2 to -4.7 in case of 1P9M. Further antioxidant potential of P. anisum using several solvents was determined. In-vitro antioxidant study and in-silico screening suggested that P. anisum ethanolic extract can be contributed in immunomodulation

Garcinoxanthones from Garcinia mangostana L. against SARS-CoV-2 infection and cytokine storm pathway inhibition: A viroinformatics study

Context: Mangosteen (Garcinia mangostana L.) is used in traditional medicine as an antibacterial, antioxidant, and anti-inflammatory. Aims: To determine the molecular mechanism and potential of garciniaxanthone derivate compounds from G. mangostana as SARS-CoV-2 antiviral and prevent cytokine storm through in silico approach. Methods: Ligand and protein samples were obtained from databases such as PubChem and Protein Databank, then drug-likeness analysis using Lipinski, Ghose, Veber, Egan, and Muege rules on SwissADME server, prediction of antiviral probability through PASSOnline server. Furthermore, molecular docking simulation with PyRx v1.0 software (Scripps Research, USA) with an academic license, identification of interactions and chemical bond positions of ligands on the target by PoseView server, 3D visualization of PyMOLv.2.5.2 software (Schrödinger, Inc., USA) with an academic license, molecular dynamics simulation for molecular stability prediction by CABS-flex v2.0 server, target prediction of antiviral candidate compounds by SwissTargetPrediction server, pathway analysis through STRING v11.5 database, and toxicity by ProTox-II server were used. Results: Garciniaxanthone C from G. mangostana was found to be a drug-like molecule with low toxicity. This can be a candidate for SARS-Cov-2 antiviral through inhibitor activity on two viral enzymes consisting of Mpro and replicase with a binding affinity value that is more negative than other garciniaxanthone derivates and is stable. Garciniaxanthone C is predicted to bind and inhibit pro-inflammatory proteins that trigger cytokine storms, such as NFKB1 and PTGS2. Conclusions: Garciniaxanthone derivative compounds from G. mangostana may be candidates for SARS-CoV-2 antiviral and preventing cytokine storm through garciniaxanthone C activity.

Positional Isomeric Cyano-Substituted Bis(2-phenylpyridine)(acetylacetonate)iridium Complexes for Efficient Organic Light-Emitting Diodes with Extended Color Range.

Bis(2-phenylpyridine)(acetylacetonate)iridium, Ir(ppy)2(acac), is a benchmark green emitter for phosphorescent organic light-emitting diodes (PhOLEDs). In this work, we reported three positional isomeric cyano-substituted Ir(ppy)2(acac) complexes, i.e., Ir(3-CN), Ir(4-CN), and Ir(10-CN), with the emission in the yellow to red region (544-625 nm). Through theoretical investigation and single-crystal analysis, it was found that the introduction of cyano substitution at various positions of the ppy ligand allows for tuning the electron distribution and coordination bond length of Ir complexes. Therefore, the charge transfer property of Ir complexes is enhanced such that the energy gap of the cyano-substituted Ir(ppy)2(acac) complexes was reduced. In addition, Ir(3-CN), Ir(4-CN), and Ir(10-CN) exhibited high PLQYs of 83, 54, and 75%, respectively, with the phosphorescence lifetime in the range of 0.79-2.08 μs. Notably, the device utilizing Ir(3-CN) as the emitter exhibited a maximum external quantum efficiency (EQE) of 25.4%, current efficiency of 56.9 cd A-1, power efficiency of 68.7 lm W-1, and brightness of 61,340 cd m-2 at 8 V. The EQE of this device remained 24.3 and 19.9% at luminances of 1,000 and 10,000 cd m-2, corresponding to the efficiency roll-off of 4.3 and 21.7%, respectively. Comparing to the Ir complexes using the ligand with an extended conjugated structure, our results demonstrated a simple molecular design strategy for phosphorescence emitters with reduced molecular weight for efficient PhOLEDs in the yellow to red color region.

Computational Study of Metal‐Organic Frameworks for Hydrogen Sulfide Adsorption: Grand Canonical Monte Carlo and Molecular Dynamics Simulations

AbstractHydrogen sulfide (H2S) is a highly toxic, and flammable acid gas that is widely present in confined spaces. However, conventional adsorption materials are inefficient and have poor reuse properties. Metal‐organic frameworks (MOFs) show potential viability as novel materials in gas adsorption. Herein, mainstream MOFs were investigated based on molecular simulation techniques to explore the differences contributing to H2S adsorption. The adsorption process of H2S in MOFs was simulated by Grand Canonical Monte Carlo (GCMC) method, and the diffusion behavior was investigated based on molecular dynamics (MD) simulations. The results showed that the interaction energy and isosteric heat of adsorption were important criteria for determining the adsorption performance of H2S. The regulation of open metal sites could help to further enhance the adsorption of H2S, and the pore structure of MOFs affected the capture of H2S. A higher self‐diffusion rate implies faster H2S capture. Hydrogen bonds affect the trapping efficiency of MOFs for H2S and the relative positions of ligands in the benzene ring cause subtle differences in adsorption. This study provides design strategies for the improvement of new high‐performing MOFs for H2S adsorption in confined spaces.

Quantifying the Electronic Effect of C4 and C4′ Positions of Bipyridine Ligand on Pd(II)/Rh(I)‐Catalyzed Conjugate Addition Reaction: A DFT Study

AbstractThe electronic effects of the bidentate ligands play a vital role in the transition metal‐catalyzed conjugate addition reactions. Here, the insertion step (rate‐determining step (RDS) of the conjugate addition) catalyzed by Pd(II)/Rh(I)‐complexes with 26 bipyridine‐type (bpy) ligands linking different substituent groups in the opposite sides (C4, C4′ position) are systematically studied by density functional theory (DFT). It is found that for both Pd(II)‐ and Rh(I)‐catalysis, the stronger the electron‐withdrawing group connecting to both C4 and C4′ positions of bpy ligands can promote the insertion step. The predominance of π‐back donation in Rh(I) and σ‐donation in Pd(II) is the main reason for above different electronic properties of Pd(II) and Rh(I)‐catalysis. This work gives enough theoretical guide to the rational design of the efficient transition metal‐based catalyst for conjugate addition.

Site-Selective Ligand Bridging among Multiple Internal Coordination Sites of a Metallomacrocycle and Its Conformational Regulation.

Metallomacrocycles with internal coordination sites have a high potential to precisely control the positions of the guest ligands and the overall shape of the assemblies by utilizing the directionality and reversibility of the coordination bonds. However, when such coordinative hosts possess multiple coordination sites, it was difficult to control to which coordination sites the incoming guest ligands bind, because such systems often result in a random, uncontrolled mixture. The metallomacrocycle that we now report, a hexanuclear palladium complex of hexapap possessing six internal coordination sites, can take two different conformations depending on the guests. One is an Alternate conformation, in which six coordination sites of pap alternatively point to Up-Down-Up-Down-Up-Down. The other is a Twisted conformation, in which the coordination sites direct Up-Middle-Down-Up-Middle-Down. Interestingly, linear ditopic α,ω-diamines are captured in three distinct cross-linking modes, and regulations between the two macrocyclic conformations have been realized by the lengths of the diamines. Furthermore, the heteroleptic site-selective bridging of two kinds of diamines has been achieved. It has been demonstrated that a slight difference in the diamine lengths leads to a significant change in the structure and selection of the produced host-guest macrocyclic complexes.