Lateral Metallation and Redistribution Reactions of Sodium Ferrates Containing Bulky 2,6-Diisopropyl-N-(trimethylsilyl)anilide Ligands

Alkali-metal ferrates containing amide groups have emerged as regioselective bases capable of promoting Fe−H exchanges of aromatic substrates. Advancing this area of heterobimetallic chemistry, a new series of sodium ferrates is introduced incorporating the bulky arylsilyl amido ligand N(SiMe₃)(Dipp) (Dipp=2,6-iPr₂-C₆H₃). Influenced by the large steric demands imposed by this amide, transamination of [NaFe(HMDS)₃] (HMDS=N(SiMe₃)₂) with an excess of HN(SiMe₃)(Dipp) led to the isolation of heteroleptic [Na(HMDS)₂Fe{N(SiMe₃)Dipp}]_∞ ( 1 ) resulting from the exchange of just one HMDS group. An alternative co-complexation approach, combining the homometallic metal amides [NaN(SiMe₃)Dipp] and [Fe{N(SiMe₃)Dipp}₂] induces lateral metallation of one Me arm from the SiMe₃ group in the iron amide furnishing tetrameric [NaFe{N(SiCH₂Me₂)Dipp}{N(SiMe₃)Dipp}]₄ ( 2 ). Reactivity studies support that this deprotonation is driven by the steric incompatibility of the single metal amides rather than the basic capability of the sodium reagent. Displaying synergistic reactivity, heteroleptic sodium ferrate 1 can selectively promote ferration of pentafluorobenzene using one of its HMDS arms to give heterotrileptic [Na{N(SiMe₃)Dipp}(HMDS)Fe(C₆F₅)]_∞ ( 4 ). Attempts to deprotonate less activated pyridine led to the isolation of NaHMDS and heteroleptic Fe(II) amide [(py)Fe{N(SiMe₃)Dipp}(HMDS)] ( 5 ), resulting from an alternative redistribution process which is favoured by the Lewis donor ability of this substrate.     

Synthetic and Structural Insights into the Zincation of Toluene: Direct Synergic Ring Metallation versus Indirect Nonsynergic Lateral Metallation

Unprecedented direct zincation of toluene can be achieved by using a bimetallic base that bypasses the acidic methyl group and instead affords a statistical mixture of the meta and para deprotonated regioisomers (see scheme).

     

Structural Insights into the Design of Synthetic Nanobody Libraries

Single domain antibodies from camelids, or nanobodies, are a unique class of antibody fragments with several advantageous characteristics: small monomeric size, high stability and solubility and easy tailoring for multiple applications. Nanobodies are gaining increasing acceptance as diagnostic tools and promising therapeutic agents in cancer and other diseases. While most nanobodies are obtained from immunized animals of the camelid family, a few synthetic nanobody libraries constructed in recent years have shown the capability of generating high quality nanobodies in terms of affinity and stability. Since this synthetic approach has important advantages over the use of animals, the recent advances are indeed encouraging. Here we review over a dozen synthetic nanobody libraries reported so far and discuss the different approaches followed in their construction and validation, with an emphasis on framework and hypervariable loop design as critical issues defining their potential as high-class nanobody sources.     

Structural and Mechanistic Insights into s‐Block Bimetallic Catalysis: Sodium Magnesiate‐Catalyzed Guanylation of Amines

To advance the catalytic applications of s‐block mixed‐metal complexes, sodium magnesiate [NaMg(CH₂SiMe₃)₃] ( 1 ) is reported as an efficient precatalyst for the guanylation of a variety of anilines and secondary amines with carbodiimides. First examples of hydrophosphination of carbodiimides by using a Mg catalyst are also described. The catalytic ability of the mixed‐metal system is much greater than that of its homometallic components [NaCH₂SiMe₃] and [Mg(CH₂SiMe₃)₂]. Stoichiometric studies suggest that magnesiate amido and guanidinate complexes are intermediates in these catalytic routes. Reactivity and kinetic studies imply that these guanylation reactions occur via (tris)amide intermediates that react with carbodiiimides in insertion steps. The rate law for the guanylation of N,N′‐diisopropylcarbodiimide with 4‐tert‐butylaniline catalyzed by 1 is first order with respect to [amine], [carbodiimide], and [catalyst], and the reaction shows a large kinetic isotopic effect, which is consistent with an amine‐assisted rate‐determining carbodiimide insertion transition state. Studies to assess the effect of sodium in these transformations denote a secondary role with little involvement in the catalytic cycle.     

