Dimeric Complex Research Articles

ZEPPI: Proteome-scale sequence-based evaluation of protein–protein interaction models

We introduce ZEPPI (Z-score Evaluation of Protein-Protein Interfaces), a framework to evaluate structural models of a complex based on sequence coevolution and conservation involving residues in protein-protein interfaces. The ZEPPI score is calculated by comparing metrics for an interface to those obtained from randomly chosen residues. Since contacting residues are defined by the structural model, this obviates the need to account for indirect interactions. Further, although ZEPPI relies on species-paired multiple sequence alignments, its focus on interfacial residues allows it to leverage quite shallow alignments. ZEPPI can be implemented on a proteome-wide scale and is applied here to millions of structural models of dimeric complexes in the Escherichia coli and human interactomes found in the PrePPI database. PrePPI's scoring function is based primarily on the evaluation of protein-protein interfaces, and ZEPPI adds a new feature to this analysis through the incorporation of evolutionary information. ZEPPI performance is evaluated through applications to experimentally determined complexes and to decoys from the CASP-CAPRI experiment. As we discuss, the standard CAPRI scores used to evaluate docking models are based on model quality and not on the ability to give yes/no answers as to whether two proteins interact. ZEPPI is able to detect weak signals from PPI models that the CAPRI scores define as incorrect and, similarly, to identify potential PPIs defined as low confidence by the current PrePPI scoring function. A number of examples that illustrate how the combination of PrePPI and ZEPPI can yield functional hypotheses are provided.

Closing the Gap Between Gas Phase and Condensed Phase: Fragmentation Studies of the Thiomethoxymethyl Complex [(bipy)Pt(CH3)2(CH2SCH3)]+

AbstractCollision‐induced dissociation (CID) of the mass‐selected cation [(bipy)Pt(CH3)2(CH2SCH3)]+ in an ion‐trap mass‐spectrometer results in the losses of the neutrals ethane, ethene, dimethyl sulfide, methane, ethyl methyl sulfide, and propane. The generation of the first four neutrals is also observed, when the isolated, dimeric complex [(bipy)Pt(CH3)2(CH2SCH3)]2[SbF6]2 is heated in the condensed phase. While the product distribution is very similar regardless of whether the complex is heated in the solid state or in solution, ethane loss, i. e. the quite rare event of an sp3‐sp3 C−C reductive elimination from a platinum(IV) complex, dominates in the gas‐phase experiment. However, when the counter anion [SbF6]− is exchanged by the more weakly coordinating anion [BAr4F]−, the amounts of ethane and ethene are increased also in the condensed phase. These sum of observations indicates the similarities of the fragmentation of [(bipy)Pt(CH3)2(CH2SCH3)]+ in both phases. Thus, a correlation of processes in both environments is possible for selected systems (and particularly for unimolecular processes), but the choice of the proper conditions is crucial for a meaningful comparison.

Characterization of Deformational Isomerization Potential and Interconversion Dynamics with Ultrafast X-ray Solution Scattering.

Dimeric complexes composed of d8 square planar metal centers and rigid bridging ligands provide model systems to understand the interplay between attractive dispersion forces and steric strain in order to assist the development of reliable methods to model metal dimer complexes more broadly. [Ir2 (dimen)4]2+ (dimen = para-diisocyanomenthane) presents a unique case study for such phenomena, as distortions of the optimal structure of a ligand with limited conformational flexibility counteract the attractive dispersive forces from the metal and ligand to yield a complex with two ground state deformational isomers. Here, we use ultrafast X-ray solution scattering (XSS) and optical transient absorption spectroscopy (OTAS) to reveal the nature of the equilibrium distribution and the exchange rate between the deformational isomers. The two ground state isomers have spectrally distinct electronic excitations that enable the selective excitation of one isomer or the other using a femtosecond duration pulse of visible light. We then track the dynamics of the nonequilibrium depletion of the electronic ground state population─often termed the ground state hole─with ultrafast XSS and OTAS, revealing a restoration of the ground state equilibrium in 2.3 ps. This combined experimental and theoretical study provides a critical test of various density functional approximations in the description of bridged d8-d8 metal complexes. The results show that density functional theory calculations can reproduce the primary experimental observations if dispersion interactions are added, and a hybrid functional, which includes exact exchange, is used.

