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Structural snapshots of base excision by the cancer-associated variant MutY N146S reveal a retaining mechanism
Abstract DNA glycosylase MutY plays a critical role in suppression of mutations resulted from oxidative damage, as highlighted by cancer-association of the human enzyme. MutY requires a highly conserved catalytic Asp residue for excision of adenines misinserted opposite 8-oxo-7,8-dihydroguanine (OG). A nearby Asn residue hydrogen bonds to the catalytic Asp in structures of MutY and its mutation to Ser is an inherited variant in human MUTYH associated with colorectal cancer. We captured structural snapshots of N146S Geobacillus stearothermophilus MutY bound to DNA containing a substrate, a transition state analog and enzyme-catalyzed abasic site products to provide insight into the base excision mechanism of MutY and the role of Asn. Surprisingly, despite the ability of N146S to excise adenine and purine (P) in vitro, albeit at slow rates, N146S-OG:P complex showed a calcium coordinated to the purine base altering its conformation to inhibit hydrolysis. We obtained crystal structures of N146S Gs MutY bound to its abasic site product by removing the calcium from crystals of N146S-OG:P complex to initiate catalysis in crystallo or by crystallization in the absence of calcium. The product structures of N146S feature enzyme-generated β-anomer abasic sites that support a retaining mechanism for MutY-catalyzed base excision.
Detection of an Iridium-Dihydrogen Complex: A Proposed Intermediate in Ionic Hydrogenation
Addition of high pressures of H2 to five-coordinate [(tBu)4(POCOP)Ir(CO)(H)]OTf [(tBu)4(POCOP) = ?3-C6H3-2,6- (OP(tBu)2)2] complexes results in observation of two new iridium-dihydrogen complexes. If the aryl moiety of the POCOP ligand is substituted with an electron withdrawing protonated dimethylamino group at the para position, hydrogen coordination is enhanced. Five-coordinate Ir-H complexes generated by addition of triflic acid to (tBu)4(POCOP)Ir(CO) species show an Ir-H 1H NMR chemical shift dependence on the number of equivalents of acid present. It is proposed that excess triflic acid in solution facilitates triflate dissociation from iridium, resulting in unsaturated five-coordinate Ir-H complexes. The five-coordinate iridium-hydride complexes were found to catalyze H/D exchange between H2 and CD3OD. The existence of the dihydrogen complexes as well as isotope exchange reactions provide evidence for proposed ionic hydrogenation mechanistic intermediates for glycerol deoxygenation.
Complexations of Ln(III) with SnS{sub 4}H and Sn{sub 2}S{sub 6}: Solvothermal syntheses and characterizations of lanthanide coordination polymers with thiostannate and polyamine mixed ligands
Polymeric lanthanide complexes with thiostannate and polyamine mixed ligands, [Ln(peha)(μ–SnS{sub 4}H)]{sub n} [Ln=La (1a), Nd (1b)] and [(Ln(tepa)(μ–OH)){sub 2}(μ–Sn{sub 2}S{sub 6})]{sub n}nH{sub 2}O [Ln=Nd (2a), Sm (2b), Gd (2c), Dy (2d)] (peha=pentaethylenehexamine, tepa=tetraethylenepentamine) were respectively prepared in peha and tepa coordinative solvents by the solvothermal methods. In 1a and 1b, the Ln{sup 3+} ions are coordinated by a hexadentate peha ligand forming [Ln(peha)]{sup 3+} units. The [SnS{sub 4}H]{sup 3−} anion chelates a [Ln(peha)]{sup 3+} unit via two S atoms and coordinates to another [Ln(peha)]{sup 3+} unit via the third S atom. As a result, the [Ln(peha)]{sup 3+} units are connected into coordination polymers [Ln(peha)(μ–SnS{sub 4}H)]{sub n} by