Macrocycle Embrace: Encapsulation of Fluoroarenes by m‐Phenylene Ethynylene Host

We report structural characterization of a new member of m‐phenylene ethynylene ring family. This shape‐persistent macrocycle also co‐crystallizes with hexafluoro‐, 1,2,4,5‐tetrafluoro‐, 1,3,5‐trifluoro, and 1,4‐difluorobenzene. The four complexes are almost isostructural, and all show the fluoroarene included into the central cavity of the macrocycle. Characterized by multiple short C?H???F?C contacts, these inclusion complexes further dimerize in the solid state into a 2+2 assembly, in which the two macrocycles embrace each other by their large hydrophobic groups that are rotated by 60° relative to one another.     

meta‐Selective C−H Arylation of Fluoroarenes and Simple Arenes

Fluorine is known to promote ortho‐C?H metalation. Based upon this reactivity, we employed an activated norbornene that traps the ortho‐palladation intermediate and is then relayed to the meta position, leading to meta‐selective C?H arylation of fluoroarenes. Deuterium experiment suggests that this meta‐arylation is initiated by ortho C?H activation and the catalytic cycle is terminated by C‐2 protonation. A dual‐ligand system is crucial for the observed high reactivity and site selectivity. Applying this approach to simple benzene or other arenes also affords arylation products with good yield and site selectivity.     

Ni‐Catalyzed Synthesis of Fluoroarenes via [2+2+2] Cycloaddition Involving α‐Fluorine Elimination

A method for direct synthesis of tetrasubstituted fluoroarenes via nickel‐catalyzed [2+2+2] cycloaddition is presented. The reaction combines one molecule of 1,1‐difluoroethylene with two molecules of alkynes and involves sequential cleavage of the C?F and C?H bonds in difluoroethylene. The catalytic cycle is established by reduction of the intermediary Ni^II fluoride with a triethylborane‐based borate.     

Structural Insights into Novel 15-Prostaglandin Dehydrogenase Inhibitors

We discovered SW033291 in a high throughput chemical screen aimed at identifying 15-prostaglandin dehydrogenase (15-PGDH) modulators. The compound exhibited inhibitory activity in in vitro biochemical and cell-based assays of 15-PGDH activity. We subsequently demonstrated that this compound, and several analogs thereof, are effective in in vivo mouse models of bone marrow transplant, colitis, and liver regeneration, where increased levels of PGE2 positively potentiate tissue regeneration. To better understand the binding of SW033291, we carried out docking studies for both the substrate, PGE2, and an inhibitor, SW033291, to 15-PGDH. Our models suggest similarities in the ways that PGE2 and SW033291 interact with key residues in the 15-PGDH-NAD+ complex. We carried out molecular dynamics simulations (MD) of SW033291 bound to this complex, in order to understand the dynamics of the binding interactions for this compound. The butyl side chain (including the sulfoxide) of SW033291 participates in crucial binding interactions that are similar to those observed for the C15-OH and the C16-C20 alkyl chain of PGE2. In addition, interactions with residues Ser138, Tyr151, and Gln148 play key roles in orienting and stabilizing SW033291 in the binding site and lead to enantioselectivity for the R-enantiomer. Finally, we compare the binding mode of (R)-S(O)-SW033291 with the binding interactions of published 15-PGDH inhibitors.     