Deciphering Charge Transfer Processes in Transition Metal Complexes from the Perspective of Ultrafast Electronic and Nuclear Motions.

Chemical transformations in charge transfer states result from the interplay between electronic dynamics and nuclear reorganization along excited-state trajectories. Here, we investigate the ultrafast structural dynamics following photoinduced electron transfer from the metal-metal-to-ligand charge transfer state of an electron donor, a Pt dimer complex, to a covalently linked electron acceptor group using ultrafast time-resolved wide-angle X-ray scattering and optical transient absorption spectroscopy methods to disentangle the interdependence of the excited-state electronic and nuclear dynamics. Following photoexcitation, Pt-Pt bond formation and contraction takes up to 1 ps, much slower than the corresponding process in analogous complexes without electron acceptor groups. Because the Pt-Pt distance change is slow with respect to excited-state electron transfer, it can affect the rate of electron transfer. These results have potential impacts on controlling electron transfer rates via structural alterations to the electron donor group, tuning the charge transfer driving force.

A conserved N-terminal motif of CUL3 contributes to assembly and E3 ligase activity of CRL3KLHL22

The CUL3-RING E3 ubiquitin ligases (CRL3s) play an essential role in response to extracellular nutrition and stress stimuli. The ubiquitin ligase function of CRL3s is activated through dimerization. However, how and why such a dimeric assembly is required for its ligase activity remains elusive. Here, we report the cryo-EM structure of the dimeric CRL3KLHL22 complex and reveal a conserved N-terminal motif in CUL3 that contributes to the dimerization assembly and the E3 ligase activity of CRL3KLHL22. We show that deletion of the CUL3 N-terminal motif impairs dimeric assembly and the E3 ligase activity of both CRL3KLHL22 and several other CRL3s. In addition, we found that the dynamics of dimeric assembly of CRL3KLHL22 generates a variable ubiquitination zone, potentially facilitating substrate recognition and ubiquitination. These findings demonstrate that a CUL3 N-terminal motif participates in the assembly process and provide insights into the assembly and activation of CRL3s.

Palladium Complexes Derived from Waste as Catalysts for C-H Functionalisation and C-N Bond Formation

Three-way catalysts (TWCs) are widely used in vehicles to convert the exhaust emissions from internal combustion engines into less toxic pollutants. After around 8–10 years of use, the declining catalytic activity of TWCs causes them to need replacing, leading to the generation of substantial amounts of spent TWC material containing precious metals, including palladium. It has previously been reported that [NnBu4]2[Pd2I6] is obtained in high yield and purity from model TWC material using a simple, inexpensive and mild reaction based on tetrabutylammonium iodide in the presence of iodine. In this contribution, it is shown that, through a simple ligand exchange reaction, this dimeric recovery complex can be converted into PdI2(dppf) (dppf = 1,1′-bis(diphenylphosphino)ferrocene), which is a direct analogue of a commonly used catalyst, PdCl2(dppf). [NnBu4]2[Pd2I6] displayed high catalytic activity in the oxidative functionalisation of benzo[h]quinoline to 10-alkoxybenzo[h]quinoline and 8-methylquinoline to 8-(methoxymethyl)quinoline in the presence of an oxidant, PhI(OAc)2. Near-quantitative conversions to the desired product were obtained using a catalyst recovered from waste under milder conditions (50 °C, 1–2 mol% Pd loading) and shorter reaction times (2 h) than those typically used in the literature. The [NnBu4]2[Pd2I6] catalyst could also be recovered and re-used multiple times after the reaction, providing additional sustainability benefits. Both [NnBu4]2[Pd2I6] and PdI2(dppf) were also found to be active in Buchwald–Hartwig amination reactions, and their performance was optimised through a Design of Experiments (DoE) study. The optimised conditions for this waste-derived palladium catalyst (1–2 mol% Pd loading, 3–6 mol% of dppf) in a bioderived solvent, cyclopentyl methyl ether (CPME), offer a more sustainable approach to C-N bond formation than comparable amination protocols.