an unprecedented tridentate μ–η{sup 1},η{sup 2}–SnS{sub 4}H bridging ligands. In 2a–2d, the Ln{sup 3+} ions are coordinated by a pentadentate tepa ligand, and two [Ln(tepa)]{sup 3+} units are joined by two μ–OH bridges to form a binuclear [(Ln(tepa)(μ–OH)){sub 2}]{sup 4+} unit. Behaving as a bidentate μ–η{sup 1}, η{sup 1}–Sn{sub 2}S{sub 6} bridging ligand, the Sn{sub 2}S{sub 6} unit connects [(Ln(tepa)(μ–OH)){sub 2}]{sup 4+} units into a neutral coordination polymer [(Ln(tepa)(μ–OH)){sub 2}(μ–Sn{sub 2}S{sub 6})]{sub n} via the trans S atoms. The Ln{sup 3+} ions are in distorted monocapped square antiprismatic and bicapped trigonal prismatic environments in [(Ln(peha)(μ–SnS{sub 4}H)]{sub n} and [(Ln(tepa)(μ–OH)){sub 2}(μ–Sn{sub 2}S{sub 6})]{sub n}, respectively. The denticities of ethylene polyamine play an important role on the formation and complexation of the thiostannate in the presence of lanthanide ions. Compounds 1a–2d show well-defined absorption edges with band gaps between 2.81 and 3.15 eV. - Graphical abstract: Lanthanide coordination polymers concerning thiostannate ligands were prepared by the solvothermal methods, and μ{sub 3}–SnS{sub 4}H and μ–Sn{sub 2}S{sub 6} ligands to Ln(III) centers were obtained. - Highlights: • Lanthanide coordination polymers were prepared in polyamines with higher denticity. • The μ–η{sup 1},η{sup 2}–SnS{sub 4}H and μ–η{sup 1},η{sup 1}–Sn{sub 2}S{sub 6} ligands to Ln(III) centers were obtained. • Effect of amine on the complexation of Ln(III) with thiostannate is observed.
A series of 2D lanthanide (III) coordination polymers constructed from 2-(pyridin-3-yl)-1H-imidazole-4,5-dicarboxylate
Reactions of 2-(pyridine-3-yl)-1H-4,5-imidazoledicarboxylic acid (H{sub 3}PyIDC) with a series of Ln(III) ions affords ten coordination polymers, namely, {l_brace}[Ln(H{sub 2}PyIDC)(HPyIDC)(H{sub 2}O){sub 2}]{center_dot}H{sub 2}O{r_brace}{sub n} [Ln=Nd (1), Sm (2), Eu (3) and Gd (4)], {l_brace}[Ln(HPyIDC)(H{sub 2}O){sub 3}]{center_dot}(H{sub 2}PyIDC){center_dot}H{sub 2}O{r_brace}{sub n} [Ln=Gd (5), Tb (6), Dy (7), Ho (8) and Er (9)], and {l_brace}[Y{sub 2}(HPyIDC){sub 2}(H{sub 2}O){sub 5}]{center_dot}(bpy){center_dot}(NO{sub 3}){sub 2}{center_dot}3H{sub 2}O{r_brace}{sub n} (10) (bpy=4,4 Prime -bipyridine). They exhibit three types of networks: complexes 1-4 are isomorphous coordination networks containing neutral 2D metal-organic layers, while complexes 5-9 are isomorphous, which consist of cationic metal-organic layers and anionic organic layers, and complex 10 is a 2D network built up from 4-connected HPyIDC{sup 2-} anion and 4-connected Y(III) ions. In addition, thermogravimetric analyses and solid-state luminescent properties of the selected complexes are investigated. They exhibit intense, characteristic emissions in the visible region at room temperature. - Graphical abstract: Structure variation of ten Ln(III) complexes is attributed to the lanthanide contraction effect and various coordination modes of H{sub 3}PyIDC ligands. Moreover, photoluminescent properties and thermal behaviors of selected complexes were investigated. Highlights: Black-Right-Pointing-Pointer A series of 2D Ln(III) coordination polymers based on H{sub 3}PyIDC were firstly obtained. Black-Right-Pointing-Pointer The structural variation is partly attributed to the lanthanide contraction effect. Black-Right-Pointing-Pointer Diverse coordination modes of H{sub 3}PyIDC ligands are observed. Black-Right-Pointing-Pointer The Gd(III) complexes with different structures controlled by different synthesis methods.