Insights into the Complexity of Weak Intermolecular Interactions Interfering in Host–Guest Systems

The recognition properties of heteroditopic hemicryptophane hosts towards anions, cations, and neutral pairs, combining both cation–π and anion–π interaction sites, were investigated to probe the complexity of interfering weak intermolecular interactions. It is suggested from NMR experiments, and supported by CASSCF/CASPT2 calculations, that the binding constants of anions can be modulated by a factor of up to 100 by varying the fluorination sites on the electron‐poor aromatic rings. Interestingly, this subtle chemical modification can also reverse the sign of cooperativity in ion‐pair recognition. Wavefunction calculations highlight how short‐ and long‐range interactions interfere in this recognition process, suggesting that a disruption of anion–π interactions can occur in the presence of a co‐bound cation. Such molecules can be viewed as prototypes for examining complex processes controlled by the competition of weak interactions.     

Insights into Structural Modifications of Valproic Acid and Their Pharmacological Profile

Valproic acid (VPA) is a well-established anticonvulsant drug discovered serendipitously and marketed for the treatment of epilepsy, migraine, bipolar disorder and neuropathic pain. Apart from this, VPA has potential therapeutic applications in other central nervous system (CNS) disorders and in various cancer types. Since the discovery of its anticonvulsant activity, substantial efforts have been made to develop structural analogues and derivatives in an attempt to increase potency and decrease adverse side effects, the most significant being teratogenicity and hepatotoxicity. Most of these compounds have shown reduced toxicity with improved potency. The simple structure of VPA offers a great advantage to its modification. This review briefly discusses the pharmacology and molecular targets of VPA. The article then elaborates on the structural modifications in VPA including amide-derivatives, acid and cyclic analogues, urea derivatives and pro-drugs, and compares their pharmacological profile with that of the parent molecule. The current challenges for the clinical use of these derivatives are also discussed. The review is expected to provide necessary knowledgebase for the further development of VPA-derived compounds.     

Boosting Conjugate Addition to Nitroolefins Using Lithium Tetraorganozincates: Synthetic Strategies and Structural Insights

We report the first transition metal catalyst- and ligand-free conjugate addition of lithium tetraorganozincates (R₄ZnLi₂) to nitroolefins. Displaying enhanced nucleophilicity combined with unique chemoselectivity and functional group tolerance, homoleptic aliphatic and aromatic R₄ZnLi₂ provide access to valuable nitroalkanes in up to 98 % yield under mild conditions (0 °C) and short reaction time (30 min). This is particularly remarkable when employing β-nitroacrylates and β-nitroenones, where despite the presence of other electrophilic groups, selective 1,4 addition to the C=C is preferred. Structural and spectroscopic studies confirmed the formation of tetraorganozincate species in solution, the nature of which has been a long debated issue, and allowed to unveil the key role played by donor additives on the aggregation and structure of these reagents. Thus, while chelating N,N,N’,N’-tetramethylethylenediamine (TMEDA) and (R,R)-N,N,N’,N’-tetramethyl-1,2-diaminocyclohexane (TMCDA) favour the formation of contacted-ion pair zincates, macrocyclic Lewis donor 12-crown-4 triggers an immediate disproportionation process of Et₄ZnLi₂ into equimolar amounts of solvent-separated Et₃ZnLi and EtLi.     

A Nucleophilicity Scale for the Reactivity of Diazaphospholenium Hydrides: Structural Insights and Synthetic Applications

Nucleophilicity parameters (N, s_N) of a group of representative diazaphospholenium hydrides were derived by kinetic investigations of their hydride transfer to a series of reference electrophiles with known electrophilicity (E) values, using the Mayr equation log k₂=s_N(N+E). The N scale covers over ten N units, ranging from the most reactive hydride donor (N=25.5) to the least of the scale (N=13.5). This discloses the highest N value ever quantified in terms of Mayr's nucleophilicity scales reported for neutral transition‐metal‐free hydride donors and implies an exceptional reactivity of this reagent. Even the least reactive hydride donor of this series is still a better hydride donor than those of many other nucleophiles such as the C?H, B?H, Si?H and transition‐metal M?H hydride donors. Structure–reactivity analysis reveals that the outstanding hydricity of 2‐H‐1,3,2‐diazaphospholene benefits from the unsaturated skeleton.     