Unravelling the role of precursors phosphine`s features in governing the reactivity of [MCl2(P-P)] (M = Pd, Pt) towards formation of thiolate complexes via S−S and S−C bond cleavage

Group 10 thiolate complexes have been in the quest zone of research due to pertinent catalytic potential. The present work unravels the role of precursor phosphine`s feature in their reactivity towards 4,6-dimethylpyrimidine-2-thiol and subsequent thiolate complex. Synthesized thiolate complexes were thoroughly characterized using elemental analyses, NMR (1H, 13C{1H}, 31P{1H}), UV–Vis spectroscopy and Single Crystal X-ray diffraction analyses. Treatment of [MCl2(PPh3)2] (M = Pd, Pt) with two equivalents of NaSC4H(4,6-Me)N2 resulted in chelated [Pd{κ-S, κ-N: SC4H(4,6-Me)2N2}{SC4H(4,6-Me)2N2}(PPh3)] (1a) as well as an expected trans compound [Pt{SC4H(4,6-Me)2N2}2(PPh3)2] (1b). A similar reaction with the chelating phosphine ‘dppm’ (dppm = 1,1-bis(diphenylphosphino)methane) as an ancillary ligand resulted in the serendipitous product of composition [Pd2(µ2-S){SC4H(4,6-Me)2N2}2(µ2-dppm)2] (2a) depending upon competitive cleavage of S-S and S-C bond. The reaction of [PdCl2(dppe)] afforded a cis configured compound [Pd{2-SC4H(4,6-Me)2N2}2(dppe)] (2b). Contrary, the similar reaction of [PdCl2(dppp)] results in removal of ‘dppp’ (1,3-bis(diphenylphosphino)propane) yielding the chelated complex [Pd{κ-S, κ-N: SC4H(4,6-Me)2N2}2] (2c). Above all, the reactivity of 4,6-dimethylpyrimidine-2-thiol significantly differs compared to unsubstituted pyrimidyl, pyridyl analogue which has been attributed to the additional richness of electrons/activation in the ring which in turn facilitates competitive reactivity pattern of S-S and S-C bond. The virtue of such activation can easily be understood by the isolation of complex [Pd2(µ2-S){SC4H(4,6-Me)2N2}2(µ2-dppm)2] (2a). Rationalization of results via DFT calculation reveals that projection angle P-M-P (ranging from ∼75 to 92°) driven structural change in the chelating phosphine and associated degree of softness in ligand molecule played a crucial role in governing the resulting product of substitution reaction as dimeric, monomeric and chelated complexes. Thus, projection angle- driven geometrical and electronic structure and variation provide opportunity and direction to efficiently derive biologically as well as academically important complexes.

Structural basis for dimerization of a paramyxovirus polymerase complex

The transcription and replication processes of non-segmented, negative-strand RNA viruses (nsNSVs) are catalyzed by a multi-functional polymerase complex composed of the large protein (L) and a cofactor protein, such as phosphoprotein (P). Previous studies have shown that the nsNSV polymerase can adopt a dimeric form, however, the structure of the dimer and its function are poorly understood. Here we determine a 2.7 Å cryo-EM structure of human parainfluenza virus type 3 (hPIV3) L–P complex with the connector domain (CD′) of a second L built, while reconstruction of the rest of the second L–P obtains a low-resolution map of the ring-like L core region. This study reveals detailed atomic features of nsNSV polymerase active site and distinct conformation of hPIV3 L with a unique β-strand latch. Furthermore, we report the structural basis of L–L dimerization, with CD′ located at the putative template entry of the adjoining L. Disruption of the L–L interface causes a defect in RNA replication that can be overcome by complementation, demonstrating that L dimerization is necessary for hPIV3 genome replication. These findings provide further insight into how nsNSV polymerases perform their functions, and suggest a new avenue for rational drug design.