Polyoxometalate-Assisted Crystallization: A General Strategy Enabling Structural Characterization of Molecular Radium Complexes
A fundamental understanding of radium (Ra) coordination chemistry has been hindered by the scarcity and radiological hazards of 226 Ra, leaving the structural characterization of molecular Ra complexes almost entirely unexplored. Here, we introduce a polyoxometalate (POM)-assisted crystallization strategy that enables single-crystal X-ray diffraction analysis of Ra–chelator complexes from microgram-scale samples. Employing the plenary Keggin anion [SiW 12 O 40 ] 4– , we isolated and structurally characterized Ra 2+ complexes of 18-crown-6 and the bis-picolinate macrocycle macropa, together with their Sr 2+ and Ba 2+ analogues. The resulting structures reveal systematic, size-dependent trends in coordination number and metal-donor distances across the alkaline earth series and provide the first direct experimental measurements of Ra–N and Ra–OCOO bond distances. Together, these results establish POM-assisted crystallization as a robust approach for obtaining solid-state structural information on Ra 2+ complexes of organic chelators, opening new opportunities to advance the coordination chemistry needed to fully realize radium’s potential in isotope production and targeted radiotherapy. More broadly, this approach expands the experimental toolkit available for studying scarce, highly radioactive elements accessible only in microgram quantities.
Human-Like Eukaryotic Translation Initiation Factor 3 from Neurospora crassa
Eukaryotic translation initiation factor 3 (eIF3) is a key regulator of translation initiation, but its in vivo assembly and molecular functions remain unclear. Here we show that eIF3 from Neurospora crassa is structurally and compositionally similar to human eIF3. N. crassa eIF3 forms a stable 12-subunit complex linked genetically and biochemically to the 13 th subunit, eIF3j, which in humans modulates mRNA start codon selection. Based on N. crassa genetic analysis, most subunits in eIF3 are essential. Subunits that can be deleted (e, h, k and l) map to the right side of the eIF3 complex, suggesting that they may coordinately regulate eIF3 function. Consistent with this model, subunits eIF3k and eIF3l are incorporated into the eIF3 complex as a pair, and their insertion depends on the presence of subunit eIF3h, a key regulator of vertebrate development. Comparisons to other eIF3 complexes suggest that eIF3 assembles around an eIF3a and eIF3c dimer, which may explain the coordinated regulation of human eIF3 levels. Taken together, these results show that Neurospora crassa eIF3 provides a tractable system for probing the structure and function of human-like eIF3 in the context of living cells.
A photochemical proposal for the preparation of ZnAl{sub 2}O{sub 4} and MgAl{sub 2}O{sub 4} thin films from β-diketonate complex precursors
Highlights: • ZnAl{sub 2}O{sub 4} and MgAl{sub 2}O{sub 4} thin films were prepared by photo-chemical method. • The Zn(II), Mg(II) and Al(III) β-diketonate complexes were used as precursors. • The photochemical reaction was monitored by UV–vis and FT-IR spectroscopy. • The results reveal spinel oxide formation and the generation of intermediate products. - Abstract: ZnAl{sub 2}O{sub 4} and MgAl{sub 2}O{sub 4} thin films were grown on Si(100) and quartz plate substrates using a photochemical method in the solid phase with thin films of β-diketonate complexes as the precursors. The films were deposited by spin-coating and subsequently photolyzed at room temperature using 254 nm UV light. The photolysis of these films results in the deposition of metal oxide thin films and fragmentation of the ligands from the coordination sphere of the complexes. The obtained samples were post-annealed at different temperatures (350–1100 °C) for 2 h and characterized by FT-Infrared spectroscopy, X-ray diffraction (XRD), X-ray photoelectron spectroscopy (XPS), atomic force miscroscopy (AFM), and UV–vis spectroscopy. The results indicate the formation of spinel-type structures and other phases. These characteristics determined the quality of the films, which were obtained from the photodeposition of ternary metal oxides.