Conventional Molecular and Novel Structural Mechanistic Insights into Orderly Organelle Interactions

The orderly organelle interaction network is prerequisite for normal life activity of cell, ensuring a balance between communication and uniqueness of organelles. Disorder organelle interaction is implicated in the occurrence and development of many diseases. An in-depth understanding of mechanisms of orderly organelle interaction helps to reveal the pathogenesis of related diseases. Chemical and genetic tools have identified the roles of specific proteins in orderly organelle interaction; however, little is known about the modes, functions and mechanisms of orderly interaction between organelles. With rapid development of imaging tools, deep-going insights into the structure feature of cell membranes have substantially improved our understanding of the mechanisms of ordered organelle interactions. This review summarizes the conventional molecular mechanism of orderly organelle interactions, and highlights the new progress regarding membrane structure and the novel structural mechanism of orderly organelle transport.     

Structural Insights into Peptides Bound to the Surface of Silica Nanopores

The structure and surface functionalization of biologically relevant silica-based hybrid materials was investigated by 2D solid-state NMR techniques combined with dynamic nuclear polarization (DNP). This approach was applied to a model system of mesoporous silica, which was modified through in-pore grafting of small peptides by solid-phase peptide synthesis (SPPS). To prove the covalent binding of the peptides on the surface, DNP-enhanced solid-state NMR was used for the detection of ¹⁵N NMR signals in natural abundance. DNP-enhanced heterocorrelation experiments with frequency switched Lee–Goldburg homonuclear proton decoupling (¹H–¹³C and ¹H–¹⁵N CP MAS FSLG HETCOR) were performed to verify the primary structure and configuration of the synthesized peptides. ¹H FSLG spectra and ¹H-²⁹Si FSLG HETCOR correlation spectra were recorded to investigate the orientation of the amino acid residues with respect to the silica surface. The combination of these NMR techniques provides detailed insights into the structure of amino acid functionalized hybrid compounds and allows for the understanding for each synthesis step during the in-pore SPPS.     

Structural and Mechanistic Insights into CO2 Activation by Nitrogenase Iron Protein

The Fe protein of nitrogenase catalyzes the ambient reduction of CO₂ when its cluster is present in the all-ferrous, [Fe₄S₄]⁰ oxidation state. Here, we report a combined structural and theoretical study that probes the unique reactivity of the all-ferrous Fe protein toward CO₂. Structural comparisons of the Azotobacter vinelandii Fe protein in the [Fe₄S₄]⁰ and [Fe₄S₄]⁺ states point to a possible asymmetric functionality of a highly conserved Arg pair in CO₂ binding and reduction. Density functional theory (DFT) calculations provide further support for the asymmetric coordination of O by the “proximal” Arg and binding of C to a unique Fe atom of the all-ferrous cluster, followed by donation of protons by the proximate guanidinium group of Arg that eventually results in the scission of a C−O bond. These results provide important mechanistic and structural insights into CO₂ activation by a surface-exposed, scaffold-held [Fe₄S₄] cluster.     

Statistical Investigation into the Structural Complementarity of Natural Products and Synthetic Compounds

The potential of new natural products as an important source for the exploration and development of new drugs and crop protection products is a long way from being exhausted. The statistical analysis of the structures of the natural and synthetically derived compounds has shown conspicuous variations in structural types in the natural products derived from different natural sources, which can be utilized in the search for individual active substances. The occasionally voiced prepossession that natural products have already been sufficiently examined and therefore no more innovations are to be expected can definitely be rejected.     