Evaluation of the Homogenous Mobility Shift Assay for Infliximab and Adalimumab Anti-drug Antibody Detection in the Clinical Laboratory.

Detecting antidrug antibodies (ADAs) against infliximab or adalimumab is useful for therapeutic drug monitoring. Various ADA detection methods exist, and antibody titer is an output in some algorithms. Homogenous mobility shift assay (HMSA) measures relative ADA concentration and determines drug-ADA complex size in vitro. However, the relevance of complex size determination in drug monitoring remains unclear. Hence, the association between complex size, ADA concentration, and sample detectable neutralizing activity was evaluated. Sera from infliximab-treated and adalimumab-treated patients who tested positive for ADA in the National Screening Service were analyzed using 3 ADA assays. HMSA determined the relative ADA concentrations and complex sizes, competitive ligand-binding assay evaluated the sample neutralizing capacity, and enzyme-linked immunosorbent assay detected immunoglobulin (Ig)G4 ADA. Most ADA-positive samples (>80%) formed drug-ADA dimer complexes, whereas 17% had dimer and multimer complexes, and 3% had multimeric complexes. Multimer presence had 100% positive predictive value for detectable neutralizing activity. ADA concentration and detectable neutralizing activity were moderately correlated (r = 0.65) in adalimumab-treated patients and strongly correlated (r = 0.81) in infliximab-treated patients. In adalimumab-treated patients, multimer presence was a stronger predictor of neutralizing activity than ADA concentration was, but not in infliximab-treated patients. However, in infliximab-treated patient samples, multimer presence revealed a distinct subset with high ADA concentrations, neutralizing activity, and IgG4 ADA. Multimers detected using HMSA had a strong positive predictive value for competitive ligand-binding assay detectable neutralizing activity. Multimeric IgG4-containing ADA-drug complexes revealed a distinct subset of infliximab-treated patient samples, whose clinical relevance merits further investigation.

Synthesis and Structure of [η5-1,2,4-(Me3Si)3C5H2]2Th(bipy) and Its Reactivity toward Small Molecules.

Halide exchange of (Cp3tms)2ThCl2 (1; Cp3tms = η5-1,2,4-(Me3Si)3C5H2) with Me3SiI furnishes (Cp3tms)2ThI2 (2), which is then reduced with potassium graphite (KC8) in the presence of 2,2'-bipyridine to give the thorium bipyridyl metallocene (Cp3tms)2Th(bipy) (3) in good yield. Complex 3 was fully characterized and readily reacted with various small molecules. For example, 3 may serve as a synthetic equivalent for the (Cp3tms)2Th(II) fragment when exposed to CuI, Ph2S2, organic azides, and CS2. Moreover, upon the addition of thiobenzophenone Ph2CS, p-methylbenzaldehyde (p-MeC6H4)CHO, benzophenone Ph2CO, amidate PhCONH(p-tolyl), seleno-ketone (p,p'-dimethoxy), selenobenzophenone (p-MeOPh)2CSe, di(p-tolyl)methanimine (p-tolyl)2C═NH, 1,2-di(benzylidene)hydrazine (PhCH═N)2, and nitriles PhCN, PhCH2CN, and Ph2CHCN C-C coupling results to give (Cp3tms)2Th[(bipy)(Ph2CS)] (8), (Cp3tms)2Th[(bipy)(p-MePhCHO)] (9), (Cp3tms)2Th[(bipy)(Ph2CO)] (10), (Cp3tms)2Th[(bipy){(p-tolylNH)(Ph)CO}] (11), (Cp3tms)2Th[(bipy){(p-MeOPh)2CSe}] (12), (Cp3tms)2Th[(bipy){(p-tolyl)2CNH}] (13), (Cp3tms)2Th[(bipy)(PhCHNN═CHPh)] (14), (Cp3tms)2Th[(bipy)(PhCN)] (16), (Cp3tms)2Th[(bipy)(PhCH2CN)] (17), and (Cp3tms)2Th[(bipy)(Ph2CHCN)] (18), respectively. However, when thiazole is added to 3, the dimeric sulfido complex [(Cp3tms)2Th]2[μ-(bipy)CH2NCHCHS]2 (15) can be isolated. Moreover, the addition of isonitriles such as Me3CNC and PhCH2NC to 3 results in C-N bond cleavage and C-C coupling processes to form the thorium isocyanido amido complexes (Cp3tms)2Th[4-(Me3C)bipy](NC) (19) and (Cp3tms)2Th[4-(PhCH2)bipy](NC) (20), respectively. Nevertheless, upon exposure of 3 to (trimethylsilyl)diazomethane Me3SiCHN2, the bis-amido complex (Cp3tms)2Th[5,6-(Me3SiCH)bipy] (21), concomitant with N2 release, is isolated.