Going around the Kok cycle of the water oxidation reaction with femtosecond X-ray crystallography
The water oxidation reaction in photosystem II (PS II) produces most of the molecular oxygen in the atmosphere, which sustains life on Earth, and in this process releases four electrons and four protons that drive the downstream process of CO 2 fixation in the photosynthetic apparatus. The catalytic center of PS II is an oxygen-bridged Mn 4 Ca complex (Mn 4 CaO 5 ) which is progressively oxidized upon the absorption of light by the chlorophyll of the PS II reaction center, and the accumulation of four oxidative equivalents in the catalytic center results in the oxidation of two waters to dioxygen in the last step. The recent emergence of X-ray free-electron lasers (XFELs) with intense femtosecond X-ray pulses has opened up opportunities to visualize this reaction in PS II as it proceeds through the catalytic cycle. In this review, we summarize our recent studies of the catalytic reaction in PS II by following the structural changes along the reaction pathway via room-temperature X-ray crystallography using XFELs. The evolution of the electron density changes at the Mn complex reveals notable structural changes, including the insertion of O X from a new water molecule, which disappears on completion of the reaction, implicating it in the O—O bond formation reaction. We were also able to follow the structural dynamics of the protein coordinating with the catalytic complex and of channels within the protein that are important for substrate and product transport, revealing well orchestrated conformational changes in response to the electronic changes at the Mn 4 Ca cluster.
Structures and Activities of Archaeal Members of the LigD 3-Phosphoesterase DNA Repair Enzyme Superfamily
LigD 3'-phosphoesterase (PE) is a component of the bacterial NHEJ apparatus that performs 3'-end-healing reactions at DNA breaks. The tertiary structure, active site and substrate specificity of bacterial PE are unique vis-a-vis other end-healing enzymes. PE homologs are present in archaea, but their properties are uncharted. Here, we demonstrate the end-healing activities of two archaeal PEs - Candidatus Korarchaeum cryptofilum PE (CkoPE; 117 amino acids) and Methanosarcina barkeri PE (MbaPE; 151 amino acids) - and we report their atomic structures at 1.1 and 2.1 {angstrom}, respectively. Archaeal PEs are minimized versions of bacterial PE, consisting of an eight-stranded {beta} barrel and a 3{sub 10} helix. Their active sites are located in a crescent-shaped groove on the barrel's outer surface, wherein two histidines and an aspartate coordinate manganese in an octahedral complex that includes two waters and a phosphate anion. The phosphate is in turn coordinated by arginine and histidine side chains. The conservation of active site architecture in bacterial and archaeal PEs, and the concordant effects of active site mutations, underscore a common catalytic mechanism, entailing transition state stabilization by manganese and the phosphate-binding arginine and histidine. Our results fortify the proposal that PEs comprise a DNA repair superfamily distributed widely among taxa.
Cyclopentadienyl coordination induces unexpected ionic Am-N bonding in an americium bipyridyl complex
Variations in bonding between trivalent lanthanides and actinides is critical for reprocessing spent nuclear fuel. The ability to tune bonding and the coordination environment in these trivalent systems is a key factor in identifying a solution for separating lanthanides and actinides. Coordination of 4,4'-bipyridine (4,4'-bpy) and trimethylsilylcyclopentadienide (Cp') to americium introduces unexpectedly ionic Am-N bonding character and unique spectroscopic properties. Here we report the structural characterization of (Cp' 3 Am) 2 (μ -4,4'-bpy) and its lanthanide analogue, (Cp' 3 Nd) 2 (μ - 4,4'-bpy), by single-crystal X-ray diffraction. Spectroscopic techniques in both solid and solution phase are performed in conjunction with theoretical calculations to probe the effects the unique coordination environment has on the electronic structure.