Structural and Magnetic Insights into the Trinuclear Ferrocenophane and Unexpected Hydrido Inverse Crown Products of Alkali‐Metal‐Mediated Manganation(II) of Ferrocene

With the aim of introducing the diisopropylamide [NiPr₂] ^? ligand to alkali‐metal‐mediated manganation (AMMMn) chemistry, the temperature‐dependent reactions of a 1:1:3 mixture of butylsodium, bis(trimethylsilylmethyl)manganese(II), and diisopropylamine with ferrocene in hexane/toluene have been investigated. Performed at reflux temperature, the reaction affords the surprising, ferrocene‐free, hydrido product [Na₂Mn₂ (μ‐H)₂{N(iPr)₂}₄]?2 toluene ( 1 ), the first Mn hydrido inverse crown complex. Repeating the reaction rationally, excluding ferrocene, produces 1 in an isolated crystalline yield of 62 %. At lower temperatures, the same bimetallic amide mixture leads to the manganation of ferrocene to generate the first trimanganese, trinuclear ferrocenophane, [{Fe(C₅H₄)₂}₃{Mn₃Na₂(NiPr₂)₂ (HNiPr₂)₂}] ( 2 ) in an isolated crystalline yield of 81 %. Both 1 and 2 have been characterised by X‐ray crystallographic studies. The magnetic properties of paramagnetic 1 and 2 have also been examined by variable‐temperature magnetisation measurements on powdered samples. For 1 , the room‐temperature value for χT is 3.45 cm³ K mol^?1, and on lowering the temperature a strong antiferromagnetic coupling between the two Mn ions is observed. For 2 , the room‐temperature value for χT is 4.06 cm³ K mol^?1, which is significantly lower than the expected value for three isolated paramagnetic Mn^II ions.     

Structural Insights into the Trp‐Cage Folding Intermediate Formation

The 20 residue long Trp‐cage is the smallest protein known, and thus has been the subject of several in vitro and in silico folding studies. Here, we report the multistate folding scenario of the miniprotein in atomic detail. We detected and characterized different intermediate states by temperature dependent NMR measurements of the ¹⁵N and ¹³C/¹⁵N labeled protein, both at neutral and acidic pH values. We developed a deconvolution technique to characterize the invisible—fully folded, unfolded and intermediate—fast exchanging states. Using nonlinear fitting methods we can obtain both the thermodynamic parameters (ΔH^F–I, T_m^F–I, ΔC_p^F–I and ΔH^I–U, T_m^I–U, ΔC_p^I–U) and the NMR chemical shifts of the conformers of the multistate unfolding process. During the unfolding of Trp‐cage distinct intermediates evolve: a fast‐exchanging intermediate is present under neutral conditions, whereas a slow‐exchanging intermediate‐pair emerges at acidic pH. The fast‐exchanging intermediate has a native‐like structure with a short α‐helix in the G¹¹–G¹⁵ segment, whereas the slow‐exchanging intermediate‐pair presents elevated dynamics, with no detectable native‐like residue contacts in which the G¹¹? P¹² peptide bond has either cis or trans conformation. Heteronuclear relaxation studies combined with MD simulations revealed the source of backbone mobility and the nature of structural rearrangements during these transitions. The ability to detect structural and dynamic information about folding intermediates in vitro provides an excellent opportunity to gain new insights into the energetic aspects of the energy landscape of protein folding. Our new experimental data offer exceptional testing ground for further computational simulations.     

Conformational Selection Mechanism Provides Structural Insights into the Optimization of APC-Asef Inhibitors

Metastasis is the major cause of death in colorectal cancer and it has been proven that inhibiting an interaction between adenomatous polyposis coli (APC) and Rho guanine nucleotide exchange factor 4 (Asef) efficaciously restrain metastasis. However, current inhibitors cannot achieve a satisfying effect in vivo and need to be optimized. In the present study, we applied molecular dynamics (MD) simulations and extensive analyses to apo and holo APC systems in order to reveal the inhibitor mechanism in detail and provide insights into optimization. MD simulations suggested that apo APC takes on a broad array of conformations and inhibitors stabilize conformation selectively. Representative structures in trajectories show specific APC-ligand interactions, explaining the different binding process. The stability and dynamic properties of systems elucidate the inherent factors of the conformation selection mechanism. Binding free energy analysis quantitatively confirms key interface residues and guide optimization. This study elucidates the conformation selection mechanism in APC-Asef inhibition and provides insights into peptide-based drug design.