Visualization of the Association of Dimeric Protein Complexes on Specific Enhancers in the Salivary Gland Nuclei of Drosophila Larva.

Transcription factors (TFs) regulate gene expression by recognizing specific target enhancers in the genome. The DNA-binding and regulatory activity of TFs depend on the presence of additional protein partners, leading to the formation of versatile and dynamic multimeric protein complexes. Visualizing these protein-protein interactions (PPIs) in the nucleus is key for decrypting the molecular cues underlying TF specificity in vivo. Over the last few years, Bimolecular Fluorescence Complementation (BiFC) has been developed in several model systems and applied in the analysis of different types of PPIs. In particular, BiFC has been applied when analyzing PPIs with hundreds of TFs in the nucleus of live Drosophila embryos. However, the visualization of PPIs at the level of specific target enhancers or genomic regions of interest awaits the advent of DNA-labelling methods that can be coupled with BiFC. Here, we present a novel experimental strategy that we have called BiFOR and that is based on the coupling of BiFC with the bacterial ANCHOR DNA-labelling system. We demonstrate that BiFOR enables the precise quantification of the enrichment of specific dimeric protein complexes on target enhancers in Drosophila salivary gland nuclei. Given its versatility and sensitivity, BiFOR could be applied more widely to other tissues during Drosophila development. Our work sets up the experimental basis for future applications of this strategy.

Interplay of Isomorphs and Polymorphs of Amidino-Copper(II) Complexes with Different Halides

To increase the number of potential materials for application as MRI contrast agents, several Cu(II) complexes were synthesized. Cu(II) complexes were chosen because they are less expensive in comparison with the presently used Gd(III), Mn(II) and other agents. Pyridine-2-carboximidamide (1), pyrimidine-2-carboximidamide (2) and pyrazole-2-carboximidamide (3) in the form of different salts along with CuCl2 and NaCl or CuBr2 and NaBr were used to obtain four Cu(II) complexes: dichloro-pyrimidine-2-carboximidamide copper(II) (4), dibromo-pyrimidine-2-carboximidamide copper(II) (5), dichloro-pirazole-2-carboximidamide copper(II) (6), and dibromo-pirazole-2-carboximidamide copper(II) (7). X-ray diffraction analysis revealed that molecular complexes 4–7 contain square planar coordinated Cu(II) atoms and their structures are very similar, as well as their packing in crystals, which allows us to consider them isomorphs. The same synthetic approach to complex preparation where NaCl or NaBr was not used brought us to the formation of dimeric complexes μ-chloro{chloro(pyridine-2-carboximidamide)copper(II)} (8) and μ-chloro{chloro(pyrimidine-2-carboximidamide)copper(II)} (9). In the dimeric complexes, two fragments which were the same as in monomeric complexes 4–7 are held together by bridging Cu-Cl bonds making the coordination of Cu equal to 5 (square pyramid). In dimeric complexes, axial Cu-Cl bonds are 2.7360 and 2.854 Å. These values are Cu-Cl bonds on the edge of existence according to statistical data from CSD. Synthesized complexes were characterized by IR spectroscopy, TGA, PXRD, EPR, and quantum chemical calculations. The higher thermal stability of monomer pyrimidine-based complexes with Cl and Br substituents makes them more prospective for further studies.