Multi-state Catalysts Modulated by Mechanical Force (Final Report)
The development of more efficient catalytic processes and new approaches to control catalytic activity and selectivity are central to the realization of more selective, atom economic, and energy efficient routes to value added chemicals and polymers. The reactivity and selectivity of a transition metal catalyst is intimately related to the ligand-sphere geometry and, in many cases, the ideal ligand geometry for one step of a catalytic cycle is poorly matched to the ideal ligand geometry for another, resulting in sub-optimal efficiency. Macroscopic mechanical forces are both large, potentially much larger than interatomic forces, and are directional and localized to an extent that differentiates them from other forms of energy input such as heat or light. As such, mechanical force represents a heretofore untapped approach to modulate catalyst geometry, with the potential to reversibly modulate catalyst geometry on the timescale of catalytic turnover or monomer enchainment. This project has addressed the fundamental challenges in material-to-molecule strain coupling associated with the development of a new class of mechanically responsive catalysts (mechanocatalysts) in which active organotransition metal catalysts are strategically embedded in a flexible polymer network such that application of external mechanical force (stretching or deformation) leads to modulation of catalyst geometry, and hence reactivity and selectivity. Our efforts during the tenure of this grant were directed toward the elucidation of force-reactivity relationships of elementary transformations that occur within the first coordination sphere of a transition metal complex employing stiff stilbene photoswitches tethered to a flexible bidentate phosphine ligand derived from MeOBiphep as molecular force probes which provide a range of compressive and extension forces to the coupled transition metal complex depending on the geometry of the stiff stilbene and length of the tethering chains. During the tenure of this grant, we have quantified the rate of C(sp 2 )-C(sp 2 ) reductive elimination from platinum(II) diaryl complexes containing bis(phosphine) force probe ligands as a function of mechanical force; compressive forces decreased the rate of reductive elimination whereas extension forces increased the rate relative to the strain-free MeOBiphep complex with a 3.4-fold change in rate over a ~290 pN range of restoring forces. In a similar manner, we have quantified the rate of oxidative addition of bromobenzene to low-ligated palladium(0) complexes containing force probe ligands as a function of mechanical force; compressive forces increase the rate of oxidative addition, whereas tensile forces decrease the rate with a ~6 fold change in rate across ~340 pN of force applied to the complexes. In both cases, experimental and computational analyses argue strongly against any significant force-induced perturbation of ground state geometry within the first coordination sphere of the reactant complexes. Rather, the force/rate behavior observed for these transformations across these ranges of forces is attributed to the coupling of force to the nuclear motion comprising the reaction coordinates for reductive elimination and oxidative addition. These results together inform the development of catalysts whose activity can be tuned by an external force that is adjusted within a catalytic cycle and suggest opportunities to experimentally map geometry changes associated with reactions in transition metal complexes and potential strategies for force-modulated catalysis.
Linear Free Energy Relationships Associated with Hydride Transfer From [(6,6'-R 2 -bpy)Re(CO) 3 H]: A Cautionary Tale in Identifying Hydrogen Bonding Effects in the Secondary Coordination Sphere
Here, six rhenium hydride complexes, [(6,6'-R 2 -bpy)Re(CO) 3 H] (bpy = 2,2'-bipyridine, R = OEt, OMe, NHMe, Me, F, Br), were synthesized. These complexes insert CO 2 to form rhenium formate complexes of the type [(6,6'-R 2 -bpy)Re(CO) 3 {OC(O)H}]. All the rhenium formate species were characterized using X-ray crystallography, which revealed that the bpy ligand is not coplanar with the metal coordination plane containing the two nitrogen donors of the bpy ligand but tilted. A solid-state structure of [(6,6'-Me 2 -bpy)Re(CO) 3 H] determined using MicroED also featured a tilted bpy ligand. The kinetics of CO 2 insertion into complexes of the type [(6,6'-R 2 -bpy)Re(CO) 3 H] were measured experimentally and the thermodynamic hydricities of [(6,6'-R 2 -bpy)Re(CO) 3 H] species were determined using theoretical calculations. A Brønsted plot constructed using the experimentally determined rate constants for CO 2 insertion and the calculated thermodynamic hydricities for [(6,6'-R 2 -bpy)Re(CO) 3 H] revealed a linear free energy relationship (LFER) between thermodynamic and kinetic hydricity. This LFER is different to the previously determined relationship for CO 2 insertion into complexes of the type [(4,4'-R 2 -bpy)Re(CO) 3 H]. At a given thermodynamic hydricity, CO 2 insertion is faster for complexes containing a 6,6'-substituted bpy ligand. This is likely in part due to the tilting observed for systems with 6,6'-substituted bpy ligands. Notably, the 6,6'-(NHMe) 2 -bpy ligand could in principle stabilize the transition state for CO 2 insertion via hydrogen bonding. This work shows that if only the rate of CO 2 insertion into [(6,6'-(NHMe) 2 -bpy)Re(CO) 3 H] is compared to [(4,4'-R 2 -bpy)Re(CO) 3 H] systems, the increase in rate could be easily attributed to hydrogen bonding, but in fact all 6,6'-substituted systems lead to faster than expected rates.