Elucidation of the Mechanisms of Inter-domain Coupling in the Monomeric State of Enzyme I by High-pressure NMR

The catalytic cycle of Enzyme I (EI), a phosphotransferase enzyme responsible for converting phosphoenolpyruvate (PEP) into pyruvate, is characterized by a series of local and global conformational rearrangements. This multistep process includes a monomer-to-dimer transition, followed by an open-to-closed rearrangement of the dimeric complex upon PEP binding. In the present study, we investigate the thermodynamics of EI dimerization using a range of high-pressure solution NMR techniques complemented by SAXS experiments. 1H-15N TROSY and 1H-13C methyl TROSY NMR spectra combined with 15N relaxation measurements revealed that a native-like engineered variant of full-length EI fully dissociates into stable monomeric state above 1.5 kbar. Conformational ensembles of EI monomeric state were generated via a recently developed protocol combining coarse-grained molecular simulations with experimental backbone residual dipolar coupling measurements. Analysis of the structural ensembles provided detailed insights into the molecular mechanisms driving formation of the catalytically competent dimeric state, and reveals that each step of EI catalytical cycle is associated with a significant reduction in either inter- or intra-domain conformational entropy. Altogether, this study completes a large body work conducted by our group on EI and establishes a comprehensive structural and dynamical description of the catalytic cycle of this prototypical multidomain, oligomeric enzyme.

Native Mass Spectrometry Dissects the Structural Dynamics of an Allosteric Heterodimer of SARS-CoV-2 Nonstructural Proteins.

Structure-based drug design, which relies on precise understanding of the target protein and its interaction with the drug candidate, is dramatically expedited by advances in computational methods for candidate prediction. Yet, the accuracy needs to be improved with more structural data from high throughput experiments, which are challenging to generate, especially for dynamic and weak associations. Herein, we applied native mass spectrometry (native MS) to rapidly characterize ligand binding of an allosteric heterodimeric complex of SARS-CoV-2 nonstructural proteins (nsp) nsp10 and nsp16 (nsp10/16), a complex essential for virus survival in the host and thus a desirable drug target. Native MS showed that the dimer is in equilibrium with monomeric states in solution. Consistent with the literature, well characterized small cosubstrate, RNA substrate, and product bind with high specificity and affinity to the dimer but not the free monomers. Unsuccessfully designed ligands bind indiscriminately to all forms. Using neutral gas collision, the nsp16 monomer with bound cosubstrate can be released from the holo dimer complex, confirming the binding to nsp16 as revealed by the crystal structure. However, we observed an unusual migration of the endogenous zinc ions bound to nsp10 to nsp16 after collisional dissociation. The metal migration can be suppressed by using surface collision with reduced precursor charge states, which presumably resulted in minimal gas-phase structural rearrangement and highlighted the importance of complementary techniques. With minimal sample input (∼μg), native MS can rapidly detect ligand binding affinities and locations in dynamic multisubunit protein complexes, demonstrating the potential of an "all-in-one" native MS assay for rapid structural profiling of protein-to-AI-based compound systems to expedite drug discovery.

Abstract 3051: JunAP, a peptide antagonist against the activator protein 1 transcription factor complex, demonstrates cancer cell cytotoxicity and reduced invasion in vitro and tumor regression in vivo in TNBC models

Abstract The activator protein 1 (AP-1) transcription factor is a dimeric complex consisting of proteins from the JUN, FOS, MAF, and ATF families. AP-1 complexes have been identified as novel therapeutic targets in cancer due to their role in tumor growth, invasion, metastasis, angiogenesis and chemoresistance. Dimerization of components of the AP-1 complex via leucine zipper domain interactions is required for DNA binding and subsequent transcriptional activity. We designed a peptide (Jun antagonizing peptide, JunAP) targeting the basic leucine zipper motif of AP-1 to antagonize AP-1 complex formation and prevent associated activity. Fluorescence polarization and DNA ELISA assays demonstrate target binding and selectivity of JunAP towards AP-1 family members, co-immunoprecipitation experiments reveal that JunAP blocks protein-protein interactions between cJun and its key binding partners, and reporter assays confirm inhibition of AP-1 transcriptional activity in vitro. Pathway analysis of RNA sequencing data confirmed by qPCR analysis shows that JunAP disrupts key pathways required for cell survival and migration. Corresponding functional in vitro assays reveal that JunAP exhibits an inhibitory effect on invasion in Boyden chamber assays and demonstrates potent cytotoxicity in Jun-dependent cells. Further, in a BT549 triple negative breast cancer subcutaneous xenograft model, administration of JunAP results in tumor regression, demonstrating the anti-cancer potential of targeting the AP-1 complex. In summary, these data support JunAP as a potent peptide antagonist of the AP-1 transcription factor family that warrants further development as a potential therapeutic option for AP-1 driven tumors. Citation Format: Karen Mendelson, Zachary F. Mattes, Siok Leong, Ricardo Ramirez, Mark Koester, Claudio Scuoppo, Julia Diehl, Erin Gallagher, Jerel Gonzales, Franco Abbate, Lila Ghamsari, Gene Merutka, Barry J. Kappel, Abi Vainstein-Haras, Jim A. Rotolo. JunAP, a peptide antagonist against the activator protein 1 transcription factor complex, demonstrates cancer cell cytotoxicity and reduced invasion in vitro and tumor regression in vivo in TNBC models [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2024; Part 1 (Regular Abstracts); 2024 Apr 5-10; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2024;84(6_Suppl):Abstract nr 3051.

N-Aryloxide-Amidinate Thorium Complexes.

An N-aryloxide-amidine ligand (1), [ONNO] ligand, integrating phenoxide (PhO-) and amidine ligands through methylene linkers, was employed in actinide chemistry. Upon reaction of the deprotonated ligand with ThCl4(DME)2 in ether, the corresponding dimer complex 2 was obtained. Upon treatment of 2 with KCp* (Cp* = Cp(Me)5) in tetrahydrofuran, the corresponding {[ONNO]ThIVCp*(LiCl)}2 (4) was obtained. In complex 2, the two ArO- arms bonded from the same ligand to different ThIV centers. In contrast, both ArO- arms coordinated to the same metal center in 4. Notably, when a mixture of 2 and bipyridine was treated with one or two equiv of KC8, the [ONNO]ThIV-bipyridyl•̅ radical dimer complex (5) and [ONNO]ThIV-bipyridyl2- dianionic dimer species (6) were obtained, respectively.

Stabilization of the retromer complex: Analysis of novel binding sites of bis-1,3-phenyl guanylhydrazone 2a to the VPS29/VPS35 interface

The stabilization of the retromer protein complex can be effective in the treatment of different neurological disorders. Following the identification of bis-1,3-phenyl guanylhydrazone 2a as an effective new compound for the treatment of amyotrophic lateral sclerosis, in this work we analyze the possible binding sites of this molecule to the VPS35/VPS29 dimer of the retromer complex. Our results show that the affinity for different sites of the protein assembly depends on compound charge and therefore slight changes in the cell microenvironment could promote different binding states. Finally, we describe a novel binding site located in a deep cleft between VPS29 and VPS35 that should be further explored to select novel molecular chaperones for the stabilization of the retromer complex.

Effects of Ring Size and Steric Encumbrance on Boron-to-Palladium Transmetalation from Arylboronic Esters.