Molecular Cobalt Catalysts for H 2 Generation with Redox Activity and Proton Relays in the Second Coordination Sphere
Two new Co(II) complexes have been synthesized and investigated as catalysts for H 2 generation. These catalysts were designed to incorporate redox-active bipyridine components and nitrogen groups, which can participate in electron and proton transfer steps in the catalytic cycle. The two catalysts differ by only one amino group, yielding a completely closed macrocycle and an open “macrocycle” complex. Removing just one nitrogen linker between the Co(II)-binding bipyridine groups has a profound impact on the molecular geometry observed by single crystal analysis. Photocatalysis experiments show that both catalysts are highly active for aqueous proton reduction at moderate pH levels, with the closed macrocycle reaching almost 2 × 10 4 turnovers of H 2 when photodriven by [Ru(2,2'-bipyridine) 3 ] 2+ using ascorbate as an electron relay and a phosphine compound as the terminal electron donor. Measurements of the electrocatalytic activity were used to investigate key steps in the mechanism of proton reduction by the molecular catalysts. The formation of a new reversible peak on addition of moderately strong acids in organic solvents suggests that protonation of the macrocycle plays an important role in H 2 generation. Onset of the catalytic current occurs near the reduction potential of the bipyridine components, suggesting that catalysis is mediated by electron transfer from the macrocycle to the cobalt center. From these observations, we propose a mechanism for catalytic proton reduction to H 2 , which involves both intramolecular proton and electron transfer steps from the macrocycle ligand to the cobalt center. In conclusion, the vital role of the second coordination sphere in the catalytic cycle places these relatively simple complexes on the pathway toward molecular catalysts that mimic the valuable features of enzymatic catalysis.
Topology‐based Visualization of Transformation Pathways in Complex Chemical Systems
Studying transformation in a chemical system by considering its energy as a function of coordinates of the system's components provides insight and changes our understanding of this process. Currently, a lack of effective visualization techniques for high-dimensional energy functions limits chemists to plot energy with respect to one or two coordinates at a time. In some complex systems, developing a comprehensive understanding requires new visualization techniques that show relationships between >all coordinates at the same time. We propose a new visualization technique that combines concepts from topological analysis, multi-dimensional scaling, and graph layout to enable the analysis of energy functions for a wide range of molecular structures. We demonstrate our technique by studying the energy function of a dimer of formic and acetic acids and a LTA zeolite structure, in which we consider diffusion of methane.
Surface speciation of yttrium and neodymium sorbed on rutile: Interpretations using the change distribution model.
The adsorption of Y3+ and Nd3+ onto rutile has been evaluated over a wide range of pH (3 11) and surface loading conditions, as well as at two ionic strengths (0.03 and 0.3 m), and temperatures (25 and 50 C). The experimental results reveal the same adsorption behavior for the two trivalent ions onto the rutile surface, with Nd3+ first adsorbing at slightly lower pH values. The adsorption of both Y3+ and Nd3+ commences at pH values below the pHznpc of rutile. The experimental results were evaluated using a charge distribution (CD) and multisite complexation (MUSIC) model, and Basic Stern layer description of the electric double layer (EDL). The coordination geometry of possible surface complexes were constrained by molecular-level information obtained from X-ray standing wave measurements and molecular dynamic (MD) simulation studies. X-ray standing wave measurements showed an inner-sphere tetradentate complex for Y3+ adsorption onto the (110) rutile surface (Zhang et al., 2004b). TheMDsimulation studies suggest additional bidentate complexes may form. The CD values for all surface species were calculated based on a bond valence interpretation of the surface complexes identified by X-ray and MD. The calculated CD values were corrected for the effect of dipole orientation of interfacial water. At low pH, the tetradentate complex provided excellent fits to the Y3+ and Nd3+ experimental data. The experimental and surface complexation modeling results show a strong pH dependence, and suggest that the tetradentate surface species hydrolyze with increasing pH. Furthermore, with increased surface loading of Y3+ on rutile the tetradentate binding mode was augmented by a hydrolyzed-bidentate Y3+ surface complex. Collectively, the experimental and surface complexation modeling results demonstrate that solution chemistry and surface loading impacts Y3+ surface speciation. The approach taken of incorporating molecular-scale information into surface complexation models (SCMs) should aid in elucidating a fundamental understating of ion-adsorption reactions.
Protonation Studies of a Mono-Dinitrogen Complex of Chromium Supported by a 12-Membered Phosphorus Macrocycle Containing Pendant Amines
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