The structure of the diol from which an arylboronic ester is derived dramatically influences the rate of transmetalation in the Suzuki-Miyaura cross-coupling reaction. Some esters undergo transmetalation more than 20 times faster than the parent arylboronic acid. Herein, investigations into the influence of arylboronic ester ring size and steric properties on the mechanism of transmetalation in the Suzuki-Miyaura reaction are described. Both factors impact the propensity of an arylboronic ester to bind to a dimeric palladium hydroxide complex. The reaction of hindered arylboronic esters derived from 1,2-diols (1,3,2-dioxaborolanes) with palladium hydroxide dimers to form a complex incorporating a Pd-O-B linkage is thermodynamically favorable, but the barrier to coordination is often higher than the barrier to arene transfer. In contrast, the analogous reaction between arylboronic esters derived from 1,3-diols (1,3,2-dioxaborinanes) and palladium hydroxide dimers is thermodynamically unfavorable, as 1,3,2-dioxaborinanes exhibit decreased electrophilicity compared to esters derived from 1,2- or 1,4-diols. These factors also influence the barrier of the arene transfer step, and in many cases, arylboronic esters that do not easily form Pd-O-B linked complexes undergo transmetalation faster than those that do because of hyperconjugative stabilization of the arene transfer transition state.

Spectroscopic and Computational Study of ZnCl2-Methanol Low-Melting-Temperature Mixtures.

Alcoholic electrolyte mixtures have wide applications in industries. In this study, a series of mixtures composed of ZnCl2 and methanol (MeOH) with ZnCl2 mol % from 6.7 to 25 were prepared, and their spectral, structural, and thermodynamic properties were studied using infrared (IR) spectroscopy, differential scanning calorimetry (DSC), and density functional theory (DFT) calculations. The DFT-assisted analysis of excess spectra, supported by 2D-correlation spectroscopy, led to the identification of the major constituents of ZnCl2-MeOH mixtures, namely, MeOH monomer, MeOH dimer, and ZnCl2-3MeOH complex, produced after dissociation of MeOH trimer which represents the bulk methanol. The Hirshfeld charge analysis showed that in the competition between the O-H···Cl hydrogen bond (H-bond) and Zn ← O coordination bond to transfer charge in ZnCl2-MeOH complexes, the latter always dominates, making MeOH positively charged. The phase diagram of the binary system showed the presence of V-shaped glass transition temperatures (Tg), characteristic of low-melting mixture solvents (LoMMSs). The present study provides insights into the microscopic properties of the system and sheds light on the understanding of the general principles to prepare deep-eutectic solvents (DESs) or LoMMSs using inorganic salts and alcoholic compounds.

The curious case of the colored crystals of N‐substituted 2‐oxo‐1,2‐dihydropyridinyl‐3‐yl amines and amides: Self‐association in the solid state

AbstractDuring a previous investigation of pyridone derivatives as inhibitors of glycogen phosphorylase, we observed that some N‐substituted 2‐oxo‐1,2‐dihydropyridinyl‐3‐yl amines and amides exhibited different colors, ranging from red to green to blue to teal. Remarkably, one compound (compound 8) could be crystallized in both a red form and a green form. To try to understand these observations, we have carried out further spectroscopic studies in the solid state and in solution employing UV‐visible spectroscopy, NMR spectroscopy, and X‐ray crystallography, along with molecular mechanics and DFT calculations on selected compounds. Evidence was obtained in the solid state for the self‐association of pyridones into dimeric complexes or near‐planar dimers induced by intermolecular hydrogen bonding and possible π‐stacking, whereas monomeric structures for two compounds were proposed in chloroform, in agreement with the DFT calculated chemical shifts. In this study, it was determined that the colors observed could not be attributed to hydrogen bonding or possible π‐bond stacking in the novel relatively unconjugated pyridone derivatives. A possible explanation for the colors is suggested: a contaminant formed by aerial oxidation of trace amounts of the 3‐aminopyridone starting material. This result contrasts with existing literature reports of UV and fluorescence spectra, which indicated distinct coloration for conjugated 2‐pyridone compounds. The spectroscopic results, including X‐ray structural data for five pyridones, contribute to a deeper understanding of structural interactions in pyridone derivatives.